Nuclear Dangers: A Resource Guide for Secondary School Teachers. Teaching Nuclear Issues.

ERIC Educational Resources Information Center

Meier, Paulette; McPherson, Beth

Provided in this guide are annotated lists of teacher and student resources for teaching and learning about nuclear issues in the secondary school. Resources are grouped into five major sections. The first section (background reading for teachers) contains books and articles focusing on nuclear issues (nuclear war; arms race/disarmament; nuclear…

Resources for Comprehensive Guidance & Counselling Programs. An Annotated List for Counsellors, Teachers, Administrators.

ERIC Educational Resources Information Center

Schlosser, Grace A.

With the growing popularity of comprehensive guidance and counseling programs in the schools, school personnel need model programs to guide them. An annotated list of suggested resources, designed to assist schools in the selection of materials to support comprehensive counseling and guidance programs, is provided here. All of the materials have…

Focus on Hinduism: Audio-Visual Resources for Teaching Religion. Occasional Publication No. 23.

ERIC Educational Resources Information Center

Dell, David; And Others

The guide presents annotated lists of audio and visual materials about the Hindu religion. The authors point out that Hinduism cannot be comprehended totally by reading books; thus the resources identified in this guide will enhance understanding based on reading. The guide is intended for use by high school and college students, teachers,…

Film Study: A Resource Guide.

ERIC Educational Resources Information Center

Manchel, Frank

This resource guide describes six popular approaches to the study of the cinema and provides a practical analysis of selected books, materials, and information about motion picture rentals. Highlighting this extensive survey of film studies are the annotated, critical bibliographies and filmographies of significant books, articles and films by and…

Resources for Responding to Doomsday 2012: An Annotated Guide

ERIC Educational Resources Information Center

Fraknoi, Andrew

2012-01-01

Educators at all levels and in all settings are getting questions these days about the approaching "end of the world" catastrophes supposedly coming in December 2012. This resource guide provides a selection of useful resources for responding to student and public questions in this arena. The latest internet myth to gain traction is the notion…

Current Materials on Barrier-Free Design. Revised.

ERIC Educational Resources Information Center

National Easter Seal Society for Crippled Children and Adults, Chicago, IL.

An eight-page annotated bibliography contains material available from the National Easter Seal Society and current material available from other sources. The annotations are grouped under design, guides, planning resources, standards/legislation, and general. Ordering information is provided. (MLF)

Project Basic Instructional Guide. Instructional Resources. Volume IV. World of Work.

ERIC Educational Resources Information Center

Maryland State Dept. of Education, Baltimore.

Designed to provide a listing of suggested resources to support the Project Basic instructional guide on the world of work, this bibliography consists of annotated listings of student-use materials (library books, films, filmstrips, kits, records, games, audio and videotapes, filmloops, transparencies, periodicals, and pamphlets) arranged…

Educators Resource Guide to WP Material for the Classroom.

ERIC Educational Resources Information Center

Potts, Peggy J.

This guide lists materials to be used in the classroom instruction of word processing technology. A listing of international, national, and regional word processing associations is followed by an annotated enumeration of resources under nine headings: (1) booklets and brochures, (2) books, (3) films, (4) handbooks, (5) machine transcription…

Resource Guide to Literature on Barrier-Free Environments with Selected Annotations.

ERIC Educational Resources Information Center

Architectural and Transportation Barriers Compliance Board, Washington, DC.

The result of a survey of barrier related literature, research, studies, and legislation completed or in progress, the resource guide lists approximately 1,500 citations regarding barrier free access for disabled persons. Bibliographic information (date, title, author, ordering and price specifications, pagination); descriptors; and a brief…

Biomes.

ERIC Educational Resources Information Center

Web Feet K-8, 2001

2001-01-01

This annotated subject guide to Web sites and additional resources focuses on biomes. Specifies age levels for resources that include Web sites, CD-ROMs and software, videos, books, audios, and magazines; includes professional resources; and presents a relevant class activity. (LRW)

Sources and Resources for Teaching about Ancient Italy.

ERIC Educational Resources Information Center

Dutra, John A.

1979-01-01

Annotates sources and resources to use in teaching secondary students about ancient Roman history, including pedagogical guides, books on various aspects of Roman civilization, reference works, journals, audiovisual and related resources, and organizations. (Author/CK)

Growing Up in a Nuclear World: A Resource Guide for Elementary School Teachers. Teaching Nuclear Issues.

ERIC Educational Resources Information Center

Meier, Paulette; McPherson, Beth

Provided in this guide are annotated lists of teacher and student resources for teaching and learning about nuclear issues in the elementary/junior high school (grades K-8). Resources are grouped into five major sections. The first section (background reading for teachers) contains books and articles focusing on nuclear issues (nuclear war; arms…

Mythology.

ERIC Educational Resources Information Center

Web Feet K-8, 2001

2001-01-01

This annotated subject guide to Web sites and additional resources focuses on mythology. Specific age levels are given for resources that include Web sites, CD-ROMs and software, videos, books, audios, and magazines; offers professional resources; and presents a relevant class activity. (LRW)

Space.

ERIC Educational Resources Information Center

Web Feet K-8, 2001

2001-01-01

This annotated subject guide to Web sites and additional resources focuses on space and astronomy. Specifies age levels for resources that include Web sites, CD-ROMS and software, videos, books, audios, and magazines; offers professional resources; and presents a relevant class activity. (LRW)

A Resource Guide on Indian Arts and Crafts for Elementary and Secondary Teachers.

ERIC Educational Resources Information Center

Fagot, Madeleine

American Indian arts and crafts reference materials (published 1923-1973) are listed in this annotated resource guide for elementary and secondary school teachers. Approximately 260 listings are given for: books, films and filmstrips, maps and charts, picture sets, magazines, bibliographies and indexes, slide kits, transparencies, distributor's…

Music Inspired by Astronomy: A Resource Guide Organized by Topic

ERIC Educational Resources Information Center

Fraknoi, Andrew

2012-01-01

This annotated resource guide presents 133 pieces of music inspired by astronomical ideas, discoveries, or history, organized in 22 subject categories. Both classical and popular music are included, but only when a clear connection to astronomy could be established. Depending on your musical tastes, you are likely to find some pieces resonating…

Educating for Peace: A Resource Guide for Teachers and Community Workers.

ERIC Educational Resources Information Center

Educating for Peace, Ottawa (Ontario).

This resource guide provides educators and community workers with a listing of written materials, audio-visual materials, and Ottawa-Carleton (Canada) area speakers dealing with peace education. The first of three parts lists 27 books, kits, and curriculum materials. For each listing, appropriate grade level, annotation, ordering address, and…

Appalachian Women. An Annotated Bibliography.

ERIC Educational Resources Information Center

Hamm, Mary Margo

This bibliography compiles annotations of 178 books, journal articles, ERIC documents, and dissertations on Appalachian women and their social, cultural, and economic environment. Entries were published 1966-93 and are listed in the following categories: (1) authors and literary criticism; (2) bibliographies and resource guides; (3) economics,…

The Right Stuff: Essential Resources for Managing Your Middle School Media Center.

ERIC Educational Resources Information Center

Manczuk, Suzanne

1999-01-01

Describes the following resources for managing a middle school media center: literature bibliographies with on-target middle school recommendations and useful annotations; resources for teaching primary sources; resources on censorship and banned books; basic Internet guides; copyright-law resources; information-literacy standards; and…

Essential Nursing References.

ERIC Educational Resources Information Center

Nursing and Health Care Perspectives, 2000

2000-01-01

This partially annotated bibliography contains these categories: abstract sources, archives, audiovisuals, bibliographies, databases, dictionaries, directories, drugs/toxicology/environmental health, grant resources, histories, indexes, Internet resources, reviews, statistical sources, and writers' manuals and guides. A supplement lists Canadian…

PACE. A Program for Acquiring Competence in Entrepreneurship. Resource Guide. Research and Development Series No. 194 D.

ERIC Educational Resources Information Center

Ohio State Univ., Columbus. National Center for Research in Vocational Education.

This Program for Acquiring Competence in Entrepreneurship (PACE) resource guide contains an "Annotated Glossary of Business Terms" and listings of sources of information. The glossary includes approximately 100 terms, of which the instructor should have a working knowledge. It may also be used as a handout for students. Sources of…

Teaching Texas History: An All-Level Resource Guide. Second Revised Edition.

ERIC Educational Resources Information Center

De Boe, David C.

This annotated resource guide offers scores of teaching aids to enrich the teaching of Texas history and geography. This edition differs from its predecessors in several ways: videocassettes replaced the section on 16mm films; the section on "Traveling Museum Exhibits" was dropped because the items were too costly for use in the typical…

ALA Guide to Medical & Health Sciences Reference

ERIC Educational Resources Information Center

ALA Editions, 2011

2011-01-01

This resource provides an annotated list of print and electronic biomedical and health-related reference sources, including Internet resources and digital image collections. Readers will find relevant research, clinical, and consumer health information resources. The emphasis is on resources within the United States, with a few representative…

Mass Communication: A Guide to Reference Sources.

ERIC Educational Resources Information Center

McGill Univ., Montreal (Quebec). McLennan Library.

For the study of mass communication in social, cultural and political contexts, this annotated resource guide presents a list of materials available in the McGill University Libraries in Montreal, Canada. As a select bibliography, the guide concentrates on current sources, although some historical coverage of newspaper and journalism is included.…

A Resource Book for Building English Proficiency.

ERIC Educational Resources Information Center

Guillen, Leonor; And Others

This resource book is a collection of articles, annotated references, and resource lists to supplement the accompanying handbook and trainer's guide for educators planning or working with English language programs for limited English proficient (LEP) students. The first part presents resources of interest to administrators adapting programs for a…

Nutrition Education Resource Guide: An Annotated Bibliography of Educational Materials for the WIC and CSF Programs. Bibliographies and Literature of Agriculture Number 24.

ERIC Educational Resources Information Center

McLaughlin, Elaine Casserly, Comp.; And Others

This resource guide to evaluated print and audiovisual nutrition materials has been developed to assist state and local staff of the Special Supplemental Program for Women, Infants and Children (WIC) and the Commodity Supplemental Foods Program (CSFP), in selecting, acquiring, and developing accurate and appropriate materials for nutrition…

Exploring the Pacific States through Literature.

ERIC Educational Resources Information Center

Doll, Carol A., Ed.

The "Exploring the United States through Literature Series" comprises seven annotated regional resource guides to selected print and nonprint materials for grades K-8. Each regional resource is divided into state sections identifying materials that relate to the history, culture, geography, resources, industries, literature and lore, and…

Guide to Civil War Books: An Annotated Selection of Modern Works on the War between the States.

ERIC Educational Resources Information Center

Barbuto, Domenica M.; Kreisel, Martha

This guide to Civil War books provides help in locating information about a specific person, battle, or campaign, as well as social or political conditions during the Civil War period. Teachers and librarians will find it useful when developing assignments or guiding students to sources for their research. This resource guide brings together books…

Learning about the Soviets: Selected Teaching Resources.

ERIC Educational Resources Information Center

Educators for Social Responsibility, Cambridge, MA.

Over 120 resources for teaching secondary and postsecondary level students about the Soviet Union, most of which have been produced since 1980, are listed in this guide. A resource list focusing on "Ten Things Soviets Say You Should Read to Understand Them" precedes annotated citations of articles; books; curricula; organizations…

German as a Second Language: Annotated Bibliography of Learning Resources, Grades 1-12.

ERIC Educational Resources Information Center

Alberta Dept. of Education, Edmonton. Language Services Branch.

The annotated bibliography of print and non-print materials for students and teachers of German includes standard student texts, audiovisual materials, student and teacher references, and other media. It is intended to guide teachers in the selection of student and instructional materials for the teaching and learning of German at the elementary…

Automated Technologies Noncommercial/Nonprofit Curriculum Guides and Resources Available for Community Colleges and Technical Institutes.

ERIC Educational Resources Information Center

Doty, Charles R.

This annotated bibliography is intended to provide community college and technical institute personnel with a listing of available curriculum guides dealing with automated technologies. Described in the handbook are a total of 31 curriculum guides that were selected because they met the following criteria: availability in the ERIC system or…

Neal-Schuman Guide to Recommended Children's Books and Media for Use with Every Elementary Subject.

ERIC Educational Resources Information Center

Matthew, Kathryn I.; Lowe, Joy L.

This resource guide is intended to help teachers and librarians integrate the best of a broad range of children's literature into the excitement of everyday learning. The guide contains annotations for contemporary children's books, videos, CD-ROMs and related media, as well as presenting inventive ideas for exploring them. An introduction…

Annotated Bibliography. Conference Materials: Strategy Conference on Education and the Economy (Washington, D.C., September 22-24, 1981).

ERIC Educational Resources Information Center

Center for Law and Education, Boston, MA.

The 22 items included in a packet distributed to participants at a 1981 conference on education and the economy are listed in this annotated bibliography, with sources for the items identified. The materials include articles, chapters from books, and monographs, as well as a resource guide and bibliography concerning rural economic and community…

Foods from an Iowa Farm. A Resource Guide.

ERIC Educational Resources Information Center

Iowa State Dept. of Agriculture and Land Stewardship, Des Moines.

Prepared for elementary and secondary teachers, this guide provides an annotated list of 72 instructional materials for teaching about farming and the products of Iowa farms. Entries, listed under the organization that provides the materials, state type of instructional material, major topics addressed, grades for which materials are appropriate,…

Russian Literature: A Guide to Reference Sources.

ERIC Educational Resources Information Center

McGill Univ., Montreal (Quebec). McLennan Library.

An annotated bibliography of general and specialized reference works for Russian and Soviet literature is intended for both students and researchers. English language and Russian language sources in the McGill University (Canada) libraries are included. Subject headings include guides (to the literature and to archival resources), encyclopedias,…

Internet Resources for Civic Educators. ERIC Digest.

ERIC Educational Resources Information Center

Pinhey, Laura A.

The Internet is an important resource for K-12 citizenship education teachers. Curriculum guides, lesson plans, government documents, conference proceedings, databases, photographs, and multimedia files provide the classroom teacher with a variety of materials including many primary sources. An annotated list of 15 World Wide Web sites are…

Community Development Resources Handbook. Inventory of Recently-Produced Resources on C.D.

ERIC Educational Resources Information Center

Roeschley, Sheila, Comp.; And Others

This guide is an annotated listing of 121 resources which are not yet available through the usual distribution channels and which might be useful to Community Development Society (CDS) members and those involved in community development. Largely produced over the last 5 years, the materials include books, chapters of books, journal articles,…

Teaching About War and its Control: A Selective Annotated Bibliography for the Social Studies Teacher.

ERIC Educational Resources Information Center

Nesbitt, William A., Ed.

A broad coverage of the war/peace field is represented by the items in this annotated bibliography and resource guide. It attempts to provide some solutions to questions about what to teach, how to teach it, and, of course, where to find materials. Both disciplines and topics appropriate to social studies courses are represented by books of…

Buyer's Guide to Environmental Media: A Directory of Books, Magazines, Films and Information Sources. Energy.

ERIC Educational Resources Information Center

Gerber, Michael, Ed.

This directory is designed to help locate energy and environmental resource materials, print and nonprint. The directory lists private and government information sources and provides an annotated guide to periodical literature. Citations of selected book titles published in 1973 include the topics of air pollution, chemical and biological…

A Guide to Free and Inexpensive Consumer Education Resources.

ERIC Educational Resources Information Center

Vickers, Carole A.

This guide contains sources of free or inexpensive consumer-education materials for use in schools or for adults. Specific contents include an annotated bibliography of 149 lists of publications dealing with consumer education materials; 77 articles in periodicals published in the 1970s; 53 audiovisuals or multimedia kits; 145 books about consumer…

New Instructional Materials on Africa South of the Sahara (1969-1970). A Supplement to Africa South of the Sahara: A Resource and Curriculum Guide.

ERIC Educational Resources Information Center

Beyer, Barry K.

This guide cites instructional materials on Africa south of the Sahara which have become available since February 1969. Acknowledging the probability of inaccuracies in the majority of the materials cited, the guide neither evaluates nor promotes items, but simply presents annotations of readings, textbooks, fact sheets, atlases, African…

A Guide to Instructional Resources for Consumers' Education.

ERIC Educational Resources Information Center

Johnston, William L.; Greenspan, Nancy B.

This annotated bibliography lists 295 selected instructional references, resources, and teaching aids for consumer education. It includes a variety of both print and nonprint materials, such as films, filmstrips, multimedia kits, games and learning packages for classroom and group instruction, textbooks for all age levels, and references for both…

Parent Resources Inventory.

ERIC Educational Resources Information Center

Alberta Education Response Centre, Edmonton.

This resource guide provides an annotated bibliography of 101 articles and newsletters of interest to parents and teachers of children in preschool through grade 3. The bibliography contains the titles and short descriptions of materials, selected with the assistance of parents and teachers from across Alberta (Canada), on a wide range of topics…

Guide to Social Science Resources in Women's Studies.

ERIC Educational Resources Information Center

Oakes, Elizabeth H.; Sheldon, Kathleen E.

This annotated bibliography describes the contents and critically evaluates 654 social science books and collections of journal articles in women's studies. The objective is to assist in research and in the organization of undergraduate or graduate courses on women. The resources are presented in nine sections. Section I covers anthropology,…

South Carolina Voices: Lessons from the Holocaust.

ERIC Educational Resources Information Center

South Carolina State Dept. of Education, Columbia. Council on the Holocaust.

This resource guide is based on interviews with survivors of the Holocaust and those who took part in liberating them from the concentration camps in World War II. The guide is divided into three main parts: (1) overviews, (2) lesson plans, and (3) student handouts. A Holocaust time line, a glossary of key terms, and an annotated bibliography are…

Learning About India: An Annotated Guide for Nonspecialists. Foreign Area Materials Center Occasional Publication No. 24.

ERIC Educational Resources Information Center

Harrison, Barbara J., Ed.

This guide to resources on India is designed to help teachers, students, librarians, and general adult readers locate materials that will help them understand Indian civilization. It is presented in five chapters. Chapter I offers three essays--"Learning About India: An Overview on Understanding India," by P. Lal; "On Teaching…

Rural Career Guidance: Abstracts of Current Research, Materials, and Practices.

ERIC Educational Resources Information Center

Far West Lab. for Educational Research and Development, San Francisco, CA.

The annotated bibliography provides a guide to the latest resource material, research findings, and/or developments in rural career guidance found in the ERIC system. Section I contains 158 citations and abstracts which have appeared in "Resources in Education" (RIE). RIE document resumes include the ERIC accession number, author(s), title,…

Global Issues: Activities and Resources for the High School Teacher.

ERIC Educational Resources Information Center

Switzer, Kenneth A.; Mulloy, Paul T.

The book is an introduction to teaching about contemporary global concerns in the high school social studies classroom. It contains background and lesson plans for seven units in addition to 39 reproducible student handouts, annotated lists of other good classroom resources, and a guide to sources of teaching materials on global issues. Topics…

Animal Rights: Selected Resources and Suggestions for Further Study.

ERIC Educational Resources Information Center

Davidoff, Donald J.

1989-01-01

Presents an annotated list of selected resources intended to serve as a guide to the growing amount of material on animal rights. Suggestions to aid in additional research include subject headings used to find books, indexes used to locate periodical articles, sources for locating organizations, and a selected list of animal rights organizations.…

Tales and Visions of the Korean War: A Guide to Internet Resources.

ERIC Educational Resources Information Center

Redstone, Victoria

2000-01-01

Provides an annotated list of Internet resources featuring lesson plans, background information, and documents pertaining to the Korean War. Highlights topics such as, but not limited to, the division of North and South Korea, a U.S. civilian massacre during the war, and a North Korean's memoir. (CMK)

SOBA: sequence ontology bioinformatics analysis.

PubMed

Moore, Barry; Fan, Guozhen; Eilbeck, Karen

2010-07-01

The advent of cheaper, faster sequencing technologies has pushed the task of sequence annotation from the exclusive domain of large-scale multi-national sequencing projects to that of research laboratories and small consortia. The bioinformatics burden placed on these laboratories, some with very little programming experience can be daunting. Fortunately, there exist software libraries and pipelines designed with these groups in mind, to ease the transition from an assembled genome to an annotated and accessible genome resource. We have developed the Sequence Ontology Bioinformatics Analysis (SOBA) tool to provide a simple statistical and graphical summary of an annotated genome. We envisage its use during annotation jamborees, genome comparison and for use by developers for rapid feedback during annotation software development and testing. SOBA also provides annotation consistency feedback to ensure correct use of terminology within annotations, and guides users to add new terms to the Sequence Ontology when required. SOBA is available at http://www.sequenceontology.org/cgi-bin/soba.cgi.

Youth, AIDS, and HIV. Resources for Educators and Policymakers, 1999-2000. A Directory of Selected National, State, and Local Resources, and an Annotated Resource Listing of Audiovisual, Print, and Software Materials for AIDS Education and HIV Prevention. Bulletin No. 99218.

ERIC Educational Resources Information Center

Wisconsin State Dept. of Public Instruction, Madison.

This resource document provides information about technical assistance and educational materials that can guide the development, implementation, and evaluation of acquired immunodeficiency syndrome (AIDS) education. The resources also offer information about programs whose goals are to prevent the spread of human immunodeficiency virus (HIV) and…

Consumer Education Resources Catalog: 16mm Films, Multi Media Kits, Video Cassettes, Simulations & Games, Printed Materials. 1978 Edition.

ERIC Educational Resources Information Center

Jones, Sandra; Neal, Kathy

This consumer education resources catalog provides an annotated guide to 16mm films, multi-media kits, video cassettes, simulations and games, and printed materials related to consumer education available from Michigan Department of Education's Regional Education Media Centers. The first major section lists available media by specific subject…

UniProtKB/Swiss-Prot, the Manually Annotated Section of the UniProt KnowledgeBase: How to Use the Entry View.

PubMed

Boutet, Emmanuel; Lieberherr, Damien; Tognolli, Michael; Schneider, Michel; Bansal, Parit; Bridge, Alan J; Poux, Sylvain; Bougueleret, Lydie; Xenarios, Ioannis

2016-01-01

The Universal Protein Resource (UniProt, http://www.uniprot.org ) consortium is an initiative of the SIB Swiss Institute of Bioinformatics (SIB), the European Bioinformatics Institute (EBI) and the Protein Information Resource (PIR) to provide the scientific community with a central resource for protein sequences and functional information. The UniProt consortium maintains the UniProt KnowledgeBase (UniProtKB), updated every 4 weeks, and several supplementary databases including the UniProt Reference Clusters (UniRef) and the UniProt Archive (UniParc).The Swiss-Prot section of the UniProt KnowledgeBase (UniProtKB/Swiss-Prot) contains publicly available expertly manually annotated protein sequences obtained from a broad spectrum of organisms. Plant protein entries are produced in the frame of the Plant Proteome Annotation Program (PPAP), with an emphasis on characterized proteins of Arabidopsis thaliana and Oryza sativa. High level annotations provided by UniProtKB/Swiss-Prot are widely used to predict annotation of newly available proteins through automatic pipelines.The purpose of this chapter is to present a guided tour of a UniProtKB/Swiss-Prot entry. We will also present some of the tools and databases that are linked to each entry.

Worth the Risk: Four Approaches to Safety in International Learning, Including Selected and Annotated Resource Guide. CBIE Research Millennium Series No. 1

ERIC Educational Resources Information Center

Myles, Wayne; Mitchell, Lynne

2000-01-01

More and more Canadians are departing the country for international study, training and work experiences. Increasingly Canadian organizations and institutions are developing programs that further this mobility. However there is a dearth of resources and a lack of guidelines related to ensuring health and safety while abroad. "Worth the…

A selective annotated bibliography for clinical audiology (1988-2008): reference works.

PubMed

Ferrer-Vinent, Susan T; Ferrer-Vinent, Ignacio J

2009-06-01

This is the 1st in a series of 3 planned companion articles that present a selected, annotated, and indexed bibliography of clinical audiology publications from 1988 to 2008. Research and preparation of the bibliography were based on published guidelines, professional audiology experience, and professional librarian experience. This article presents reference works (dictionaries, encyclopedias, handbooks, and manuals). The future planned articles will cover other monographs, periodicals, and online resources. Audiologists and librarians can use these lists as a guide when seeking clinical audiology literature.

A Selected Bibliography of Educational Sources.

ERIC Educational Resources Information Center

Campbell, Janet; And Others

Focusing on materials available at the California State University at Long Beach Library, this annotated bibliography lists resources in seven subject categories pertaining to education: (1) guides to the professional educational literature; (2) books about education research methodology; (3) encyclopedias and dictionaries; (4) tests and…

Rights & Responsibilities.

ERIC Educational Resources Information Center

Online-Offline, 2000

2000-01-01

This theme issue guides teachers and students to annotated listings of Web sites, CD-ROMs and computer software, videos, books, and additional resources that deal with topics related to rights and responsibilities. Sidebar features discuss animal rights, handling money responsibly, and taking responsibility for the environment. (Contains Three…

Films in Early Childhood Education.

ERIC Educational Resources Information Center

Cooke, Gary, Comp.

This annotated bibliography provides descriptions of films concerning child development and various approaches to early childhood education. Some are for classroom use, and others are intended as guides and resource materials for teachers. Attachments give addresses and phone numbers of film distributors and addresses, managers and phone number of…

Resource Letter PD-1 on Particle Detectors

ERIC Educational Resources Information Center

Trower, W. Peter

1970-01-01

Intended to guide college physicists to literature on nuclear and sub-nuclear particle detectors. The paper contains a discussion of (1) interactions of particles with matter and (2) individual particle detectors, each section being followed by an annotated bibliography of selected reference materials. Rankings are given to the articles on the…

Sesquicentennial: Gold Rush to Golden Statehood.

ERIC Educational Resources Information Center

Sabato, George

1998-01-01

Provides an annotated bibliography of educational resources that can be used to support instructional units on the Gold Rush or the sesquicentennial of California's statehood. The materials include workbooks, videos, teacher's guides, monographs, and magazines. Offers a brief history of the Gold Rush and a set of relevant discussion questions.…

Teacher's Guide to the Future.

ERIC Educational Resources Information Center

Murphy, Elaine M.; Cancellier, Patricia

1982-01-01

A brief introduction to futures education, an annotated listing of resources, and three ready-to-use student activities are provided. The introduction discusses the benefits of futures education; for example, it encourages students to make responsible decisions about the future. Next, it lists a variety of techniques developed by futurists to…

New Feminist Scholarship: A Guide to Bibliographies.

ERIC Educational Resources Information Center

Williamson, Jane

This partially annotated bibliography lists 391 bibliographies, resource lists, and literature reviews on women. The entries, published in the late 1960s and throughout the 1970s, are classified alphabetically by author into 30 categories including a general category, anthropology and sociology, art and music, child care, criminal justice,…

Choosing a President, 1968: The American Political Process.

ERIC Educational Resources Information Center

Tufts Univ., Medford, MA. Lincoln Filene Center for Citizenship and Public Affairs.

The student text portion of this set contains an account of the 1968 presidential election, from the state primaries to the election of Richard M. Nixon. The Teacher's Guide outlines objectives, teaching strategies, discussion questions, vocabulary, and an annotated listing of resources which includes educational and commercial films as well as…

The Internet: A Selective Annotated Bibliography of Print Material.

ERIC Educational Resources Information Center

Giguere, Marlene

1993-01-01

Describes 38 introductory print materials the novice may consult before using the Internet, including guides and directories to resources; general information about the Internet; materials about Internet applications such as electronic mail, remote login, and file transfer; and information about Internet tools such as Archie, Gopher, and WAIS…

CATH-Gene3D: Generation of the Resource and Its Use in Obtaining Structural and Functional Annotations for Protein Sequences.

PubMed

Dawson, Natalie L; Sillitoe, Ian; Lees, Jonathan G; Lam, Su Datt; Orengo, Christine A

2017-01-01

This chapter describes the generation of the data in the CATH-Gene3D online resource and how it can be used to study protein domains and their evolutionary relationships. Methods will be presented for: comparing protein structures, recognizing homologs, predicting domain structures within protein sequences, and subclassifying superfamilies into functionally pure families, together with a guide on using the webpages.

A Teacher's Science Companion.

ERIC Educational Resources Information Center

Perry, Phyllis J.

The purpose of this guide is to highlight some broad areas in which teachers and other adults have exceptional opportunities to encourage and enjoy teaching children science. Each area in the book provides some hands-on ideas for projects as well as an annotated list of readily available resources that might prove helpful on the topic at hand. The…

Reading Materials in Large Print: A Resource Guide. Reference Circular No. 97-02.

ERIC Educational Resources Information Center

Mendle, Gillian, Comp.

This reference circular contains information about large-print materials. Section 1 is an annotated list of selected sources of large-print materials available for purchase or loan. The sources are publishers or distributors, specialized libraries, and associations for persons with visual impairments. Several of these sources also provide general…

Legal Information Resources: A Guide for Maryland Libraries.

ERIC Educational Resources Information Center

Miller, Michael S., Ed.

This guidebook and annotated bibliography is designed to provide a basic listing of sources of state (Maryland), federal, and some general law for the non-law library community, and to offer some insight into the suggested approaches for dealing with legal reference inquiries. Listings of contributors and members of the Task Force on Improving…

International Relations: A Student's Guide to Reference Resources.

ERIC Educational Resources Information Center

Silvester, Elizabeth

Intended for students, this annotated bibliography describes reference materials in International Relations that may be found in either the McLennan or Law Library of McGill University. Scope includes political science, international law, and related areas in the social and behavioral sciences, but titles which relate to the foreign relations of a…

Acid Rain: A Resource Guide for Classroom, Laboratory, Field, and Debate Topics.

ERIC Educational Resources Information Center

Stoss, Frederick W.

1987-01-01

Provides a partially annotated bibliography of journals and book chapters which deal with acid rain. Includes selections which provide background information, ideas for introducing acid rain into science or social studies curricula, inventories of audio-visual aids, and non-print media to supplement classroom, laboratory, and field instruction.…

The RIF Guide to Encouraging Young Readers. A Fun-filled Sourcebook of over 200 Favorite Reading Activities of Kids and Parents from Across the Country, Plus an Annotated List of Books and Resources.

ERIC Educational Resources Information Center

Graves, Ruth, Ed.

Based on the notion that reading is both fun and fundamental, this book contains a stimulating array of activities that parents can use to engage their children in reading from the toddler stage through primary school. The first section provides information on how to use the guide, and some tips for encouraging young readers. The second and major…

A Selected and Annotated Resource List of Materials on the Holocaust.

ERIC Educational Resources Information Center

B'nai B'rith, New York, NY. Anti-Defamation League.

This guide for students, teachers, and librarians in secondary schools lists over 200 books and films about the Holocaust. The contents have been selected to help students and others find out what happened during the Holocaust, understand some of the reasons for it, develop a better understanding of the Jewish people, and reflect on their own…

Teaching World History in the Twenty-First Century: A Resource Book

ERIC Educational Resources Information Center

Roupp, Heidi, Ed.

2009-01-01

This practical handbook is designed to help anyone who is preparing to teach a world history course--or wants to teach it better. It opens with Peter Stearns's essay "Where Did World History Come From?" and closes with Jerry Bentley's annotated bibliographic guide to the essential content knowledge for teaching world history. In between,…

Selecting and Using a Core-Reference Collection. Second Edition.

ERIC Educational Resources Information Center

Nichols, Margaret Irby

Core-reference collections are the small number of sources which meet the basic needs of all libraries, and the purpose of this guide is to assist libraries in the selection, acquisition, and use of these resources. Section I, structured like an annotated bibliography, focuses on the selection of those works which should constitute the main…

Science Fiction: An Annotated Bibliography of Selected Resources in the University Libraries SUNY/Albany.

ERIC Educational Resources Information Center

Osielski, Mary Y., Comp.

This bibliography is a guide to sources of information in the field of science fiction which are available in the University Libraries at the State University of New York (SUNY) at Albany. Other libraries may find it useful as a reference tool for expanding their science fiction collections. Emphasis is on works which deal primarily with science…

A guide to best practices for Gene Ontology (GO) manual annotation

PubMed Central

Balakrishnan, Rama; Harris, Midori A.; Huntley, Rachael; Van Auken, Kimberly; Cherry, J. Michael

2013-01-01

The Gene Ontology Consortium (GOC) is a community-based bioinformatics project that classifies gene product function through the use of structured controlled vocabularies. A fundamental application of the Gene Ontology (GO) is in the creation of gene product annotations, evidence-based associations between GO definitions and experimental or sequence-based analysis. Currently, the GOC disseminates 126 million annotations covering >374 000 species including all the kingdoms of life. This number includes two classes of GO annotations: those created manually by experienced biocurators reviewing the literature or by examination of biological data (1.1 million annotations covering 2226 species) and those generated computationally via automated methods. As manual annotations are often used to propagate functional predictions between related proteins within and between genomes, it is critical to provide accurate consistent manual annotations. Toward this goal, we present here the conventions defined by the GOC for the creation of manual annotation. This guide represents the best practices for manual annotation as established by the GOC project over the past 12 years. We hope this guide will encourage research communities to annotate gene products of their interest to enhance the corpus of GO annotations available to all. Database URL: http://www.geneontology.org PMID:23842463

An annotated bibliography of selected guides for stream habitat improvement in the Pacific Northwest

USGS Publications Warehouse

Keim, R.F.; Price, A.B.; Hardin, T. S.; Skaugset, Arne E.; Bateman, D.S.; Gresswell, R.E.; Tesch, S. D.

2004-01-01

This annotated bibliography is a response to widespread interest in stream habitat improvement in the Pacific Northwest by land managers, governmental and nongovernmental organizations, and the lay public. Several guides to stream habitat improvement have been written in the past, but may not be easily accessible to people from diverse backgrounds. This annotated bibliography reviews 11 guides to stream habitat improvement so that readers can find literature appropriate to their needs. All reviews begin with summaries of the contents, stated audiences, and goals of each guide. Reviews also include subjective comments on the strengths and weaknesses of each guide. Finally, this bibliography includes recommendations of guides and combinations of guides judged most useful for a range of purposes. 

Elementary Health: Authorized Resources Annotated List.

ERIC Educational Resources Information Center

Alberta Dept. of Education, Edmonton. Curriculum Standards Branch.

This comprehensive, annotated resource list is designed to assist in selecting resources authorized by the Alberta (Canada) Education Department for the elementary health classroom (Grades 1-6). Within each grade and topic, annotated entries for basic learning resources are listed, followed by support learning resources and authorized teaching…

Russian Lyric Diction: A Practical Guide with Introduction and Annotations and a Bibliography with Annotations on Selected Sources

ERIC Educational Resources Information Center

Grayson, Craig M.

2012-01-01

The purpose of this dissertation is twofold-to investigate, in brief, the available guides to Russian lyric diction and to present my own comprehensive guide, which gives singers the tools to prepare the pronunciation of Russian vocal pieces independently. The survey examines four guides to Russian lyric diction found in popular anthologies or…

How High the Sky? How Far the Moon? Women Scientists Today - An Educational Program for Girls and Women in Math and Science, Lafayette, Colorado.

ERIC Educational Resources Information Center

Menard, Sharon L.

This packet of resource materials contains four sections: curriculum activities, a career guide for women, a role models list, and an annotated bibliography. These materials deal with women in science and mathematics and cover primary through high school educational levels. Skill Activities are outlined for use at various (K-12) levels which were…

Case Studies in Describing Scientific Research Efforts as Linked Data

NASA Astrophysics Data System (ADS)

Gandara, A.; Villanueva-Rosales, N.; Gates, A.

2013-12-01

The Web is growing with numerous scientific resources, prompting increased efforts in information management to consider integration and exchange of scientific resources. Scientists have many options to share scientific resources on the Web; however, existing options provide limited support to scientists in annotating and relating research resources resulting from a scientific research effort. Moreover, there is no systematic approach to documenting scientific research and sharing it on the Web. This research proposes the Collect-Annotate-Refine-Publish (CARP) Methodology as an approach for guiding documentation of scientific research on the Semantic Web as scientific collections. Scientific collections are structured descriptions about scientific research that make scientific results accessible based on context. In addition, scientific collections enhance the Linked Data data space and can be queried by machines. Three case studies were conducted on research efforts at the Cyber-ShARE Research Center of Excellence in order to assess the effectiveness of the methodology to create scientific collections. The case studies exposed the challenges and benefits of leveraging the Semantic Web and Linked Data data space to facilitate access, integration and processing of Web-accessible scientific resources and research documentation. As such, we present the case study findings and lessons learned in documenting scientific research using CARP.

Automated Patent Categorization and Guided Patent Search using IPC as Inspired by MeSH and PubMed.

PubMed

Eisinger, Daniel; Tsatsaronis, George; Bundschus, Markus; Wieneke, Ulrich; Schroeder, Michael

2013-04-15

Document search on PubMed, the pre-eminent database for biomedical literature, relies on the annotation of its documents with relevant terms from the Medical Subject Headings ontology (MeSH) for improving recall through query expansion. Patent documents are another important information source, though they are considerably less accessible. One option to expand patent search beyond pure keywords is the inclusion of classification information: Since every patent is assigned at least one class code, it should be possible for these assignments to be automatically used in a similar way as the MeSH annotations in PubMed. In order to develop a system for this task, it is necessary to have a good understanding of the properties of both classification systems. This report describes our comparative analysis of MeSH and the main patent classification system, the International Patent Classification (IPC). We investigate the hierarchical structures as well as the properties of the terms/classes respectively, and we compare the assignment of IPC codes to patents with the annotation of PubMed documents with MeSH terms.Our analysis shows a strong structural similarity of the hierarchies, but significant differences of terms and annotations. The low number of IPC class assignments and the lack of occurrences of class labels in patent texts imply that current patent search is severely limited. To overcome these limits, we evaluate a method for the automated assignment of additional classes to patent documents, and we propose a system for guided patent search based on the use of class co-occurrence information and external resources.

Automated Patent Categorization and Guided Patent Search using IPC as Inspired by MeSH and PubMed

PubMed Central

2013-01-01

Document search on PubMed, the pre-eminent database for biomedical literature, relies on the annotation of its documents with relevant terms from the Medical Subject Headings ontology (MeSH) for improving recall through query expansion. Patent documents are another important information source, though they are considerably less accessible. One option to expand patent search beyond pure keywords is the inclusion of classification information: Since every patent is assigned at least one class code, it should be possible for these assignments to be automatically used in a similar way as the MeSH annotations in PubMed. In order to develop a system for this task, it is necessary to have a good understanding of the properties of both classification systems. This report describes our comparative analysis of MeSH and the main patent classification system, the International Patent Classification (IPC). We investigate the hierarchical structures as well as the properties of the terms/classes respectively, and we compare the assignment of IPC codes to patents with the annotation of PubMed documents with MeSH terms. Our analysis shows a strong structural similarity of the hierarchies, but significant differences of terms and annotations. The low number of IPC class assignments and the lack of occurrences of class labels in patent texts imply that current patent search is severely limited. To overcome these limits, we evaluate a method for the automated assignment of additional classes to patent documents, and we propose a system for guided patent search based on the use of class co-occurrence information and external resources. PMID:23734562

Books in Spanish for Children and Young Adults: An Annotated Guide (Libros Infantiles y Juveniles en Espanol: Una Guia Anotada).

ERIC Educational Resources Information Center

Schon, Isabel

Intended to aid teachers, librarians, and others in the selection of Spanish-language books for children in grades K-12, the annotated guide includes books by Hispanic authors which highlight the lifestyle, folklore, heroes, history, fiction, poetry, theatre, and classical literature of Hispanic cultures. Most books included in the guide have been…

An Annotated Guide of Available Films. English for Speakers of Other Languages (ESOL) Secondary Centers. Beginning and Intermediate Levels.

ERIC Educational Resources Information Center

Hughes, Linda; Nahmani, Lois

This guide to films appropriate for junior and senior high school classes of English as a second language (ESL) includes general comments on the use of films in ESL instruction, notes on how to use the film guide, an outline of procedures and class activities for the presentation of films, and an annotated filmography. The films are listed in two…

Plant genome and transcriptome annotations: from misconceptions to simple solutions

PubMed Central

Bolger, Marie E; Arsova, Borjana; Usadel, Björn

2018-01-01

Abstract Next-generation sequencing has triggered an explosion of available genomic and transcriptomic resources in the plant sciences. Although genome and transcriptome sequencing has become orders of magnitudes cheaper and more efficient, often the functional annotation process is lagging behind. This might be hampered by the lack of a comprehensive enumeration of simple-to-use tools available to the plant researcher. In this comprehensive review, we present (i) typical ontologies to be used in the plant sciences, (ii) useful databases and resources used for functional annotation, (iii) what to expect from an annotated plant genome, (iv) an automated annotation pipeline and (v) a recipe and reference chart outlining typical steps used to annotate plant genomes/transcriptomes using publicly available resources. PMID:28062412

Mitochondrial Disease Sequence Data Resource (MSeqDR): a global grass-roots consortium to facilitate deposition, curation, annotation, and integrated analysis of genomic data for the mitochondrial disease clinical and research communities.

PubMed

Falk, Marni J; Shen, Lishuang; Gonzalez, Michael; Leipzig, Jeremy; Lott, Marie T; Stassen, Alphons P M; Diroma, Maria Angela; Navarro-Gomez, Daniel; Yeske, Philip; Bai, Renkui; Boles, Richard G; Brilhante, Virginia; Ralph, David; DaRe, Jeana T; Shelton, Robert; Terry, Sharon F; Zhang, Zhe; Copeland, William C; van Oven, Mannis; Prokisch, Holger; Wallace, Douglas C; Attimonelli, Marcella; Krotoski, Danuta; Zuchner, Stephan; Gai, Xiaowu

2015-03-01

Success rates for genomic analyses of highly heterogeneous disorders can be greatly improved if a large cohort of patient data is assembled to enhance collective capabilities for accurate sequence variant annotation, analysis, and interpretation. Indeed, molecular diagnostics requires the establishment of robust data resources to enable data sharing that informs accurate understanding of genes, variants, and phenotypes. The "Mitochondrial Disease Sequence Data Resource (MSeqDR) Consortium" is a grass-roots effort facilitated by the United Mitochondrial Disease Foundation to identify and prioritize specific genomic data analysis needs of the global mitochondrial disease clinical and research community. A central Web portal (https://mseqdr.org) facilitates the coherent compilation, organization, annotation, and analysis of sequence data from both nuclear and mitochondrial genomes of individuals and families with suspected mitochondrial disease. This Web portal provides users with a flexible and expandable suite of resources to enable variant-, gene-, and exome-level sequence analysis in a secure, Web-based, and user-friendly fashion. Users can also elect to share data with other MSeqDR Consortium members, or even the general public, either by custom annotation tracks or through the use of a convenient distributed annotation system (DAS) mechanism. A range of data visualization and analysis tools are provided to facilitate user interrogation and understanding of genomic, and ultimately phenotypic, data of relevance to mitochondrial biology and disease. Currently available tools for nuclear and mitochondrial gene analyses include an MSeqDR GBrowse instance that hosts optimized mitochondrial disease and mitochondrial DNA (mtDNA) specific annotation tracks, as well as an MSeqDR locus-specific database (LSDB) that curates variant data on more than 1300 genes that have been implicated in mitochondrial disease and/or encode mitochondria-localized proteins. MSeqDR is integrated with a diverse array of mtDNA data analysis tools that are both freestanding and incorporated into an online exome-level dataset curation and analysis resource (GEM.app) that is being optimized to support needs of the MSeqDR community. In addition, MSeqDR supports mitochondrial disease phenotyping and ontology tools, and provides variant pathogenicity assessment features that enable community review, feedback, and integration with the public ClinVar variant annotation resource. A centralized Web-based informed consent process is being developed, with implementation of a Global Unique Identifier (GUID) system to integrate data deposited on a given individual from different sources. Community-based data deposition into MSeqDR has already begun. Future efforts will enhance capabilities to incorporate phenotypic data that enhance genomic data analyses. MSeqDR will fill the existing void in bioinformatics tools and centralized knowledge that are necessary to enable efficient nuclear and mtDNA genomic data interpretation by a range of shareholders across both clinical diagnostic and research settings. Ultimately, MSeqDR is focused on empowering the global mitochondrial disease community to better define and explore mitochondrial diseases. Copyright © 2014 Elsevier Inc. All rights reserved.

Mitochondrial Disease Sequence Data Resource (MSeqDR): A global grass-roots consortium to facilitate deposition, curation, annotation, and integrated analysis of genomic data for the mitochondrial disease clinical and research communities

PubMed Central

Falk, Marni J.; Shen, Lishuang; Gonzalez, Michael; Leipzig, Jeremy; Lott, Marie T.; Stassen, Alphons P.M.; Diroma, Maria Angela; Navarro-Gomez, Daniel; Yeske, Philip; Bai, Renkui; Boles, Richard G.; Brilhante, Virginia; Ralph, David; DaRe, Jeana T.; Shelton, Robert; Terry, Sharon; Zhang, Zhe; Copeland, William C.; van Oven, Mannis; Prokisch, Holger; Wallace, Douglas C.; Attimonelli, Marcella; Krotoski, Danuta; Zuchner, Stephan; Gai, Xiaowu

2014-01-01

Success rates for genomic analyses of highly heterogeneous disorders can be greatly improved if a large cohort of patient data is assembled to enhance collective capabilities for accurate sequence variant annotation, analysis, and interpretation. Indeed, molecular diagnostics requires the establishment of robust data resources to enable data sharing that informs accurate understanding of genes, variants, and phenotypes. The “Mitochondrial Disease Sequence Data Resource (MSeqDR) Consortium” is a grass-roots effort facilitated by the United Mitochondrial Disease Foundation to identify and prioritize specific genomic data analysis needs of the global mitochondrial disease clinical and research community. A central Web portal (https://mseqdr.org) facilitates the coherent compilation, organization, annotation, and analysis of sequence data from both nuclear and mitochondrial genomes of individuals and families with suspected mitochondrial disease. This Web portal provides users with a flexible and expandable suite of resources to enable variant-, gene-, and exome-level sequence analysis in a secure, Web-based, and user-friendly fashion. Users can also elect to share data with other MSeqDR Consortium members, or even the general public, either by custom annotation tracks or through use of a convenient distributed annotation system (DAS) mechanism. A range of data visualization and analysis tools are provided to facilitate user interrogation and understanding of genomic, and ultimately phenotypic, data of relevance to mitochondrial biology and disease. Currently available tools for nuclear and mitochondrial gene analyses include an MSeqDR GBrowse instance that hosts optimized mitochondrial disease and mitochondrial DNA (mtDNA) specific annotation tracks, as well as an MSeqDR locus-specific database (LSDB) that curates variant data on more than 1,300 genes that have been implicated in mitochondrial disease and/or encode mitochondria-localized proteins. MSeqDR is integrated with a diverse array of mtDNA data analysis tools that are both freestanding and incorporated into an online exome-level dataset curation and analysis resource (GEM.app) that is being optimized to support needs of the MSeqDR community. In addition, MSeqDR supports mitochondrial disease phenotyping and ontology tools, and provides variant pathogenicity assessment features that enable community review, feedback, and integration with the public ClinVar variant annotation resource. A centralized Web-based informed consent process is being developed, with implementation of a Global Unique Identifier (GUID) system to integrate data deposited on a given individual from different sources. Community-based data deposition into MSeqDR has already begun. Future efforts will enhance capabilities to incorporate phenotypic data that enhance genomic data analyses. MSeqDR will fill the existing void in bioinformatics tools and centralized knowledge that are necessary to enable efficient nuclear and mtDNA genomic data interpretation by a range of shareholders across both clinical diagnostic and research settings. Ultimately, MSeqDR is focused on empowering the global mitochondrial disease community to better define and explore mitochondrial disease. PMID:25542617

The UniProtKB guide to the human proteome

PubMed Central

Breuza, Lionel; Poux, Sylvain; Estreicher, Anne; Famiglietti, Maria Livia; Magrane, Michele; Tognolli, Michael; Bridge, Alan; Baratin, Delphine; Redaschi, Nicole

2016-01-01

Advances in high-throughput and advanced technologies allow researchers to routinely perform whole genome and proteome analysis. For this purpose, they need high-quality resources providing comprehensive gene and protein sets for their organisms of interest. Using the example of the human proteome, we will describe the content of a complete proteome in the UniProt Knowledgebase (UniProtKB). We will show how manual expert curation of UniProtKB/Swiss-Prot is complemented by expert-driven automatic annotation to build a comprehensive, high-quality and traceable resource. We will also illustrate how the complexity of the human proteome is captured and structured in UniProtKB. Database URL: www.uniprot.org PMID:26896845

A Guide to Orientation Materials for Refugees and their Sponsors. A Selected, Annotated Bibliography Supplement.

ERIC Educational Resources Information Center

Center for Applied Linguistics, Washington, DC. Language and Orientation Resource Center.

An annotated bibliography of materials for the orientation of refugees and their sponsors is a supplement to "A Guide to Orientation Materials for Indochinese Refugees and their Sponsors," and includes 40 entries for materials pertinent to many other, non-Indochinese refugee groups. The materials are grouped alphabetically by the…

Prevention Bibliography 1991-1992: An Annotated Guide to Information on Alcohol, Tobacco, and Other Drug Use among Youth.

ERIC Educational Resources Information Center

Sieber, Robert G.; Austin, Gregory

The second in a series of annual guides to the literature on alcohol, tobacco, and other drug use among American youth and its prevention, this annotated bibliography for June 1991-June 1992 attempts to bridge the communication gap between practitioners and researchers. This bibliography consists of an indexed collection of 237 references with…

A Selected Annotated Bibliography on Work Time Options.

ERIC Educational Resources Information Center

Ivantcho, Barbara

This annotated bibliography is divided into three sections. Section I contains annotations of general publications on work time options. Section II presents resources on flexitime and the compressed work week. In Section III are found resources related to these reduced work time options: permanent part-time employment, job sharing, voluntary…

International Early Childhood Resources from Educational Research Abstracts Online (ERA)

ERIC Educational Resources Information Center

International Journal of Early Years Education, 2007

2007-01-01

This annotated bibliography provides abstracts for 12 resources relating to early childhood around the world. Each annotation contains: title; author name(s); Source (name of journal in which the resource was published); ISSN of the journal in which the resource was published; Issue (journal citation information for the resource within the…

International Early Childhood Resources from Educational Research Abstracts (ERA) Online

ERIC Educational Resources Information Center

International Journal of Early Years Education, 2011

2011-01-01

This annotated bibliography provides abstracts for 17 resources relating to early childhood around the world. Each annotation contains: title; author name(s); source (name of journal in which the resource was published); ISSN of the journal in which the resource was published; and issue (journal citation information for the resource within the…

International Early Childhood Resources from Educational Research Abstracts Online (ERA)

ERIC Educational Resources Information Center

International Journal of Early Years Education, 2006

2006-01-01

This annotated bibliography provides abstracts for 18 resources relating to early childhood around the world. Each annotation contains: title; author name(s); Source (name of journal in which the resource was published); ISSN of the journal in which the resource was published; Issue (journal citation information for the resource within the…

1974-75 NCTE Guide to Teaching Materials for English, Grades 7-12: An Annotated Listing of Textbooks and Related Materials for Secondary Schools Prepared by the NCTE Staff.

ERIC Educational Resources Information Center

National Council of Teachers of English, Urbana, IL.

This guide contains 550 annotations for English anthologies, textbooks, workbooks, multimedia packages, and other materials for grades 7-12. Works of literature, audiovisual materials, and professional publications are included only when integrally related to specific, listed instructional materials. Entries are grouped into the following subject…

Resource Letter ETC-1: extraterrestrial civilization.

PubMed

Kuiper, T B; Brin, G D

1989-01-01

This Resource Letter provides a guide to the literature about intelligent life beyond the human sphere of exploration. It offers a starting point for professionals and academics interested in participating in the debate about the existence of other technological civilizations or in the search for extraterrestrial intelligence (SETI). It can also serve as a reference for teaching. This Letter is not intended as an exhaustive bibliography, but several extensive bibliographies have been cited. The letter E after an item indicates elementary, nontechnical material of general interest to persons becoming informed in the field. Intermediate level material, of a somewhat more specialized nature, is indicated by the Letter I. The annotation A indicates advanced, technical material. An asterisk (*) precedes items to be included in an accompanying Reprint Book.

International Early Childhood Resources from Educational Research Abstracts Online (ERA)

ERIC Educational Resources Information Center

International Journal of Early Years Education, 2004

2004-01-01

This annotated bibliography provides abstracts for 14 resources relating to early childhood around the world. Each annotation contains: title; author name(s); Educational Research Abstract; Abstract number; Source (name of journal in which the resource was published); ISSN of the journal in which the resource was published; and Issue (journal…

Developing a Resource Center in Consumer Education: An Annotated Bibliography.

ERIC Educational Resources Information Center

Garman, E. Thomas; And Others

The rationale behind this annotated bibliography of over 1300 items is that every consumer education teacher needs numerous classroom resources to provide for the individual needs of his students, and these resources should be balanced in representing all content areas. The resource materials included, mostly booklets and pamphlets for classroom…

Information extraction from Italian medical reports: An ontology-driven approach.

PubMed

Viani, Natalia; Larizza, Cristiana; Tibollo, Valentina; Napolitano, Carlo; Priori, Silvia G; Bellazzi, Riccardo; Sacchi, Lucia

2018-03-01

In this work, we propose an ontology-driven approach to identify events and their attributes from episodes of care included in medical reports written in Italian. For this language, shared resources for clinical information extraction are not easily accessible. The corpus considered in this work includes 5432 non-annotated medical reports belonging to patients with rare arrhythmias. To guide the information extraction process, we built a domain-specific ontology that includes the events and the attributes to be extracted, with related regular expressions. The ontology and the annotation system were constructed on a development set, while the performance was evaluated on an independent test set. As a gold standard, we considered a manually curated hospital database named TRIAD, which stores most of the information written in reports. The proposed approach performs well on the considered Italian medical corpus, with a percentage of correct annotations above 90% for most considered clinical events. We also assessed the possibility to adapt the system to the analysis of another language (i.e., English), with promising results. Our annotation system relies on a domain ontology to extract and link information in clinical text. We developed an ontology that can be easily enriched and translated, and the system performs well on the considered task. In the future, it could be successfully used to automatically populate the TRIAD database. Copyright © 2017 Elsevier B.V. All rights reserved.

K-8 Collection.

ERIC Educational Resources Information Center

Web Feet, 2001

2001-01-01

This annotated subject guide to Web sites for grades K-8 focuses on biography, dinosaurs, fairy tales and folk tales, history, math, science, and calendar connections for December observances. Specific grade levels are indicated for each annotation. (LRW)

Annotated Bibliography of Children's Literature Resources on War, Terrorism, and Disaster since 1945: By Continents/Countries for Grades K-8

ERIC Educational Resources Information Center

Gangi, Jane M.

2009-01-01

This article presents an annotated bibliography of children's literature resources on war, terrorism, and disaster since 1945. This annotated bibliography focuses on grades K-8 from different continents/countries, including (1) Africa; (2) Asia; (3) The Caribbean; (4) Central and South America; (5) Europe; and (6) The Middle East.

Menominee Indian Tribe of Wisconsin. Part I: Inventory of Resources; Part II: Annotated Bibliography. Report No. 230.

ERIC Educational Resources Information Center

Stephens, Wayne E.; And Others

Designed to provide data and resource materials needed by the Menominee Restoration Committee and others involved in reservation organizational and development planning, this report covers the present status of the Menominee tribal resources and presents an annotated bibliography. The resource inventory includes maps, tables, and charts and is…

Youth, AIDS, and HIV: Resources for Educators and Policymakers, 1995. Bulletin 95244. Revised.

ERIC Educational Resources Information Center

Wisconsin State Dept. of Public Instruction, Madison.

This directory lists selected national, state, and local resources, and provides an annotated listing of various materials for AIDS education and HIV prevention. Telephone numbers and hours of operation are provided for national, state, and local resources--a brief statement of each agency's purview is also given. Annotated resources are divided…

SAS- Semantic Annotation Service for Geoscience resources on the web

NASA Astrophysics Data System (ADS)

Elag, M.; Kumar, P.; Marini, L.; Li, R.; Jiang, P.

2015-12-01

There is a growing need for increased integration across the data and model resources that are disseminated on the web to advance their reuse across different earth science applications. Meaningful reuse of resources requires semantic metadata to realize the semantic web vision for allowing pragmatic linkage and integration among resources. Semantic metadata associates standard metadata with resources to turn them into semantically-enabled resources on the web. However, the lack of a common standardized metadata framework as well as the uncoordinated use of metadata fields across different geo-information systems, has led to a situation in which standards and related Standard Names abound. To address this need, we have designed SAS to provide a bridge between the core ontologies required to annotate resources and information systems in order to enable queries and analysis over annotation from a single environment (web). SAS is one of the services that are provided by the Geosematnic framework, which is a decentralized semantic framework to support the integration between models and data and allow semantically heterogeneous to interact with minimum human intervention. Here we present the design of SAS and demonstrate its application for annotating data and models. First we describe how predicates and their attributes are extracted from standards and ingested in the knowledge-base of the Geosemantic framework. Then we illustrate the application of SAS in annotating data managed by SEAD and annotating simulation models that have web interface. SAS is a step in a broader approach to raise the quality of geoscience data and models that are published on the web and allow users to better search, access, and use of the existing resources based on standard vocabularies that are encoded and published using semantic technologies.

French as a Second Language. Annotated Bibliography of Learning Resources: Beginning Level. Early Childhood Services - Grade 12.

ERIC Educational Resources Information Center

Alberta Dept. of Education, Edmonton. Language Services Branch.

This annotated bibliography of instructional resources for Alberta (Canada) introductory French second language teaching in early childhood, elementary, and secondary education consists of citations in 10 categories: audio/video recordings; communicative activity resources (primarily texts and workbooks); dictionaries and vocabulary handbooks;…

IMG ER: a system for microbial genome annotation expert review and curation.

PubMed

Markowitz, Victor M; Mavromatis, Konstantinos; Ivanova, Natalia N; Chen, I-Min A; Chu, Ken; Kyrpides, Nikos C

2009-09-01

A rapidly increasing number of microbial genomes are sequenced by organizations worldwide and are eventually included into various public genome data resources. The quality of the annotations depends largely on the original dataset providers, with erroneous or incomplete annotations often carried over into the public resources and difficult to correct. We have developed an Expert Review (ER) version of the Integrated Microbial Genomes (IMG) system, with the goal of supporting systematic and efficient revision of microbial genome annotations. IMG ER provides tools for the review and curation of annotations of both new and publicly available microbial genomes within IMG's rich integrated genome framework. New genome datasets are included into IMG ER prior to their public release either with their native annotations or with annotations generated by IMG ER's annotation pipeline. IMG ER tools allow addressing annotation problems detected with IMG's comparative analysis tools, such as genes missed by gene prediction pipelines or genes without an associated function. Over the past year, IMG ER was used for improving the annotations of about 150 microbial genomes.

Necklace: combining reference and assembled transcriptomes for more comprehensive RNA-Seq analysis.

PubMed

Davidson, Nadia M; Oshlack, Alicia

2018-05-01

RNA sequencing (RNA-seq) analyses can benefit from performing a genome-guided and de novo assembly, in particular for species where the reference genome or the annotation is incomplete. However, tools for integrating an assembled transcriptome with reference annotation are lacking. Necklace is a software pipeline that runs genome-guided and de novo assembly and combines the resulting transcriptomes with reference genome annotations. Necklace constructs a compact but comprehensive superTranscriptome out of the assembled and reference data. Reads are subsequently aligned and counted in preparation for differential expression testing. Necklace allows a comprehensive transcriptome to be built from a combination of assembled and annotated transcripts, which results in a more comprehensive transcriptome for the majority of organisms. In addition RNA-seq data are mapped back to this newly created superTranscript reference to enable differential expression testing with standard methods.

An Atlas of annotations of Hydra vulgaris transcriptome.

PubMed

Evangelista, Daniela; Tripathi, Kumar Parijat; Guarracino, Mario Rosario

2016-09-22

RNA sequencing takes advantage of the Next Generation Sequencing (NGS) technologies for analyzing RNA transcript counts with an excellent accuracy. Trying to interpret this huge amount of data in biological information is still a key issue, reason for which the creation of web-resources useful for their analysis is highly desiderable. Starting from a previous work, Transcriptator, we present the Atlas of Hydra's vulgaris, an extensible web tool in which its complete transcriptome is annotated. In order to provide to the users an advantageous resource that include the whole functional annotated transcriptome of Hydra vulgaris water polyp, we implemented the Atlas web-tool contains 31.988 accesible and downloadable transcripts of this non-reference model organism. Atlas, as a freely available resource, can be considered a valuable tool to rapidly retrieve functional annotation for transcripts differentially expressed in Hydra vulgaris exposed to the distinct experimental treatments. WEB RESOURCE URL: http://www-labgtp.na.icar.cnr.it/Atlas .

NCTE (National Council of Teachers of English) Guide to Teaching Materials for English, Grades 7-12; An Annotated Listing of Textbooks and Related Materials for Secondary Schools Prepared by the NCTE Staff. 1975-76 Supplement.

ERIC Educational Resources Information Center

National Council of Teachers of English, Urbana, IL.

This supplement to the "NCTE Guide to Teaching Materials for English, Grades 7-12" contains annotations for English anthologies, textbooks, workbooks, multimedia packages, and other materials for the junior high and high school levels. Works of literature, audiovisual materials, and professional publications are included when related to specific,…

ANALYTiC: An Active Learning System for Trajectory Classification.

PubMed

Soares Junior, Amilcar; Renso, Chiara; Matwin, Stan

2017-01-01

The increasing availability and use of positioning devices has resulted in large volumes of trajectory data. However, semantic annotations for such data are typically added by domain experts, which is a time-consuming task. Machine-learning algorithms can help infer semantic annotations from trajectory data by learning from sets of labeled data. Specifically, active learning approaches can minimize the set of trajectories to be annotated while preserving good performance measures. The ANALYTiC web-based interactive tool visually guides users through this annotation process.

AgBase: supporting functional modeling in agricultural organisms

PubMed Central

McCarthy, Fiona M.; Gresham, Cathy R.; Buza, Teresia J.; Chouvarine, Philippe; Pillai, Lakshmi R.; Kumar, Ranjit; Ozkan, Seval; Wang, Hui; Manda, Prashanti; Arick, Tony; Bridges, Susan M.; Burgess, Shane C.

2011-01-01

AgBase (http://www.agbase.msstate.edu/) provides resources to facilitate modeling of functional genomics data and structural and functional annotation of agriculturally important animal, plant, microbe and parasite genomes. The website is redesigned to improve accessibility and ease of use, including improved search capabilities. Expanded capabilities include new dedicated pages for horse, cat, dog, cotton, rice and soybean. We currently provide 590 240 Gene Ontology (GO) annotations to 105 454 gene products in 64 different species, including GO annotations linked to transcripts represented on agricultural microarrays. For many of these arrays, this provides the only functional annotation available. GO annotations are available for download and we provide comprehensive, species-specific GO annotation files for 18 different organisms. The tools available at AgBase have been expanded and several existing tools improved based upon user feedback. One of seven new tools available at AgBase, GOModeler, supports hypothesis testing from functional genomics data. We host several associated databases and provide genome browsers for three agricultural pathogens. Moreover, we provide comprehensive training resources (including worked examples and tutorials) via links to Educational Resources at the AgBase website. PMID:21075795

What should students learn about complementary and alternative medicine?

PubMed

Gaster, Barak; Unterborn, John N; Scott, Richard B; Schneeweiss, Ronald

2007-10-01

With thousands of complementary and alternative medicine (CAM) treatments currently being used in the United States today, it is challenging to design a concise body of CAM content which will fit into already overly full curricula for health care students. The purpose of this article is to outline key principles which 15 National Center for Complementary and Alternative Medicine-funded education programs found useful when developing CAM course-work and selecting CAM content. Three key guiding principles are discussed: teach foundational CAM competencies to give students a framework for learning about CAM; choose specific content on the basis of evidence, demographics and condition (what conditions are most appropriate for CAM therapies?); and finally, provide students with skills for future learning, including where to find reliable information about CAM and how to search the scientific literature and assess the results of CAM research. Most of the programs developed evidence-based guides to help students find reliable CAM resources. The cumulative experiences of the 15 programs have been compiled, and an annotated table outlining the most highly recommended resources about CAM is presented.

Marky: a tool supporting annotation consistency in multi-user and iterative document annotation projects.

PubMed

Pérez-Pérez, Martín; Glez-Peña, Daniel; Fdez-Riverola, Florentino; Lourenço, Anália

2015-02-01

Document annotation is a key task in the development of Text Mining methods and applications. High quality annotated corpora are invaluable, but their preparation requires a considerable amount of resources and time. Although the existing annotation tools offer good user interaction interfaces to domain experts, project management and quality control abilities are still limited. Therefore, the current work introduces Marky, a new Web-based document annotation tool equipped to manage multi-user and iterative projects, and to evaluate annotation quality throughout the project life cycle. At the core, Marky is a Web application based on the open source CakePHP framework. User interface relies on HTML5 and CSS3 technologies. Rangy library assists in browser-independent implementation of common DOM range and selection tasks, and Ajax and JQuery technologies are used to enhance user-system interaction. Marky grants solid management of inter- and intra-annotator work. Most notably, its annotation tracking system supports systematic and on-demand agreement analysis and annotation amendment. Each annotator may work over documents as usual, but all the annotations made are saved by the tracking system and may be further compared. So, the project administrator is able to evaluate annotation consistency among annotators and across rounds of annotation, while annotators are able to reject or amend subsets of annotations made in previous rounds. As a side effect, the tracking system minimises resource and time consumption. Marky is a novel environment for managing multi-user and iterative document annotation projects. Compared to other tools, Marky offers a similar visually intuitive annotation experience while providing unique means to minimise annotation effort and enforce annotation quality, and therefore corpus consistency. Marky is freely available for non-commercial use at http://sing.ei.uvigo.es/marky. Copyright © 2014 Elsevier Ireland Ltd. All rights reserved.

Differentiating signals to make biological sense - A guide through databases for MS-based non-targeted metabolomics.

PubMed

Gil de la Fuente, Alberto; Grace Armitage, Emily; Otero, Abraham; Barbas, Coral; Godzien, Joanna

2017-09-01

Metabolite identification is one of the most challenging steps in metabolomics studies and reflects one of the greatest bottlenecks in the entire workflow. The success of this step determines the success of the entire research, therefore the quality at which annotations are given requires special attention. A variety of tools and resources are available to aid metabolite identification or annotation, offering different and often complementary functionalities. In preparation for this article, almost 50 databases were reviewed, from which 17 were selected for discussion, chosen for their online ESI-MS functionality. The general characteristics and functions of each database is discussed in turn, considering the advantages and limitations of each along with recommendations for optimal use of each tool, as derived from experiences encountered at the Centre for Metabolomics and Bioanalysis (CEMBIO) in Madrid. These databases were evaluated considering their utility in non-targeted metabolomics, including aspects such as identifier assignment, structural assignment and interpretation of results. © 2017 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

PATtyFams: Protein families for the microbial genomes in the PATRIC database

DOE PAGES

Davis, James J.; Gerdes, Svetlana; Olsen, Gary J.; ...

2016-02-08

The ability to build accurate protein families is a fundamental operation in bioinformatics that influences comparative analyses, genome annotation, and metabolic modeling. For several years we have been maintaining protein families for all microbial genomes in the PATRIC database (Pathosystems Resource Integration Center, patricbrc.org) in order to drive many of the comparative analysis tools that are available through the PATRIC website. However, due to the burgeoning number of genomes, traditional approaches for generating protein families are becoming prohibitive. In this report, we describe a new approach for generating protein families, which we call PATtyFams. This method uses the k-mer-based functionmore » assignments available through RAST (Rapid Annotation using Subsystem Technology) to rapidly guide family formation, and then differentiates the function-based groups into families using a Markov Cluster algorithm (MCL). In conclusion, this new approach for generating protein families is rapid, scalable and has properties that are consistent with alignment-based methods.« less

PATtyFams: Protein families for the microbial genomes in the PATRIC database

DOE Office of Scientific and Technical Information (OSTI.GOV)

Davis, James J.; Gerdes, Svetlana; Olsen, Gary J.

The ability to build accurate protein families is a fundamental operation in bioinformatics that influences comparative analyses, genome annotation, and metabolic modeling. For several years we have been maintaining protein families for all microbial genomes in the PATRIC database (Pathosystems Resource Integration Center, patricbrc.org) in order to drive many of the comparative analysis tools that are available through the PATRIC website. However, due to the burgeoning number of genomes, traditional approaches for generating protein families are becoming prohibitive. In this report, we describe a new approach for generating protein families, which we call PATtyFams. This method uses the k-mer-based functionmore » assignments available through RAST (Rapid Annotation using Subsystem Technology) to rapidly guide family formation, and then differentiates the function-based groups into families using a Markov Cluster algorithm (MCL). In conclusion, this new approach for generating protein families is rapid, scalable and has properties that are consistent with alignment-based methods.« less

The Energy Education Bibliography. An Annotated Bibliography of Key Resources for Energy and Conservation Education.

ERIC Educational Resources Information Center

Scherner, Sharon; And Others

The annotated bibliography lists approximately 180 energy and conservation education resources. The bibliography is intended to aid K-12 classroom teachers and curriculum developers identify key resources as they develop and implement energy education programs. Sample topics in the works listed deal with the story of natural gas, living with…

Semantic biomedical resource discovery: a Natural Language Processing framework.

PubMed

Sfakianaki, Pepi; Koumakis, Lefteris; Sfakianakis, Stelios; Iatraki, Galatia; Zacharioudakis, Giorgos; Graf, Norbert; Marias, Kostas; Tsiknakis, Manolis

2015-09-30

A plethora of publicly available biomedical resources do currently exist and are constantly increasing at a fast rate. In parallel, specialized repositories are been developed, indexing numerous clinical and biomedical tools. The main drawback of such repositories is the difficulty in locating appropriate resources for a clinical or biomedical decision task, especially for non-Information Technology expert users. In parallel, although NLP research in the clinical domain has been active since the 1960s, progress in the development of NLP applications has been slow and lags behind progress in the general NLP domain. The aim of the present study is to investigate the use of semantics for biomedical resources annotation with domain specific ontologies and exploit Natural Language Processing methods in empowering the non-Information Technology expert users to efficiently search for biomedical resources using natural language. A Natural Language Processing engine which can "translate" free text into targeted queries, automatically transforming a clinical research question into a request description that contains only terms of ontologies, has been implemented. The implementation is based on information extraction techniques for text in natural language, guided by integrated ontologies. Furthermore, knowledge from robust text mining methods has been incorporated to map descriptions into suitable domain ontologies in order to ensure that the biomedical resources descriptions are domain oriented and enhance the accuracy of services discovery. The framework is freely available as a web application at ( http://calchas.ics.forth.gr/ ). For our experiments, a range of clinical questions were established based on descriptions of clinical trials from the ClinicalTrials.gov registry as well as recommendations from clinicians. Domain experts manually identified the available tools in a tools repository which are suitable for addressing the clinical questions at hand, either individually or as a set of tools forming a computational pipeline. The results were compared with those obtained from an automated discovery of candidate biomedical tools. For the evaluation of the results, precision and recall measurements were used. Our results indicate that the proposed framework has a high precision and low recall, implying that the system returns essentially more relevant results than irrelevant. There are adequate biomedical ontologies already available, sufficiency of existing NLP tools and quality of biomedical annotation systems for the implementation of a biomedical resources discovery framework, based on the semantic annotation of resources and the use on NLP techniques. The results of the present study demonstrate the clinical utility of the application of the proposed framework which aims to bridge the gap between clinical question in natural language and efficient dynamic biomedical resources discovery.

Construction of an annotated corpus to support biomedical information extraction

PubMed Central

Thompson, Paul; Iqbal, Syed A; McNaught, John; Ananiadou, Sophia

2009-01-01

Background Information Extraction (IE) is a component of text mining that facilitates knowledge discovery by automatically locating instances of interesting biomedical events from huge document collections. As events are usually centred on verbs and nominalised verbs, understanding the syntactic and semantic behaviour of these words is highly important. Corpora annotated with information concerning this behaviour can constitute a valuable resource in the training of IE components and resources. Results We have defined a new scheme for annotating sentence-bound gene regulation events, centred on both verbs and nominalised verbs. For each event instance, all participants (arguments) in the same sentence are identified and assigned a semantic role from a rich set of 13 roles tailored to biomedical research articles, together with a biological concept type linked to the Gene Regulation Ontology. To our knowledge, our scheme is unique within the biomedical field in terms of the range of event arguments identified. Using the scheme, we have created the Gene Regulation Event Corpus (GREC), consisting of 240 MEDLINE abstracts, in which events relating to gene regulation and expression have been annotated by biologists. A novel method of evaluating various different facets of the annotation task showed that average inter-annotator agreement rates fall within the range of 66% - 90%. Conclusion The GREC is a unique resource within the biomedical field, in that it annotates not only core relationships between entities, but also a range of other important details about these relationships, e.g., location, temporal, manner and environmental conditions. As such, it is specifically designed to support bio-specific tool and resource development. It has already been used to acquire semantic frames for inclusion within the BioLexicon (a lexical, terminological resource to aid biomedical text mining). Initial experiments have also shown that the corpus may viably be used to train IE components, such as semantic role labellers. The corpus and annotation guidelines are freely available for academic purposes. PMID:19852798

GFam: a platform for automatic annotation of gene families.

PubMed

Sasidharan, Rajkumar; Nepusz, Tamás; Swarbreck, David; Huala, Eva; Paccanaro, Alberto

2012-10-01

We have developed GFam, a platform for automatic annotation of gene/protein families. GFam provides a framework for genome initiatives and model organism resources to build domain-based families, derive meaningful functional labels and offers a seamless approach to propagate functional annotation across periodic genome updates. GFam is a hybrid approach that uses a greedy algorithm to chain component domains from InterPro annotation provided by its 12 member resources followed by a sequence-based connected component analysis of un-annotated sequence regions to derive consensus domain architecture for each sequence and subsequently generate families based on common architectures. Our integrated approach increases sequence coverage by 7.2 percentage points and residue coverage by 14.6 percentage points higher than the coverage relative to the best single-constituent database within InterPro for the proteome of Arabidopsis. The true power of GFam lies in maximizing annotation provided by the different InterPro data sources that offer resource-specific coverage for different regions of a sequence. GFam's capability to capture higher sequence and residue coverage can be useful for genome annotation, comparative genomics and functional studies. GFam is a general-purpose software and can be used for any collection of protein sequences. The software is open source and can be obtained from http://www.paccanarolab.org/software/gfam/.

BμG@Sbase—a microbial gene expression and comparative genomic database

PubMed Central

Witney, Adam A.; Waldron, Denise E.; Brooks, Lucy A.; Tyler, Richard H.; Withers, Michael; Stoker, Neil G.; Wren, Brendan W.; Butcher, Philip D.; Hinds, Jason

2012-01-01

The reducing cost of high-throughput functional genomic technologies is creating a deluge of high volume, complex data, placing the burden on bioinformatics resources and tool development. The Bacterial Microarray Group at St George's (BμG@S) has been at the forefront of bacterial microarray design and analysis for over a decade and while serving as a hub of a global network of microbial research groups has developed BμG@Sbase, a microbial gene expression and comparative genomic database. BμG@Sbase (http://bugs.sgul.ac.uk/bugsbase/) is a web-browsable, expertly curated, MIAME-compliant database that stores comprehensive experimental annotation and multiple raw and analysed data formats. Consistent annotation is enabled through a structured set of web forms, which guide the user through the process following a set of best practices and controlled vocabulary. The database currently contains 86 expertly curated publicly available data sets (with a further 124 not yet published) and full annotation information for 59 bacterial microarray designs. The data can be browsed and queried using an explorer-like interface; integrating intuitive tree diagrams to present complex experimental details clearly and concisely. Furthermore the modular design of the database will provide a robust platform for integrating other data types beyond microarrays into a more Systems analysis based future. PMID:21948792

BμG@Sbase--a microbial gene expression and comparative genomic database.

PubMed

Witney, Adam A; Waldron, Denise E; Brooks, Lucy A; Tyler, Richard H; Withers, Michael; Stoker, Neil G; Wren, Brendan W; Butcher, Philip D; Hinds, Jason

2012-01-01

The reducing cost of high-throughput functional genomic technologies is creating a deluge of high volume, complex data, placing the burden on bioinformatics resources and tool development. The Bacterial Microarray Group at St George's (BμG@S) has been at the forefront of bacterial microarray design and analysis for over a decade and while serving as a hub of a global network of microbial research groups has developed BμG@Sbase, a microbial gene expression and comparative genomic database. BμG@Sbase (http://bugs.sgul.ac.uk/bugsbase/) is a web-browsable, expertly curated, MIAME-compliant database that stores comprehensive experimental annotation and multiple raw and analysed data formats. Consistent annotation is enabled through a structured set of web forms, which guide the user through the process following a set of best practices and controlled vocabulary. The database currently contains 86 expertly curated publicly available data sets (with a further 124 not yet published) and full annotation information for 59 bacterial microarray designs. The data can be browsed and queried using an explorer-like interface; integrating intuitive tree diagrams to present complex experimental details clearly and concisely. Furthermore the modular design of the database will provide a robust platform for integrating other data types beyond microarrays into a more Systems analysis based future.

MIPS bacterial genomes functional annotation benchmark dataset.

PubMed

Tetko, Igor V; Brauner, Barbara; Dunger-Kaltenbach, Irmtraud; Frishman, Goar; Montrone, Corinna; Fobo, Gisela; Ruepp, Andreas; Antonov, Alexey V; Surmeli, Dimitrij; Mewes, Hans-Wernen

2005-05-15

Any development of new methods for automatic functional annotation of proteins according to their sequences requires high-quality data (as benchmark) as well as tedious preparatory work to generate sequence parameters required as input data for the machine learning methods. Different program settings and incompatible protocols make a comparison of the analyzed methods difficult. The MIPS Bacterial Functional Annotation Benchmark dataset (MIPS-BFAB) is a new, high-quality resource comprising four bacterial genomes manually annotated according to the MIPS functional catalogue (FunCat). These resources include precalculated sequence parameters, such as sequence similarity scores, InterPro domain composition and other parameters that could be used to develop and benchmark methods for functional annotation of bacterial protein sequences. These data are provided in XML format and can be used by scientists who are not necessarily experts in genome annotation. BFAB is available at http://mips.gsf.de/proj/bfab

Annotated Bibliography of the Air Force Human Resources Laboratory Technical Reports - 1979.

DTIC Science & Technology

1981-05-01

Force Human Resources Laboratory, March 1980. (Covers all AFHRL projects.) NTIS. This document provides the academic and industrial R&D community with...D-AI02 04𔃾 AIR FORCE HUMAN RESOURCES LAB BROOKS AF TX F/G 5/2 ANNOTATED BIBLIOGRAPHY OF THE AIR FORCE HUMAN RESOURCES LABORAT--ETC(U) MAY 81 E M...OF THE AIR FORCE HUMAN RESOURCES LABORATORY TECHNICAL REPORTS - 1979U M By M Esther M. Barlow A N TECHNICAL SERVICES DIVISION Brooks Air Force Base

Annotated Bibliography of Special Education Instructional Materials: Supplement.

ERIC Educational Resources Information Center

Cook, Iva Dean, Comp.

Presented is an annotated bibliography of instructional materials available through the West Virginia College of Graduate Studies Special Education Instructional Materials Center (SEIMC). Materials are grouped into the following major categories: art, curriculum guides, guidance, health and safety, homemaking, language arts, mathematics, music,…

Annotated Videography. Part 3. [Revised].

ERIC Educational Resources Information Center

United States Holocaust Memorial Museum, Washington, DC.

This annotated videography has been designed to identify videotapes addressing Holocaust history that have been used effectively in classrooms and are available readily to most communities. The guide is divided into 15 topical categories, including: life before the Holocaust; perpetrators; propaganda; racism; antisemitism; mosaic of victims;…

Inclusion: An Annotated Bibliography.

ERIC Educational Resources Information Center

Moore, Caroline; Carter, Susanne

This annotated bibliography is a compilation of recently published literature about inclusion of students with disabilities in the mainstream of school and community life. The 279 resources are organized into 19 topical areas and are indexed by more than 200 subject descriptors. Within each section, resources are displayed alphabetically by author…

Genome re-annotation: a wiki solution?

PubMed Central

Salzberg, Steven L

2007-01-01

The annotation of most genomes becomes outdated over time, owing in part to our ever-improving knowledge of genomes and in part to improvements in bioinformatics software. Unfortunately, annotation is rarely if ever updated and resources to support routine reannotation are scarce. Wiki software, which would allow many scientists to edit each genome's annotation, offers one possible solution. PMID:17274839

Library Guides to Business Information.

ERIC Educational Resources Information Center

Harris, Jamie L., Comp.

This collection of library guides is designed to introduce undergraduate students at Chicago State University to basic business reference sources. Annotated bibliographies cover the subject areas of business management, marketing, and finance. Guides in the collection include: (1) Researching the Company (Chicago and Illinois business and national…

A Selective United Nations Guide.

ERIC Educational Resources Information Center

Petty, Johnese G.

This annotated, selective bibliography is a guide to the history of the United Nations, its publications, and four of the 14 specialized agencies and their publications. It is organized under the following headings: biographies, guides, official records, indexes and abstracts, laws, yearbooks, bibliographies, directories, statistics, periodicals,…

American Revolution, Fitness, Presidents, U.S., Rocks & Minerals, Spelling, Vocabulary.

ERIC Educational Resources Information Center

Web Feet, 2002

2002-01-01

This annotated subject guide to Web sites for grades K-8 focuses on the American Revolution, fitness, U.S. Presidents, rocks and minerals, spelling, vocabulary, and calendar connections for Women's History Month and other March observations. Specific grade levels are indicated for each annotation. (LRW)

Coping and Adaptation: An Annotated Bibliography and Study Guide.

ERIC Educational Resources Information Center

Coelho, George V., Ed.; Irving, Richard I., Ed.

This annotated bibliography concerns the styles and strategies used to cope with stressful situations and to adapt to pathological conditions, and provides mental health researchers and practitioners with recent, relevant mental health information on theoretical, developmental, clinical, behavioral, and social issues about coping and adaptation.…

Resources for Helping Young Children Deal with Death.

ERIC Educational Resources Information Center

Wass, Hannelore

This bibliography contains selected resources (1965-1983) to help parents and teachers assist young children with death-related concerns. Included are materials for adults: an annotated list of books on death (13 citations); a bibliography of articles about children and death from recent literature (50 citations); and an annotated list of…

The Career Education Resource Center Annotated Catalog, 1978-1979.

ERIC Educational Resources Information Center

Keene, Lois, Ed.

This catalog provides an annotated list of the career education materials which may be borrowed for previewing from the Career Education Resource Center in Colorado. Covering materials of interest to educators in kindergarten through postsecondary programs, the catalog includes items produced by classroom teachers, commercial publishers, business…

AphidBase: A centralized bioinformatic resource for annotation of the pea aphid genome

PubMed Central

Legeai, Fabrice; Shigenobu, Shuji; Gauthier, Jean-Pierre; Colbourne, John; Rispe, Claude; Collin, Olivier; Richards, Stephen; Wilson, Alex C. C.; Tagu, Denis

2015-01-01

AphidBase is a centralized bioinformatic resource that was developed to facilitate community annotation of the pea aphid genome by the International Aphid Genomics Consortium (IAGC). The AphidBase Information System designed to organize and distribute genomic data and annotations for a large international community was constructed using open source software tools from the Generic Model Organism Database (GMOD). The system includes Apollo and GBrowse utilities as well as a wiki, blast search capabilities and a full text search engine. AphidBase strongly supported community cooperation and coordination in the curation of gene models during community annotation of the pea aphid genome. AphidBase can be accessed at http://www.aphidbase.com. PMID:20482635

Annual Editions: Early Childhood Education 06/07

ERIC Educational Resources Information Center

Paciorek, Karen Menke, Ed.

2006-01-01

This 27th edition of "Annual Editions: Early Childhood Education" provides convenient, inexpensive access to current articles selected from the best of the public press. Organizational features include: an annotated listing of selected World Wide Web sites; an annotated table of contents; a topic guide; a general introduction; brief overviews for…

College and University Rankings: Part 2--An Annotated Bibliography of Analysis, Criticism, and Evaluation.

ERIC Educational Resources Information Center

Hattendorf, Lynn C.

1987-01-01

This annotated bibliography of recent articles and books on academic rankings updates an article in the Spring 1986 "RQ." Items are listed by subject and ranking in general; individual guides; subject areas including accounting, advertising, biogeography, business, communications, data communications, economics, music, publishing,…

Teaching Adult Vocational Education Learners. Annotated and Selected Bibliography. Final Report.

ERIC Educational Resources Information Center

Warner, Larry S.; Humburg, Renae

This selected annotated bibliography contains eighty-three entries (includes books, reports, guides, papers, and articles) relevant to teaching adult vocational education learners. The citations are organized alphabetically by author and each one includes some or all of the following: source, title, sponsoring agency, publisher, city, state, date,…

Numeracy Books for Adult Learners. An Annotated Bibliography.

ERIC Educational Resources Information Center

Ciancone, Thomas

This annotated bibliography profiles 27 print publications about and for adults whose mathematics skills are below the eighth-grade level. Entries describing the following materials are presented: 5 handbooks/guides (including an introduction to numeracy teaching, adult numeracy training pack, and manual for teaching place value); 2 publications…

The Chicago American Indian Community, 1893-1988. Annotated Bibliography and Guide to Sources in Chicago.

ERIC Educational Resources Information Center

Beck, David

This annotated bibliography identifies and describes documentary evidence of Chicago's American Indian population since the 1893 World's Columbian Exposition. Sources include studies and reports generated by Indian community organizations and agencies, community newsletters, newspapers, oral histories, grant applications, personal papers, and…

A Guide to Orientation Materials for Indochinese Refugees and Their Sponsors. A Selected, Annotated Bibliography.

ERIC Educational Resources Information Center

Center for Applied Linguistics, Washington, DC. Language and Orientation Resource Center.

This is an annotated bibliography of orientation materials for Indochinese refugees and their sponsors. The materials have been grouped under fourteen headings: community services, consumer education, culture, education, employment, family planning and child care, finances, health, housing, legal problems, nutrition, sponsorship and resettlement,…

Teacher Education Program Evaluation: An Annotated Bibliography and Guide to Research.

ERIC Educational Resources Information Center

Ayers, Jerry B.; Berney, Mary F.

This book includes an annotated bibliography of the essentials needed to conduct an effective evaluation of a teacher education program. Specific information on evaluation includes: (1) general evaluation techniques, (2) evaluation of candidates and students, (3) evaluation of the knowledge base, (4) quality controls, (5) evaluation of laboratory…

Systemic Planning: An Annotated Bibliography and Literature Guide. Exchange Bibliography No. 91.

ERIC Educational Resources Information Center

Catanese, Anthony James

Systemic planning is an operational approach to using scientific rigor and qualitative judgment in a complementary manner. It integrates rigorous techniques and methods from systems analysis, cybernetics, decision theory, and work programing. The annotated reference sources in this bibliography include those works that have been most influential…

Microcomputers and the Media Specialist: An Annotated Bibliography.

ERIC Educational Resources Information Center

Miller, Inabeth

An overview of the literature reflecting the rapid development of interest in microcomputer use in education since 1978 is followed by an annotated bibliography which lists books, articles, and ERIC documents in nine categories. The first section includes materials of general interest--historical background, guides to using computers in the…

Careers; Current Events; Government, U.S.; Insects; Science Experiments; Terrorism, War on.

ERIC Educational Resources Information Center

Web Feet, 2001

2001-01-01

This annotated subject guide to Web sites for grades K-8 focuses on careers, current events, government, insects, science experiments, the war on terrorism, and calendar connections for Martin Luther King Day and other January observances. Specific grade levels are indicated for each annotation. (LRW)

WORKSHOPS FOR THE HANDICAPPED, AN ANNOTATED BIBLIOGRAPHY--NO. 3.

ERIC Educational Resources Information Center

PERKINS, DOROTHY C.; AND OTHERS

THESE 126 ANNOTATIONS ARE THE THIRD VOLUME OF A CONTINUING SERIES OF BIBLIOGRAPHIES LISTING ARTICLES APPEARING IN JOURNALS AND CONFERENCE, RESEARCH, AND PROJECT REPORTS. LISTINGS INCLUDE TESTS, TEST RESULTS, STAFF TRAINING PROGRAMS, GUIDES FOR COUNSELORS AND TEACHERS, AND ARCHITECTURAL PLANNING, AND RELATE TO THE MENTALLY RETARDED, EMOTIONALLY…

A new approach for annotation of transposable elements using small RNA mapping

PubMed Central

El Baidouri, Moaine; Kim, Kyung Do; Abernathy, Brian; Arikit, Siwaret; Maumus, Florian; Panaud, Olivier; Meyers, Blake C.; Jackson, Scott A.

2015-01-01

Transposable elements (TEs) are mobile genomic DNA sequences found in most organisms. They so densely populate the genomes of many eukaryotic species that they are often the major constituents. With the rapid generation of many plant genome sequencing projects over the past few decades, there is an urgent need for improved TE annotation as a prerequisite for genome-wide studies. Analogous to the use of RNA-seq for gene annotation, we propose a new method for de novo TE annotation that uses as a guide 24 nt-siRNAs that are a part of TE silencing pathways. We use this new approach, called TASR (for Transposon Annotation using Small RNAs), for de novo annotation of TEs in Arabidopsis, rice and soybean and demonstrate that this strategy can be successfully applied for de novo TE annotation in plants. Executable PERL is available for download from: http://tasr-pipeline.sourceforge.net/ PMID:25813049

The Biological Reference Repository (BioR): a rapid and flexible system for genomics annotation.

PubMed

Kocher, Jean-Pierre A; Quest, Daniel J; Duffy, Patrick; Meiners, Michael A; Moore, Raymond M; Rider, David; Hossain, Asif; Hart, Steven N; Dinu, Valentin

2014-07-01

The Biological Reference Repository (BioR) is a toolkit for annotating variants. BioR stores public and user-specific annotation sources in indexed JSON-encoded flat files (catalogs). The BioR toolkit provides the functionality to combine and retrieve annotation from these catalogs via the command-line interface. Several catalogs from commonly used annotation sources and instructions for creating user-specific catalogs are provided. Commands from the toolkit can be combined with other UNIX commands for advanced annotation processing. We also provide instructions for the development of custom annotation pipelines. The package is implemented in Java and makes use of external tools written in Java and Perl. The toolkit can be executed on Mac OS X 10.5 and above or any Linux distribution. The BioR application, quickstart, and user guide documents and many biological examples are available at http://bioinformaticstools.mayo.edu. © The Author 2014. Published by Oxford University Press.

Resources on Campus Governance and Employment Relations, 1967-1977. With Essay, Annotations, and Indexes.

ERIC Educational Resources Information Center

Tice, Terrence N.

An annotated bibliography containing 1,110 items from 1967 through early 1977 and other relevant resources covers virtually all the significant material on campus collective bargaining and closely related issues regarding campus governance and employment relations. It complements five publications from 1972-76 and indexes both authors and…

Annotated Bibliography of Alcohol, Other Drug, and Violence Prevention Resources, 2006-2008

ERIC Educational Resources Information Center

Segars, Lance, Ed.; Akinola, Olayinka, Ed.

2009-01-01

The U.S. Department of Education's Higher Education Center for Alcohol and Other Drug Abuse and Violence Prevention has developed this annotated bibliography to provide those interested in prevention at colleges and universities--and in surrounding communities--with a ready reference of current, important, and available information resources.…

A Selected Annotated Bibliography on the Analysis of Water Resources System, Volume 2.

ERIC Educational Resources Information Center

Kriss, Carol; And Others

Presented is an annotated bibliography of some recent selected publications pertaining to the application of systems analysis techniques for defining and evaluating alternative solutions to water resource problems. Both subject and author indices are provided. Keywords are listed at the end of each abstract. The abstracted material emphasizes the…

A Selected Annotated Bibliography on the Analysis of Water Resource Systems.

ERIC Educational Resources Information Center

Gysi, Marshall; And Others

Presented is an annotated bibliography of some selected publications pertaining to the application of systems analysis techniques to water resource problems. The majority of the references included in this bibliography have been published within the last five years. About half of the entries have informative abstracts and keywords following the…

The Africa Collection: An Annotated Historical Resource Bibliography for the Student of Africa.

ERIC Educational Resources Information Center

Lynn, Karen

This annotated bibliographic collection of resources on Africa including non-fiction, fiction, texts, poetry, draft papers, addresses, periodicals, film, records, and travel agencies is designed to aid secondary students and their teachers interested in research on Africa. An instructional approach is taken, drawing upon examples to demonstrate…

An infrastructure for ontology-based information systems in biomedicine: RICORDO case study.

PubMed

Wimalaratne, Sarala M; Grenon, Pierre; Hoehndorf, Robert; Gkoutos, Georgios V; de Bono, Bernard

2012-02-01

The article presents an infrastructure for supporting the semantic interoperability of biomedical resources based on the management (storing and inference-based querying) of their ontology-based annotations. This infrastructure consists of: (i) a repository to store and query ontology-based annotations; (ii) a knowledge base server with an inference engine to support the storage of and reasoning over ontologies used in the annotation of resources; (iii) a set of applications and services allowing interaction with the integrated repository and knowledge base. The infrastructure is being prototyped and developed and evaluated by the RICORDO project in support of the knowledge management of biomedical resources, including physiology and pharmacology models and associated clinical data. The RICORDO toolkit and its source code are freely available from http://ricordo.eu/relevant-resources. sarala@ebi.ac.uk.

Guide to investment and trade in the forest-product sectors of Southeast Asia: Indonesia, Malaysia, and the Philippines. Working paper

DOE Office of Scientific and Technical Information (OSTI.GOV)

Krutilia, K.

1988-01-01

Declining timber resources, an increase in value-added wood-base processing, new export markets, and a growing stress on joint ventures have been key factors in the rapid evolution since 1975 of Southeast Asia's forest products industry. The report profiles the industry and its prospects in Indonesia, the Philippines, and Malaysia, each of which differs with respect to stage of wood-industry development and investment climate. The countries' forest management policies, timber resources, and the status of their wood-based processing industries are reviewed first, followed by an overview of the business environment in each country, the latter covering policies toward foreign investment (includingmore » the increasingly important investments from other less-developed countries), investment licensing and regulation, taxation, exporting/importing regulations, and policies governing currency and capital controls. Includes a 5-page list of references and a short annotated bibliography.« less

The Internet and Library and Information Services: A Review, Analysis, and Annotated Bibliography. Occasional Papers No. 202.

ERIC Educational Resources Information Center

Liu, Lewis-Guodo

This work provides a review and analysis of the literature and an annotated bibliography of 446 sources on the Internet and library and information services. The bibliography is divided alphabetically according to the following topics: academic libraries and scholarly research; bibliographies, directories, guides, and glossaries; business…

An Annotated Bibliography of the Gestalt Methods, Techniques, and Therapy

ERIC Educational Resources Information Center

Prewitt-Diaz, Joseph O.

The purpose of this annotated bibliography is to provide the reader with a guide to relevant research in the area of Gestalt therapy, techniques, and methods. The majority of the references are journal articles written within the last 5 years or documents easily obtained through interlibrary loans from local libraries. These references were…

Teaching Diversity and Aging through Active Learning Strategies: An Annotated Bibliography.

ERIC Educational Resources Information Center

Fried, Stephen B.; Mehrotra, Chandra M.

Covering 10 topical areas, this annotated bibliography offers a guide to journal articles, book chapters, monographs, and books useful for teaching diversity and aging through active learning. Active learning experiences may help expand students' awareness of elements of their own diversity, broaden their world view, and enhance their culturally…

Kaleidoscope: A Multicultural Booklist for Grades K-8. Third Edition. NCTE Bibliography Series.

ERIC Educational Resources Information Center

Yokota, Junko, Ed.

The third edition of this annotated bibliography collection offers students, teachers, and librarians a helpful guide to the best multicultural literature (published between 1996 and 1998) for elementary and middle school readers. With approximately 600 annotations on topics and formats including picture story books, realistic fiction, history and…

Entrepreneurship Theories and Their Use in Rural Development. An Annotated Bibliography.

ERIC Educational Resources Information Center

Frederick, Martha; Long, Celeste A.

Entrepreneurship has been one of the major issues in rural education. This annotated bibliography is a guide to theoretical material and to more recent empirical work on entrepreneurs in different economic climates. The material was gathered to enable rural development strategists who want to promote local independent business development to build…

Bibliography of Law-Related Curriculum Materials: Annotated (Second Edition). Working Notes No. 10.

ERIC Educational Resources Information Center

Davison, Susan E., Ed.

This annotated bibliography cites over 1,000 elementary- and secondary-level materials dealing with the philosophy, substance, and pedagogy of law-related education. It lists textbooks, curriculum kits and guides, journals and newsletters, and books that can serve as reference or supplementary materials. The bibliography is divided by topic into…

Counselor's Information Service. A Quarterly Annotated Bibliography of Current Literature on Educational and Vocational Guidance. Volume 32, Number 1.

ERIC Educational Resources Information Center

B'nai B'rith, Washington, DC. Career and Counseling Services.

This quarterly annotated bibliography of current literature on educational and vocational guidance describes various pamphlets, guides and brochures which provide occupational information, educational, vocational and personal guidance, guidance administration and procedures, information on student aids and aids for the teacher. Additional guidance…

Asian Theatre: A Study Guide and Annotated Bibliography. "Theatre Perspectives" No. 1.

ERIC Educational Resources Information Center

Brandon, James R., Ed.; Wichmann, Elizabeth, Ed.

This study guide/bibliography is intended to help the English language reader find materials for the study of Asian theatre. Containing 1,348 entries, the guide is the most extensive bibliography published to date. The guide is organized by geographical area: an initial chapter on Asia is followed by chapters on each of 16 countries: Burma,…

High-throughput comparison, functional annotation, and metabolic modeling of plant genomes using the PlantSEED resource

USDA-ARS?s Scientific Manuscript database

The increasing number of sequenced plant genomes is placing new demands on the methods applied to analyze, annotate, and model these genomes. Today's annotation pipelines result in inconsistent gene assignments that complicate comparative analyses and prevent efficient construction of metabolic mode...

A Resource on Behavioral Terminology: An Annotated Bibliography of "On Terms" Articles in "The Behavior Analyst"

ERIC Educational Resources Information Center

Carr, James E.; Briggs, Adam M.

2011-01-01

An annotated bibliography that summarizes the "On Terms" articles on behavior-analytic terminology from "The Behavior Analyst" is provided. Thirty-five articles published between 1979 and 2010 were identified, annotated, and classified using common behavior analysis course content frameworks. (Contains 1 table.)

BioCreative V CDR task corpus: a resource for chemical disease relation extraction.

PubMed

Li, Jiao; Sun, Yueping; Johnson, Robin J; Sciaky, Daniela; Wei, Chih-Hsuan; Leaman, Robert; Davis, Allan Peter; Mattingly, Carolyn J; Wiegers, Thomas C; Lu, Zhiyong

2016-01-01

Community-run, formal evaluations and manually annotated text corpora are critically important for advancing biomedical text-mining research. Recently in BioCreative V, a new challenge was organized for the tasks of disease named entity recognition (DNER) and chemical-induced disease (CID) relation extraction. Given the nature of both tasks, a test collection is required to contain both disease/chemical annotations and relation annotations in the same set of articles. Despite previous efforts in biomedical corpus construction, none was found to be sufficient for the task. Thus, we developed our own corpus called BC5CDR during the challenge by inviting a team of Medical Subject Headings (MeSH) indexers for disease/chemical entity annotation and Comparative Toxicogenomics Database (CTD) curators for CID relation annotation. To ensure high annotation quality and productivity, detailed annotation guidelines and automatic annotation tools were provided. The resulting BC5CDR corpus consists of 1500 PubMed articles with 4409 annotated chemicals, 5818 diseases and 3116 chemical-disease interactions. Each entity annotation includes both the mention text spans and normalized concept identifiers, using MeSH as the controlled vocabulary. To ensure accuracy, the entities were first captured independently by two annotators followed by a consensus annotation: The average inter-annotator agreement (IAA) scores were 87.49% and 96.05% for the disease and chemicals, respectively, in the test set according to the Jaccard similarity coefficient. Our corpus was successfully used for the BioCreative V challenge tasks and should serve as a valuable resource for the text-mining research community.Database URL: http://www.biocreative.org/tasks/biocreative-v/track-3-cdr/. Published by Oxford University Press 2016. This work is written by US Government employees and is in the public domain in the United States.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Larsen, A.

This study examines various energy resources in Utah including oil impregnated rocks (oil shale and oil sand deposits), geothermal, coal, uranium, oil and natural gas in terms of the following dimensions: resurce potential and location; resource technology, development and production status; resource development requirements; potential environmental and socio-economic impacts; and transportation tradeoffs. The advantages of minemouth power plants in comparison to combined cycle or hybrid power plants are also examined. Annotative bibliographies of the energy resources are presented in the appendices. Specific topics summarized in these annotative bibliographies include: economics, environmental impacts, water requirements, production technology, and siting requirements.

Ensembl core software resources: storage and programmatic access for DNA sequence and genome annotation.

PubMed

Ruffier, Magali; Kähäri, Andreas; Komorowska, Monika; Keenan, Stephen; Laird, Matthew; Longden, Ian; Proctor, Glenn; Searle, Steve; Staines, Daniel; Taylor, Kieron; Vullo, Alessandro; Yates, Andrew; Zerbino, Daniel; Flicek, Paul

2017-01-01

The Ensembl software resources are a stable infrastructure to store, access and manipulate genome assemblies and their functional annotations. The Ensembl 'Core' database and Application Programming Interface (API) was our first major piece of software infrastructure and remains at the centre of all of our genome resources. Since its initial design more than fifteen years ago, the number of publicly available genomic, transcriptomic and proteomic datasets has grown enormously, accelerated by continuous advances in DNA-sequencing technology. Initially intended to provide annotation for the reference human genome, we have extended our framework to support the genomes of all species as well as richer assembly models. Cross-referenced links to other informatics resources facilitate searching our database with a variety of popular identifiers such as UniProt and RefSeq. Our comprehensive and robust framework storing a large diversity of genome annotations in one location serves as a platform for other groups to generate and maintain their own tailored annotation. We welcome reuse and contributions: our databases and APIs are publicly available, all of our source code is released with a permissive Apache v2.0 licence at http://github.com/Ensembl and we have an active developer mailing list ( http://www.ensembl.org/info/about/contact/index.html ). http://www.ensembl.org. © The Author(s) 2017. Published by Oxford University Press.

Inside KidVid: The Essential Parents' Guide to Video.

ERIC Educational Resources Information Center

MacAlpine, Loretta

This guide aims to help parents choose stimulating, educational, and fun videos for their children from the more than 7,000 currently available. The guide includes: 10 tips for evaluating and choosing videos; interviews with and advice from experts; annotated descriptions of more than 400 recommended videos; essential information such as suggested…

A Guide to Research in Education with Appended Informational Aids.

ERIC Educational Resources Information Center

Smith, Barbara J.

THis annotated bibliography is designed to help students beginning educational research at Pattee Library of Pennsylvania State University Libraries. Grouped in sections A through H in the body of the guide by the type of information they contain, items listed include: bibliographies, guides to theses and dissertations; indexes and abstracts;…

China: A Guide to Reference Sources in English and Chinese.

ERIC Educational Resources Information Center

Chen, Su, Comp.; Slavin, Suzy M., Ed.

This guide to selected reference sources in the McGill University (Quebec) Library for Sinology (the study of the language, history, literature, and civilization of China) contains annotated listings for English and Chinese language materials in the following categories: (1) guides to the literature (6 references); (2) encyclopedias (3…

Genome3D: a UK collaborative project to annotate genomic sequences with predicted 3D structures based on SCOP and CATH domains.

PubMed

Lewis, Tony E; Sillitoe, Ian; Andreeva, Antonina; Blundell, Tom L; Buchan, Daniel W A; Chothia, Cyrus; Cuff, Alison; Dana, Jose M; Filippis, Ioannis; Gough, Julian; Hunter, Sarah; Jones, David T; Kelley, Lawrence A; Kleywegt, Gerard J; Minneci, Federico; Mitchell, Alex; Murzin, Alexey G; Ochoa-Montaño, Bernardo; Rackham, Owen J L; Smith, James; Sternberg, Michael J E; Velankar, Sameer; Yeats, Corin; Orengo, Christine

2013-01-01

Genome3D, available at http://www.genome3d.eu, is a new collaborative project that integrates UK-based structural resources to provide a unique perspective on sequence-structure-function relationships. Leading structure prediction resources (DomSerf, FUGUE, Gene3D, pDomTHREADER, Phyre and SUPERFAMILY) provide annotations for UniProt sequences to indicate the locations of structural domains (structural annotations) and their 3D structures (structural models). Structural annotations and 3D model predictions are currently available for three model genomes (Homo sapiens, E. coli and baker's yeast), and the project will extend to other genomes in the near future. As these resources exploit different strategies for predicting structures, the main aim of Genome3D is to enable comparisons between all the resources so that biologists can see where predictions agree and are therefore more trusted. Furthermore, as these methods differ in whether they build their predictions using CATH or SCOP, Genome3D also contains the first official mapping between these two databases. This has identified pairs of similar superfamilies from the two resources at various degrees of consensus (532 bronze pairs, 527 silver pairs and 370 gold pairs).

MetaStorm: A Public Resource for Customizable Metagenomics Annotation

PubMed Central

Arango-Argoty, Gustavo; Singh, Gargi; Heath, Lenwood S.; Pruden, Amy; Xiao, Weidong; Zhang, Liqing

2016-01-01

Metagenomics is a trending research area, calling for the need to analyze large quantities of data generated from next generation DNA sequencing technologies. The need to store, retrieve, analyze, share, and visualize such data challenges current online computational systems. Interpretation and annotation of specific information is especially a challenge for metagenomic data sets derived from environmental samples, because current annotation systems only offer broad classification of microbial diversity and function. Moreover, existing resources are not configured to readily address common questions relevant to environmental systems. Here we developed a new online user-friendly metagenomic analysis server called MetaStorm (http://bench.cs.vt.edu/MetaStorm/), which facilitates customization of computational analysis for metagenomic data sets. Users can upload their own reference databases to tailor the metagenomics annotation to focus on various taxonomic and functional gene markers of interest. MetaStorm offers two major analysis pipelines: an assembly-based annotation pipeline and the standard read annotation pipeline used by existing web servers. These pipelines can be selected individually or together. Overall, MetaStorm provides enhanced interactive visualization to allow researchers to explore and manipulate taxonomy and functional annotation at various levels of resolution. PMID:27632579

MetaStorm: A Public Resource for Customizable Metagenomics Annotation.

PubMed

Arango-Argoty, Gustavo; Singh, Gargi; Heath, Lenwood S; Pruden, Amy; Xiao, Weidong; Zhang, Liqing

2016-01-01

Metagenomics is a trending research area, calling for the need to analyze large quantities of data generated from next generation DNA sequencing technologies. The need to store, retrieve, analyze, share, and visualize such data challenges current online computational systems. Interpretation and annotation of specific information is especially a challenge for metagenomic data sets derived from environmental samples, because current annotation systems only offer broad classification of microbial diversity and function. Moreover, existing resources are not configured to readily address common questions relevant to environmental systems. Here we developed a new online user-friendly metagenomic analysis server called MetaStorm (http://bench.cs.vt.edu/MetaStorm/), which facilitates customization of computational analysis for metagenomic data sets. Users can upload their own reference databases to tailor the metagenomics annotation to focus on various taxonomic and functional gene markers of interest. MetaStorm offers two major analysis pipelines: an assembly-based annotation pipeline and the standard read annotation pipeline used by existing web servers. These pipelines can be selected individually or together. Overall, MetaStorm provides enhanced interactive visualization to allow researchers to explore and manipulate taxonomy and functional annotation at various levels of resolution.

Functional Annotation of the Arabidopsis Genome Using Controlled Vocabularies1

PubMed Central

Berardini, Tanya Z.; Mundodi, Suparna; Reiser, Leonore; Huala, Eva; Garcia-Hernandez, Margarita; Zhang, Peifen; Mueller, Lukas A.; Yoon, Jungwoon; Doyle, Aisling; Lander, Gabriel; Moseyko, Nick; Yoo, Danny; Xu, Iris; Zoeckler, Brandon; Montoya, Mary; Miller, Neil; Weems, Dan; Rhee, Seung Y.

2004-01-01

Controlled vocabularies are increasingly used by databases to describe genes and gene products because they facilitate identification of similar genes within an organism or among different organisms. One of The Arabidopsis Information Resource's goals is to associate all Arabidopsis genes with terms developed by the Gene Ontology Consortium that describe the molecular function, biological process, and subcellular location of a gene product. We have also developed terms describing Arabidopsis anatomy and developmental stages and use these to annotate published gene expression data. As of March 2004, we used computational and manual annotation methods to make 85,666 annotations representing 26,624 unique loci. We focus on associating genes to controlled vocabulary terms based on experimental data from the literature and use The Arabidopsis Information Resource-developed PubSearch software to facilitate this process. Each annotation is tagged with a combination of evidence codes, evidence descriptions, and references that provide a robust means to assess data quality. Annotation of all Arabidopsis genes will allow quantitative comparisons between sets of genes derived from sources such as microarray experiments. The Arabidopsis annotation data will also facilitate annotation of newly sequenced plant genomes by using sequence similarity to transfer annotations to homologous genes. In addition, complete and up-to-date annotations will make unknown genes easy to identify and target for experimentation. Here, we describe the process of Arabidopsis functional annotation using a variety of data sources and illustrate several ways in which this information can be accessed and used to infer knowledge about Arabidopsis and other plant species. PMID:15173566

Structuring osteosarcoma knowledge: an osteosarcoma-gene association database based on literature mining and manual annotation.

PubMed

Poos, Kathrin; Smida, Jan; Nathrath, Michaela; Maugg, Doris; Baumhoer, Daniel; Neumann, Anna; Korsching, Eberhard

2014-01-01

Osteosarcoma (OS) is the most common primary bone cancer exhibiting high genomic instability. This genomic instability affects multiple genes and microRNAs to a varying extent depending on patient and tumor subtype. Massive research is ongoing to identify genes including their gene products and microRNAs that correlate with disease progression and might be used as biomarkers for OS. However, the genomic complexity hampers the identification of reliable biomarkers. Up to now, clinico-pathological factors are the key determinants to guide prognosis and therapeutic treatments. Each day, new studies about OS are published and complicate the acquisition of information to support biomarker discovery and therapeutic improvements. Thus, it is necessary to provide a structured and annotated view on the current OS knowledge that is quick and easily accessible to researchers of the field. Therefore, we developed a publicly available database and Web interface that serves as resource for OS-associated genes and microRNAs. Genes and microRNAs were collected using an automated dictionary-based gene recognition procedure followed by manual review and annotation by experts of the field. In total, 911 genes and 81 microRNAs related to 1331 PubMed abstracts were collected (last update: 29 October 2013). Users can evaluate genes and microRNAs according to their potential prognostic and therapeutic impact, the experimental procedures, the sample types, the biological contexts and microRNA target gene interactions. Additionally, a pathway enrichment analysis of the collected genes highlights different aspects of OS progression. OS requires pathways commonly deregulated in cancer but also features OS-specific alterations like deregulated osteoclast differentiation. To our knowledge, this is the first effort of an OS database containing manual reviewed and annotated up-to-date OS knowledge. It might be a useful resource especially for the bone tumor research community, as specific information about genes or microRNAs is quick and easily accessible. Hence, this platform can support the ongoing OS research and biomarker discovery. Database URL: http://osteosarcoma-db.uni-muenster.de. © The Author(s) 2014. Published by Oxford University Press.

Structuring osteosarcoma knowledge: an osteosarcoma-gene association database based on literature mining and manual annotation

PubMed Central

Poos, Kathrin; Smida, Jan; Nathrath, Michaela; Maugg, Doris; Baumhoer, Daniel; Neumann, Anna; Korsching, Eberhard

2014-01-01

Osteosarcoma (OS) is the most common primary bone cancer exhibiting high genomic instability. This genomic instability affects multiple genes and microRNAs to a varying extent depending on patient and tumor subtype. Massive research is ongoing to identify genes including their gene products and microRNAs that correlate with disease progression and might be used as biomarkers for OS. However, the genomic complexity hampers the identification of reliable biomarkers. Up to now, clinico-pathological factors are the key determinants to guide prognosis and therapeutic treatments. Each day, new studies about OS are published and complicate the acquisition of information to support biomarker discovery and therapeutic improvements. Thus, it is necessary to provide a structured and annotated view on the current OS knowledge that is quick and easily accessible to researchers of the field. Therefore, we developed a publicly available database and Web interface that serves as resource for OS-associated genes and microRNAs. Genes and microRNAs were collected using an automated dictionary-based gene recognition procedure followed by manual review and annotation by experts of the field. In total, 911 genes and 81 microRNAs related to 1331 PubMed abstracts were collected (last update: 29 October 2013). Users can evaluate genes and microRNAs according to their potential prognostic and therapeutic impact, the experimental procedures, the sample types, the biological contexts and microRNA target gene interactions. Additionally, a pathway enrichment analysis of the collected genes highlights different aspects of OS progression. OS requires pathways commonly deregulated in cancer but also features OS-specific alterations like deregulated osteoclast differentiation. To our knowledge, this is the first effort of an OS database containing manual reviewed and annotated up-to-date OS knowledge. It might be a useful resource especially for the bone tumor research community, as specific information about genes or microRNAs is quick and easily accessible. Hence, this platform can support the ongoing OS research and biomarker discovery. Database URL: http://osteosarcoma-db.uni-muenster.de PMID:24865352

Evaluating children's conservation biology learning at the zoo.

PubMed

Jensen, Eric

2014-08-01

Millions of children visit zoos every year with parents or schools to encounter wildlife firsthand. Public conservation education is a requirement for membership in professional zoo associations. However, in recent years zoos have been criticized for failing to educate the public on conservation issues and related biological concepts, such as animal adaptation to habitats. I used matched pre- and postvisit mixed methods questionnaires to investigate the educational value of zoo visits for children aged 7-15 years. The questionnaires gathered qualitative data from these individuals, including zoo-related thoughts and an annotated drawing of a habitat. A content analysis of these qualitative data produced the quantitative data reported in this article. I evaluated the relative learning outcomes of educator-guided and unguided zoo visits at London Zoo, both in terms of learning about conservation biology (measured by annotated drawings) and changing attitudes toward wildlife conservation (measured using thought-listing data). Forty-one percent of educator-guided visits and 34% of unguided visits resulted in conservation biology-related learning. Negative changes in children's understanding of animals and their habitats were more prevalent in unguided zoo visits. Overall, my results show the potential educational value of visiting zoos for children. However, they also suggest that zoos' standard unguided interpretive materials are insufficient for achieving the best outcomes for visiting children. These results support a theoretical model of conservation biology learning that frames conservation educators as toolmakers who develop conceptual resources to enhance children's understanding of science. © 2014 Society for Conservation Biology.

An Annotated Bibliography of Verbal Behavior Articles Published outside of "The Analysis of Verbal Behavior: 2016"

ERIC Educational Resources Information Center

Lechago, Sarah A.; Jackson, Rachel E.; Oda, Fernanda S.

2017-01-01

An annotated bibliography is provided that summarizes journal articles on verbal behavior published outside of "The Analysis of Verbal Behavior" in 2016, the primary journal for scholarship in this area. Thirty-seven such articles were identified and annotated as a resource for practitioners, researchers, and educators.

An Annotated Bibliography of Verbal Behavior Scholarship Published outside of "The Analysis of Verbal Behavior": 2014

ERIC Educational Resources Information Center

Carr, James E.; Nosik, Melissa R.; Lechago, Sarah A.; Phillips, Lauren

2015-01-01

This annotated bibliography summarizes journal articles on verbal behavior published outside of "The Analysis of Verbal Behavior," the primary journal for scholarship in this area. Seventeen such articles were published in 2014 and are annotated as a resource for practitioners, researchers, and educators.

An Annotated Bibliography of Verbal Behavior Articles Published outside of "The Analysis of Verbal Behavior": 2015

ERIC Educational Resources Information Center

Lechago, Sarah A.; Phillips, Lauren A.

2016-01-01

An annotated bibliography is provided that summarizes journal articles on verbal behavior published outside of "The Analysis of Verbal Behavior" in 2015, the primary journal for scholarship in this area. Thirty such articles were identified and annotated as a resource for practitioners, researchers, and educators.

Sourcebook for Sex Equality: In-Service Training. An Annotated Listing of Materials and Media for Affirmative Action In-Service Training. Bibliographic Series, 2.

ERIC Educational Resources Information Center

Hulme, Marylin A., Comp.

The materials contained in this annotated bibliography include films, slide shows, information resources, evaluation materials, sample workshop formats, and guidelines for sex-fair and race-fair materials and group activities. The bibliography is divided into four sections: (1) "General Resources" includes readings in sex role stereotyping,…

Home Furnishings Merchandising. A Suggested Interdisciplinary Guide.

ERIC Educational Resources Information Center

Wray, Ralph D.; Hayden, Margaret B.

This curriculum guide contains three sections: introduction, curriculum material, and an annotated bibliography. Introductory information provides an overview of the home furnishings merchandising area, aptitudes needed, and career opportunities; discusses potential career ladders, which are divided into entry level, middle management, and…

Easy Online Access to Helpful Internet Guides.

ERIC Educational Resources Information Center

Tuss, Joan

1993-01-01

Lists recommended guides to the Internet that are available electronically. Basic commands needed to use anonymous ftp (file transfer protocol) are explained. An annotation and command formats to access, scan, retrieve, and exit each file are included for 11 titles. (EAM)

Sourcebook for English Teachers: Directed Reading/Teaching Guides for Selected Literacy Works. Volume 2.

ERIC Educational Resources Information Center

Ley, Terry C., Ed.

This sourcebook presents reading guides for 27 literary works frequently used by secondary school English teachers. The guides contain an overview of the work, a pool of instructional objectives for each work, a variety of activities, a series of discussion options, suggestions for evaluation, and annotated lists of related works. Included are:…

Guide to Datasets for Research and Policymaking in Child Care and Early Education

ERIC Educational Resources Information Center

Romero, Mariajose; Douglas-Hall, Ayana

2009-01-01

This Guide is an annotated bibliography of existing large scale data sets that provide useful information to policymakers, researchers, state administrators, and others in the field of child care and early education. The Guide follows an ecological approach to research and policy in the field: it brings attention not only to children themselves,…

Sourcebook for English Teachers: Directed Reading/Teaching Guides for Selected Literary Works. Volume 1.

ERIC Educational Resources Information Center

Ley, Terry C., Ed.

This sourcebook presents reading guides for 22 literary works frequently used by secondary school English teachers. The guides contain an overview of the work, a pool of instructional objectives for each work, a variety of activities, a series of discussion options, suggestions for evaluation, and annotated lists of related works. Included are:…

Sourcebook for English Teachers: Directed Reading/Teaching Guides for Selected Literacy Works. Volume 3.

ERIC Educational Resources Information Center

Ley, Terry C., Ed.

This sourcebook presents reading guides for 39 literary works frequently used by scondary school English teachers. The guides contain an overview of the work, a pool of instructional objectives for each work, a variety of activities, a series of discussion options, suggestions for evaluation, and annotated lists of related works. Included are:…

Overview of the Portable Guides to Investigating Child Abuse: Update 2000. Juvenile Justice Bulletin.

ERIC Educational Resources Information Center

McNaughton, Janet

In response to requests from law enforcement professionals for guidelines on investigating child abuse and neglect, the Office of Juvenile Justice and Delinquency Prevention developed the Portable Guides to Investigating Child Abuse series. This document is a synposis of each Portable Guide and provides annotated bibliographies of the series. The…

MicroScope—an integrated microbial resource for the curation and comparative analysis of genomic and metabolic data

PubMed Central

Vallenet, David; Belda, Eugeni; Calteau, Alexandra; Cruveiller, Stéphane; Engelen, Stefan; Lajus, Aurélie; Le Fèvre, François; Longin, Cyrille; Mornico, Damien; Roche, David; Rouy, Zoé; Salvignol, Gregory; Scarpelli, Claude; Thil Smith, Adam Alexander; Weiman, Marion; Médigue, Claudine

2013-01-01

MicroScope is an integrated platform dedicated to both the methodical updating of microbial genome annotation and to comparative analysis. The resource provides data from completed and ongoing genome projects (automatic and expert annotations), together with data sources from post-genomic experiments (i.e. transcriptomics, mutant collections) allowing users to perfect and improve the understanding of gene functions. MicroScope (http://www.genoscope.cns.fr/agc/microscope) combines tools and graphical interfaces to analyse genomes and to perform the manual curation of gene annotations in a comparative context. Since its first publication in January 2006, the system (previously named MaGe for Magnifying Genomes) has been continuously extended both in terms of data content and analysis tools. The last update of MicroScope was published in 2009 in the Database journal. Today, the resource contains data for >1600 microbial genomes, of which ∼300 are manually curated and maintained by biologists (1200 personal accounts today). Expert annotations are continuously gathered in the MicroScope database (∼50 000 a year), contributing to the improvement of the quality of microbial genomes annotations. Improved data browsing and searching tools have been added, original tools useful in the context of expert annotation have been developed and integrated and the website has been significantly redesigned to be more user-friendly. Furthermore, in the context of the European project Microme (Framework Program 7 Collaborative Project), MicroScope is becoming a resource providing for the curation and analysis of both genomic and metabolic data. An increasing number of projects are related to the study of environmental bacterial (meta)genomes that are able to metabolize a large variety of chemical compounds that may be of high industrial interest. PMID:23193269

NCBI disease corpus: a resource for disease name recognition and concept normalization.

PubMed

Doğan, Rezarta Islamaj; Leaman, Robert; Lu, Zhiyong

2014-02-01

Information encoded in natural language in biomedical literature publications is only useful if efficient and reliable ways of accessing and analyzing that information are available. Natural language processing and text mining tools are therefore essential for extracting valuable information, however, the development of powerful, highly effective tools to automatically detect central biomedical concepts such as diseases is conditional on the availability of annotated corpora. This paper presents the disease name and concept annotations of the NCBI disease corpus, a collection of 793 PubMed abstracts fully annotated at the mention and concept level to serve as a research resource for the biomedical natural language processing community. Each PubMed abstract was manually annotated by two annotators with disease mentions and their corresponding concepts in Medical Subject Headings (MeSH®) or Online Mendelian Inheritance in Man (OMIM®). Manual curation was performed using PubTator, which allowed the use of pre-annotations as a pre-step to manual annotations. Fourteen annotators were randomly paired and differing annotations were discussed for reaching a consensus in two annotation phases. In this setting, a high inter-annotator agreement was observed. Finally, all results were checked against annotations of the rest of the corpus to assure corpus-wide consistency. The public release of the NCBI disease corpus contains 6892 disease mentions, which are mapped to 790 unique disease concepts. Of these, 88% link to a MeSH identifier, while the rest contain an OMIM identifier. We were able to link 91% of the mentions to a single disease concept, while the rest are described as a combination of concepts. In order to help researchers use the corpus to design and test disease identification methods, we have prepared the corpus as training, testing and development sets. To demonstrate its utility, we conducted a benchmarking experiment where we compared three different knowledge-based disease normalization methods with a best performance in F-measure of 63.7%. These results show that the NCBI disease corpus has the potential to significantly improve the state-of-the-art in disease name recognition and normalization research, by providing a high-quality gold standard thus enabling the development of machine-learning based approaches for such tasks. The NCBI disease corpus, guidelines and other associated resources are available at: http://www.ncbi.nlm.nih.gov/CBBresearch/Dogan/DISEASE/. Published by Elsevier Inc.

RNA-Seq analysis and annotation of a draft blueberry genome assembly identifies candidate genes involved in fruit ripening, biosynthesis of bioactive compounds, and stage-specific alternative splicing.

PubMed

Gupta, Vikas; Estrada, April D; Blakley, Ivory; Reid, Rob; Patel, Ketan; Meyer, Mason D; Andersen, Stig Uggerhøj; Brown, Allan F; Lila, Mary Ann; Loraine, Ann E

2015-01-01

Blueberries are a rich source of antioxidants and other beneficial compounds that can protect against disease. Identifying genes involved in synthesis of bioactive compounds could enable the breeding of berry varieties with enhanced health benefits. Toward this end, we annotated a previously sequenced draft blueberry genome assembly using RNA-Seq data from five stages of berry fruit development and ripening. Genome-guided assembly of RNA-Seq read alignments combined with output from ab initio gene finders produced around 60,000 gene models, of which more than half were similar to proteins from other species, typically the grape Vitis vinifera. Comparison of gene models to the PlantCyc database of metabolic pathway enzymes identified candidate genes involved in synthesis of bioactive compounds, including bixin, an apocarotenoid with potential disease-fighting properties, and defense-related cyanogenic glycosides, which are toxic. Cyanogenic glycoside (CG) biosynthetic enzymes were highly expressed in green fruit, and a candidate CG detoxification enzyme was up-regulated during fruit ripening. Candidate genes for ethylene, anthocyanin, and 400 other biosynthetic pathways were also identified. Homology-based annotation using Blast2GO and InterPro assigned Gene Ontology terms to around 15,000 genes. RNA-Seq expression profiling showed that blueberry growth, maturation, and ripening involve dynamic gene expression changes, including coordinated up- and down-regulation of metabolic pathway enzymes and transcriptional regulators. Analysis of RNA-seq alignments identified developmentally regulated alternative splicing, promoter use, and 3' end formation. We report genome sequence, gene models, functional annotations, and RNA-Seq expression data that provide an important new resource enabling high throughput studies in blueberry.

Clothing/Apparel and Accessories Merchandising. A Suggested Interdisciplinary Guide.

ERIC Educational Resources Information Center

Wray, Ralph D.; Hayden, Margaret B.

This curriculum guide contains three sections: introduction, curriculum material, and an annotated bibliography. Introductory information provides an overview of the clothing/apparel and accessories merchandising area, aptitudes needed, and career opportunities; discusses potential career ladders, which are divided into entry level, middle…

Horticulture.

ERIC Educational Resources Information Center

Aitken, James

This curriculum guide is intended to assist vocational instructors in preparing students for entry-level employment in the field of horticulture and getting them ready for advanced training in the workplace. The package contains a validated competency/skill and task list, an instructor's guide, and an annotated bibliography. The following…

EST-PAC a web package for EST annotation and protein sequence prediction

PubMed Central

Strahm, Yvan; Powell, David; Lefèvre, Christophe

2006-01-01

With the decreasing cost of DNA sequencing technology and the vast diversity of biological resources, researchers increasingly face the basic challenge of annotating a larger number of expressed sequences tags (EST) from a variety of species. This typically consists of a series of repetitive tasks, which should be automated and easy to use. The results of these annotation tasks need to be stored and organized in a consistent way. All these operations should be self-installing, platform independent, easy to customize and amenable to using distributed bioinformatics resources available on the Internet. In order to address these issues, we present EST-PAC a web oriented multi-platform software package for expressed sequences tag (EST) annotation. EST-PAC provides a solution for the administration of EST and protein sequence annotations accessible through a web interface. Three aspects of EST annotation are automated: 1) searching local or remote biological databases for sequence similarities using Blast services, 2) predicting protein coding sequence from EST data and, 3) annotating predicted protein sequences with functional domain predictions. In practice, EST-PAC integrates the BLASTALL suite, EST-Scan2 and HMMER in a relational database system accessible through a simple web interface. EST-PAC also takes advantage of the relational database to allow consistent storage, powerful queries of results and, management of the annotation process. The system allows users to customize annotation strategies and provides an open-source data-management environment for research and education in bioinformatics. PMID:17147782

Accessing the SEED genome databases via Web services API: tools for programmers.

PubMed

Disz, Terry; Akhter, Sajia; Cuevas, Daniel; Olson, Robert; Overbeek, Ross; Vonstein, Veronika; Stevens, Rick; Edwards, Robert A

2010-06-14

The SEED integrates many publicly available genome sequences into a single resource. The database contains accurate and up-to-date annotations based on the subsystems concept that leverages clustering between genomes and other clues to accurately and efficiently annotate microbial genomes. The backend is used as the foundation for many genome annotation tools, such as the Rapid Annotation using Subsystems Technology (RAST) server for whole genome annotation, the metagenomics RAST server for random community genome annotations, and the annotation clearinghouse for exchanging annotations from different resources. In addition to a web user interface, the SEED also provides Web services based API for programmatic access to the data in the SEED, allowing the development of third-party tools and mash-ups. The currently exposed Web services encompass over forty different methods for accessing data related to microbial genome annotations. The Web services provide comprehensive access to the database back end, allowing any programmer access to the most consistent and accurate genome annotations available. The Web services are deployed using a platform independent service-oriented approach that allows the user to choose the most suitable programming platform for their application. Example code demonstrate that Web services can be used to access the SEED using common bioinformatics programming languages such as Perl, Python, and Java. We present a novel approach to access the SEED database. Using Web services, a robust API for access to genomics data is provided, without requiring large volume downloads all at once. The API ensures timely access to the most current datasets available, including the new genomes as soon as they come online.

A Linked Data-Based Collaborative Annotation System for Increasing Learning Achievements

ERIC Educational Resources Information Center

Zarzour, Hafed; Sellami, Mokhtar

2017-01-01

With the emergence of the Web 2.0, collaborative annotation practices have become more mature in the field of learning. In this context, several recent studies have shown the powerful effects of the integration of annotation mechanism in learning process. However, most of these studies provide poor support for semantically structured resources,…

The Protein Information Resource: an integrated public resource of functional annotation of proteins

PubMed Central

Wu, Cathy H.; Huang, Hongzhan; Arminski, Leslie; Castro-Alvear, Jorge; Chen, Yongxing; Hu, Zhang-Zhi; Ledley, Robert S.; Lewis, Kali C.; Mewes, Hans-Werner; Orcutt, Bruce C.; Suzek, Baris E.; Tsugita, Akira; Vinayaka, C. R.; Yeh, Lai-Su L.; Zhang, Jian; Barker, Winona C.

2002-01-01

The Protein Information Resource (PIR) serves as an integrated public resource of functional annotation of protein data to support genomic/proteomic research and scientific discovery. The PIR, in collaboration with the Munich Information Center for Protein Sequences (MIPS) and the Japan International Protein Information Database (JIPID), produces the PIR-International Protein Sequence Database (PSD), the major annotated protein sequence database in the public domain, containing about 250 000 proteins. To improve protein annotation and the coverage of experimentally validated data, a bibliography submission system is developed for scientists to submit, categorize and retrieve literature information. Comprehensive protein information is available from iProClass, which includes family classification at the superfamily, domain and motif levels, structural and functional features of proteins, as well as cross-references to over 40 biological databases. To provide timely and comprehensive protein data with source attribution, we have introduced a non-redundant reference protein database, PIR-NREF. The database consists of about 800 000 proteins collected from PIR-PSD, SWISS-PROT, TrEMBL, GenPept, RefSeq and PDB, with composite protein names and literature data. To promote database interoperability, we provide XML data distribution and open database schema, and adopt common ontologies. The PIR web site (http://pir.georgetown.edu/) features data mining and sequence analysis tools for information retrieval and functional identification of proteins based on both sequence and annotation information. The PIR databases and other files are also available by FTP (ftp://nbrfa.georgetown.edu/pir_databases). PMID:11752247

Native American Resources Annotated Bibliography of Print and Non-Print Materials. A Model Program in Multi-Ethnic Heritage Studies.

ERIC Educational Resources Information Center

Mankato State Univ., Minn.

This is an annotated bibliography of print and nonprint materials for programs in Native American Studies. It is divided into elementary level materials and secondary level materials. Each section is arranged alphabetically by subject. Most subject headings in this resource begin with a name of a tribe, nation, or a geographical area. General…

Prostate Cancer Biospecimen Cohort Study

DTIC Science & Technology

2016-10-01

goal of the study is development of a Prostate Cancer Biorepository Network (PCBN) resource site with high quality and well-annotated urine , blood...with no coordinating center and each site will be responsible for maintaining/storing their own data/ samples . 15. SUBJECT TERMS Prostate cancer...Biorepository Network (PCBN) resource site with high quality and well-annotated urine , blood, and tissue specimens as part of a multi-institutional Department of

Feasibility of Leveraging Crowd Sourcing for the Creation of a Large Scale Annotated Resource for Hindi English Code Switched Data: A Pilot Annotation

DTIC Science & Technology

2011-11-01

Proceedings of the 9th Workshop on Asian Language Resources, pages 36–40, Chiang Mai , Thailand, November 12 and 13, 2011. Feasibility of Leveraging... Chiang Mai , Thailand on November 12-13, 2011. Sponsored in part by AOARD and ONR. U.S. Government or Federal Rights License. 14. ABSTRACT Linguistic

Sourcebook for Sex Equality: Small Presses. An Annotated Listing of Small Presses and Alternative Sources for Books and Media. Bibliographic Series, 1.

ERIC Educational Resources Information Center

Hulme, Marylin A., Comp.

This briefly annotated guide to non-sexist and non-racist educational materials suppliers includes small presses, non-profit educational firms, women's sections of professional and trade organizations, task forces in State educational departments, and feminist publishers, bookstores and distributors. Aimed at assisting librarians and teachers in…

School Sexuality Education: Opposition and Answers. Materials from the Katharine Dexter McCormick Library: A Selective, Annotated Bibliography.

ERIC Educational Resources Information Center

Modig, Zeau D., Ed.

This annotated bibliography was compiled as a guide for educators, administrators, counselors, parents, and everyone concerned about the opponents of sexuality education in schools, their arguments, and their tactics. Entries were chosen to represent a variety of materials in terms of both format and content. This bibliography is divided into…

Annotated Bibliography on Apartheid.

ERIC Educational Resources Information Center

Totten, Sam, ed.

1985-01-01

This annotated listing on apartheid in South Africa cites general resources, classroom materials, fiction, poetry, audio visuals, and organizations and associations. Also included are a glossary and a brief chronology of South Africa's apartheid system. (RM)

Welding.

ERIC Educational Resources Information Center

Baldwin, Harold; Whitney, Gregory

This curriculum guide is intended to assist vocational instructors in preparing students for entry-level employment as welders and preparing them for advanced training in the workplace. The package contains an overview of new and emerging welding technologies, a competency/skill and task list, an instructor's guide, and an annotated bibliography.…

The Biofuel Feedstock Genomics Resource: a web-based portal and database to enable functional genomics of plant biofuel feedstock species.

PubMed

Childs, Kevin L; Konganti, Kranti; Buell, C Robin

2012-01-01

Major feedstock sources for future biofuel production are likely to be high biomass producing plant species such as poplar, pine, switchgrass, sorghum and maize. One active area of research in these species is genome-enabled improvement of lignocellulosic biofuel feedstock quality and yield. To facilitate genomic-based investigations in these species, we developed the Biofuel Feedstock Genomic Resource (BFGR), a database and web-portal that provides high-quality, uniform and integrated functional annotation of gene and transcript assembly sequences from species of interest to lignocellulosic biofuel feedstock researchers. The BFGR includes sequence data from 54 species and permits researchers to view, analyze and obtain annotation at the gene, transcript, protein and genome level. Annotation of biochemical pathways permits the identification of key genes and transcripts central to the improvement of lignocellulosic properties in these species. The integrated nature of the BFGR in terms of annotation methods, orthologous/paralogous relationships and linkage to seven species with complete genome sequences allows comparative analyses for biofuel feedstock species with limited sequence resources. Database URL: http://bfgr.plantbiology.msu.edu.

Eagle-i: Making Invisible Resources, Visible

PubMed Central

Haendel, M.; Wilson, M.; Torniai, C.; Segerdell, E.; Shaffer, C.; Frost, R.; Bourges, D.; Brownstein, J.; McInnerney, K.

2010-01-01

RP-134 The eagle-i Consortium – Dartmouth College, Harvard Medical School, Jackson State University, Morehouse School of Medicine, Montana State University, Oregon Health and Science University (OHSU), the University of Alaska, the University of Hawaii, and the University of Puerto Rico – aims to make invisible resources for scientific research visible by developing a searchable network of resource repositories at research institutions nationwide. Now in early development, it is hoped that the system will scale beyond the consortium at the end of the two-year pilot. Data Model & Ontology: The eagle-i ontology development team at the OHSU Library is generating the data model and ontologies necessary for resource indexing and querying. Our indexing system will enable cores and research labs to represent resources within a defined vocabulary, leading to more effective searches and better linkage between data types. This effort is being guided by active discussions within the ontology community (http://RRontology.tk) bringing together relevant preexisting ontologies in a logical framework. The goal of these discussions is to provide context for interoperability and domain-wide standards for resource types used throughout biomedical research. Research community feedback is welcomed. Architecture Development, led by a team at Harvard, includes four main components: tools for data collection, management and curation; an institutional resource repository; a federated network; and a central search application. Each participating institution will populate and manage their repository locally, using data collection and curation tools. To help improve search performance, data tools will support the semi-automatic annotation of resources. A central search application will use a federated protocol to broadcast queries to all repositories and display aggregated results. The search application will leverage the eagle-i ontologies to help guide users to valid queries via auto-suggestions and taxonomy browsing and improve search result quality via concept-based search and synonym expansion. Website: http://eagle-i.org. NIH/NCRR ARRA award #U24RR029825

Educational Film Guide for Middle Eastern Studies.

ERIC Educational Resources Information Center

Greenman, Joseph; Joachim, Ann

This annotated guide lists 16mm. films on the Middle East for use in grades K-12 and with adults. The Middle East refers to a vast area extending from eastern Afghanistan and the northern Caucasus to the western coast of Morocco and the southern periphery of the Sahara. The guide does not list films according to their merits. Rather, it includes…

TogoTable: cross-database annotation system using the Resource Description Framework (RDF) data model.

PubMed

Kawano, Shin; Watanabe, Tsutomu; Mizuguchi, Sohei; Araki, Norie; Katayama, Toshiaki; Yamaguchi, Atsuko

2014-07-01

TogoTable (http://togotable.dbcls.jp/) is a web tool that adds user-specified annotations to a table that a user uploads. Annotations are drawn from several biological databases that use the Resource Description Framework (RDF) data model. TogoTable uses database identifiers (IDs) in the table as a query key for searching. RDF data, which form a network called Linked Open Data (LOD), can be searched from SPARQL endpoints using a SPARQL query language. Because TogoTable uses RDF, it can integrate annotations from not only the reference database to which the IDs originally belong, but also externally linked databases via the LOD network. For example, annotations in the Protein Data Bank can be retrieved using GeneID through links provided by the UniProt RDF. Because RDF has been standardized by the World Wide Web Consortium, any database with annotations based on the RDF data model can be easily incorporated into this tool. We believe that TogoTable is a valuable Web tool, particularly for experimental biologists who need to process huge amounts of data such as high-throughput experimental output. © The Author(s) 2014. Published by Oxford University Press on behalf of Nucleic Acids Research.

An annotated corpus with nanomedicine and pharmacokinetic parameters

PubMed Central

Lewinski, Nastassja A; Jimenez, Ivan; McInnes, Bridget T

2017-01-01

A vast amount of data on nanomedicines is being generated and published, and natural language processing (NLP) approaches can automate the extraction of unstructured text-based data. Annotated corpora are a key resource for NLP and information extraction methods which employ machine learning. Although corpora are available for pharmaceuticals, resources for nanomedicines and nanotechnology are still limited. To foster nanotechnology text mining (NanoNLP) efforts, we have constructed a corpus of annotated drug product inserts taken from the US Food and Drug Administration’s Drugs@FDA online database. In this work, we present the development of the Engineered Nanomedicine Database corpus to support the evaluation of nanomedicine entity extraction. The data were manually annotated for 21 entity mentions consisting of nanomedicine physicochemical characterization, exposure, and biologic response information of 41 Food and Drug Administration-approved nanomedicines. We evaluate the reliability of the manual annotations and demonstrate the use of the corpus by evaluating two state-of-the-art named entity extraction systems, OpenNLP and Stanford NER. The annotated corpus is available open source and, based on these results, guidelines and suggestions for future development of additional nanomedicine corpora are provided. PMID:29066897

Potential use of geothermal resources in the Snake River Basin: an environmental overview. Volume II. Annotated bibliography

DOE Office of Scientific and Technical Information (OSTI.GOV)

Spencer, S.G.; Russell, B.F.; Sullivan, J.F.

This volume is a partially annotated bibliography of reference materials pertaining to the seven KGRA's. The bibliography is divided into sections by program element as follows: terrestrial ecology, aquatic ecology, heritage resources, socioeconomics and demography, geology, geothermal, soils, hydrology and water quality, seismicity, and subsidence. Cross-referencing is available for those references which are applicable to specific KGRA's. (MHR)

Navigating highly homologous genes in a molecular diagnostic setting: a resource for clinical next-generation sequencing.

PubMed

Mandelker, Diana; Schmidt, Ryan J; Ankala, Arunkanth; McDonald Gibson, Kristin; Bowser, Mark; Sharma, Himanshu; Duffy, Elizabeth; Hegde, Madhuri; Santani, Avni; Lebo, Matthew; Funke, Birgit

2016-12-01

Next-generation sequencing (NGS) is now routinely used to interrogate large sets of genes in a diagnostic setting. Regions of high sequence homology continue to be a major challenge for short-read technologies and can lead to false-positive and false-negative diagnostic errors. At the scale of whole-exome sequencing (WES), laboratories may be limited in their knowledge of genes and regions that pose technical hurdles due to high homology. We have created an exome-wide resource that catalogs highly homologous regions that is tailored toward diagnostic applications. This resource was developed using a mappability-based approach tailored to current Sanger and NGS protocols. Gene-level and exon-level lists delineate regions that are difficult or impossible to analyze via standard NGS. These regions are ranked by degree of affectedness, annotated for medical relevance, and classified by the type of homology (within-gene, different functional gene, known pseudogene, uncharacterized noncoding region). Additionally, we provide a list of exons that cannot be analyzed by short-amplicon Sanger sequencing. This resource can help guide clinical test design, supplemental assay implementation, and results interpretation in the context of high homology.Genet Med 18 12, 1282-1289.

Archaeology: A Guide to Reference Sources.

ERIC Educational Resources Information Center

Morrison, Doreen, Comp.

This bibliographic guide lists reference sources available at McGill University for research in prehistory and non-classical archaeology. No exclusively biographical sources have been included, but many of the encyclopedias and handbooks contain biographical information and are annotated accordingly. Titles are listed in the following categories:…

Testing Information Sources for Educators. ERIC/TME Report 94.

ERIC Educational Resources Information Center

Fabiano, Emily; O'Brien, Nancy

This guide provides annotated lists of books, journals, indexes, and computer-based services and organizations that are sources of test information. The guide directs educators to test information about assessing academic ability, aptitude, achievement, personality, vocational aptitude, and intelligence, as well as specialized topics such as…

Guide to Special Information in Scientific and Engineering Journals.

ERIC Educational Resources Information Center

Harris, Mary Elizabeth

This annotated bibliography lists 203 special features or special issues of science and technology periodicals with emphasis on compilations of information that appear in periodicals on a regular basis. Subjects covered in the guide include aeronautics, air-conditioning and refrigeration engineering, astronomy, automobiles, biology, botany,…

Gene Ontology annotations at SGD: new data sources and annotation methods

PubMed Central

Hong, Eurie L.; Balakrishnan, Rama; Dong, Qing; Christie, Karen R.; Park, Julie; Binkley, Gail; Costanzo, Maria C.; Dwight, Selina S.; Engel, Stacia R.; Fisk, Dianna G.; Hirschman, Jodi E.; Hitz, Benjamin C.; Krieger, Cynthia J.; Livstone, Michael S.; Miyasato, Stuart R.; Nash, Robert S.; Oughtred, Rose; Skrzypek, Marek S.; Weng, Shuai; Wong, Edith D.; Zhu, Kathy K.; Dolinski, Kara; Botstein, David; Cherry, J. Michael

2008-01-01

The Saccharomyces Genome Database (SGD; http://www.yeastgenome.org/) collects and organizes biological information about the chromosomal features and gene products of the budding yeast Saccharomyces cerevisiae. Although published data from traditional experimental methods are the primary sources of evidence supporting Gene Ontology (GO) annotations for a gene product, high-throughput experiments and computational predictions can also provide valuable insights in the absence of an extensive body of literature. Therefore, GO annotations available at SGD now include high-throughput data as well as computational predictions provided by the GO Annotation Project (GOA UniProt; http://www.ebi.ac.uk/GOA/). Because the annotation method used to assign GO annotations varies by data source, GO resources at SGD have been modified to distinguish data sources and annotation methods. In addition to providing information for genes that have not been experimentally characterized, GO annotations from independent sources can be compared to those made by SGD to help keep the literature-based GO annotations current. PMID:17982175

Evaluating Functional Annotations of Enzymes Using the Gene Ontology.

PubMed

Holliday, Gemma L; Davidson, Rebecca; Akiva, Eyal; Babbitt, Patricia C

2017-01-01

The Gene Ontology (GO) (Ashburner et al., Nat Genet 25(1):25-29, 2000) is a powerful tool in the informatics arsenal of methods for evaluating annotations in a protein dataset. From identifying the nearest well annotated homologue of a protein of interest to predicting where misannotation has occurred to knowing how confident you can be in the annotations assigned to those proteins is critical. In this chapter we explore what makes an enzyme unique and how we can use GO to infer aspects of protein function based on sequence similarity. These can range from identification of misannotation or other errors in a predicted function to accurate function prediction for an enzyme of entirely unknown function. Although GO annotation applies to any gene products, we focus here a describing our approach for hierarchical classification of enzymes in the Structure-Function Linkage Database (SFLD) (Akiva et al., Nucleic Acids Res 42(Database issue):D521-530, 2014) as a guide for informed utilisation of annotation transfer based on GO terms.

A semi-automatic annotation tool for cooking video

NASA Astrophysics Data System (ADS)

Bianco, Simone; Ciocca, Gianluigi; Napoletano, Paolo; Schettini, Raimondo; Margherita, Roberto; Marini, Gianluca; Gianforme, Giorgio; Pantaleo, Giuseppe

2013-03-01

In order to create a cooking assistant application to guide the users in the preparation of the dishes relevant to their profile diets and food preferences, it is necessary to accurately annotate the video recipes, identifying and tracking the foods of the cook. These videos present particular annotation challenges such as frequent occlusions, food appearance changes, etc. Manually annotate the videos is a time-consuming, tedious and error-prone task. Fully automatic tools that integrate computer vision algorithms to extract and identify the elements of interest are not error free, and false positive and false negative detections need to be corrected in a post-processing stage. We present an interactive, semi-automatic tool for the annotation of cooking videos that integrates computer vision techniques under the supervision of the user. The annotation accuracy is increased with respect to completely automatic tools and the human effort is reduced with respect to completely manual ones. The performance and usability of the proposed tool are evaluated on the basis of the time and effort required to annotate the same video sequences.

Next Generation Models for Storage and Representation of Microbial Biological Annotation

DOE Office of Scientific and Technical Information (OSTI.GOV)

Quest, Daniel J; Land, Miriam L; Brettin, Thomas S

2010-01-01

Background Traditional genome annotation systems were developed in a very different computing era, one where the World Wide Web was just emerging. Consequently, these systems are built as centralized black boxes focused on generating high quality annotation submissions to GenBank/EMBL supported by expert manual curation. The exponential growth of sequence data drives a growing need for increasingly higher quality and automatically generated annotation. Typical annotation pipelines utilize traditional database technologies, clustered computing resources, Perl, C, and UNIX file systems to process raw sequence data, identify genes, and predict and categorize gene function. These technologies tightly couple the annotation software systemmore » to hardware and third party software (e.g. relational database systems and schemas). This makes annotation systems hard to reproduce, inflexible to modification over time, difficult to assess, difficult to partition across multiple geographic sites, and difficult to understand for those who are not domain experts. These systems are not readily open to scrutiny and therefore not scientifically tractable. The advent of Semantic Web standards such as Resource Description Framework (RDF) and OWL Web Ontology Language (OWL) enables us to construct systems that address these challenges in a new comprehensive way. Results Here, we develop a framework for linking traditional data to OWL-based ontologies in genome annotation. We show how data standards can decouple hardware and third party software tools from annotation pipelines, thereby making annotation pipelines easier to reproduce and assess. An illustrative example shows how TURTLE (Terse RDF Triple Language) can be used as a human readable, but also semantically-aware, equivalent to GenBank/EMBL files. Conclusions The power of this approach lies in its ability to assemble annotation data from multiple databases across multiple locations into a representation that is understandable to researchers. In this way, all researchers, experimental and computational, will more easily understand the informatics processes constructing genome annotation and ultimately be able to help improve the systems that produce them.« less

Energy and Environmental Issues in Eastern Europe and Central Asia: An Annotated Guide to Information Resources

DOE Office of Scientific and Technical Information (OSTI.GOV)

Gant, K.S.

2000-10-09

Energy and environmental problems undermine the potential for sustained economic development and contribute to political and economic instability in the strategically important region surrounding the Caspian and Black Seas. Many organizations supporting efforts to resolve problems in this region have found that consensus building--a prerequisite for action--is a difficult process. Reaching agreement on priorities for investment, technical collaboration, and policy incentives depends upon informed decision-making by governments and local stakeholders. And while vast quantities of data and numerous analyses and reports are more accessible than ever, wading through the many potential sources in search of timely and relevant data ismore » a formidable task. To facilitate more successful data searches and retrieval, this document provides annotated references to over 200 specific information sources, and over twenty primary search engines and data retrieval services, that provide relevant and timely information related to the environment, energy, and economic development around the Caspian and Black Seas. This document is an advance copy of the content that Oak Ridge National Laboratory (ORNL) plans to transfer to the web in HTML format to facilitate interactive search and retrieval of information using standard web-browser software.« less

Guide to preparing SAND reports. Revised

DOE Office of Scientific and Technical Information (OSTI.GOV)

Locke, T.K.

1996-04-01

This guide contains basic information needed to produce a SAND report. Its guidelines reflect DOE regulation and Sandia policy. The guide includes basic writing instructions in an annotated sample report; guidance for organization, format, and layout of reports produced by line organizations; and information about conference papers, journal articles, and brochures. The appendixes contain sections on Sandia`s preferred usage, equations, references, copyrights and permissions, and publishing terms.

GUIDEseq: a bioconductor package to analyze GUIDE-Seq datasets for CRISPR-Cas nucleases.

PubMed

Zhu, Lihua Julie; Lawrence, Michael; Gupta, Ankit; Pagès, Hervé; Kucukural, Alper; Garber, Manuel; Wolfe, Scot A

2017-05-15

Genome editing technologies developed around the CRISPR-Cas9 nuclease system have facilitated the investigation of a broad range of biological questions. These nucleases also hold tremendous promise for treating a variety of genetic disorders. In the context of their therapeutic application, it is important to identify the spectrum of genomic sequences that are cleaved by a candidate nuclease when programmed with a particular guide RNA, as well as the cleavage efficiency of these sites. Powerful new experimental approaches, such as GUIDE-seq, facilitate the sensitive, unbiased genome-wide detection of nuclease cleavage sites within the genome. Flexible bioinformatics analysis tools for processing GUIDE-seq data are needed. Here, we describe an open source, open development software suite, GUIDEseq, for GUIDE-seq data analysis and annotation as a Bioconductor package in R. The GUIDEseq package provides a flexible platform with more than 60 adjustable parameters for the analysis of datasets associated with custom nuclease applications. These parameters allow data analysis to be tailored to different nuclease platforms with different length and complexity in their guide and PAM recognition sequences or their DNA cleavage position. They also enable users to customize sequence aggregation criteria, and vary peak calling thresholds that can influence the number of potential off-target sites recovered. GUIDEseq also annotates potential off-target sites that overlap with genes based on genome annotation information, as these may be the most important off-target sites for further characterization. In addition, GUIDEseq enables the comparison and visualization of off-target site overlap between different datasets for a rapid comparison of different nuclease configurations or experimental conditions. For each identified off-target, the GUIDEseq package outputs mapped GUIDE-Seq read count as well as cleavage score from a user specified off-target cleavage score prediction algorithm permitting the identification of genomic sequences with unexpected cleavage activity. The GUIDEseq package enables analysis of GUIDE-data from various nuclease platforms for any species with a defined genomic sequence. This software package has been used successfully to analyze several GUIDE-seq datasets. The software, source code and documentation are freely available at http://www.bioconductor.org/packages/release/bioc/html/GUIDEseq.html .

The Music Industry Conference Guide for Music Educators. A Supplement to the Music Educators Journal.

ERIC Educational Resources Information Center

Music Educators Journal, 1988

1988-01-01

This supplement is a comprehensive guide to the music industry designed for music teachers. Included are tips for contacting music businesses and suggestions on ordering music, robes, instruments, computer software, and other supplies. Includes an annotated directory of Music Industry Conference members. (JDH)

A Guide to Employability Skills Materials.

ERIC Educational Resources Information Center

Kromhout, Ora M.; And Others

This guide identifies existing employability skills materials and provides annotations to assist the reader in selecting materials. To assist Florida educators in relating employability skills to educational goals, Florida goals and standards are presented. A Topic Index to Titles first provides a topic outline of skills areas based on The Florida…

Public Administration: A Bibliography of Selected Reference Sources.

ERIC Educational Resources Information Center

Brustman, Mary Jane

This guide presents an annotated list of selected reference sources in public administration. All of the sources listed are found at the Graduate Library for Public Affairs and Policy (GLPP) located at the State University of New York, Albany. Detailed, exhaustive guides in literature, research, indexes, abstracts, statistical sources, government…

California Library Laws, 2008

ERIC Educational Resources Information Center

Smith, Paul G., Ed.

2008-01-01

"California Library Laws 2008" is a selective guide to state laws and related materials that most directly affect the everyday operations of public libraries and organizations that work with public libraries. It is intended as a convenient reference, not as a replacement for the annotated codes or for legal advice. The guide is organized…

VOCATIONAL ADJUSTMENT AND THE DEAF--A GUIDE AND ANNOTATED BIBLIOGRAPHY.

ERIC Educational Resources Information Center

LERMAN, ALAN

WRITTEN FOR THOSE INTERESTED IN THE VOCATIONAL TRAINING, PLACEMENT, REHABILITATION, AND EVALUATION OF DEAF WORKERS, THE GUIDE REVIEWS LITERATURE WRITTEN ON WORK ADJUSTMENT, VOCATIONAL INTERESTS, PLACEMENT, STATUS, AND ADJUSTMENT OF DEAF ADULTS. A CRITIQUE OF STUDIES ON DEAF WORKERS AND EVALUATION OF VARIOUS INFORMATION-GATHERING TECHNIQUES…

Kinder Lernen Deutsch. Materials Project Part I. Revised.

ERIC Educational Resources Information Center

American Association of Teachers of German.

The Kinder Lernen Deutsch (LKD) materials evaluation project identifies materials appropriate for the elementary school German classrooms in grades K-8. This guide consists of an annotated bibliography, with ratings, of these materials. The guiding principles by which the materials were assessed were: use of the communicative approach; integration…

Theatre and Cinema Architecture: A Guide to Information Sources.

ERIC Educational Resources Information Center

Stoddard, Richard

This annotated bibliography cites works related to theatres, movie houses, opera houses, and dance facilities. It is divided into three parts: general references, theatre architecture, and cinema architecture. The part on general references includes bibliographies and periodicals. The second and main part of the guide, on theatre architecture,…

Free-Loan Media for French: A Teacher's Guide.

ERIC Educational Resources Information Center

Veitz, M. Frances, Ed.

Designed to assist French instructors in introducing France to their students, this guidebook provides an annotated list of over 300 audio-visual materials and realia that are available on a free-loan basis. The guide lists films, videotapes, filmstrips, slide collections, pamphlets, factsheets, posters, records, tapes, and booklets available in…

Planetarium Educator's Workshop Guide. International Planetarium Society Special Report No. 10.

ERIC Educational Resources Information Center

Friedman, Alan; And Others

Presented is a workshop guide for planetarium educators. Seven modules and four appendices focus on organizational patterns, learning theories, questioning strategies, activities for the planetarium, and incorporating all of the above into teaching. The four appendices include a list of the 1978 workshop participants, an annotated bibliography for…

The distributed annotation system.

PubMed

Dowell, R D; Jokerst, R M; Day, A; Eddy, S R; Stein, L

2001-01-01

Currently, most genome annotation is curated by centralized groups with limited resources. Efforts to share annotations transparently among multiple groups have not yet been satisfactory. Here we introduce a concept called the Distributed Annotation System (DAS). DAS allows sequence annotations to be decentralized among multiple third-party annotators and integrated on an as-needed basis by client-side software. The communication between client and servers in DAS is defined by the DAS XML specification. Annotations are displayed in layers, one per server. Any client or server adhering to the DAS XML specification can participate in the system; we describe a simple prototype client and server example. The DAS specification is being used experimentally by Ensembl, WormBase, and the Berkeley Drosophila Genome Project. Continued success will depend on the readiness of the research community to adopt DAS and provide annotations. All components are freely available from the project website http://www.biodas.org/.

MicroScope in 2017: an expanding and evolving integrated resource for community expertise of microbial genomes

PubMed Central

Vallenet, David; Calteau, Alexandra; Cruveiller, Stéphane; Gachet, Mathieu; Lajus, Aurélie; Josso, Adrien; Mercier, Jonathan; Renaux, Alexandre; Rollin, Johan; Rouy, Zoe; Roche, David; Scarpelli, Claude; Médigue, Claudine

2017-01-01

The annotation of genomes from NGS platforms needs to be automated and fully integrated. However, maintaining consistency and accuracy in genome annotation is a challenging problem because millions of protein database entries are not assigned reliable functions. This shortcoming limits the knowledge that can be extracted from genomes and metabolic models. Launched in 2005, the MicroScope platform (http://www.genoscope.cns.fr/agc/microscope) is an integrative resource that supports systematic and efficient revision of microbial genome annotation, data management and comparative analysis. Effective comparative analysis requires a consistent and complete view of biological data, and therefore, support for reviewing the quality of functional annotation is critical. MicroScope allows users to analyze microbial (meta)genomes together with post-genomic experiment results if any (i.e. transcriptomics, re-sequencing of evolved strains, mutant collections, phenotype data). It combines tools and graphical interfaces to analyze genomes and to perform the expert curation of gene functions in a comparative context. Starting with a short overview of the MicroScope system, this paper focuses on some major improvements of the Web interface, mainly for the submission of genomic data and on original tools and pipelines that have been developed and integrated in the platform: computation of pan-genomes and prediction of biosynthetic gene clusters. Today the resource contains data for more than 6000 microbial genomes, and among the 2700 personal accounts (65% of which are now from foreign countries), 14% of the users are performing expert annotations, on at least a weekly basis, contributing to improve the quality of microbial genome annotations. PMID:27899624

Bibliographie annotee de ressources complementaires. Etudes sociales: Secondaire, 7e a 12e (Annotated Bibliography of Further Resources. Social Studies: Secondary School, Grades 7-12).

ERIC Educational Resources Information Center

Soucy, Claire, Comp.; Hebert, Lorraine, Comp.

This annotated bibliography offers resources for teaching the social studies for grades 7 through 12. Subject areas include: (1) grade 7 - culture of Canada and Japan, as well as multicultural and bilingual Canada; (2) grade 8 - the geography of Canada, the United States, and the case of Brazil in South America; (3) grade 9 - economic perspectives…

An Audio-Visual Resource Notebook for Adult Consumer Education. An Annotated Bibliography of Selected Audio-Visual Aids for Adult Consumer Education, with Special Emphasis on Materials for Elderly, Low-Income and Handicapped Consumers.

ERIC Educational Resources Information Center

Virginia State Dept. of Agriculture and Consumer Services, Richmond, VA.

This document is an annotated bibliography of audio-visual aids in the field of consumer education, intended especially for use among low-income, elderly, and handicapped consumers. It was developed to aid consumer education program planners in finding audio-visual resources to enhance their presentations. Materials listed include 293 resources…

MicroScope-an integrated resource for community expertise of gene functions and comparative analysis of microbial genomic and metabolic data.

PubMed

Médigue, Claudine; Calteau, Alexandra; Cruveiller, Stéphane; Gachet, Mathieu; Gautreau, Guillaume; Josso, Adrien; Lajus, Aurélie; Langlois, Jordan; Pereira, Hugo; Planel, Rémi; Roche, David; Rollin, Johan; Rouy, Zoe; Vallenet, David

2017-09-12

The overwhelming list of new bacterial genomes becoming available on a daily basis makes accurate genome annotation an essential step that ultimately determines the relevance of thousands of genomes stored in public databanks. The MicroScope platform (http://www.genoscope.cns.fr/agc/microscope) is an integrative resource that supports systematic and efficient revision of microbial genome annotation, data management and comparative analysis. Starting from the results of our syntactic, functional and relational annotation pipelines, MicroScope provides an integrated environment for the expert annotation and comparative analysis of prokaryotic genomes. It combines tools and graphical interfaces to analyze genomes and to perform the manual curation of gene function in a comparative genomics and metabolic context. In this article, we describe the free-of-charge MicroScope services for the annotation and analysis of microbial (meta)genomes, transcriptomic and re-sequencing data. Then, the functionalities of the platform are presented in a way providing practical guidance and help to the nonspecialists in bioinformatics. Newly integrated analysis tools (i.e. prediction of virulence and resistance genes in bacterial genomes) and original method recently developed (the pan-genome graph representation) are also described. Integrated environments such as MicroScope clearly contribute, through the user community, to help maintaining accurate resources. © The Author 2017. Published by Oxford University Press.

The Universal Protein Resource (UniProt): an expanding universe of protein information.

PubMed

Wu, Cathy H; Apweiler, Rolf; Bairoch, Amos; Natale, Darren A; Barker, Winona C; Boeckmann, Brigitte; Ferro, Serenella; Gasteiger, Elisabeth; Huang, Hongzhan; Lopez, Rodrigo; Magrane, Michele; Martin, Maria J; Mazumder, Raja; O'Donovan, Claire; Redaschi, Nicole; Suzek, Baris

2006-01-01

The Universal Protein Resource (UniProt) provides a central resource on protein sequences and functional annotation with three database components, each addressing a key need in protein bioinformatics. The UniProt Knowledgebase (UniProtKB), comprising the manually annotated UniProtKB/Swiss-Prot section and the automatically annotated UniProtKB/TrEMBL section, is the preeminent storehouse of protein annotation. The extensive cross-references, functional and feature annotations and literature-based evidence attribution enable scientists to analyse proteins and query across databases. The UniProt Reference Clusters (UniRef) speed similarity searches via sequence space compression by merging sequences that are 100% (UniRef100), 90% (UniRef90) or 50% (UniRef50) identical. Finally, the UniProt Archive (UniParc) stores all publicly available protein sequences, containing the history of sequence data with links to the source databases. UniProt databases continue to grow in size and in availability of information. Recent and upcoming changes to database contents, formats, controlled vocabularies and services are described. New download availability includes all major releases of UniProtKB, sequence collections by taxonomic division and complete proteomes. A bibliography mapping service has been added, and an ID mapping service will be available soon. UniProt databases can be accessed online at http://www.uniprot.org or downloaded at ftp://ftp.uniprot.org/pub/databases/.

Neurocarta: aggregating and sharing disease-gene relations for the neurosciences.

PubMed

Portales-Casamar, Elodie; Ch'ng, Carolyn; Lui, Frances; St-Georges, Nicolas; Zoubarev, Anton; Lai, Artemis Y; Lee, Mark; Kwok, Cathy; Kwok, Willie; Tseng, Luchia; Pavlidis, Paul

2013-02-26

Understanding the genetic basis of diseases is key to the development of better diagnoses and treatments. Unfortunately, only a small fraction of the existing data linking genes to phenotypes is available through online public resources and, when available, it is scattered across multiple access tools. Neurocarta is a knowledgebase that consolidates information on genes and phenotypes across multiple resources and allows tracking and exploring of the associations. The system enables automatic and manual curation of evidence supporting each association, as well as user-enabled entry of their own annotations. Phenotypes are recorded using controlled vocabularies such as the Disease Ontology to facilitate computational inference and linking to external data sources. The gene-to-phenotype associations are filtered by stringent criteria to focus on the annotations most likely to be relevant. Neurocarta is constantly growing and currently holds more than 30,000 lines of evidence linking over 7,000 genes to 2,000 different phenotypes. Neurocarta is a one-stop shop for researchers looking for candidate genes for any disorder of interest. In Neurocarta, they can review the evidence linking genes to phenotypes and filter out the evidence they're not interested in. In addition, researchers can enter their own annotations from their experiments and analyze them in the context of existing public annotations. Neurocarta's in-depth annotation of neurodevelopmental disorders makes it a unique resource for neuroscientists working on brain development.

Document Delivery: An Annotated Selective Bibliography.

ERIC Educational Resources Information Center

Khalil, Mounir A.; Katz, Suzanne R.

1992-01-01

Presents a selective annotated bibliography of 61 items that deal with topics related to document delivery, including networks; hypertext; interlibrary loan; computer security; electronic publishing; copyright; online catalogs; resource sharing; electronic mail; electronic libraries; optical character recognition; microcomputers; liability issues;…

RATT: Rapid Annotation Transfer Tool

PubMed Central

Otto, Thomas D.; Dillon, Gary P.; Degrave, Wim S.; Berriman, Matthew

2011-01-01

Second-generation sequencing technologies have made large-scale sequencing projects commonplace. However, making use of these datasets often requires gene function to be ascribed genome wide. Although tool development has kept pace with the changes in sequence production, for tasks such as mapping, de novo assembly or visualization, genome annotation remains a challenge. We have developed a method to rapidly provide accurate annotation for new genomes using previously annotated genomes as a reference. The method, implemented in a tool called RATT (Rapid Annotation Transfer Tool), transfers annotations from a high-quality reference to a new genome on the basis of conserved synteny. We demonstrate that a Mycobacterium tuberculosis genome or a single 2.5 Mb chromosome from a malaria parasite can be annotated in less than five minutes with only modest computational resources. RATT is available at http://ratt.sourceforge.net. PMID:21306991

Guide to Reference Sources on Africa, Asia, Latin America and the Caribbean, Middle East and North Africa, and Russia and East Europe: Selected and Annotated.

ERIC Educational Resources Information Center

Kennedy, James R., Jr.; And Others

This selected annotated bibliography of reference sources is designed to help college students prepare for the future by identifying critical sources on the societies and cultures of most of the world's people who have long been neglected in higher education. Encyclopedias, handbooks, and yearbooks are listed first under each area. Next are the…

Protein Information Resource: a community resource for expert annotation of protein data

PubMed Central

Barker, Winona C.; Garavelli, John S.; Hou, Zhenglin; Huang, Hongzhan; Ledley, Robert S.; McGarvey, Peter B.; Mewes, Hans-Werner; Orcutt, Bruce C.; Pfeiffer, Friedhelm; Tsugita, Akira; Vinayaka, C. R.; Xiao, Chunlin; Yeh, Lai-Su L.; Wu, Cathy

2001-01-01

The Protein Information Resource, in collaboration with the Munich Information Center for Protein Sequences (MIPS) and the Japan International Protein Information Database (JIPID), produces the most comprehensive and expertly annotated protein sequence database in the public domain, the PIR-International Protein Sequence Database. To provide timely and high quality annotation and promote database interoperability, the PIR-International employs rule-based and classification-driven procedures based on controlled vocabulary and standard nomenclature and includes status tags to distinguish experimentally determined from predicted protein features. The database contains about 200 000 non-redundant protein sequences, which are classified into families and superfamilies and their domains and motifs identified. Entries are extensively cross-referenced to other sequence, classification, genome, structure and activity databases. The PIR web site features search engines that use sequence similarity and database annotation to facilitate the analysis and functional identification of proteins. The PIR-Inter­national databases and search tools are accessible on the PIR web site at http://pir.georgetown.edu/ and at the MIPS web site at http://www.mips.biochem.mpg.de. The PIR-International Protein Sequence Database and other files are also available by FTP. PMID:11125041

Concept annotation in the CRAFT corpus.

PubMed

Bada, Michael; Eckert, Miriam; Evans, Donald; Garcia, Kristin; Shipley, Krista; Sitnikov, Dmitry; Baumgartner, William A; Cohen, K Bretonnel; Verspoor, Karin; Blake, Judith A; Hunter, Lawrence E

2012-07-09

Manually annotated corpora are critical for the training and evaluation of automated methods to identify concepts in biomedical text. This paper presents the concept annotations of the Colorado Richly Annotated Full-Text (CRAFT) Corpus, a collection of 97 full-length, open-access biomedical journal articles that have been annotated both semantically and syntactically to serve as a research resource for the biomedical natural-language-processing (NLP) community. CRAFT identifies all mentions of nearly all concepts from nine prominent biomedical ontologies and terminologies: the Cell Type Ontology, the Chemical Entities of Biological Interest ontology, the NCBI Taxonomy, the Protein Ontology, the Sequence Ontology, the entries of the Entrez Gene database, and the three subontologies of the Gene Ontology. The first public release includes the annotations for 67 of the 97 articles, reserving two sets of 15 articles for future text-mining competitions (after which these too will be released). Concept annotations were created based on a single set of guidelines, which has enabled us to achieve consistently high interannotator agreement. As the initial 67-article release contains more than 560,000 tokens (and the full set more than 790,000 tokens), our corpus is among the largest gold-standard annotated biomedical corpora. Unlike most others, the journal articles that comprise the corpus are drawn from diverse biomedical disciplines and are marked up in their entirety. Additionally, with a concept-annotation count of nearly 100,000 in the 67-article subset (and more than 140,000 in the full collection), the scale of conceptual markup is also among the largest of comparable corpora. The concept annotations of the CRAFT Corpus have the potential to significantly advance biomedical text mining by providing a high-quality gold standard for NLP systems. The corpus, annotation guidelines, and other associated resources are freely available at http://bionlp-corpora.sourceforge.net/CRAFT/index.shtml.

Concept annotation in the CRAFT corpus

PubMed Central

2012-01-01

Background Manually annotated corpora are critical for the training and evaluation of automated methods to identify concepts in biomedical text. Results This paper presents the concept annotations of the Colorado Richly Annotated Full-Text (CRAFT) Corpus, a collection of 97 full-length, open-access biomedical journal articles that have been annotated both semantically and syntactically to serve as a research resource for the biomedical natural-language-processing (NLP) community. CRAFT identifies all mentions of nearly all concepts from nine prominent biomedical ontologies and terminologies: the Cell Type Ontology, the Chemical Entities of Biological Interest ontology, the NCBI Taxonomy, the Protein Ontology, the Sequence Ontology, the entries of the Entrez Gene database, and the three subontologies of the Gene Ontology. The first public release includes the annotations for 67 of the 97 articles, reserving two sets of 15 articles for future text-mining competitions (after which these too will be released). Concept annotations were created based on a single set of guidelines, which has enabled us to achieve consistently high interannotator agreement. Conclusions As the initial 67-article release contains more than 560,000 tokens (and the full set more than 790,000 tokens), our corpus is among the largest gold-standard annotated biomedical corpora. Unlike most others, the journal articles that comprise the corpus are drawn from diverse biomedical disciplines and are marked up in their entirety. Additionally, with a concept-annotation count of nearly 100,000 in the 67-article subset (and more than 140,000 in the full collection), the scale of conceptual markup is also among the largest of comparable corpora. The concept annotations of the CRAFT Corpus have the potential to significantly advance biomedical text mining by providing a high-quality gold standard for NLP systems. The corpus, annotation guidelines, and other associated resources are freely available at http://bionlp-corpora.sourceforge.net/CRAFT/index.shtml. PMID:22776079

Core French: A Selected Annotated Resource List.

ERIC Educational Resources Information Center

Boyd, J. A.; Mollica, Anthony

1985-01-01

This is an annotated bibliography of: readers, workbooks, conversation books, cultural sources and readings, flash cards, duplicating or line masters, and media kits submitted by publishers as applicable to French second language instruction from kindergarten through senior high school levels. (MSE)

proGenomes: a resource for consistent functional and taxonomic annotations of prokaryotic genomes.

PubMed

Mende, Daniel R; Letunic, Ivica; Huerta-Cepas, Jaime; Li, Simone S; Forslund, Kristoffer; Sunagawa, Shinichi; Bork, Peer

2017-01-04

The availability of microbial genomes has opened many new avenues of research within microbiology. This has been driven primarily by comparative genomics approaches, which rely on accurate and consistent characterization of genomic sequences. It is nevertheless difficult to obtain consistent taxonomic and integrated functional annotations for defined prokaryotic clades. Thus, we developed proGenomes, a resource that provides user-friendly access to currently 25 038 high-quality genomes whose sequences and consistent annotations can be retrieved individually or by taxonomic clade. These genomes are assigned to 5306 consistent and accurate taxonomic species clusters based on previously established methodology. proGenomes also contains functional information for almost 80 million protein-coding genes, including a comprehensive set of general annotations and more focused annotations for carbohydrate-active enzymes and antibiotic resistance genes. Additionally, broad habitat information is provided for many genomes. All genomes and associated information can be downloaded by user-selected clade or multiple habitat-specific sets of representative genomes. We expect that the availability of high-quality genomes with comprehensive functional annotations will promote advances in clinical microbial genomics, functional evolution and other subfields of microbiology. proGenomes is available at http://progenomes.embl.de. © The Author(s) 2016. Published by Oxford University Press on behalf of Nucleic Acids Research.

Dual Career Couple Relationships. An Annotated Bibliography, for Conference Presented by The Women's Resources and Research Center (University of California, Davis, April 11-12, 1980). UCD-Women's Resources and Research Center Working Paper Series No. 20.

ERIC Educational Resources Information Center

Knowles, Em Claire

This annotated bibliography of readings related to dual career couple relationships is divided into eleven areas of focus. Sections included are (1) Alternatives to Rigid Work Imperatives; (2) Child Rearing in Dual Career Families; (3) Collaboration Strategies for Coping; (4) Definition, Trend, and Historical Perspective of Dual Career Couples;…

Annotating spatio-temporal datasets for meaningful analysis in the Web

NASA Astrophysics Data System (ADS)

Stasch, Christoph; Pebesma, Edzer; Scheider, Simon

2014-05-01

More and more environmental datasets that vary in space and time are available in the Web. This comes along with an advantage of using the data for other purposes than originally foreseen, but also with the danger that users may apply inappropriate analysis procedures due to lack of important assumptions made during the data collection process. In order to guide towards a meaningful (statistical) analysis of spatio-temporal datasets available in the Web, we have developed a Higher-Order-Logic formalism that captures some relevant assumptions in our previous work [1]. It allows to proof on meaningful spatial prediction and aggregation in a semi-automated fashion. In this poster presentation, we will present a concept for annotating spatio-temporal datasets available in the Web with concepts defined in our formalism. Therefore, we have defined a subset of the formalism as a Web Ontology Language (OWL) pattern. It allows capturing the distinction between the different spatio-temporal variable types, i.e. point patterns, fields, lattices and trajectories, that in turn determine whether a particular dataset can be interpolated or aggregated in a meaningful way using a certain procedure. The actual annotations that link spatio-temporal datasets with the concepts in the ontology pattern are provided as Linked Data. In order to allow data producers to add the annotations to their datasets, we have implemented a Web portal that uses a triple store at the backend to store the annotations and to make them available in the Linked Data cloud. Furthermore, we have implemented functions in the statistical environment R to retrieve the RDF annotations and, based on these annotations, to support a stronger typing of spatio-temporal datatypes guiding towards a meaningful analysis in R. [1] Stasch, C., Scheider, S., Pebesma, E., Kuhn, W. (2014): "Meaningful spatial prediction and aggregation", Environmental Modelling & Software, 51, 149-165.

iELM—a web server to explore short linear motif-mediated interactions

PubMed Central

Weatheritt, Robert J.; Jehl, Peter; Dinkel, Holger; Gibson, Toby J.

2012-01-01

The recent expansion in our knowledge of protein–protein interactions (PPIs) has allowed the annotation and prediction of hundreds of thousands of interactions. However, the function of many of these interactions remains elusive. The interactions of Eukaryotic Linear Motif (iELM) web server provides a resource for predicting the function and positional interface for a subset of interactions mediated by short linear motifs (SLiMs). The iELM prediction algorithm is based on the annotated SLiM classes from the Eukaryotic Linear Motif (ELM) resource and allows users to explore both annotated and user-generated PPI networks for SLiM-mediated interactions. By incorporating the annotated information from the ELM resource, iELM provides functional details of PPIs. This can be used in proteomic analysis, for example, to infer whether an interaction promotes complex formation or degradation. Furthermore, details of the molecular interface of the SLiM-mediated interactions are also predicted. This information is displayed in a fully searchable table, as well as graphically with the modular architecture of the participating proteins extracted from the UniProt and Phospho.ELM resources. A network figure is also presented to aid the interpretation of results. The iELM server supports single protein queries as well as large-scale proteomic submissions and is freely available at http://i.elm.eu.org. PMID:22638578

Corpus annotation for mining biomedical events from literature

PubMed Central

Kim, Jin-Dong; Ohta, Tomoko; Tsujii, Jun'ichi

2008-01-01

Background Advanced Text Mining (TM) such as semantic enrichment of papers, event or relation extraction, and intelligent Question Answering have increasingly attracted attention in the bio-medical domain. For such attempts to succeed, text annotation from the biological point of view is indispensable. However, due to the complexity of the task, semantic annotation has never been tried on a large scale, apart from relatively simple term annotation. Results We have completed a new type of semantic annotation, event annotation, which is an addition to the existing annotations in the GENIA corpus. The corpus has already been annotated with POS (Parts of Speech), syntactic trees, terms, etc. The new annotation was made on half of the GENIA corpus, consisting of 1,000 Medline abstracts. It contains 9,372 sentences in which 36,114 events are identified. The major challenges during event annotation were (1) to design a scheme of annotation which meets specific requirements of text annotation, (2) to achieve biology-oriented annotation which reflect biologists' interpretation of text, and (3) to ensure the homogeneity of annotation quality across annotators. To meet these challenges, we introduced new concepts such as Single-facet Annotation and Semantic Typing, which have collectively contributed to successful completion of a large scale annotation. Conclusion The resulting event-annotated corpus is the largest and one of the best in quality among similar annotation efforts. We expect it to become a valuable resource for NLP (Natural Language Processing)-based TM in the bio-medical domain. PMID:18182099

Linking Disparate Datasets of the Earth Sciences with the SemantEco Annotator

NASA Astrophysics Data System (ADS)

Seyed, P.; Chastain, K.; McGuinness, D. L.

2013-12-01

Use of Semantic Web technologies for data management in the Earth sciences (and beyond) has great potential but is still in its early stages, since the challenges of translating data into a more explicit or semantic form for immediate use within applications has not been fully addressed. In this abstract we help address this challenge by introducing the SemantEco Annotator, which enables anyone, regardless of expertise, to semantically annotate tabular Earth Science data and translate it into linked data format, while applying the logic inherent in community-standard vocabularies to guide the process. The Annotator was conceived under a desire to unify dataset content from a variety of sources under common vocabularies, for use in semantically-enabled web applications. Our current use case employs linked data generated by the Annotator for use in the SemantEco environment, which utilizes semantics to help users explore, search, and visualize water or air quality measurement and species occurrence data through a map-based interface. The generated data can also be used immediately to facilitate discovery and search capabilities within 'big data' environments. The Annotator provides a method for taking information about a dataset, that may only be known to its maintainers, and making it explicit, in a uniform and machine-readable fashion, such that a person or information system can more easily interpret the underlying structure and meaning. Its primary mechanism is to enable a user to formally describe how columns of a tabular dataset relate and/or describe entities. For example, if a user identifies columns for latitude and longitude coordinates, we can infer the data refers to a point that can be plotted on a map. Further, it can be made explicit that measurements of 'nitrate' and 'NO3-' are of the same entity through vocabulary assignments, thus more easily utilizing data sets that use different nomenclatures. The Annotator provides an extensive and searchable library of vocabularies to assist the user in locating terms to describe observed entities, their properties, and relationships. The Annotator leverages vocabulary definitions of these concepts to guide the user in describing data in a logically consistent manner. The vocabularies made available through the Annotator are open, as is the Annotator itself. We have taken a step towards making semantic annotation/translation of data more accessible. Our vision for the Annotator is as a tool that can be integrated into a semantic data 'workbench' environment, which would allow semantic annotation of a variety of data formats, using standard vocabularies. These vocabularies involved enable search for similar datasets, and integration with any semantically-enabled applications for analysis and visualization.

Annotated chemical patent corpus: a gold standard for text mining.

PubMed

Akhondi, Saber A; Klenner, Alexander G; Tyrchan, Christian; Manchala, Anil K; Boppana, Kiran; Lowe, Daniel; Zimmermann, Marc; Jagarlapudi, Sarma A R P; Sayle, Roger; Kors, Jan A; Muresan, Sorel

2014-01-01

Exploring the chemical and biological space covered by patent applications is crucial in early-stage medicinal chemistry activities. Patent analysis can provide understanding of compound prior art, novelty checking, validation of biological assays, and identification of new starting points for chemical exploration. Extracting chemical and biological entities from patents through manual extraction by expert curators can take substantial amount of time and resources. Text mining methods can help to ease this process. To validate the performance of such methods, a manually annotated patent corpus is essential. In this study we have produced a large gold standard chemical patent corpus. We developed annotation guidelines and selected 200 full patents from the World Intellectual Property Organization, United States Patent and Trademark Office, and European Patent Office. The patents were pre-annotated automatically and made available to four independent annotator groups each consisting of two to ten annotators. The annotators marked chemicals in different subclasses, diseases, targets, and modes of action. Spelling mistakes and spurious line break due to optical character recognition errors were also annotated. A subset of 47 patents was annotated by at least three annotator groups, from which harmonized annotations and inter-annotator agreement scores were derived. One group annotated the full set. The patent corpus includes 400,125 annotations for the full set and 36,537 annotations for the harmonized set. All patents and annotated entities are publicly available at www.biosemantics.org.

Annotated Chemical Patent Corpus: A Gold Standard for Text Mining

PubMed Central

Akhondi, Saber A.; Klenner, Alexander G.; Tyrchan, Christian; Manchala, Anil K.; Boppana, Kiran; Lowe, Daniel; Zimmermann, Marc; Jagarlapudi, Sarma A. R. P.; Sayle, Roger; Kors, Jan A.; Muresan, Sorel

2014-01-01

Exploring the chemical and biological space covered by patent applications is crucial in early-stage medicinal chemistry activities. Patent analysis can provide understanding of compound prior art, novelty checking, validation of biological assays, and identification of new starting points for chemical exploration. Extracting chemical and biological entities from patents through manual extraction by expert curators can take substantial amount of time and resources. Text mining methods can help to ease this process. To validate the performance of such methods, a manually annotated patent corpus is essential. In this study we have produced a large gold standard chemical patent corpus. We developed annotation guidelines and selected 200 full patents from the World Intellectual Property Organization, United States Patent and Trademark Office, and European Patent Office. The patents were pre-annotated automatically and made available to four independent annotator groups each consisting of two to ten annotators. The annotators marked chemicals in different subclasses, diseases, targets, and modes of action. Spelling mistakes and spurious line break due to optical character recognition errors were also annotated. A subset of 47 patents was annotated by at least three annotator groups, from which harmonized annotations and inter-annotator agreement scores were derived. One group annotated the full set. The patent corpus includes 400,125 annotations for the full set and 36,537 annotations for the harmonized set. All patents and annotated entities are publicly available at www.biosemantics.org. PMID:25268232

Newspaper Indexes, Guides, Directories, and Union Lists. No. 4.

ERIC Educational Resources Information Center

Fikes, Robert, Jr.

This annotated bibliography lists 52 citations for U.S. and foreign newspaper indexes, summaries, guides and directories, and union lists held by San Diego State University Libraries. Entries are arranged alphabetically in the above categories by main entry, followed by imprint, frequency and/or date of publication, volumes held by the library,…

RIF's [Reading is Fundamental] Guide to Book Selection 1973.

ERIC Educational Resources Information Center

Smithsonian Institution, Washington, DC. National Reading is Fun-damental Program.

This book guide is an annotated list of available paperback titles for elementary school children for use by "Reading is FUNdamental" program directors. Some high-interest, low-vocabulary titles suitable for older children as well as special booklists for black, American Indian, and Spanish-speaking children are also included. All books…

Air University Suggested Professional Reading Guide.

ERIC Educational Resources Information Center

Air Univ., Maxwell AFB, AL.

One of six related documents intended for the Air Force officer, the enlisted man, or the civilian, this reading guide contains an annotated list of 26 publications that support Project Warrior and provide information about military history and the Air Force heritage. The books are listed in sequence according to a reading ease index, which…

California Library Laws, 2009

ERIC Educational Resources Information Center

Smith, Paul G., Ed.

2009-01-01

California Library Laws 2009 is a selective guide to state laws and related materials that most directly affect the everyday operations of public libraries and organizations that work with public libraries. It is intended as a convenient reference, not as a replacement for the annotated codes or for legal advice. The guide is organized as follows.…

A Guide to Courseware Authoring Options in ESL/FL Instruction.

ERIC Educational Resources Information Center

Hampson, S. L.

A guide to courseware authoring aids for computer-assisted language instruction (CALIS) gives suggestions for the selection and use of programing options and provides an annotated listing of those options. Introductory sections discuss the use of computer-assisted language teaching, the selection of quality courseware, the types of authoring aids…

Aids to English Language Teaching: Information Guide No. 4.

ERIC Educational Resources Information Center

British Council, London (England). English-Teaching Information Centre.

This is an annotated guide to English language instructional materials useful for both native and non-native speakers of English at primary and secondary levels. Materials relate to and are available in Great Britain; prices and addresses of publishers and suppliers are included. The sections cover: (1) Visual aids specifically designed for…

An Annotated Guide to Audio-Visual Materials for Teaching Shakespeare.

ERIC Educational Resources Information Center

Albert, Richard N.

Audio-visual materials, found in a variety of periodicals, catalogs, and reference works, are listed in this guide to expedite the process of finding appropriate classroom materials for a study of William Shakespeare in the classroom. Separate listings of films, filmstrips, and recordings are provided, with subdivisions for "The Plays"…

Manufacturing Math Classes: An Instructional Program Guide for Manufacturing Workers.

ERIC Educational Resources Information Center

McBride, Pamela G.; And Others

This program guide documents a manufacturing job family curriculum that develops competence in generic work force education skills through three courses: Reading Rulers, Charts, and Gauges and Math for Manufacturing Workers I and II. An annotated table of contents lists a brief description of the questions answered in each section. An introduction…

What Shall I Read on Japan? An Introductory Guide. Twelfth Edition.

ERIC Educational Resources Information Center

Marks, Alfred H.

This highly selective annotated list of works may be read with profit by the serious beginning student or casual reader interested in things Japanese. As many entries as possible from the earlier editions have been retained. All new materials cited were reviewed. Included are reference books, guides, fiction, novels, translations, research…

Asia: A Guide to Basic Books. 1971 Supplement.

ERIC Educational Resources Information Center

Embree, Ainslie T., Comp.; And Others

This selective bibliography, compiled and annotated by Asian specialists, is intended for the general reader as a continuation of Asia: A Guide to Basic Books published in 1966. The purpose is to identify 156 books covering extensive subject areas about Asia. The supplement is a geographically arranged into four major sections: General Asia, South…

From data repositories to submission portals: rethinking the role of domain-specific databases in CollecTF.

PubMed

Kılıç, Sefa; Sagitova, Dinara M; Wolfish, Shoshannah; Bely, Benoit; Courtot, Mélanie; Ciufo, Stacy; Tatusova, Tatiana; O'Donovan, Claire; Chibucos, Marcus C; Martin, Maria J; Erill, Ivan

2016-01-01

Domain-specific databases are essential resources for the biomedical community, leveraging expert knowledge to curate published literature and provide access to referenced data and knowledge. The limited scope of these databases, however, poses important challenges on their infrastructure, visibility, funding and usefulness to the broader scientific community. CollecTF is a community-oriented database documenting experimentally validated transcription factor (TF)-binding sites in the Bacteria domain. In its quest to become a community resource for the annotation of transcriptional regulatory elements in bacterial genomes, CollecTF aims to move away from the conventional data-repository paradigm of domain-specific databases. Through the adoption of well-established ontologies, identifiers and collaborations, CollecTF has progressively become also a portal for the annotation and submission of information on transcriptional regulatory elements to major biological sequence resources (RefSeq, UniProtKB and the Gene Ontology Consortium). This fundamental change in database conception capitalizes on the domain-specific knowledge of contributing communities to provide high-quality annotations, while leveraging the availability of stable information hubs to promote long-term access and provide high-visibility to the data. As a submission portal, CollecTF generates TF-binding site information through direct annotation of RefSeq genome records, definition of TF-based regulatory networks in UniProtKB entries and submission of functional annotations to the Gene Ontology. As a database, CollecTF provides enhanced search and browsing, targeted data exports, binding motif analysis tools and integration with motif discovery and search platforms. This innovative approach will allow CollecTF to focus its limited resources on the generation of high-quality information and the provision of specialized access to the data.Database URL: http://www.collectf.org/. © The Author(s) 2016. Published by Oxford University Press.

Genome and proteome annotation: organization, interpretation and integration

PubMed Central

Reeves, Gabrielle A.; Talavera, David; Thornton, Janet M.

2008-01-01

Recent years have seen a huge increase in the generation of genomic and proteomic data. This has been due to improvements in current biological methodologies, the development of new experimental techniques and the use of computers as support tools. All these raw data are useless if they cannot be properly analysed, annotated, stored and displayed. Consequently, a vast number of resources have been created to present the data to the wider community. Annotation tools and databases provide the means to disseminate these data and to comprehend their biological importance. This review examines the various aspects of annotation: type, methodology and availability. Moreover, it puts a special interest on novel annotation fields, such as that of phenotypes, and highlights the recent efforts focused on the integrating annotations. PMID:19019817

HopBase: a unified resource for Humulus genomics

PubMed Central

Hill, Steven T.; Sudarsanam, Ramcharan

2017-01-01

Abstract Hop (Humulus lupulus L. var lupulus) is a dioecious plant of worldwide significance, used primarily for bittering and flavoring in brewing beer. Studies on the medicinal properties of several unique compounds produced by hop have led to additional interest from pharmacy and healthcare industries as well as livestock production as a natural antibiotic. Genomic research in hop has resulted a published draft genome and transcriptome assemblies. As research into the genomics of hop has gained interest, there is a critical need for centralized online genomic resources. To support the growing research community, we report the development of an online resource "HopBase.org." In addition to providing a gene annotation to the existing Shinsuwase draft genome, HopBase makes available genome assemblies and annotations for both the cultivar “Teamaker” and male hop accession number USDA 21422M. These genome assemblies, gene annotations, along with other common data, coupled with a genome browser and BLAST database enable the hop community to enter the genomic age. The HopBase genomic resource is accessible at http://hopbase.org and http://hopbase.cgrb.oregonstate.edu. PMID:28415075

PhytoPath: an integrative resource for plant pathogen genomics.

PubMed

Pedro, Helder; Maheswari, Uma; Urban, Martin; Irvine, Alistair George; Cuzick, Alayne; McDowall, Mark D; Staines, Daniel M; Kulesha, Eugene; Hammond-Kosack, Kim Elizabeth; Kersey, Paul Julian

2016-01-04

PhytoPath (www.phytopathdb.org) is a resource for genomic and phenotypic data from plant pathogen species, that integrates phenotypic data for genes from PHI-base, an expertly curated catalog of genes with experimentally verified pathogenicity, with the Ensembl tools for data visualization and analysis. The resource is focused on fungi, protists (oomycetes) and bacterial plant pathogens that have genomes that have been sequenced and annotated. Genes with associated PHI-base data can be easily identified across all plant pathogen species using a BioMart-based query tool and visualized in their genomic context on the Ensembl genome browser. The PhytoPath resource contains data for 135 genomic sequences from 87 plant pathogen species, and 1364 genes curated for their role in pathogenicity and as targets for chemical intervention. Support for community annotation of gene models is provided using the WebApollo online gene editor, and we are working with interested communities to improve reference annotation for selected species. © The Author(s) 2015. Published by Oxford University Press on behalf of Nucleic Acids Research.

An integrative strategy to identify the entire protein coding potential of prokaryotic genomes by proteogenomics.

PubMed

Omasits, Ulrich; Varadarajan, Adithi R; Schmid, Michael; Goetze, Sandra; Melidis, Damianos; Bourqui, Marc; Nikolayeva, Olga; Québatte, Maxime; Patrignani, Andrea; Dehio, Christoph; Frey, Juerg E; Robinson, Mark D; Wollscheid, Bernd; Ahrens, Christian H

2017-12-01

Accurate annotation of all protein-coding sequences (CDSs) is an essential prerequisite to fully exploit the rapidly growing repertoire of completely sequenced prokaryotic genomes. However, large discrepancies among the number of CDSs annotated by different resources, missed functional short open reading frames (sORFs), and overprediction of spurious ORFs represent serious limitations. Our strategy toward accurate and complete genome annotation consolidates CDSs from multiple reference annotation resources, ab initio gene prediction algorithms and in silico ORFs (a modified six-frame translation considering alternative start codons) in an integrated proteogenomics database (iPtgxDB) that covers the entire protein-coding potential of a prokaryotic genome. By extending the PeptideClassifier concept of unambiguous peptides for prokaryotes, close to 95% of the identifiable peptides imply one distinct protein, largely simplifying downstream analysis. Searching a comprehensive Bartonella henselae proteomics data set against such an iPtgxDB allowed us to unambiguously identify novel ORFs uniquely predicted by each resource, including lipoproteins, differentially expressed and membrane-localized proteins, novel start sites and wrongly annotated pseudogenes. Most novelties were confirmed by targeted, parallel reaction monitoring mass spectrometry, including unique ORFs and single amino acid variations (SAAVs) identified in a re-sequenced laboratory strain that are not present in its reference genome. We demonstrate the general applicability of our strategy for genomes with varying GC content and distinct taxonomic origin. We release iPtgxDBs for B. henselae , Bradyrhizobium diazoefficiens and Escherichia coli and the software to generate both proteogenomics search databases and integrated annotation files that can be viewed in a genome browser for any prokaryote. © 2017 Omasits et al.; Published by Cold Spring Harbor Laboratory Press.

BioModels.net Web Services, a free and integrated toolkit for computational modelling software.

PubMed

Li, Chen; Courtot, Mélanie; Le Novère, Nicolas; Laibe, Camille

2010-05-01

Exchanging and sharing scientific results are essential for researchers in the field of computational modelling. BioModels.net defines agreed-upon standards for model curation. A fundamental one, MIRIAM (Minimum Information Requested in the Annotation of Models), standardises the annotation and curation process of quantitative models in biology. To support this standard, MIRIAM Resources maintains a set of standard data types for annotating models, and provides services for manipulating these annotations. Furthermore, BioModels.net creates controlled vocabularies, such as SBO (Systems Biology Ontology) which strictly indexes, defines and links terms used in Systems Biology. Finally, BioModels Database provides a free, centralised, publicly accessible database for storing, searching and retrieving curated and annotated computational models. Each resource provides a web interface to submit, search, retrieve and display its data. In addition, the BioModels.net team provides a set of Web Services which allows the community to programmatically access the resources. A user is then able to perform remote queries, such as retrieving a model and resolving all its MIRIAM Annotations, as well as getting the details about the associated SBO terms. These web services use established standards. Communications rely on SOAP (Simple Object Access Protocol) messages and the available queries are described in a WSDL (Web Services Description Language) file. Several libraries are provided in order to simplify the development of client software. BioModels.net Web Services make one step further for the researchers to simulate and understand the entirety of a biological system, by allowing them to retrieve biological models in their own tool, combine queries in workflows and efficiently analyse models.

MicroScope in 2017: an expanding and evolving integrated resource for community expertise of microbial genomes.

PubMed

Vallenet, David; Calteau, Alexandra; Cruveiller, Stéphane; Gachet, Mathieu; Lajus, Aurélie; Josso, Adrien; Mercier, Jonathan; Renaux, Alexandre; Rollin, Johan; Rouy, Zoe; Roche, David; Scarpelli, Claude; Médigue, Claudine

2017-01-04

The annotation of genomes from NGS platforms needs to be automated and fully integrated. However, maintaining consistency and accuracy in genome annotation is a challenging problem because millions of protein database entries are not assigned reliable functions. This shortcoming limits the knowledge that can be extracted from genomes and metabolic models. Launched in 2005, the MicroScope platform (http://www.genoscope.cns.fr/agc/microscope) is an integrative resource that supports systematic and efficient revision of microbial genome annotation, data management and comparative analysis. Effective comparative analysis requires a consistent and complete view of biological data, and therefore, support for reviewing the quality of functional annotation is critical. MicroScope allows users to analyze microbial (meta)genomes together with post-genomic experiment results if any (i.e. transcriptomics, re-sequencing of evolved strains, mutant collections, phenotype data). It combines tools and graphical interfaces to analyze genomes and to perform the expert curation of gene functions in a comparative context. Starting with a short overview of the MicroScope system, this paper focuses on some major improvements of the Web interface, mainly for the submission of genomic data and on original tools and pipelines that have been developed and integrated in the platform: computation of pan-genomes and prediction of biosynthetic gene clusters. Today the resource contains data for more than 6000 microbial genomes, and among the 2700 personal accounts (65% of which are now from foreign countries), 14% of the users are performing expert annotations, on at least a weekly basis, contributing to improve the quality of microbial genome annotations. © The Author(s) 2016. Published by Oxford University Press on behalf of Nucleic Acids Research.

GONUTS: the Gene Ontology Normal Usage Tracking System

PubMed Central

Renfro, Daniel P.; McIntosh, Brenley K.; Venkatraman, Anand; Siegele, Deborah A.; Hu, James C.

2012-01-01

The Gene Ontology Normal Usage Tracking System (GONUTS) is a community-based browser and usage guide for Gene Ontology (GO) terms and a community system for general GO annotation of proteins. GONUTS uses wiki technology to allow registered users to share and edit notes on the use of each term in GO, and to contribute annotations for specific genes of interest. By providing a site for generation of third-party documentation at the granularity of individual terms, GONUTS complements the official documentation of the Gene Ontology Consortium. To provide examples for community users, GONUTS displays the complete GO annotations from seven model organisms: Saccharomyces cerevisiae, Dictyostelium discoideum, Caenorhabditis elegans, Drosophila melanogaster, Danio rerio, Mus musculus and Arabidopsis thaliana. To support community annotation, GONUTS allows automated creation of gene pages for gene products in UniProt. GONUTS will improve the consistency of annotation efforts across genome projects, and should be useful in training new annotators and consumers in the production of GO annotations and the use of GO terms. GONUTS can be accessed at http://gowiki.tamu.edu. The source code for generating the content of GONUTS is available upon request. PMID:22110029

An Educator's Guide to the Literature Dealing with the Rationale for Steroid Use, Effects They Have on Body Composition and Performance, with Solutions to Preventing Steroid Abuse in Youth.

ERIC Educational Resources Information Center

Dawson, Tim R.

This study provides information about steroids and recommends programs to educators and coaches who are involved with educating students about steroid abuse. The first part of the study contains annotations that examine the rationale and motivation of those who have used anabolic steroids. The next part of the study contains annotations that…

Measuring Attitudes Toward Reading. An Annotated ERIC Bibliography.

ERIC Educational Resources Information Center

Hahn, Christine T., Comp.

This 30-item annotated bibliography provides access to information concerning the development and use of tests and procedures for evaluating student attitudes toward reading. Based upon a computer search of five data bases--Educational Resources Information Center (ERIC), Psychological Abstracts, Exceptional Child Education Abstracts, Sociological…

An Annotated Bibliography of Research on Reading and Adults Learning English as a Second Language.

ERIC Educational Resources Information Center

Burt, Miriam, Comp.; Florez, MaryAnn, Comp.; Terrill, Lynda, Comp.; Van Duzer, Carol, Comp.

This annotated bibliography contains 27 references regarding research on reading and adults learning English as a Second Language (ESL). None of the resources are more than 10 years old. (Adjunct ERIC Clearinghouse for ESL Literacy Education) (KFT)

An Annotated Bibliography for Art.

ERIC Educational Resources Information Center

Minnesota State Dept. of Education, St. Paul. Div. of Instruction.

The annotated bibliography presents approximately 450 references about art for elementary, secondary, and professional levels. It is presented in three sections. Section one identifies 19 resources about art from a professional or teaching perspective. Included are books explaining how to teach various techniques to students of beginning or…

ERAIZDA: a model for holistic annotation of animal infectious and zoonotic diseases

PubMed Central

Buza, Teresia M.; Jack, Sherman W.; Kirunda, Halid; Khaitsa, Margaret L.; Lawrence, Mark L.; Pruett, Stephen; Peterson, Daniel G.

2015-01-01

There is an urgent need for a unified resource that integrates trans-disciplinary annotations of emerging and reemerging animal infectious and zoonotic diseases. Such data integration will provide wonderful opportunity for epidemiologists, researchers and health policy makers to make data-driven decisions designed to improve animal health. Integrating emerging and reemerging animal infectious and zoonotic disease data from a large variety of sources into a unified open-access resource provides more plausible arguments to achieve better understanding of infectious and zoonotic diseases. We have developed a model for interlinking annotations of these diseases. These diseases are of particular interest because of the threats they pose to animal health, human health and global health security. We demonstrated the application of this model using brucellosis, an infectious and zoonotic disease. Preliminary annotations were deposited into VetBioBase database (http://vetbiobase.igbb.msstate.edu). This database is associated with user-friendly tools to facilitate searching, retrieving and downloading of disease-related information. Database URL: http://vetbiobase.igbb.msstate.edu PMID:26581408

MyWEST: my Web Extraction Software Tool for effective mining of annotations from web-based databanks.

PubMed

Masseroli, Marco; Stella, Andrea; Meani, Natalia; Alcalay, Myriam; Pinciroli, Francesco

2004-12-12

High-throughput technologies create the necessity to mine large amounts of gene annotations from diverse databanks, and to integrate the resulting data. Most databanks can be interrogated only via Web, for a single gene at a time, and query results are generally available only in the HTML format. Although some databanks provide batch retrieval of data via FTP, this requires expertise and resources for locally reimplementing the databank. We developed MyWEST, a tool aimed at researchers without extensive informatics skills or resources, which exploits user-defined templates to easily mine selected annotations from different Web-interfaced databanks, and aggregates and structures results in an automatically updated database. Using microarray results from a model system of retinoic acid-induced differentiation, MyWEST effectively gathered relevant annotations from various biomolecular databanks, highlighted significant biological characteristics and supported a global approach to the understanding of complex cellular mechanisms. MyWEST is freely available for non-profit use at http://www.medinfopoli.polimi.it/MyWEST/

The Evidence and Conclusion Ontology (ECO): Supporting GO Annotations.

PubMed

Chibucos, Marcus C; Siegele, Deborah A; Hu, James C; Giglio, Michelle

2017-01-01

The Evidence and Conclusion Ontology (ECO) is a community resource for describing the various types of evidence that are generated during the course of a scientific study and which are typically used to support assertions made by researchers. ECO describes multiple evidence types, including evidence resulting from experimental (i.e., wet lab) techniques, evidence arising from computational methods, statements made by authors (whether or not supported by evidence), and inferences drawn by researchers curating the literature. In addition to summarizing the evidence that supports a particular assertion, ECO also offers a means to document whether a computer or a human performed the process of making the annotation. Incorporating ECO into an annotation system makes it possible to leverage the structure of the ontology such that associated data can be grouped hierarchically, users can select data associated with particular evidence types, and quality control pipelines can be optimized. Today, over 30 resources, including the Gene Ontology, use the Evidence and Conclusion Ontology to represent both evidence and how annotations are made.

Socioeconomic resources in medicine: review of the literature.

PubMed Central

Austin, T

1984-01-01

In this era of intense competition in medicine, it is essential for health sciences librarians to keep abreast of the new and varied socioeconomic influences in the medical environment. A list of socioeconomic resources is provided to help meet this objective. A citation analysis of the Socioeconomic Bibliographic Information (SIB) database was used as a selection criterion. An annotated list of ninety journals, newspapers, and newsletters is included, which provides title of publication, publisher, cost, index information, and special characteristics. In addition, publishers and associations that provide socioeconomic information are listed, and an annotated list of standard statistical resource books is given. PMID:6378285

VectorBase: a data resource for invertebrate vector genomics

PubMed Central

Lawson, Daniel; Arensburger, Peter; Atkinson, Peter; Besansky, Nora J.; Bruggner, Robert V.; Butler, Ryan; Campbell, Kathryn S.; Christophides, George K.; Christley, Scott; Dialynas, Emmanuel; Hammond, Martin; Hill, Catherine A.; Konopinski, Nathan; Lobo, Neil F.; MacCallum, Robert M.; Madey, Greg; Megy, Karine; Meyer, Jason; Redmond, Seth; Severson, David W.; Stinson, Eric O.; Topalis, Pantelis; Birney, Ewan; Gelbart, William M.; Kafatos, Fotis C.; Louis, Christos; Collins, Frank H.

2009-01-01

VectorBase (http://www.vectorbase.org) is an NIAID-funded Bioinformatic Resource Center focused on invertebrate vectors of human pathogens. VectorBase annotates and curates vector genomes providing a web accessible integrated resource for the research community. Currently, VectorBase contains genome information for three mosquito species: Aedes aegypti, Anopheles gambiae and Culex quinquefasciatus, a body louse Pediculus humanus and a tick species Ixodes scapularis. Since our last report VectorBase has initiated a community annotation system, a microarray and gene expression repository and controlled vocabularies for anatomy and insecticide resistance. We have continued to develop both the software infrastructure and tools for interrogating the stored data. PMID:19028744

Towards Semantic Modelling of Business Processes for Networked Enterprises

NASA Astrophysics Data System (ADS)

Furdík, Karol; Mach, Marián; Sabol, Tomáš

The paper presents an approach to the semantic modelling and annotation of business processes and information resources, as it was designed within the FP7 ICT EU project SPIKE to support creation and maintenance of short-term business alliances and networked enterprises. A methodology for the development of the resource ontology, as a shareable knowledge model for semantic description of business processes, is proposed. Systematically collected user requirements, conceptual models implied by the selected implementation platform as well as available ontology resources and standards are employed in the ontology creation. The process of semantic annotation is described and illustrated using an example taken from a real application case.

Home Economics: An Annotated Bibliography.

ERIC Educational Resources Information Center

Beasley, Georgia Blair, Comp.

This annotated bibliography is an attempt to provide a fairly extensive listing of available resource materials related to home economics. It does not attempt to include materials listed in readily available catalogs produced by commercial sources, government agencies, or other agencies which normally supply their lists to teachers. The…

Adaptation Scolaire: Bibliographie annotee (Scholastic Adaptation: Annotated Bibliography).

ERIC Educational Resources Information Center

Alberta Dept. of Education, Edmonton. Language Services Branch.

This annotated bibliography on resources concerning scholastic adaptation for students with exceptionalities was based on information collected by the Alberta Ministry of Education (Candada) from publishing houses and university presses. From the 350 submissions received, the 42 entries in this bibliography represent the materials chosen as the…

Adolescent Fertility: Selected, Annotated Resources for the International Community.

ERIC Educational Resources Information Center

Ogden, Celia

This bibliography on adolescent fertility contains over 300 annotations of articles, audiovisual materials, books, charts, comic books, games, journals, papers, pamphlets, and packets. With a few exceptions entries were published from 1974 through 1978; they are categorized according to geographic section: World, Africa, Asia, Europe, Latin…

English Language Learners: Annotated Bibliography

ERIC Educational Resources Information Center

Hector-Mason, Anestine; Bardack, Sarah

2010-01-01

This annotated bibliography represents a first step toward compiling a comprehensive overview of current research on issues related to English language learners (ELLs). It is intended to be a resource for researchers, policymakers, administrators, and educators who are engaged in efforts to bridge the divide between research, policy, and practice…

Developing Professionalism in the Child Care Industry. An Instructional Program Guide for Child Care Workers.

ERIC Educational Resources Information Center

Johnson, Ann; And Others

This program guide documents a child care job family curriculum that develops competence in generic work force education skills through two minicourses: Basic Issues in Child Care and Child Development Associate. An annotated table of contents lists a brief description of the questions answered in each section. An introduction presents a program…

A Reader's Guide for Parents of Children with Mental, Physical, or Emotional Disabilities. An Update.

ERIC Educational Resources Information Center

Moore, Cory; And Others

Intended for parents of children with disabilities, the guide lists and provides information on helpful books. Part I presents annotations on books relevant to all disabilities. Topics covered include personal accounts, early intervention at home, special education rights, and disabled adults. Part II focuses on specific disabilities: autism,…

The Mass Media: A Student's Guide to Reference Sources.

ERIC Educational Resources Information Center

McGill Univ., Montreal (Quebec). McLennan Library.

This guide to materials available in the McLennan Library is intended to assist students in locating information and literature necessary for sociological studies of the mass media (excluding film). It does not deal with the more technical aspects of the media or the "how to" literature. The annotations are arranged under the following headings:…

Selected reference aids for small medical libraries.

PubMed

Duncan, H F

1970-04-01

This annotated list of 178 items is compiled as a guide to the development of the reference collection in a small medical library.Arrangement, following the pattern of the previous revision, is by broad subject groups. Titles are chiefly in English. Textbooks in subject fields have been omitted since these are covered adequately in several comprehensive guides to the literature.

Camping and Backpacking. A Guide to Information Sources. Volume 2 in the Sports, Games and Pastimes Information Guide Series.

ERIC Educational Resources Information Center

Clotfelter, Cecil F.; Clotfelter, Mary L.

Sources of information regarding camping, backpacking, and related activities are annotated in a comprehensive listing of books, films and other non-print media, pamphlets, and periodicals largely dating from 1960. The volume contains chapters pertaining to: general directories, general camping, organized camping, camp related activities,…

Where Have All the Flowers Gone? A Reference Guide and Sourcebook to Ecological Literature.

ERIC Educational Resources Information Center

1970

Published as a reference guide and sourcebook to ecological literature, this anthology includes books, magazine articles, children's books, and films pertinent to ecology and the environment. A one paragraph annotation is provided for books and films, and all items are cross-indexed within 24 categories: agriculture, air pollution, animals and…

Environmental Toxicology: A Guide to Information Sources. Volume 7 in the "Man and the Environment Information Guide" Series.

ERIC Educational Resources Information Center

Rudd, Robert L.

This annotated bibliography on environmental toxicology brings together a diverse set of information sources from the physical, social, and natural sciences. These sources include periodical literature, government documents, scientific journals, and teaching materials. The volume is divided into sixteen sections organized into four parts: (1)…

Asia: A Guide to Basic Books.

ERIC Educational Resources Information Center

Embree, Ainslie T., Comp.; And Others

Three hundred and sixteen books dating from 1915 to 1966 with the majority published in the 1950s and 1960s are listed in this annotated bibliography. The purpose of the guide is to identify basic books on Asia which are especially useful for teachers, mature students, and adults who want to increase their knowledge and understanding of Asian…

Guide to Special Information in Scientific and Engineering Journals.

ERIC Educational Resources Information Center

Harris, Mary Elizabeth

This update of a 1983 annotated bibliography lists 298 special features or special issues of science and technology periodicals with emphasis on compilations of information that appear in periodicals on a regular basis. In addition to the 203 entries listed in the original edition, 95 new entries are included. Subjects covered in the guide include…

The Read-Aloud Handbook. Fourth Edition. Revised and Updated.

ERIC Educational Resources Information Center

Trelease, Jim

This new edition of a guide which has made reading aloud a special pleasure for millions of people offers a chance for a new generation of parents, teachers, grandparents, and siblings to discover the rewards--and the necessity--of reading aloud. The guide provides an up-to-date annotated bibliography ("treasury") of more than 1200…

A Selected Bibliography of Dictionaries. General Information Series, No. 9. Indochinese Refugee Education Guides.

ERIC Educational Resources Information Center

Center for Applied Linguistics, Arlington, VA.

This is a selected, annotated bibliography of dictionaries useful to Indochinese refugees. The purpose of this guide is to provide the American teacher or sponsor with information on the use, limitations and availability of monolingual and bilingual dictionaries which can be used by refugees. The bibliography is preceded by notes on problems with…

Family Literacy: Community & Family Life Materials. A Guide to Recent and Recommended Books.

ERIC Educational Resources Information Center

Lane, Martha A.; And Others

The books in this family literacy guide are listed alphabetically by title in each of three sections. The author, publisher, copyright date, reading level, type of book, number of pages, International Standard Book Number, price, and annotation comprise each entry. The topic of the family contains 11 titles: "Angry Feelings"; "Beginning with…

Gay and Lesbian Studies. A Research Guide for the UCLA Libraries.

ERIC Educational Resources Information Center

Walker, Walt Cat

Designed to aid students and other researchers in finding information about gays, lesbians, and homosexuality, this guide contains a collection of annotated bibliographies, or pathfinders, of both gay and general reference sources in each of 14 disciplines and lists of some major gay and lesbian works in each area. The materials listed are based…

Variation resources at UC Santa Cruz.

PubMed

Thomas, Daryl J; Trumbower, Heather; Kern, Andrew D; Rhead, Brooke L; Kuhn, Robert M; Haussler, David; Kent, W James

2007-01-01

The variation resources within the University of California Santa Cruz Genome Browser include polymorphism data drawn from public collections and analyses of these data, along with their display in the context of other genomic annotations. Primary data from dbSNP is included for many organisms, with added information including genomic alleles and orthologous alleles for closely related organisms. Display filtering and coloring is available by variant type, functional class or other annotations. Annotation of potential errors is highlighted and a genomic alignment of the variant's flanking sequence is displayed. HapMap allele frequencies and linkage disequilibrium (LD) are available for each HapMap population, along with non-human primate alleles. The browsing and analysis tools, downloadable data files and links to documentation and other information can be found at http://genome.ucsc.edu/.

Standardized description of scientific evidence using the Evidence Ontology (ECO)

PubMed Central

Chibucos, Marcus C.; Mungall, Christopher J.; Balakrishnan, Rama; Christie, Karen R.; Huntley, Rachael P.; White, Owen; Blake, Judith A.; Lewis, Suzanna E.; Giglio, Michelle

2014-01-01

The Evidence Ontology (ECO) is a structured, controlled vocabulary for capturing evidence in biological research. ECO includes diverse terms for categorizing evidence that supports annotation assertions including experimental types, computational methods, author statements and curator inferences. Using ECO, annotation assertions can be distinguished according to the evidence they are based on such as those made by curators versus those automatically computed or those made via high-throughput data review versus single test experiments. Originally created for capturing evidence associated with Gene Ontology annotations, ECO is now used in other capacities by many additional annotation resources including UniProt, Mouse Genome Informatics, Saccharomyces Genome Database, PomBase, the Protein Information Resource and others. Information on the development and use of ECO can be found at http://evidenceontology.org. The ontology is freely available under Creative Commons license (CC BY-SA 3.0), and can be downloaded in both Open Biological Ontologies and Web Ontology Language formats at http://code.google.com/p/evidenceontology. Also at this site is a tracker for user submission of term requests and questions. ECO remains under active development in response to user-requested terms and in collaborations with other ontologies and database resources. Database URL: Evidence Ontology Web site: http://evidenceontology.org PMID:25052702

Concomitant prediction of function and fold at the domain level with GO-based profiles.

PubMed

Lopez, Daniel; Pazos, Florencio

2013-01-01

Predicting the function of newly sequenced proteins is crucial due to the pace at which these raw sequences are being obtained. Almost all resources for predicting protein function assign functional terms to whole chains, and do not distinguish which particular domain is responsible for the allocated function. This is not a limitation of the methodologies themselves but it is due to the fact that in the databases of functional annotations these methods use for transferring functional terms to new proteins, these annotations are done on a whole-chain basis. Nevertheless, domains are the basic evolutionary and often functional units of proteins. In many cases, the domains of a protein chain have distinct molecular functions, independent from each other. For that reason resources with functional annotations at the domain level, as well as methodologies for predicting function for individual domains adapted to these resources are required.We present a methodology for predicting the molecular function of individual domains, based on a previously developed database of functional annotations at the domain level. The approach, which we show outperforms a standard method based on sequence searches in assigning function, concomitantly predicts the structural fold of the domains and can give hints on the functionally important residues associated to the predicted function.

RICD: a rice indica cDNA database resource for rice functional genomics.

PubMed

Lu, Tingting; Huang, Xuehui; Zhu, Chuanrang; Huang, Tao; Zhao, Qiang; Xie, Kabing; Xiong, Lizhong; Zhang, Qifa; Han, Bin

2008-11-26

The Oryza sativa L. indica subspecies is the most widely cultivated rice. During the last few years, we have collected over 20,000 putative full-length cDNAs and over 40,000 ESTs isolated from various cDNA libraries of two indica varieties Guangluai 4 and Minghui 63. A database of the rice indica cDNAs was therefore built to provide a comprehensive web data source for searching and retrieving the indica cDNA clones. Rice Indica cDNA Database (RICD) is an online MySQL-PHP driven database with a user-friendly web interface. It allows investigators to query the cDNA clones by keyword, genome position, nucleotide or protein sequence, and putative function. It also provides a series of information, including sequences, protein domain annotations, similarity search results, SNPs and InDels information, and hyperlinks to gene annotation in both The Rice Annotation Project Database (RAP-DB) and The TIGR Rice Genome Annotation Resource, expression atlas in RiceGE and variation report in Gramene of each cDNA. The online rice indica cDNA database provides cDNA resource with comprehensive information to researchers for functional analysis of indica subspecies and for comparative genomics. The RICD database is available through our website http://www.ncgr.ac.cn/ricd.

Consumer Education Materials: An Annotated List. Revised Edition.

ERIC Educational Resources Information Center

Alberta Consumer and Corporate Affairs, Edmonton. Resource Centre.

This annotated list is intended to help K-12 librarians and teachers identify consumer education materials. All materials listed are in the Alberta Consumer and Corporate Affairs Resource Centre, Edmonton, Alberta, Canada. The materials treat a wide variety of topics including advertising, purchasing, budgets, business education, conservation of…

Children: Health, Education, and Change. A Selected, Annotated Bibliography. Annotated Bibliography #6.

ERIC Educational Resources Information Center

Michigan State Univ., East Lansing. Non-Formal Education Information Center.

Compiled from the resource collection of Michigan State University's Non-Formal Education (NFE) Information Center, this bibliography contains over 100 references to international publications related to children's education, environment, development, labor, and health, and the training of persons involved in child education, development, and…

Resources for Improving Principal Effectiveness. Annotated Bibliography of Packaged Training Programs.

ERIC Educational Resources Information Center

Gaddy, C. Stephen

This annotated bibliography of commercially prepared training materials for management and leadership development programs offers 10 topical sections of references applicable to school principal training. Entries were selected by using the following criteria: (1) programs dealing too specifically with management in sales, manufacturing, finance,…

Program Evaluation in the Arts. An Annotated Bibliography.

ERIC Educational Resources Information Center

Wildemuth, Barbara M., Comp.; Eichinger, Debra S., Comp.

This 56-item annotated bibliography gives teachers and administrators access to information on the evaluation of school fine arts programs. Based upon a computer search of the Educational Resources Information Center (ERIC) data base, it cites project reports, journal articles, and dissertations published from 1963 to 1976. Citations of elementary…

Parenting: An Annotated Bibliography, 1965-1987.

ERIC Educational Resources Information Center

Feinberg, Sandra; And Others

This annotated bibliography on parenting resources is designed to assist parents and those who work with them to locate books on the many and complex topics that affect family life. The materials included encompass the various stages of parenting, from pregnancy and childbirth through the parenting of adult children. The many topics covered…

Conflict Resolution and Peace Studies: An Annotated Bibliography. Ethnic Studies Bulletin, Number Nine.

ERIC Educational Resources Information Center

Connecticut Univ., Storrs. Thut (I.N.) World Education Center.

This annotated bibliography of resources dealing with conflict resolution and peace studies was compiled for the use of elementary, secondary, and college educators. The listing is alphabetical by author. Included are handbooks for teachers, course outlines, anthologies of journal articles, bibliographies of curriculum materials, background…

Design and Applications of a GeoSemantic Framework for Integration of Data and Model Resources in Hydrologic Systems

NASA Astrophysics Data System (ADS)

Elag, M.; Kumar, P.

2016-12-01

Hydrologists today have to integrate resources such as data and models, which originate and reside in multiple autonomous and heterogeneous repositories over the Web. Several resource management systems have emerged within geoscience communities for sharing long-tail data, which are collected by individual or small research groups, and long-tail models, which are developed by scientists or small modeling communities. While these systems have increased the availability of resources within geoscience domains, deficiencies remain due to the heterogeneity in the methods, which are used to describe, encode, and publish information about resources over the Web. This heterogeneity limits our ability to access the right information in the right context so that it can be efficiently retrieved and understood without the Hydrologist's mediation. A primary challenge of the Web today is the lack of the semantic interoperability among the massive number of resources, which already exist and are continually being generated at rapid rates. To address this challenge, we have developed a decentralized GeoSemantic (GS) framework, which provides three sets of micro-web services to support (i) semantic annotation of resources, (ii) semantic alignment between the metadata of two resources, and (iii) semantic mediation among Standard Names. Here we present the design of the framework and demonstrate its application for semantic integration between data and models used in the IML-CZO. First we show how the IML-CZO data are annotated using the Semantic Annotation Services. Then we illustrate how the Resource Alignment Services and Knowledge Integration Services are used to create a semantic workflow among TopoFlow model, which is a spatially-distributed hydrologic model and the annotated data. Results of this work are (i) a demonstration of how the GS framework advances the integration of heterogeneous data and models of water-related disciplines by seamless handling of their semantic heterogeneity, (ii) an introduction of new paradigm for reusing existing and new standards as well as tools and models without the need of their implementation in the Cyberinfrastructures of water-related disciplines, and (iii) an investigation of a methodology by which distributed models can be coupled in a workflow using the GS services.

Books and Other Resources for Education about the August 21, 2017, Solar Eclipse

NASA Astrophysics Data System (ADS)

Pasachoff, Jay M.; Fraknoi, Andrew; Kentrianakis, Michael

2017-06-01

As part of our work to reach and educate the 300+ million Americans of all ages about observing the August 21 solar eclipse, especially by being outdoors in the path of totality but also for those who will see only partial phases, we have compiled annotated lists of books, pamphlets, travel guides, websites, and other information useful for teachers, students, and the general public and made them available on the web, at conferences, and through webinars. Our list includes new eclipse books by David Barron, Anthony Aveni, Frank Close, Tyler Nordgren, John Dvorak, Michael Bakich, and others. We list websites accessible to the general public including those of the International Astronomical Union Working Group on Eclipses (http://eclipses.info, which has links to all the sites listed below); the AAS Eclipse 2017 Task Force (http://eclipse2017.aas.org); NASA Heliophysics (http://eclipse.nasa.gov); Fred Espenak (the updated successor to his authoritative "NASA website": http://EclipseWise.com); Michael Zeiler (http://GreatAmericanEclipse.com); Xavier Jubier (http://xjubier.free.fr/en/site_pages/solar_eclipses/); Jay Anderson (meteorology: http://eclipsophile.com); NASA's Eyes (http://eyes.nasa.gov/eyes-on-eclipse.html and its related app); the Astronomical Society of the Pacific (http://www.astrosociety.org/eclipse); Dan McGlaun (http://eclipse2017.org/); Bill Kramer (http://eclipse-chasers.com). Specialized guides include Dennis Schatz and Andrew Fraknoi's Solar Science for teachers (from the National Science Teachers Association:http://www.nsta.org/publications/press/extras/files/solarscience/SolarScienceInsert.pdf), and a printing with expanded eclipse coverage of Jay Pasachoff's, Peterson Field Guide to the Stars and Planets (14th printing of the fourth edition, 2016: http://solarcorona.com).A version of our joint list is to be published in the July issue of the American Journal of Physics as a Resource Letter on Eclipses, adding to JMP's 2010, "Resource Letter SP-1 on Solar Physics," AJP, 78, September, 890-901.

TriAnnot: A Versatile and High Performance Pipeline for the Automated Annotation of Plant Genomes

PubMed Central

Leroy, Philippe; Guilhot, Nicolas; Sakai, Hiroaki; Bernard, Aurélien; Choulet, Frédéric; Theil, Sébastien; Reboux, Sébastien; Amano, Naoki; Flutre, Timothée; Pelegrin, Céline; Ohyanagi, Hajime; Seidel, Michael; Giacomoni, Franck; Reichstadt, Mathieu; Alaux, Michael; Gicquello, Emmanuelle; Legeai, Fabrice; Cerutti, Lorenzo; Numa, Hisataka; Tanaka, Tsuyoshi; Mayer, Klaus; Itoh, Takeshi; Quesneville, Hadi; Feuillet, Catherine

2012-01-01

In support of the international effort to obtain a reference sequence of the bread wheat genome and to provide plant communities dealing with large and complex genomes with a versatile, easy-to-use online automated tool for annotation, we have developed the TriAnnot pipeline. Its modular architecture allows for the annotation and masking of transposable elements, the structural, and functional annotation of protein-coding genes with an evidence-based quality indexing, and the identification of conserved non-coding sequences and molecular markers. The TriAnnot pipeline is parallelized on a 712 CPU computing cluster that can run a 1-Gb sequence annotation in less than 5 days. It is accessible through a web interface for small scale analyses or through a server for large scale annotations. The performance of TriAnnot was evaluated in terms of sensitivity, specificity, and general fitness using curated reference sequence sets from rice and wheat. In less than 8 h, TriAnnot was able to predict more than 83% of the 3,748 CDS from rice chromosome 1 with a fitness of 67.4%. On a set of 12 reference Mb-sized contigs from wheat chromosome 3B, TriAnnot predicted and annotated 93.3% of the genes among which 54% were perfectly identified in accordance with the reference annotation. It also allowed the curation of 12 genes based on new biological evidences, increasing the percentage of perfect gene prediction to 63%. TriAnnot systematically showed a higher fitness than other annotation pipelines that are not improved for wheat. As it is easily adaptable to the annotation of other plant genomes, TriAnnot should become a useful resource for the annotation of large and complex genomes in the future. PMID:22645565

Towards a complete map of the human long non-coding RNA transcriptome.

PubMed

Uszczynska-Ratajczak, Barbara; Lagarde, Julien; Frankish, Adam; Guigó, Roderic; Johnson, Rory

2018-05-23

Gene maps, or annotations, enable us to navigate the functional landscape of our genome. They are a resource upon which virtually all studies depend, from single-gene to genome-wide scales and from basic molecular biology to medical genetics. Yet present-day annotations suffer from trade-offs between quality and size, with serious but often unappreciated consequences for downstream studies. This is particularly true for long non-coding RNAs (lncRNAs), which are poorly characterized compared to protein-coding genes. Long-read sequencing technologies promise to improve current annotations, paving the way towards a complete annotation of lncRNAs expressed throughout a human lifetime.

The Comprehensive Phytopathogen Genomics Resource: a web-based resource for data-mining plant pathogen genomes.

PubMed

Hamilton, John P; Neeno-Eckwall, Eric C; Adhikari, Bishwo N; Perna, Nicole T; Tisserat, Ned; Leach, Jan E; Lévesque, C André; Buell, C Robin

2011-01-01

The Comprehensive Phytopathogen Genomics Resource (CPGR) provides a web-based portal for plant pathologists and diagnosticians to view the genome and trancriptome sequence status of 806 bacterial, fungal, oomycete, nematode, viral and viroid plant pathogens. Tools are available to search and analyze annotated genome sequences of 74 bacterial, fungal and oomycete pathogens. Oomycete and fungal genomes are obtained directly from GenBank, whereas bacterial genome sequences are downloaded from the A Systematic Annotation Package (ASAP) database that provides curation of genomes using comparative approaches. Curated lists of bacterial genes relevant to pathogenicity and avirulence are also provided. The Plant Pathogen Transcript Assemblies Database provides annotated assemblies of the transcribed regions of 82 eukaryotic genomes from publicly available single pass Expressed Sequence Tags. Data-mining tools are provided along with tools to create candidate diagnostic markers, an emerging use for genomic sequence data in plant pathology. The Plant Pathogen Ribosomal DNA (rDNA) database is a resource for pathogens that lack genome or transcriptome data sets and contains 131 755 rDNA sequences from GenBank for 17 613 species identified as plant pathogens and related genera. Database URL: http://cpgr.plantbiology.msu.edu.

Multicultural Early Childhood Education Bibliography and Resource List.

ERIC Educational Resources Information Center

Mock, Karen R., Comp.

Compiled for early childhood educators, this list of resources for multicultural education provides a total of 153 entries in the categories of readings for teachers, curriculum materials, nonprint media, children's books, resource bibliographies and catalogues, Canadian periodicals, and resource agencies. Brief annotations accompany most entries.…

Improving Microbial Genome Annotations in an Integrated Database Context

PubMed Central

Chen, I-Min A.; Markowitz, Victor M.; Chu, Ken; Anderson, Iain; Mavromatis, Konstantinos; Kyrpides, Nikos C.; Ivanova, Natalia N.

2013-01-01

Effective comparative analysis of microbial genomes requires a consistent and complete view of biological data. Consistency regards the biological coherence of annotations, while completeness regards the extent and coverage of functional characterization for genomes. We have developed tools that allow scientists to assess and improve the consistency and completeness of microbial genome annotations in the context of the Integrated Microbial Genomes (IMG) family of systems. All publicly available microbial genomes are characterized in IMG using different functional annotation and pathway resources, thus providing a comprehensive framework for identifying and resolving annotation discrepancies. A rule based system for predicting phenotypes in IMG provides a powerful mechanism for validating functional annotations, whereby the phenotypic traits of an organism are inferred based on the presence of certain metabolic reactions and pathways and compared to experimentally observed phenotypes. The IMG family of systems are available at http://img.jgi.doe.gov/. PMID:23424620

Automatic annotation of histopathological images using a latent topic model based on non-negative matrix factorization

PubMed Central

Cruz-Roa, Angel; Díaz, Gloria; Romero, Eduardo; González, Fabio A.

2011-01-01

Histopathological images are an important resource for clinical diagnosis and biomedical research. From an image understanding point of view, the automatic annotation of these images is a challenging problem. This paper presents a new method for automatic histopathological image annotation based on three complementary strategies, first, a part-based image representation, called the bag of features, which takes advantage of the natural redundancy of histopathological images for capturing the fundamental patterns of biological structures, second, a latent topic model, based on non-negative matrix factorization, which captures the high-level visual patterns hidden in the image, and, third, a probabilistic annotation model that links visual appearance of morphological and architectural features associated to 10 histopathological image annotations. The method was evaluated using 1,604 annotated images of skin tissues, which included normal and pathological architectural and morphological features, obtaining a recall of 74% and a precision of 50%, which improved a baseline annotation method based on support vector machines in a 64% and 24%, respectively. PMID:22811960

Data Acquisition and Linguistic Resources

NASA Astrophysics Data System (ADS)

Strassel, Stephanie; Christianson, Caitlin; McCary, John; Staderman, William; Olive, Joseph

All human language technology demands substantial quantities of data for system training and development, plus stable benchmark data to measure ongoing progress. While creation of high quality linguistic resources is both costly and time consuming, such data has the potential to profoundly impact not just a single evaluation program but language technology research in general. GALE's challenging performance targets demand linguistic data on a scale and complexity never before encountered. Resources cover multiple languages (Arabic, Chinese, and English) and multiple genres -- both structured (newswire and broadcast news) and unstructured (web text, including blogs and newsgroups, and broadcast conversation). These resources include significant volumes of monolingual text and speech, parallel text, and transcribed audio combined with multiple layers of linguistic annotation, ranging from word aligned parallel text and Treebanks to rich semantic annotation.

Boston: An Urban Community. Boston's Black Letters: From Phillis Wheatley to W. E. B. DuBois. Culture and Its Conflicts: The Example of Nineteenth-century Boston. The Emerging Immigrants of Boston. Annotated Reading Lists.

ERIC Educational Resources Information Center

Jenkins, Hugh M.; And Others

These three annotated reading guides were developed for courses offered at the Boston Public Library under the National Endowment for the Humanities Learning Library Program. The permutations in style and content of black Boston literature are exemplified in this collection of 18 writings to serve as an index to the cultural and social life of the…

Leveraging Comparative Genomics to Identify and Functionally Characterize Genes Associated with Sperm Phenotypes in Python bivittatus (Burmese Python)

PubMed Central

Rutllant, Josep

2016-01-01

Comparative genomics approaches provide a means of leveraging functional genomics information from a highly annotated model organism's genome (such as the mouse genome) in order to make physiological inferences about the role of genes and proteins in a less characterized organism's genome (such as the Burmese python). We employed a comparative genomics approach to produce the functional annotation of Python bivittatus genes encoding proteins associated with sperm phenotypes. We identify 129 gene-phenotype relationships in the python which are implicated in 10 specific sperm phenotypes. Results obtained through our systematic analysis identified subsets of python genes exhibiting associations with gene ontology annotation terms. Functional annotation data was represented in a semantic scatter plot. Together, these newly annotated Python bivittatus genome resources provide a high resolution framework from which the biology relating to reptile spermatogenesis, fertility, and reproduction can be further investigated. Applications of our research include (1) production of genetic diagnostics for assessing fertility in domestic and wild reptiles; (2) enhanced assisted reproduction technology for endangered and captive reptiles; and (3) novel molecular targets for biotechnology-based approaches aimed at reducing fertility and reproduction of invasive reptiles. Additional enhancements to reptile genomic resources will further enhance their value. PMID:27200191

Leveraging Comparative Genomics to Identify and Functionally Characterize Genes Associated with Sperm Phenotypes in Python bivittatus (Burmese Python).

PubMed

Irizarry, Kristopher J L; Rutllant, Josep

2016-01-01

Comparative genomics approaches provide a means of leveraging functional genomics information from a highly annotated model organism's genome (such as the mouse genome) in order to make physiological inferences about the role of genes and proteins in a less characterized organism's genome (such as the Burmese python). We employed a comparative genomics approach to produce the functional annotation of Python bivittatus genes encoding proteins associated with sperm phenotypes. We identify 129 gene-phenotype relationships in the python which are implicated in 10 specific sperm phenotypes. Results obtained through our systematic analysis identified subsets of python genes exhibiting associations with gene ontology annotation terms. Functional annotation data was represented in a semantic scatter plot. Together, these newly annotated Python bivittatus genome resources provide a high resolution framework from which the biology relating to reptile spermatogenesis, fertility, and reproduction can be further investigated. Applications of our research include (1) production of genetic diagnostics for assessing fertility in domestic and wild reptiles; (2) enhanced assisted reproduction technology for endangered and captive reptiles; and (3) novel molecular targets for biotechnology-based approaches aimed at reducing fertility and reproduction of invasive reptiles. Additional enhancements to reptile genomic resources will further enhance their value.

Solving the Problem: Genome Annotation Standards before the Data Deluge.

PubMed

Klimke, William; O'Donovan, Claire; White, Owen; Brister, J Rodney; Clark, Karen; Fedorov, Boris; Mizrachi, Ilene; Pruitt, Kim D; Tatusova, Tatiana

2011-10-15

The promise of genome sequencing was that the vast undiscovered country would be mapped out by comparison of the multitude of sequences available and would aid researchers in deciphering the role of each gene in every organism. Researchers recognize that there is a need for high quality data. However, different annotation procedures, numerous databases, and a diminishing percentage of experimentally determined gene functions have resulted in a spectrum of annotation quality. NCBI in collaboration with sequencing centers, archival databases, and researchers, has developed the first international annotation standards, a fundamental step in ensuring that high quality complete prokaryotic genomes are available as gold standard references. Highlights include the development of annotation assessment tools, community acceptance of protein naming standards, comparison of annotation resources to provide consistent annotation, and improved tracking of the evidence used to generate a particular annotation. The development of a set of minimal standards, including the requirement for annotated complete prokaryotic genomes to contain a full set of ribosomal RNAs, transfer RNAs, and proteins encoding core conserved functions, is an historic milestone. The use of these standards in existing genomes and future submissions will increase the quality of databases, enabling researchers to make accurate biological discoveries.

Solving the Problem: Genome Annotation Standards before the Data Deluge

PubMed Central

Klimke, William; O'Donovan, Claire; White, Owen; Brister, J. Rodney; Clark, Karen; Fedorov, Boris; Mizrachi, Ilene; Pruitt, Kim D.; Tatusova, Tatiana

2011-01-01

The promise of genome sequencing was that the vast undiscovered country would be mapped out by comparison of the multitude of sequences available and would aid researchers in deciphering the role of each gene in every organism. Researchers recognize that there is a need for high quality data. However, different annotation procedures, numerous databases, and a diminishing percentage of experimentally determined gene functions have resulted in a spectrum of annotation quality. NCBI in collaboration with sequencing centers, archival databases, and researchers, has developed the first international annotation standards, a fundamental step in ensuring that high quality complete prokaryotic genomes are available as gold standard references. Highlights include the development of annotation assessment tools, community acceptance of protein naming standards, comparison of annotation resources to provide consistent annotation, and improved tracking of the evidence used to generate a particular annotation. The development of a set of minimal standards, including the requirement for annotated complete prokaryotic genomes to contain a full set of ribosomal RNAs, transfer RNAs, and proteins encoding core conserved functions, is an historic milestone. The use of these standards in existing genomes and future submissions will increase the quality of databases, enabling researchers to make accurate biological discoveries. PMID:22180819

An Annotated Bibliography on Movement Education.

ERIC Educational Resources Information Center

Rizzitiello, Theresa, G.

This bibliography is a collection of selected resources significant to a deeper understanding of the many aspects and definitions of movement education. The one hundred seventy-three annotations are arranged and ordered in a pattern to reflect an overview of both theory and practice, the latter examined under the headings of basic movement,…

Expressive Therapies, the ARTS and the Exceptional Child. (An Annotated Bibliography).

ERIC Educational Resources Information Center

Minar, Virginia, Comp.; And Others

The annotated bibliography lists approximately 500 citations (1967-1978) regarding the arts and exceptional children in preschool through grade 8. It is explained that the bibliography was designed to provide concrete material and ideas for teachers and therapists working with exceptional children in mainstreamed, resource room, or special class…

Questionnaires for research: an annotated bibliography on design, construction, and use.

Treesearch

Dale R. Potter; Kathryn M. Sharpe; John C. Hendee; Roger N. Clark

1972-01-01

Questionnaires as social science tools are used increasingly to study people aspects of outdoor recreation and other natural resource fields. An annotated bibliography including subjective evaluations of each article and a keyword list is presented for 193 references to aid researchers and managers in the design, construction, and use of mail questionnaires.

Managerial and Organizational Career Development: An Annotated Bibliography.

ERIC Educational Resources Information Center

Maddox, E. Nick; And Others

1988-01-01

This annotated bibliography is an extension of an earlier work published in the "Career Planning and Adult Development Journal" in 1983. It represents a cross-sectional look at the expanding field of career development as it relates to organizational behavior and human resource management disciplines and practice. Citations are included of 295…

An Introduction to Youth with Disabilities: Annotated Bibliography. CYDLINE Reviews.

ERIC Educational Resources Information Center

Minnesota Univ., Minneapolis. National Center for Youth with Disabilities.

The annotated bibliography describes resources covering a wide range of issues related to disabled youth and their families. The 38 bibliographic citations date from 1980 to 1989 and are grouped into the following categories: psychosocial issues, health issues, educational issues, and community living. Information is also provided on services of…

Adult Literacy and Television: An Annotated Bibliography.

ERIC Educational Resources Information Center

Centre for Literacy, Montreal (Quebec).

This annotated bibliography was developed for the Centre for Literacy of Quebec's 2000 Summer Literacy Institute, "Adult Literacy and Television: Has a Familiar Resource Been Overlooked?" and contains 49 citations of Canadian, British, and American research in the field of adult literacy and television from the 1960s to the year 2000. The…

Annotation of Korean Learner Corpora for Particle Error Detection

ERIC Educational Resources Information Center

Lee, Sun-Hee; Jang, Seok Bae; Seo, Sang-Kyu

2009-01-01

In this study, we focus on particle errors and discuss an annotation scheme for Korean learner corpora that can be used to extract heuristic patterns of particle errors efficiently. We investigate different properties of particle errors so that they can be later used to identify learner errors automatically, and we provide resourceful annotation…

Handbook of Reference Sources. Second Edition.

ERIC Educational Resources Information Center

Nichols, Margaret Irby

Designed to serve as a selection aid for small public libraries and to list important sources available through the major resource centers of the Texas Library System, this bibliography lists 804 annotated reference sources with 126 additional works named within the annotations. The books are grouped into 18 major areas, each of which is broken…

Education and Training. Annotated Bibliography. Author and Subject Index.

ERIC Educational Resources Information Center

United Nations Food and Agriculture Organization, Rome (Italy).

Food and Agriculture Organization (FAO) publications and documents issued by the Human Resources and Institutions division and by other technical divisions in the technical, economic, and social fields are selected, annotated and indexed in this bibliography. Documents issued prior to 1967 are not included but can be found in the Rural…

ERAIZDA: a model for holistic annotation of animal infectious and zoonotic diseases.

PubMed

Buza, Teresia M; Jack, Sherman W; Kirunda, Halid; Khaitsa, Margaret L; Lawrence, Mark L; Pruett, Stephen; Peterson, Daniel G

2015-01-01

There is an urgent need for a unified resource that integrates trans-disciplinary annotations of emerging and reemerging animal infectious and zoonotic diseases. Such data integration will provide wonderful opportunity for epidemiologists, researchers and health policy makers to make data-driven decisions designed to improve animal health. Integrating emerging and reemerging animal infectious and zoonotic disease data from a large variety of sources into a unified open-access resource provides more plausible arguments to achieve better understanding of infectious and zoonotic diseases. We have developed a model for interlinking annotations of these diseases. These diseases are of particular interest because of the threats they pose to animal health, human health and global health security. We demonstrated the application of this model using brucellosis, an infectious and zoonotic disease. Preliminary annotations were deposited into VetBioBase database (http://vetbiobase.igbb.msstate.edu). This database is associated with user-friendly tools to facilitate searching, retrieving and downloading of disease-related information. Database URL: http://vetbiobase.igbb.msstate.edu. © The Author(s) 2015. Published by Oxford University Press.

Optimizing Search and Ranking in Folksonomy Systems by Exploiting Context Information

NASA Astrophysics Data System (ADS)

Abel, Fabian; Henze, Nicola; Krause, Daniel

Tagging systems enable users to annotate resources with freely chosen keywords. The evolving bunch of tag assignments is called folksonomy and there exist already some approaches that exploit folksonomies to improve resource retrieval. In this paper, we analyze and compare graph-based ranking algorithms: FolkRank and SocialPageRank. We enhance these algorithms by exploiting the context of tags, and evaluate the results on the GroupMe! dataset. In GroupMe!, users can organize and maintain arbitrary Web resources in self-defined groups. When users annotate resources in GroupMe!, this can be interpreted in context of a certain group. The grouping activity itself is easy for users to perform. However, it delivers valuable semantic information about resources and their context. We present GRank that uses the context information to improve and optimize the detection of relevant search results, and compare different strategies for ranking result lists in folksonomy systems.

On the Effect of Group Structures on Ranking Strategies in Folksonomies

NASA Astrophysics Data System (ADS)

Abel, Fabian; Henze, Nicola; Krause, Daniel; Kriesell, Matthias

Folksonomies have shown interesting potential for improving information discovery and exploration. Recent folksonomy systems explore the use of tag assignments, which combine Web resources with annotations (tags), and the users that have created the annotations. This article investigates on the effect of grouping resources in folksonomies, i.e. creating sets of resources, and using this additional structure for the tasks of search & ranking, and for tag recommendations. We propose several group-sensitive extensions of graph-based search and recommendation algorithms, and compare them with non group-sensitive versions. Our experiments show that the quality of search result ranking can be significantly improved by introducing and exploiting the grouping of resources (one-tailed t-Test, level of significance α=0.05). Furthermore, tag recommendations profit from the group context, and it is possible to make very good recommendations even for untagged resources- which currently known tag recommendation algorithms cannot fulfill.

A Guide to the Recorded Distribution of Endangered, Threatened and Rare Species in Michigan. Providing a Bibliographic Discussion of the Subject, Annotated List of Reference Sources and Directory of Local Nature Associations, Centers, Agencies, and University Field Stations.

ERIC Educational Resources Information Center

Yakes, Nancy A.

This document is a guide to sources of information on endangered species distribution in Michigan. It was prepared for CETA (Comprehensive Employment and Training Act) students who will collect the documents. The guide is divided into three major sections. The first section includes an introduction (briefly discussing endangered, rare, threatened…

Transcriptomic resources for the medicinal legume Mucuna pruriens: de novo transcriptome assembly, annotation, identification and validation of EST-SSR markers.

PubMed

Sathyanarayana, N; Pittala, Ranjith Kumar; Tripathi, Pankaj Kumar; Chopra, Ratan; Singh, Heikham Russiachand; Belamkar, Vikas; Bhardwaj, Pardeep Kumar; Doyle, Jeff J; Egan, Ashley N

2017-05-25

The medicinal legume Mucuna pruriens (L.) DC. has attracted attention worldwide as a source of the anti-Parkinson's drug L-Dopa. It is also a popular green manure cover crop that offers many agronomic benefits including high protein content, nitrogen fixation and soil nutrients. The plant currently lacks genomic resources and there is limited knowledge on gene expression, metabolic pathways, and genetics of secondary metabolite production. Here, we present transcriptomic resources for M. pruriens, including a de novo transcriptome assembly and annotation, as well as differential transcript expression analyses between root, leaf, and pod tissues. We also develop microsatellite markers and analyze genetic diversity and population structure within a set of Indian germplasm accessions. One-hundred ninety-one million two hundred thirty-three thousand two hundred forty-two bp cleaned reads were assembled into 67,561 transcripts with mean length of 626 bp and N50 of 987 bp. Assembled sequences were annotated using BLASTX against public databases with over 80% of transcripts annotated. We identified 7,493 simple sequence repeat (SSR) motifs, including 787 polymorphic repeats between the parents of a mapping population. 134 SSRs from expressed sequenced tags (ESTs) were screened against 23 M. pruriens accessions from India, with 52 EST-SSRs retained after quality control. Population structure analysis using a Bayesian framework implemented in fastSTRUCTURE showed nearly similar groupings as with distance-based (neighbor-joining) and principal component analyses, with most of the accessions clustering per geographical origins. Pair-wise comparison of transcript expression in leaves, roots and pods identified 4,387 differentially expressed transcripts with the highest number occurring between roots and leaves. Differentially expressed transcripts were enriched with transcription factors and transcripts annotated as belonging to secondary metabolite pathways. The M. pruriens transcriptomic resources generated in this study provide foundational resources for gene discovery and development of molecular markers. Polymorphic SSRs identified can be used for genetic diversity, marker-trait analyses, and development of functional markers for crop improvement. The results of differential expression studies can be used to investigate genes involved in L-Dopa synthesis and other key metabolic pathways in M. pruriens.

Improved methods and resources for paramecium genomics: transcription units, gene annotation and gene expression.

PubMed

Arnaiz, Olivier; Van Dijk, Erwin; Bétermier, Mireille; Lhuillier-Akakpo, Maoussi; de Vanssay, Augustin; Duharcourt, Sandra; Sallet, Erika; Gouzy, Jérôme; Sperling, Linda

2017-06-26

The 15 sibling species of the Paramecium aurelia cryptic species complex emerged after a whole genome duplication that occurred tens of millions of years ago. Given extensive knowledge of the genetics and epigenetics of Paramecium acquired over the last century, this species complex offers a uniquely powerful system to investigate the consequences of whole genome duplication in a unicellular eukaryote as well as the genetic and epigenetic mechanisms that drive speciation. High quality Paramecium gene models are important for research using this system. The major aim of the work reported here was to build an improved gene annotation pipeline for the Paramecium lineage. We generated oriented RNA-Seq transcriptome data across the sexual process of autogamy for the model species Paramecium tetraurelia. We determined, for the first time in a ciliate, candidate P. tetraurelia transcription start sites using an adapted Cap-Seq protocol. We developed TrUC, multi-threaded Perl software that in conjunction with TopHat mapping of RNA-Seq data to a reference genome, predicts transcription units for the annotation pipeline. We used EuGene software to combine annotation evidence. The high quality gene structural annotations obtained for P. tetraurelia were used as evidence to improve published annotations for 3 other Paramecium species. The RNA-Seq data were also used for differential gene expression analysis, providing a gene expression atlas that is more sensitive than the previously established microarray resource. We have developed a gene annotation pipeline tailored for the compact genomes and tiny introns of Paramecium species. A novel component of this pipeline, TrUC, predicts transcription units using Cap-Seq and oriented RNA-Seq data. TrUC could prove useful beyond Paramecium, especially in the case of high gene density. Accurate predictions of 3' and 5' UTR will be particularly valuable for studies of gene expression (e.g. nucleosome positioning, identification of cis regulatory motifs). The P. tetraurelia improved transcriptome resource, gene annotations for P. tetraurelia, P. biaurelia, P. sexaurelia and P. caudatum, and Paramecium-trained EuGene configuration are available through ParameciumDB ( http://paramecium.i2bc.paris-saclay.fr ). TrUC software is freely distributed under a GNU GPL v3 licence ( https://github.com/oarnaiz/TrUC ).

CRISPR-Mediated Base Editing Enables Efficient Disruption of Eukaryotic Genes through Induction of STOP Codons.

PubMed

Billon, Pierre; Bryant, Eric E; Joseph, Sarah A; Nambiar, Tarun S; Hayward, Samuel B; Rothstein, Rodney; Ciccia, Alberto

2017-09-21

Standard CRISPR-mediated gene disruption strategies rely on Cas9-induced DNA double-strand breaks (DSBs). Here, we show that CRISPR-dependent base editing efficiently inactivates genes by precisely converting four codons (CAA, CAG, CGA, and TGG) into STOP codons without DSB formation. To facilitate gene inactivation by induction of STOP codons (iSTOP), we provide access to a database of over 3.4 million single guide RNAs (sgRNAs) for iSTOP (sgSTOPs) targeting 97%-99% of genes in eight eukaryotic species, and we describe a restriction fragment length polymorphism (RFLP) assay that allows the rapid detection of iSTOP-mediated editing in cell populations and clones. To simplify the selection of sgSTOPs, our resource includes annotations for off-target propensity, percentage of isoforms targeted, prediction of nonsense-mediated decay, and restriction enzymes for RFLP analysis. Additionally, our database includes sgSTOPs that could be employed to precisely model over 32,000 cancer-associated nonsense mutations. Altogether, this work provides a comprehensive resource for DSB-free gene disruption by iSTOP. Copyright © 2017 Elsevier Inc. All rights reserved.

Workplace Literacy: A Resource Book.

ERIC Educational Resources Information Center

Guglielmino, Lucy Madsen; Byran, Valerie C.

This resource book provides information on developing a workplace literacy program, descriptions of Florida Workplace Literacy Programs, and an annotated bibliography of resources. An introduction discusses the problem of basic skills deficiencies, projections that indicate the problem will increase, the Florida context, and benefits realized when…

Assistive Technology Resource Directory.

ERIC Educational Resources Information Center

Council for Exceptional Children, Reston, VA. Center for Special Education Technology.

This annotated directory of resources is designed to assist in locating key organizations, agencies, and projects that are involved in the delivery of assistive technology services at the national, state, and local levels. Resources described include three federal agencies, nine national associations, five rehabilitation engineering centers, four…

Functional Annotations of Paralogs: A Blessing and a Curse

PubMed Central

Zallot, Rémi; Harrison, Katherine J.; Kolaczkowski, Bryan; de Crécy-Lagard, Valérie

2016-01-01

Gene duplication followed by mutation is a classic mechanism of neofunctionalization, producing gene families with functional diversity. In some cases, a single point mutation is sufficient to change the substrate specificity and/or the chemistry performed by an enzyme, making it difficult to accurately separate enzymes with identical functions from homologs with different functions. Because sequence similarity is often used as a basis for assigning functional annotations to genes, non-isofunctional gene families pose a great challenge for genome annotation pipelines. Here we describe how integrating evolutionary and functional information such as genome context, phylogeny, metabolic reconstruction and signature motifs may be required to correctly annotate multifunctional families. These integrative analyses can also lead to the discovery of novel gene functions, as hints from specific subgroups can guide the functional characterization of other members of the family. We demonstrate how careful manual curation processes using comparative genomics can disambiguate subgroups within large multifunctional families and discover their functions. We present the COG0720 protein family as a case study. We also discuss strategies to automate this process to improve the accuracy of genome functional annotation pipelines. PMID:27618105

'RetinoGenetics': a comprehensive mutation database for genes related to inherited retinal degeneration.

PubMed

Ran, Xia; Cai, Wei-Jun; Huang, Xiu-Feng; Liu, Qi; Lu, Fan; Qu, Jia; Wu, Jinyu; Jin, Zi-Bing

2014-01-01

Inherited retinal degeneration (IRD), a leading cause of human blindness worldwide, is exceptionally heterogeneous with clinical heterogeneity and genetic variety. During the past decades, tremendous efforts have been made to explore the complex heterogeneity, and massive mutations have been identified in different genes underlying IRD with the significant advancement of sequencing technology. In this study, we developed a comprehensive database, 'RetinoGenetics', which contains informative knowledge about all known IRD-related genes and mutations for IRD. 'RetinoGenetics' currently contains 4270 mutations in 186 genes, with detailed information associated with 164 phenotypes from 934 publications and various types of functional annotations. Then extensive annotations were performed to each gene using various resources, including Gene Ontology, KEGG pathways, protein-protein interaction, mutational annotations and gene-disease network. Furthermore, by using the search functions, convenient browsing ways and intuitive graphical displays, 'RetinoGenetics' could serve as a valuable resource for unveiling the genetic basis of IRD. Taken together, 'RetinoGenetics' is an integrative, informative and updatable resource for IRD-related genetic predispositions. Database URL: http://www.retinogenetics.org/. © The Author(s) 2014. Published by Oxford University Press.

The Plant Genome Integrative Explorer Resource: PlantGenIE.org.

PubMed

Sundell, David; Mannapperuma, Chanaka; Netotea, Sergiu; Delhomme, Nicolas; Lin, Yao-Cheng; Sjödin, Andreas; Van de Peer, Yves; Jansson, Stefan; Hvidsten, Torgeir R; Street, Nathaniel R

2015-12-01

Accessing and exploring large-scale genomics data sets remains a significant challenge to researchers without specialist bioinformatics training. We present the integrated PlantGenIE.org platform for exploration of Populus, conifer and Arabidopsis genomics data, which includes expression networks and associated visualization tools. Standard features of a model organism database are provided, including genome browsers, gene list annotation, Blast homology searches and gene information pages. Community annotation updating is supported via integration of WebApollo. We have produced an RNA-sequencing (RNA-Seq) expression atlas for Populus tremula and have integrated these data within the expression tools. An updated version of the ComPlEx resource for performing comparative plant expression analyses of gene coexpression network conservation between species has also been integrated. The PlantGenIE.org platform provides intuitive access to large-scale and genome-wide genomics data from model forest tree species, facilitating both community contributions to annotation improvement and tools supporting use of the included data resources to inform biological insight. © 2015 The Authors. New Phytologist © 2015 New Phytologist Trust.

NoGOA: predicting noisy GO annotations using evidences and sparse representation.

PubMed

Yu, Guoxian; Lu, Chang; Wang, Jun

2017-07-21

Gene Ontology (GO) is a community effort to represent functional features of gene products. GO annotations (GOA) provide functional associations between GO terms and gene products. Due to resources limitation, only a small portion of annotations are manually checked by curators, and the others are electronically inferred. Although quality control techniques have been applied to ensure the quality of annotations, the community consistently report that there are still considerable noisy (or incorrect) annotations. Given the wide application of annotations, however, how to identify noisy annotations is an important but yet seldom studied open problem. We introduce a novel approach called NoGOA to predict noisy annotations. NoGOA applies sparse representation on the gene-term association matrix to reduce the impact of noisy annotations, and takes advantage of sparse representation coefficients to measure the semantic similarity between genes. Secondly, it preliminarily predicts noisy annotations of a gene based on aggregated votes from semantic neighborhood genes of that gene. Next, NoGOA estimates the ratio of noisy annotations for each evidence code based on direct annotations in GOA files archived on different periods, and then weights entries of the association matrix via estimated ratios and propagates weights to ancestors of direct annotations using GO hierarchy. Finally, it integrates evidence-weighted association matrix and aggregated votes to predict noisy annotations. Experiments on archived GOA files of six model species (H. sapiens, A. thaliana, S. cerevisiae, G. gallus, B. Taurus and M. musculus) demonstrate that NoGOA achieves significantly better results than other related methods and removing noisy annotations improves the performance of gene function prediction. The comparative study justifies the effectiveness of integrating evidence codes with sparse representation for predicting noisy GO annotations. Codes and datasets are available at http://mlda.swu.edu.cn/codes.php?name=NoGOA .

High-performance web services for querying gene and variant annotation.

PubMed

Xin, Jiwen; Mark, Adam; Afrasiabi, Cyrus; Tsueng, Ginger; Juchler, Moritz; Gopal, Nikhil; Stupp, Gregory S; Putman, Timothy E; Ainscough, Benjamin J; Griffith, Obi L; Torkamani, Ali; Whetzel, Patricia L; Mungall, Christopher J; Mooney, Sean D; Su, Andrew I; Wu, Chunlei

2016-05-06

Efficient tools for data management and integration are essential for many aspects of high-throughput biology. In particular, annotations of genes and human genetic variants are commonly used but highly fragmented across many resources. Here, we describe MyGene.info and MyVariant.info, high-performance web services for querying gene and variant annotation information. These web services are currently accessed more than three million times permonth. They also demonstrate a generalizable cloud-based model for organizing and querying biological annotation information. MyGene.info and MyVariant.info are provided as high-performance web services, accessible at http://mygene.info and http://myvariant.info . Both are offered free of charge to the research community.

National Mesothelioma Virtual Bank: a standard based biospecimen and clinical data resource to enhance translational research.

PubMed

Amin, Waqas; Parwani, Anil V; Schmandt, Linda; Mohanty, Sambit K; Farhat, Ghada; Pople, Andrew K; Winters, Sharon B; Whelan, Nancy B; Schneider, Althea M; Milnes, John T; Valdivieso, Federico A; Feldman, Michael; Pass, Harvey I; Dhir, Rajiv; Melamed, Jonathan; Becich, Michael J

2008-08-13

Advances in translational research have led to the need for well characterized biospecimens for research. The National Mesothelioma Virtual Bank is an initiative which collects annotated datasets relevant to human mesothelioma to develop an enterprising biospecimen resource to fulfill researchers' need. The National Mesothelioma Virtual Bank architecture is based on three major components: (a) common data elements (based on College of American Pathologists protocol and National North American Association of Central Cancer Registries standards), (b) clinical and epidemiologic data annotation, and (c) data query tools. These tools work interoperably to standardize the entire process of annotation. The National Mesothelioma Virtual Bank tool is based upon the caTISSUE Clinical Annotation Engine, developed by the University of Pittsburgh in cooperation with the Cancer Biomedical Informatics Grid (caBIG, see http://cabig.nci.nih.gov). This application provides a web-based system for annotating, importing and searching mesothelioma cases. The underlying information model is constructed utilizing Unified Modeling Language class diagrams, hierarchical relationships and Enterprise Architect software. The database provides researchers real-time access to richly annotated specimens and integral information related to mesothelioma. The data disclosed is tightly regulated depending upon users' authorization and depending on the participating institute that is amenable to the local Institutional Review Board and regulation committee reviews. The National Mesothelioma Virtual Bank currently has over 600 annotated cases available for researchers that include paraffin embedded tissues, tissue microarrays, serum and genomic DNA. The National Mesothelioma Virtual Bank is a virtual biospecimen registry with robust translational biomedical informatics support to facilitate basic science, clinical, and translational research. Furthermore, it protects patient privacy by disclosing only de-identified datasets to assure that biospecimens can be made accessible to researchers.

INDIGO – INtegrated Data Warehouse of MIcrobial GenOmes with Examples from the Red Sea Extremophiles

PubMed Central

Alam, Intikhab; Antunes, André; Kamau, Allan Anthony; Ba alawi, Wail; Kalkatawi, Manal; Stingl, Ulrich; Bajic, Vladimir B.

2013-01-01

Background The next generation sequencing technologies substantially increased the throughput of microbial genome sequencing. To functionally annotate newly sequenced microbial genomes, a variety of experimental and computational methods are used. Integration of information from different sources is a powerful approach to enhance such annotation. Functional analysis of microbial genomes, necessary for downstream experiments, crucially depends on this annotation but it is hampered by the current lack of suitable information integration and exploration systems for microbial genomes. Results We developed a data warehouse system (INDIGO) that enables the integration of annotations for exploration and analysis of newly sequenced microbial genomes. INDIGO offers an opportunity to construct complex queries and combine annotations from multiple sources starting from genomic sequence to protein domain, gene ontology and pathway levels. This data warehouse is aimed at being populated with information from genomes of pure cultures and uncultured single cells of Red Sea bacteria and Archaea. Currently, INDIGO contains information from Salinisphaera shabanensis, Haloplasma contractile, and Halorhabdus tiamatea - extremophiles isolated from deep-sea anoxic brine lakes of the Red Sea. We provide examples of utilizing the system to gain new insights into specific aspects on the unique lifestyle and adaptations of these organisms to extreme environments. Conclusions We developed a data warehouse system, INDIGO, which enables comprehensive integration of information from various resources to be used for annotation, exploration and analysis of microbial genomes. It will be regularly updated and extended with new genomes. It is aimed to serve as a resource dedicated to the Red Sea microbes. In addition, through INDIGO, we provide our Automatic Annotation of Microbial Genomes (AAMG) pipeline. The INDIGO web server is freely available at http://www.cbrc.kaust.edu.sa/indigo. PMID:24324765

The De Novo Transcriptome and Its Functional Annotation in the Seed Beetle Callosobruchus maculatus.

PubMed

Sayadi, Ahmed; Immonen, Elina; Bayram, Helen; Arnqvist, Göran

2016-01-01

Despite their unparalleled biodiversity, the genomic resources available for beetles (Coleoptera) remain relatively scarce. We present an integrative and high quality annotated transcriptome of the beetle Callosobruchus maculatus, an important and cosmopolitan agricultural pest as well as an emerging model species in ecology and evolutionary biology. Using Illumina sequencing technology, we sequenced 492 million read pairs generated from 51 samples of different developmental stages (larvae, pupae and adults) of C. maculatus. Reads were de novo assembled using the Trinity software, into a single combined assembly as well as into three separate assemblies based on data from the different developmental stages. The combined assembly generated 218,192 transcripts and 145,883 putative genes. Putative genes were annotated with the Blast2GO software and the Trinotate pipeline. In total, 33,216 putative genes were successfully annotated using Blastx against the Nr (non-redundant) database and 13,382 were assigned to 34,100 Gene Ontology (GO) terms. We classified 5,475 putative genes into Clusters of Orthologous Groups (COG) and 116 metabolic pathways maps were predicted based on the annotation. Our analyses suggested that the transcriptional specificity increases with ontogeny. For example, out of 33,216 annotated putative genes, 51 were only expressed in larvae, 63 only in pupae and 171 only in adults. Our study illustrates the importance of including samples from several developmental stages when the aim is to provide an integrative and high quality annotated transcriptome. Our results will represent an invaluable resource for those working with the ecology, evolution and pest control of C. maculatus, as well for comparative studies of the transcriptomics and genomics of beetles more generally.

The De Novo Transcriptome and Its Functional Annotation in the Seed Beetle Callosobruchus maculatus

PubMed Central

Sayadi, Ahmed; Immonen, Elina; Bayram, Helen

2016-01-01

Despite their unparalleled biodiversity, the genomic resources available for beetles (Coleoptera) remain relatively scarce. We present an integrative and high quality annotated transcriptome of the beetle Callosobruchus maculatus, an important and cosmopolitan agricultural pest as well as an emerging model species in ecology and evolutionary biology. Using Illumina sequencing technology, we sequenced 492 million read pairs generated from 51 samples of different developmental stages (larvae, pupae and adults) of C. maculatus. Reads were de novo assembled using the Trinity software, into a single combined assembly as well as into three separate assemblies based on data from the different developmental stages. The combined assembly generated 218,192 transcripts and 145,883 putative genes. Putative genes were annotated with the Blast2GO software and the Trinotate pipeline. In total, 33,216 putative genes were successfully annotated using Blastx against the Nr (non-redundant) database and 13,382 were assigned to 34,100 Gene Ontology (GO) terms. We classified 5,475 putative genes into Clusters of Orthologous Groups (COG) and 116 metabolic pathways maps were predicted based on the annotation. Our analyses suggested that the transcriptional specificity increases with ontogeny. For example, out of 33,216 annotated putative genes, 51 were only expressed in larvae, 63 only in pupae and 171 only in adults. Our study illustrates the importance of including samples from several developmental stages when the aim is to provide an integrative and high quality annotated transcriptome. Our results will represent an invaluable resource for those working with the ecology, evolution and pest control of C. maculatus, as well for comparative studies of the transcriptomics and genomics of beetles more generally. PMID:27442123

SEED Servers: High-Performance Access to the SEED Genomes, Annotations, and Metabolic Models

PubMed Central

Aziz, Ramy K.; Devoid, Scott; Disz, Terrence; Edwards, Robert A.; Henry, Christopher S.; Olsen, Gary J.; Olson, Robert; Overbeek, Ross; Parrello, Bruce; Pusch, Gordon D.; Stevens, Rick L.; Vonstein, Veronika; Xia, Fangfang

2012-01-01

The remarkable advance in sequencing technology and the rising interest in medical and environmental microbiology, biotechnology, and synthetic biology resulted in a deluge of published microbial genomes. Yet, genome annotation, comparison, and modeling remain a major bottleneck to the translation of sequence information into biological knowledge, hence computational analysis tools are continuously being developed for rapid genome annotation and interpretation. Among the earliest, most comprehensive resources for prokaryotic genome analysis, the SEED project, initiated in 2003 as an integration of genomic data and analysis tools, now contains >5,000 complete genomes, a constantly updated set of curated annotations embodied in a large and growing collection of encoded subsystems, a derived set of protein families, and hundreds of genome-scale metabolic models. Until recently, however, maintaining current copies of the SEED code and data at remote locations has been a pressing issue. To allow high-performance remote access to the SEED database, we developed the SEED Servers (http://www.theseed.org/servers): four network-based servers intended to expose the data in the underlying relational database, support basic annotation services, offer programmatic access to the capabilities of the RAST annotation server, and provide access to a growing collection of metabolic models that support flux balance analysis. The SEED servers offer open access to regularly updated data, the ability to annotate prokaryotic genomes, the ability to create metabolic reconstructions and detailed models of metabolism, and access to hundreds of existing metabolic models. This work offers and supports a framework upon which other groups can build independent research efforts. Large integrations of genomic data represent one of the major intellectual resources driving research in biology, and programmatic access to the SEED data will provide significant utility to a broad collection of potential users. PMID:23110173

INDIGO - INtegrated data warehouse of microbial genomes with examples from the red sea extremophiles.

PubMed

Alam, Intikhab; Antunes, André; Kamau, Allan Anthony; Ba Alawi, Wail; Kalkatawi, Manal; Stingl, Ulrich; Bajic, Vladimir B

2013-01-01

The next generation sequencing technologies substantially increased the throughput of microbial genome sequencing. To functionally annotate newly sequenced microbial genomes, a variety of experimental and computational methods are used. Integration of information from different sources is a powerful approach to enhance such annotation. Functional analysis of microbial genomes, necessary for downstream experiments, crucially depends on this annotation but it is hampered by the current lack of suitable information integration and exploration systems for microbial genomes. We developed a data warehouse system (INDIGO) that enables the integration of annotations for exploration and analysis of newly sequenced microbial genomes. INDIGO offers an opportunity to construct complex queries and combine annotations from multiple sources starting from genomic sequence to protein domain, gene ontology and pathway levels. This data warehouse is aimed at being populated with information from genomes of pure cultures and uncultured single cells of Red Sea bacteria and Archaea. Currently, INDIGO contains information from Salinisphaera shabanensis, Haloplasma contractile, and Halorhabdus tiamatea - extremophiles isolated from deep-sea anoxic brine lakes of the Red Sea. We provide examples of utilizing the system to gain new insights into specific aspects on the unique lifestyle and adaptations of these organisms to extreme environments. We developed a data warehouse system, INDIGO, which enables comprehensive integration of information from various resources to be used for annotation, exploration and analysis of microbial genomes. It will be regularly updated and extended with new genomes. It is aimed to serve as a resource dedicated to the Red Sea microbes. In addition, through INDIGO, we provide our Automatic Annotation of Microbial Genomes (AAMG) pipeline. The INDIGO web server is freely available at http://www.cbrc.kaust.edu.sa/indigo.

War Peace Film Guide. Revised Edition.

ERIC Educational Resources Information Center

Dowling, John

This filmography is a selective listing of 287 films dealing with the topics of war and peace for use with K-12 and college students and with adults. The annotated guide will be of use to anyone planning a world affairs program and of special value to those interested in the problem of war. A wide variety of subject areas are treated in the films.…

Teaching Business Ethics: A Practical Guide and Case Studies. SBDC Professional Enrichment.

ERIC Educational Resources Information Center

Collins, Denis; Page, Laura V.

This teaching guide is for instructors who wish to include a discussion of ethical dilemmas in their regular business seminars and workshops. It discusses why it is essential to teach ethics and how to do so. It reviews the format of specially annotated ethics cases that are designed to help teach business ethics and shows how to use them. These…

Selected Resources and Bibliography

ERIC Educational Resources Information Center

New Directions for Higher Education, 2011

2011-01-01

This chapter provides an annotated bibliography of resources pertaining to international branch campuses (IBCs). This collection of references has been selected to represent the breadth of emerging scholarship on cross-border higher education and is intended to provide further resources on a range of concerns surrounding cross-border higher…

Temporal Annotation in the Clinical Domain

PubMed Central

Styler, William F.; Bethard, Steven; Finan, Sean; Palmer, Martha; Pradhan, Sameer; de Groen, Piet C; Erickson, Brad; Miller, Timothy; Lin, Chen; Savova, Guergana; Pustejovsky, James

2014-01-01

This article discusses the requirements of a formal specification for the annotation of temporal information in clinical narratives. We discuss the implementation and extension of ISO-TimeML for annotating a corpus of clinical notes, known as the THYME corpus. To reflect the information task and the heavily inference-based reasoning demands in the domain, a new annotation guideline has been developed, “the THYME Guidelines to ISO-TimeML (THYME-TimeML)”. To clarify what relations merit annotation, we distinguish between linguistically-derived and inferentially-derived temporal orderings in the text. We also apply a top performing TempEval 2013 system against this new resource to measure the difficulty of adapting systems to the clinical domain. The corpus is available to the community and has been proposed for use in a SemEval 2015 task. PMID:29082229

A Folksonomy-Based Lightweight Resource Annotation Metadata Schema for Personalized Hypermedia Learning Resource Delivery

ERIC Educational Resources Information Center

Lau, Simon Boung-Yew; Lee, Chien-Sing; Singh, Yashwant Prasad

2015-01-01

With the proliferation of social Web applications, users can now collaboratively author, share and access hypermedia learning resources, contributing to richer learning experiences outside formal education. These resources may or may not be educational. However, they can be harnessed for educational purposes by adapting and personalizing them to…

Focus on Firearms. Biblio Alert! New Resources for Preventing Injury and Violence.

ERIC Educational Resources Information Center

National Center for Education in Maternal and Child Health, Arlington, VA.

This annotated bibliography provides information on important resources on firearm injuries. It is divided into two sections: (1) New Resources, including journal articles (28 titles), reports and books (15 titles), other resources (13 titles), and popular press (3 titles); and (2) Classics, including journal articles (10 titles), reports and…

BioUSeR: a semantic-based tool for retrieving Life Science web resources driven by text-rich user requirements

PubMed Central

2013-01-01

Background Open metadata registries are a fundamental tool for researchers in the Life Sciences trying to locate resources. While most current registries assume that resources are annotated with well-structured metadata, evidence shows that most of the resource annotations simply consists of informal free text. This reality must be taken into account in order to develop effective techniques for resource discovery in Life Sciences. Results BioUSeR is a semantic-based tool aimed at retrieving Life Sciences resources described in free text. The retrieval process is driven by the user requirements, which consist of a target task and a set of facets of interest, both expressed in free text. BioUSeR is able to effectively exploit the available textual descriptions to find relevant resources by using semantic-aware techniques. Conclusions BioUSeR overcomes the limitations of the current registries thanks to: (i) rich specification of user information needs, (ii) use of semantics to manage textual descriptions, (iii) retrieval and ranking of resources based on user requirements. PMID:23635042

The Holocaust in Books and Films. A Selected, Annotated List.

ERIC Educational Resources Information Center

Muffs, Judith Herschlag, Ed.

This is an annotated list of over 400 resource books and films on Jewish history before the Holocaust, the history and development of Nazism, experiences during the Holocaust and its aftermath, and the phenomenon of prejudice and anti-Semitism. Designed primarily for teachers and librarians in secondary schools and to some extent in elementary…

Steps for Creating a Specialized Corpus and Developing an Annotated Frequency-Based Vocabulary List

ERIC Educational Resources Information Center

Toriida, Marie-Claude

2016-01-01

This article provides introductory, step-by-step explanations of how to make a specialized corpus and an annotated frequency-based vocabulary list. One of my objectives is to help teachers, instructors, program administrators, and graduate students with little experience in this field be able to do so using free resources. Instructions are first…

Multimedia Materials for Afro-American Studies. A Curriculum Orientation and Annotated Bibliography of Resources.

ERIC Educational Resources Information Center

Johnson, Harry Alleyn, Ed.

Four black professionals (an educational media specialist, an educator, a sociologist, and a historian) present their views on relevant education for minority students from the vantage point of their respective disciplines. An extensive annotated list of non-print media, plus a bibliography of 100 paperback books, provides a body of instructional…

American Indian Women and Mathematics: An Annotated Bibliography of Selected Resources.

ERIC Educational Resources Information Center

Christensen, Rosemary; And Others

An annotated bibliography, compiled as part of a 1-year project to look at factors affecting the participation and performance of Minnesota Indian girls in mathematics, contains 64 entries, dating between 1967 and 1982. Because Indian Students in general leave the public schools underprepared for jobs, and because the plight of Indian women is…

Automated and Accurate Estimation of Gene Family Abundance from Shotgun Metagenomes

PubMed Central

Nayfach, Stephen; Bradley, Patrick H.; Wyman, Stacia K.; Laurent, Timothy J.; Williams, Alex; Eisen, Jonathan A.; Pollard, Katherine S.; Sharpton, Thomas J.

2015-01-01

Shotgun metagenomic DNA sequencing is a widely applicable tool for characterizing the functions that are encoded by microbial communities. Several bioinformatic tools can be used to functionally annotate metagenomes, allowing researchers to draw inferences about the functional potential of the community and to identify putative functional biomarkers. However, little is known about how decisions made during annotation affect the reliability of the results. Here, we use statistical simulations to rigorously assess how to optimize annotation accuracy and speed, given parameters of the input data like read length and library size. We identify best practices in metagenome annotation and use them to guide the development of the Shotgun Metagenome Annotation Pipeline (ShotMAP). ShotMAP is an analytically flexible, end-to-end annotation pipeline that can be implemented either on a local computer or a cloud compute cluster. We use ShotMAP to assess how different annotation databases impact the interpretation of how marine metagenome and metatranscriptome functional capacity changes across seasons. We also apply ShotMAP to data obtained from a clinical microbiome investigation of inflammatory bowel disease. This analysis finds that gut microbiota collected from Crohn’s disease patients are functionally distinct from gut microbiota collected from either ulcerative colitis patients or healthy controls, with differential abundance of metabolic pathways related to host-microbiome interactions that may serve as putative biomarkers of disease. PMID:26565399

PATRIC, the bacterial bioinformatics database and analysis resource.

PubMed

Wattam, Alice R; Abraham, David; Dalay, Oral; Disz, Terry L; Driscoll, Timothy; Gabbard, Joseph L; Gillespie, Joseph J; Gough, Roger; Hix, Deborah; Kenyon, Ronald; Machi, Dustin; Mao, Chunhong; Nordberg, Eric K; Olson, Robert; Overbeek, Ross; Pusch, Gordon D; Shukla, Maulik; Schulman, Julie; Stevens, Rick L; Sullivan, Daniel E; Vonstein, Veronika; Warren, Andrew; Will, Rebecca; Wilson, Meredith J C; Yoo, Hyun Seung; Zhang, Chengdong; Zhang, Yan; Sobral, Bruno W

2014-01-01

The Pathosystems Resource Integration Center (PATRIC) is the all-bacterial Bioinformatics Resource Center (BRC) (http://www.patricbrc.org). A joint effort by two of the original National Institute of Allergy and Infectious Diseases-funded BRCs, PATRIC provides researchers with an online resource that stores and integrates a variety of data types [e.g. genomics, transcriptomics, protein-protein interactions (PPIs), three-dimensional protein structures and sequence typing data] and associated metadata. Datatypes are summarized for individual genomes and across taxonomic levels. All genomes in PATRIC, currently more than 10,000, are consistently annotated using RAST, the Rapid Annotations using Subsystems Technology. Summaries of different data types are also provided for individual genes, where comparisons of different annotations are available, and also include available transcriptomic data. PATRIC provides a variety of ways for researchers to find data of interest and a private workspace where they can store both genomic and gene associations, and their own private data. Both private and public data can be analyzed together using a suite of tools to perform comparative genomic or transcriptomic analysis. PATRIC also includes integrated information related to disease and PPIs. All the data and integrated analysis and visualization tools are freely available. This manuscript describes updates to the PATRIC since its initial report in the 2007 NAR Database Issue.

PATRIC, the bacterial bioinformatics database and analysis resource

PubMed Central

Wattam, Alice R.; Abraham, David; Dalay, Oral; Disz, Terry L.; Driscoll, Timothy; Gabbard, Joseph L.; Gillespie, Joseph J.; Gough, Roger; Hix, Deborah; Kenyon, Ronald; Machi, Dustin; Mao, Chunhong; Nordberg, Eric K.; Olson, Robert; Overbeek, Ross; Pusch, Gordon D.; Shukla, Maulik; Schulman, Julie; Stevens, Rick L.; Sullivan, Daniel E.; Vonstein, Veronika; Warren, Andrew; Will, Rebecca; Wilson, Meredith J.C.; Yoo, Hyun Seung; Zhang, Chengdong; Zhang, Yan; Sobral, Bruno W.

2014-01-01

The Pathosystems Resource Integration Center (PATRIC) is the all-bacterial Bioinformatics Resource Center (BRC) (http://www.patricbrc.org). A joint effort by two of the original National Institute of Allergy and Infectious Diseases-funded BRCs, PATRIC provides researchers with an online resource that stores and integrates a variety of data types [e.g. genomics, transcriptomics, protein–protein interactions (PPIs), three-dimensional protein structures and sequence typing data] and associated metadata. Datatypes are summarized for individual genomes and across taxonomic levels. All genomes in PATRIC, currently more than 10 000, are consistently annotated using RAST, the Rapid Annotations using Subsystems Technology. Summaries of different data types are also provided for individual genes, where comparisons of different annotations are available, and also include available transcriptomic data. PATRIC provides a variety of ways for researchers to find data of interest and a private workspace where they can store both genomic and gene associations, and their own private data. Both private and public data can be analyzed together using a suite of tools to perform comparative genomic or transcriptomic analysis. PATRIC also includes integrated information related to disease and PPIs. All the data and integrated analysis and visualization tools are freely available. This manuscript describes updates to the PATRIC since its initial report in the 2007 NAR Database Issue. PMID:24225323

Mediagraphy: Print and Nonprint Resources.

ERIC Educational Resources Information Center

Educational Media and Technology Yearbook, 1999

1999-01-01

Provides annotated listings for current journals, books, ERIC documents, articles, and nonprint resources in the following categories: artificial intelligence/robotics/electronic performance support systems; computer-assisted instruction; distance education; educational research; educational technology; information science and technology;…

Partnerships panel: natural, resource partnerships: literature synthesis and research agenda

Treesearch

Steve Selin; Nancy Myers

1995-01-01

This paper presents a summary of an annotated bibliography on natural resource partnerships. Resource areas and management functions addressed in the partnership literature are examined. Partnership research is summarized and broken into categories including: Partnership outcomes, assessing the potential for partnerships, characteristics of successful partnerships,...

Immersive Education, an Annotated Webliography

ERIC Educational Resources Information Center

Pricer, Wayne F.

2011-01-01

In this second installment of a two-part feature on immersive education a webliography will provide resources discussing the use of various types of computer simulations including: (a) augmented reality, (b) virtual reality programs, (c) gaming resources for teaching with technology, (d) virtual reality lab resources, (e) virtual reality standards…

The SEED and the Rapid Annotation of microbial genomes using Subsystems Technology (RAST)

PubMed Central

Overbeek, Ross; Olson, Robert; Pusch, Gordon D.; Olsen, Gary J.; Davis, James J.; Disz, Terry; Edwards, Robert A.; Gerdes, Svetlana; Parrello, Bruce; Shukla, Maulik; Vonstein, Veronika; Wattam, Alice R.; Xia, Fangfang; Stevens, Rick

2014-01-01

In 2004, the SEED (http://pubseed.theseed.org/) was created to provide consistent and accurate genome annotations across thousands of genomes and as a platform for discovering and developing de novo annotations. The SEED is a constantly updated integration of genomic data with a genome database, web front end, API and server scripts. It is used by many scientists for predicting gene functions and discovering new pathways. In addition to being a powerful database for bioinformatics research, the SEED also houses subsystems (collections of functionally related protein families) and their derived FIGfams (protein families), which represent the core of the RAST annotation engine (http://rast.nmpdr.org/). When a new genome is submitted to RAST, genes are called and their annotations are made by comparison to the FIGfam collection. If the genome is made public, it is then housed within the SEED and its proteins populate the FIGfam collection. This annotation cycle has proven to be a robust and scalable solution to the problem of annotating the exponentially increasing number of genomes. To date, >12 000 users worldwide have annotated >60 000 distinct genomes using RAST. Here we describe the interconnectedness of the SEED database and RAST, the RAST annotation pipeline and updates to both resources. PMID:24293654

The SEED and the Rapid Annotation of microbial genomes using Subsystems Technology (RAST).

PubMed

Overbeek, Ross; Olson, Robert; Pusch, Gordon D; Olsen, Gary J; Davis, James J; Disz, Terry; Edwards, Robert A; Gerdes, Svetlana; Parrello, Bruce; Shukla, Maulik; Vonstein, Veronika; Wattam, Alice R; Xia, Fangfang; Stevens, Rick

2014-01-01

In 2004, the SEED (http://pubseed.theseed.org/) was created to provide consistent and accurate genome annotations across thousands of genomes and as a platform for discovering and developing de novo annotations. The SEED is a constantly updated integration of genomic data with a genome database, web front end, API and server scripts. It is used by many scientists for predicting gene functions and discovering new pathways. In addition to being a powerful database for bioinformatics research, the SEED also houses subsystems (collections of functionally related protein families) and their derived FIGfams (protein families), which represent the core of the RAST annotation engine (http://rast.nmpdr.org/). When a new genome is submitted to RAST, genes are called and their annotations are made by comparison to the FIGfam collection. If the genome is made public, it is then housed within the SEED and its proteins populate the FIGfam collection. This annotation cycle has proven to be a robust and scalable solution to the problem of annotating the exponentially increasing number of genomes. To date, >12 000 users worldwide have annotated >60 000 distinct genomes using RAST. Here we describe the interconnectedness of the SEED database and RAST, the RAST annotation pipeline and updates to both resources.

Annotated Resource List of Peace Education Resources Available from Wilmington College Peace Resource Center, Hiroshima/Nagasaki Memorial Collection.

ERIC Educational Resources Information Center

Wilmington Coll., OH. Peace Resource Center.

Over 130 print and nonprint peace education resources for use with adult groups and elementary, secondary, and college students are described. Audiovisuals may be rented and books may be purchased from the Wilmington College (Ohio) Peace Resource Center. Audiovisuals, including slides, videotapes and videotape cassettes, and 16mm films, are…

Marketable energy resources in Alabama: a partially annotated research bibliography

DOE Office of Scientific and Technical Information (OSTI.GOV)

Not Available

1982-04-01

This bibliography has been compiled to provide a guide to the published research, both basic and applied, on the commercial potential and possible energy contribution of selected domestic renewable and non-renewable energy resources in Alabama. Some of the renewable and non-renewable energy resources documented in published form and highlighted in this bibliography include coal, oil, small-scale hydroelectric power, natural gas, wind energy, waste wood, and uranium. Citations dealing mainly with solar energy can be obtained by contacting organizations involved in the development of solar energy. The information for this publication was derived from a number of sources; including the Geologicalmore » Survey of Alabama, Office of State Planning and Federal Program's Planning Reference Service, US Department of Energy's Technical Information Center at Oak Ridge, Tennessee, School of Mines and Energy Development of the University of Alabama, Mineral Resources Institute and State Mine Experiment Station of the University of Alabama. Each citation is complete insofar as the information was available to the compiler. Most abstracts contain some summary information on uses, technology, and economics. These summaries are not meant to be exhaustive. Users of the bibliography should deal directly with the Technical Information Center, US Department of Energy, PO Box 62, Oak Ridge, Tennessee 37830, or the supporting organization or project investigator as to the availability of copies of completed projects in report or book form. (PSB)« less

MSeqDR: A Centralized Knowledge Repository and Bioinformatics Web Resource to Facilitate Genomic Investigations in Mitochondrial Disease.

PubMed

Shen, Lishuang; Diroma, Maria Angela; Gonzalez, Michael; Navarro-Gomez, Daniel; Leipzig, Jeremy; Lott, Marie T; van Oven, Mannis; Wallace, Douglas C; Muraresku, Colleen Clarke; Zolkipli-Cunningham, Zarazuela; Chinnery, Patrick F; Attimonelli, Marcella; Zuchner, Stephan; Falk, Marni J; Gai, Xiaowu

2016-06-01

MSeqDR is the Mitochondrial Disease Sequence Data Resource, a centralized and comprehensive genome and phenome bioinformatics resource built by the mitochondrial disease community to facilitate clinical diagnosis and research investigations of individual patient phenotypes, genomes, genes, and variants. A central Web portal (https://mseqdr.org) integrates community knowledge from expert-curated databases with genomic and phenotype data shared by clinicians and researchers. MSeqDR also functions as a centralized application server for Web-based tools to analyze data across both mitochondrial and nuclear DNA, including investigator-driven whole exome or genome dataset analyses through MSeqDR-Genesis. MSeqDR-GBrowse genome browser supports interactive genomic data exploration and visualization with custom tracks relevant to mtDNA variation and mitochondrial disease. MSeqDR-LSDB is a locus-specific database that currently manages 178 mitochondrial diseases, 1,363 genes associated with mitochondrial biology or disease, and 3,711 pathogenic variants in those genes. MSeqDR Disease Portal allows hierarchical tree-style disease exploration to evaluate their unique descriptions, phenotypes, and causative variants. Automated genomic data submission tools are provided that capture ClinVar compliant variant annotations. PhenoTips will be used for phenotypic data submission on deidentified patients using human phenotype ontology terminology. The development of a dynamic informed patient consent process to guide data access is underway to realize the full potential of these resources. © 2016 WILEY PERIODICALS, INC.

MSeqDR: A Centralized Knowledge Repository and Bioinformatics Web Resource to Facilitate Genomic Investigations in Mitochondrial Disease

PubMed Central

Shen, Lishuang; Diroma, Maria Angela; Gonzalez, Michael; Navarro-Gomez, Daniel; Leipzig, Jeremy; Lott, Marie T.; van Oven, Mannis; Wallace, Douglas C.; Muraresku, Colleen Clarke; Zolkipli-Cunningham, Zarazuela; Chinnery, Patrick F.; Attimonelli, Marcella; Zuchner, Stephan

2016-01-01

MSeqDR is the Mitochondrial Disease Sequence Data Resource, a centralized and comprehensive genome and phenome bioinformatics resource built by the mitochondrial disease community to facilitate clinical diagnosis and research investigations of individual patient phenotypes, genomes, genes, and variants. A central Web portal (https://mseqdr.org) integrates community knowledge from expert-curated databases with genomic and phenotype data shared by clinicians and researchers. MSeqDR also functions as a centralized application server for Web-based tools to analyze data across both mitochondrial and nuclear DNA, including investigator-driven whole exome or genome dataset analyses through MSeqDR-Genesis. MSeqDR-GBrowse supports interactive genomic data exploration and visualization with custom tracks relevant to mtDNA variation and disease. MSeqDR-LSDB is a locus specific database that currently manages 178 mitochondrial diseases, 1,363 genes associated with mitochondrial biology or disease, and 3,711 pathogenic variants in those genes. MSeqDR Disease Portal allows hierarchical tree-style disease exploration to evaluate their unique descriptions, phenotypes, and causative variants. Automated genomic data submission tools are provided that capture ClinVar-compliant variant annotations. PhenoTips is used for phenotypic data submission on de-identified patients using human phenotype ontology terminology. Development of a dynamic informed patient consent process to guide data access is underway to realize the full potential of these resources. PMID:26919060

MSeqDR mvTool: A mitochondrial DNA Web and API resource for comprehensive variant annotation, universal nomenclature collation, and reference genome conversion.

PubMed

Shen, Lishuang; Attimonelli, Marcella; Bai, Renkui; Lott, Marie T; Wallace, Douglas C; Falk, Marni J; Gai, Xiaowu

2018-06-01

Accurate mitochondrial DNA (mtDNA) variant annotation is essential for the clinical diagnosis of diverse human diseases. Substantial challenges to this process include the inconsistency in mtDNA nomenclatures, the existence of multiple reference genomes, and a lack of reference population frequency data. Clinicians need a simple bioinformatics tool that is user-friendly, and bioinformaticians need a powerful informatics resource for programmatic usage. Here, we report the development and functionality of the MSeqDR mtDNA Variant Tool set (mvTool), a one-stop mtDNA variant annotation and analysis Web service. mvTool is built upon the MSeqDR infrastructure (https://mseqdr.org), with contributions of expert curated data from MITOMAP (https://www.mitomap.org) and HmtDB (https://www.hmtdb.uniba.it/hmdb). mvTool supports all mtDNA nomenclatures, converts variants to standard rCRS- and HGVS-based nomenclatures, and annotates novel mtDNA variants. Besides generic annotations from dbNSFP and Variant Effect Predictor (VEP), mvTool provides allele frequencies in more than 47,000 germline mitogenomes, and disease and pathogenicity classifications from MSeqDR, Mitomap, HmtDB and ClinVar (Landrum et al., 2013). mvTools also provides mtDNA somatic variants annotations. "mvTool API" is implemented for programmatic access using inputs in VCF, HGVS, or classical mtDNA variant nomenclatures. The results are reported as hyperlinked html tables, JSON, Excel, and VCF formats. MSeqDR mvTool is freely accessible at https://mseqdr.org/mvtool.php. © 2018 Wiley Periodicals, Inc.

RNA-Rocket: an RNA-Seq analysis resource for infectious disease research

PubMed Central

Warren, Andrew S.; Aurrecoechea, Cristina; Brunk, Brian; Desai, Prerak; Emrich, Scott; Giraldo-Calderón, Gloria I.; Harb, Omar; Hix, Deborah; Lawson, Daniel; Machi, Dustin; Mao, Chunhong; McClelland, Michael; Nordberg, Eric; Shukla, Maulik; Vosshall, Leslie B.; Wattam, Alice R.; Will, Rebecca; Yoo, Hyun Seung; Sobral, Bruno

2015-01-01

Motivation: RNA-Seq is a method for profiling transcription using high-throughput sequencing and is an important component of many research projects that wish to study transcript isoforms, condition specific expression and transcriptional structure. The methods, tools and technologies used to perform RNA-Seq analysis continue to change, creating a bioinformatics challenge for researchers who wish to exploit these data. Resources that bring together genomic data, analysis tools, educational material and computational infrastructure can minimize the overhead required of life science researchers. Results: RNA-Rocket is a free service that provides access to RNA-Seq and ChIP-Seq analysis tools for studying infectious diseases. The site makes available thousands of pre-indexed genomes, their annotations and the ability to stream results to the bioinformatics resources VectorBase, EuPathDB and PATRIC. The site also provides a combination of experimental data and metadata, examples of pre-computed analysis, step-by-step guides and a user interface designed to enable both novice and experienced users of RNA-Seq data. Availability and implementation: RNA-Rocket is available at rnaseq.pathogenportal.org. Source code for this project can be found at github.com/cidvbi/PathogenPortal. Contact: anwarren@vt.edu Supplementary information: Supplementary materials are available at Bioinformatics online. PMID:25573919

RNA-Rocket: an RNA-Seq analysis resource for infectious disease research.

PubMed

Warren, Andrew S; Aurrecoechea, Cristina; Brunk, Brian; Desai, Prerak; Emrich, Scott; Giraldo-Calderón, Gloria I; Harb, Omar; Hix, Deborah; Lawson, Daniel; Machi, Dustin; Mao, Chunhong; McClelland, Michael; Nordberg, Eric; Shukla, Maulik; Vosshall, Leslie B; Wattam, Alice R; Will, Rebecca; Yoo, Hyun Seung; Sobral, Bruno

2015-05-01

RNA-Seq is a method for profiling transcription using high-throughput sequencing and is an important component of many research projects that wish to study transcript isoforms, condition specific expression and transcriptional structure. The methods, tools and technologies used to perform RNA-Seq analysis continue to change, creating a bioinformatics challenge for researchers who wish to exploit these data. Resources that bring together genomic data, analysis tools, educational material and computational infrastructure can minimize the overhead required of life science researchers. RNA-Rocket is a free service that provides access to RNA-Seq and ChIP-Seq analysis tools for studying infectious diseases. The site makes available thousands of pre-indexed genomes, their annotations and the ability to stream results to the bioinformatics resources VectorBase, EuPathDB and PATRIC. The site also provides a combination of experimental data and metadata, examples of pre-computed analysis, step-by-step guides and a user interface designed to enable both novice and experienced users of RNA-Seq data. RNA-Rocket is available at rnaseq.pathogenportal.org. Source code for this project can be found at github.com/cidvbi/PathogenPortal. anwarren@vt.edu Supplementary materials are available at Bioinformatics online. © The Author 2015. Published by Oxford University Press.

An Annotated Reading List for Concurrent Engineering

DTIC Science & Technology

1989-07-01

The seven tools are sometimes referred to as the seven old tools.) -9- Ishikawa , Kaoru , What is Total Quality Control? The Japanese Way, Prentice-Hall...some solutions. * Ishikawa (1982) presents a practical guide (with easy to use tools) for implementing qual- ity control at the working level...study of, :-, ieering for the last two years. Is..ikawa, Kaoru , Guide to Quality Control, Kraus International Publications, White Plains, NY, 1982. The

Developmental Gene Discovery in a Hemimetabolous Insect: De Novo Assembly and Annotation of a Transcriptome for the Cricket Gryllus bimaculatus

PubMed Central

Zeng, Victor; Ewen-Campen, Ben; Horch, Hadley W.; Roth, Siegfried; Mito, Taro; Extavour, Cassandra G.

2013-01-01

Most genomic resources available for insects represent the Holometabola, which are insects that undergo complete metamorphosis like beetles and flies. In contrast, the Hemimetabola (direct developing insects), representing the basal branches of the insect tree, have very few genomic resources. We have therefore created a large and publicly available transcriptome for the hemimetabolous insect Gryllus bimaculatus (cricket), a well-developed laboratory model organism whose potential for functional genetic experiments is currently limited by the absence of genomic resources. cDNA was prepared using mRNA obtained from adult ovaries containing all stages of oogenesis, and from embryo samples on each day of embryogenesis. Using 454 Titanium pyrosequencing, we sequenced over four million raw reads, and assembled them into 21,512 isotigs (predicted transcripts) and 120,805 singletons with an average coverage per base pair of 51.3. We annotated the transcriptome manually for over 400 conserved genes involved in embryonic patterning, gametogenesis, and signaling pathways. BLAST comparison of the transcriptome against the NCBI non-redundant protein database (nr) identified significant similarity to nr sequences for 55.5% of transcriptome sequences, and suggested that the transcriptome may contain 19,874 unique transcripts. For predicted transcripts without significant similarity to known sequences, we assessed their similarity to other orthopteran sequences, and determined that these transcripts contain recognizable protein domains, largely of unknown function. We created a searchable, web-based database to allow public access to all raw, assembled and annotated data. This database is to our knowledge the largest de novo assembled and annotated transcriptome resource available for any hemimetabolous insect. We therefore anticipate that these data will contribute significantly to more effective and higher-throughput deployment of molecular analysis tools in Gryllus. PMID:23671567

Resources for Using a Global Approach in Elementary Social Studies. TeachERIC Resource Series, No. 2.

ERIC Educational Resources Information Center

Social Science Education Consortium, Inc., Boulder, CO.

This annotated bibliography, one of four separate resources in the "Teach ERIC Resource Series," cites materials that will help elementary teachers incorporate a global approach into social studies instruction. All materials listed are available through the ERIC system and in journal articles. The purpose of the Series is to help familiarize…

Educational Equity Options. A Resource Bibliography.

ERIC Educational Resources Information Center

Martino, Susan; Watson, Jennifer

This selected list of educational resources includes 44 video items, 23 books, 9 posters, and 24 educational equity organizations and resource centers. Video materials and books are classified according to appropriate age groups and student abilities. All items are annotated. Topics of the videos and books include career choices, special needs…

Annotated Bibliography of Mathematics Resources. Program Resources.

ERIC Educational Resources Information Center

Markus, Nancy L.

Two bibliographies that review 18 books and resource materials that adult educators can use to teach mathematics in adult literacy classes are included. The materials are suggested to help teachers implement an effective, successful mathematics program, using many of the strategies recommended by the National Council of Teachers of Mathematics.…

Recreation and scenic resources in Alaska: an annotated bibliography.

Treesearch

Robert M. Muth; Sally Anne Fitchet

1976-01-01

This bibliography provides descriptions of material published on recreation and scenic resources in Alaska. Included are publications on research and supporting material in the form of studies and reports, proposals, plans, historical and cultural references, bibliographic documents, and popular books and articles describing the resources of Alaska and issues relating...

Evidence-based gene models for structural and functional annotations of the oil palm genome.

PubMed

Chan, Kuang-Lim; Tatarinova, Tatiana V; Rosli, Rozana; Amiruddin, Nadzirah; Azizi, Norazah; Halim, Mohd Amin Ab; Sanusi, Nik Shazana Nik Mohd; Jayanthi, Nagappan; Ponomarenko, Petr; Triska, Martin; Solovyev, Victor; Firdaus-Raih, Mohd; Sambanthamurthi, Ravigadevi; Murphy, Denis; Low, Eng-Ti Leslie

2017-09-08

Oil palm is an important source of edible oil. The importance of the crop, as well as its long breeding cycle (10-12 years) has led to the sequencing of its genome in 2013 to pave the way for genomics-guided breeding. Nevertheless, the first set of gene predictions, although useful, had many fragmented genes. Classification and characterization of genes associated with traits of interest, such as those for fatty acid biosynthesis and disease resistance, were also limited. Lipid-, especially fatty acid (FA)-related genes are of particular interest for the oil palm as they specify oil yields and quality. This paper presents the characterization of the oil palm genome using different gene prediction methods and comparative genomics analysis, identification of FA biosynthesis and disease resistance genes, and the development of an annotation database and bioinformatics tools. Using two independent gene-prediction pipelines, Fgenesh++ and Seqping, 26,059 oil palm genes with transcriptome and RefSeq support were identified from the oil palm genome. These coding regions of the genome have a characteristic broad distribution of GC 3 (fraction of cytosine and guanine in the third position of a codon) with over half the GC 3 -rich genes (GC 3  ≥ 0.75286) being intronless. In comparison, only one-seventh of the oil palm genes identified are intronless. Using comparative genomics analysis, characterization of conserved domains and active sites, and expression analysis, 42 key genes involved in FA biosynthesis in oil palm were identified. For three of them, namely EgFABF, EgFABH and EgFAD3, segmental duplication events were detected. Our analysis also identified 210 candidate resistance genes in six classes, grouped by their protein domain structures. We present an accurate and comprehensive annotation of the oil palm genome, focusing on analysis of important categories of genes (GC 3 -rich and intronless), as well as those associated with important functions, such as FA biosynthesis and disease resistance. The study demonstrated the advantages of having an integrated approach to gene prediction and developed a computational framework for combining multiple genome annotations. These results, available in the oil palm annotation database ( http://palmxplore.mpob.gov.my ), will provide important resources for studies on the genomes of oil palm and related crops. This article was reviewed by Alexander Kel, Igor Rogozin, and Vladimir A. Kuznetsov.

Mediagraphy: Print and Nonprint Resources.

ERIC Educational Resources Information Center

Educational Media and Technology Yearbook, 1996

1996-01-01

This annotated list includes media-related resources classified under the following headings: artificial intelligence and robotics, CD-ROM, computer-assisted instruction, databases and online searching, distance education, educational research, educational technology, electronic publishing, information science and technology, instructional design…

Mediagraphy: Print and Nonprint Resources.

ERIC Educational Resources Information Center

Educational Media and Technology Yearbook, 1997

1997-01-01

This annotated list includes media-related resources classified under the following headings: artificial intelligence and robotics, CD-ROM, computer-assisted instruction, databases and online searching, distance education, educational research, educational technology, electronic publishing, information science and technology, instructional design…

Una Introduccion a los Jovenes con Discapacidades: Bibliografia Anotada. Revisiones de CYDLINE (An Introduction to Youth with Disabilities: Annotated Bibliography. CYDINE Reviews).

ERIC Educational Resources Information Center

Minnesota Univ., Minneapolis. National Center for Youth with Disabilities.

This Spanish-language annotated bibliography describes English-language resources covering a wide range of issues related to disabled youth and their families. The 38 bibliographic citations date from 1980 to 1989 and are grouped into the following categories: psychosocial issues, health issues, educational issues, and community living.…

Expansion of DSSTox: Leveraging public data to create a semantic cheminformatics resource with quality annotations for support of U.S. EPA applications. (American Chemical Society)

EPA Science Inventory

The expansion of chemical-bioassay data in the public domain is a boon to science; however, the difficulty in establishing accurate linkages from CAS registry number (CASRN) to structure, or for properly annotating names and synonyms for a particular structure is well known. DSS...

Teacher's Resource Handbook for Asian Studies: An Annotated Bibliography of Curriculum Materials, Preschool through Grade Twelve.

ERIC Educational Resources Information Center

Hawkins, John N.

This handbook is an annotated bibliography of 1,586 instructional materials for teaching about Asia. Existing materials are identified that can be used by precollegiate teachers of all subject areas. The handbook is arranged by grade levels--preschool to grade 3, grades 4-6, junior high, senior high, and ungraded. Within each section, materials…

Nutrition and the Elderly: A Selected Annotated Bibliography for Nutrition and Health Professionals. Bibliographies of Literature and Agriculture No. 34.

ERIC Educational Resources Information Center

Cox, Evelyn, Comp.; Sandberg, Janet, Comp.

This annotated bibliography of information on nutrition and the elderly was written for nutrition professionals, health care providers, and organizations that work with older adults. The focus is primarily on nutrition in the United States. The bibliography includes 399 citations of both print and nonprint resources that are readily available to…

An Integrated Encyclopedia of DNA Elements in the Human Genome

PubMed Central

2012-01-01

Summary The human genome encodes the blueprint of life, but the function of the vast majority of its nearly three billion bases is unknown. The Encyclopedia of DNA Elements (ENCODE) project has systematically mapped regions of transcription, transcription factor association, chromatin structure, and histone modification. These data enabled us to assign biochemical functions for 80% of the genome, in particular outside of the well-studied protein-coding regions. Many discovered candidate regulatory elements are physically associated with one another and with expressed genes, providing new insights into the mechanisms of gene regulation. The newly identified elements also show a statistical correspondence to sequence variants linked to human disease, and can thereby guide interpretation of this variation. Overall the project provides new insights into the organization and regulation of our genes and genome, and an expansive resource of functional annotations for biomedical research. PMID:22955616

EGASP: the human ENCODE Genome Annotation Assessment Project

PubMed Central

Guigó, Roderic; Flicek, Paul; Abril, Josep F; Reymond, Alexandre; Lagarde, Julien; Denoeud, France; Antonarakis, Stylianos; Ashburner, Michael; Bajic, Vladimir B; Birney, Ewan; Castelo, Robert; Eyras, Eduardo; Ucla, Catherine; Gingeras, Thomas R; Harrow, Jennifer; Hubbard, Tim; Lewis, Suzanna E; Reese, Martin G

2006-01-01

Background We present the results of EGASP, a community experiment to assess the state-of-the-art in genome annotation within the ENCODE regions, which span 1% of the human genome sequence. The experiment had two major goals: the assessment of the accuracy of computational methods to predict protein coding genes; and the overall assessment of the completeness of the current human genome annotations as represented in the ENCODE regions. For the computational prediction assessment, eighteen groups contributed gene predictions. We evaluated these submissions against each other based on a 'reference set' of annotations generated as part of the GENCODE project. These annotations were not available to the prediction groups prior to the submission deadline, so that their predictions were blind and an external advisory committee could perform a fair assessment. Results The best methods had at least one gene transcript correctly predicted for close to 70% of the annotated genes. Nevertheless, the multiple transcript accuracy, taking into account alternative splicing, reached only approximately 40% to 50% accuracy. At the coding nucleotide level, the best programs reached an accuracy of 90% in both sensitivity and specificity. Programs relying on mRNA and protein sequences were the most accurate in reproducing the manually curated annotations. Experimental validation shows that only a very small percentage (3.2%) of the selected 221 computationally predicted exons outside of the existing annotation could be verified. Conclusion This is the first such experiment in human DNA, and we have followed the standards established in a similar experiment, GASP1, in Drosophila melanogaster. We believe the results presented here contribute to the value of ongoing large-scale annotation projects and should guide further experimental methods when being scaled up to the entire human genome sequence. PMID:16925836

Draft genome of the American Eel (Anguilla rostrata).

PubMed

Pavey, Scott A; Laporte, Martin; Normandeau, Eric; Gaudin, Jérémy; Letourneau, Louis; Boisvert, Sébastien; Corbeil, Jacques; Audet, Céline; Bernatchez, Louis

2017-07-01

Freshwater eels (Anguilla sp.) have large economic, cultural, ecological and aesthetic importance worldwide, but they suffered more than 90% decline in global stocks over the past few decades. Proper genetic resources, such as sequenced, assembled and annotated genomes, are essential to help plan sustainable recoveries by identifying physiological, biochemical and genetic mechanisms that caused the declines or that may lead to recoveries. Here, we present the first sequenced genome of the American eel. This genome contained 305 043 contigs (N50 = 7397) and 79 209 scaffolds (N50 = 86 641) for a total size of 1.41 Gb, which is in the middle of the range of previous estimations for this species. In addition, protein-coding regions, including introns and flanking regions, are very well represented in the genome, as 95.2% of the 458 core eukaryotic genes and 98.8% of the 248 ultra-conserved subset were represented in the assembly and a total of 26 564 genes were annotated for future functional genomics studies. We performed a candidate gene analysis to compare three genes among all three freshwater eel species and, congruent with the phylogenetic relationships, Japanese eel (A. japanica) exhibited the most divergence. Overall, the sequenced genome presented in this study is a crucial addition to the presently available genetic tools to help guide future conservation efforts of freshwater eels. © 2016 John Wiley & Sons Ltd.

Experimental annotation of post-translational features and translated coding regions in the pathogen Salmonella Typhimurium

DOE Office of Scientific and Technical Information (OSTI.GOV)

Ansong, Charles; Tolic, Nikola; Purvine, Samuel O.

Complete and accurate genome annotation is crucial for comprehensive and systematic studies of biological systems. For example systems biology-oriented genome scale modeling efforts greatly benefit from accurate annotation of protein-coding genes to develop proper functioning models. However, determining protein-coding genes for most new genomes is almost completely performed by inference, using computational predictions with significant documented error rates (> 15%). Furthermore, gene prediction programs provide no information on biologically important post-translational processing events critical for protein function. With the ability to directly measure peptides arising from expressed proteins, mass spectrometry-based proteomics approaches can be used to augment and verify codingmore » regions of a genomic sequence and importantly detect post-translational processing events. In this study we utilized “shotgun” proteomics to guide accurate primary genome annotation of the bacterial pathogen Salmonella Typhimurium 14028 to facilitate a systems-level understanding of Salmonella biology. The data provides protein-level experimental confirmation for 44% of predicted protein-coding genes, suggests revisions to 48 genes assigned incorrect translational start sites, and uncovers 13 non-annotated genes missed by gene prediction programs. We also present a comprehensive analysis of post-translational processing events in Salmonella, revealing a wide range of complex chemical modifications (70 distinct modifications) and confirming more than 130 signal peptide and N-terminal methionine cleavage events in Salmonella. This study highlights several ways in which proteomics data applied during the primary stages of annotation can improve the quality of genome annotations, especially with regards to the annotation of mature protein products.« less

Ethnic Heritage Project General Bibliography.

ERIC Educational Resources Information Center

Berman, Edward H.

The document lists approximately 280 ethnic heritage-related materials. Bibliographic citations for anthologies, plays, speeches, autobiographies, films, filmstrips, study guides, curriculum outlines, learning activities, and critical and historical studies for works published from 1950 through 1976 are annotated. The materials consider cultural…

A Selective Bibliography on School Materials: Selection and Censorship.

ERIC Educational Resources Information Center

Folke, Carolyn, Comp.

Prepared as a guide for Wisconsin school administrators selecting school instructional materials, this bibliography provides annotations of 57 useful readings on the selection and censorship of school materials. Journal articles, monographs, and ERIC documents are included. (RAA)

The Chinchilla Research Resource Database: resource for an otolaryngology disease model

PubMed Central

Shimoyama, Mary; Smith, Jennifer R.; De Pons, Jeff; Tutaj, Marek; Khampang, Pawjai; Hong, Wenzhou; Erbe, Christy B.; Ehrlich, Garth D.; Bakaletz, Lauren O.; Kerschner, Joseph E.

2016-01-01

The long-tailed chinchilla (Chinchilla lanigera) is an established animal model for diseases of the inner and middle ear, among others. In particular, chinchilla is commonly used to study diseases involving viral and bacterial pathogens and polymicrobial infections of the upper respiratory tract and the ear, such as otitis media. The value of the chinchilla as a model for human diseases prompted the sequencing of its genome in 2012 and the more recent development of the Chinchilla Research Resource Database (http://crrd.mcw.edu) to provide investigators with easy access to relevant datasets and software tools to enhance their research. The Chinchilla Research Resource Database contains a complete catalog of genes for chinchilla and, for comparative purposes, human. Chinchilla genes can be viewed in the context of their genomic scaffold positions using the JBrowse genome browser. In contrast to the corresponding records at NCBI, individual gene reports at CRRD include functional annotations for Disease, Gene Ontology (GO) Biological Process, GO Molecular Function, GO Cellular Component and Pathway assigned to chinchilla genes based on annotations from the corresponding human orthologs. Data can be retrieved via keyword and gene-specific searches. Lists of genes with similar functional attributes can be assembled by leveraging the hierarchical structure of the Disease, GO and Pathway vocabularies through the Ontology Search and Browser tool. Such lists can then be further analyzed for commonalities using the Gene Annotator (GA) Tool. All data in the Chinchilla Research Resource Database is freely accessible and downloadable via the CRRD FTP site or using the download functions available in the search and analysis tools. The Chinchilla Research Resource Database is a rich resource for researchers using, or considering the use of, chinchilla as a model for human disease. Database URL: http://crrd.mcw.edu PMID:27173523

Mediagraphy: Print and Nonprint Resources.

ERIC Educational Resources Information Center

Price, Brooke, Ed.

2001-01-01

Lists media-related journals, books, ERIC documents, journal articles, and nonprint resources published in 1999-2000. The annotated entries are classified under the following headings: artificial intelligence; computer assisted instruction; distance education; educational research; educational technology; information science and technology;…

Mediagraphy: Print and Nonprint Resources.

ERIC Educational Resources Information Center

Burdett, Anna E.

2003-01-01

Lists media-related journals, books, ERIC documents, journal articles, and nonprint resources published in 2001-2002. The annotated entries are classified under the following headings: artificial intelligence; computer assisted instruction; distance education; educational research; educational technology; information science and technology;…

Resource Letter PE-1: Physics and the Environment

ERIC Educational Resources Information Center

Shonle, John I.

1974-01-01

Presents a Resource Letter on air pollution, noise pollution, transportation, and solid waste for the purpose of acquainting college physicists with some of the literature and teaching aids. Included are five bibliographies of which four are annotated. (CC)

A method for the development of disease-specific reference standards vocabularies from textual biomedical literature resources

PubMed Central

Wang, Liqin; Bray, Bruce E.; Shi, Jianlin; Fiol, Guilherme Del; Haug, Peter J.

2017-01-01

Objective Disease-specific vocabularies are fundamental to many knowledge-based intelligent systems and applications like text annotation, cohort selection, disease diagnostic modeling, and therapy recommendation. Reference standards are critical in the development and validation of automated methods for disease-specific vocabularies. The goal of the present study is to design and test a generalizable method for the development of vocabulary reference standards from expert-curated, disease-specific biomedical literature resources. Methods We formed disease-specific corpora from literature resources like textbooks, evidence-based synthesized online sources, clinical practice guidelines, and journal articles. Medical experts annotated and adjudicated disease-specific terms in four classes (i.e., causes or risk factors, signs or symptoms, diagnostic tests or results, and treatment). Annotations were mapped to UMLS concepts. We assessed source variation, the contribution of each source to build disease-specific vocabularies, the saturation of the vocabularies with respect to the number of used sources, and the generalizability of the method with different diseases. Results The study resulted in 2588 string-unique annotations for heart failure in four classes, and 193 and 425 respectively for pulmonary embolism and rheumatoid arthritis in treatment class. Approximately 80% of the annotations were mapped to UMLS concepts. The agreement among heart failure sources ranged between 0.28 and 0.46. The contribution of these sources to the final vocabulary ranged between 18% and 49%. With the sources explored, the heart failure vocabulary reached near saturation in all four classes with the inclusion of minimal six sources (or between four to seven sources if only counting terms occurred in two or more sources). It took fewer sources to reach near saturation for the other two diseases in terms of the treatment class. Conclusions We developed a method for the development of disease-specific reference vocabularies. Expert-curated biomedical literature resources are substantial for acquiring disease-specific medical knowledge. It is feasible to reach near saturation in a disease-specific vocabulary using a relatively small number of literature sources. PMID:26971304

AnnoSys—implementation of a generic annotation system for schema-based data using the example of biodiversity collection data

PubMed Central

Kusber, W.-H.; Tschöpe, O.; Güntsch, A.; Berendsohn, W. G.

2017-01-01

Abstract Biological research collections holding billions of specimens world-wide provide the most important baseline information for systematic biodiversity research. Increasingly, specimen data records become available in virtual herbaria and data portals. The traditional (physical) annotation procedure fails here, so that an important pathway of research documentation and data quality control is broken. In order to create an online annotation system, we analysed, modeled and adapted traditional specimen annotation workflows. The AnnoSys system accesses collection data from either conventional web resources or the Biological Collection Access Service (BioCASe) and accepts XML-based data standards like ABCD or DarwinCore. It comprises a searchable annotation data repository, a user interface, and a subscription based message system. We describe the main components of AnnoSys and its current and planned interoperability with biodiversity data portals and networks. Details are given on the underlying architectural model, which implements the W3C OpenAnnotation model and allows the adaptation of AnnoSys to different problem domains. Advantages and disadvantages of different digital annotation and feedback approaches are discussed. For the biodiversity domain, AnnoSys proposes best practice procedures for digital annotations of complex records. Database URL: https://annosys.bgbm.fu-berlin.de/AnnoSys/AnnoSys PMID:28365735

Autobiographical and Biographical Resources for History of Psychology.

ERIC Educational Resources Information Center

Ware, Mark E.

This document presents a variety of resources for students to use in preparing class presentations and historical research projects on the history of psychology. The resources pertain to historical figures in the field of psychology. Many of the references included in this bibliography are annotated and the names of the psychologists contained…

Using Linked Data to Annotate and Search Educational Video Resources for Supporting Distance Learning

ERIC Educational Resources Information Center

Yu, Hong Qing; Pedrinaci, C.; Dietze, S.; Domingue, J.

2012-01-01

Multimedia educational resources play an important role in education, particularly for distance learning environments. With the rapid growth of the multimedia web, large numbers of educational video resources are increasingly being created by several different organizations. It is crucial to explore, share, reuse, and link these educational…

Quantum Computing: Selected Internet Resources for Librarians, Researchers, and the Casually Curious

ERIC Educational Resources Information Center

Cirasella, Jill

2009-01-01

This article presents an annotated selection of the most important and informative Internet resources for learning about quantum computing, finding quantum computing literature, and tracking quantum computing news. All of the quantum computing resources described in this article are freely available, English-language web sites that fall into one…

Native Peoples: Department of Education Resources Pertaining to Indians, Inuit, and Metis. Curriculum Support Series.

ERIC Educational Resources Information Center

Manitoba Dept. of Education, Winnipeg.

Intended for teachers, librarians, and other interested people, the annotated listing contains citations for multimedia resources pertaining to North American Indians, Inuits, and Metis, available from the Manitoba Department of Education Library, Film Services, and School Broadcasts. Titles of over 900 resources, many published since 1960, are…

AggNet: Deep Learning From Crowds for Mitosis Detection in Breast Cancer Histology Images.

PubMed

Albarqouni, Shadi; Baur, Christoph; Achilles, Felix; Belagiannis, Vasileios; Demirci, Stefanie; Navab, Nassir

2016-05-01

The lack of publicly available ground-truth data has been identified as the major challenge for transferring recent developments in deep learning to the biomedical imaging domain. Though crowdsourcing has enabled annotation of large scale databases for real world images, its application for biomedical purposes requires a deeper understanding and hence, more precise definition of the actual annotation task. The fact that expert tasks are being outsourced to non-expert users may lead to noisy annotations introducing disagreement between users. Despite being a valuable resource for learning annotation models from crowdsourcing, conventional machine-learning methods may have difficulties dealing with noisy annotations during training. In this manuscript, we present a new concept for learning from crowds that handle data aggregation directly as part of the learning process of the convolutional neural network (CNN) via additional crowdsourcing layer (AggNet). Besides, we present an experimental study on learning from crowds designed to answer the following questions. 1) Can deep CNN be trained with data collected from crowdsourcing? 2) How to adapt the CNN to train on multiple types of annotation datasets (ground truth and crowd-based)? 3) How does the choice of annotation and aggregation affect the accuracy? Our experimental setup involved Annot8, a self-implemented web-platform based on Crowdflower API realizing image annotation tasks for a publicly available biomedical image database. Our results give valuable insights into the functionality of deep CNN learning from crowd annotations and prove the necessity of data aggregation integration.

Type-Separated Bytecode - Its Construction and Evaluation

NASA Astrophysics Data System (ADS)

Adler, Philipp; Amme, Wolfram

A lot of constrained systems still use interpreters to run mobile applications written in Java. These interpreters demand for only a few resources. On the other hand, it is difficult to apply optimizations during the runtime of the application. Annotations could be used to achieve a simpler and faster code analysis, which would allow optimizations even for interpreters on constrained devices. Unfortunately, there is no viable way of transporting annotations to and verifying them at the code consumer. In this paper we present type-separated bytecode as an intermediate representation which allows to safely transport annotations as type-extensions. We have implemented several versions of this system and show that it is possible to obtain a performance comparable to Java Bytecode, even though we use a type-separated system with annotations.

The aquatic animals' transcriptome resource for comparative functional analysis.

PubMed

Chou, Chih-Hung; Huang, Hsi-Yuan; Huang, Wei-Chih; Hsu, Sheng-Da; Hsiao, Chung-Der; Liu, Chia-Yu; Chen, Yu-Hung; Liu, Yu-Chen; Huang, Wei-Yun; Lee, Meng-Lin; Chen, Yi-Chang; Huang, Hsien-Da

2018-05-09

Aquatic animals have great economic and ecological importance. Among them, non-model organisms have been studied regarding eco-toxicity, stress biology, and environmental adaptation. Due to recent advances in next-generation sequencing techniques, large amounts of RNA-seq data for aquatic animals are publicly available. However, currently there is no comprehensive resource exist for the analysis, unification, and integration of these datasets. This study utilizes computational approaches to build a new resource of transcriptomic maps for aquatic animals. This aquatic animal transcriptome map database dbATM provides de novo assembly of transcriptome, gene annotation and comparative analysis of more than twenty aquatic organisms without draft genome. To improve the assembly quality, three computational tools (Trinity, Oases and SOAPdenovo-Trans) were employed to enhance individual transcriptome assembly, and CAP3 and CD-HIT-EST software were then used to merge these three assembled transcriptomes. In addition, functional annotation analysis provides valuable clues to gene characteristics, including full-length transcript coding regions, conserved domains, gene ontology and KEGG pathways. Furthermore, all aquatic animal genes are essential for comparative genomics tasks such as constructing homologous gene groups and blast databases and phylogenetic analysis. In conclusion, we establish a resource for non model organism aquatic animals, which is great economic and ecological importance and provide transcriptomic information including functional annotation and comparative transcriptome analysis. The database is now publically accessible through the URL http://dbATM.mbc.nctu.edu.tw/ .

School/Work Transition. A Bibliography.

ERIC Educational Resources Information Center

Florida State Univ., Tallahassee. Center for Instructional Development and Services.

This annotated bibliography contains 55 citations of materials that contain information on transitional programs for the physically or mentally challenged or disadvantaged students. Citations include descriptive, evaluative, and research reports; guides; information analyses; opinion papers; and reference materials. Materials for inclusion in this…

Developing a disease outbreak event corpus.

PubMed

Conway, Mike; Kawazoe, Ai; Chanlekha, Hutchatai; Collier, Nigel

2010-09-28

In recent years, there has been a growth in work on the use of information extraction technologies for tracking disease outbreaks from online news texts, yet publicly available evaluation standards (and associated resources) for this new area of research have been noticeably lacking. This study seeks to create a "gold standard" data set against which to test how accurately disease outbreak information extraction systems can identify the semantics of disease outbreak events. Additionally, we hope that the provision of an annotation scheme (and associated corpus) to the community will encourage open evaluation in this new and growing application area. We developed an annotation scheme for identifying infectious disease outbreak events in news texts. An event--in the context of our annotation scheme--consists minimally of geographical (eg, country and province) and disease name information. However, the scheme also allows for the rich encoding of other domain salient concepts (eg, international travel, species, and food contamination). The work resulted in a 200-document corpus of event-annotated disease outbreak reports that can be used to evaluate the accuracy of event detection algorithms (in this case, for the BioCaster biosurveillance online news information extraction system). In the 200 documents, 394 distinct events were identified (mean 1.97 events per document, range 0-25 events per document). We also provide a download script and graphical user interface (GUI)-based event browsing software to facilitate corpus exploration. In summary, we present an annotation scheme and corpus that can be used in the evaluation of disease outbreak event extraction algorithms. The annotation scheme and corpus were designed both with the particular evaluation requirements of the BioCaster system in mind as well as the wider need for further evaluation resources in this growing research area.

The Bologna Annotation Resource (BAR 3.0): improving protein functional annotation

PubMed Central

Casadio, Rita

2017-01-01

Abstract BAR 3.0 updates our server BAR (Bologna Annotation Resource) for predicting protein structural and functional features from sequence. We increase data volume, query capabilities and information conveyed to the user. The core of BAR 3.0 is a graph-based clustering procedure of UniProtKB sequences, following strict pairwise similarity criteria (sequence identity ≥40% with alignment coverage ≥90%). Each cluster contains the available annotation downloaded from UniProtKB, GO, PFAM and PDB. After statistical validation, GO terms and PFAM domains are cluster-specific and annotate new sequences entering the cluster after satisfying similarity constraints. BAR 3.0 includes 28 869 663 sequences in 1 361 773 clusters, of which 22.2% (22 241 661 sequences) and 47.4% (24 555 055 sequences) have at least one validated GO term and one PFAM domain, respectively. 1.4% of the clusters (36% of all sequences) include PDB structures and the cluster is associated to a hidden Markov model that allows building template-target alignment suitable for structural modeling. Some other 3 399 026 sequences are singletons. BAR 3.0 offers an improved search interface, allowing queries by UniProtKB-accession, Fasta sequence, GO-term, PFAM-domain, organism, PDB and ligand/s. When evaluated on the CAFA2 targets, BAR 3.0 largely outperforms our previous version and scores among state-of-the-art methods. BAR 3.0 is publicly available and accessible at http://bar.biocomp.unibo.it/bar3. PMID:28453653

Collective dynamics of social annotation

PubMed Central

Cattuto, Ciro; Barrat, Alain; Baldassarri, Andrea; Schehr, Gregory; Loreto, Vittorio

2009-01-01

The enormous increase of popularity and use of the worldwide web has led in the recent years to important changes in the ways people communicate. An interesting example of this fact is provided by the now very popular social annotation systems, through which users annotate resources (such as web pages or digital photographs) with keywords known as “tags.” Understanding the rich emergent structures resulting from the uncoordinated actions of users calls for an interdisciplinary effort. In particular concepts borrowed from statistical physics, such as random walks (RWs), and complex networks theory, can effectively contribute to the mathematical modeling of social annotation systems. Here, we show that the process of social annotation can be seen as a collective but uncoordinated exploration of an underlying semantic space, pictured as a graph, through a series of RWs. This modeling framework reproduces several aspects, thus far unexplained, of social annotation, among which are the peculiar growth of the size of the vocabulary used by the community and its complex network structure that represents an externalization of semantic structures grounded in cognition and that are typically hard to access. PMID:19506244

A large-scale evaluation of computational protein function prediction

PubMed Central

Radivojac, Predrag; Clark, Wyatt T; Ronnen Oron, Tal; Schnoes, Alexandra M; Wittkop, Tobias; Sokolov, Artem; Graim, Kiley; Funk, Christopher; Verspoor, Karin; Ben-Hur, Asa; Pandey, Gaurav; Yunes, Jeffrey M; Talwalkar, Ameet S; Repo, Susanna; Souza, Michael L; Piovesan, Damiano; Casadio, Rita; Wang, Zheng; Cheng, Jianlin; Fang, Hai; Gough, Julian; Koskinen, Patrik; Törönen, Petri; Nokso-Koivisto, Jussi; Holm, Liisa; Cozzetto, Domenico; Buchan, Daniel W A; Bryson, Kevin; Jones, David T; Limaye, Bhakti; Inamdar, Harshal; Datta, Avik; Manjari, Sunitha K; Joshi, Rajendra; Chitale, Meghana; Kihara, Daisuke; Lisewski, Andreas M; Erdin, Serkan; Venner, Eric; Lichtarge, Olivier; Rentzsch, Robert; Yang, Haixuan; Romero, Alfonso E; Bhat, Prajwal; Paccanaro, Alberto; Hamp, Tobias; Kassner, Rebecca; Seemayer, Stefan; Vicedo, Esmeralda; Schaefer, Christian; Achten, Dominik; Auer, Florian; Böhm, Ariane; Braun, Tatjana; Hecht, Maximilian; Heron, Mark; Hönigschmid, Peter; Hopf, Thomas; Kaufmann, Stefanie; Kiening, Michael; Krompass, Denis; Landerer, Cedric; Mahlich, Yannick; Roos, Manfred; Björne, Jari; Salakoski, Tapio; Wong, Andrew; Shatkay, Hagit; Gatzmann, Fanny; Sommer, Ingolf; Wass, Mark N; Sternberg, Michael J E; Škunca, Nives; Supek, Fran; Bošnjak, Matko; Panov, Panče; Džeroski, Sašo; Šmuc, Tomislav; Kourmpetis, Yiannis A I; van Dijk, Aalt D J; ter Braak, Cajo J F; Zhou, Yuanpeng; Gong, Qingtian; Dong, Xinran; Tian, Weidong; Falda, Marco; Fontana, Paolo; Lavezzo, Enrico; Di Camillo, Barbara; Toppo, Stefano; Lan, Liang; Djuric, Nemanja; Guo, Yuhong; Vucetic, Slobodan; Bairoch, Amos; Linial, Michal; Babbitt, Patricia C; Brenner, Steven E; Orengo, Christine; Rost, Burkhard; Mooney, Sean D; Friedberg, Iddo

2013-01-01

Automated annotation of protein function is challenging. As the number of sequenced genomes rapidly grows, the overwhelming majority of protein products can only be annotated computationally. If computational predictions are to be relied upon, it is crucial that the accuracy of these methods be high. Here we report the results from the first large-scale community-based Critical Assessment of protein Function Annotation (CAFA) experiment. Fifty-four methods representing the state-of-the-art for protein function prediction were evaluated on a target set of 866 proteins from eleven organisms. Two findings stand out: (i) today’s best protein function prediction algorithms significantly outperformed widely-used first-generation methods, with large gains on all types of targets; and (ii) although the top methods perform well enough to guide experiments, there is significant need for improvement of currently available tools. PMID:23353650

The coffee genome hub: a resource for coffee genomes

PubMed Central

Dereeper, Alexis; Bocs, Stéphanie; Rouard, Mathieu; Guignon, Valentin; Ravel, Sébastien; Tranchant-Dubreuil, Christine; Poncet, Valérie; Garsmeur, Olivier; Lashermes, Philippe; Droc, Gaëtan

2015-01-01

The whole genome sequence of Coffea canephora, the perennial diploid species known as Robusta, has been recently released. In the context of the C. canephora genome sequencing project and to support post-genomics efforts, we developed the Coffee Genome Hub (http://coffee-genome.org/), an integrative genome information system that allows centralized access to genomics and genetics data and analysis tools to facilitate translational and applied research in coffee. We provide the complete genome sequence of C. canephora along with gene structure, gene product information, metabolism, gene families, transcriptomics, syntenic blocks, genetic markers and genetic maps. The hub relies on generic software (e.g. GMOD tools) for easy querying, visualizing and downloading research data. It includes a Genome Browser enhanced by a Community Annotation System, enabling the improvement of automatic gene annotation through an annotation editor. In addition, the hub aims at developing interoperability among other existing South Green tools managing coffee data (phylogenomics resources, SNPs) and/or supporting data analyses with the Galaxy workflow manager. PMID:25392413

Teacher Resources Catalogue.

ERIC Educational Resources Information Center

Alberta Dept. of Education, Edmonton. Special Educational Services Branch.

This annotated bibliography contains approximately 90 selected print and media resources to help Alberta (Canada) teachers implement special education programs. Items were selected to ensure that content fits the curriculum, the content is current, the conceptual level is appropriate, there is Canadian content, and controversial issues are treated…

The Feds and the Environment.

ERIC Educational Resources Information Center

Coyle, Daniel

1979-01-01

Lists and annotates recurrent federal publications that contain basic statistical data on pollution levels and controls, natural resources and wildlife conservation, water resources supply and development, weather and ocean conditions, federal aid programs, and the environmental impact of energy development. It also lists continuing bibliographies…

Resources for Community Organizing.

ERIC Educational Resources Information Center

Valadez, Cristina, Comp.

This document is composed of two parts: a bibliography of community organizing and support materials and a directory of community organizing resource centers. The 25 bibliographic entries are grouped according to subject, and include author, title, publication date, publisher, number of pages, annotation, and ordering information. Subjects…

Semantic annotation of consumer health questions.

PubMed

Kilicoglu, Halil; Ben Abacha, Asma; Mrabet, Yassine; Shooshan, Sonya E; Rodriguez, Laritza; Masterton, Kate; Demner-Fushman, Dina

2018-02-06

Consumers increasingly use online resources for their health information needs. While current search engines can address these needs to some extent, they generally do not take into account that most health information needs are complex and can only fully be expressed in natural language. Consumer health question answering (QA) systems aim to fill this gap. A major challenge in developing consumer health QA systems is extracting relevant semantic content from the natural language questions (question understanding). To develop effective question understanding tools, question corpora semantically annotated for relevant question elements are needed. In this paper, we present a two-part consumer health question corpus annotated with several semantic categories: named entities, question triggers/types, question frames, and question topic. The first part (CHQA-email) consists of relatively long email requests received by the U.S. National Library of Medicine (NLM) customer service, while the second part (CHQA-web) consists of shorter questions posed to MedlinePlus search engine as queries. Each question has been annotated by two annotators. The annotation methodology is largely the same between the two parts of the corpus; however, we also explain and justify the differences between them. Additionally, we provide information about corpus characteristics, inter-annotator agreement, and our attempts to measure annotation confidence in the absence of adjudication of annotations. The resulting corpus consists of 2614 questions (CHQA-email: 1740, CHQA-web: 874). Problems are the most frequent named entities, while treatment and general information questions are the most common question types. Inter-annotator agreement was generally modest: question types and topics yielded highest agreement, while the agreement for more complex frame annotations was lower. Agreement in CHQA-web was consistently higher than that in CHQA-email. Pairwise inter-annotator agreement proved most useful in estimating annotation confidence. To our knowledge, our corpus is the first focusing on annotation of uncurated consumer health questions. It is currently used to develop machine learning-based methods for question understanding. We make the corpus publicly available to stimulate further research on consumer health QA.

Netbook User’s Guide and Installation Manual.

DTIC Science & Technology

1997-01-31

The general purpose of Netbook is to add value to the information available online, by developing a collaborative environment within which that...information can be effectively accessed, stored, annotated, and structured. Netbook is a prototype tool that provides users with the capacity for

Selected Reference Books of 1971-72

ERIC Educational Resources Information Center

Sheehy, Eugene P.

1973-01-01

The purpose of this annotated list is to present a selection of recent scholarly and foreign works of interest to reference workers in university libraries. The citations are listed under the following headings: guide, bibliography, encyclopedias, dictionaries, newspapers, dissertations, biography, genealogy, literature, education, sociology,…

Realistic Library Research Methods: Bibliographic Sources Annotated.

ERIC Educational Resources Information Center

Kushon, Susan G.; Wells, Bernice

This guide gives an overview of basic library research methods with emphasis upon developing an understanding of library organization and professional services. Commonly used bibliographic techniques are described for various published and unpublished, print and nonprint materials. Standard reference sources (bibliographies, encyclopedias, annual…

Entrepreneurship Education Materials.

ERIC Educational Resources Information Center

Muzzo, John F., Ed.; And Others

This annotated bibliography is intended to provide instructors and trainers with a variety of materials that may be used to design or supplement a self-employment/small business management training program. The materials listed include lesson plans, handbooks, workbooks, textbooks, tests, test keys, instruction guides, videocassettes, pamphlets,…

The what, where, how and why of gene ontology—a primer for bioinformaticians

PubMed Central

du Plessis, Louis; Škunca, Nives

2011-01-01

With high-throughput technologies providing vast amounts of data, it has become more important to provide systematic, quality annotations. The Gene Ontology (GO) project is the largest resource for cataloguing gene function. Nonetheless, its use is not yet ubiquitous and is still fraught with pitfalls. In this review, we provide a short primer to the GO for bioinformaticians. We summarize important aspects of the structure of the ontology, describe sources and types of functional annotations, survey measures of GO annotation similarity, review typical uses of GO and discuss other important considerations pertaining to the use of GO in bioinformatics applications. PMID:21330331

Natural-Annotation-based Unsupervised Construction of Korean-Chinese Domain Dictionary

NASA Astrophysics Data System (ADS)

Liu, Wuying; Wang, Lin

2018-03-01

The large-scale bilingual parallel resource is significant to statistical learning and deep learning in natural language processing. This paper addresses the automatic construction issue of the Korean-Chinese domain dictionary, and presents a novel unsupervised construction method based on the natural annotation in the raw corpus. We firstly extract all Korean-Chinese word pairs from Korean texts according to natural annotations, secondly transform the traditional Chinese characters into the simplified ones, and finally distill out a bilingual domain dictionary after retrieving the simplified Chinese words in an extra Chinese domain dictionary. The experimental results show that our method can automatically build multiple Korean-Chinese domain dictionaries efficiently.

Gifted Gay, Lesbian, Bisexual, and Transgender Annotated Bibliography: A Resource for Educators of Gifted Secondary GLBT Students

ERIC Educational Resources Information Center

Treat, Alena R.; Whittenburg, Becky

2006-01-01

This bibliography makes available to educators and others a comprehensive resource for information regarding gifted youth who are gay, lesbian, bisexual, transgender or questioning their sexual orientation and/or gender identity (G/GLBTQ). It includes articles, brochures, books, lesson plans, staff development, video media, and Web resources. As…

Parental Involvement in the Educational Process of Children with Special Needs. An Annotated Report. [Final Report] and Research Analysis.

ERIC Educational Resources Information Center

Kreger, Robert D.

A listing of resources is presented for parents of handicapped children. Resources are categorized according to the following types: programs, organizations, products, and additional resources; federally funded programs; national parent organizations; local parent training; and handbooks, book lists, and media. Entries are organized according to…

Pseudomonas Genome Database: facilitating user-friendly, comprehensive comparisons of microbial genomes.

PubMed

Winsor, Geoffrey L; Van Rossum, Thea; Lo, Raymond; Khaira, Bhavjinder; Whiteside, Matthew D; Hancock, Robert E W; Brinkman, Fiona S L

2009-01-01

Pseudomonas aeruginosa is a well-studied opportunistic pathogen that is particularly known for its intrinsic antimicrobial resistance, diverse metabolic capacity, and its ability to cause life threatening infections in cystic fibrosis patients. The Pseudomonas Genome Database (http://www.pseudomonas.com) was originally developed as a resource for peer-reviewed, continually updated annotation for the Pseudomonas aeruginosa PAO1 reference strain genome. In order to facilitate cross-strain and cross-species genome comparisons with other Pseudomonas species of importance, we have now expanded the database capabilities to include all Pseudomonas species, and have developed or incorporated methods to facilitate high quality comparative genomics. The database contains robust assessment of orthologs, a novel ortholog clustering method, and incorporates five views of the data at the sequence and annotation levels (Gbrowse, Mauve and custom views) to facilitate genome comparisons. A choice of simple and more flexible user-friendly Boolean search features allows researchers to search and compare annotations or sequences within or between genomes. Other features include more accurate protein subcellular localization predictions and a user-friendly, Boolean searchable log file of updates for the reference strain PAO1. This database aims to continue to provide a high quality, annotated genome resource for the research community and is available under an open source license.

Crowdsourcing for error detection in cortical surface delineations.

PubMed

Ganz, Melanie; Kondermann, Daniel; Andrulis, Jonas; Knudsen, Gitte Moos; Maier-Hein, Lena

2017-01-01

With the recent trend toward big data analysis, neuroimaging datasets have grown substantially in the past years. While larger datasets potentially offer important insights for medical research, one major bottleneck is the requirement for resources of medical experts needed to validate automatic processing results. To address this issue, the goal of this paper was to assess whether anonymous nonexperts from an online community can perform quality control of MR-based cortical surface delineations derived by an automatic algorithm. So-called knowledge workers from an online crowdsourcing platform were asked to annotate errors in automatic cortical surface delineations on 100 central, coronal slices of MR images. On average, annotations for 100 images were obtained in less than an hour. When using expert annotations as reference, the crowd on average achieves a sensitivity of 82 % and a precision of 42 %. Merging multiple annotations per image significantly improves the sensitivity of the crowd (up to 95 %), but leads to a decrease in precision (as low as 22 %). Our experiments show that the detection of errors in automatic cortical surface delineations generated by anonymous untrained workers is feasible. Future work will focus on increasing the sensitivity of our method further, such that the error detection tasks can be handled exclusively by the crowd and expert resources can be focused on error correction.

The Eimeria Transcript DB: an integrated resource for annotated transcripts of protozoan parasites of the genus Eimeria

PubMed Central

Rangel, Luiz Thibério; Novaes, Jeniffer; Durham, Alan M.; Madeira, Alda Maria B. N.; Gruber, Arthur

2013-01-01

Parasites of the genus Eimeria infect a wide range of vertebrate hosts, including chickens. We have recently reported a comparative analysis of the transcriptomes of Eimeria acervulina, Eimeria maxima and Eimeria tenella, integrating ORESTES data produced by our group and publicly available Expressed Sequence Tags (ESTs). All cDNA reads have been assembled, and the reconstructed transcripts have been submitted to a comprehensive functional annotation pipeline. Additional studies included orthology assignment across apicomplexan parasites and clustering analyses of gene expression profiles among different developmental stages of the parasites. To make all this body of information publicly available, we constructed the Eimeria Transcript Database (EimeriaTDB), a web repository that provides access to sequence data, annotation and comparative analyses. Here, we describe the web interface, available sequence data sets and query tools implemented on the site. The main goal of this work is to offer a public repository of sequence and functional annotation data of reconstructed transcripts of parasites of the genus Eimeria. We believe that EimeriaTDB will represent a valuable and complementary resource for the Eimeria scientific community and for those researchers interested in comparative genomics of apicomplexan parasites. Database URL: http://www.coccidia.icb.usp.br/eimeriatdb/ PMID:23411718

The history of the CATH structural classification of protein domains.

PubMed

Sillitoe, Ian; Dawson, Natalie; Thornton, Janet; Orengo, Christine

2015-12-01

This article presents a historical review of the protein structure classification database CATH. Together with the SCOP database, CATH remains comprehensive and reasonably up-to-date with the now more than 100,000 protein structures in the PDB. We review the expansion of the CATH and SCOP resources to capture predicted domain structures in the genome sequence data and to provide information on the likely functions of proteins mediated by their constituent domains. The establishment of comprehensive function annotation resources has also meant that domain families can be functionally annotated allowing insights into functional divergence and evolution within protein families. Copyright © 2015 The Authors. Published by Elsevier B.V. All rights reserved.

COMP Superscalar, an interoperable programming framework

NASA Astrophysics Data System (ADS)

Badia, Rosa M.; Conejero, Javier; Diaz, Carlos; Ejarque, Jorge; Lezzi, Daniele; Lordan, Francesc; Ramon-Cortes, Cristian; Sirvent, Raul

2015-12-01

COMPSs is a programming framework that aims to facilitate the parallelization of existing applications written in Java, C/C++ and Python scripts. For that purpose, it offers a simple programming model based on sequential development in which the user is mainly responsible for (i) identifying the functions to be executed as asynchronous parallel tasks and (ii) annotating them with annotations or standard Python decorators. A runtime system is in charge of exploiting the inherent concurrency of the code, automatically detecting and enforcing the data dependencies between tasks and spawning these tasks to the available resources, which can be nodes in a cluster, clouds or grids. In cloud environments, COMPSs provides scalability and elasticity features allowing the dynamic provision of resources.

DNASU plasmid and PSI:Biology-Materials repositories: resources to accelerate biological research

PubMed Central

Seiler, Catherine Y.; Park, Jin G.; Sharma, Amit; Hunter, Preston; Surapaneni, Padmini; Sedillo, Casey; Field, James; Algar, Rhys; Price, Andrea; Steel, Jason; Throop, Andrea; Fiacco, Michael; LaBaer, Joshua

2014-01-01

The mission of the DNASU Plasmid Repository is to accelerate research by providing high-quality, annotated plasmid samples and online plasmid resources to the research community through the curated DNASU database, website and repository (http://dnasu.asu.edu or http://dnasu.org). The collection includes plasmids from grant-funded, high-throughput cloning projects performed in our laboratory, plasmids from external researchers, and large collections from consortia such as the ORFeome Collaboration and the NIGMS-funded Protein Structure Initiative: Biology (PSI:Biology). Through DNASU, researchers can search for and access detailed information about each plasmid such as the full length gene insert sequence, vector information, associated publications, and links to external resources that provide additional protein annotations and experimental protocols. Plasmids can be requested directly through the DNASU website. DNASU and the PSI:Biology-Materials Repositories were previously described in the 2010 NAR Database Issue (Cormier, C.Y., Mohr, S.E., Zuo, D., Hu, Y., Rolfs, A., Kramer, J., Taycher, E., Kelley, F., Fiacco, M., Turnbull, G. et al. (2010) Protein Structure Initiative Material Repository: an open shared public resource of structural genomics plasmids for the biological community. Nucleic Acids Res., 38, D743–D749.). In this update we will describe the plasmid collection and highlight the new features in the website redesign, including new browse/search options, plasmid annotations and a dynamic vector mapping feature that was developed in collaboration with LabGenius. Overall, these plasmid resources continue to enable research with the goal of elucidating the role of proteins in both normal biological processes and disease. PMID:24225319

High-throughput comparison, functional annotation, and metabolic modeling of plant genomes using the PlantSEED resource

PubMed Central

Seaver, Samuel M. D.; Gerdes, Svetlana; Frelin, Océane; Lerma-Ortiz, Claudia; Bradbury, Louis M. T.; Zallot, Rémi; Hasnain, Ghulam; Niehaus, Thomas D.; El Yacoubi, Basma; Pasternak, Shiran; Olson, Robert; Pusch, Gordon; Overbeek, Ross; Stevens, Rick; de Crécy-Lagard, Valérie; Ware, Doreen; Hanson, Andrew D.; Henry, Christopher S.

2014-01-01

The increasing number of sequenced plant genomes is placing new demands on the methods applied to analyze, annotate, and model these genomes. Today’s annotation pipelines result in inconsistent gene assignments that complicate comparative analyses and prevent efficient construction of metabolic models. To overcome these problems, we have developed the PlantSEED, an integrated, metabolism-centric database to support subsystems-based annotation and metabolic model reconstruction for plant genomes. PlantSEED combines SEED subsystems technology, first developed for microbial genomes, with refined protein families and biochemical data to assign fully consistent functional annotations to orthologous genes, particularly those encoding primary metabolic pathways. Seamless integration with its parent, the prokaryotic SEED database, makes PlantSEED a unique environment for cross-kingdom comparative analysis of plant and bacterial genomes. The consistent annotations imposed by PlantSEED permit rapid reconstruction and modeling of primary metabolism for all plant genomes in the database. This feature opens the unique possibility of model-based assessment of the completeness and accuracy of gene annotation and thus allows computational identification of genes and pathways that are restricted to certain genomes or need better curation. We demonstrate the PlantSEED system by producing consistent annotations for 10 reference genomes. We also produce a functioning metabolic model for each genome, gapfilling to identify missing annotations and proposing gene candidates for missing annotations. Models are built around an extended biomass composition representing the most comprehensive published to date. To our knowledge, our models are the first to be published for seven of the genomes analyzed. PMID:24927599

High-throughput comparison, functional annotation, and metabolic modeling of plant genomes using the PlantSEED resource.

PubMed

Seaver, Samuel M D; Gerdes, Svetlana; Frelin, Océane; Lerma-Ortiz, Claudia; Bradbury, Louis M T; Zallot, Rémi; Hasnain, Ghulam; Niehaus, Thomas D; El Yacoubi, Basma; Pasternak, Shiran; Olson, Robert; Pusch, Gordon; Overbeek, Ross; Stevens, Rick; de Crécy-Lagard, Valérie; Ware, Doreen; Hanson, Andrew D; Henry, Christopher S

2014-07-01

The increasing number of sequenced plant genomes is placing new demands on the methods applied to analyze, annotate, and model these genomes. Today's annotation pipelines result in inconsistent gene assignments that complicate comparative analyses and prevent efficient construction of metabolic models. To overcome these problems, we have developed the PlantSEED, an integrated, metabolism-centric database to support subsystems-based annotation and metabolic model reconstruction for plant genomes. PlantSEED combines SEED subsystems technology, first developed for microbial genomes, with refined protein families and biochemical data to assign fully consistent functional annotations to orthologous genes, particularly those encoding primary metabolic pathways. Seamless integration with its parent, the prokaryotic SEED database, makes PlantSEED a unique environment for cross-kingdom comparative analysis of plant and bacterial genomes. The consistent annotations imposed by PlantSEED permit rapid reconstruction and modeling of primary metabolism for all plant genomes in the database. This feature opens the unique possibility of model-based assessment of the completeness and accuracy of gene annotation and thus allows computational identification of genes and pathways that are restricted to certain genomes or need better curation. We demonstrate the PlantSEED system by producing consistent annotations for 10 reference genomes. We also produce a functioning metabolic model for each genome, gapfilling to identify missing annotations and proposing gene candidates for missing annotations. Models are built around an extended biomass composition representing the most comprehensive published to date. To our knowledge, our models are the first to be published for seven of the genomes analyzed.

Resources for Performance-Based Education.

ERIC Educational Resources Information Center

Houston, W. Robert; And Others

This volume presents annotations of resources on performance-based teacher education. The materials, produced after 1967, include films, slide/tapes, modules, programmed texts, and multimedia kits for training pre- and in-service educational personnel. The materials are indexed according to both competency categories and key words, descriptions,…

Nutrition Books and Resources 1971.

ERIC Educational Resources Information Center

Hawaii Dietetic Association, Honolulu.

This is an annotated bibliography listing books, resources, and films and filmstrips on the subject of nutrition. Sections include: Food Sense; Controlling Your Weight; Feeding Your Family; Food for Teens; Learning and Teaching Nutrition; Other Sources; and Films and Filmstrips. The material is in pamphlet form. (LK)

Audiovisual Resources for Family Programming.

ERIC Educational Resources Information Center

Jordan, Barbara; Stackpole, Noreen

This directory contains annotated descriptions and source information for more than 1,700 nonprint items on topics of interest to parents, parent educators, social workers, school and community groups, and librarians developing collections on family resources. The directory consists mainly of videotapes but also includes games, kits,…

Beatrix Potter: Seeing Beauty in the Simplest Things.

ERIC Educational Resources Information Center

Brodie, Carolyn S.

2002-01-01

Discusses the life and works of Beatrix Potter. Suggests ideas for related extension activities and provides an annotated bibliography, including books in the Peter Rabbit series; selected publications based on the Peter Rabbit series; Web resources; books about Beatrix Potter; and additional print resources. (LRW)

Cultural Awareness: A Resource Bibliography.

ERIC Educational Resources Information Center

Schmidt, Velma E.; McNeill, Earldene

This annotated bibliography cites books for children and resource materials such as books and articles, bibliographies, catalogs, and periodicals for adults which deal with various aspects of different cultures. Posters, pictures, records, films, filmstrips, slides, dolls, and museums which pertain to particular cultures are also listed. Separate…

Microbial Genome Analysis and Comparisons: Web-based Protocols and Resources

USDA-ARS?s Scientific Manuscript database

Fully annotated genome sequences of many microorganisms are publicly available as a resource. However, in-depth analysis of these genomes using specialized tools is required to derive meaningful information. We describe here the utility of three powerful publicly available genome databases and ana...

Bibliography of Nuclear Education Resources.

ERIC Educational Resources Information Center

Alexander, Susan, Ed.

Provided in this bibliography is a listing of nuclear education books and resource materials. Entries (most of which are annotated) are presented under these headings: action; arms control and negotiations; arms race; the arts; atomic energy; atomic testing; bibliographies; civil defense; conference proceedings; conflict solving; conversion;…

Copyright Resources for School Librarians

ERIC Educational Resources Information Center

Johnson, Yvonne M.; Johnson, Nicole M.

2016-01-01

This article provides a collection of annotated citations for online resources of interest to school librarians; the focus is on copyright law, related information, and guidelines. The citations are organized by themes based on common issues. Copyright protects originally created works, including movies, recorded music performances, novels,…

Genome Annotation Generator: a simple tool for generating and correcting WGS annotation tables for NCBI submission.

PubMed

Geib, Scott M; Hall, Brian; Derego, Theodore; Bremer, Forest T; Cannoles, Kyle; Sim, Sheina B

2018-04-01

One of the most overlooked, yet critical, components of a whole genome sequencing (WGS) project is the submission and curation of the data to a genomic repository, most commonly the National Center for Biotechnology Information (NCBI). While large genome centers or genome groups have developed software tools for post-annotation assembly filtering, annotation, and conversion into the NCBI's annotation table format, these tools typically require back-end setup and connection to an Structured Query Language (SQL) database and/or some knowledge of programming (Perl, Python) to implement. With WGS becoming commonplace, genome sequencing projects are moving away from the genome centers and into the ecology or biology lab, where fewer resources are present to support the process of genome assembly curation. To fill this gap, we developed software to assess, filter, and transfer annotation and convert a draft genome assembly and annotation set into the NCBI annotation table (.tbl) format, facilitating submission to the NCBI Genome Assembly database. This software has no dependencies, is compatible across platforms, and utilizes a simple command to perform a variety of simple and complex post-analysis, pre-NCBI submission WGS project tasks. The Genome Annotation Generator is a consistent and user-friendly bioinformatics tool that can be used to generate a .tbl file that is consistent with the NCBI submission pipeline. The Genome Annotation Generator achieves the goal of providing a publicly available tool that will facilitate the submission of annotated genome assemblies to the NCBI. It is useful for any individual researcher or research group that wishes to submit a genome assembly of their study system to the NCBI.

Genome Annotation Generator: a simple tool for generating and correcting WGS annotation tables for NCBI submission

PubMed Central

Hall, Brian; Derego, Theodore; Bremer, Forest T; Cannoles, Kyle

2018-01-01

Abstract Background One of the most overlooked, yet critical, components of a whole genome sequencing (WGS) project is the submission and curation of the data to a genomic repository, most commonly the National Center for Biotechnology Information (NCBI). While large genome centers or genome groups have developed software tools for post-annotation assembly filtering, annotation, and conversion into the NCBI’s annotation table format, these tools typically require back-end setup and connection to an Structured Query Language (SQL) database and/or some knowledge of programming (Perl, Python) to implement. With WGS becoming commonplace, genome sequencing projects are moving away from the genome centers and into the ecology or biology lab, where fewer resources are present to support the process of genome assembly curation. To fill this gap, we developed software to assess, filter, and transfer annotation and convert a draft genome assembly and annotation set into the NCBI annotation table (.tbl) format, facilitating submission to the NCBI Genome Assembly database. This software has no dependencies, is compatible across platforms, and utilizes a simple command to perform a variety of simple and complex post-analysis, pre-NCBI submission WGS project tasks. Findings The Genome Annotation Generator is a consistent and user-friendly bioinformatics tool that can be used to generate a .tbl file that is consistent with the NCBI submission pipeline Conclusions The Genome Annotation Generator achieves the goal of providing a publicly available tool that will facilitate the submission of annotated genome assemblies to the NCBI. It is useful for any individual researcher or research group that wishes to submit a genome assembly of their study system to the NCBI. PMID:29635297

Teaching Woodwinds.

ERIC Educational Resources Information Center

New York State Education Dept., Albany. Bureau of General Education Curriculum Development.

The guide contains suggestions for the selection, repair, and care of woodwind instruments and equipment; goals and procedures for beginning, intermediate, and advanced levels of study; and specific annotated reference lists. The book is arranged into five major sections by type of instrument: flute, oboe, clarinet, saxophone and bassoon. Each…

Catalogs of Audiovisual Materials: A Guide to Government Sources.

ERIC Educational Resources Information Center

Dale, Doris Cruger

This annotated bibliography lists 53 federally published catalogs and bibliographies which identify films and other audiovisual materials produced or sponsored by government agencies; some also include commercially produced audiovisual and/or print materials. Publications are listed alphabetically by government agency or department, and…

Shakespeare: A Student's Guide to Basic Reference Sources.

ERIC Educational Resources Information Center

Claener, Anne, Comp.

Basic and standard reference materials dealing with William Shakespeare are listed in this bibliography. Annotated entries are grouped under the following headings: concordances, dictionaries, encyclopedias and handbooks, and bibliographies. The section on bibliographies is further divided into lists of editions of Shakespeare's work, general…

Libraries and Literacy: Making It Work. An Annotated Bibliography

ERIC Educational Resources Information Center

Lamontagne, Manon

2007-01-01

This bibliography was compiled for The Centre for Literacy's 2007 Summer Institute--"Libraries and Literacy: Making It Work." The literature represented here includes research studies, descriptive articles, guides and manuals. Selections address the principles, "best practices" and assessment of library involvement in literacy…

MIPS: curated databases and comprehensive secondary data resources in 2010.

PubMed

Mewes, H Werner; Ruepp, Andreas; Theis, Fabian; Rattei, Thomas; Walter, Mathias; Frishman, Dmitrij; Suhre, Karsten; Spannagl, Manuel; Mayer, Klaus F X; Stümpflen, Volker; Antonov, Alexey

2011-01-01

The Munich Information Center for Protein Sequences (MIPS at the Helmholtz Center for Environmental Health, Neuherberg, Germany) has many years of experience in providing annotated collections of biological data. Selected data sets of high relevance, such as model genomes, are subjected to careful manual curation, while the bulk of high-throughput data is annotated by automatic means. High-quality reference resources developed in the past and still actively maintained include Saccharomyces cerevisiae, Neurospora crassa and Arabidopsis thaliana genome databases as well as several protein interaction data sets (MPACT, MPPI and CORUM). More recent projects are PhenomiR, the database on microRNA-related phenotypes, and MIPS PlantsDB for integrative and comparative plant genome research. The interlinked resources SIMAP and PEDANT provide homology relationships as well as up-to-date and consistent annotation for 38,000,000 protein sequences. PPLIPS and CCancer are versatile tools for proteomics and functional genomics interfacing to a database of compilations from gene lists extracted from literature. A novel literature-mining tool, EXCERBT, gives access to structured information on classified relations between genes, proteins, phenotypes and diseases extracted from Medline abstracts by semantic analysis. All databases described here, as well as the detailed descriptions of our projects can be accessed through the MIPS WWW server (http://mips.helmholtz-muenchen.de).

MIPS: curated databases and comprehensive secondary data resources in 2010

PubMed Central

Mewes, H. Werner; Ruepp, Andreas; Theis, Fabian; Rattei, Thomas; Walter, Mathias; Frishman, Dmitrij; Suhre, Karsten; Spannagl, Manuel; Mayer, Klaus F.X.; Stümpflen, Volker; Antonov, Alexey

2011-01-01

The Munich Information Center for Protein Sequences (MIPS at the Helmholtz Center for Environmental Health, Neuherberg, Germany) has many years of experience in providing annotated collections of biological data. Selected data sets of high relevance, such as model genomes, are subjected to careful manual curation, while the bulk of high-throughput data is annotated by automatic means. High-quality reference resources developed in the past and still actively maintained include Saccharomyces cerevisiae, Neurospora crassa and Arabidopsis thaliana genome databases as well as several protein interaction data sets (MPACT, MPPI and CORUM). More recent projects are PhenomiR, the database on microRNA-related phenotypes, and MIPS PlantsDB for integrative and comparative plant genome research. The interlinked resources SIMAP and PEDANT provide homology relationships as well as up-to-date and consistent annotation for 38 000 000 protein sequences. PPLIPS and CCancer are versatile tools for proteomics and functional genomics interfacing to a database of compilations from gene lists extracted from literature. A novel literature-mining tool, EXCERBT, gives access to structured information on classified relations between genes, proteins, phenotypes and diseases extracted from Medline abstracts by semantic analysis. All databases described here, as well as the detailed descriptions of our projects can be accessed through the MIPS WWW server (http://mips.helmholtz-muenchen.de). PMID:21109531

Improving Program Design and Assessment with Broadening Participation Resources

NASA Astrophysics Data System (ADS)

Siegfried, D.; Johnson, A.; Thomas, S. H.; Fauver, A.; Detrick, L.

2012-12-01

Many theoretical and research-based approaches suggest how to best use mentoring to enhance an undergraduate research program. The Institute for Broadening Participation's Pathways to Engineering and Pathways to Ocean Sciences projects synthesized a set of mentoring studies, theoretical sources, and other texts pertinent to undergraduate research program design into a suite of practical tools that includes an online mentoring manual, an online reference library of mentoring and diversity literature, and practical guides such as Using Social Media to Build Diversity in Your REU. The overall goal is to provide easy-to-access resources that can assist faculty and program directors in implementing or honing the mentoring elements in their research programs for undergraduates. IBP's Online Mentoring Manual addresses common themes, such as modeling, student self-efficacy, career development, retention and evaluation. The Online Diversity Reference Library provides a comprehensive, annotated selection of key policy documents, research studies, intervention studies, and other texts on broadening participation in science, technology, engineering and mathematics. IBP's suite of tools provides the theoretical underpinnings and research findings that can help leaders in education integrate site-appropriate mentoring elements into their educational programs. Program directors and faculty from a variety of program types and disciplines have benefitted from using the Manual and other resources. IBP continues the work of translating and synthesizing theory to practice and welcomes your participation and partnership in that effort.

COPRED: prediction of fold, GO molecular function and functional residues at the domain level.

PubMed

López, Daniel; Pazos, Florencio

2013-07-15

Only recently the first resources devoted to the functional annotation of proteins at the domain level started to appear. The next step is to develop specific methodologies for predicting function at the domain level based on these resources, and to implement them in web servers to be used by the community. In this work, we present COPRED, a web server for the concomitant prediction of fold, molecular function and functional sites at the domain level, based on a methodology for domain molecular function prediction and a resource of domain functional annotations previously developed and benchmarked. COPRED can be freely accessed at http://csbg.cnb.csic.es/copred. The interface works in all standard web browsers. WebGL (natively supported by most browsers) is required for the in-line preview and manipulation of protein 3D structures. The website includes a detailed help section and usage examples. pazos@cnb.csic.es.

VectorBase: an updated bioinformatics resource for invertebrate vectors and other organisms related with human diseases

PubMed Central

Giraldo-Calderón, Gloria I.; Emrich, Scott J.; MacCallum, Robert M.; Maslen, Gareth; Dialynas, Emmanuel; Topalis, Pantelis; Ho, Nicholas; Gesing, Sandra; Madey, Gregory; Collins, Frank H.; Lawson, Daniel

2015-01-01

VectorBase is a National Institute of Allergy and Infectious Diseases supported Bioinformatics Resource Center (BRC) for invertebrate vectors of human pathogens. Now in its 11th year, VectorBase currently hosts the genomes of 35 organisms including a number of non-vectors for comparative analysis. Hosted data range from genome assemblies with annotated gene features, transcript and protein expression data to population genetics including variation and insecticide-resistance phenotypes. Here we describe improvements to our resource and the set of tools available for interrogating and accessing BRC data including the integration of Web Apollo to facilitate community annotation and providing Galaxy to support user-based workflows. VectorBase also actively supports our community through hands-on workshops and online tutorials. All information and data are freely available from our website at https://www.vectorbase.org/. PMID:25510499

AdjScales: Visualizing Differences between Adjectives for Language Learners

NASA Astrophysics Data System (ADS)

Sheinman, Vera; Tokunaga, Takenobu

In this study we introduce AdjScales, a method for scaling similar adjectives by their strength. It combines existing Web-based computational linguistic techniques in order to automatically differentiate between similar adjectives that describe the same property by strength. Though this kind of information is rarely present in most of the lexical resources and dictionaries, it may be useful for language learners that try to distinguish between similar words. Additionally, learners might gain from a simple visualization of these differences using unidimensional scales. The method is evaluated by comparison with annotation on a subset of adjectives from WordNet by four native English speakers. It is also compared against two non-native speakers of English. The collected annotation is an interesting resource in its own right. This work is a first step toward automatic differentiation of meaning between similar words for language learners. AdjScales can be useful for lexical resource enhancement.

Resources for Performance-Based Education. Supplement A.

ERIC Educational Resources Information Center

Houston, W. Robert; And Others

This document is a supplement to the annotated bibliography "Resources for Performance-Based Education," published by the New York State Education Department (ED 076 555). The supplement adds new instructional modules, films, slide/tapes, programmed materials, video tapes, and other nontextbook materials useful for supporting performance-based…

New Funding Opportunity: Biospecimen Core Resource | Office of Cancer Clinical Proteomics Research

Cancer.gov

The purpose of this notice is to notify the community that the National Cancer Institute's (NCI’s) Office of Cancer Clinical Proteomics Research (OCCPR) is seeking sources to establish a Biospecimen Core Resource (BCR), capable of receiving, qualifying, processing, and distributing annotated biospecimens.

Small Business Bibliography.

ERIC Educational Resources Information Center

Anderson, Wendell, Ed.

Intended as a resource for both experienced businesspeople and those new to business, this annotated bibliography provides a list of books, pamphlets, periodicals, and videotapes of value in solving specific business problems. The bibliography begins with a list of resources recommended for the library of every small business and a survey of…

The Resource Directory: Designing Your Success.

ERIC Educational Resources Information Center

Bowers, Richard A.

1995-01-01

Discusses computer software and system design in the information industry and provides an annotated bibliography of 31 resources that address the issue of design. Highlights include competition, color use, hardware and presentation design, content and packaging, screen design, graphics, and interactive multimedia. A sidebar reviews and rates seven…

A Short Bibliography on Library/Media Leadership.

ERIC Educational Resources Information Center

Stanford Univ., CA. ERIC Clearinghouse on Information Resources.

Prepared for distribution at the 1975 Annual Convention of the Association for Educational Communications and Technology, this bibliography was assembled from the Current Index to Journals in Education (CIJE) and Resources in Education (RIE) computer files of the Educational Resources Information Center (ERIC). Annotated CIJE and RIE entries…

Annotated Bibliography on Population, Resources and Environment Relationships.

ERIC Educational Resources Information Center

Hollander, Seth

The National Audubon Society is concerned with dependencies of wildlife and life support systems on this planet. Recognizing the role humans play in the interrelationships, Dr. Russell W. Peterson, Audubon's president, established the Population Program within the society's Environmental Policy Analysis Department to: analyze population, resource,…

Exploring the Universe: An Introductory Bibliography in Astronomy.

ERIC Educational Resources Information Center

Fraknoi, Andrew

Arranged in five sections, this annotated bibliography cites over 40 introductory level resources on astronomy published between 1972 and 1981. A note on the availability of these resources precedes sections covering general introductory books, magazines featuring non-technical articles, general books for readers with slight background,…

The Bologna Annotation Resource (BAR 3.0): improving protein functional annotation.

PubMed

Profiti, Giuseppe; Martelli, Pier Luigi; Casadio, Rita

2017-07-03

BAR 3.0 updates our server BAR (Bologna Annotation Resource) for predicting protein structural and functional features from sequence. We increase data volume, query capabilities and information conveyed to the user. The core of BAR 3.0 is a graph-based clustering procedure of UniProtKB sequences, following strict pairwise similarity criteria (sequence identity ≥40% with alignment coverage ≥90%). Each cluster contains the available annotation downloaded from UniProtKB, GO, PFAM and PDB. After statistical validation, GO terms and PFAM domains are cluster-specific and annotate new sequences entering the cluster after satisfying similarity constraints. BAR 3.0 includes 28 869 663 sequences in 1 361 773 clusters, of which 22.2% (22 241 661 sequences) and 47.4% (24 555 055 sequences) have at least one validated GO term and one PFAM domain, respectively. 1.4% of the clusters (36% of all sequences) include PDB structures and the cluster is associated to a hidden Markov model that allows building template-target alignment suitable for structural modeling. Some other 3 399 026 sequences are singletons. BAR 3.0 offers an improved search interface, allowing queries by UniProtKB-accession, Fasta sequence, GO-term, PFAM-domain, organism, PDB and ligand/s. When evaluated on the CAFA2 targets, BAR 3.0 largely outperforms our previous version and scores among state-of-the-art methods. BAR 3.0 is publicly available and accessible at http://bar.biocomp.unibo.it/bar3. © The Author(s) 2017. Published by Oxford University Press on behalf of Nucleic Acids Research.

Make It and Take It: Computer-Based Resources for Lesson Planning.

ERIC Educational Resources Information Center

Brown, Tasha; Cargill, Debby; Hostetler, Jan; Joyner, Susan; Phillips, Vanessa

This document is part lesson planner and idea resource and part annotated bibliography of electronic resources. The lesson planner is divided into four parts. Part one, "Tables to Go," contains different tables that can be used for a variety of exercises at all levels of the English-as-a-Second-Language (ESL) classroom. Part two, "Exploring the…

Alternative and Asset-Based Evaluation and Assessment in Language Teaching and Literacy: Resources for Research, Classroom Instruction and Evaluation of Language Competence

ERIC Educational Resources Information Center

Eaton, Sarah Elaine

2011-01-01

This annotated bibliography surveys key resources and research related specifically to language learning and literacy. It focuses on resources that will be valuable to teaching professionals and researchers who specialize in the areas of foreign and second language teaching, language arts and first and second language literacy. Significant…

An Adult Prescriptive Program for Levels of Employment--Career Oriented Education (Apple Core). Bulletin #1258. An Adult Education Curriculum Guide Based on Instructional Materials Related to the Occupational Needs of Employees. Booklet 3. Annotated Bibliography.

ERIC Educational Resources Information Center

Bureau of Occupational and Adult Education (DHEW/OE), Washington, DC. Div. of Adult Education.

This booklet along with six others comprises a curriculum guide developed for adult education supervisors and teachers of undereducated workers or job seekers whose inability to develop the skills and obtain the knowledge necessary to meet the requirements of the working world are primarily due to a lack of competence in reading and math skills.…

Metabolomics-based chemotaxonomy of root endophytic fungi for natural products discovery.

PubMed

Maciá-Vicente, Jose G; Shi, Yan-Ni; Cheikh-Ali, Zakaria; Grün, Peter; Glynou, Kyriaki; Kia, Sevda Haghi; Piepenbring, Meike; Bode, Helge B

2018-03-01

Fungi are prolific producers of natural products routinely screened for biotechnological applications, and those living endophytically within plants attract particular attention because of their purported chemical diversity. However, the harnessing of their biosynthetic potential is hampered by a large and often cryptic phylogenetic and ecological diversity, coupled with a lack of large-scale natural products' dereplication studies. To guide efforts to discover new chemistries among root-endophytic fungi, we analyzed the natural products produced by 822 strains using an untargeted UPLC-ESI-MS/MS-based approach and linked the patterns of chemical features to fungal lineages. We detected 17 809 compounds of which 7951 were classified in 1992 molecular families, whereas the remaining were considered unique chemistries. Our approach allowed to annotate 1191 compounds with different degrees of accuracy, many of which had known fungal origins. Approximately 61% of the compounds were specific of a fungal order, and differences were observed across lineages in the diversity and characteristics of their chemistries. Chemical profiles also showed variable chemosystematic values across lineages, ranging from relative homogeneity to high heterogeneity among related fungi. Our results provide an extensive resource to dereplicate fungal natural products and may assist future discovery programs by providing a guide for the selection of target fungi. © 2018 Society for Applied Microbiology and John Wiley & Sons Ltd.

A computational platform to maintain and migrate manual functional annotations for BioCyc databases.

PubMed

Walsh, Jesse R; Sen, Taner Z; Dickerson, Julie A

2014-10-12

BioCyc databases are an important resource for information on biological pathways and genomic data. Such databases represent the accumulation of biological data, some of which has been manually curated from literature. An essential feature of these databases is the continuing data integration as new knowledge is discovered. As functional annotations are improved, scalable methods are needed for curators to manage annotations without detailed knowledge of the specific design of the BioCyc database. We have developed CycTools, a software tool which allows curators to maintain functional annotations in a model organism database. This tool builds on existing software to improve and simplify annotation data imports of user provided data into BioCyc databases. Additionally, CycTools automatically resolves synonyms and alternate identifiers contained within the database into the appropriate internal identifiers. Automating steps in the manual data entry process can improve curation efforts for major biological databases. The functionality of CycTools is demonstrated by transferring GO term annotations from MaizeCyc to matching proteins in CornCyc, both maize metabolic pathway databases available at MaizeGDB, and by creating strain specific databases for metabolic engineering.

The Energy Crisis -- Aids to Study.

ERIC Educational Resources Information Center

McDaniel, Margaret, Comp.

Over one-hundred citations, the majority of which are current works dating from the seventies, are provided in this annotated bibliography focusing on energy. Entries include books, pamphlets, reports, magazine articles, bibliographies, newsletters, and curriculum materials, such as audiovisual aids, guides and units, and simulations which will be…

Ames Energy: A Consumer's Guide to Energy Conservation.

ERIC Educational Resources Information Center

Women's Support Network, Inc., Santa Rosa, CA.

Presented is an annotated bibliography of energy-related materials for the consumer. Materials (which include books, videotape recordings, magazines, pamphlets, and other media) are arranged by subject area. These area include: (1) earth sheltered buildings; (2) fuels; (3) general (including general energy conservation and insulation); (4) heat…

Farmworker Health-Related Bibliography.

ERIC Educational Resources Information Center

National Association of Farmworker Organizations, Washington, DC.

Documents pertaining to migrant and seasonal farmworker health comprise this bibliography of over 300 entries, nearly 100 of them annotated. The purpose of the bibliography is to provide health groups within the National Association of Farmworker Organizations with literature which may guide further research related to the provision of health care…

User's guide [Chapter 3

Treesearch

Nicholas L. Crookston; Donald C. E. Robinson; Sarah J. Beukema

2003-01-01

The Fire and Fuels Extension (FFE) to the Forest Vegetation Simulator (FVS) simulates fuel dynamics and potential fire behavior over time, in the context of stand development and management. This chapter presents the model's options, provides annotated examples, describes the outputs, and describes how to use and apply the model.

LS-SNP/PDB: annotated non-synonymous SNPs mapped to Protein Data Bank structures.

PubMed

Ryan, Michael; Diekhans, Mark; Lien, Stephanie; Liu, Yun; Karchin, Rachel

2009-06-01

LS-SNP/PDB is a new WWW resource for genome-wide annotation of human non-synonymous (amino acid changing) SNPs. It serves high-quality protein graphics rendered with UCSF Chimera molecular visualization software. The system is kept up-to-date by an automated, high-throughput build pipeline that systematically maps human nsSNPs onto Protein Data Bank structures and annotates several biologically relevant features. LS-SNP/PDB is available at (http://ls-snp.icm.jhu.edu/ls-snp-pdb) and via links from protein data bank (PDB) biology and chemistry tabs, UCSC Genome Browser Gene Details and SNP Details pages and PharmGKB Gene Variants Downloads/Cross-References pages.

The Human Phenotype Ontology: Semantic Unification of Common and Rare Disease

PubMed Central

Groza, Tudor; Köhler, Sebastian; Moldenhauer, Dawid; Vasilevsky, Nicole; Baynam, Gareth; Zemojtel, Tomasz; Schriml, Lynn Marie; Kibbe, Warren Alden; Schofield, Paul N.; Beck, Tim; Vasant, Drashtti; Brookes, Anthony J.; Zankl, Andreas; Washington, Nicole L.; Mungall, Christopher J.; Lewis, Suzanna E.; Haendel, Melissa A.; Parkinson, Helen; Robinson, Peter N.

2015-01-01

The Human Phenotype Ontology (HPO) is widely used in the rare disease community for differential diagnostics, phenotype-driven analysis of next-generation sequence-variation data, and translational research, but a comparable resource has not been available for common disease. Here, we have developed a concept-recognition procedure that analyzes the frequencies of HPO disease annotations as identified in over five million PubMed abstracts by employing an iterative procedure to optimize precision and recall of the identified terms. We derived disease models for 3,145 common human diseases comprising a total of 132,006 HPO annotations. The HPO now comprises over 250,000 phenotypic annotations for over 10,000 rare and common diseases and can be used for examining the phenotypic overlap among common diseases that share risk alleles, as well as between Mendelian diseases and common diseases linked by genomic location. The annotations, as well as the HPO itself, are freely available. PMID:26119816

DOE Office of Scientific and Technical Information (OSTI.GOV)

Groza, Tudor; Köhler, Sebastian; Moldenhauer, Dawid

The Human Phenotype Ontology (HPO) is widely used in the rare disease community for differential diagnostics, phenotype-driven analysis of next-generation sequence-variation data, and translational research, but a comparable resource has not been available for common disease. Here, we have developed a concept-recognition procedure that analyzes the frequencies of HPO disease annotations as identified in over five million PubMed abstracts by employing an iterative procedure to optimize precision and recall of the identified terms. We derived disease models for 3,145 common human diseases comprising a total of 132,006 HPO annotations. The HPO now comprises over 250,000 phenotypic annotations for over 10,000more » rare and common diseases and can be used for examining the phenotypic overlap among common diseases that share risk alleles, as well as between Mendelian diseases and common diseases linked by genomic location. The annotations, as well as the HPO itself, are freely available.« less

A Resource of Quantitative Functional Annotation for Homo sapiens Genes.

PubMed

Taşan, Murat; Drabkin, Harold J; Beaver, John E; Chua, Hon Nian; Dunham, Julie; Tian, Weidong; Blake, Judith A; Roth, Frederick P

2012-02-01

The body of human genomic and proteomic evidence continues to grow at ever-increasing rates, while annotation efforts struggle to keep pace. A surprisingly small fraction of human genes have clear, documented associations with specific functions, and new functions continue to be found for characterized genes. Here we assembled an integrated collection of diverse genomic and proteomic data for 21,341 human genes and make quantitative associations of each to 4333 Gene Ontology terms. We combined guilt-by-profiling and guilt-by-association approaches to exploit features unique to the data types. Performance was evaluated by cross-validation, prospective validation, and by manual evaluation with the biological literature. Functional-linkage networks were also constructed, and their utility was demonstrated by identifying candidate genes related to a glioma FLN using a seed network from genome-wide association studies. Our annotations are presented-alongside existing validated annotations-in a publicly accessible and searchable web interface.

Issues with RNA-seq analysis in non-model organisms: A salmonid example.

PubMed

Sundaram, Arvind; Tengs, Torstein; Grimholt, Unni

2017-10-01

High throughput sequencing (HTS) is useful for many purposes as exemplified by the other topics included in this special issue. The purpose of this paper is to look into the unique challenges of using this technology in non-model organisms where resources such as genomes, functional genome annotations or genome complexity provide obstacles not met in model organisms. To describe these challenges, we narrow our scope to RNA sequencing used to study differential gene expression in response to pathogen challenge. As a demonstration species we chose Atlantic salmon, which has a sequenced genome with poor annotation and an added complexity due to many duplicated genes. We find that our RNA-seq analysis pipeline deciphers between duplicates despite high sequence identity. However, annotation issues provide problems in linking differentially expressed genes to pathways. Also, comparing results between approaches and species are complicated due to lack of standardized annotation. Copyright © 2017 Elsevier Ltd. All rights reserved.

Resource Directory of Hispanic Educational Materials on Child Abuse Prevention.

ERIC Educational Resources Information Center

Hill, Nancy; And Others

This annotated resource directory lists brochures, booklets, audiovisual materials, charts, and other educational materials, most of which are available in both English and Spanish, that address the following issues: (1) child abuse; (2) child development; (3) parenting skills; (4) mental health; (5) self-esteem; (6) stress management; (7) family…