U41 HG002273-13
Progress Report Publication List
5 U41 HG002273-14 – Period covered 12/01/2012 – 11/30/2013
Aranguren ME, Fernández-Breis JT, Mungall C, Antezana E, González AR, & Wilkinson MD. 2013. OPPLGalaxy, a Galaxy tool for enhancing ontology exploitation as part of bioinformatics workflows. Journal of
biomedical semantics, 4(1), 2.PMID:23286517
Bada, M, Sitnikov D, Blake J, Hunter L. 2013. Occurrence of Gene Ontology, Protein Ontology, and NCBI
Taxonomy Concepts in Text toward Automatic Gene Ontology Annotation. BioLink Paper at 2013 BioLink
Special Interest Group: Roles for text mining in biomedical knowledge discovery and translational medicine.
Balakrishnan R, Harris MA, Huntley R, Van Auken K, Cherry JM. 2013. A guide to best practices for Gene
Ontology (GO) manual annotation. Database (Oxford). 2013 Jul 9;2013:bat054. PMC3706743
Blake JA. 2013. Ten Quick Tips for Using the Gene Ontology PMC3828149 PLoS Comput Biol. 2013
November; 9(11):
Dutkowski J, Kramer M, Surma MA, Balakrishnan R, Cherry JM, Krogan NJ, Ideker T. 2013. A gene ontology
inferred from molecular networks. Nat Biotechnol. 2013 Jan;31(1):38-45. PMID: 23242164
The Gene Ontology Consortium. 2013. Gene Ontology Annotations and Resources. Nucleic Acids Research,
41(Database issue), D530-535. PMC3531070
Hill DP, Adams N, Bada M, Batchelor C, Berardini TZ, Dietze H, Drabkin HJ, et al. 2013. Dovetailing biology
and chemistry: integrating the Gene Ontology with the ChEBI chemical ontology. BMC genomics, 14(1),
513. PMC3733925
Meehan T, Vasilevsky N, Mungall C, Dougall D, Haendel M, Blake J, & Diehl A. 2013. Ontology based
molecular signatures for immune cell types via gene expression analysis. BMC Bioinformatics, 14(1),
263. PMID:24004649
Mutowo-Meullenet P, Huntley RP, Dimmer EC, Alam-Faruque Y, Sawford T, Jesus Martin M, O'Donovan C,
Apweiler R. 2013. Use of Gene Ontology Annotation to understand the peroxisome proteome in humans.
Database (Oxford). 2013 Jan 17;2013:bas062. PMC3548334
Roncaglia P, Martone ME, Hill DP, Berardini TZ, Foulger RE, Imam FT, Drabkin H, et al. 2013. The Gene
Ontology (GO) Cellular Component Ontology: integration with SAO (Subcellular Anatomy Ontology) and other
recent developments. Journal of Biomedical Semantics, 4(1), 20. PMID:24093723
Tripathi S, Christie KR, Balakrishnan R, Huntley R, Hill DP, Thommesen L, Blake JA, Kuiper M, Lægreid A.
Gene Ontology annotation of sequence-specific DNA binding transcription factors: setting the stage for a largescale curation effort. 2013. Database (Oxford). 2013 Aug 27;2013:bat062. PMC3753819
UniProt Consortium. 2013. Update on activities at the Universal Protein Resource (UniProt) in 2013. Nucleic
Acids Res. 2013 Jan;41(Database issue):D43-7. PMC3531094
Progress Report Presentations List
5 U41 HG002273-14 – Period covered 12/01/2013 – 11/30/2014
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U41 HG002273-13
Blake J. Gene Ontology: Functional Annotations for Comparative Genomics. 15 Genome Standards
Consortium Meeting. Washington DC. April 23, 2013.
th
Christie K and Huntley R. Making Gene Ontology Annotations for Transcription Factors. - Workshop at the EBI
for the NTNU group annotating transcription factors and their target genes (small group workshop). February 78 2013, Hinxton, UK.
Drabkin H. Increased expressivity of mouse protein function representation using the gene ontology;
Proteomics 2013, July 15-17; Philadelphia PA
Dietz H. TermGenie - Granting Biocurators' Wishes for the Gene Ontology 2013 BioCurators, Cambridge,
UK, SlideShare- Increased Expressivity of Gene Ontology Annotations
Huntley R. The Gene Ontology Resource - Common Misconceptions and Improving Accuracy. Automated
Function Prediction SIG at ISMB/ECCB July 20 2013, Berlin, Germany.
Munoz-Torres M. Web Apollo: Lessons learned from community based biocuration efforts. 2013
sbvIMPROVER Symposium. Athens, Greece.
Mutowo P. Use of Gene Ontology Annotation to understand the peroxisome proteome in humans. Biocuration
April 2013, Cambridge, UK.
Progress Report Posters/Meetings List
5 U41 HG002273-14 – Period covered 12/01/2012 – 11/30/2013
AmiGO 2: An Adventure in Flatland 2013 International Biocuration Conference, Cambridge, UK.
Representation of apoptosis in the Gene Ontology File:BioCuration2013.pdf 2013 International Biocuration
Conference, Cambridge, UK.
Huntley R. Protein2GO: A curation tool for Gene Ontology. 2013 International Biocuration Conference,
Cambridge, UK.
Huntley R. The Gene Ontology Resource - Common Misconceptions and Improving Accuracy. Automated
Function Prediction SIG at ISMB/ECCB July 20 2013, Berlin, Germany.
Mutowo-Muellenet P and Shypitsyna A. The UniProt-GOA resource. EMBL-EBI Open Day, Hinxton. November
7 2013.
Huntley R. The UniProt-GOA resource. EMBL-EBI Open Day, Hinxton. March 14 2013.
Progress Report Tutorials List
5 U41 HG002273-14 – Period covered 12/01/2012 – 11/30/2013
Mutowo P. EBI Bioinformatics Roadshow January 2013 Zimbabwe.
Huntley R. Using the Gene Ontology. EMBL-EBI Industry Programme Workshop: "A practical overview of
biomedical ontologies". April 17-18 2013, Hinxton, UK.
Rachael Huntley trained two GeneDB curators in GO annotation. October 18 2013, Hinxton.
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