Ontology application and use at the ENCODE DCC

Database

Volumn 2015, Issue , 2015, Pages

  Malladi, Venkat S ^a   Erickson, Drew T ^a   Podduturi, Nikhil R ^a   Rowe, Laurence D ^a   Chan, Esther T ^a   Davidson, Jean M ^a   Hitz, Benjamin C ^a   Ho, Marcus ^a   Lee, Brian T ^b   Miyasato, Stuart ^a   Roe, Gregory R ^a   Simison, Matt ^a   Sloan, Cricket A ^a   Strattan, J Seth ^a   Tanaka, Forrest ^a   Kent, W James ^b   Cherry, J Michael ^a   Hong, Eurie L ^a  

^a STANFORD UNIVERSITY SCHOOL OF MEDICINE   (United States)

^b University of California Santa Cruz   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ANIMAL; GENE ONTOLOGY; GENE REGULATORY NETWORK; GENETIC DATABASE; GENETIC TRANSCRIPTION; HUMAN; INFORMATION PROCESSING; MOLECULAR GENETICS; MOUSE; PHYSIOLOGY; PROCEDURES;

ANIMALS; DATA CURATION; DATABASES, GENETIC; GENE ONTOLOGY; GENE REGULATORY NETWORKS; HUMANS; MICE; MOLECULAR SEQUENCE ANNOTATION; TRANSCRIPTION, GENETIC;

EID: 84943150249     PISSN: 17580463     EISSN: None     Source Type: Journal    
DOI: 10.1093/database/bav010     Document Type: Article

References (29)

1. ENCODE Project Consortium. (2012) An integrated encyclopedia of DNA elements in the human genome. Nature, 489, 57-74.
2. Rosenbloom, K.R., Sloan, C.A., Malladi, V.S. et al. (2013) ENCODE data in the UCSC genome browser: Year 5 update. Nucleic Acids Res., 41(Database issue), D56-D63.
3. Mouse ENCODE Consortium, Stamatoyannopolous, J.A., Snyder, M. et al. (2012) An encyclopedia of mouse DNA elements (Mouse ENCODE). Genome Biol., 13, 418.
4. Ho, J.W., Jung, Y.L, Lui, T. et al. (2014) Comparative analysis of metazoan chromatin organization. Nature, 512, 449-452.
5. Boyle, A.P., Araya, C.L., Brdlik, C. et al. (2014) Comparative analysis of regulatory information and circuits across distance species. Nature, 512, 453-456.
6. Gerstein, M.B., Rozowsky, J., Yan, K.K. et al. (2014) Comparative analysis of the transcriptome across distance species. Nature, 512, 445-448.
7. Rosenbloom, K.R., Dreszer, T.R., Long, J.C. et al. (2012) ENCODE whole-genome data in the UCSC Genome Browser: Update 2012. Nucleic Acids Res., 40(Database issue), D912-D917.
8. Washington, N.L., Stinson, E.O., Perry, M.D. et al. (2011) The modENCODE Data Coordination Center: Lessons in harvesting comprehensive experimental details. Database, 2011, bar023.
9. The Gene Ontology Consortium. (2001) Creating the gene ontology resource: Design and implementation. Genome Res., 8, 1425-1433.
10. Ashburner, M., Ball, C.A., Blake, J.A. et al. (2000) Gene Ontology: Tool for the unification of biology. Nat. Genet., 25, 25-29.
11. Mungall, C.J., Torniai, C., Gkoutos, G.V. et al. (2012) Uberon, an integrativemulti-species anatomy ontology. Genome Biol., 13, R5.
12. Grumbling, G., Strelets V and The FlyBase Consortium. (2006) FlyBase: Anatomical data, images and queries. Nucleic Acids Res., 34(Database issue), D484-D488.
13. Lee, R.Y. and Sternberg, P.W. (2003) Building a cell and anatomy ontology of Caenorhabditis elegans. Comp. Funct. Genomics, 4, 121-126.
14. Brad, J., Rhee, S.Y. and Ashburner, M. (2005) An ontology for cell types. Genome Biol., 6, R21.
15. Malone, J., Holloway, E., Adamusiak, T et al. (2010) Modeling sample variables with an experimental factor ontology. Bioinformatics, 26, 1112-1118.
16. Hastings, J., de Matos, P., Dekker, A. et al. (2013) The ChEBI reference database and ontology for biologically relevant chemistry: Enhancements for 2013. Nucleic Acids Res., 41(Database issue), D456-D463.
17. Brikmann, R.R., Courtot, M., Derom, D. et al. (2010) Modeling biomedical experimental processes with OBI. J. Biomed. Semantics, 1(Suppl 1), S7.
18. Eilbeck, K., Lewis, S.E., Mungall, C.J et al. (2005) The Sequence Ontology: A tool for the unification of genome annotations. Genome Biol., 6, R44.
19. Whetzel, P.L., Noy, N.F., Shah, N.H. et al. (2011) BioPortal: Enhanced functionality via new Web services from the National Center for Biomedical Ontology to access and use ontologies in software applications. Nucleic Acids Res., 39(Web Server Issue), W541-W545.
20. Côté, R., Reisinger, F., Martens, L. et al. (2010) The Ontology Lookup Service: Bigger and better. Nucleic Acids Res., 38(Suppl 2). W155-W160.
21. Vercryysse, S., Venkatesan, A., Kulper, M. (2012) OLSVis: An animated, interactive visual browser for bio-ontologies. BMC Bioinformatics, 13, 116.
22. Sacco, G.M. (2007) Research results in dynamic taxonomy and faceted search systems. Paper presented at the FIND'07 Workshop on Dynamic Taxonomies and Faceted Search, Regensburg, Germany.
23. The Gene Ontology Consortium. (2011) The Gene Ontology: Enhancements for 2011. Nucleic Acids Res., 40(Database issue), D559-D564.
24. Natale, D.A., Arighi, C.N., Barker, W.C. et al. (2011) The Protein Ontology: A structured representation of protein forms and complexes. Nucleic Acids Res., 39, D539-D545.
25. Ison, J., Kalas?, M., Jonassen, I. et al. (2013) EDAM: An ontology of bioinformatics operations, types of data and identifiers, topics and formats. Bioinformatics, 29, 1325-1332.
26. Walls, R.L, Deck, J., Guralnick, R. et al. (2014) Semantics in support of biodiversity knowledge discovery: An introduction to the biological collections ontology and related ontologies. PLoS One, 9, e89606.
27. Gostev, M., Faulconbridge, A., Brandizi, M. et al. (2012) The BioSample Database (BioSD) at the European Bioinformatics Institute. Nucleic Acids Res., 40(Database issue), D64-D70.
28. Barret, T., Clark, K., Gevorgyan, R. et al. (2012) BioProject and Biosample databases at NCBI: Facilitating capture and organization of metadata. Nucleic Acids Res., 40(Database issue), D57-D63.
29. Jupp, S., Malone, J. Bolleman, J. et al. (2014) The EBI RDF platform: Linked open data for the life sciences. Bioinformatics. 30, 1338-1339.