Publications, Talks, Posters 2014

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List of Papers published by GOC in 2014 (Chronologically, most recent first)

  • Ascensao JA, Dolan ME, Hill, DP and Blake JA. 2014. Methodology for the inference of gene function from phenotype data. BMC Bioinformatics. 15:405 doi:10.1186/s12859-014-0405-z.
  • The Gene Ontology Consortium. 2014. Gene Ontology Consortium: Going Forward. Nucl. Acids Res. Database Issue doi: 10.1093/nar/gku1179.
  • Dietze H, Berardini TZ, Foulger RE, Hill DP, Lomax J, Osumi-Sutherland D, Roncaglia P and Mungall CJ. 2014. TermGenie – a web-application for pattern-based ontology class generation, Journal of Biomedical Semantics 5:48 DOI: 10.1186/2041-1480-5-48.
  • Mungall, C. J., Dietze, H., & Osumi-Sutherland, D. (2014). Use of OWL within the Gene Ontology. In M. Keet & V. Tamma (Eds.), Proceedings of the 11th International Workshop on OWL: Experiences and Directions (OWLED 2014) (pp. 25–36). Riva del Garda, Italy, October 17-18, 2014. doi:10.1101/010090.
  • Masson P, Hulo C, de Castro E, Foulger R, Poux S, Bridge A, Lomax J, Bougueleret L, Xenarios I, Le Mercier P. 2014. "An integrated ontology resource to explore and study host-virus relationships." PLoS One. Sep 18;9(9):e108075. doi: 10.1371/journal.pone.0108075. eCollection 2014. PMID 25233094.
  • Mao Y, Van Auken K, Li D, Arighi CN, McQuilton P, Hayman GT, Tweedie S, Schaeffer ML, Laulederkind SJF Wang SJ, Gobeill J, Ruch P, Luu AT, Kim JJ, Chiang JH, Chen YD, Yang CJ, Liu H, Zhu D, Li Y, Yu H, Emadzadeh E, Gonzalez G, Chen JM, Dai HJ, Lu Z. Overview of the Gene Ontology Task at BioCreative IV. Database (Oxford). 2014 Aug 25;2014. pii: bau086. doi: 10.1093/database/bau086. Print 2014. PMID:25157073, PMCID: PMC4142793.
  • Van Auken K, Schaeffer ML, McQuilton P, Laulederkind SJF, Li D, Wang SJ, Hayman GT, Tweedie S, Arighi CN, Done J, Müller HM, Sternberg PW, Mao Y, Wei CH, Lu Z. BC4GO: A Full-Text Corpus for the BioCreative IV GO Task.Database (Oxford). 2014 Jul 28;2014. pii: bau074. doi: 10.1093/database/bau074. Print 2014. PMID: 25070993, PMCID: PMC4112614.
  • Chibucos MC, Mungall CJ, Balakrishnan R, Christie KR, Huntley RP, White O, Blake JA, Lewis SE, Giglio M. Standardized description of scientific evidence using the Evidence Ontology (ECO). Database (Oxford). 2014 Jul 22;2014. pii:bau075. doi: 10.1093/database/bau075. Print 2014. PubMed PMID: 25052702; PubMed Central PMCID: PMC4105709.
  • Alam-Faruque Y, Hill DP, Dimmer EC, Harris MA, Foulger RE, Tweedie S, Attrill H, Howe DG, Thomas SR, Davidson D, Woolf AS, Blake JA, Mungall CJ, O'Donovan C, Apweiler R, Huntley RP. Representing kidney development using the gene ontology. PLoS One. 2014 Jun 18;9(6):e99864. doi: 10.1371/journal.pone.0099864. eCollection 2014. PubMed PMID: 24941002; PubMed Central PMCID: PMC4062467.
  • Haendel MA, Balhoff JP, Bastian FB, Blackburn DC, Blake JA, Bradford Y, Comte A, Dahdul WM, Dececchi TA, Druzinsky RE, Hayamizu TF, Ibrahim N, Lewis SE, Mabee PM, Niknejad A, Robinson-Rechavi M, Sereno PC, Mungall CJ. Unification of multi-species vertebrate anatomy ontologies for comparative biology in Uberon. J Biomed Semantics. 2014 May 19;5:21. doi: 10.1186/2041-1480-5-21. eCollection 2014. PubMed PMID: 25009735; PubMed Central PMCID: PMC4089931.
  • Huntley RP, Harris MA, Alam-Faruque Y, Blake JA, Carbon S, Dietze H, Dimmer EC, Foulger RE, Hill DP, Khodiyar VK, Lock A, Lomax J, Lovering RC, Mutowo-Meullenet P, Sawford T, Van Auken K, Wood V, Mungall CJ. A method for increasing expressivity of Gene Ontology annotations using a compositional approach. BMC Bioinformatics. 2014 May 21;15:155. doi: 10.1186/1471-2105-15-155. PubMed PMID: 24885854; PubMed Central PMCID: PMC4039540.
  • Andersson R, Gebhard C, Miguel-Escalada I, Hoof I, Bornholdt J, Boyd M, Chen Y, Zhao X, Schmidl C, Suzuki T, Ntini E, Arner E, Valen E, Li K, Schwarzfischer L, Glatz D, Raithel J, Lilje B, Rapin N, Bagger FO, Jørgensen M, Andersen PR, Bertin N, Rackham O, Burroughs AM, Baillie JK, Ishizu Y, Shimizu Y, Furuhata E, Maeda S, Negishi Y, Mungall CJ, Meehan TF, Lassmann T, Itoh M, Kawaji H, Kondo N, Kawai J, Lennartsson A, Daub CO, Heutink P, Hume DA, Jensen TH, Suzuki H, Hayashizaki Y, Müller F; FANTOM Consortium, Forrest AR, Carninci P, Rehli M, Sandelin A. An atlas of active enhancers across human cell types and tissues. Nature. 2014 Mar 27;507(7493):455-61. doi: 10.1038/nature12787. PubMed PMID: 24670763.
  • Huntley RP, Sawford T, Martin MJ, O'Donovan C. Understanding how and why the Gene Ontology and its annotations evolve: the GO within UniProt. Gigascience. 2014 Mar 18;3(1):4. doi: 10.1186/2047-217X-3-4. PubMed PMID: 24641996; PubMed Central PMCID: PMC3995153.
  • Wick HC, Drabkin H, Ngu H, Sackman M, Fournier C, Haggett J, Blake JA, Bianchi DW, Slonim DK. DFLAT: functional annotation for human development. BMC Bioinformatics. 2014 Feb 7;15:45. doi: 10.1186/1471-2105-15-45. PubMed PMID: 24507166; PubMed Central PMCID: PMC3928322.
  • Rachael P. Huntley; Tony Sawford; Prudence Mutowo-Meullenet; Aleksandra Shypitsyna; Carlos Bonilla; Maria J. Martin; Claire O'Donovan. "The GOA database: gene ontology annotation updates for 2015." Nucleic Acids Research 2014 doi: 10.1093/nar/gku1113 PMID 25378336.

2014 GO-centric Talks

Presenter Talk/Poster Title Date Venue Audience
David Osumi-Sutherland (EBI) Alternative perspectives on the GO and its annotations December 16th Centre for Cardiovascular Genetics, University College London Cardiovascular biologists (mostly clinical researchers)
Judith Blake (Jackson Lab) Keynote: Modeling Glycolysis in the Gene Ontology: All Roads Lead to Pyruvate December 11-13 ISCB 12th Annual Rocky Mountain Bioinformatics Conference Computation biologists and bio-informaticians
Paul Thomas (USC) Introduction to the GO and annotation processes December 5 2014 Synapse Annotation Jamboree, Broad Institute, Cambridge MA Synapse biologists and neurological disease geneticists
Rebecca Foulger (UCL) Using Gene Ontology to Characterise Key Players in Parkinson's Disease November 3rd 2014 Parkinson's UK Research Conference, York PD researchers, clinicians, some PD patients, and Parkinson's UK.
Paul Thomas (USC) Lecture: Gene function annotation October 21 2014 Programming for Biology Course, Cold Spring Harbor NY Graduate students and postdoctoral students in bioinformatics
David Osumi-Sutherland (EBI) Use of OWL within the Gene Ontology October 17th 2014 OWLED, Riva Del Garda, Italy Computer scientists
Paul Thomas (USC) Modeling the evolution of gene function using the Gene Ontology October 16 2014 Center for Genomic Regulation, Barcelona, Spain Computational biologists and bioinformaticians
Prudence Mutowo (UniProtGOA) How scientists use GO 25 September 2014 University of Minas Gerais. Belo Horizonte Brazil Masters, PhD and postdocs
Prudence Mutowo (UniProtGOA The Peroxisome case study- benefits of a focused GO annotation effort 25 September 2014 University of Minas Gerais. Belo Horizonte Brazil Masters, PhD and postdocs
Judith Blake (Jackson Lab) Impact of Biomedical Ontologies on Data Harmonization and Computational Analysis Pipelines Sept 15-16 NIEHS-EPA Workshop for the Development of a Framework for Environmental Health Science Language. Broad coalition of environmental and health scientists
Rachael Huntley UniProt and the CAFA challenge 12 July 2014 Automated function prediction SIG at ISMB/ECCB, Boston, USA PhDs, Postdocs and PIs in automated function prediction
Judith Blake (Jackson Lab) Representation of Biology in the Gene Ontology July 11 BioOntologies SIG at ISMB 2014 Bio-ontology developers and users
Paola Roncaglia (EBI) Introduction to the Gene Ontology and to GO annotation 23-24 June 2014 Practical Course "Bioinformatics: Computer Methods in Molecular Biology" Masters, PhD and postdocs
Rachael Huntley Introduction to the Gene Ontology and to GO annotation 11-15 January 2014 Plant and Animal Genome Conference, San Diego, USA PhDs and Postdocs
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2014 GO-centric Posters

Presenter Poster Title Date Venue Audience
Rebecca Foulger and Paul Denny (UCL) Using Gene Ontology to Characterise Key Players in Parkinson's Disease 3rd-4th Nov 2014 Parkinson’s UK Research Conference, York Parkinson’s researchers & clinicians
Rebecca Foulger (UCL) Using Gene Ontology to Characterise Key Players in Parkinson's Disease 3rd-4th Oct 2014 2nd International Parkinson's Disease Symposium, Luxembourg PD researchers & clinicians, and PD-map
Ruth Lovering (UCL) The Cardiovascular Gene Annotation Initiative: Impact on data analysis 25-26th Sept 2014 British Atherosclerosis Society meeting, Cambridge Cardiovascular researchers & clinicians
Suzanna Lewis (LBL) PAINT: A Phylogenetic Annotation INferencing Tool 21-24 September 2014 Genome Informatics: Wellcome Trust Scientific Conferences Bioinformatics
David Hill (MGI) Modeling Glycolysis in The Gene Ontology: All Roads Lead to Pyruvate 7th-10th Sept 2014 ECCB' 14 Computational Biologists
Paul Denny and Rebecca Foulger (UCL) Using Gene Ontology to Characterise Key Players in Parkinson's Disease July 23rd 2014 UK Parkinson’s Disease Consortium Celebration Day Parkinson’s researchers
Rachael Huntley (GOA) UniProt and the CAFA challenge July 11-15 2014 Automated function prediction SIG at ISMB/ECCB, Boston, USA PhDs, Postdocs and PIs in automated function prediction
Rebecca Foulger (UCL) Using Gene Ontology to Characterise Key Players in Parkinson's Disease June 19th 2014 UCL Neuroscience Symposium UCL Neuroscience researchers
Helen Attrill (FlyBase) Gene Groups in FlyBase March 26-30 2014 55th Annual Drosophila Research Conference Drosophila Researchers
Dmitry Sitnikov (MGI) Cellular Localization, Functional, and Biological Process Curation of microRNA Literature March 17-18 2014 MicroRNA as Biomarkers and Diagnostics microRNA researchers
Karen Christie (MGI) Comprehensive Gene Ontology annotation of ciliary genes in the mouse, Mus musculus March 2-7 2014 Keystone Symposia: Cilia, Development and Human Disease ciliary researchers
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2014 GO-centric Workshops

  • May 1st-2nd 2014, UCL GO annotation workshop for UCL students and researchers. Organized and run by Ruth Lovering (UCL).
  • October 25-29th 2014. Introduction to Gene Ontology and GO annotation training. masters, PhD and postdoc participants. Organised and run by Prudence Mutowo (UniProt0GOA)
  • November 11-13th 2014. EBI Ambassador training workshop at NTNU, Trondheim, Norway. Audience: Masters and PhD students, Postdocs, established faculty staff. Introduction to EBI resourses with focus on Networks and Pathways. Introduction to GO as an important ontology for molecular biologists in general. GO was refered to in many of the tutorials including a hands-on session of BINGO. Organised and run Birgit Meldal (EBI IntAct & Complex Portal)

2014 GO Tutoring and Mentoring Activities

The MGI group mentored a Jackson Laboratory Summer Student Program intern, Nikolai Renedo from Tufts University, in an ontology development project.

Judith Blake is an INBRE mentor for Jason Castro, an Assistant Professor at Bates College. He is a neuroscientist combining neuroinformatics, electrophysiology, and anatomy in his investigations of the functioning of specific neurons in the mouse.

The EBI GO group was involved in supervising a PhD student in a program on "Foundations and Ethics of Life Sciences".

The UCL team undertook a full term (Oct-Dec) of teaching MSc students and informed 23 UCL MSc students about Gene Ontology and other bioinformatic resources.