Literature DB >> 18629098

Building a cell and anatomy ontology of Caenorhabditis elegans.

Raymond Y N Lee1, Paul W Sternberg.   

Abstract

We are endowed with a rich knowledge about Caenorhabditis elegans. Its stereotyped anatomy and development has stimulated research and resulted in the accumulation of cell-based information concerning gene expression, and the role of specific cells in developmental signalling and behavioural circuits. To make the information more accessible to sophisticated queries and automated retrieval systems, WormBase has begun to construct a C. elegans cell and anatomy ontology. Here we present our strategies and progress.

Entities:  

Year:  2003        PMID: 18629098      PMCID: PMC2447384          DOI: 10.1002/cfg.248

Source DB:  PubMed          Journal:  Comp Funct Genomics        ISSN: 1531-6912


  13 in total

1.  Predictive value of compression ultrasonography for deep vein thrombosis in symptomatic outpatients: clinical implications of the site of vein noncompressibility.

Authors:  B G Birdwell; G E Raskob; T L Whitsett; S S Durica; P C Comp; J N George; T L Tytle; W L Owen; P A McKee
Journal:  Arch Intern Med       Date:  2000-02-14

2.  Post-embryonic development in the ventral cord of Caenorhabditis elegans.

Authors:  J E Sulston
Journal:  Philos Trans R Soc Lond B Biol Sci       Date:  1976-08-10       Impact factor: 6.237

3.  Post-embryonic cell lineages of the nematode, Caenorhabditis elegans.

Authors:  J E Sulston; H R Horvitz
Journal:  Dev Biol       Date:  1977-03       Impact factor: 3.582

4.  The embryonic cell lineage of the nematode Caenorhabditis elegans.

Authors:  J E Sulston; E Schierenberg; J G White; J N Thomson
Journal:  Dev Biol       Date:  1983-11       Impact factor: 3.582

5.  Gonadal cell lineages of the nematode Panagrellus redivivus and implications for evolution by the modification of cell lineage.

Authors:  P W Sternberg; H R Horvitz
Journal:  Dev Biol       Date:  1981-11       Impact factor: 3.582

6.  The Caenorhabditis elegans male: postembryonic development of nongonadal structures.

Authors:  J E Sulston; D G Albertson; J N Thomson
Journal:  Dev Biol       Date:  1980-08       Impact factor: 3.582

7.  The postembryonic cell lineages of the hermaphrodite and male gonads in Caenorhabditis elegans.

Authors:  J Kimble; D Hirsh
Journal:  Dev Biol       Date:  1979-06       Impact factor: 3.582

8.  Electron microscopical reconstruction of the anterior sensory anatomy of the nematode Caenorhabditis elegans.?2UU.

Authors:  S Ward; N Thomson; J G White; S Brenner
Journal:  J Comp Neurol       Date:  1975-04-01       Impact factor: 3.215

9.  Formation of the vulva in Caenorhabditis elegans: a paradigm for organogenesis.

Authors:  R Sharma-Kishore; J G White; E Southgate; B Podbilewicz
Journal:  Development       Date:  1999-02       Impact factor: 6.868

10.  Symmetry breakage in the development of one-armed gonads in nematodes.

Authors:  M A Félix; P W Sternberg
Journal:  Development       Date:  1996-07       Impact factor: 6.868

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  18 in total

Review 1.  Representing ontogeny through ontology: a developmental biologist's guide to the gene ontology.

Authors:  David P Hill; Tanya Z Berardini; Douglas G Howe; Kimberly M Van Auken
Journal:  Mol Reprod Dev       Date:  2010-04       Impact factor: 2.609

2.  Using WormBase: A Genome Biology Resource for Caenorhabditis elegans and Related Nematodes.

Authors:  Christian Grove; Scott Cain; Wen J Chen; Paul Davis; Todd Harris; Kevin L Howe; Ranjana Kishore; Raymond Lee; Michael Paulini; Daniela Raciti; Mary Ann Tuli; Kimberly Van Auken; Gary Williams
Journal:  Methods Mol Biol       Date:  2018

3.  Automated generation of gene summaries at the Alliance of Genome Resources.

Authors:  Ranjana Kishore; Valerio Arnaboldi; Ceri E Van Slyke; Juancarlos Chan; Robert S Nash; Jose M Urbano; Mary E Dolan; Stacia R Engel; Mary Shimoyama; Paul W Sternberg; The Alliance Of Genome Resources
Journal:  Database (Oxford)       Date:  2020-01-01       Impact factor: 3.451

4.  Text mining in the biocuration workflow: applications for literature curation at WormBase, dictyBase and TAIR.

Authors:  Kimberly Van Auken; Petra Fey; Tanya Z Berardini; Robert Dodson; Laurel Cooper; Donghui Li; Juancarlos Chan; Yuling Li; Siddhartha Basu; Hans-Michael Muller; Rex Chisholm; Eva Huala; Paul W Sternberg
Journal:  Database (Oxford)       Date:  2012-11-17       Impact factor: 3.451

5.  PhenomeNET: a whole-phenome approach to disease gene discovery.

Authors:  Robert Hoehndorf; Paul N Schofield; Georgios V Gkoutos
Journal:  Nucleic Acids Res       Date:  2011-07-06       Impact factor: 16.971

6.  The modENCODE Data Coordination Center: lessons in harvesting comprehensive experimental details.

Authors:  Nicole L Washington; E O Stinson; Marc D Perry; Peter Ruzanov; Sergio Contrino; Richard Smith; Zheng Zha; Rachel Lyne; Adrian Carr; Paul Lloyd; Ellen Kephart; Sheldon J McKay; Gos Micklem; Lincoln D Stein; Suzanna E Lewis
Journal:  Database (Oxford)       Date:  2011-08-19       Impact factor: 3.451

Review 7.  Ontology application and use at the ENCODE DCC.

Authors:  Venkat S Malladi; Drew T Erickson; Nikhil R Podduturi; Laurence D Rowe; Esther T Chan; Jean M Davidson; Benjamin C Hitz; Marcus Ho; Brian T Lee; Stuart Miyasato; Gregory R Roe; Matt Simison; Cricket A Sloan; J Seth Strattan; Forrest Tanaka; W James Kent; J Michael Cherry; Eurie L Hong
Journal:  Database (Oxford)       Date:  2015-03-16       Impact factor: 3.451

8.  Overlapping cell population expression profiling and regulatory inference in C. elegans.

Authors:  Joshua Burdick; Travis Walton; Elicia Preston; Amanda Zacharias; Arjun Raj; John Isaac Murray
Journal:  BMC Genomics       Date:  2016-02-29       Impact factor: 3.969

9.  Evaluation of research in biomedical ontologies.

Authors:  Robert Hoehndorf; Michel Dumontier; Georgios V Gkoutos
Journal:  Brief Bioinform       Date:  2012-09-08       Impact factor: 11.622

10.  Representation of anatomy in online atlases and databases: a survey and collection of patterns for interface design.

Authors:  Melissa D Clarkson
Journal:  BMC Dev Biol       Date:  2016-05-21       Impact factor: 1.978

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