Publications, Talks, Posters 2010-2012

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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.

Publications (alphabetical)

Alam-Faruque Y, Dimmer EC, Huntley RP, O'Donovan C, Scambler P, Apweiler R. The Renal Gene Ontology Annotation Initiative. Organogenesis 6 (2) April/May June 2010: 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. Feb;28(2):128-30.

Mungall C, Gkoutos G, Smith C, Haendel M, Lewis S, Ashburner M. Integrating phenotype ontologies across multiple species. Genome Biology, 11(1):R2, 2010.

Diehl AD, Augustine AD, Blake JA, Cowell LG, Gold TS, GondrÃ-Lewis TA, Masci AM, Meehan TF, Morel PA, NIAID Cell Ontology Working Group, Nijnik A, Peters B, Pulendran B, Scheuerman RH, Yao QA, Zand MS, and Mungall CJ. Hematopoietic Cell Types: Prototype for a Revised Cell Ontology. Journal of Biomedical Informatics, (accepted), 2010.

Gene Ontology Consortium. 2010. The Gene Ontology in 2010: extensions and refinements. Nucleic Acids Res. 2010 January; 38(Database issue): D331–D335.

Khodiyar VK, Dimmer EC, Huntley RP and Lovering RC. Fundamentals of gene ontology functional annotation, in Knowledge-based Bioinformatics, G. Alterovitz and M. Ramoni, Editors. 2010, Wiley: Boston, Massachusetts. p. 171-208

Leonelli S, Diehl AD, Christie KR, Harris MA, Lomax J. How the Gene Ontology Evolves. Genome Biology [ready for submission]

Mungall CJ, Bada M, Berardini TZ, Deegan J, Ireland A, Harris MA, Hill DP, Lomax J. Cross-Product Extensions of the Gene Ontology. Journal of Biomedical Informatics, In Press, Uncorrected Proof, 2010. PDF.

Trudy Torto-Alalibo, Candace W. Collmer, Michelle Gwinn-Giglio, Magdalen Lindeberg, Shaowu Meng, Marcus C. Chibucos, Tsai-Tien Tseng, Jane Lomax, Bryan Bieh, Amelia Ireland, David Bird, Ralph A. Dean, Jeremy D. Glasner, Nicole Perna, Joao C. Setubal1, Alan Collmer and Brett M. Tyler. Unifying Themes in Microbial Associations with Animal and Plant Hosts Described Using the Gene Ontology. Microbiology and Molecular Biology Reviews [accepted pending acceptance of revisions]

Deegan et al is accepted pending acceptance of minor revisions

In Progress/Proposed

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.

Technical Reports / Standards

Tutorials (chronological)

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.

Talks (chronological)

  • Alam-Faruque Y, [1] 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

Posters (chronological)

  • 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)

Project-Generated Resources

  1. 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.
  2. 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).
  3. 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.
  4. 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 GO monthly releases are available in RDF XML or a MySQL database dump.
  5. GO Consortium Tools are the AmiGO browser for the GO database resource and the OBO-Edit ontology editing tool; both are open-source applications (
  6. 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.
  7. 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.
  8. GO Teaching Resources include tutorials, presentations and posters provided by members of the GO Consortium (
  9. 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. (

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