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…

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:…

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:…

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.

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…

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…

Resource Guide: Selected Early Childhood/Early Intervention Training Materials. 8th Edition.

ERIC Educational Resources Information Center

Catlett, Camille, Comp.; Winton, Pamela J., Comp.

This resource guide is intended to identify both primary and supplementary resources for designing preservice and inservice training on early intervention programs for children with disabilities. The instructional materials are described and listed in three sections. The first section provides annotated descriptions of instructional materials in…

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…

State Minimum Competency Testing Programs. Resource Catalog. Final Report.

ERIC Educational Resources Information Center

Mills, Gladys H.

Focusing on state-mandated minimum competency testing programs, this annotated bibliography cites 200 items selected from more than 700. The Resource Catalog is intended for state education policy makers and therefore includes resource and study guides; legislative and board action; conference speeches, reports and proceedings; curriculum guides,…

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…

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…

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 resource guide lists information on 1341 references (1960-1975) on barrier-free environments for elderly and/or handicapped persons. Each citation contains bibliographic information (author, title, ordering information and source), descriptors, and a brief abstract. Resources are arranged according to the following categories (sample subtopics…

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,…

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…

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…

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.…

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…

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.…

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…

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.

Marketing the Arts: A Selected and Annotated Bibliography.

ERIC Educational Resources Information Center

Nakamoto, Kent, Comp.; Levin, Kathi, Comp.

Compiled from the marketing, arts, and arts management literature, this selected list includes materials ranging from theoretical articles and reports of studies to practical guides for marketing techniques. It consists of three sections: Primary Sources, Secondary Sources, and Surveys. Of particular interest to the arts administrator, the first…

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…

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…

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.…

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…

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…

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…

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…

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…

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

The Special Relationship: The United States as the British Have Seen It. A Selective Reading List by British Writers.

ERIC Educational Resources Information Center

Wright, Esmond, Comp.

The selective annotated bibliography is a reader's guide to aspects of the American past and present as seen by British writers since the 1940s. Approximately 250 entries provide a sampling of how British students of United States studies perceive the New World. Childrens books are omitted. Nine categories are organized alphabetically by author.…

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…

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…

Education and Older People. Selected Bibliographies on Ageing 2.

ERIC Educational Resources Information Center

Norton, Dianne, Comp.

These annotated bibliographies are intended to assist researchers, students, and other practitioners interested in the topic of education and aging. How-to guides, research studies, literature reviews, essays, state-of-the-art reviews, and program descriptions are included. Works are arranged by the following subject areas: general, learning…

Counselor's Guide to Manpower Information; An Annotated Bibliography of Government Publications.

ERIC Educational Resources Information Center

Smith, Gerard C.

This selected bibliography of materials published by all Federal and many state agencies from 1962 to 1968 is divided into four sections. One deals with occupational and industry manpower literature, including occupational outlook service information, occupational and industry manpower studies, job descriptions, and Federal government careers. The…

An Annotated Bibliography for Health Occupations: A Guide for Teachers and Students.

ERIC Educational Resources Information Center

Solon, Lindy

The bibliography is designed to assist teachers and students at the secondary level in selecting printed and audiovisual materials related to health occupations. The 115 items relate to the following occupations: dental assistant, medical laboratory aide, practical nurse, nurse assistant, rehabilitation aide, physical therapy aide, radiologic…

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…

Taking the Law into Your Own Hands.

ERIC Educational Resources Information Center

Pedzich, Joan

1993-01-01

Describes how to select materials needed by the growing legal self-help movement, the importance of currency, and publishers in the field. An annotated bibliography of 25 titles includes general guides and books focusing on estate planning, going to court, contracts, animals, immigration, domestic issues, real estate, and bankruptcy. (KRN)

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…

Reference. Advisory List of Instructional Media.

ERIC Educational Resources Information Center

North Carolina State Dept. of Public Education, Raleigh.

The reference books featured in this annotated bibliography were selected from those titles that publishers submitted to the North Carolina Department of Public Instruction for review. As such, it is not a comprehensive list of all reference titles in print. This guide organizes the 33 titles into major subject categories: (1) Arts…

Soft Skills Training: An Annotated Guide to Selected Programs.

ERIC Educational Resources Information Center

Leigh, Wilhelmina A.; Lee, Deitra H.; Lindquist, Malinda A.

This guidebook presents data from a two-part study that reviewed existing literature on soft work skills, defined soft skills, and determined their importance to employers. The study also identified programs that were teaching those skills. Researchers contacted 90 organizations, asking for detailed written materials about themselves. The 53 that…

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…

A Guide to Non-Sexist Children's books.

ERIC Educational Resources Information Center

Adell, Judith, Comp.; Klein, Hilary Dole, Comp.

The 141 books listed in this annotated bibliography were selected becasue they portray boys and girls as people who have the same kinds of frailties and strengths. The books are divided into four general categories; preschool through third grade, third grade through seventh grade, seventh grade through twelfth grade, and all ages. Each category…

Information on Child Abuse: A Selected Bibliography of Federal Government Publications. Research Guide.

ERIC Educational Resources Information Center

Dodge, Timothy

The overall topic of this annotated bibliography, directed to users of the Auburn University libraries, is child abuse. It contains 63 federal government publications in 4 major areas: (1) definitions and prevalence of child abuse, including child pornography and pedophilia, family violence, abductions, and emotional abuse; (2) recent legislation,…

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.…

This Land Is Our Land: A Guide to Multicultural Literature for Children and Young Adults.

ERIC Educational Resources Information Center

Helbig, Alethea K.; Perkins, Agnes Regan

This annotated bibliography of recent works of fiction, oral tradition, and poetry about the experiences and traditions of African-Americans, Asian-Americans, Hispanic-Americans and Native-Americans provides a one-stop selection tool. Only those works mainly about minority characters are presented, and inclusion decisions were made based on…

Religious Books for Children: An Annotated Bibliography. Third Revised Edition.

ERIC Educational Resources Information Center

Dole, Patricia Pearl

This bibliography is a guide for selecting children's books with overt religious themes and for the evaluation of this area in library collections. It is designed to be both current and critical, and can be used by church and synagogue libraries, directors of religious education, parents, and public or school libraries. The bibliography is…

What Shall Our Children Read? A Selected Bibliography of American Indian Literature for Young People.

ERIC Educational Resources Information Center

Blank, Ruth

The 178 titles in the annotated bibliography represent a variety of American Indian and Alaska Native topics and literature from 1953 to 1980 (primarily the 1970's). Serving as a guide for teachers and Native American parents, the bibliography alphabetically lists published material non-stereotypic of American Indians and suitable for teaching…

English Department Midi Course Curriculum for Juniors and Seniors at Norton High School.

ERIC Educational Resources Information Center

Zwicker, Lucille; And Others

This curriculum guide presents syllabi for seventeen ten-week "midi-courses" for juniors and seniors in high school. For each course, the syllabi contain a course description, goals, subject matter, materials, an annotated list of audio-visual aids, a list of behavioral objectives, some suggested activities, a glossary of terms, and a selection of…

A Guide to Reviews of Books, Plays, Films: A Selected Bibliography.

ERIC Educational Resources Information Center

Miller, Elaine N.

Forty reference sources for book, play, and film reviews are listed in this annotated bibliography: most of the titles cited are periodical indexes. A general section lists sources not restricted by subject or which contain references to all three kinds of reviews. Subsequent sections are the broad subject categories of humanities, science, social…

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…

Something to Chew On: Canadian Fiction for Young Adults.

ERIC Educational Resources Information Center

Pederson, Beverley

An annotated bibliography of fiction about Canada or written by Canadian authors is presented. The list is intended as a guide for Canadian young adult readers in search of a literature they can identify as their own. It can also be used by librarians and teachers who need assistance in selecting novels and short stories for young Canadians. Over…

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…

The Vietnam Era: A Guide to Teaching Resources.

ERIC Educational Resources Information Center

Indochina Curriculum Group, Cambridge, MA.

This annotated resource guide contains information and learning activities on the Vietnam War for use by high school history teachers. Annotations of primary source materials, resource materials, textbooks, general interest books, and film and slide shows from several competing points of view are included. The developers believe that students who…

Traumatic Brain Injury and Special Education: An Information Resource Guide.

ERIC Educational Resources Information Center

Stevens, Alice M.

This resource guide of annotated references on traumatic brain injury (TBI) was created to help educators locate information from such disciplines as neurology, neuropsychology, rehabilitation, and pediatric medicine. Twenty-four resources published from 1990 to 1994 are listed, with annotations. The resources include research reports/reviews,…

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…

The Special-Needs Reading List: An Annotated Guide to the Best Publications for Parents and Professionals.

ERIC Educational Resources Information Center

Sweeney, Wilma K.

This annotated resource guide lists books, periodicals, and organizations relevant to the needs of parents of children with disabilities. The books and periodicals were chosen as being up-to-date, accurate, written in parent-friendly language, written with a parent's information or support needs in mind, generally affordable, or considered a…

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

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…

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…

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…

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)

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.

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.

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)

How disordered is my protein and what is its disorder for? A guide through the “dark side” of the protein universe

PubMed Central

Lieutaud, Philippe; Uversky, Alexey V.; Uversky, Vladimir N.; Longhi, Sonia

2016-01-01

ABSTRACT In the last 2 decades it has become increasingly evident that a large number of proteins are either fully or partially disordered. Intrinsically disordered proteins lack a stable 3D structure, are ubiquitous and fulfill essential biological functions. Their conformational heterogeneity is encoded in their amino acid sequences, thereby allowing intrinsically disordered proteins or regions to be recognized based on properties of these sequences. The identification of disordered regions facilitates the functional annotation of proteins and is instrumental for delineating boundaries of protein domains amenable to structural determination with X-ray crystallization. This article discusses a comprehensive selection of databases and methods currently employed to disseminate experimental and putative annotations of disorder, predict disorder and identify regions involved in induced folding. It also provides a set of detailed instructions that should be followed to perform computational analysis of disorder. PMID:28232901

Moving toward more community-oriented transportation strategies for the San Francisco Bay Area : a resource guide

DOT National Transportation Integrated Search

1996-12-01

This resource guide provides a list of references with annotations, including many how to guides, for use by local jurisdictions, developers, transit operators and citizens groups that are interested in planning, designing, reviewing and implementing...

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,…

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;…

Resource Guide to Competency-Based Vocational Education: Distributive Education.

ERIC Educational Resources Information Center

Foster, Phillip R., Comp.

This resource guide for classroom teachers contains annotations of resources representing recent instructional development in competency-based education for distributive education. It is also intended to assist curriculum specialists, administrators, and supervisors in development of performance-based instructional programs. The guide is divided…

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…

Resource Guide to Competency-Based Vocational Education: Health Occupations.

ERIC Educational Resources Information Center

Foster, Phillip R., Comp.

This resource guide for classroom teachers contains annotations of resources representing recent instructional development in competency-based education for health occupations. It is also intended to assist curriculum specialists, administrators, and supervisors in development of performance-based instructional programs. The guide is divided into…

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.…

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,…

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…

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.

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.

Indians and Eskimos of Canada: A Student's Guide to Reference Resources.

ERIC Educational Resources Information Center

Slavin, Suzy M.

Emphasizing reference resources for ethnological research on Canadian American Indians and Eskimos, this guide constitutes a revised and expanded edition of an earlier student's guide entitled "Canadian Ethnology" and includes both reference sources and annotated bibliographic references for the following: (1) Handbooks (8 references);…

Bibliographies and Annotations from Speakers and Class Participants.

ERIC Educational Resources Information Center

California Univ., Berkeley. Office of Resources for International and Area Studies.

This annotated bibliography focuses on recent children's literature that deals with other cultures. The books in the bibliography are set in or about Africa (29 selections), Ancient Egypt (3 selections), East Asia (20 selections), India (7 selections), Latin America (3 selections), Middle East (5 selections), and Russia (9 selections). The…

Adolescent Literacy Resources: An Annotated Bibliography. Second Edition 2009

ERIC Educational Resources Information Center

Center on Instruction, 2009

2009-01-01

This annotated bibliography updated from a 2007 edition, is intended as a resource for technical assistance providers as they work with states on adolescent literacy. This revision includes current research and documents of practical use in guiding improvements in grades 4-12 reading instruction in the content areas and in interventions for…

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,…

Literacy and Basic Education: A Selected, Annotated Bibliography. Annotated Bibliography #3.

ERIC Educational Resources Information Center

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

A selected annotated bibliography on literacy and basic education, including contributions from practitioners in the worldwide non-formal education network and compiled for them, has three interrelated themes: integration of literacy programs with broader development efforts; the learner-centered or "psycho-social" approach to literacy,…

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;…

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)

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.

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,…

Learning to Live Safely: Persisting Life Situation No. 6. A Resource Guide for the Wisconsin EMR Curriculum.

ERIC Educational Resources Information Center

Quackenboss, Rita, Ed.; And Others

Presented in the resource guide for the Wisconsin curriculum for educable mentally retarded students are safety education teaching units. Learning to Live Safely" is the sixth in a series of persisting life situations. The guide lists behavioral objectives, activities, and annotated resource materials (with distributors' addresses) for…

A Guide to Outdoor Education Resources and Programs for the Handicapped. Outdoor Education for the Handicapped.

ERIC Educational Resources Information Center

Kentucky Univ., Lexington.

The resource guide is designed to assist educators, park resource persons, and parents of disabled children in locating and identifying sources of information for developing, implementing, and evaluating outdoor education programs for all disabled children and youth. The guide has two main parts. The first part contains an annotated bibliography…

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,…

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…

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…

Projects, Training, and Strategies for Generating Income: A Selected Annotated Bibliography. Annotated Bibliography #4.

ERIC Educational Resources Information Center

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

A selected annotated bibliography on projects, training, and strategies for generating income, intended for persons actively engaged in non-formal education for development, reflects a growing number of projects on income generation by and for women's groups, and a reliance upon indigenous associations and group action. Documents dating from 1969…

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…

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…

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…

Sharing and reusing multimedia multilingual educational resources in medicine.

PubMed

Zdrahal, Zdenek; Knoth, Petr; Mulholland, Paul; Collins, Trevor

2013-01-01

The paper describes the Eurogene portal for sharing and reusing multilingual multimedia educational resources in human genetics. The content is annotated using concepts of two ontologies and a topic hierarchy. The ontology annotation is used to guide search and for calculating semantically similar content. Educational resources can be aggregated into learning packages. The system is in routine use since 2009.

A Selected Annotated Bibliography of Material Relating to Racism, Blacks, Chicanos, Native Americans and Multi-Ethnicity. Vol. 4.

ERIC Educational Resources Information Center

Michigan Education Association, East Lansing. Div. of Minority Affairs.

Volume Four of this selected annotated bibliography is composed of the most recently discovered materials, pertaining to blacks, Latinos, Native Americans, multi-ethnicity and racism. Like the three previous annotated bibliographies, it is considered to reflect only that material which is held to be most representative and most relevant in terms…

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.…

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…

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,…

PFAAT version 2.0: a tool for editing, annotating, and analyzing multiple sequence alignments.

PubMed

Caffrey, Daniel R; Dana, Paul H; Mathur, Vidhya; Ocano, Marco; Hong, Eun-Jong; Wang, Yaoyu E; Somaroo, Shyamal; Caffrey, Brian E; Potluri, Shobha; Huang, Enoch S

2007-10-11

By virtue of their shared ancestry, homologous sequences are similar in their structure and function. Consequently, multiple sequence alignments are routinely used to identify trends that relate to function. This type of analysis is particularly productive when it is combined with structural and phylogenetic analysis. Here we describe the release of PFAAT version 2.0, a tool for editing, analyzing, and annotating multiple sequence alignments. Support for multiple annotations is a key component of this release as it provides a framework for most of the new functionalities. The sequence annotations are accessible from the alignment and tree, where they are typically used to label sequences or hyperlink them to related databases. Sequence annotations can be created manually or extracted automatically from UniProt entries. Once a multiple sequence alignment is populated with sequence annotations, sequences can be easily selected and sorted through a sophisticated search dialog. The selected sequences can be further analyzed using statistical methods that explicitly model relationships between the sequence annotations and residue properties. Residue annotations are accessible from the alignment viewer and are typically used to designate binding sites or properties for a particular residue. Residue annotations are also searchable, and allow one to quickly select alignment columns for further sequence analysis, e.g. computing percent identities. Other features include: novel algorithms to compute sequence conservation, mapping conservation scores to a 3D structure in Jmol, displaying secondary structure elements, and sorting sequences by residue composition. PFAAT provides a framework whereby end-users can specify knowledge for a protein family in the form of annotation. The annotations can be combined with sophisticated analysis to test hypothesis that relate to sequence, structure and function.

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.

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…

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 .

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…

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)

Bilingualism and Education in the United States: A Resource Guide.

ERIC Educational Resources Information Center

Karski, Joan Leonard

The guide is intended to introduce education professionals and interested groups to government resources and provide strategies for obtaining information on bilingualism and education in the United States. It consists primarily of annotated listings of federal government publications, but also includes some state and international resources. An…

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,…

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…

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…

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,…

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,…

Planning for Nursing Needs and Resources.

ERIC Educational Resources Information Center

Foerst, Helen V.; Gareau, Florence E.

To aid state and local manpower planning for nursing needs and resources, this guide presents basic principles and procedures essential to identifying needs and examining resources effectively. A wide range of resource and annotated reference lists present survey and study reports, background material, tools for planning, and a guide to…

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…

Articles Pertinent to the Campus Press: A Selected Annotated Bibliography

ERIC Educational Resources Information Center

Ardoin, Birthney

1974-01-01

Contains a selected annotated bibliography of 51 items covering articles published from January through August, 1974, organized under the following categories: advertising, broadcasting, media criticism, editorial policy, graphics, job opportunities, pedagogy, and photography. (RB)

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;…

Evaluating Computational Gene Ontology Annotations.

PubMed

Škunca, Nives; Roberts, Richard J; Steffen, Martin

2017-01-01

Two avenues to understanding gene function are complementary and often overlapping: experimental work and computational prediction. While experimental annotation generally produces high-quality annotations, it is low throughput. Conversely, computational annotations have broad coverage, but the quality of annotations may be variable, and therefore evaluating the quality of computational annotations is a critical concern.In this chapter, we provide an overview of strategies to evaluate the quality of computational annotations. First, we discuss why evaluating quality in this setting is not trivial. We highlight the various issues that threaten to bias the evaluation of computational annotations, most of which stem from the incompleteness of biological databases. Second, we discuss solutions that address these issues, for example, targeted selection of new experimental annotations and leveraging the existing experimental annotations.

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.

Annotated Bibliography of Textbooks and Reference Materials in Marine Sciences. Provisional Edition. Intergovernmental Oceanographic Commission, Technical Series.

ERIC Educational Resources Information Center

United Nations Educational, Scientific, and Cultural Organization, Paris (France). Intergovernmental Oceanographic Commission.

Presented is an annotated bibliography based on selected materials from a preliminary survey of existing bibliographies, publishers' listings, and other sources. It is intended to serve educators and researchers, especially those in countries where marine sciences are just developing. One hundred annotated and 450 non-annotated entries are…

The Occupational Aspirations of Minority College Students: An Annotated Bibliography as Related to Graduate Business Education. Research Report.

ERIC Educational Resources Information Center

Davis, E. Leta

An annotated bibliography on the occupational aspirations of minority college students as related to graduate business education is presented with most entries dated 1964 to 1978. Twenty-two selected studies relating to minority aspirations are annotated. In addition, supplementary materials include 51 entries without annotations, 15 nonannotated…

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.

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,…

Resources for Ensuring Quality School-to-Work Opportunities for Young Women. Draft.

ERIC Educational Resources Information Center

Wider Opportunities for Women, Inc., Washington, DC.

This annotated bibliography lists 49 resources for ensuring high quality school-to-work opportunities for young women. These resources are grouped into 10 categories: print material for middle and high school girls; videos for middle and high school girls; administrator/school guides; curriculum guides/resources for teachers; resources for…

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…

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…

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"…

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…

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…

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…

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…

Ontology-guided organ detection to retrieve web images of disease manifestation: towards the construction of a consumer-based health image library.

PubMed

Chen, Yang; Ren, Xiaofeng; Zhang, Guo-Qiang; Xu, Rong

2013-01-01

Visual information is a crucial aspect of medical knowledge. Building a comprehensive medical image base, in the spirit of the Unified Medical Language System (UMLS), would greatly benefit patient education and self-care. However, collection and annotation of such a large-scale image base is challenging. To combine visual object detection techniques with medical ontology to automatically mine web photos and retrieve a large number of disease manifestation images with minimal manual labeling effort. As a proof of concept, we first learnt five organ detectors on three detection scales for eyes, ears, lips, hands, and feet. Given a disease, we used information from the UMLS to select affected body parts, ran the pretrained organ detectors on web images, and combined the detection outputs to retrieve disease images. Compared with a supervised image retrieval approach that requires training images for every disease, our ontology-guided approach exploits shared visual information of body parts across diseases. In retrieving 2220 web images of 32 diseases, we reduced manual labeling effort to 15.6% while improving the average precision by 3.9% from 77.7% to 81.6%. For 40.6% of the diseases, we improved the precision by 10%. The results confirm the concept that the web is a feasible source for automatic disease image retrieval for health image database construction. Our approach requires a small amount of manual effort to collect complex disease images, and to annotate them by standard medical ontology terms.

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…

The Atomic Papers: A citizen's guide to selected books and articles on the bomb, the arms race, nuclear power, the peace movement, and related issues

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

Burns, G.

The Atomic Papers annotates over 800 books published since 1945 and approximately 300 periodical articles since 1980 on every facet of the nuclear dilemma: the development and effects of the bomb, the arms race, nuclear proliferation, and the peace movement. Work on both sides of the nuclear power controversy also receives substantial attention. All references are to English-language material, and nearly half are to work published since 1980. The concluding chapter, ''The Art of Fission,'' describes over one hundred novels and stories with nuclear themes published since 1945--and, in a few cases, before that date.

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…

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…

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:…

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)…

Resources on Law-Related Education: Documents and Journal Articles in ERIC. Yearbook No. 3.

ERIC Educational Resources Information Center

Healy, Langdon T., Ed.; Vontz, Thomas S., Ed.

This ERIC resource is a guide to the array of law-related education (LRE) resources available to teachers. The annotated bibliography offers resources for essential knowledge of the law, innovative teaching methods, and guides to national LRE programs. Included in this collection are abstracts of LRE documents and journal articles, arranged…

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…

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…

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…

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…

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…

A Selective, Annotated Bibliography for the Language Laboratory, 1959-1971.

ERIC Educational Resources Information Center

Keck, Mary Ellen B., Comp.; Smith, William Flint, Comp.

This annotated bibliography lists 163 selected books, articles, and research reports concerning the language laboratory published from 1959 to 1972. It is intended for foreign language teachers and administrators seeking information on the planning, administration, operation, and installation of mediated language instruction. The bibliography is…

CONTINUING EDUCATION FOR WOMEN, A SELECTED ANNOTATED BIBLIOGRAPHY.

ERIC Educational Resources Information Center

SPIEGEL, JEANNE

A BIBLIOGRAPHY OF MATERIALS WAS PREPARED ON THE SUBJECT OF THE ECONOMIC, SOCIAL, AND PSYCHOLOGICAL CHALLENGES CONFRONTING WOMEN IN DEVELOPING THEIR CAPABILITIES THROUGH CONTINUING EDUCATION. SELECTIONS ARE NOT EVALUATED, BUT ANNOTATIONS SUMMARIZE CONTENT AND FINDINGS. INCLUDED ARE 30 BOOKS, REPORTS, AND PAMPHLETS, 24 PERIODICAL ARTICLES, FOUR…

A Call to Standardize Preanalytic Data Elements for Biospecimens, Part II.

PubMed

Robb, James A; Bry, Lynn; Sluss, Patrick M; Wagar, Elizabeth A; Kennedy, Mary F

2015-09-01

Biospecimens must have appropriate clinical annotation (data) to ensure optimal quality for both patient care and research. Additional clinical preanalytic variables are the focus of this continuing study. To complete the identification of the essential preanalytic variables (data fields) that can, and in some instances should, be attached to every collected biospecimen by adding the additional specific variables for clinical chemistry and microbiology to our original 170 variables. The College of American Pathologists Diagnostic Intelligence and Health Information Technology Committee sponsored a second Biorepository Working Group to complete the list of preanalytic variables for annotating biospecimens. Members of the second Biorepository Working Group are experts in clinical pathology and microbiology. Additional preanalytic area-specific variables were identified and ranked along with definitions and potential negative impacts if the variable is not attached to the biospecimen. The draft manuscript was reviewed by additional national and international stakeholders. Four additional required preanalytic variables were identified specifically for clinical chemistry and microbiology biospecimens that can be used as a guide for site-specific implementation into patient care and research biorepository processes. In our collective experience, selecting which of the many preanalytic variables to attach to any specific set of biospecimens used for patient care and/or research is often difficult. The additional ranked list should be of practical benefit when selecting preanalytic variables for a given biospecimen collection.

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…

Non-Formal Education and Agriculture: A Selected Annotated Bibliography. Annotated Bibliography #10.

ERIC Educational Resources Information Center

Sullivan, Karen Collamore; And Others

Intended for those actively engaged in nonformal education for development, this annotated bibliography contains approximately 300 references to documents that highlight issues concerning food production, distribution, and consumption. It also demonstrates education's role in enhancing developmental efforts to alleviate world hunger. Materials are…

Annotating ebony on the fly.

PubMed

Kohn, Michael H; Wittkopp, Patricia J

2007-07-01

The distinctive black phenotype of ebony mutants has made it one of the most widely used phenotypic markers in Drosophila genetics. Without doubt, ebony showcases the fruits of the fly community's labours to annotate gene function. As of this writing, FlyBase lists 142 references, 1277 fly stocks, 15 phenotypes and 44 alleles. In addition to its namesake pigmentation phenotype, ebony mutants affect other traits, including phototaxis and courtship. With phenotypic consequences of ebony variants readily apparent in the laboratory, does natural selection also see them in the wild? In this issue of Molecular Ecology, Pool & Aquadro investigate this question and found signs of natural selection on the ebony gene that appear to have resulted from selection for darker pigmentation at higher elevations in sub-Saharan populations of Drosophila melanogaster. Such findings from population genomic analysis of wild-derived strains should be included in gene annotations to provide a more holistic view of a gene's function. The evolutionary annotation of ebony added by Pool & Aquadro substantiates that pigmentation can be adaptive and implicates elevation as an important selective factor. This is important progress because the selective factors seem to differ between populations and species. In addition, the study raises issues to consider when extrapolating from selection at the molecular level to selection at the phenotypic level.

Health Communication: A Selected, Annotated Bibliography. Second Edition.

ERIC Educational Resources Information Center

Kreps, Gary L.

Selected on the basis of their clarity, comprehensiveness, and representativeness within the health communication field of study, the items in this annotated bibliography are intended for use by those wishing to develop health communication educational programs or conduct health communication research. The 42 titles deal with a variety of topics,…

Productivity: A Selected, Annotated Bibliography, 1976-78.

ERIC Educational Resources Information Center

Brand, Horst, Comp.; Belitsky, Harvey A., Comp.

This selective bibliography provides annotated references for 1,200 books and articles published between 1976 and 1978 which concern productivity--the relation between physical output and input. Publications deal with concepts and methods; measurement of levels and trends; the sources of productivity change (such as technology and research); the…

RADIOISOTOPE EXPERIMENTS IN HIGH SCHOOL BIOLOGY, AN ANNOTATED SELECTED BIBLIOGRAPHY.

ERIC Educational Resources Information Center

HURLBURT, EVELYN M.

SELECTED REFERENCES ON THE USE OF RADIOISOTOPES IN BIOLOGY ARE CONTAINED IN THIS ANNOTATED BIBLIOGRAPHY FOR SECONDARY SCHOOL STUDENTS. MATERIALS INCLUDED WERE PUBLISHED AFTER 1960 AND DEAL WITH THE PROPERTIES OF RADIATION, SIMPLE RADIATION DETECTION PROCEDURES, AND TECHNIQUES FOR USING RADIOISOTOPES EXPERIMENTALLY. THE REFERENCES ARE LISTED IN…

Academic Library Literature, 1981-1984: A Selective, Annotated Bibliography.

ERIC Educational Resources Information Center

Dolak, Frank J.

This annotated bibliography provides citations for selected English language journal articles and books that stress and address general, broad concerns of the academic library. Following citations of two bibliographies, the citations are presented in six general categories: (l) budgeting (12 titles); (2) decision making (9 titles); (3) directing…

MEGANTE: A Web-Based System for Integrated Plant Genome Annotation

PubMed Central

Numa, Hisataka; Itoh, Takeshi

2014-01-01

The recent advancement of high-throughput genome sequencing technologies has resulted in a considerable increase in demands for large-scale genome annotation. While annotation is a crucial step for downstream data analyses and experimental studies, this process requires substantial expertise and knowledge of bioinformatics. Here we present MEGANTE, a web-based annotation system that makes plant genome annotation easy for researchers unfamiliar with bioinformatics. Without any complicated configuration, users can perform genomic sequence annotations simply by uploading a sequence and selecting the species to query. MEGANTE automatically runs several analysis programs and integrates the results to select the appropriate consensus exon–intron structures and to predict open reading frames (ORFs) at each locus. Functional annotation, including a similarity search against known proteins and a functional domain search, are also performed for the predicted ORFs. The resultant annotation information is visualized with a widely used genome browser, GBrowse. For ease of analysis, the results can be downloaded in Microsoft Excel format. All of the query sequences and annotation results are stored on the server side so that users can access their own data from virtually anywhere on the web. The current release of MEGANTE targets 24 plant species from the Brassicaceae, Fabaceae, Musaceae, Poaceae, Salicaceae, Solanaceae, Rosaceae and Vitaceae families, and it allows users to submit a sequence up to 10 Mb in length and to save up to 100 sequences with the annotation information on the server. The MEGANTE web service is available at https://megante.dna.affrc.go.jp/. PMID:24253915

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…

MIPS: analysis and annotation of genome information in 2007

PubMed Central

Mewes, H. W.; Dietmann, S.; Frishman, D.; Gregory, R.; Mannhaupt, G.; Mayer, K. F. X.; Münsterkötter, M.; Ruepp, A.; Spannagl, M.; Stümpflen, V.; Rattei, T.

2008-01-01

The Munich Information Center for Protein Sequences (MIPS-GSF, Neuherberg, Germany) combines automatic processing of large amounts of sequences with manual annotation of selected model genomes. Due to the massive growth of the available data, the depth of annotation varies widely between independent databases. Also, the criteria for the transfer of information from known to orthologous sequences are diverse. To cope with the task of global in-depth genome annotation has become unfeasible. Therefore, our efforts are dedicated to three levels of annotation: (i) the curation of selected genomes, in particular from fungal and plant taxa (e.g. CYGD, MNCDB, MatDB), (ii) the comprehensive, consistent, automatic annotation employing exhaustive methods for the computation of sequence similarities and sequence-related attributes as well as the classification of individual sequences (SIMAP, PEDANT and FunCat) and (iii) the compilation of manually curated databases for protein interactions based on scrutinized information from the literature to serve as an accepted set of reliable annotated interaction data (MPACT, MPPI, CORUM). All databases and tools described as well as the detailed descriptions of our projects can be accessed through the MIPS web server (http://mips.gsf.de). PMID:18158298

MIPS: analysis and annotation of genome information in 2007.

PubMed

Mewes, H W; Dietmann, S; Frishman, D; Gregory, R; Mannhaupt, G; Mayer, K F X; Münsterkötter, M; Ruepp, A; Spannagl, M; Stümpflen, V; Rattei, T

2008-01-01

The Munich Information Center for Protein Sequences (MIPS-GSF, Neuherberg, Germany) combines automatic processing of large amounts of sequences with manual annotation of selected model genomes. Due to the massive growth of the available data, the depth of annotation varies widely between independent databases. Also, the criteria for the transfer of information from known to orthologous sequences are diverse. To cope with the task of global in-depth genome annotation has become unfeasible. Therefore, our efforts are dedicated to three levels of annotation: (i) the curation of selected genomes, in particular from fungal and plant taxa (e.g. CYGD, MNCDB, MatDB), (ii) the comprehensive, consistent, automatic annotation employing exhaustive methods for the computation of sequence similarities and sequence-related attributes as well as the classification of individual sequences (SIMAP, PEDANT and FunCat) and (iii) the compilation of manually curated databases for protein interactions based on scrutinized information from the literature to serve as an accepted set of reliable annotated interaction data (MPACT, MPPI, CORUM). All databases and tools described as well as the detailed descriptions of our projects can be accessed through the MIPS web server (http://mips.gsf.de).

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…

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…

Women, Islam, and Pakistan: A Selected Annotated Bibliography. Fulbright-Hays Summer Seminar Abroad Project.

ERIC Educational Resources Information Center

Phillips, Brenda

This bibliography features selected books, book chapters, research projects, and journal articles, published between 1953 and 1994, about the social, legal, economic, educational political, and professional position of Muslim Pakistani women. Sixteen of the references are annotated. An additional 41 bibliographic references to other materials, not…

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…

Higher Education Opportunities for Minorities and Women--Annotated Selections. 1989 Edition.

ERIC Educational Resources Information Center

Young, William C., Comp.; Hicks, Edward L., Comp.

Developed to assist parents and students in finding sources of postsecondary financial aid, this annotated listing provides a brief summary of the basic information about a selected list of financial aid sources designed primarily for minority groups and women, or available to all students. The listings provide names and addresses, background…

What's New in Children's Literature for the Children of Louisiana? A Selected Annotated Bibliography with Readability Levels (Selected) and Associated Louisiana Content Standards

ERIC Educational Resources Information Center

Webre, Elizabeth C.

2011-01-01

An annotated list of children's books published within the last 15 years and related to Louisiana culture, environment, and economics are linked to the Louisiana Content Standards. Readability levels of selected books are included, providing guidance as to whether a book is appropriate for independent student use. The thirty-three books listed are…

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…

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…

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

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…

Hand in Hand: Selected Reprints and Annotated Bibliography on Working with Students Who Are Deaf-Blind.

ERIC Educational Resources Information Center

Huebner, Kathleen Mary, Ed.; And Others

The items in this collection of reprints and an annotated bibliography were selected because of their value to classroom teachers working with deaf-blind students. Reprinted articles, originally published in various periodicals between 1978 and 1993, are grouped into five categories: (1) communication, (2) orientation and mobility, (3) functional…

Gender, Education and Development: A Partially Annotated and Selective Bibliography. Education Research Paper.

ERIC Educational Resources Information Center

Brock, Colin; Cammish, Nadine; Aedo-Richmond, Ruth; Narayanan, Aparna; Njoroge, Rose

This partially annotated and selected bibliography lists several hundred publications on the topics of gender and gender and education at the global level and in countries located in the following areas: Sub-Saharan Africa, North Africa and the Middle East, Asia, South Asia, Southeast Asia, Central and East Asia, Latin America, and Tropical Island…

RADIOISOTOPE TECHNIQUES FOR INSTRUCTION IN THE BIOLOGICAL SCIENCES, A LIST OF ANNOTATED REFERENCES.

ERIC Educational Resources Information Center

HURLBURT, EVELYN M.

REFERENCES TO BIOLOGICAL EXPERIMENTS THAT EMPHASIZE THE USE OF RADIOISOTOPES AS TRACERS ARE INCLUDED IN THIS ANNOTATED BIBLIOGRAPHY. MATERIALS INCLUDED ARE CONSIDERED TO BE READILY AVAILABLE AND WERE PUBLISHED AFTER 1960. SECTION I IS COMPOSED OF SELECTED SOURCES. ENTRIES INCLUDE (1) COMPLETE CITATIONS, (2) A BRIEF ANNOTATION, AND (3) LISTS OF…

Annotations of Early Childhood Assessment Instruments.

ERIC Educational Resources Information Center

Texas Education Agency, Austin.

An annotated listing of selected instruments which may be appropriate for the young child who appears to be handicapped and who may be placed in an early childhood unit for the handicapped is provided. The list is not comprehensive nor does it contain annotations from all companies which produce this type of material. It is offered to apprise…

Math for Learning, Math for Life: An Annotated Bibliography.

ERIC Educational Resources Information Center

Elliott, Claire

This document presents a total of 109 references and annotations of works that are in some way related to the topic of math for learning and life. Section 1 presents 68 annotated references with keywords drawn from the Canadian Literacy Thesaurus. Selected topics covered in the listed publications are as follows: numeracy as social practice; the…

BioSAVE: display of scored annotation within a sequence context.

PubMed

Pollock, Richard F; Adryan, Boris

2008-03-20

Visualization of sequence annotation is a common feature in many bioinformatics tools. For many applications it is desirable to restrict the display of such annotation according to a score cutoff, as biological interpretation can be difficult in the presence of the entire data. Unfortunately, many visualisation solutions are somewhat static in the way they handle such score cutoffs. We present BioSAVE, a sequence annotation viewer with on-the-fly selection of visualisation thresholds for each feature. BioSAVE is a versatile OS X program for visual display of scored features (annotation) within a sequence context. The program reads sequence and additional supplementary annotation data (e.g., position weight matrix matches, conservation scores, structural domains) from a variety of commonly used file formats and displays them graphically. Onscreen controls then allow for live customisation of these graphics, including on-the-fly selection of visualisation thresholds for each feature. Possible applications of the program include display of transcription factor binding sites in a genomic context or the visualisation of structural domain assignments in protein sequences and many more. The dynamic visualisation of these annotations is useful, e.g., for the determination of cutoff values of predicted features to match experimental data. Program, source code and exemplary files are freely available at the BioSAVE homepage.

BioSAVE: Display of scored annotation within a sequence context

PubMed Central

Pollock, Richard F; Adryan, Boris

2008-01-01

Background Visualization of sequence annotation is a common feature in many bioinformatics tools. For many applications it is desirable to restrict the display of such annotation according to a score cutoff, as biological interpretation can be difficult in the presence of the entire data. Unfortunately, many visualisation solutions are somewhat static in the way they handle such score cutoffs. Results We present BioSAVE, a sequence annotation viewer with on-the-fly selection of visualisation thresholds for each feature. BioSAVE is a versatile OS X program for visual display of scored features (annotation) within a sequence context. The program reads sequence and additional supplementary annotation data (e.g., position weight matrix matches, conservation scores, structural domains) from a variety of commonly used file formats and displays them graphically. Onscreen controls then allow for live customisation of these graphics, including on-the-fly selection of visualisation thresholds for each feature. Conclusion Possible applications of the program include display of transcription factor binding sites in a genomic context or the visualisation of structural domain assignments in protein sequences and many more. The dynamic visualisation of these annotations is useful, e.g., for the determination of cutoff values of predicted features to match experimental data. Program, source code and exemplary files are freely available at the BioSAVE homepage. PMID:18366701

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)

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

NegGOA: negative GO annotations selection using ontology structure.

PubMed

Fu, Guangyuan; Wang, Jun; Yang, Bo; Yu, Guoxian

2016-10-01

Predicting the biological functions of proteins is one of the key challenges in the post-genomic era. Computational models have demonstrated the utility of applying machine learning methods to predict protein function. Most prediction methods explicitly require a set of negative examples-proteins that are known not carrying out a particular function. However, Gene Ontology (GO) almost always only provides the knowledge that proteins carry out a particular function, and functional annotations of proteins are incomplete. GO structurally organizes more than tens of thousands GO terms and a protein is annotated with several (or dozens) of these terms. For these reasons, the negative examples of a protein can greatly help distinguishing true positive examples of the protein from such a large candidate GO space. In this paper, we present a novel approach (called NegGOA) to select negative examples. Specifically, NegGOA takes advantage of the ontology structure, available annotations and potentiality of additional annotations of a protein to choose negative examples of the protein. We compare NegGOA with other negative examples selection algorithms and find that NegGOA produces much fewer false negatives than them. We incorporate the selected negative examples into an efficient function prediction model to predict the functions of proteins in Yeast, Human, Mouse and Fly. NegGOA also demonstrates improved accuracy than these comparing algorithms across various evaluation metrics. In addition, NegGOA is less suffered from incomplete annotations of proteins than these comparing methods. The Matlab and R codes are available at https://sites.google.com/site/guoxian85/neggoa gxyu@swu.edu.cn Supplementary data are available at Bioinformatics online. © The Author 2016. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

A Selected Annotated Bibliography of Material Relating to Racism, Blacks, Chicanos, Native Americans and Multi-Ethnicity. Vol. 2.

ERIC Educational Resources Information Center

Michigan Education Association, East Lansing. Div. of Minority Affairs.

The second in the series, this selected annotated bibliography deals with new and recently discovered materials that address racism, Blacks, Chicanos, native Americans, and multi-ethnicity. This bibliography is considered to be not all inclusive but to reflect only on that material which is considered to be most representative of the realities…

A Selected Annotated Bibliography of Material Relating to Racism, Blacks, Chicanos, Native Americans and Multi-Ethnicity. Vol. 3.

ERIC Educational Resources Information Center

Michigan Education Association, East Lansing. Div. of Minority Affairs.

The third in the series, this selected annotated bibliography is composed of the most recently discovered materials pertaining to Blacks, Latinos, Native Americans, multi-ethnicity, and racism. It is said to reflect only that material considered most representative and most relevant in terms of the involvement and contributions that Third World…

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

An Annotated and Cross-Referenced Bibliography on Computer Security and Access Control in Computer Systems.

ERIC Educational Resources Information Center

Bergart, Jeffrey G.; And Others

This paper represents a careful study of published works on computer security and access control in computer systems. The study includes a selective annotated bibliography of some eighty-five important published results in the field and, based on these papers, analyzes the state of the art. In annotating these works, the authors try to be…

The Function of Annotations in the Comprehension of Scientific Texts: Cognitive Load Effects and the Impact of Verbal Ability

ERIC Educational Resources Information Center

Wallen, Erik; Plass, Jan L.; Brunken, Roland

2005-01-01

Students participated in a study (n = 98) investigating the effectiveness of three types of annotations on three learning outcome measures. The annotations were designed to support the cognitive processes in the comprehension of scientific texts, with a function to aid either the process of selecting relevant information, organizing the…

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)

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

Is the Juice Worth the Squeeze? Costs and Benefits of Multiple Human Annotators for Clinical Text De-identification.

PubMed

Carrell, David S; Cronkite, David J; Malin, Bradley A; Aberdeen, John S; Hirschman, Lynette

2016-08-05

Clinical text contains valuable information but must be de-identified before it can be used for secondary purposes. Accurate annotation of personally identifiable information (PII) is essential to the development of automated de-identification systems and to manual redaction of PII. Yet the accuracy of annotations may vary considerably across individual annotators and annotation is costly. As such, the marginal benefit of incorporating additional annotators has not been well characterized. This study models the costs and benefits of incorporating increasing numbers of independent human annotators to identify the instances of PII in a corpus. We used a corpus with gold standard annotations to evaluate the performance of teams of annotators of increasing size. Four annotators independently identified PII in a 100-document corpus consisting of randomly selected clinical notes from Family Practice clinics in a large integrated health care system. These annotations were pooled and validated to generate a gold standard corpus for evaluation. Recall rates for all PII types ranged from 0.90 to 0.98 for individual annotators to 0.998 to 1.0 for teams of three, when meas-ured against the gold standard. Median cost per PII instance discovered during corpus annotation ranged from $ 0.71 for an individual annotator to $ 377 for annotations discovered only by a fourth annotator. Incorporating a second annotator into a PII annotation process reduces unredacted PII and improves the quality of annotations to 0.99 recall, yielding clear benefit at reasonable cost; the cost advantages of annotation teams larger than two diminish rapidly.

Active learning reduces annotation time for clinical concept extraction.

PubMed

Kholghi, Mahnoosh; Sitbon, Laurianne; Zuccon, Guido; Nguyen, Anthony

2017-10-01

To investigate: (1) the annotation time savings by various active learning query strategies compared to supervised learning and a random sampling baseline, and (2) the benefits of active learning-assisted pre-annotations in accelerating the manual annotation process compared to de novo annotation. There are 73 and 120 discharge summary reports provided by Beth Israel institute in the train and test sets of the concept extraction task in the i2b2/VA 2010 challenge, respectively. The 73 reports were used in user study experiments for manual annotation. First, all sequences within the 73 reports were manually annotated from scratch. Next, active learning models were built to generate pre-annotations for the sequences selected by a query strategy. The annotation/reviewing time per sequence was recorded. The 120 test reports were used to measure the effectiveness of the active learning models. When annotating from scratch, active learning reduced the annotation time up to 35% and 28% compared to a fully supervised approach and a random sampling baseline, respectively. Reviewing active learning-assisted pre-annotations resulted in 20% further reduction of the annotation time when compared to de novo annotation. The number of concepts that require manual annotation is a good indicator of the annotation time for various active learning approaches as demonstrated by high correlation between time rate and concept annotation rate. Active learning has a key role in reducing the time required to manually annotate domain concepts from clinical free text, either when annotating from scratch or reviewing active learning-assisted pre-annotations. Copyright © 2017 Elsevier B.V. All rights reserved.

Knowledge Representation and Management. From Ontology to Annotation. Findings from the Yearbook 2015 Section on Knowledge Representation and Management.

PubMed

Charlet, J; Darmoni, S J

2015-08-13

To summarize the best papers in the field of Knowledge Representation and Management (KRM). A comprehensive review of medical informatics literature was performed to select some of the most interesting papers of KRM published in 2014. Four articles were selected, two focused on annotation and information retrieval using an ontology. The two others focused mainly on ontologies, one dealing with the usage of a temporal ontology in order to analyze the content of narrative document, one describing a methodology for building multilingual ontologies. Semantic models began to show their efficiency, coupled with annotation tools.

Open PHACTS computational protocols for in silico target validation of cellular phenotypic screens: knowing the knowns† †The authors declare no competing interests. ‡ ‡Electronic supplementary information (ESI) available: Pipeline Pilot protocols, xls file with the output of the Pipeline Pilot protocols, KNIME workflows, and supplementary figures showing the Pipeline Pilot protocols. See DOI: 10.1039/c6md00065g Click here for additional data file.

PubMed Central

Zdrazil, B.; Neefs, J.-M.; Van Vlijmen, H.; Herhaus, C.; Caracoti, A.; Brea, J.; Roibás, B.; Loza, M. I.; Queralt-Rosinach, N.; Furlong, L. I.; Gaulton, A.; Bartek, L.; Senger, S.; Chichester, C.; Engkvist, O.; Evelo, C. T.; Franklin, N. I.; Marren, D.; Ecker, G. F.

2016-01-01

Phenotypic screening is in a renaissance phase and is expected by many academic and industry leaders to accelerate the discovery of new drugs for new biology. Given that phenotypic screening is per definition target agnostic, the emphasis of in silico and in vitro follow-up work is on the exploration of possible molecular mechanisms and efficacy targets underlying the biological processes interrogated by the phenotypic screening experiments. Herein, we present six exemplar computational protocols for the interpretation of cellular phenotypic screens based on the integration of compound, target, pathway, and disease data established by the IMI Open PHACTS project. The protocols annotate phenotypic hit lists and allow follow-up experiments and mechanistic conclusions. The annotations included are from ChEMBL, ChEBI, GO, WikiPathways and DisGeNET. Also provided are protocols which select from the IUPHAR/BPS Guide to PHARMACOLOGY interaction file selective compounds to probe potential targets and a correlation robot which systematically aims to identify an overlap of active compounds in both the phenotypic as well as any kinase assay. The protocols are applied to a phenotypic pre-lamin A/C splicing assay selected from the ChEMBL database to illustrate the process. The computational protocols make use of the Open PHACTS API and data and are built within the Pipeline Pilot and KNIME workflow tools. PMID:27774140

A multilingual gold-standard corpus for biomedical concept recognition: the Mantra GSC

PubMed Central

Clematide, Simon; Akhondi, Saber A; van Mulligen, Erik M; Rebholz-Schuhmann, Dietrich

2015-01-01

Objective To create a multilingual gold-standard corpus for biomedical concept recognition. Materials and methods We selected text units from different parallel corpora (Medline abstract titles, drug labels, biomedical patent claims) in English, French, German, Spanish, and Dutch. Three annotators per language independently annotated the biomedical concepts, based on a subset of the Unified Medical Language System and covering a wide range of semantic groups. To reduce the annotation workload, automatically generated preannotations were provided. Individual annotations were automatically harmonized and then adjudicated, and cross-language consistency checks were carried out to arrive at the final annotations. Results The number of final annotations was 5530. Inter-annotator agreement scores indicate good agreement (median F-score 0.79), and are similar to those between individual annotators and the gold standard. The automatically generated harmonized annotation set for each language performed equally well as the best annotator for that language. Discussion The use of automatic preannotations, harmonized annotations, and parallel corpora helped to keep the manual annotation efforts manageable. The inter-annotator agreement scores provide a reference standard for gauging the performance of automatic annotation techniques. Conclusion To our knowledge, this is the first gold-standard corpus for biomedical concept recognition in languages other than English. Other distinguishing features are the wide variety of semantic groups that are being covered, and the diversity of text genres that were annotated. PMID:25948699

Annotation Graphs: A Graph-Based Visualization for Meta-Analysis of Data Based on User-Authored Annotations.

PubMed

Zhao, Jian; Glueck, Michael; Breslav, Simon; Chevalier, Fanny; Khan, Azam

2017-01-01

User-authored annotations of data can support analysts in the activity of hypothesis generation and sensemaking, where it is not only critical to document key observations, but also to communicate insights between analysts. We present annotation graphs, a dynamic graph visualization that enables meta-analysis of data based on user-authored annotations. The annotation graph topology encodes annotation semantics, which describe the content of and relations between data selections, comments, and tags. We present a mixed-initiative approach to graph layout that integrates an analyst's manual manipulations with an automatic method based on similarity inferred from the annotation semantics. Various visual graph layout styles reveal different perspectives on the annotation semantics. Annotation graphs are implemented within C8, a system that supports authoring annotations during exploratory analysis of a dataset. We apply principles of Exploratory Sequential Data Analysis (ESDA) in designing C8, and further link these to an existing task typology in the visualization literature. We develop and evaluate the system through an iterative user-centered design process with three experts, situated in the domain of analyzing HCI experiment data. The results suggest that annotation graphs are effective as a method of visually extending user-authored annotations to data meta-analysis for discovery and organization of ideas.

The evolution of function within the Nudix homology clan

PubMed Central

Srouji, John R.; Xu, Anting; Park, Annsea; Kirsch, Jack F.

2017-01-01

ABSTRACT The Nudix homology clan encompasses over 80,000 protein domains from all three domains of life, defined by homology to each other. Proteins with a domain from this clan fall into four general functional classes: pyrophosphohydrolases, isopentenyl diphosphate isomerases (IDIs), adenine/guanine mismatch‐specific adenine glycosylases (A/G‐specific adenine glycosylases), and nonenzymatic activities such as protein/protein interaction and transcriptional regulation. The largest group, pyrophosphohydrolases, encompasses more than 100 distinct hydrolase specificities. To understand the evolution of this vast number of activities, we assembled and analyzed experimental and structural data for 205 Nudix proteins collected from the literature. We corrected erroneous functions or provided more appropriate descriptions for 53 annotations described in the Gene Ontology Annotation database in this family, and propose 275 new experimentally‐based annotations. We manually constructed a structure‐guided sequence alignment of 78 Nudix proteins. Using the structural alignment as a seed, we then made an alignment of 347 “select” Nudix homology domains, curated from structurally determined, functionally characterized, or phylogenetically important Nudix domains. Based on our review of Nudix pyrophosphohydrolase structures and specificities, we further analyzed a loop region downstream of the Nudix hydrolase motif previously shown to contact the substrate molecule and possess known functional motifs. This loop region provides a potential structural basis for the functional radiation and evolution of substrate specificity within the hydrolase family. Finally, phylogenetic analyses of the 347 select protein domains and of the complete Nudix homology clan revealed general monophyly with regard to function and a few instances of probable homoplasy. Proteins 2017; 85:775–811. © 2016 Wiley Periodicals, Inc. PMID:27936487

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

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.

Selected Annotated Bibliography of Recent Research on Rural Life on Prince Edward Island. Community Studies, Report No. 1.

ERIC Educational Resources Information Center

MacDonald, Allan F.; O'Connell, Harold J.

A review of research literature was the first step in a program of rural development and planning on Prince Edward Island. This bibliography containing 80 annotations of extended research reports from 1960-71 is the result of that search. The bibliography is divided into 4 main subject areas within which the annotations appear in alphabetical…

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…

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

Qcorp: an annotated classification corpus of Chinese health questions.

PubMed

Guo, Haihong; Na, Xu; Li, Jiao

2018-03-22

Health question-answering (QA) systems have become a typical application scenario of Artificial Intelligent (AI). An annotated question corpus is prerequisite for training machines to understand health information needs of users. Thus, we aimed to develop an annotated classification corpus of Chinese health questions (Qcorp) and make it openly accessible. We developed a two-layered classification schema and corresponding annotation rules on basis of our previous work. Using the schema, we annotated 5000 questions that were randomly selected from 5 Chinese health websites within 6 broad sections. 8 annotators participated in the annotation task, and the inter-annotator agreement was evaluated to ensure the corpus quality. Furthermore, the distribution and relationship of the annotated tags were measured by descriptive statistics and social network map. The questions were annotated using 7101 tags that covers 29 topic categories in the two-layered schema. In our released corpus, the distribution of questions on the top-layered categories was treatment of 64.22%, diagnosis of 37.14%, epidemiology of 14.96%, healthy lifestyle of 10.38%, and health provider choice of 4.54% respectively. Both the annotated health questions and annotation schema were openly accessible on the Qcorp website. Users can download the annotated Chinese questions in CSV, XML, and HTML format. We developed a Chinese health question corpus including 5000 manually annotated questions. It is openly accessible and would contribute to the intelligent health QA system development.

Bibliocable.

ERIC Educational Resources Information Center

Cable Television Information Center, Washington, DC.

This selective, annotated bibliography covers 67 items published on cable television from 1968 to 1972. The books, articles, and report literature included here deal with these topics: introduction, background, access, applications, economic aspects, franchising, regulation, and technology. Each annotation includes sources and ordering…

A review and evaluation of the Langley Research Center's Scientific and Technical Information Program. Results of phase 5. Design and evaluation of STI systems: A selected, annotated bibliography

NASA Technical Reports Server (NTRS)

Pinelli, T. E.; Hinnebusch, P. A.; Jaffe, J. M.

1981-01-01

A selected, annotated bibliography of literature citations related to the design and evaluation of STI systems is presented. The use of manual and machine-readable literature searches; the review of numerous books, periodicals reports, and papers; and the selection and annotation of literature citations were required. The bibliography was produced because the information was needed to develop the methodology for the review and evaluation project, and a survey of the literature did not reveal the existence of a single published source of information pertinent to the subject. Approximately 200 citations are classified in four subject areas. The areas include information - general; information systems - design and evaluation, including information products and services; information - use and need; and information - economics.

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.

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…

A multilingual gold-standard corpus for biomedical concept recognition: the Mantra GSC.

PubMed

Kors, Jan A; Clematide, Simon; Akhondi, Saber A; van Mulligen, Erik M; Rebholz-Schuhmann, Dietrich

2015-09-01

To create a multilingual gold-standard corpus for biomedical concept recognition. We selected text units from different parallel corpora (Medline abstract titles, drug labels, biomedical patent claims) in English, French, German, Spanish, and Dutch. Three annotators per language independently annotated the biomedical concepts, based on a subset of the Unified Medical Language System and covering a wide range of semantic groups. To reduce the annotation workload, automatically generated preannotations were provided. Individual annotations were automatically harmonized and then adjudicated, and cross-language consistency checks were carried out to arrive at the final annotations. The number of final annotations was 5530. Inter-annotator agreement scores indicate good agreement (median F-score 0.79), and are similar to those between individual annotators and the gold standard. The automatically generated harmonized annotation set for each language performed equally well as the best annotator for that language. The use of automatic preannotations, harmonized annotations, and parallel corpora helped to keep the manual annotation efforts manageable. The inter-annotator agreement scores provide a reference standard for gauging the performance of automatic annotation techniques. To our knowledge, this is the first gold-standard corpus for biomedical concept recognition in languages other than English. Other distinguishing features are the wide variety of semantic groups that are being covered, and the diversity of text genres that were annotated. © The Author 2015. Published by Oxford University Press on behalf of the American Medical Informatics Association.

Articles Pertinent to the Campus Press: A Selected Annotated Bibliography

ERIC Educational Resources Information Center

Ardoin, Birthney; And Others

1977-01-01

Lists and annotates articles dealing with such topics as advertising, audience analysis, broadcasting, broadcast law, criticism and defense of media, editorial policy and methods, media policy and methods, journalism education, press law, and school publications. (GW)

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

Real-time image annotation by manifold-based biased Fisher discriminant analysis

NASA Astrophysics Data System (ADS)

Ji, Rongrong; Yao, Hongxun; Wang, Jicheng; Sun, Xiaoshuai; Liu, Xianming

2008-01-01

Automatic Linguistic Annotation is a promising solution to bridge the semantic gap in content-based image retrieval. However, two crucial issues are not well addressed in state-of-art annotation algorithms: 1. The Small Sample Size (3S) problem in keyword classifier/model learning; 2. Most of annotation algorithms can not extend to real-time online usage due to their low computational efficiencies. This paper presents a novel Manifold-based Biased Fisher Discriminant Analysis (MBFDA) algorithm to address these two issues by transductive semantic learning and keyword filtering. To address the 3S problem, Co-Training based Manifold learning is adopted for keyword model construction. To achieve real-time annotation, a Bias Fisher Discriminant Analysis (BFDA) based semantic feature reduction algorithm is presented for keyword confidence discrimination and semantic feature reduction. Different from all existing annotation methods, MBFDA views image annotation from a novel Eigen semantic feature (which corresponds to keywords) selection aspect. As demonstrated in experiments, our manifold-based biased Fisher discriminant analysis annotation algorithm outperforms classical and state-of-art annotation methods (1.K-NN Expansion; 2.One-to-All SVM; 3.PWC-SVM) in both computational time and annotation accuracy with a large margin.

Freedom of Speech: A Selected, Annotated Basic Bibliography.

ERIC Educational Resources Information Center

Tedford, Thomas L.

Restricted to books on freedom of speech, this annotated bibliography offers a list of 38 references pertinent to the subject. Also included is a list of 18 ERIC documents on freedom of speech, and information on how to order them. (JC)

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)

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

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…

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,…

Sheep genome functional annotation reveals proximal regulatory elements contributed to the evolution of modern breeds.

PubMed

Naval-Sanchez, Marina; Nguyen, Quan; McWilliam, Sean; Porto-Neto, Laercio R; Tellam, Ross; Vuocolo, Tony; Reverter, Antonio; Perez-Enciso, Miguel; Brauning, Rudiger; Clarke, Shannon; McCulloch, Alan; Zamani, Wahid; Naderi, Saeid; Rezaei, Hamid Reza; Pompanon, Francois; Taberlet, Pierre; Worley, Kim C; Gibbs, Richard A; Muzny, Donna M; Jhangiani, Shalini N; Cockett, Noelle; Daetwyler, Hans; Kijas, James

2018-02-28

Domestication fundamentally reshaped animal morphology, physiology and behaviour, offering the opportunity to investigate the molecular processes driving evolutionary change. Here we assess sheep domestication and artificial selection by comparing genome sequence from 43 modern breeds (Ovis aries) and their Asian mouflon ancestor (O. orientalis) to identify selection sweeps. Next, we provide a comparative functional annotation of the sheep genome, validated using experimental ChIP-Seq of sheep tissue. Using these annotations, we evaluate the impact of selection and domestication on regulatory sequences and find that sweeps are significantly enriched for protein coding genes, proximal regulatory elements of genes and genome features associated with active transcription. Finally, we find individual sites displaying strong allele frequency divergence are enriched for the same regulatory features. Our data demonstrate that remodelling of gene expression is likely to have been one of the evolutionary forces that drove phenotypic diversification of this common livestock species.

AnnotateGenomicRegions: a web application.

PubMed

Zammataro, Luca; DeMolfetta, Rita; Bucci, Gabriele; Ceol, Arnaud; Muller, Heiko

2014-01-01

Modern genomic technologies produce large amounts of data that can be mapped to specific regions in the genome. Among the first steps in interpreting the results is annotation of genomic regions with known features such as genes, promoters, CpG islands etc. Several tools have been published to perform this task. However, using these tools often requires a significant amount of bioinformatics skills and/or downloading and installing dedicated software. Here we present AnnotateGenomicRegions, a web application that accepts genomic regions as input and outputs a selection of overlapping and/or neighboring genome annotations. Supported organisms include human (hg18, hg19), mouse (mm8, mm9, mm10), zebrafish (danRer7), and Saccharomyces cerevisiae (sacCer2, sacCer3). AnnotateGenomicRegions is accessible online on a public server or can be installed locally. Some frequently used annotations and genomes are embedded in the application while custom annotations may be added by the user. The increasing spread of genomic technologies generates the need for a simple-to-use annotation tool for genomic regions that can be used by biologists and bioinformaticians alike. AnnotateGenomicRegions meets this demand. AnnotateGenomicRegions is an open-source web application that can be installed on any personal computer or institute server. AnnotateGenomicRegions is available at: http://cru.genomics.iit.it/AnnotateGenomicRegions.

AnnotateGenomicRegions: a web application

PubMed Central

2014-01-01

Background Modern genomic technologies produce large amounts of data that can be mapped to specific regions in the genome. Among the first steps in interpreting the results is annotation of genomic regions with known features such as genes, promoters, CpG islands etc. Several tools have been published to perform this task. However, using these tools often requires a significant amount of bioinformatics skills and/or downloading and installing dedicated software. Results Here we present AnnotateGenomicRegions, a web application that accepts genomic regions as input and outputs a selection of overlapping and/or neighboring genome annotations. Supported organisms include human (hg18, hg19), mouse (mm8, mm9, mm10), zebrafish (danRer7), and Saccharomyces cerevisiae (sacCer2, sacCer3). AnnotateGenomicRegions is accessible online on a public server or can be installed locally. Some frequently used annotations and genomes are embedded in the application while custom annotations may be added by the user. Conclusions The increasing spread of genomic technologies generates the need for a simple-to-use annotation tool for genomic regions that can be used by biologists and bioinformaticians alike. AnnotateGenomicRegions meets this demand. AnnotateGenomicRegions is an open-source web application that can be installed on any personal computer or institute server. AnnotateGenomicRegions is available at: http://cru.genomics.iit.it/AnnotateGenomicRegions. PMID:24564446

Organizational Communication in Health Care Settings: A Selected Annotated Bibliography.

ERIC Educational Resources Information Center

Taylor, James A.; And Others

This annotated bibliography on health related subjects lists more than 300 items emphasizing the relationships between communication, occupational role, technology, organizational design, and institutional policy. Items are classified (and cross-indexed) according to the following variables: organizational design, policy, communication,…

People: Annotated Multiethnic Bibliography K-12.

ERIC Educational Resources Information Center

Gilmore, Dolores D., Comp.; Petrie, Kenneth, Comp.

This annotated bibliography has been compiled to assist personnel in the selection of multiethnic media for schools. The bibliography includes sections entitled "Asian Americans,""Jewish Americans,""Mexican Americans,""Native Americans,""Puerto Rican Americans,""Other Hyphenated Americans," and "All Americans (Multiethnic)." The entries for the…

Appropriate Technology--A Selected, Annotated Bibliography No. 8.

ERIC Educational Resources Information Center

Andree, Carolyn

Presented is an annotated bibliography of "appropriate technology" (AT) publications. The bibliography is divided into the following sections. Philosophy and overview section includes works describing the interrelationship of technology with other facets of development; place of technology in international relations; criteria for…

Articles on Mass Communication in U.S. and Foreign Journals: A Selected Annotated Bibliography--October, November, December 1978.

ERIC Educational Resources Information Center

McKerns, Joseph P.; Delahaye, Alfred N.

1979-01-01

Lists and annotates more than 200 articles on mass communication, grouped according to topic. Topics include advertising, broadcasting, courts and law, education for journalism, international, management, public relations, and visual communications. (GT)

The KIT Motion-Language Dataset.

PubMed

Plappert, Matthias; Mandery, Christian; Asfour, Tamim

2016-12-01

Linking human motion and natural language is of great interest for the generation of semantic representations of human activities as well as for the generation of robot activities based on natural language input. However, although there have been years of research in this area, no standardized and openly available data set exists to support the development and evaluation of such systems. We, therefore, propose the Karlsruhe Institute of Technology (KIT) Motion-Language Dataset, which is large, open, and extensible. We aggregate data from multiple motion capture databases and include them in our data set using a unified representation that is independent of the capture system or marker set, making it easy to work with the data regardless of its origin. To obtain motion annotations in natural language, we apply a crowd-sourcing approach and a web-based tool that was specifically build for this purpose, the Motion Annotation Tool. We thoroughly document the annotation process itself and discuss gamification methods that we used to keep annotators motivated. We further propose a novel method, perplexity-based selection, which systematically selects motions for further annotation that are either under-represented in our data set or that have erroneous annotations. We show that our method mitigates the two aforementioned problems and ensures a systematic annotation process. We provide an in-depth analysis of the structure and contents of our resulting data set, which, as of October 10, 2016, contains 3911 motions with a total duration of 11.23 hours and 6278 annotations in natural language that contain 52,903 words. We believe this makes our data set an excellent choice that enables more transparent and comparable research in this important area.

TwiMed: Twitter and PubMed Comparable Corpus of Drugs, Diseases, Symptoms, and Their Relations

PubMed Central

Miyao, Yusuke; Collier, Nigel

2017-01-01

Background Work on pharmacovigilance systems using texts from PubMed and Twitter typically target at different elements and use different annotation guidelines resulting in a scenario where there is no comparable set of documents from both Twitter and PubMed annotated in the same manner. Objective This study aimed to provide a comparable corpus of texts from PubMed and Twitter that can be used to study drug reports from these two sources of information, allowing researchers in the area of pharmacovigilance using natural language processing (NLP) to perform experiments to better understand the similarities and differences between drug reports in Twitter and PubMed. Methods We produced a corpus comprising 1000 tweets and 1000 PubMed sentences selected using the same strategy and annotated at entity level by the same experts (pharmacists) using the same set of guidelines. Results The resulting corpus, annotated by two pharmacists, comprises semantically correct annotations for a set of drugs, diseases, and symptoms. This corpus contains the annotations for 3144 entities, 2749 relations, and 5003 attributes. Conclusions We present a corpus that is unique in its characteristics as this is the first corpus for pharmacovigilance curated from Twitter messages and PubMed sentences using the same data selection and annotation strategies. We believe this corpus will be of particular interest for researchers willing to compare results from pharmacovigilance systems (eg, classifiers and named entity recognition systems) when using data from Twitter and from PubMed. We hope that given the comprehensive set of drug names and the annotated entities and relations, this corpus becomes a standard resource to compare results from different pharmacovigilance studies in the area of NLP. PMID:28468748

TwiMed: Twitter and PubMed Comparable Corpus of Drugs, Diseases, Symptoms, and Their Relations.

PubMed

Alvaro, Nestor; Miyao, Yusuke; Collier, Nigel

2017-05-03

Work on pharmacovigilance systems using texts from PubMed and Twitter typically target at different elements and use different annotation guidelines resulting in a scenario where there is no comparable set of documents from both Twitter and PubMed annotated in the same manner. This study aimed to provide a comparable corpus of texts from PubMed and Twitter that can be used to study drug reports from these two sources of information, allowing researchers in the area of pharmacovigilance using natural language processing (NLP) to perform experiments to better understand the similarities and differences between drug reports in Twitter and PubMed. We produced a corpus comprising 1000 tweets and 1000 PubMed sentences selected using the same strategy and annotated at entity level by the same experts (pharmacists) using the same set of guidelines. The resulting corpus, annotated by two pharmacists, comprises semantically correct annotations for a set of drugs, diseases, and symptoms. This corpus contains the annotations for 3144 entities, 2749 relations, and 5003 attributes. We present a corpus that is unique in its characteristics as this is the first corpus for pharmacovigilance curated from Twitter messages and PubMed sentences using the same data selection and annotation strategies. We believe this corpus will be of particular interest for researchers willing to compare results from pharmacovigilance systems (eg, classifiers and named entity recognition systems) when using data from Twitter and from PubMed. We hope that given the comprehensive set of drug names and the annotated entities and relations, this corpus becomes a standard resource to compare results from different pharmacovigilance studies in the area of NLP. ©Nestor Alvaro, Yusuke Miyao, Nigel Collier. Originally published in JMIR Public Health and Surveillance (http://publichealth.jmir.org), 03.05.2017.

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…

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.

Peaceful Peoples: An Annotated Bibliography.

ERIC Educational Resources Information Center

Bonta, Bruce D.

This annotated bibliography includes 438 selected references to books, journal articles, essays within edited volumes, and dissertations that provide significant information about peaceful societies. Peaceful societies are groups that have developed harmonious social structures that allow them to get along with each other, and with outsiders,…

A Selected, Annotated Bibliography for Fitness Educators.

ERIC Educational Resources Information Center

Whitehead, James R.

1992-01-01

This annotated bibliography, designed for practitioners and those involved in improving practice, contains 218 citations on topics related to youth physical fitness. Topics include children's fitness and activity status; contents of, and rationale for, fitness education; program suggestions, methods, and strategies; drug problems; and fitness…

Selected and Annotated Bibliography on the Processes of Change.

ERIC Educational Resources Information Center

Kurland, Norman D., Comp.; Miller, Richard I., Comp.

Over 170 books, booklets, articles, bibliographies, periodicals, and unpublished items on anthropology, sociology, education, industry, and technology, medicine, political science, and psychology are listed in this annotated bibliography on the processes of change. These documents, which treat such subjects as educational change, social and…

Religion and Communication: A Selected, Annotated Basic Bibliography.

ERIC Educational Resources Information Center

Tate, Eugene D.; McConnell, Kathleen

This annotated bibliography provides a broad perspective on the way religion and communication relate to one another. Forty-two references are listed in the areas of (1) "Religion and Communication Theory"; (2) "Religion and Language"; (3) "Televangelism and Televangelists"; (4) "Historical Roots of Religion and…

Rhetoric of India: A Selected, Interdisciplinary Bibliography.

ERIC Educational Resources Information Center

Chandler, Daniel Ross

Focusing on the philosophical and religious literature of India, this updated annotated bibliography discusses 33 books published between 1961 and 1993. Books annotated in the bibliography discuss: the foundations of Indian culture, the rhetorical tradition, Indian literary traditions, the historical-cultural context, toward a rhetorical-cultural…

Public Relations: Selected, Annotated Bibliography.

ERIC Educational Resources Information Center

Demo, Penny

Designed for students and practitioners of public relations (PR), this annotated bibliography focuses on recent journal articles and ERIC documents. The 34 citations include the following: (1) surveys of public relations professionals on career-related education; (2) literature reviews of research on measurement and evaluation of PR and…

Articles on Mass Communication in U.S. and Foreign Journals: A Selected Annotated Bibliography--January, February, March 1979.

ERIC Educational Resources Information Center

McKerns, Joseph P.; Delahaye, Alfred N.

1979-01-01

Lists and annotates more than 200 articles on mass communication, grouped according to topic. Topics include advertising, broadcasting, courts and law, government and media, history and biography, international, management, public relations, and visual communication. (GT)

Rural Development Literature 1976-1977: An Updated Annotated Bibliography.

ERIC Educational Resources Information Center

Buzzard, Shirley, Comp.

More than 100 books and articles on rural development published during 1976-77 are annotated in this selective bibliography. Concentrating on social science literature, the bibliography is interdisciplinary in nature, spanning agricultural economics, anthropology, community development, community health, and rural sociology. Types of works…

A Selected Annotated Bibliography of Educational Materials for Teachers of Limited English Speaking Vocational Students and a Selected Review of Its Literature. Technical Assistance Services: Illinois Special Needs Populations.

ERIC Educational Resources Information Center

McCarthy, JoAnn; Kang, Margaret

The annotated bibliography contained in the second part of this two-part document is a presentation of the literature related to the field of English language teaching within a vocational training framework. The review, the first two/thirds of the document, addresses itself primarily to the monolingual vocational teacher who may not have at his or…

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…

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.…

Semantic annotation in biomedicine: the current landscape.

PubMed

Jovanović, Jelena; Bagheri, Ebrahim

2017-09-22

The abundance and unstructured nature of biomedical texts, be it clinical or research content, impose significant challenges for the effective and efficient use of information and knowledge stored in such texts. Annotation of biomedical documents with machine intelligible semantics facilitates advanced, semantics-based text management, curation, indexing, and search. This paper focuses on annotation of biomedical entity mentions with concepts from relevant biomedical knowledge bases such as UMLS. As a result, the meaning of those mentions is unambiguously and explicitly defined, and thus made readily available for automated processing. This process is widely known as semantic annotation, and the tools that perform it are known as semantic annotators.Over the last dozen years, the biomedical research community has invested significant efforts in the development of biomedical semantic annotation technology. Aiming to establish grounds for further developments in this area, we review a selected set of state of the art biomedical semantic annotators, focusing particularly on general purpose annotators, that is, semantic annotation tools that can be customized to work with texts from any area of biomedicine. We also examine potential directions for further improvements of today's annotators which could make them even more capable of meeting the needs of real-world applications. To motivate and encourage further developments in this area, along the suggested and/or related directions, we review existing and potential practical applications and benefits of semantic annotators.

Analysis of disease-associated objects at the Rat Genome Database

PubMed Central

Wang, Shur-Jen; Laulederkind, Stanley J. F.; Hayman, G. T.; Smith, Jennifer R.; Petri, Victoria; Lowry, Timothy F.; Nigam, Rajni; Dwinell, Melinda R.; Worthey, Elizabeth A.; Munzenmaier, Diane H.; Shimoyama, Mary; Jacob, Howard J.

2013-01-01

The Rat Genome Database (RGD) is the premier resource for genetic, genomic and phenotype data for the laboratory rat, Rattus norvegicus. In addition to organizing biological data from rats, the RGD team focuses on manual curation of gene–disease associations for rat, human and mouse. In this work, we have analyzed disease-associated strains, quantitative trait loci (QTL) and genes from rats. These disease objects form the basis for seven disease portals. Among disease portals, the cardiovascular disease and obesity/metabolic syndrome portals have the highest number of rat strains and QTL. These two portals share 398 rat QTL, and these shared QTL are highly concentrated on rat chromosomes 1 and 2. For disease-associated genes, we performed gene ontology (GO) enrichment analysis across portals using RatMine enrichment widgets. Fifteen GO terms, five from each GO aspect, were selected to profile enrichment patterns of each portal. Of the selected biological process (BP) terms, ‘regulation of programmed cell death’ was the top enriched term across all disease portals except in the obesity/metabolic syndrome portal where ‘lipid metabolic process’ was the most enriched term. ‘Cytosol’ and ‘nucleus’ were common cellular component (CC) annotations for disease genes, but only the cancer portal genes were highly enriched with ‘nucleus’ annotations. Similar enrichment patterns were observed in a parallel analysis using the DAVID functional annotation tool. The relationship between the preselected 15 GO terms and disease terms was examined reciprocally by retrieving rat genes annotated with these preselected terms. The individual GO term–annotated gene list showed enrichment in physiologically related diseases. For example, the ‘regulation of blood pressure’ genes were enriched with cardiovascular disease annotations, and the ‘lipid metabolic process’ genes with obesity annotations. Furthermore, we were able to enhance enrichment of neurological diseases by combining ‘G-protein coupled receptor binding’ annotated genes with ‘protein kinase binding’ annotated genes. Database URL: http://rgd.mcw.edu PMID:23794737

Articles on Mass Communication in U.S. and Foreign Journals: A Selected Annotated Bibliography--July, August, September 1979.

ERIC Educational Resources Information Center

Delahaye, Alfred N.; McKerns, Joseph P.

1979-01-01

Lists and annotates more than 200 articles on mass communication, grouped according to topic. Topics include advertising, broadcasting, courts and law, journalism education, history and biography, international, public relations, visual communication, and women and media. (GT)

Skin Cancer Education Materials: Selected Annotations.

ERIC Educational Resources Information Center

National Cancer Inst. (NIH), Bethesda, MD.

This annotated bibliography presents 85 entries on a variety of approaches to cancer education. The entries are grouped under three broad headings, two of which contain smaller sub-divisions. The first heading, Public Education, contains prevention and general information, and non-print materials. The second heading, Professional Education,…

Sexually Transmitted Diseases: A Selective, Annotated Bibliography.

ERIC Educational Resources Information Center

Planned Parenthood Federation of America, Inc., New York, NY. Education Dept.

This document contains a reference sheet and an annotated bibliography concerned with sexually transmitted diseases (STD). The reference sheet provides a brief, accurate overview of STDs which includes both statistical and background information. The bibliography contains 83 entries, listed alphabetically, that deal with STDs. Books and articles…

Training Methodology. Part 3: Instructional Methods and Techniques; an Annotated Bibliography.

ERIC Educational Resources Information Center

National Inst. of Mental Health (DHEW), Bethesda, MD.

One of a series of bibliographies within a larger series on mental health inservice training and training methodology, this publication contains 346 abstracts, annotations, and other recent selected references (largely 1960-68) on apprenticeship, coaching, programmed instruction, correspondence study, lectures, group discussion, meetings,…

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…

Persuasion: Attitude/Behavior Change. A Selected, Annotated Bibliography.

ERIC Educational Resources Information Center

Benoit, William L.

Designed for teachers, students and researchers of the psychological dimensions of attitude and behavior change, this annotated bibliography lists books, bibliographies and articles on the subject ranging from general introductions and surveys through specific research studies, and from theoretical position essays to literature reviews. The 42…

Articles on Mass Communication in U.S. and Foreign Journals: A Selected Annotated Bibliography--April, May, June 1979.

ERIC Educational Resources Information Center

McKerns, Joseph P.; Delahaye, Alfred N.

1979-01-01

Lists and annotates 200 articles on mass communication, grouped according to topic. Topics include advertising, audience and communicator analysis, broadcasting, courts and law, education for journalism, government and media, international, management, public relations, and visual communication. (GT)

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…

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…

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…

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…

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…

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…

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.

An effective approach for annotation of protein families with low sequence similarity and conserved motifs: identifying GDSL hydrolases across the plant kingdom.

PubMed

Vujaklija, Ivan; Bielen, Ana; Paradžik, Tina; Biđin, Siniša; Goldstein, Pavle; Vujaklija, Dušica

2016-02-18

The massive accumulation of protein sequences arising from the rapid development of high-throughput sequencing, coupled with automatic annotation, results in high levels of incorrect annotations. In this study, we describe an approach to decrease annotation errors of protein families characterized by low overall sequence similarity. The GDSL lipolytic family comprises proteins with multifunctional properties and high potential for pharmaceutical and industrial applications. The number of proteins assigned to this family has increased rapidly over the last few years. In particular, the natural abundance of GDSL enzymes reported recently in plants indicates that they could be a good source of novel GDSL enzymes. We noticed that a significant proportion of annotated sequences lack specific GDSL motif(s) or catalytic residue(s). Here, we applied motif-based sequence analyses to identify enzymes possessing conserved GDSL motifs in selected proteomes across the plant kingdom. Motif-based HMM scanning (Viterbi decoding-VD and posterior decoding-PD) and the here described PD/VD protocol were successfully applied on 12 selected plant proteomes to identify sequences with GDSL motifs. A significant number of identified GDSL sequences were novel. Moreover, our scanning approach successfully detected protein sequences lacking at least one of the essential motifs (171/820) annotated by Pfam profile search (PfamA) as GDSL. Based on these analyses we provide a curated list of GDSL enzymes from the selected plants. CLANS clustering and phylogenetic analysis helped us to gain a better insight into the evolutionary relationship of all identified GDSL sequences. Three novel GDSL subfamilies as well as unreported variations in GDSL motifs were discovered in this study. In addition, analyses of selected proteomes showed a remarkable expansion of GDSL enzymes in the lycophyte, Selaginella moellendorffii. Finally, we provide a general motif-HMM scanner which is easily accessible through the graphical user interface ( http://compbio.math.hr/ ). Our results show that scanning with a carefully parameterized motif-HMM is an effective approach for annotation of protein families with low sequence similarity and conserved motifs. The results of this study expand current knowledge and provide new insights into the evolution of the large GDSL-lipase family in land plants.

Abstracting/Annotating. ERIC Processing Manual, Section VI.

ERIC Educational Resources Information Center

Brandhorst, Ted, Ed.

Rules and guidelines are provided for the preparation of abstracts and annotations for documents and journal articles entering the ERIC database. Various types of abstracts are defined, including the Informative, Indicative, and mixed Informative-Indicative. Advice is given on how to select the abstract type appropriate for the particular…

Articles on Mass Communication in U.S. and Foreign Journals: A Selected Annotated Bibliography--October, November, December 1979.

ERIC Educational Resources Information Center

McKerns, Joseph P.; Delahaye, Alfred N.

1980-01-01

Lists and annotates more than 200 articles on mass communication, grouped according to topic. Topics include advertising, broadcasting, courts and law, criticism and defense of media, history and biography, international, public relations, visual communication, and women and media. (GT)

Nutrition & Adolescent Pregnancy: A Selected Annotated Bibliography.

ERIC Educational Resources Information Center

National Agricultural Library (USDA), Washington, DC.

This annotated bibliography on nutrition and adolescent pregnancy is intended to be a source of technical assistance for nurses, nutritionists, physicians, educators, social workers, and other personnel concerned with improving the health of teenage mothers and their babies. It is divided into two major sections. The first section lists selected…

Staff Differentiation. An Annotated Bibliography.

ERIC Educational Resources Information Center

Marin County Superintendent of Schools, Corte Madera, CA.

This annotated bibliography reviews selected literature focusing on the concept of staff differentiation. Included are 62 items (dated 1966-1970), along with a list of mailing addresses where copies of individual items can be obtained. Also a list of 31 staff differentiation projects receiving financial assistance from the U.S. Office of Education…

Environment and the Community: An Annotated Bibliography.

ERIC Educational Resources Information Center

Department of Housing and Urban Development, Washington, DC.

Three hundred and nine citations of books, reports, and articles dating from 1964 to 1971 are included in this annotated bibliography, intended as a selection tool for concerned citizens, architects, builders, and city planners emphasizing the environment of American cities and communities. It is topically arranged into sixteen broad sections with…

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…

Migrant Education: An Annotated Bibliography.

ERIC Educational Resources Information Center

Palmer, Barbara C., Comp.

Materials selected for inclusion in the annotated bibliography of 139 publications from 1970 to 1980 give a general understanding of the lives of migrant children, their educational needs and problems, and various attempts made to meet those needs. The bibliography, a valuable tool for researchers and teachers in migrant education, includes books,…

Selected Annotated Bibliography of Deaf-Blind Prevocational Training Literature.

ERIC Educational Resources Information Center

Stoddard, Denis W.; Glazer, Jamie

Presented is an annotated bibliography of 47 documents relating to prevocational training of deaf-blind children. Entries include books, journal articles, conference proceedings, and regional center reports and usually provide information on author, title, source, publication date, and a review (including a brief description of the type and…

An Annotated Bibliography of Adult ESL Instructional Materials.

ERIC Educational Resources Information Center

Escobar, Joanna Sculley; Daugherty, John

This annotated bibliography of adult English as a second language (ESL) student materials, available at the Illinois ESL/Adult Basic Education (ABE) Services Center, was prepared for adult ESL administrators, coordinators, teachers, and teacher aides to provide a representative sampling of materials available and to assist in the selection of…

Work and Family Functioning: An Annotated Bibliography Selected from Family Database.

ERIC Educational Resources Information Center

Davis, Mari, Comp.

This annotated bibliography lists works published in Australia on issues regarding work obligations and family responsibilities. All works cited are included in Australia's FAMILY database. The following topics are covered: (1) adolescents and attitudes to employment (14 citations); (2) the aged and employment (20 citations); (3) career…

Annotated Psychodynamic Bibliography for Residents in Psychiatry

PubMed Central

CALIGOR, EVE

1996-01-01

The author provides an annotated bibliography to introduce psychodynamic psychotherapy and psychoanalysis to residents in psychiatry. The emphasis of the selection is on relevance to practice. The entries are grouped by topic, levels of difficulty are noted, and readings are identified as being of either current or historic relevance. PMID:22700303

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,…

Best Books of 1977

ERIC Educational Resources Information Center

Gerhardt, Lillian N.; And Others

1977-01-01

School Library Journal book review editors have selected and annotated their choices for the best children's and young adults' books from those books that were submitted for review during 1977 by general book trade book publishers. Included in the annotations are: author, title, publisher, price, and recommended reading and interest levels. (JPF)

Ethical Responsibility in Communication: A Selected, Annotated Bibliography. Fourth Edition.

ERIC Educational Resources Information Center

Johannesen, Richard L.

Representing works published between 1970 and 1984, this annotated bibliography identifies a variety of readings that explore fundamental issues of ethics in interpersonal, public, and mass communication, and that examine from an ethical viewpoint how to and whether to employ particular communication tactics or techniques. The bibliography…

Selected Bibliography of Egyptian Educational Materials. Vol. 5, No. 1, 1979.

ERIC Educational Resources Information Center

Al-Ahram Center for Scientific Translations, Cairo (Egypt).

This annotated bibliography contains 166 English language annotations of newspaper, journal, and government publications from Egypt on the topic of education. All items were published in 1979. The items are categorized by subject areas including: adult education, art education; basic education; child care, education and psychology; demographic…

Personal Assistance Services (PAS): Toward Universal Access to Support. Annotated Bibliography.

ERIC Educational Resources Information Center

Racino, Julie Ann

This annotated bibliography provides approximately 100 summaries and evaluations of documents, published from 1979 to 1995, on personal assistance services (PAS) for individuals with disabilities. Studies and articles were selected for inclusion based upon their capacity to inform the development of PAS models, including conceptual, policy, and…

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…

Collection Evaluation Techniques: A Short, Selective, Practical, Current, Annotated Bibliography, 1990-1998. RUSA Occasional Papers Number 24.

ERIC Educational Resources Information Center

Strohl, Bonnie, Comp.

This bibliography contains annotations of 110 journal articles on topics related to library collection evaluation techniques, including academic library collections, access-vs-ownership, "Books for College Libraries," business collections, the OCLC/AMIGOS Collection Analysis CD, circulation data, citation-checking, collection bias,…

Children and Poetry: A Selective, Annotated Bibliography.

ERIC Educational Resources Information Center

Haviland, Virginia; Smith, William Jay

This annotated bibliography of over 120 books was compiled to call attention to poetry for children that is both pleasing and rewarding. Omitted are traditional materials such as Mother Goose rhymes, textbooks, and collections designed especially for the classroom. Sample illustrations from the books noted and lines from poems are reproduced…

Preparing Teachers for Urban Schools: An Annotated Bibliography for Teacher Education.

ERIC Educational Resources Information Center

Clothier, Grant; And Others

This annotated bibliography developed by Cooperative Urban Teacher Education (CUTE) staff members presents a selective reading list for undergraduate teacher education candidates preparing to work in inner-city schools. An interdisciplinary team composed of a psychiatrist, a sociologist, and teacher educators categorized the 187 entries under the…

Argumentation Theory. [A Selected Annotated Bibliography].

ERIC Educational Resources Information Center

Benoit, William L.

Materials dealing with aspects of argumentation theory are cited in this annotated bibliography. The 50 citations are organized by topic as follows: (1) argumentation; (2) the nature of argument; (3) traditional perspectives on argument; (4) argument diagrams; (5) Chaim Perelman's theory of rhetoric; (6) the evaluation of argument; (7) argument…

Gender, Science, and Technology: A Selected Annotated Bibliography.

ERIC Educational Resources Information Center

Eldredge, Mary; And Others

1990-01-01

Presents 196 annotated listings of works on science, technology, and gender, under 9 headings: Biography and History; Women Scientists; Science Education; Feminists Look at Science and Technology; Effects of Technology on Women; Medicine and Reproductive Technologies in Women's Lives; Women and Evolution; Women and Agriculture; and Gender,…

The Suburban Press; First Steps toward an Annotated Bibliography. Suburban Press Research Series No. 16 and 17.

ERIC Educational Resources Information Center

Northern Illinois Univ., De Kalb. Suburban Press Research Center.

This bibliography lists journal articles concerning various aspects of the suburban press. Annotated selections, arranged alphabetically according to journal title, are gathered from the following periodicals: "Advertising Age,""Business Week,""Columbia Journalism Review,""Editor and Publisher,""Grassroots Editor,""Journalism…

Program Evaluation in Alternative Education: An Annotated Bibliography. Teacher Education Forum; Volume 4, Number 17.

ERIC Educational Resources Information Center

Esp, Barbara

The Forum Series is a collection of papers dealing with all phases of teacher education including inservice training and graduate study. This selection is an annotated bibliography in two parts: (1) Evaluation Issues and Methods; and (2) Studies of Alternative Environments. (DMT)

Nutrition and Mental Retardation. An Annotated Bibliography, 1964-1970.

ERIC Educational Resources Information Center

Springer, Ninfa Saturnino

This annotated bibliography is primarily organized for nutritionists. It presents selected articles published from 1964 to the present. All aspects of nutrition in mental retardation are covered excepting inborn errors of metabolism. Sections are included on: (1) nutrition, birthweight, and mental retardation; (2) nutrition, growth, and mental…

Communication and Politics: A Selected, Annotated Bibliography.

ERIC Educational Resources Information Center

Kaid, Lynda Lee; And Others

Noting that the study of communication in political settings is an increasingly popular and important area of teaching and research in many disciplines, this 51-item annotated bibliography reflects the interdisciplinary nature of the field and is designed to incorporate varying approaches to the subject matter. With few exceptions, the books and…

Articles on Mass Communication in U.S. and Foreign Journals: A Selected Annotated Bibliography

ERIC Educational Resources Information Center

McKerns, Joseph P.; Delahaye, Alfred N.

1978-01-01

Lists and annotates 212 journal articles on mass communication, grouped according to topic. Topics include audience and communicator analysis, broadcasting, communication theory, courts and law, criticism and defense of media, journalism education, government and media, history and biography, international topics, and public relations. (GW)

Consumer Health

ERIC Educational Resources Information Center

Bibel, Barbara

2010-01-01

This article presents an annotated bibliography of 19 titles that focus on cancer and health-care reform. These include: (1) Anderson, John W. "Stand by Her: A Breast Cancer Guide for Men." AMACOM: American Management Assn.; (2) Carstensen, Laura L. "A Long Bright Future: An Action Plan for a Lifetime of Happiness, Health, and Financial Security."…

Sourcebook on Parenting and Child Care.

ERIC Educational Resources Information Center

Carpenter, Kathryn Hammell

Intended as a guide to parenting materials for parents and professionals who work with parents, this sourcebook and annotated bibliography of 940 entries is divided into five parts. Topical chapters in each part list and describe books and journals categorized as popular titles, professional titles, and directories. Chapters in part 1 list and…

Tests and Testing for Bilingual Children: A Bibliography of Literature.

ERIC Educational Resources Information Center

Kirsch, Judith, Comp.

This annotated listing cites tests, guides, dissertations, journal articles, research reports, reference materials, and conference papers and proceedings regarding tests and testing for bilingual children. Items cited were published between 1964-81. The listing is one of a series of bibliographies from a computerized database, Bilingual Education…

A bookshelf in public health, medical care, and allied fields.

PubMed

La Rocco, A; Jones, B

1972-01-01

This bibliography of nonserial publications consists of 610 annotations. It is intended as a guide to the development of a collection for librarians and for health professionals in research and education. References are mostly to publications from 1960. Titles are in English. Both primary and secondary sources are cited.

Computer Applications in Education: The Best of ERIC 1991.

ERIC Educational Resources Information Center

McLaughlin, Pamela

This annotated bibliography is the sixth annual compilation of the abstracts of 228 documents added to the ERIC database during the year 1991 in the area of computer applications in elementary and secondary schools. The types of materials included are administrator guides, bibliographies, conference papers, evaluative reports, literature reviews,…

Jewish Studies: A Guide to Reference Sources.

ERIC Educational Resources Information Center

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

An annotated bibliography to the reference sources for Jewish Studies in the McLennan Library of McGill University (Canada) is presented. Any titles in Hebrew characters are listed by their transliterated equivalents. There is also a list of relevant Library of Congress Subject Headings. General reference sources listed are: encyclopedias,…

Economics: A Guide to Reference Sources.

ERIC Educational Resources Information Center

Mason, Mary, Comp.

Approximately 84 reference materials on economics located in the McLennan Library, McGill University (Montreal), are cited in this annotated bibliography. The bibliography serves to provide an overview of the printed bibliographic and reference sources useful for the study of economics. Financial and business sources and statistical compendia and…

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…

Native Peoples of Canada: A Guide to Reference Sources.

ERIC Educational Resources Information Center

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

Brief annotations accompany the 104 entries in this bibliography which emphasizes sources for ethnological research about Native peoples of Canada dating from 1913 to 1985. Materials reflecting concerns of social anthropology and historical approaches to the study of Native peoples are also included, but linguistics and archaeology are covered…

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.…

Bibliography...Books for Children. 1983 Edition.

ERIC Educational Resources Information Center

Roedder, Kathleen R., Comp.; And Others

Intended for use by librarians, teachers, parents, and community workers as a guide to good children's literature, this annotated bibliography contains more than 1,000 entries. Each entry provides author and title, publisher, date of publication, price, International Standard Book Number (ISBN), and appropriate age levels. The entries are arranged…

Bibliography of Books for Children.

ERIC Educational Resources Information Center

Roedder, Kathleen R., Comp.; Sidorsky, Phyllis G., Comp.

Intended for use by librarians, teachers, parents, and community workers as a guide to good children's literature, this annotated bibliography contains more than 1,000 entries. Each entry provides author and title, publisher, date of publication, price, and International Standard Book Number (ISBN). Age level is also indicated. The entries are…

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…

A Language-teaching Bibliography.

ERIC Educational Resources Information Center

Centre for Information on Language Teaching, London (England).

This annotated bibliography provides a guide to books on the theory and practice of language teaching. Instructional materials for classroom use are not included. Eight sections of materials are contained in the work: (1) language, (2) language teaching, (3) English for speakers of other languages, (4) French, (5) German, (6) Italian, (7) Russian…

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,…

Buddhism: A Brief Guide to Reference Sources.

ERIC Educational Resources Information Center

Drost, Jerry

The annotated bibliography lists 48 articles, atlases, dictionaries, bibliographies, and general and subject indexes on Buddhism. The bibliography is intended to provide college students with an introduction to the more complex literature of Buddhism and to stimulate further research and study. Topics include the history of Buddhism; the practice…

Life Science, A Process Approach, Second Edition: Revised, 1970.

ERIC Educational Resources Information Center

Phare, Wayne; And Others

Seventeen scientific processes are identified and annotated; some suggestions for activities to demonstrate them are given. These processes are used as headings in the teacher's guide to succeeding units on biological classifications, microbiology, physiology of plants and animals, chick embryology and ecology. Similar headings are usually used in…

Anthropology: Guide to Reference Sources.

ERIC Educational Resources Information Center

Mason, Mary G., Ed.

More than 80 anthropology source materials concentrating on cultural and social anthropology are cited in this annotated bibliography. Materials, located in the McLennan Library at McGill University (Montreal), are listed according to type of material. Library of Congress call numbers are presented; dates of publication range from 1950 to 1985.…

Comparison of methods for library construction and short read annotation of shellfish viral metagenomes.

PubMed

Wei, Hong-Ying; Huang, Sheng; Wang, Jiang-Yong; Gao, Fang; Jiang, Jing-Zhe

2018-03-01

The emergence and widespread use of high-throughput sequencing technologies have promoted metagenomic studies on environmental or animal samples. Library construction for metagenome sequencing and annotation of the produced sequence reads are important steps in such studies and influence the quality of metagenomic data. In this study, we collected some marine mollusk samples, such as Crassostrea hongkongensis, Chlamys farreri, and Ruditapes philippinarum, from coastal areas in South China. These samples were divided into two batches to compare two library construction methods for shellfish viral metagenome. Our analysis showed that reverse-transcribing RNA into cDNA and then amplifying it simultaneously with DNA by whole genome amplification (WGA) yielded a larger amount of DNA compared to using only WGA or WTA (whole transcriptome amplification). Moreover, higher quality libraries were obtained by agarose gel extraction rather than with AMPure bead size selection. However, the latter can also provide good results if combined with the adjustment of the filter parameters. This, together with its simplicity, makes it a viable alternative. Finally, we compared three annotation tools (BLAST, DIAMOND, and Taxonomer) and two reference databases (NCBI's NR and Uniprot's Uniref). Considering the limitations of computing resources and data transfer speed, we propose the use of DIAMOND with Uniref for annotating metagenomic short reads as its running speed can guarantee a good annotation rate. This study may serve as a useful reference for selecting methods for Shellfish viral metagenome library construction and read annotation.

The CHEMDNER corpus of chemicals and drugs and its annotation principles.

PubMed

Krallinger, Martin; Rabal, Obdulia; Leitner, Florian; Vazquez, Miguel; Salgado, David; Lu, Zhiyong; Leaman, Robert; Lu, Yanan; Ji, Donghong; Lowe, Daniel M; Sayle, Roger A; Batista-Navarro, Riza Theresa; Rak, Rafal; Huber, Torsten; Rocktäschel, Tim; Matos, Sérgio; Campos, David; Tang, Buzhou; Xu, Hua; Munkhdalai, Tsendsuren; Ryu, Keun Ho; Ramanan, S V; Nathan, Senthil; Žitnik, Slavko; Bajec, Marko; Weber, Lutz; Irmer, Matthias; Akhondi, Saber A; Kors, Jan A; Xu, Shuo; An, Xin; Sikdar, Utpal Kumar; Ekbal, Asif; Yoshioka, Masaharu; Dieb, Thaer M; Choi, Miji; Verspoor, Karin; Khabsa, Madian; Giles, C Lee; Liu, Hongfang; Ravikumar, Komandur Elayavilli; Lamurias, Andre; Couto, Francisco M; Dai, Hong-Jie; Tsai, Richard Tzong-Han; Ata, Caglar; Can, Tolga; Usié, Anabel; Alves, Rui; Segura-Bedmar, Isabel; Martínez, Paloma; Oyarzabal, Julen; Valencia, Alfonso

2015-01-01

The automatic extraction of chemical information from text requires the recognition of chemical entity mentions as one of its key steps. When developing supervised named entity recognition (NER) systems, the availability of a large, manually annotated text corpus is desirable. Furthermore, large corpora permit the robust evaluation and comparison of different approaches that detect chemicals in documents. We present the CHEMDNER corpus, a collection of 10,000 PubMed abstracts that contain a total of 84,355 chemical entity mentions labeled manually by expert chemistry literature curators, following annotation guidelines specifically defined for this task. The abstracts of the CHEMDNER corpus were selected to be representative for all major chemical disciplines. Each of the chemical entity mentions was manually labeled according to its structure-associated chemical entity mention (SACEM) class: abbreviation, family, formula, identifier, multiple, systematic and trivial. The difficulty and consistency of tagging chemicals in text was measured using an agreement study between annotators, obtaining a percentage agreement of 91. For a subset of the CHEMDNER corpus (the test set of 3,000 abstracts) we provide not only the Gold Standard manual annotations, but also mentions automatically detected by the 26 teams that participated in the BioCreative IV CHEMDNER chemical mention recognition task. In addition, we release the CHEMDNER silver standard corpus of automatically extracted mentions from 17,000 randomly selected PubMed abstracts. A version of the CHEMDNER corpus in the BioC format has been generated as well. We propose a standard for required minimum information about entity annotations for the construction of domain specific corpora on chemical and drug entities. The CHEMDNER corpus and annotation guidelines are available at: http://www.biocreative.org/resources/biocreative-iv/chemdner-corpus/.

The CHEMDNER corpus of chemicals and drugs and its annotation principles

PubMed Central

2015-01-01

The automatic extraction of chemical information from text requires the recognition of chemical entity mentions as one of its key steps. When developing supervised named entity recognition (NER) systems, the availability of a large, manually annotated text corpus is desirable. Furthermore, large corpora permit the robust evaluation and comparison of different approaches that detect chemicals in documents. We present the CHEMDNER corpus, a collection of 10,000 PubMed abstracts that contain a total of 84,355 chemical entity mentions labeled manually by expert chemistry literature curators, following annotation guidelines specifically defined for this task. The abstracts of the CHEMDNER corpus were selected to be representative for all major chemical disciplines. Each of the chemical entity mentions was manually labeled according to its structure-associated chemical entity mention (SACEM) class: abbreviation, family, formula, identifier, multiple, systematic and trivial. The difficulty and consistency of tagging chemicals in text was measured using an agreement study between annotators, obtaining a percentage agreement of 91. For a subset of the CHEMDNER corpus (the test set of 3,000 abstracts) we provide not only the Gold Standard manual annotations, but also mentions automatically detected by the 26 teams that participated in the BioCreative IV CHEMDNER chemical mention recognition task. In addition, we release the CHEMDNER silver standard corpus of automatically extracted mentions from 17,000 randomly selected PubMed abstracts. A version of the CHEMDNER corpus in the BioC format has been generated as well. We propose a standard for required minimum information about entity annotations for the construction of domain specific corpora on chemical and drug entities. The CHEMDNER corpus and annotation guidelines are available at: http://www.biocreative.org/resources/biocreative-iv/chemdner-corpus/ PMID:25810773

APPRIS: annotation of principal and alternative splice isoforms

PubMed Central

Rodriguez, Jose Manuel; Maietta, Paolo; Ezkurdia, Iakes; Pietrelli, Alessandro; Wesselink, Jan-Jaap; Lopez, Gonzalo; Valencia, Alfonso; Tress, Michael L.

2013-01-01

Here, we present APPRIS (http://appris.bioinfo.cnio.es), a database that houses annotations of human splice isoforms. APPRIS has been designed to provide value to manual annotations of the human genome by adding reliable protein structural and functional data and information from cross-species conservation. The visual representation of the annotations provided by APPRIS for each gene allows annotators and researchers alike to easily identify functional changes brought about by splicing events. In addition to collecting, integrating and analyzing reliable predictions of the effect of splicing events, APPRIS also selects a single reference sequence for each gene, here termed the principal isoform, based on the annotations of structure, function and conservation for each transcript. APPRIS identifies a principal isoform for 85% of the protein-coding genes in the GENCODE 7 release for ENSEMBL. Analysis of the APPRIS data shows that at least 70% of the alternative (non-principal) variants would lose important functional or structural information relative to the principal isoform. PMID:23161672

Enhanced functionalities for annotating and indexing clinical text with the NCBO Annotator.

PubMed

Tchechmedjiev, Andon; Abdaoui, Amine; Emonet, Vincent; Melzi, Soumia; Jonnagaddala, Jitendra; Jonquet, Clement

2018-06-01

Second use of clinical data commonly involves annotating biomedical text with terminologies and ontologies. The National Center for Biomedical Ontology Annotator is a frequently used annotation service, originally designed for biomedical data, but not very suitable for clinical text annotation. In order to add new functionalities to the NCBO Annotator without hosting or modifying the original Web service, we have designed a proxy architecture that enables seamless extensions by pre-processing of the input text and parameters, and post processing of the annotations. We have then implemented enhanced functionalities for annotating and indexing free text such as: scoring, detection of context (negation, experiencer, temporality), new output formats and coarse-grained concept recognition (with UMLS Semantic Groups). In this paper, we present the NCBO Annotator+, a Web service which incorporates these new functionalities as well as a small set of evaluation results for concept recognition and clinical context detection on two standard evaluation tasks (Clef eHealth 2017, SemEval 2014). The Annotator+ has been successfully integrated into the SIFR BioPortal platform-an implementation of NCBO BioPortal for French biomedical terminologies and ontologies-to annotate English text. A Web user interface is available for testing and ontology selection (http://bioportal.lirmm.fr/ncbo_annotatorplus); however the Annotator+ is meant to be used through the Web service application programming interface (http://services.bioportal.lirmm.fr/ncbo_annotatorplus). The code is openly available, and we also provide a Docker packaging to enable easy local deployment to process sensitive (e.g. clinical) data in-house (https://github.com/sifrproject). andon.tchechmedjiev@lirmm.fr. Supplementary data are available at Bioinformatics online.

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,…

Private School Education in the U.S. An Annotated Bibliography, 1950-1980.

ERIC Educational Resources Information Center

Songe, Alice H.

This selective and annotated bibliography represents the body of literature published on nonpublic elementary and secondary education between 1950 and 1980, as well as some important titles that appeared in 1981. The work covers all aspects of independent and church-related schools--their aims and objectives, history, administration, and…

An Annotated Bibliography of Isotonic Weight-Training Methods.

ERIC Educational Resources Information Center

Wysong, John V.

This literature study was conducted to compare and evaluate various types and techniques of weight lifting so that a weight lifting program could be selected or devised for a secondary school. Annotations of 32 research reports, journal articles, and monographs on isotonic strength training are presented. The literature in the first part of the…

Censorship of Sexual Materials: A Selected, Annotated Basic Bibliography.

ERIC Educational Resources Information Center

Tedford, Thomas L.

The 37 references in this annotated bibliography are compiled for researchers of information on the censorship of sexual materials from ancient times to present. The materials include case studies, histories, essays, and opinion pieces about the use and regulation of "obscenity" in literature, pictorial art, radio broadcasting, the mail, film, and…

Annotated Selected Bibliography & Index for Teaching African-American Learners: Culturally Responsive Pedagogy Project.

ERIC Educational Resources Information Center

Hilliard, Asa G.

This annotated bibliography and index presents nearly 2,000 references that are substantially unique to African or African American teaching and learning. Designed to support teacher education, the bibliography features references that were chosen if they were culturally relevant, recognized the African or African American experience, and drew…

Association for Teacher Education in Europe (ATEE) Seminar on Practical Experience in Teacher Education (Gargnano, Italy, June 28-July 1, 1995). Select Annotated Bibliography.

ERIC Educational Resources Information Center

Macrae, Sheila, Comp.; Manning, Patricia, Comp; Moon, Bob, Comp.

1996-01-01

This annotated bibliography offers information from presentations at a 1995 seminar on practical teaching experience in preservice teacher education programs throughout Europe. Each entry includes a brief abstract of the presentation and a list of keywords. (SM)

Latin America: Books for High Schools. An Annotated Bibliography.

ERIC Educational Resources Information Center

Farrell, Robert V., Comp.; Hohenstein, John F., Comp.

This bibliography, intended for use as a selection tool for social studies programs and libraries in order to supply secondary students and teachers with recent Latin American books, contains 171 annotated bibliographic citations prepared by the center for Inter-American Relations after examination of more than 1200 books for comprehensiveness,…

Global Climate Change. Selected Annotated Bibliography. Second Edition.

ERIC Educational Resources Information Center

Jones, Douglas E.

This annotated bibliography on global climate change contains 27 articles designed to expand the breadth and depth of information presented in the Global Change Information Packet. Most articles were chosen from journals likely to be available in most medium-sized public or college libraries. The articles cover a variety of topics related to…

Selected Bibliography of Educational Materials: Algeria, Libya, Morocco, Tunisia. Volume 7, Number 4, 1973.

ERIC Educational Resources Information Center

Azzouz, Azzedine; And Others

This annotated bibliography contains 108 English language annotations of newspapers and government publications covering educational materials of interest to North Africans. The materials relate a clear trend toward increased awareness of Arab and Islamic heritage and the adaptation of education to a multilingual population. Citations are…

Selected Bibliography of Educational Materials: Algeria, Libya, Morocco, Tunisia. Volume 8, Number 1, 1974.

ERIC Educational Resources Information Center

Azzouz, Azzedine; And Others

This annotated bibliography contains 100 English-language annotations of newspapers and government publications covering educational topics of interest to North Africans. The majority of the items cited were published in 1974. Citations are categorized by country: Algeria, Libya, Morocco, and Tunisia. Within these major categories are subtopics…

Ethical Issues in Health Services: A Report and Annotated Bibliography.

ERIC Educational Resources Information Center

Carmody, James

This publication identifies, discusses, and lists areas for further research for five ethical issues related to health services: 1) the right to health care; 2) death and euthanasia; 3) human experimentation; 4) genetic engineering; and, 5) abortion. Following a discussion of each issue is a selected annotated bibliography covering the years 1967…

Aviation and the Environment. A Selected, Annotated Bibliography Related to Aviation's Responses Toward Improving the Environment.

ERIC Educational Resources Information Center

Marshall, Jane

This informal, brief bibliography attempts to stress the positive side of aviation, annotating documents that explain how the airlines, aircraft engine manufacturers, government agencies, military aviation, and general aviation are meeting their responsibilities in solving environmental problems. Topics arousing public concern are identified:…

Family Support Services. A Review of the Literature and Selected Annotated Bibliography.

ERIC Educational Resources Information Center

Wolcott, Ilene

This document contains a literature review and annotated bibliography on family support services in Australia and overseas. Literature relating to services for families with dependent adolescent children as well as young children is included. The review and bibliography concentrate primarily on community-based services defined in the literature as…

Job Creation in Rural Areas: A Select Annotated Bibliography.

ERIC Educational Resources Information Center

Pankratz, John

1989-01-01

This annotated bibliography is designed to assist rural leaders seeking ways to effectively structure successful job development projects in their communities. The 120 entries are listed in the main body alphabetically by author, and are grouped in the index into categories reflecting Thomas's "seven hallmarks of successful rural development": (1)…

Selected Bibliography of Educational Materials: Algeria, Libya, Morocco, Tunisia. Volume 8, Number 2, 1974.

ERIC Educational Resources Information Center

Azzouz, Azzedine; And Others

This bibliography contains 100 English-language annotations of newspaper articles and government publications from four North African nations. Most of the items were published in 1974. Annotations are categorized by topic: philosophy and theory of education, educational level, adult education, teacher training, teaching methods and aids, artistic…

Selected Bibliography of Educational Materials: Algeria, Libya, Morocco, Tunisia. Vol. 6, No. 3. 1972.

ERIC Educational Resources Information Center

Azzouz, Azzedine; And Others

English language annotations of articles from 13 French language periodicals covering educational materials of interest to North Africans are included in this annotated bibliography. Citations are categorized by country. Topics touch on philosophy and theory of education, educational statistics, education organization by grade and type, adult…

Ethical Issues in Social Work. An Annotated Bibliography.

ERIC Educational Resources Information Center

Elliott, Martha W., Comp.

Designed as a practical aid to social work students and practitioners interested in approaching the ethical issues inherent in social work practice, this annotated bibliography lists over 500 books and articles, most of which were published between 1970 and 1983. The bibliography has two main parts, of which the first consists of selections from…

Multi-Cultural Education: Selected Bibliography (Annotated). Research Report, Vol. 10, No. 1.

ERIC Educational Resources Information Center

Louisiana State Univ., Baton Rouge. Bureau of Educational Materials and Research.

This annotated bibliography contains citations of reports, papers, and journal articles in the ERIC data bases and from other sources, on the subject of multicultural education. The references cite works of both theoretical and practical natures. Information on availability of the materials is included in the citation. (JD)

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…

Hard-Core Unemployment: A Selected, Annotated Bibliography.

ERIC Educational Resources Information Center

Cameron, Colin, Comp.; Menon, Anila Bhatt, Comp.

This annotated bibliography contains references to various films, articles, and books on the subject of hard-core unemployment, and is divided into the following sections: (1) The Sociology of the Hard-Core Milieu, (2) Training Programs, (3) Business and the Hard-Core, (4) Citations of Miscellaneous References on Hard-Core Unemployment, (5)…

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…

Articles on Mass Communication in U.S. and Foreign Journals: A Selected Annotated Bibliography--January, February, March 1980.

ERIC Educational Resources Information Center

McKerns, Joseph P.; Delahaye, Alfred N.

1980-01-01

Lists and annotates more than 250 articles on mass communication, grouped according to topic. Topics include advertising, audience and communicator analysis, broadcasting, community journalism, courts and law, criticism and defense of media, education for journalism, history and biography, international, management, public relations, visual…

A proposed research program in information processing

NASA Technical Reports Server (NTRS)

Schorr, Herbert

1992-01-01

The goal of the Formalized Software Development (FSD) project was to demonstrate improvements productivity of software development and maintenance through the use of a new software lifecycle paradigm. The paradigm calls for the mechanical, but human-guided, derivation of software implementations from formal specifications of the desired software behavior. It relies on altering a system's specification and rederiving its implementation as the standard technology for software maintenance. A system definition for this paradigm is composed of a behavioral specification together with a body of annotations that control the derivation of executable code from the specification. Annotations generally achieve the selection of certain data representations and/or algorithms that are consistent with, but not mandated by, the behavioral specification. In doing this, they may yield systems which exhibit only certain behaviors among multiple alternatives permitted by the behavioral specification. The FSD project proposed to construct a testbed in which to explore the realization of this new paradigm. The testbed was to provide operational support environment for software design, implementation, and maintenance. The testbed was proposed to provide highly automated support for individual programmers ('programming in the small'), but not to address the additional needs of programming teams ('programming in the large'). The testbed proposed to focus on supporting rapid construction and evolution of useful prototypes of software systems, as opposed to focusing on the problems of achieving production quality performance of systems.

The visualCMAT: A web-server to select and interpret correlated mutations/co-evolving residues in protein families.

PubMed

Suplatov, Dmitry; Sharapova, Yana; Timonina, Daria; Kopylov, Kirill; Švedas, Vytas

2018-04-01

The visualCMAT web-server was designed to assist experimental research in the fields of protein/enzyme biochemistry, protein engineering, and drug discovery by providing an intuitive and easy-to-use interface to the analysis of correlated mutations/co-evolving residues. Sequence and structural information describing homologous proteins are used to predict correlated substitutions by the Mutual information-based CMAT approach, classify them into spatially close co-evolving pairs, which either form a direct physical contact or interact with the same ligand (e.g. a substrate or a crystallographic water molecule), and long-range correlations, annotate and rank binding sites on the protein surface by the presence of statistically significant co-evolving positions. The results of the visualCMAT are organized for a convenient visual analysis and can be downloaded to a local computer as a content-rich all-in-one PyMol session file with multiple layers of annotation corresponding to bioinformatic, statistical and structural analyses of the predicted co-evolution, or further studied online using the built-in interactive analysis tools. The online interactivity is implemented in HTML5 and therefore neither plugins nor Java are required. The visualCMAT web-server is integrated with the Mustguseal web-server capable of constructing large structure-guided sequence alignments of protein families and superfamilies using all available information about their structures and sequences in public databases. The visualCMAT web-server can be used to understand the relationship between structure and function in proteins, implemented at selecting hotspots and compensatory mutations for rational design and directed evolution experiments to produce novel enzymes with improved properties, and employed at studying the mechanism of selective ligand's binding and allosteric communication between topologically independent sites in protein structures. The web-server is freely available at https://biokinet.belozersky.msu.ru/visualcmat and there are no login requirements.

Oil and development in the Arabian Gulf: A selected annotated bibliography

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

Sharif, W.I.

1985-01-01

This past decade has witnessed a vast proliferation of literature on the Arabian Gulf region. In this book the author provides a systematic guide to the literature in order to assist those conducting research on the area. The author is primarily concerned with the national, regional and international role of Arabian Gulf oil between 1973 and 1983. He includes more general sources, however, if they are partly devoted to the subject or if they provide information essential to the understanding of the particular economic systems or the place of Arabian Gulf oil within the world energy situation. Sources of amore » technical nature have been excluded, such as those dealing with the science and technology of Arab oil. The main languages of the material selected for inclusion are English and Arabic, with French, German, Italian, and Spanish sources in smaller number. The Arabic sources are appended separately after the Western language sections in each chapter. The sources of information cited include books, monographs, articles, journals, theses, annual reports, directories, government documents, and various unpublished papers and documents.« less

A selective annotated bibliography for clinical audiology (1989-2009): books.

PubMed

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

2010-12-01

This is the 2nd in a series of 3 planned companion articles that present a selected, annotated, and indexed bibliography of clinical audiology publications from 1989 through 2009. Research and preparation of the bibliography were based on published guidelines, professional audiology experience, and professional librarian experience. The first article in the series covered reference works. This article focuses on other books. The planned third companion article will present periodicals and online resources. Audiologists and librarians can use this bibliography to help them identify relevant clinical audiology literature.

Hymenoptera Genome Database: integrating genome annotations in HymenopteraMine

PubMed Central

Elsik, Christine G.; Tayal, Aditi; Diesh, Colin M.; Unni, Deepak R.; Emery, Marianne L.; Nguyen, Hung N.; Hagen, Darren E.

2016-01-01

We report an update of the Hymenoptera Genome Database (HGD) (http://HymenopteraGenome.org), a model organism database for insect species of the order Hymenoptera (ants, bees and wasps). HGD maintains genomic data for 9 bee species, 10 ant species and 1 wasp, including the versions of genome and annotation data sets published by the genome sequencing consortiums and those provided by NCBI. A new data-mining warehouse, HymenopteraMine, based on the InterMine data warehousing system, integrates the genome data with data from external sources and facilitates cross-species analyses based on orthology. New genome browsers and annotation tools based on JBrowse/WebApollo provide easy genome navigation, and viewing of high throughput sequence data sets and can be used for collaborative genome annotation. All of the genomes and annotation data sets are combined into a single BLAST server that allows users to select and combine sequence data sets to search. PMID:26578564

An Annotated Bibliography of Slide Library Literature. Bibliographic Studies No. 3.

ERIC Educational Resources Information Center

Hess, Stanley W.

Intended as a guide to the current literature of non-book librarianship dealing with the care and administration of slide collections, this listing surveys post-1960 imprints which emphasize organization, control, indexing, cataloging, general planning, acquisition, and the unique requirements of specialized area collections such as fine arts.…

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,…

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…

Succession Planning and Management: A Guide to Organizational Systems and Practices

ERIC Educational Resources Information Center

Berke, David

2005-01-01

The purpose of succession-related practices is to ensure that there are ready replacements for key positions in an organization so that turnover will not negatively affect the organization's performance. CCL first published an annotated bibliography on succession planning in 1995. That bibliography focused primarily on the link between succession…

The LOGO Processor; A Guide for System Programmers.

ERIC Educational Resources Information Center

Weiner, Walter B.; And Others

A detailed specification of the LOGO programing system is given. The level of description is intended to enable system programers to design LOGO processors of their own. The discussion of storage allocation and garbage collection algorithms is virtually complete. An annotated LOGO system listing for the PDP-10 computer system may be obtained on…

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…

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…

How the Schools Can Meet the Needs of the Children of Divorce.

ERIC Educational Resources Information Center

Gay, Velva Bere

The responsiblity of the school in dealing with children of divorced parents was studied. An annotated bibliography provides a guide to sources offering suggestions for school personnel seeking greater understanding of the problem of divorce. The bibliography is divided into sections on: (1) understanding family breakdown, in which statistics,…

An Educator's Guide to the Literature Dealing with Teenage Suicide.

ERIC Educational Resources Information Center

Woodruff, John

This report was written to provide educators with information on their role in dealing with the problem of adolescent suicide. A review of current literature was conducted to give educators accurate teenage suicide information, and an annotated bibliography of relevant citations from that review is included. Thirty entries are organized in the…

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…

"Tropic of Cancer" and the Censors: A Case Study and Bibliographic Guide to the Literature.

ERIC Educational Resources Information Center

Kincaid, Larry; Koger, Grove

1997-01-01

Traces the history of Henry Miller's novel "Tropic of Cancer"--censored in England and America for being too obscene--from its inception in 1932 to its vindication by the United States judicial system 30 years later. Also includes an annotated bibliography of related literature. (AEF)

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)

Educators' Guide to Great Lakes Materials: Books, Films, Maps and Pamphlets for Classroom Use.

ERIC Educational Resources Information Center

Johnson, Pam

This annotated bibliography presents Great Lakes information for grades six through nine classroom use. It is meant to facilitate and encourage Great Lakes study, particularly of Lakes Michigan and Superior. Material is presented on history, science, lake management, environmental concerns, and recreational use. Included are both fiction and…

A Bookshelf in Public Health, Medical Care, and Allied Fields

PubMed Central

La Rocco, August; Jones, Barbara

1972-01-01

This bibliography of nonserial publications consists of 610 annotations. It is intended as a guide to the development of a collection for librarians and for health professionals in research and education. References are mostly to publications from 1960. Titles are in English. Both primary and secondary sources are cited. PMID:4554218

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

ERIC Educational Resources Information Center

Hansen-Krening, Nancy, Ed.; Aoki, Elaine M., Ed.; Mizokawa, Donald T., Ed.

The fourth edition of this annotated bibliography collection offers students, teachers, and librarians a helpful guide to the best multicultural literature (published from 1999 to 2001) for elementary and middle school readers. The book continues a tradition of promoting unity through diversity by highlighting fiction and nonfiction published by…

Ontology design patterns to disambiguate relations between genes and gene products in GENIA

PubMed Central

2011-01-01

Motivation Annotated reference corpora play an important role in biomedical information extraction. A semantic annotation of the natural language texts in these reference corpora using formal ontologies is challenging due to the inherent ambiguity of natural language. The provision of formal definitions and axioms for semantic annotations offers the means for ensuring consistency as well as enables the development of verifiable annotation guidelines. Consistent semantic annotations facilitate the automatic discovery of new information through deductive inferences. Results We provide a formal characterization of the relations used in the recent GENIA corpus annotations. For this purpose, we both select existing axiom systems based on the desired properties of the relations within the domain and develop new axioms for several relations. To apply this ontology of relations to the semantic annotation of text corpora, we implement two ontology design patterns. In addition, we provide a software application to convert annotated GENIA abstracts into OWL ontologies by combining both the ontology of relations and the design patterns. As a result, the GENIA abstracts become available as OWL ontologies and are amenable for automated verification, deductive inferences and other knowledge-based applications. Availability Documentation, implementation and examples are available from http://www-tsujii.is.s.u-tokyo.ac.jp/GENIA/. PMID:22166341

AGORA : Organellar genome annotation from the amino acid and nucleotide references.

PubMed

Jung, Jaehee; Kim, Jong Im; Jeong, Young-Sik; Yi, Gangman

2018-03-29

Next-generation sequencing (NGS) technologies have led to the accumulation of highthroughput sequence data from various organisms in biology. To apply gene annotation of organellar genomes for various organisms, more optimized tools for functional gene annotation are required. Almost all gene annotation tools are mainly focused on the chloroplast genome of land plants or the mitochondrial genome of animals.We have developed a web application AGORA for the fast, user-friendly, and improved annotations of organellar genomes. AGORA annotates genes based on a BLAST-based homology search and clustering with selected reference sequences from the NCBI database or user-defined uploaded data. AGORA can annotate the functional genes in almost all mitochondrion and plastid genomes of eukaryotes. The gene annotation of a genome with an exon-intron structure within a gene or inverted repeat region is also available. It provides information of start and end positions of each gene, BLAST results compared with the reference sequence, and visualization of gene map by OGDRAW. Users can freely use the software, and the accessible URL is https://bigdata.dongguk.edu/gene_project/AGORA/.The main module of the tool is implemented by the python and php, and the web page is built by the HTML and CSS to support all browsers. gangman@dongguk.edu.

Estimating False Positive Contamination in Crater Annotations from Citizen Science Data

NASA Astrophysics Data System (ADS)

Tar, P. D.; Bugiolacchi, R.; Thacker, N. A.; Gilmour, J. D.

2017-01-01

Web-based citizen science often involves the classification of image features by large numbers of minimally trained volunteers, such as the identification of lunar impact craters under the Moon Zoo project. Whilst such approaches facilitate the analysis of large image data sets, the inexperience of users and ambiguity in image content can lead to contamination from false positive identifications. We give an approach, using Linear Poisson Models and image template matching, that can quantify levels of false positive contamination in citizen science Moon Zoo crater annotations. Linear Poisson Models are a form of machine learning which supports predictive error modelling and goodness-of-fits, unlike most alternative machine learning methods. The proposed supervised learning system can reduce the variability in crater counts whilst providing predictive error assessments of estimated quantities of remaining true verses false annotations. In an area of research influenced by human subjectivity, the proposed method provides a level of objectivity through the utilisation of image evidence, guided by candidate crater identifications.

Proteomics informed by transcriptomics for characterising active transposable elements and genome annotation in Aedes aegypti.

PubMed

Maringer, Kevin; Yousuf, Amjad; Heesom, Kate J; Fan, Jun; Lee, David; Fernandez-Sesma, Ana; Bessant, Conrad; Matthews, David A; Davidson, Andrew D

2017-01-19

Aedes aegypti is a vector for the (re-)emerging human pathogens dengue, chikungunya, yellow fever and Zika viruses. Almost half of the Ae. aegypti genome is comprised of transposable elements (TEs). Transposons have been linked to diverse cellular processes, including the establishment of viral persistence in insects, an essential step in the transmission of vector-borne viruses. However, up until now it has not been possible to study the overall proteome derived from an organism's mobile genetic elements, partly due to the highly divergent nature of TEs. Furthermore, as for many non-model organisms, incomplete genome annotation has hampered proteomic studies on Ae. aegypti. We analysed the Ae. aegypti proteome using our new proteomics informed by transcriptomics (PIT) technique, which bypasses the need for genome annotation by identifying proteins through matched transcriptomic (rather than genomic) data. Our data vastly increase the number of experimentally confirmed Ae. aegypti proteins. The PIT analysis also identified hotspots of incomplete genome annotation, and showed that poor sequence and assembly quality do not explain all annotation gaps. Finally, in a proof-of-principle study, we developed criteria for the characterisation of proteomically active TEs. Protein expression did not correlate with a TE's genomic abundance at different levels of classification. Most notably, long terminal repeat (LTR) retrotransposons were markedly enriched compared to other elements. PIT was superior to 'conventional' proteomic approaches in both our transposon and genome annotation analyses. We present the first proteomic characterisation of an organism's repertoire of mobile genetic elements, which will open new avenues of research into the function of transposon proteins in health and disease. Furthermore, our study provides a proof-of-concept that PIT can be used to evaluate a genome's annotation to guide annotation efforts which has the potential to improve the efficiency of annotation projects in non-model organisms. PIT therefore represents a valuable new tool to study the biology of the important vector species Ae. aegypti, including its role in transmitting emerging viruses of global public health concern.

Literature on the Deaf-Blind -- An Annotated Bibliography.

ERIC Educational Resources Information Center

Blea, William A., Comp.; Hobron, Robert, Comp.

The annotated bibliography of literature on the deaf-blind covers both a wide variety of sources and a lengthy period of time. Entries are listed by category: selected books; articles from American Annals of the Deaf, 1848-1970; articles from New Beacon, 1922-1970; articles from New Outlook for the Blind, 1907-1970; articles from Volta Review,…

Annotated Bibliography: Afro-American, Hispano and Amerind; with Amerinc; with Audio-Visual Materials List.

ERIC Educational Resources Information Center

Haberbosch, John F.; And Others

Readings and audiovisual materials, selected especially for educators, related to the study of Afro-American, Hispano-American, and American Indian cultures are included in this 366-item annotated bibliography covering the period from 1861 to 1968. Historical, cultural, and biographical materials are included for each of the three cultures as well…

Nitrogen and Phosphorus in Water, An Annotated Selected Bibliography of Their Biological Effects.

ERIC Educational Resources Information Center

Mackenthun, Kenneth M.

Included in this bibliography are annotations of quantitative data on the content or concentration of nitrogen and phosphorus in plants and animals, the contribution to water of these elements from various sources (soil, fertilizers, excretion, sewage, precipitation, urban run-off), and the effect their presence has on aquatic standing crops and…

Selected Bibliography of Educational Materials: Maghreb, Algeria, Libya, Morocco, Tunisia. Vol. 9, No. 3, 1975.

ERIC Educational Resources Information Center

Azzouz, Azzedine, Comp.; And Others

The bibliography presents 91 English language annotations of newspaper articles, journals, and government publications about education in Algeria, Libya, Morocco, and Tunisia. Although the title also includes Maghreb, this issue does not contain any annotations for that country. All articles were published during the period July-September 1975.…

Selected Bibliography of Educational Materials: Algeria, Libya, Morocco, Tunisia. Volume 6, Number 2, 1972.

ERIC Educational Resources Information Center

Azzouz, Azzedine; And Others

Annotations of articles, written in English, provide the content for an annotated bibliography of educational materials written in French useful to those with an interest in North Africa. Sections on Algeria, Libya, Morocco, and Tunisia cover topics such as the philosophy and theory of education, educational organization, adult education, teacher…

Significant U.S. 20th Century Education Books: Biblio-Historical Essay.

ERIC Educational Resources Information Center

Parker, Franklin

Presented in historical context, the books listed in this annotated bibliography offer insights into professional education concerns and can help teachers know about the great ideas and themes of their field, and what the best and most provocative books are today. The bibliography begins with books that list and annotate topically selected best…

Annotated Bibliography of Research in the Teaching of English

ERIC Educational Resources Information Center

Beach, Richard; Bigelow, Martha; Brendler, Beth; Coffino, Kara; Dillon, Deborah; Frederick, Amy; Gabrielli, Michelle; Helman, Lori; Ngo, Bic; O'Brien, David; Rambow, Adam; Scharber, Cassie; Sethi, Jenna; Braaksma, Martine; Janssen, Tanja; Thein, Amanda Haertling; Liang, Lauren; Stornaiuolo, Amy

2012-01-01

This November issue of "Research in the Teaching of English" ("RTE") once again contains the Annual Annotated Bibliography of "RTE." This bibliography includes abstracts of selected empirical research studies as well as titles of other related studies and books published between summer 2011 and summer 2012. As was the case with the 2010 and 2011…

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…

Annotated Bibliography, Part Two, Final Report for Phase I, Rural Shared Services.

ERIC Educational Resources Information Center

Northern Montana Coll., Havre.

Part Two of a four-part report, designed to identify, evaluate, and synthesize shared services research and development efforts conducted throughout the nation, presents an annotated bibliography of 32 books and 36 articles which describe various attempts to improve rural education. The 68 publications dating from 1958 to 1968 were selected by a…

Ethnic Folklife Dissertations from the United States and Canada, 1960-1980. A Selected, Annotated Bibliography.

ERIC Educational Resources Information Center

Kerst, Catherine Hiebert

This annotated bibliography lists over 220 multi-disciplinary Ph.D. dissertations written between 1960 and 1980 on the subject of indigenous and immigrant ethnic folklife in the United States and Canada. Only dissertations providing substantial attention to traditional forms of ethnic folk culture in context were considered. The concept of…

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…

An Annotated Selective Bibliography on Human Performance in Fault Diagnosis Tasks. Technical Report 435. Final Report.

ERIC Educational Resources Information Center

Johnson, William B.; And Others

This annotated bibliography developed in connection with an ongoing investigation of the use of computer simulations for fault diagnosis training cites 61 published works taken predominantly from the disciplines of engineering, psychology, and education. A review of the existing literature included computer searches of the past ten years of…

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…

AutoFACT: An Automatic Functional Annotation and Classification Tool

PubMed Central

Koski, Liisa B; Gray, Michael W; Lang, B Franz; Burger, Gertraud

2005-01-01

Background Assignment of function to new molecular sequence data is an essential step in genomics projects. The usual process involves similarity searches of a given sequence against one or more databases, an arduous process for large datasets. Results We present AutoFACT, a fully automated and customizable annotation tool that assigns biologically informative functions to a sequence. Key features of this tool are that it (1) analyzes nucleotide and protein sequence data; (2) determines the most informative functional description by combining multiple BLAST reports from several user-selected databases; (3) assigns putative metabolic pathways, functional classes, enzyme classes, GeneOntology terms and locus names; and (4) generates output in HTML, text and GFF formats for the user's convenience. We have compared AutoFACT to four well-established annotation pipelines. The error rate of functional annotation is estimated to be only between 1–2%. Comparison of AutoFACT to the traditional top-BLAST-hit annotation method shows that our procedure increases the number of functionally informative annotations by approximately 50%. Conclusion AutoFACT will serve as a useful annotation tool for smaller sequencing groups lacking dedicated bioinformatics staff. It is implemented in PERL and runs on LINUX/UNIX platforms. AutoFACT is available at . PMID:15960857

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.

New directions in biomedical text annotation: definitions, guidelines and corpus construction

PubMed Central

Wilbur, W John; Rzhetsky, Andrey; Shatkay, Hagit

2006-01-01

Background While biomedical text mining is emerging as an important research area, practical results have proven difficult to achieve. We believe that an important first step towards more accurate text-mining lies in the ability to identify and characterize text that satisfies various types of information needs. We report here the results of our inquiry into properties of scientific text that have sufficient generality to transcend the confines of a narrow subject area, while supporting practical mining of text for factual information. Our ultimate goal is to annotate a significant corpus of biomedical text and train machine learning methods to automatically categorize such text along certain dimensions that we have defined. Results We have identified five qualitative dimensions that we believe characterize a broad range of scientific sentences, and are therefore useful for supporting a general approach to text-mining: focus, polarity, certainty, evidence, and directionality. We define these dimensions and describe the guidelines we have developed for annotating text with regard to them. To examine the effectiveness of the guidelines, twelve annotators independently annotated the same set of 101 sentences that were randomly selected from current biomedical periodicals. Analysis of these annotations shows 70–80% inter-annotator agreement, suggesting that our guidelines indeed present a well-defined, executable and reproducible task. Conclusion We present our guidelines defining a text annotation task, along with annotation results from multiple independently produced annotations, demonstrating the feasibility of the task. The annotation of a very large corpus of documents along these guidelines is currently ongoing. These annotations form the basis for the categorization of text along multiple dimensions, to support viable text mining for experimental results, methodology statements, and other forms of information. We are currently developing machine learning methods, to be trained and tested on the annotated corpus, that would allow for the automatic categorization of biomedical text along the general dimensions that we have presented. The guidelines in full detail, along with annotated examples, are publicly available. PMID:16867190

Active learning: a step towards automating medical concept extraction.

PubMed

Kholghi, Mahnoosh; Sitbon, Laurianne; Zuccon, Guido; Nguyen, Anthony

2016-03-01

This paper presents an automatic, active learning-based system for the extraction of medical concepts from clinical free-text reports. Specifically, (1) the contribution of active learning in reducing the annotation effort and (2) the robustness of incremental active learning framework across different selection criteria and data sets are determined. The comparative performance of an active learning framework and a fully supervised approach were investigated to study how active learning reduces the annotation effort while achieving the same effectiveness as a supervised approach. Conditional random fields as the supervised method, and least confidence and information density as 2 selection criteria for active learning framework were used. The effect of incremental learning vs standard learning on the robustness of the models within the active learning framework with different selection criteria was also investigated. The following 2 clinical data sets were used for evaluation: the Informatics for Integrating Biology and the Bedside/Veteran Affairs (i2b2/VA) 2010 natural language processing challenge and the Shared Annotated Resources/Conference and Labs of the Evaluation Forum (ShARe/CLEF) 2013 eHealth Evaluation Lab. The annotation effort saved by active learning to achieve the same effectiveness as supervised learning is up to 77%, 57%, and 46% of the total number of sequences, tokens, and concepts, respectively. Compared with the random sampling baseline, the saving is at least doubled. Incremental active learning is a promising approach for building effective and robust medical concept extraction models while significantly reducing the burden of manual annotation. © The Author 2015. Published by Oxford University Press on behalf of the American Medical Informatics Association. All rights reserved. For Permissions, please email: journals.permissions@oup.com.

A tool for selecting SNPs for association studies based on observed linkage disequilibrium patterns.

PubMed

De La Vega, Francisco M; Isaac, Hadar I; Scafe, Charles R

2006-01-01

The design of genetic association studies using single-nucleotide polymorphisms (SNPs) requires the selection of subsets of the variants providing high statistical power at a reasonable cost. SNPs must be selected to maximize the probability that a causative mutation is in linkage disequilibrium (LD) with at least one marker genotyped in the study. The HapMap project performed a genome-wide survey of genetic variation with about a million SNPs typed in four populations, providing a rich resource to inform the design of association studies. A number of strategies have been proposed for the selection of SNPs based on observed LD, including construction of metric LD maps and the selection of haplotype tagging SNPs. Power calculations are important at the study design stage to ensure successful results. Integrating these methods and annotations can be challenging: the algorithms required to implement these methods are complex to deploy, and all the necessary data and annotations are deposited in disparate databases. Here, we present the SNPbrowser Software, a freely available tool to assist in the LD-based selection of markers for association studies. This stand-alone application provides fast query capabilities and swift visualization of SNPs, gene annotations, power, haplotype blocks, and LD map coordinates. Wizards implement several common SNP selection workflows including the selection of optimal subsets of SNPs (e.g. tagging SNPs). Selected SNPs are screened for their conversion potential to either TaqMan SNP Genotyping Assays or the SNPlex Genotyping System, two commercially available genotyping platforms, expediting the set-up of genetic studies with an increased probability of success.

Semantic Annotations and Querying of Web Data Sources

NASA Astrophysics Data System (ADS)

Hornung, Thomas; May, Wolfgang

A large part of the Web, actually holding a significant portion of the useful information throughout the Web, consists of views on hidden databases, provided by numerous heterogeneous interfaces that are partly human-oriented via Web forms ("Deep Web"), and partly based on Web Services (only machine accessible). In this paper we present an approach for annotating these sources in a way that makes them citizens of the Semantic Web. We illustrate how queries can be stated in terms of the ontology, and how the annotations are used to selected and access appropriate sources and to answer the queries.

TRAP: automated classification, quantification and annotation of tandemly repeated sequences.

PubMed

Sobreira, Tiago José P; Durham, Alan M; Gruber, Arthur

2006-02-01

TRAP, the Tandem Repeats Analysis Program, is a Perl program that provides a unified set of analyses for the selection, classification, quantification and automated annotation of tandemly repeated sequences. TRAP uses the results of the Tandem Repeats Finder program to perform a global analysis of the satellite content of DNA sequences, permitting researchers to easily assess the tandem repeat content for both individual sequences and whole genomes. The results can be generated in convenient formats such as HTML and comma-separated values. TRAP can also be used to automatically generate annotation data in the format of feature table and GFF files.

An Annotated Bibliography of Selected Projects, Theses, and Dissertations on the American Indian by Arizona State University Students from 1943-1974.

ERIC Educational Resources Information Center

Mech, Joyce, Comp.

Fifty-five published projects, theses, and dissertations dealing with the Native American and written by Arizona State University students are listed in this annotated bibliography. Arranged alphabetically according to authors and topics, the publications cover the period from 1943 to 1974. Topics include: (1) attitudes/achievement, (2)…

Atlases in the Collection of Moellering Memorial Library, Valparaiso University. A Selected and Annotated Bibliography.

ERIC Educational Resources Information Center

Hess, Elmer B., Comp.

Following a brief discussion of the evolution of the atlas and its importance as a library reference tool, an annotated description is provided of each atlas found in this university library collection. Items in the bibliography are arranged in the following categories: (1) world atlases; (2) regional atlases; (3) national atlases; (4) state…

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…

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…

Puerto Rican Migration: The Return Flow = La Migracion Puertorriquena: El Reflujo a la Isla.

ERIC Educational Resources Information Center

Vivo, Paquita, Comp.

This is a guide to materials and research on Puerto Ricans who have returned to Puerto Rico after living in the United States. Part 1 is an annotated bibliography of books, journal articles, printed documents, doctoral dissertations, master's theses, journalistic accounts, and unpublished papers on characteristics of Puerto Rican return migrants;…

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,…

Extending the Five-Foot Bookshelf: More Essential Books for Professionals Who Serve Teens.

ERIC Educational Resources Information Center

Rosenzweig, Susan

2000-01-01

Provides annotated bibliographies for five books that are recommended professional reading for librarians serving teens. Topics include American Indian stereotypes in the media; a leadership guide for school library media specialists; views of teens; how teens who are different are often outcasts; and tips for public library young adult services.…

Guide to Theses and Dissertations: An International Bibliography of Bibliographies. Revised and Enlarged Edition.

ERIC Educational Resources Information Center

Reynolds, Michael M.

Annotations on 2,948 bibliographies of dissertations, theses, and research completed and in progress for graduate degrees are presented. The bibliographies, produced through 1983 and most of 1984, are specialized and usually subject-oriented and cover current and retrospective research in the United States and throughout the world. The annotations…

MeSH-informed enrichment analysis and MeSH-guided semantic similarity among functional terms and gene products in chicken

USDA-ARS?s Scientific Manuscript database

Such Biomedical vocabularies and ontologies aid in recapitulating biological knowledge. The annotation of gene products is mainly accelerated by Gene Ontology (GO) and more recently by Medical Subject Headings (MeSH). MeSH is the National Library of Medicine's controlled vocabulary and it is making ...

Books for Teens: Stressing the Higher Values: A CSLA Bibliography.

ERIC Educational Resources Information Center

Tyson, Edith S.

This annotated bibliography is intended as a general background guide for volunteer librarians in churches and synagogues. It is assumed that the user has little knowledge of contemporary literature for youth in grades 7 through 12, but is aware that their reading needs are not identical to those of younger children or adults. Rather than listing…

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,…

A Basic Reference Shelf on Simulation and Gaming. A Series One Paper from ERIC at Stanford.

ERIC Educational Resources Information Center

Twelker, Paul A.

A short, preliminary discussion of simulation and gaming outlines the various instructional and research techniques which come under the more general heading and lists the properties of each. Six sections of annotated, bibliographic entries serve as a guide to the literature on simulation and gaming. Documents are grouped under the following…

Women in Occupations and Equity Issues: An Annotated Bibliographical Guide to the Literature.

ERIC Educational Resources Information Center

Caliguri, Joseph P.; Krueger, Jack P.

Consisting of items published between 1977 and 1981, this 445-item bibliography focuses on women in education, government, business, and industry. Topics covered include nontraditional careers for women, sex role stereotypes, and role models for young women. There is also an emphasis on affirmative action cases and programs. Other major topics…

Sonic-boom research: Selected bibliography with annotation

NASA Technical Reports Server (NTRS)

Hubbard, H. H.; Maglieri, D. J.; Stephens, D. G.

1986-01-01

Citations of selected documents are included which represent the state of the art of technology in each of the following subject areas: prediction, measurement, and minimization of steady-flight sonic booms; prediction and measurement of accelerating-flight sonic booms; sonic-boom propagation; the effects of sonic booms on people, communities, structures, animals, birds, and terrain; and sonic-boom simulator technology. Documents are listed in chronological order in each section of the paper, with key documents and associated annotation listed first. The sources are given along with acquisition numbers, when available, to expedite the acquisition of copies of the documents.

Assembling the Setaria italica L. Beauv. genome into nine chromosomes and insights into regions affecting growth and drought tolerance

PubMed Central

Tsai, Kevin J.; Lu, Mei-Yeh Jade; Yang, Kai-Jung; Li, Mengyun; Teng, Yuchuan; Chen, Shihmay; Ku, Maurice S. B.; Li, Wen-Hsiung

2016-01-01

The diploid C4 plant foxtail millet (Setaria italica L. Beauv.) is an important crop in many parts of Africa and Asia for the vast consumption of its grain and ability to grow in harsh environments, but remains understudied in terms of complete genomic architecture. To date, there have been only two genome assembly and annotation efforts with neither assembly reaching over 86% of the estimated genome size. We have combined de novo assembly with custom reference-guided improvements on a popular cultivar of foxtail millet and have achieved a genome assembly of 477 Mbp in length, which represents over 97% of the estimated 490 Mbp. The assembly anchors over 98% of the predicted genes to the nine assembled nuclear chromosomes and contains more functional annotation gene models than previous assemblies. Our annotation has identified a large number of unique gene ontology terms related to metabolic activities, a region of chromosome 9 with several growth factor proteins, and regions syntenic with pearl millet or maize genomic regions that have been previously shown to affect growth. The new assembly and annotation for this important species can be used for detailed investigation and future innovations in growth for millet and other grains. PMID:27734962

Assembling the Setaria italica L. Beauv. genome into nine chromosomes and insights into regions affecting growth and drought tolerance.

PubMed

Tsai, Kevin J; Lu, Mei-Yeh Jade; Yang, Kai-Jung; Li, Mengyun; Teng, Yuchuan; Chen, Shihmay; Ku, Maurice S B; Li, Wen-Hsiung

2016-10-13

The diploid C 4 plant foxtail millet (Setaria italica L. Beauv.) is an important crop in many parts of Africa and Asia for the vast consumption of its grain and ability to grow in harsh environments, but remains understudied in terms of complete genomic architecture. To date, there have been only two genome assembly and annotation efforts with neither assembly reaching over 86% of the estimated genome size. We have combined de novo assembly with custom reference-guided improvements on a popular cultivar of foxtail millet and have achieved a genome assembly of 477 Mbp in length, which represents over 97% of the estimated 490 Mbp. The assembly anchors over 98% of the predicted genes to the nine assembled nuclear chromosomes and contains more functional annotation gene models than previous assemblies. Our annotation has identified a large number of unique gene ontology terms related to metabolic activities, a region of chromosome 9 with several growth factor proteins, and regions syntenic with pearl millet or maize genomic regions that have been previously shown to affect growth. The new assembly and annotation for this important species can be used for detailed investigation and future innovations in growth for millet and other grains.

Extending SEQenv: a taxa-centric approach to environmental annotations of 16S rDNA sequences

PubMed Central

Jeffries, Thomas C.; Ijaz, Umer Z.; Hamonts, Kelly

2017-01-01

Understanding how the environment selects a given taxon and the diversity patterns that emerge as a result of environmental filtering can dramatically improve our ability to analyse any environment in depth as well as advancing our knowledge on how the response of different taxa can impact each other and ecosystem functions. Most of the work investigating microbial biogeography has been site-specific, and logical environmental factors, rather than geographical location, may be more influential on microbial diversity. SEQenv, a novel pipeline aiming to provide environmental annotations of sequences emerged to provide a consistent description of the environmental niches using the ENVO ontology. While the pipeline provides a list of environmental terms on the basis of sample datasets and, therefore, the annotations obtained are at the dataset level, it lacks a taxa centric approach to environmental annotation. The work here describes an extension developed to enhance the SEQenv pipeline, which provided the means to directly generate environmental annotations for taxa under different contexts. 16S rDNA amplicon datasets belonging to distinct biomes were selected to illustrate the applicability of the extended SEQenv pipeline. A literature survey of the results demonstrates the immense importance of sequence level environmental annotations by illustrating the distribution of both taxa across environments as well as the various environmental sources of a specific taxon. Significantly enhancing the SEQenv pipeline in the process, this information would be valuable to any biologist seeking to understand the various taxa present in the habitat and the environment they originated from, enabling a more thorough analysis of which lineages are abundant in certain habitats and the recovery of patterns in taxon distribution across different habitats and environmental gradients. PMID:29038749

Hymenoptera Genome Database: integrating genome annotations in HymenopteraMine.

PubMed

Elsik, Christine G; Tayal, Aditi; Diesh, Colin M; Unni, Deepak R; Emery, Marianne L; Nguyen, Hung N; Hagen, Darren E

2016-01-04

We report an update of the Hymenoptera Genome Database (HGD) (http://HymenopteraGenome.org), a model organism database for insect species of the order Hymenoptera (ants, bees and wasps). HGD maintains genomic data for 9 bee species, 10 ant species and 1 wasp, including the versions of genome and annotation data sets published by the genome sequencing consortiums and those provided by NCBI. A new data-mining warehouse, HymenopteraMine, based on the InterMine data warehousing system, integrates the genome data with data from external sources and facilitates cross-species analyses based on orthology. New genome browsers and annotation tools based on JBrowse/WebApollo provide easy genome navigation, and viewing of high throughput sequence data sets and can be used for collaborative genome annotation. All of the genomes and annotation data sets are combined into a single BLAST server that allows users to select and combine sequence data sets to search. © The Author(s) 2015. Published by Oxford University Press on behalf of Nucleic Acids Research.

Generation of an annotated reference standard for vaccine adverse event reports.

PubMed

Foster, Matthew; Pandey, Abhishek; Kreimeyer, Kory; Botsis, Taxiarchis

2018-07-05

As part of a collaborative project between the US Food and Drug Administration (FDA) and the Centers for Disease Control and Prevention for the development of a web-based natural language processing (NLP) workbench, we created a corpus of 1000 Vaccine Adverse Event Reporting System (VAERS) reports annotated for 36,726 clinical features, 13,365 temporal features, and 22,395 clinical-temporal links. This paper describes the final corpus, as well as the methodology used to create it, so that clinical NLP researchers outside FDA can evaluate the utility of the corpus to aid their own work. The creation of this standard went through four phases: pre-training, pre-production, production-clinical feature annotation, and production-temporal annotation. The pre-production phase used a double annotation followed by adjudication strategy to refine and finalize the annotation model while the production phases followed a single annotation strategy to maximize the number of reports in the corpus. An analysis of 30 reports randomly selected as part of a quality control assessment yielded accuracies of 0.97, 0.96, and 0.83 for clinical features, temporal features, and clinical-temporal associations, respectively and speaks to the quality of the corpus. Copyright © 2018 Elsevier Ltd. All rights reserved.

Transportation Noise Bibliography

DOT National Transportation Integrated Search

1975-07-01

This overview of the scope of current activity provides annotated bibliographic data relating to selections which range from short journal articles to longer research reports and conference proceedings. The items have been selected on the basis of to...

Selected Reference Books of 1999.

ERIC Educational Resources Information Center

McIlvaine, Eileen

2000-01-01

Presents annotated bibliographies of a selection of recent scholarly and general reference works under the subject headings of publishing, periodical indexes, philosophy and religion, literature, music, art, photography, social sciences, business, history, and new editions. (LRW)

pocketZebra: a web-server for automated selection and classification of subfamily-specific binding sites by bioinformatic analysis of diverse protein families

PubMed Central

Suplatov, Dmitry; Kirilin, Eugeny; Arbatsky, Mikhail; Takhaveev, Vakil; Švedas, Vytas

2014-01-01

The new web-server pocketZebra implements the power of bioinformatics and geometry-based structural approaches to identify and rank subfamily-specific binding sites in proteins by functional significance, and select particular positions in the structure that determine selective accommodation of ligands. A new scoring function has been developed to annotate binding sites by the presence of the subfamily-specific positions in diverse protein families. pocketZebra web-server has multiple input modes to meet the needs of users with different experience in bioinformatics. The server provides on-site visualization of the results as well as off-line version of the output in annotated text format and as PyMol sessions ready for structural analysis. pocketZebra can be used to study structure–function relationship and regulation in large protein superfamilies, classify functionally important binding sites and annotate proteins with unknown function. The server can be used to engineer ligand-binding sites and allosteric regulation of enzymes, or implemented in a drug discovery process to search for potential molecular targets and novel selective inhibitors/effectors. The server, documentation and examples are freely available at http://biokinet.belozersky.msu.ru/pocketzebra and there are no login requirements. PMID:24852248

When Whole-Genome Alignments Just Won't Work: kSNP v2 Software for Alignment-Free SNP Discovery and Phylogenetics of Hundreds of Microbial Genomes

PubMed Central

Gardner, Shea N.; Hall, Barry G.

2013-01-01

Effective use of rapid and inexpensive whole genome sequencing for microbes requires fast, memory efficient bioinformatics tools for sequence comparison. The kSNP v2 software finds single nucleotide polymorphisms (SNPs) in whole genome data. kSNP v2 has numerous improvements over kSNP v1 including SNP gene annotation; better scaling for draft genomes available as assembled contigs or raw, unassembled reads; a tool to identify the optimal value of k; distribution of packages of executables for Linux and Mac OS X for ease of installation and user-friendly use; and a detailed User Guide. SNP discovery is based on k-mer analysis, and requires no multiple sequence alignment or the selection of a single reference genome. Most target sets with hundreds of genomes complete in minutes to hours. SNP phylogenies are built by maximum likelihood, parsimony, and distance, based on all SNPs, only core SNPs, or SNPs present in some intermediate user-specified fraction of targets. The SNP-based trees that result are consistent with known taxonomy. kSNP v2 can handle many gigabases of sequence in a single run, and if one or more annotated genomes are included in the target set, SNPs are annotated with protein coding and other information (UTRs, etc.) from Genbank file(s). We demonstrate application of kSNP v2 on sets of viral and bacterial genomes, and discuss in detail analysis of a set of 68 finished E. coli and Shigella genomes and a set of the same genomes to which have been added 47 assemblies and four “raw read” genomes of H104:H4 strains from the recent European E. coli outbreak that resulted in both bloody diarrhea and hemolytic uremic syndrome (HUS), and caused at least 50 deaths. PMID:24349125

When whole-genome alignments just won't work: kSNP v2 software for alignment-free SNP discovery and phylogenetics of hundreds of microbial genomes.

PubMed

Gardner, Shea N; Hall, Barry G

2013-01-01

Effective use of rapid and inexpensive whole genome sequencing for microbes requires fast, memory efficient bioinformatics tools for sequence comparison. The kSNP v2 software finds single nucleotide polymorphisms (SNPs) in whole genome data. kSNP v2 has numerous improvements over kSNP v1 including SNP gene annotation; better scaling for draft genomes available as assembled contigs or raw, unassembled reads; a tool to identify the optimal value of k; distribution of packages of executables for Linux and Mac OS X for ease of installation and user-friendly use; and a detailed User Guide. SNP discovery is based on k-mer analysis, and requires no multiple sequence alignment or the selection of a single reference genome. Most target sets with hundreds of genomes complete in minutes to hours. SNP phylogenies are built by maximum likelihood, parsimony, and distance, based on all SNPs, only core SNPs, or SNPs present in some intermediate user-specified fraction of targets. The SNP-based trees that result are consistent with known taxonomy. kSNP v2 can handle many gigabases of sequence in a single run, and if one or more annotated genomes are included in the target set, SNPs are annotated with protein coding and other information (UTRs, etc.) from Genbank file(s). We demonstrate application of kSNP v2 on sets of viral and bacterial genomes, and discuss in detail analysis of a set of 68 finished E. coli and Shigella genomes and a set of the same genomes to which have been added 47 assemblies and four "raw read" genomes of H104:H4 strains from the recent European E. coli outbreak that resulted in both bloody diarrhea and hemolytic uremic syndrome (HUS), and caused at least 50 deaths.

MicroScope: a platform for microbial genome annotation and comparative genomics

PubMed Central

Vallenet, D.; Engelen, S.; Mornico, D.; Cruveiller, S.; Fleury, L.; Lajus, A.; Rouy, Z.; Roche, D.; Salvignol, G.; Scarpelli, C.; Médigue, C.

2009-01-01

The initial outcome of genome sequencing is the creation of long text strings written in a four letter alphabet. The role of in silico sequence analysis is to assist biologists in the act of associating biological knowledge with these sequences, allowing investigators to make inferences and predictions that can be tested experimentally. A wide variety of software is available to the scientific community, and can be used to identify genomic objects, before predicting their biological functions. However, only a limited number of biologically interesting features can be revealed from an isolated sequence. Comparative genomics tools, on the other hand, by bringing together the information contained in numerous genomes simultaneously, allow annotators to make inferences based on the idea that evolution and natural selection are central to the definition of all biological processes. We have developed the MicroScope platform in order to offer a web-based framework for the systematic and efficient revision of microbial genome annotation and comparative analysis (http://www.genoscope.cns.fr/agc/microscope). Starting with the description of the flow chart of the annotation processes implemented in the MicroScope pipeline, and the development of traditional and novel microbial annotation and comparative analysis tools, this article emphasizes the essential role of expert annotation as a complement of automatic annotation. Several examples illustrate the use of implemented tools for the review and curation of annotations of both new and publicly available microbial genomes within MicroScope’s rich integrated genome framework. The platform is used as a viewer in order to browse updated annotation information of available microbial genomes (more than 440 organisms to date), and in the context of new annotation projects (117 bacterial genomes). The human expertise gathered in the MicroScope database (about 280,000 independent annotations) contributes to improve the quality of microbial genome annotation, especially for genomes initially analyzed by automatic procedures alone. Database URLs: http://www.genoscope.cns.fr/agc/mage and http://www.genoscope.cns.fr/agc/microcyc PMID:20157493

MicroScope: a platform for microbial genome annotation and comparative genomics.

PubMed

Vallenet, D; Engelen, S; Mornico, D; Cruveiller, S; Fleury, L; Lajus, A; Rouy, Z; Roche, D; Salvignol, G; Scarpelli, C; Médigue, C

2009-01-01

The initial outcome of genome sequencing is the creation of long text strings written in a four letter alphabet. The role of in silico sequence analysis is to assist biologists in the act of associating biological knowledge with these sequences, allowing investigators to make inferences and predictions that can be tested experimentally. A wide variety of software is available to the scientific community, and can be used to identify genomic objects, before predicting their biological functions. However, only a limited number of biologically interesting features can be revealed from an isolated sequence. Comparative genomics tools, on the other hand, by bringing together the information contained in numerous genomes simultaneously, allow annotators to make inferences based on the idea that evolution and natural selection are central to the definition of all biological processes. We have developed the MicroScope platform in order to offer a web-based framework for the systematic and efficient revision of microbial genome annotation and comparative analysis (http://www.genoscope.cns.fr/agc/microscope). Starting with the description of the flow chart of the annotation processes implemented in the MicroScope pipeline, and the development of traditional and novel microbial annotation and comparative analysis tools, this article emphasizes the essential role of expert annotation as a complement of automatic annotation. Several examples illustrate the use of implemented tools for the review and curation of annotations of both new and publicly available microbial genomes within MicroScope's rich integrated genome framework. The platform is used as a viewer in order to browse updated annotation information of available microbial genomes (more than 440 organisms to date), and in the context of new annotation projects (117 bacterial genomes). The human expertise gathered in the MicroScope database (about 280,000 independent annotations) contributes to improve the quality of microbial genome annotation, especially for genomes initially analyzed by automatic procedures alone.Database URLs: http://www.genoscope.cns.fr/agc/mage and http://www.genoscope.cns.fr/agc/microcyc.

Growing up and Growing Older: Books for Young Readers©: An Annotated Booklist of Literature to Promote Positive Aging (Preschool-Third Grade)

ERIC Educational Resources Information Center

McGuire, Sandra L.

2016-01-01

Early children's literature plays a major role in attitude formation. The attitudes children form about aging will play an important role in how successfully they age. This annotated booklist is a compilation of carefully selected early children's literature that contains positive, meaningful portrayals of older adults and promotes positive aging.…

Smoking: The Health Consequences of Tobacco Use. An Annotated Bibliography with Analytical Introduction. Science and Social Responsibility Series, No. 2.

ERIC Educational Resources Information Center

Schmitz, Cecilia M.; Gray, Richard A.

This volume contains an extensive introduction to the health consequences of tobacco use and extended annotations of the most important English-language monographs and articles to appear on the subject in the 1980s and 1990s arranged in classified order under select headings. The introductory analytical essay by Richard A. Gray covers: early and…

The Economic Aspects of Non-Formal Education: A Selected Annotated Bibliography. Program of Studies in Non-Formal Education, Supplementary Series. Paper No. 3.

ERIC Educational Resources Information Center

Mannan, M. A.

The 303 items in the annotated bibliography are arrayed under four headings: (1) general literature--economic issues, (2) general literature--nonformal education, (3) economics of nonformal education (including cost-benefit analysis, investment and return in human capital, and economics of on-the-job training and retraining), and (4) planning and…

An Annotated List of Historically and Scientifically Important Works Published Before 1900 in the Library of The National Bureau of Standards.

ERIC Educational Resources Information Center

Terner, Janet

The purpose of this project was to specifically identify important works within the National Bureau of Standards library collection of approximately 125,000 items that are generally acknowledged to be pertinent to the development of modern science and technology. Presented is an annotated list including 197 items selected from the pre-1900…

A Selected Bibliography on Language Input To Young Children. CAL-ERIC/CLL Series on Languages and Linguistics.

ERIC Educational Resources Information Center

Andersen, Elaine S., Comp.

Thirty-one papers and reports dealing with recent work on language input to children are listed in this annotated bibliography. The annotations, which are descriptive rather than evaluative, summarize the design of each study, the nature of the data, and some of the results and conclusions. Entries by P. Broen, J. Bynon, L. Cherry, J. M. Crawford,…

MimoSA: a system for minimotif annotation

PubMed Central

2010-01-01

Background Minimotifs are short peptide sequences within one protein, which are recognized by other proteins or molecules. While there are now several minimotif databases, they are incomplete. There are reports of many minimotifs in the primary literature, which have yet to be annotated, while entirely novel minimotifs continue to be published on a weekly basis. Our recently proposed function and sequence syntax for minimotifs enables us to build a general tool that will facilitate structured annotation and management of minimotif data from the biomedical literature. Results We have built the MimoSA application for minimotif annotation. The application supports management of the Minimotif Miner database, literature tracking, and annotation of new minimotifs. MimoSA enables the visualization, organization, selection and editing functions of minimotifs and their attributes in the MnM database. For the literature components, Mimosa provides paper status tracking and scoring of papers for annotation through a freely available machine learning approach, which is based on word correlation. The paper scoring algorithm is also available as a separate program, TextMine. Form-driven annotation of minimotif attributes enables entry of new minimotifs into the MnM database. Several supporting features increase the efficiency of annotation. The layered architecture of MimoSA allows for extensibility by separating the functions of paper scoring, minimotif visualization, and database management. MimoSA is readily adaptable to other annotation efforts that manually curate literature into a MySQL database. Conclusions MimoSA is an extensible application that facilitates minimotif annotation and integrates with the Minimotif Miner database. We have built MimoSA as an application that integrates dynamic abstract scoring with a high performance relational model of minimotif syntax. MimoSA's TextMine, an efficient paper-scoring algorithm, can be used to dynamically rank papers with respect to context. PMID:20565705

Wide coverage biomedical event extraction using multiple partially overlapping corpora

PubMed Central

2013-01-01

Background Biomedical events are key to understanding physiological processes and disease, and wide coverage extraction is required for comprehensive automatic analysis of statements describing biomedical systems in the literature. In turn, the training and evaluation of extraction methods requires manually annotated corpora. However, as manual annotation is time-consuming and expensive, any single event-annotated corpus can only cover a limited number of semantic types. Although combined use of several such corpora could potentially allow an extraction system to achieve broad semantic coverage, there has been little research into learning from multiple corpora with partially overlapping semantic annotation scopes. Results We propose a method for learning from multiple corpora with partial semantic annotation overlap, and implement this method to improve our existing event extraction system, EventMine. An evaluation using seven event annotated corpora, including 65 event types in total, shows that learning from overlapping corpora can produce a single, corpus-independent, wide coverage extraction system that outperforms systems trained on single corpora and exceeds previously reported results on two established event extraction tasks from the BioNLP Shared Task 2011. Conclusions The proposed method allows the training of a wide-coverage, state-of-the-art event extraction system from multiple corpora with partial semantic annotation overlap. The resulting single model makes broad-coverage extraction straightforward in practice by removing the need to either select a subset of compatible corpora or semantic types, or to merge results from several models trained on different individual corpora. Multi-corpus learning also allows annotation efforts to focus on covering additional semantic types, rather than aiming for exhaustive coverage in any single annotation effort, or extending the coverage of semantic types annotated in existing corpora. PMID:23731785

Evaluation and integration of functional annotation pipelines for newly sequenced organisms: the potato genome as a test case.

PubMed

Amar, David; Frades, Itziar; Danek, Agnieszka; Goldberg, Tatyana; Sharma, Sanjeev K; Hedley, Pete E; Proux-Wera, Estelle; Andreasson, Erik; Shamir, Ron; Tzfadia, Oren; Alexandersson, Erik

2014-12-05

For most organisms, even if their genome sequence is available, little functional information about individual genes or proteins exists. Several annotation pipelines have been developed for functional analysis based on sequence, 'omics', and literature data. However, researchers encounter little guidance on how well they perform. Here, we used the recently sequenced potato genome as a case study. The potato genome was selected since its genome is newly sequenced and it is a non-model plant even if there is relatively ample information on individual potato genes, and multiple gene expression profiles are available. We show that the automatic gene annotations of potato have low accuracy when compared to a "gold standard" based on experimentally validated potato genes. Furthermore, we evaluate six state-of-the-art annotation pipelines and show that their predictions are markedly dissimilar (Jaccard similarity coefficient of 0.27 between pipelines on average). To overcome this discrepancy, we introduce a simple GO structure-based algorithm that reconciles the predictions of the different pipelines. We show that the integrated annotation covers more genes, increases by over 50% the number of highly co-expressed GO processes, and obtains much higher agreement with the gold standard. We find that different annotation pipelines produce different results, and show how to integrate them into a unified annotation that is of higher quality than each single pipeline. We offer an improved functional annotation of both PGSC and ITAG potato gene models, as well as tools that can be applied to additional pipelines and improve annotation in other organisms. This will greatly aid future functional analysis of '-omics' datasets from potato and other organisms with newly sequenced genomes. The new potato annotations are available with this paper.

Common data model for natural language processing based on two existing standard information models: CDA+GrAF.

PubMed

Meystre, Stéphane M; Lee, Sanghoon; Jung, Chai Young; Chevrier, Raphaël D

2012-08-01

An increasing need for collaboration and resources sharing in the Natural Language Processing (NLP) research and development community motivates efforts to create and share a common data model and a common terminology for all information annotated and extracted from clinical text. We have combined two existing standards: the HL7 Clinical Document Architecture (CDA), and the ISO Graph Annotation Format (GrAF; in development), to develop such a data model entitled "CDA+GrAF". We experimented with several methods to combine these existing standards, and eventually selected a method wrapping separate CDA and GrAF parts in a common standoff annotation (i.e., separate from the annotated text) XML document. Two use cases, clinical document sections, and the 2010 i2b2/VA NLP Challenge (i.e., problems, tests, and treatments, with their assertions and relations), were used to create examples of such standoff annotation documents, and were successfully validated with the XML schemata provided with both standards. We developed a tool to automatically translate annotation documents from the 2010 i2b2/VA NLP Challenge format to GrAF, and automatically generated 50 annotation documents using this tool, all successfully validated. Finally, we adapted the XSL stylesheet provided with HL7 CDA to allow viewing annotation XML documents in a web browser, and plan to adapt existing tools for translating annotation documents between CDA+GrAF and the UIMA and GATE frameworks. This common data model may ease directly comparing NLP tools and applications, combining their output, transforming and "translating" annotations between different NLP applications, and eventually "plug-and-play" of different modules in NLP applications. Copyright © 2011 Elsevier Inc. All rights reserved.

A call to standardize preanalytic data elements for biospecimens.

PubMed

Robb, James A; Gulley, Margaret L; Fitzgibbons, Patrick L; Kennedy, Mary F; Cosentino, L Mark; Washington, Kay; Dash, Rajesh C; Branton, Philip A; Jewell, Scott D; Lapham, Rosanna L

2014-04-01

Biospecimens must have appropriate clinical annotation (data) to ensure optimal quality for both patient care and research. Clinical preanalytic variables are the focus of this study. To define the essential preanalytic variables (data fields) that should be attached to every collected biospecimen and to provide a complete list of such variables, along with their relative importance, which can vary, depending on downstream use, institutional needs, and information technology capabilities. The College of American Pathologists Diagnostic Intelligence and Health Information Technology Committee sponsored a Biorepository Working Group to develop a ranked list of the preanalytic variables for annotating biospecimens. Members of the working group were experts in anatomic, clinical, and molecular pathology; biobanking; medical informatics; and accreditation. Several members had experience with federal government programs, such as the National Cancer Institute's Biospecimens and Biorepository Branch and the National Cancer Institute's Community Cancer Center Program. Potential preanalytic variables were identified and ranked along with available supporting evidence, definitions, and potential negative effects if the variable was not attached to the biospecimen. Additional national and international stakeholders reviewed the draft manuscript. The ranked listing of 170 preanalytic variables produced can be used as a guide for site-specific implementation into patient care and/or research biorepository processes. Conclusions.-In our collective experience, it is often difficult to choose which of the many preanalytic variables to attach to any specific set of biospecimens used for patient care and/or research. The provided ranked list should aid in the selection of preanalytic variables for a given biospecimen collection.

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.

Selected Reference Books of 1998-99.

ERIC Educational Resources Information Center

McIlvaine, Eileen

1999-01-01

Presents an annotated bibliography of selected reference books published between 1998 and 1999 under subject headings for biography, journalism, mythology, languages and literature, architecture and city planning, political science, economics, history, and new editions and supplements. (LRW)

Selected Reference Books of 2000/2001.

ERIC Educational Resources Information Center

McIlvaine, Eileen

2002-01-01

Presents an annotated list of selected recent scholarly and general reference works under the subject categories of archives; literature; music; psychology; sociology; black studies; women's studies; history and area studies; and new editions and supplements. (LRW)

Trees and Shrubs of the Penobscot Experimental Forest, Penobscot County, Maine

Treesearch

Lawrence O. Safford; Robert M. Frank; Elbert L., Jr. Little

1969-01-01

A reference guide for scientists, students, and visitors to the Penobscot Experimental Forest. A research unit of the Northeastern Forest Experiment Station, the 4,000-acre site is located in southern Penobscot County near Bangor. Includes the history and a description of the physical features of the Penobscot, an annotated list of 103 species of woody plants and...

An Annotated Bibliography Dealing with Some Implications of Two Art Education Reform Movements.

ERIC Educational Resources Information Center

Molinaro, Julia A.

Efforts to renew cultural literacy and reform arts education sponsored by the National Endowment for the Arts and the Getty Center for Education in the Arts suggest fundamental changes relating to the scope of art curricula. The single greatest drawback of existing art curricula and the guides that teachers use is the emphasis on skill development…

Teaching on Weekends and in Shopping Centers. A Guide for Colleges and Universities.

ERIC Educational Resources Information Center

East, James R.

A directory of 233 weekend and 30 shopping center programs in the United States and Canada is presented, along with a general discussion of these types of programs and an annotated bibliography. The listing for each program includes: the institution's name, address, and contact person; the funding sources; the date the program was started; the…

Elucidating high-dimensional cancer hallmark annotation via enriched ontology.

PubMed

Yan, Shankai; Wong, Ka-Chun

2017-09-01

Cancer hallmark annotation is a promising technique that could discover novel knowledge about cancer from the biomedical literature. The automated annotation of cancer hallmarks could reveal relevant cancer transformation processes in the literature or extract the articles that correspond to the cancer hallmark of interest. It acts as a complementary approach that can retrieve knowledge from massive text information, advancing numerous focused studies in cancer research. Nonetheless, the high-dimensional nature of cancer hallmark annotation imposes a unique challenge. To address the curse of dimensionality, we compared multiple cancer hallmark annotation methods on 1580 PubMed abstracts. Based on the insights, a novel approach, UDT-RF, which makes use of ontological features is proposed. It expands the feature space via the Medical Subject Headings (MeSH) ontology graph and utilizes novel feature selections for elucidating the high-dimensional cancer hallmark annotation space. To demonstrate its effectiveness, state-of-the-art methods are compared and evaluated by a multitude of performance metrics, revealing the full performance spectrum on the full set of cancer hallmarks. Several case studies are conducted, demonstrating how the proposed approach could reveal novel insights into cancers. https://github.com/cskyan/chmannot. Copyright © 2017 Elsevier Inc. All rights reserved.

Essential Annotation Schema for Ecology (EASE)-A framework supporting the efficient data annotation and faceted navigation in ecology.

PubMed

Pfaff, Claas-Thido; Eichenberg, David; Liebergesell, Mario; König-Ries, Birgitta; Wirth, Christian

2017-01-01

Ecology has become a data intensive science over the last decades which often relies on the reuse of data in cross-experimental analyses. However, finding data which qualifies for the reuse in a specific context can be challenging. It requires good quality metadata and annotations as well as efficient search strategies. To date, full text search (often on the metadata only) is the most widely used search strategy although it is known to be inaccurate. Faceted navigation is providing a filter mechanism which is based on fine granular metadata, categorizing search objects along numeric and categorical parameters relevant for their discovery. Selecting from these parameters during a full text search creates a system of filters which allows to refine and improve the results towards more relevance. We developed a framework for the efficient annotation and faceted navigation in ecology. It consists of an XML schema for storing the annotation of search objects and is accompanied by a vocabulary focused on ecology to support the annotation process. The framework consolidates ideas which originate from widely accepted metadata standards, textbooks, scientific literature, and vocabularies as well as from expert knowledge contributed by researchers from ecology and adjacent disciplines.

Postoperative seizure outcome-guided machine learning for interictal electrocorticography in neocortical epilepsy.

PubMed

Park, Seong-Cheol; Chung, Chun Kee

2018-06-01

The objective of this study was to introduce a new machine learning guided by outcome of resective epilepsy surgery defined as the presence/absence of seizures to improve data mining for interictal pathological activities in neocortical epilepsy. Electrocorticographies for 39 patients with medically intractable neocortical epilepsy were analyzed. We separately analyzed 38 frequencies from 0.9 to 800 Hz including both high-frequency activities and low-frequency activities to select bands related to seizure outcome. An automatic detector using amplitude-duration-number thresholds was used. Interictal electrocorticography data sets of 8 min for each patient were selected. In the first training data set of 20 patients, the automatic detector was optimized to best differentiate the seizure-free group from not-seizure-free-group based on ranks of resection percentages of activities detected using a genetic algorithm. The optimization was validated in a different data set of 19 patients. There were 16 (41%) seizure-free patients. The mean follow-up duration was 21 ± 11 mo (range, 13-44 mo). After validation, frequencies significantly related to seizure outcome were 5.8, 8.4-25, 30, 36, 52, and 75 among low-frequency activities and 108 and 800 Hz among high-frequency activities. Resection for 5.8, 8.4-25, 108, and 800 Hz activities consistently improved seizure outcome. Resection effects of 17-36, 52, and 75 Hz activities on seizure outcome were variable according to thresholds. We developed and validated an automated detector for monitoring interictal pathological and inhibitory/physiological activities in neocortical epilepsy using a data-driven approach through outcome-guided machine learning. NEW & NOTEWORTHY Outcome-guided machine learning based on seizure outcome was used to improve detections for interictal electrocorticographic low- and high-frequency activities. This method resulted in better separation of seizure outcome groups than others reported in the literature. The automatic detector can be trained without human intervention and no prior information. It is based only on objective seizure outcome data without relying on an expert's manual annotations. Using the method, we could find and characterize pathological and inhibitory activities.

Sickle Cell: A Selected Resource Bibliography.

ERIC Educational Resources Information Center

National Center for Education in Maternal and Child Health, Washington, DC.

This annotated, selective bibliography lists the following types of educational and informational material on both sickle cell disease and trait: (1) professional education materials; (2) fact sheets, pamphlets, and brochures; and (3) audiovisual material. A selected list of references is provided for the following topic areas: (1) genetic…

[Medicinal plant DNA marker assisted breeding (Ⅱ) the assistant identification of SNPs assisted identification and breeding research of high yield Perilla frutescens new variety].

PubMed

Shen, Qi; Zhang, Dong; Sun, Wei; Zhang, Yu-Jun; Shang, Zhi-Wei; Chen, Shi-Lin

2017-05-01

Perilla frutescens is one of 60 kinds of food and medicine plants in the initial directory announced by health ministry of China. With the development of Perilla domain in recent , the breeding and application of good varieties has become the main bottleneck of its development. This study reported that applied to the system selection, add to marker-assisted method to breed perilla varieties. Through the whole genome sequencing and consistency matching, annotated the mutation locus according to genome data, and comparison analysis with Perilla common variants database, finally selected 30 non-synonymous mutation SNPs used as characteristic markers of Zhongyan Feishu No.1. those SNP marker were used as chosen standard of Perilla varieties. Finally breeding new perilla variety Zhongyan Feishu No.1, which possess to characters of the leaf and seed dual-used, high yield, high resistance, and could used to green fertilizer. The Zhongyan Feishu No.1 acquired the plant new varieties identification of Beijing city , the identification numbers is 2016054. Marker assisted identification guide new varieties breeding in plants, which can provide a new reference for breeding of medicinal plants. Copyright© by the Chinese Pharmaceutical Association.

Aspects of U.S. Information Policy: An Annotated Bibliography of Federal Laws, Policies, Regulations, Congressional Hearings with Related Monographs, Serials and Studies from the Private Sector.

ERIC Educational Resources Information Center

National Commission on Libraries and Information Science, Washington, DC.

This annotated bibliography covers the period from 1974 to 1981, with primary emphasis on documents and publications produced between 1978 and 1981. The majority of the publications cited are U.S. government documents; however, the last section includes relevant monographs, journal articles, and conference papers that were selected by the National…

Economic Aspects of Agricultural Development in Africa. A Selective Annotated Reading List of Reports and Studies Concerning 40 African Countries During the Period 1960 - 1969.

ERIC Educational Resources Information Center

Neville-Rolfe, Edmund, Comp.

Some 1394 research studies from various African countries are annotated in this bibliography, which is divided into 37 country sections with a separate section (Africa General) for studies dealing with the continent as a whole, with geographical regions, or with groups of countries. The publications listed and summarized were published primarily…

Sequencing, annotation and comparative analysis of nine BACs of giant panda (Ailuropoda melanoleuca).

PubMed

Zheng, Yang; Cai, Jing; Li, JianWen; Li, Bo; Lin, Runmao; Tian, Feng; Wang, XiaoLing; Wang, Jun

2010-01-01

A 10-fold BAC library for giant panda was constructed and nine BACs were selected to generate finish sequences. These BACs could be used as a validation resource for the de novo assembly accuracy of the whole genome shotgun sequencing reads of giant panda newly generated by the Illumina GA sequencing technology. Complete sanger sequencing, assembly, annotation and comparative analysis were carried out on the selected BACs of a joint length 878 kb. Homologue search and de novo prediction methods were used to annotate genes and repeats. Twelve protein coding genes were predicted, seven of which could be functionally annotated. The seven genes have an average gene size of about 41 kb, an average coding size of about 1.2 kb and an average exon number of 6 per gene. Besides, seven tRNA genes were found. About 27 percent of the BAC sequence is composed of repeats. A phylogenetic tree was constructed using neighbor-join algorithm across five species, including giant panda, human, dog, cat and mouse, which reconfirms dog as the most related species to giant panda. Our results provide detailed sequence and structure information for new genes and repeats of giant panda, which will be helpful for further studies on the giant panda.

A Select Bibliography of Books on Labor Issues.

ERIC Educational Resources Information Center

American Federation of Labor and Congress of Industrial Organizations, Washington, DC.

This annotated bibliography of 90 books on labor issues presents selections in the following areas: labor history, biographies, contemporary issues, labor economics and labor relations, labor law, labor unions, women and work, and reference books. (DB)

Processing sequence annotation data using the Lua programming language.

PubMed

Ueno, Yutaka; Arita, Masanori; Kumagai, Toshitaka; Asai, Kiyoshi

2003-01-01

The data processing language in a graphical software tool that manages sequence annotation data from genome databases should provide flexible functions for the tasks in molecular biology research. Among currently available languages we adopted the Lua programming language. It fulfills our requirements to perform computational tasks for sequence map layouts, i.e. the handling of data containers, symbolic reference to data, and a simple programming syntax. Upon importing a foreign file, the original data are first decomposed in the Lua language while maintaining the original data schema. The converted data are parsed by the Lua interpreter and the contents are stored in our data warehouse. Then, portions of annotations are selected and arranged into our catalog format to be depicted on the sequence map. Our sequence visualization program was successfully implemented, embedding the Lua language for processing of annotation data and layout script. The program is available at http://staff.aist.go.jp/yutaka.ueno/guppy/.

Assessing the impact of telestration on surgical telementoring: A randomized controlled trial.

PubMed

Budrionis, Andrius; Hasvold, Per; Hartvigsen, Gunnar; Bellika, Johan Gustav

2016-01-01

Using graphical annotations in surgical telementoring promises vast improvements in both clinical and educational outcomes. However, these assumptions do not consider the potential patient safety risks resulting from this feature. Major differences in regulations regarding the implementation of telestration encourage an assessment of the utility of this feature on the outcomes of telementoring sessions. Eight students participated in a randomized controlled trial, comparing verbal with annotation-supplemented telementoring via video conferencing. A remote mentor guided the participants through four localization exercises, identifying the features in a still laparoscopic surgery scene using a laparoscopic simulator. Clinical and educational outcomes were assessed; the time consumption and quality of mentoring were determined. The study revealed no significant difference in localizing the intervention between the studied methods, while educational outcomes favoured verbal mentoring. Telestration-supplemented guidance was considerably faster and resulted in fewer miscommunications between the mentor and mentee. The initial hypothesis of the major clinical and education benefits of telestration in telementoring was not supported. A potential 33% decrease in the duration of the mentored episodes is expected due to the ability to annotate live video content. However, the impact of time saving on the outcome of the procedure remains unclear. Regardless of the quantitative measures, most of the participants and the mentor agreed that graphical annotations provide advantages over verbal guidance. © The Author(s) 2015.

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.

Told through the wine: A liquid chromatography-mass spectrometry interplatform comparison reveals the influence of the global approach on the final annotated metabolites in non-targeted metabolomics.

PubMed

Díaz, Ramon; Gallart-Ayala, Hector; Sancho, Juan V; Nuñez, Oscar; Zamora, Tatiana; Martins, Claudia P B; Hernández, Félix; Hernández-Cassou, Santiago; Saurina, Javier; Checa, Antonio

2016-02-12

This work focuses on the influence of the selected LC-HRMS platform on the final annotated compounds in non-targeted metabolomics. Two platforms that differed in columns, mobile phases, gradients, chromatographs, mass spectrometers (Orbitrap [Platform#1] and Q-TOF [Platform#2]), data processing and marker selection protocols were compared. A total of 42 wines samples from three different protected denomination of origin (PDO) were analyzed. At the feature level, good (O)PLS-DA models were obtained for both platforms (Q(2)[Platform#1]=0.89, 0.83 and 0.72; Q(2)[Platform#2]=0.86, 0.86 and 0.77 for Penedes, Ribera del Duero and Rioja wines respectively) with 100% correctly classified samples in all cases. At the annotated metabolite level, platforms proposed 9 and 8 annotated metabolites respectively which were identified by matching standards or the MS/MS spectra of the compounds. At this stage, there was no coincidence among platforms regarding the suggested metabolites. When screened on the raw data, 6 and 5 of these compounds were detected on the other platform with a similar trend. Some of the detected metabolites showed complimentary information when integrated on biological pathways. Through the use of some examples at the annotated metabolite level, possible explanations of this initial divergence on the results are presented. This work shows the complications that may arise on the comparison of non-targeted metabolomics platforms even when metabolite focused approaches are used in the identification. Copyright © 2016 Elsevier B.V. All rights reserved.

Selected Survey of Educational Law and Policy Literature.

ERIC Educational Resources Information Center

Piele, Philip K., Comp.

1983-01-01

Annotations from three issues of "Current Index to Journals in Education" were selected on the basis of anticipated reader interest. Articles dealing with elementary and secondary education organized by subjects are followed by articles dealing with postsecondary education. (MLF)

Collection Development Plan.

ERIC Educational Resources Information Center

Minnesota State Law Library, St. Paul.

This collection development plan of the Minnesota State Law Library includes detailed information on policies and annotations. After an overview of the Library's collection, general policy guidelines on the following are discussed: material selection; principles of selection; exclusions; gifts; interlibrary loan; cooperation; replacements;…

Automated Gene Ontology annotation for anonymous sequence data.

PubMed

Hennig, Steffen; Groth, Detlef; Lehrach, Hans

2003-07-01

Gene Ontology (GO) is the most widely accepted attempt to construct a unified and structured vocabulary for the description of genes and their products in any organism. Annotation by GO terms is performed in most of the current genome projects, which besides generality has the advantage of being very convenient for computer based classification methods. However, direct use of GO in small sequencing projects is not easy, especially for species not commonly represented in public databases. We present a software package (GOblet), which performs annotation based on GO terms for anonymous cDNA or protein sequences. It uses the species independent GO structure and vocabulary together with a series of protein databases collected from various sites, to perform a detailed GO annotation by sequence similarity searches. The sensitivity and the reference protein sets can be selected by the user. GOblet runs automatically and is available as a public service on our web server. The paper also addresses the reliability of automated GO annotations by using a reference set of more than 6000 human proteins. The GOblet server is accessible at http://goblet.molgen.mpg.de.

pocketZebra: a web-server for automated selection and classification of subfamily-specific binding sites by bioinformatic analysis of diverse protein families.

PubMed

Suplatov, Dmitry; Kirilin, Eugeny; Arbatsky, Mikhail; Takhaveev, Vakil; Svedas, Vytas

2014-07-01

The new web-server pocketZebra implements the power of bioinformatics and geometry-based structural approaches to identify and rank subfamily-specific binding sites in proteins by functional significance, and select particular positions in the structure that determine selective accommodation of ligands. A new scoring function has been developed to annotate binding sites by the presence of the subfamily-specific positions in diverse protein families. pocketZebra web-server has multiple input modes to meet the needs of users with different experience in bioinformatics. The server provides on-site visualization of the results as well as off-line version of the output in annotated text format and as PyMol sessions ready for structural analysis. pocketZebra can be used to study structure-function relationship and regulation in large protein superfamilies, classify functionally important binding sites and annotate proteins with unknown function. The server can be used to engineer ligand-binding sites and allosteric regulation of enzymes, or implemented in a drug discovery process to search for potential molecular targets and novel selective inhibitors/effectors. The server, documentation and examples are freely available at http://biokinet.belozersky.msu.ru/pocketzebra and there are no login requirements. © The Author(s) 2014. Published by Oxford University Press on behalf of Nucleic Acids Research.

Databases and Networking for Development. The Organization of Information in Europe in the Field of Policy and Planning for Developing Countries.

ERIC Educational Resources Information Center

Lindsay, John

This work suggests that better organization of existing sources of information available in Europe and better application of these sources to training can result in improved understanding of how information systems work, and it provides an annotated list of some of these sources. The guide opens with an introduction to public policy and urban…

The Soviet Union and Eastern Europe: A Bibliographic Guide to Recommended Books for Small and Medium-Sized Libraries and School Media Centers.

ERIC Educational Resources Information Center

Horak, Stephan M.

Intended to aid librarians in small- and medium-sized libraries and media centers, this annotated bibliography lists 1,555 books focusing on the Soviet Union and Eastern Europe. The book is divided into four parts: (1) "General and Interrelated Themes--Union of the Soviet Socialist Republics and Eastern European Countries"; (2)…

Comparison of three microarray probe annotation pipelines: differences in strategies and their effect on downstream analysis

PubMed Central

Neerincx, Pieter BT; Casel, Pierrot; Prickett, Dennis; Nie, Haisheng; Watson, Michael; Leunissen, Jack AM; Groenen, Martien AM; Klopp, Christophe

2009-01-01

Background Reliable annotation linking oligonucleotide probes to target genes is essential for functional biological analysis of microarray experiments. We used the IMAD, OligoRAP and sigReannot pipelines to update the annotation for the ARK-Genomics Chicken 20 K array as part of a joined EADGENE/SABRE workshop. In this manuscript we compare their annotation strategies and results. Furthermore, we analyse the effect of differences in updated annotation on functional analysis for an experiment involving Eimeria infected chickens and finally we propose guidelines for optimal annotation strategies. Results IMAD, OligoRAP and sigReannot update both annotation and estimated target specificity. The 3 pipelines can assign oligos to target specificity categories although with varying degrees of resolution. Target specificity is judged based on the amount and type of oligo versus target-gene alignments (hits), which are determined by filter thresholds that users can adjust based on their experimental conditions. Linking oligos to annotation on the other hand is based on rigid rules, which differ between pipelines. For 52.7% of the oligos from a subset selected for in depth comparison all pipelines linked to one or more Ensembl genes with consensus on 44.0%. In 31.0% of the cases none of the pipelines could assign an Ensembl gene to an oligo and for the remaining 16.3% the coverage differed between pipelines. Differences in updated annotation were mainly due to different thresholds for hybridisation potential filtering of oligo versus target-gene alignments and different policies for expanding annotation using indirect links. The differences in updated annotation packages had a significant effect on GO term enrichment analysis with consensus on only 67.2% of the enriched terms. Conclusion In addition to flexible thresholds to determine target specificity, annotation tools should provide metadata describing the relationships between oligos and the annotation assigned to them. These relationships can then be used to judge the varying degrees of reliability allowing users to fine-tune the balance between reliability and coverage. This is important as it can have a significant effect on functional microarray analysis as exemplified by the lack of consensus on almost one third of the terms found with GO term enrichment analysis based on updated IMAD, OligoRAP or sigReannot annotation. PMID:19615109

Comparison of three microarray probe annotation pipelines: differences in strategies and their effect on downstream analysis.

PubMed

Neerincx, Pieter Bt; Casel, Pierrot; Prickett, Dennis; Nie, Haisheng; Watson, Michael; Leunissen, Jack Am; Groenen, Martien Am; Klopp, Christophe

2009-07-16

Reliable annotation linking oligonucleotide probes to target genes is essential for functional biological analysis of microarray experiments. We used the IMAD, OligoRAP and sigReannot pipelines to update the annotation for the ARK-Genomics Chicken 20 K array as part of a joined EADGENE/SABRE workshop. In this manuscript we compare their annotation strategies and results. Furthermore, we analyse the effect of differences in updated annotation on functional analysis for an experiment involving Eimeria infected chickens and finally we propose guidelines for optimal annotation strategies. IMAD, OligoRAP and sigReannot update both annotation and estimated target specificity. The 3 pipelines can assign oligos to target specificity categories although with varying degrees of resolution. Target specificity is judged based on the amount and type of oligo versus target-gene alignments (hits), which are determined by filter thresholds that users can adjust based on their experimental conditions. Linking oligos to annotation on the other hand is based on rigid rules, which differ between pipelines.For 52.7% of the oligos from a subset selected for in depth comparison all pipelines linked to one or more Ensembl genes with consensus on 44.0%. In 31.0% of the cases none of the pipelines could assign an Ensembl gene to an oligo and for the remaining 16.3% the coverage differed between pipelines. Differences in updated annotation were mainly due to different thresholds for hybridisation potential filtering of oligo versus target-gene alignments and different policies for expanding annotation using indirect links. The differences in updated annotation packages had a significant effect on GO term enrichment analysis with consensus on only 67.2% of the enriched terms. In addition to flexible thresholds to determine target specificity, annotation tools should provide metadata describing the relationships between oligos and the annotation assigned to them. These relationships can then be used to judge the varying degrees of reliability allowing users to fine-tune the balance between reliability and coverage. This is important as it can have a significant effect on functional microarray analysis as exemplified by the lack of consensus on almost one third of the terms found with GO term enrichment analysis based on updated IMAD, OligoRAP or sigReannot annotation.

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…