Publications, Talks, Posters 2010-2012

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Note there is now a GO group on Mendeley: http://www.mendeley.com/groups/1250271/gene-ontology-consortium/papers/

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)

  • Dutkowski J, Kramer M, Surma MA, Balakrishnan R, Cherry JM, Krogan NJ, Ideker T. A gene ontology inferred from molecular networks. Nat Biotechnol. 2012 Dec 16. doi: 10.1038/nbt.2463.
  • Park J, Costanzo MC, Balakrishnan R, Cherry JM, Hong EL. CvManGO, a method for leveraging computational predictions to improve literature-based Gene Ontology annotations.Database (Oxford). 2012 Mar 20;2012:bas001. doi: 10.1093/database/bas001.
  • Alam-Faruque Y, Huntley RP, Khodiyar VK, Camon EB, Dimmer EC, Sawford T, Martin MJ, O'Donovan C, Talmud PJ, Scambler P, Apweiler R, Lovering RC. 2011. The impact of focused Gene Ontology curation of specific mammalian systems. PLoS One. 2011;6(12):e27541. Epub 2011 Dec 9. PMID 22174742
  • 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. PMID 20885853
  • 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.
  • Erick Antezana, Aravind Venkatesan, Chris Mungall, Vladimir Mironov1 and Martin Kuiper. 2010. ONTO-ToolKit: enabling bio-ontology engineering via Galaxy. BMC Bioinformatics 2010, 11(Suppl 12):S8doi:10.1186/1471-2105-11-S12-S8
  • Barrell D., Dimmer E., Huntley R.P., Binns D., O'Donovan C., Apweiler R. 2009. The GOA database in 2009 - an integrated Gene Ontology Annotation resource. Nucleic Acids Research 2009 37: D396-D403.
  • 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]
  • Costanzo MC, Park J, Balakrishnan R, Cherry JM, Hong EL. Using computational predictions to improve literature-based Gene Ontology annotations: a feasibility study. Database (Oxford). 2011 Mar 15;2011:bar004.
  • 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.
  • du Plessis L, Skunca N, Dessimoz C. The what, where, how and why of gene ontology--a primer for bioinformaticians. Brief Bioinform. 2011 Feb 17. [Epub ahead of print]
  • Gene Ontology Consortium. 2010. The Gene Ontology in 2010: extensions and refinements. Nucleic Acids Res 38(Database issue): D331-D335.
  • Hill DP, Berardini TZ, Howe DG, Van Auken KM. Representing ontogeny through ontology: a developmental biologist's guide to the gene ontology. Mol Reprod Dev. 2010 Apr;77(4):314-29.
  • 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. ISBN-10: 0470748311
  • Khodiyar VK, Hill DP, Howe D, Berardini TZ, Tweedie S, Talmud PJ, Breckenridge R, Bhattarcharya S, Riley P, Scambler P, Lovering RC. 2011. The representation of heart development in the gene ontology. Dev Biol. 2011 Jun 1;354(1):9-17
  • Laulederkind SJ, Shimoyama M, Hayman GT, Lowry TF, Nigam R, Petri V, Smith JR, Wang SJ, de Pons J, Kowalski G, Liu W, Rood W, Munzenmaier DH, Dwinell MR, Twigger SN, Jacob HJ; RGD Team. 2011. The Rat Genome Database curation tool suite: a set of optimized software tools enabling efficient acquisition, organization, and presentation of biological data. Database (Oxford). 2011:bar002.
  • Leonelli S, Diehl AD, Christie KR, Harris MA, Lomax J. How the Gene Ontology evolves. BMC Bioinformatics. 2011 Aug 5;12(1):325.
  • 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 38(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.
  • Pfreundt U, James DP, Tweedie S, Wilson D, Teichmann SA, Adryan B. 2010 FlyTF: improved annotation and enhanced functionality of the Drosophila transcription factor database. Nucleic Acids Res. 38(Database issue): D443-7
  • 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.
  • Shimoyama M, Smith JR, Hayman T, Laulederkind S, Lowry T, Nigam R, Petri V, Wang SJ, Dwinell M, Jacob H; RGD Team. 2011 RGD: a comparative genomics platform. Hum Genomics 5(2):124-9.
  • 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.
  • Van Auken K, Jaffery J, Chan J, Müller HM, Sternberg PW. Semi-automated curation of protein subcellular localization: a text mining-based approach to Gene Ontology (GO) Cellular Component curation. BMC Bioinformatics. 2009 Jul 21;10:228.

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.

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.

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.
  • D. Li (TAIR), "Accessing GO annotations from TAIR". 21st International Conference on Arabidopsis Research, Yokohama, Japan. 06-10 June 2010.
  • K. Dreher (TAIR). "TAIR: Bringing Together Data for the Global Plant Biology Community". American Society of Plant Biologists Annual Meeting. Montreal, Canada. 2 August 2010.
  • R. Lovering and V. Khodiyar (BHF). GO annotation workshop, University College London, Staff and PhD students. 22-23rd September 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.
  • R. Lovering and V. Khodiyar (BHF). GO annotation MSc module, University College London, Genetics of human disease MSc students. 16 November 2010 to 11th February 2011.
  • 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.
  • R. Lovering and V. Khodiyar (BHF). GO annotation workshop, University College London, Staff and PhD students. 6-7th April 2011.
  • R. Lovering and V. Khodiyar (BHF). GO annotation workshop, University College London, Staff and PhD students. 27-28th September 2011.
  • R. Lovering and V. Khodiyar (BHF). GO annotation workshop, University College London, Staff and PhD students. 24-25th April 2012.
  • R. Lovering and V. Khodiyar (BHF). GO annotation day, University College London, Staff and PhD students. 17th July 2012.
  • R. Lovering and A. Lock (PomBase). GO annotation workshop, University College London, Staff and PhD students. 10-11th September 2011.

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
  • 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.
  • R Lovering (BHF-UCL) Bringing Gene Ontology to cardiovascular research. University College London partners Cardiometabolic Network meeting (September 2010)
  • V Khodiyar (BHF-UCL) Cross-species annotation of cardiovascular processes. University College London partners Cardiometabolic Network meeting (September 2010)
  • Alam-Faruque Y, Representing kidney development biology in Gene Ontology October 2010 EBI Industry Workshop on Ontology Development and Engineering held at EBI
  • Laulederkind S, (RGD), “Gene Curation Software at the Rat Genome Database (RGD)”. 4th International BioCuration Conference (October 2010)
  • Su AI, Howe DG. 2010. Mining the Gene Wiki to Prioritize Literature Curation Eforts. , FWCS 2010
  • Eurie L. Hong, Using Computational predictions to improve literature-based GO annotations, CSHL Genome Informatics Meeting. (November 2011)
  • Henning Hermjakob (EBI) presented the Cardiovascular Gene Ontology Initiative under the title Human Protein Knowledgebase for the Heart and Soul. HUPO 2011 World Congress, Geneva, Switzerland (September 2011)
  • R Lovering (BHF-UCL) HVP and GO annotation, during the Cardiac Genetics Interest Satellite Group meeting, Human Variome Project Biennial Meeting, Paris (June 2012)

Posters (chronological)

  • R. Balakrishnan, Chris Mungall, Amelia Ireland, Emily Dimmer, Shahid Manzoor and J. M. Cherry. Title: Sticking to the Rules: Automated Checks for GO Consortium Annotations. Fifth International Biocuration Conference (April 2012).
  • 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.
  • Tutaj M, et al. (RGD), “Curating the Rat Genome: RGD’s Automated Data Integration Pipelines Maximize Coverage”. ISMB (July 2010)
  • Alam-Faruque Y, et al. (GOA), Title: "The Renal Gene Ontology Annotation (GOA) Initiative"; Kidney Research UK Fellows Day (September 2010)
  • Lovering R, et al (BHF-UCL, GOA) Bringing Gene Ontology to cardiovascular research. University College London partners Cardiometabolic Network meeting (September 2010)
  • Khodiyar V, et al (BHF-UCL, GOA) Cross-species annotation of cardiovascular processes. University College London partners Cardiometabolic Network meeting (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)
  • Smith J. R., et al. (RGD), " The Rat Genome Database: Resources for Genomics Research”. XVIIIth International Workshop on Genetic Systems in the Rat (December 2010)
  • Lovering R, et al (BHF-UCL, GOA) Bringing Gene Ontology to cardiovascular research. Computational Biology Symposium, University College London (February 2011)
  • Park J., et al. (SGD), Using Computational predictions to improve Literature based Gene Ontology (GO) annotations. CSHL Yeast Cell Biology Meeting. (August 2011)
  • Lovering R, et al (BHF-UCL, GOA) Bringing Gene Ontology to cardiovascular research. ENFIN Enabling Systems Biology Conference & Bioinformatics Workshop

University College London (April 2011)

  • Lovering R, et al (BHF-UCL, GOA) Can HVP GO further? Expanding human Gene Ontology…… Human Variome Project Biennial Meeting, Paris, France (June 2012)
  • Lovering R, et al (BHF-UCL, GOA) The impact of focused Gene Ontology annotation efforts on high-throughput data analysis. 2nd Annual Computational Life and Medical Sciences Symposium, University College London (June 2012)

Project-Generated Resources

  1. The Gene Ontologies: As of Dec. 2010, the Gene Ontologies include Molecular Function (8,908 terms), Biological Process (19,913 terms), and Cellular Component (2,775 terms). 100% of the terms are defined. 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 http://www.godatabase.org/dev/database/. 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 (http://www.geneontology.org/GO.tools.html).
  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 (http://www.geneontology.org/GO.teaching.resources.html).
  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. (http://www.geneontology.org/GO.indices.html).
  10. GOMine (Stanford): Implementation of InterMine for GO. GOMine should serve as a fast search and retrieval tool for GO data without having to know sql or the database table structure.

Publications by external groups that rely on the GO

View all publications for 2010 in the GO bibliography

Other publications of note:

return to 2010 Progress Reports