Publications, Talks, Posters 2010-2012
Here we list publications, tutorials, talks and posters focused primarily on the GO and use of the GO, and presented by GOC members during 2010 reporting year.
- Alam-Faruque Y, Dimmer EC, Huntley RP, O'Donovan C, Scambler P, Apweiler R. 2010. The Renal Gene Ontology Annotation Initiative. Organogenesis 6(2): 71-75
- Alterovitz G, Xiang M, Hill DP, Lomax J, Liu J, Cherkassky M, Mungall C, Harris MA, Dolan ME, Blake JA, Ramoni MF. 2010. Ontology Engineering. Nat Biotechnol 28(2):128-30.
- Ammari M, McCarthy FM, Nanduri B, Pinchuk LM. 2010. Analysis of Bovine Viral Diarrhea Viruses-infected monocytes: identification of cytopathic and non-cytopathic biotype differences. BMC Bioinformatics 11 Suppl 6:S9.
- Blake JA, Bult CJ, Kadin JA, Richardson JE, Eppig JT; the Mouse Genome Database Group. 2010. The mouse genome database (MGD): premier model organism resource for mammalian genomics and genetics. Nucleic Acids Res. [Epub ahead of print]
- Deegan JI, Dimmer EC, Mungall CJ. 2010. Formalization of taxon-based constraints to detect inconsistencies in annotation and ontology development. BMC Bioinformatics 11(1): 530.
- Diehl AD, Augustine AD, Blake JA, Cowell LG, Gold TS, Gondré-Lewis TA, Masci AM, Meehan TF, Morel PA, Nijnik A, Peters B, Pulendran B, Scheuerman RH, Yao QA, Zand MS, Mungall CJ. 2010. Hematopoietic cell types: Prototype for a revised Cell Ontology. J Biomed Inform. [Epub ahead of print] doi:10.1016/j.jbi.2010.01.006.
- Gene Ontology Consortium. 2010. The Gene Ontology in 2010: extensions and refinements. Nucleic Acids Res 38(Database issue): D331-D335.
- Huntley RP, Dimmer EC, Apweiler R. 2010. Practical applications of the Gene Ontology resource. In Problem Solving Handbook in Computational Biology, LS Heath and N Ramakrishnan, Editors. Springer: New York, NY. ISBN 978-0-387-09759-6
- Khodiyar VK, Dimmer EC, Huntley RP, Lovering RC. 2010. Fundamentals of gene ontology functional annotation. In Knowledge-based Bioinformatics, G Alterovitz and M Ramoni, Editors. Wiley: Boston, MA.
- Leonelli S, Diehl AD, Christie KR, Harris MA, Lomax J. How the Gene Ontology evolves. BMC Bioinformatics [submitted].
- Manda P, Freeman MG, Bridges SM, Jankun-Kelly TJ, Nanduri B, McCarthy FM, Burgess SC. 2010. GOModeler--a tool for hypothesis-testing of functional genomics datasets. BMC Bioinformatics 11 Suppl 6: S29.
- Mi H, Dong Q, Muruganujan A, Gaudet P, Lewis S, Thomas PD. 2010. PANTHER version 7: improved phylogenetic trees, orthologs and collaboration with the Gene Ontology Consortium. Nuclei Acids Res 8(Database issue): D204-D210.
- Mungall CJ, Bada M, Berardini TZ, Deegan J, Ireland A, Harris MA, Hill DP, Lomax J. 2010. Cross-product extensions of the Gene Ontology. J Biomed Inform [Epub ahead of print]. doi:10.1016/j.jbi.2010.02.002. PDF.
- Mungall CJ, Batchelor C, Eilbeck K. 2010. Evolution of the Sequence Ontology terms and relationships. J Biomed Inform [Epub ahead of print].
- Mungall CJ, Gkoutos G, Smith C, Haendel M, Lewis S, Ashburner M. Integrating phenotype ontologies across multiple species. Genome Biology, 11(1):R2, 2010.
- Reese MG, Moore B, Batchelor C, Salas F, Cunningham F, Marth GT, Stein L, Flicek P, Yandell M, Eilbeck K. 2010. A standard variation file format for human genome sequences. Genome Biol 11(8):R88.
- Torto-Alalibo T, Collmer CW, Gwinn-Giglio M, Lindeberg M, Meng S, Chibucos MC, Tseng TT, Lomax J, Bieh B, Ireland A, Bird D, Dean RA, Glasner JD, Perna N, Setubal JC, Collmer A, Tyler BM. 2010. Unifying themes in microbial associations with animal and plant hosts described using the Gene Ontology. Microbiol Mol Biol Rev [accepted for publication]
- van den Berg BH, McCarthy FM, Lamont SJ, Burgess SC. 2010. Re-annotation is an essential step in systems biology modeling of functional genomics data. PLoS One 5(5): e10642.
C Mungall, P D'Eustachio: integrating GO and pathway data. Draft available on request
C Mungall, SJ Carbon: the GO compositional term request system. Draft available on request
D Hill, C Mungall, J Lomax, T Berardini, H Drabkin [+ others] GOCHE/CHEBI paper - in progress.
Yasmin Alam-Faruque, Rebecca Foulger, Doug Howe, David Hill, Midori Harris, Emily Dimmer, Rachael Huntley, Susan Tweedie, Judith Blake, Randall Thomas, Duncan Davidson, Jamie Davies, Adrian Woolf, Sanjay Jain, Peter Scambler, Rolf Apweiler. Representing Renal Development Biology in Gene Ontology - A report on outcome of the Kidney Development Ontology Content Meeting - in progress.
Yasmin Alam-Faruque, Ruth Lovering, Emily Dimmer, Varsha Khodyar, Rachael Huntley, Philippa Talmud, Peter Scambler, Rolf Apweiler. The importance of focused Gene Ontology curation of specific mammalian systems - in progress.
Technical Reports / Standards
- E. Dimmer (GOA). Trained 5 SIB curators in GO annotation. Geneva. February 2010.
- E. Dimmer (GOA). GO/GOA tutorial. Perspectives in clinical proteomics training workshop. EBI Hinxton. 17-18th March 2010.
- R. Huntley (GOA). "Describing Plant Gene Products Using GO/GOA." Plant Bioinformatics Hands-on training at EBI. EMBL-EBI, Hinxton, Cambridge. 29-31 March 2010.
- E. Dimmer (GOA). Trained 4 UniProtKB curators in GO annotation. EBI Hinxton. April 2010.
- V. Wood (PomBase), S. Oliver (U Cambridge), M. Harris (MGI), S. Tweedie (FlyBase). GO annotation practical, Cambridge University systems biology students. 8 November 2010.
- J. R. Smith (RGD). "Introduction to Biomedical Ontologies #4- Ontology Term Enrichment Using RatMine". Posted on Scivee.tv, YouTube, and Vimeo.com 19 November 2010.
- R. Huntley (GOA). "Introduction to the Gene Ontology and GO annotation resources." Proteomics Bioinformatics Joint EBI-Wellcome Trust workshop. EMBL-EBI, Hinxton, Cambridge. 12-18 December 2010.
- Alam-Faruque Y,  Renal GOA Initiative HSF March 2010
- R Apweiler, Talk at the Joint British Renal Society/ Renal Association Annual Conference May 2010 about Bioinformatics resources for renal scientists and in particular the Renal GOA Initiative
- C Mungall, has_part in GO
- M Haendel, C Mungall Uberon, CL and GO
- C Mungall GO-pathway integration
- Mike Bada and Karen Eilbeck Toward a richer representation of sequence variation in the Sequence Ontology. September 2010 AIMM workshop at the European Conference on Computational Biology.
- Alam-Faruque Y, Representing kidney development biology in Gene Ontology October 2010 EBI Industry Workshop on Ontology Development and Engineering held at EBI
- Alam-Faruque Y, et al. (GOA), Title: "The Renal Gene Ontology Annotation (GOA) Initiative"; Joint British Renal Society/ Renal Association Annual Conference (May 2010)
- Fisk D et al. (SGD), Title: "Annotation Across Species: SGD and the Reference Genome Project"; Model Organism to Human Biology Conference. File:FiskMO2HB-2010v2.pdf (June 2010)
- Christie K et al. (SGD), Title: "Improving the Representation of Transcription in the Gene Ontology (GO)"; EMBO Gene Transcription in Yeast (June 2010)
- Blake J, et al. (GOC), Title: "Improving Logical Relationships in the Gene Ontology"; ISMB Bio-Ontologies SIG (July 2010)
- Drabkin HJ et al. (MGI), Title: "Proteins, Pathways, and Macromolecular Complexes"; ISMB (July 2010)
- Meehan TF et al. (GOC), Title: "Logically defining hematopoietic cell types in the Cell Ontology by cross-product extensions"; ISMB Bio-Ontologies SIG (July 2010)
- Gaudet P, Lee E, Livestone, M, Dolinski K, Lewis SE, Thomas P. Functional Gene Ontology Annotation across Species using PAINT. Poster presented at the ISMB meeting. Boston, July 2010.
- Alam-Faruque Y, et al. (GOA), Title: "The Renal Gene Ontology Annotation (GOA) Initiative"; Kidney Research UK Fellows Day (September 2010)
- Van Auken K, Fang R, Chan J, Mueller HM, Sternberg P (WB), Title: "Combining Support Vector Machines (SVMs) with Textpresso Category Searches for Improved Data Type Curation Efficiency at WormBase"; 4th International BioCuration Conference (October 2010)
- The Gene Ontologies: As of Dec. 2009, the Gene Ontologies include Molecular Function (8,657 terms), Biological Process (17, 553 terms), and Cellular Component (2,613 terms). The ontologies including definitions are available at the GO Web site in a variety of formats including OWL, RDF, XML, and OBO.
- The Sequence Ontology is provided for download in 4 different forms. It is provided for editing as so-xp.obo which includes the raw cross product terms, and is intended for use with a reasoner. It is provided fully reasoned with the implicit links fully written out, for use without a reasoner as so.obo. Two subsets of SO are maintained for specialized uses: a version for natural language programming (l_s_f.obo) and subset of SO feature for automated annotation pipelines (sofa.obo).
- GO Associations files for the major model organisms are provided in OBO, tab delimited and XML formats that include evidence assertions, citations, synonyms and other accIDs and Xrefs.
- The GO Database is developed and maintained by software engineers located in the Stanford and LBNL GO groups. The MySQL database, API documentation, schema diagrams and full descriptions of all tables are freely available at http://www.godatabase.org/dev/database/. GO monthly releases are available in RDF XML or a MySQL database dump.
- GO Consortium Tools are the AmiGO browser for the GO database resource and the OBO-Edit ontology editing tool; both are open-source applications (http://www.geneontology.org/GO.tools.html).
- Many GO Tools for mining GO data have been developed and can be accessed from the GO Web Site. Tools can map granular GO terms to more general parent terms, and can facilitate the access to GO information from gene-set input files. Several are particularly useful for analysis of microarray data.
- GO Browsers: Several browsing tools have been developed and are available via the GO Web site. The AmiGO browser is provided by the GOC for access to the GO database.
- GO Teaching Resources include tutorials, presentations and posters provided by members of the GO Consortium (http://www.geneontology.org/GO.teaching.resources.html).
- Indices mapping other classification systems to the GO provided at the GO Web site include translations of Swiss-Prot keywords, TIGR/EGAD, GenProtEC, InterPro keywords, and the Enzyme Commission set. (http://www.geneontology.org/GO.indices.html).
Publications by external groups that rely on the GO
View all publications for 2010 in the GO bibliography
Other publications of note:
- Biomedical Discovery Acceleration, with Applications to Craniofacial Development PLoS Comp Bio, 2010, Leach et al -- this publication makes novel use of the GO cross products.