GOA December 2013: Difference between revisions

From GO Wiki
Jump to navigation Jump to search
Line 147: Line 147:


=Other Highlights=
=Other Highlights=
TO DO

Revision as of 10:57, 29 November 2013

UniProt Gene Ontology Annotation Summary, December 2013

Overview

The UniProt GO Annotation project (UniProt-GOA) at the European Bioinformatics Institute has been a member of the GO Consortium since 2001. All UniProt curators are actively involved in curating UniProtKB entries with Gene Ontology terms during the UniProt literature curation process, providing both high-quality manual GO annotations in addition to their contributions to electronic GO annotation pipelines. The multi-species nature of UniProtKB means that the GO Annotation project is able to assist in the GO curation of proteins from over 430,000 taxonomic groups.

The core UniProt-GOA project staff are primarily responsible for supplying the GO Consortium with manual and electronic GO annotations to the human proteome. UniProt-GOA staff not only manually annotate, but coordinate and check the integration of GO annotations from other curation efforts at the EBI (including from InterPro, IntAct and Reactome). The UniProt-GOA dataset is supplemented with manual annotations from 35 annotating groups, including all members of the GO Consortium, as well as a number of external groups which produce relevant functional data. Nine electronic annotation pipelines are incorporated into the UniProt-GOA dataset, which provide the vast majority of annotations for non-model organism species. UniProt-GOA is therefore able to consolidate multiple sources of specialised knowledge, ensuring the UniProt-GOA resource remains a key up-to-date reference for a large number of research communities.

Staff:

Claire O'Donovan

Maria Martin

Rachael Huntley*

Prudence Mutowo-Muellenet

Tony Sawford*

Aleksandra Shypitsyna

UniProt contributors (EBI, Hinxton, UK; SIB, Geneva, Switzerland; and PIR, Washington DC): Ioannis Xenarios, Lydie Bougueleret

Ghislaine Argoud-Puy, Andrea Auchinchloss, Kristian Axelsen, Marie-Claude Blatter, Emmanuel Boutet, Lionel Breuza, Alan Bridge, Gayatri Chavali, Elena Cibrian-Uhalte, Elizabeth Coudert, Isabelle Cusin, Paula Duek Roggli, Anne Estreicher, Livia Famiglietti, Marc Feuermann, Arnaud Gos, Nadine Gruaz-Gumowski, Reija Hieta, Ursula Hinz, Chantal Hulo, Janet James, Florence Jungo, Guillaume Keller, Kati Laiho, Duncan Legge, Philippe Lemercier, Damien Lieberherr, Michele Magrane, Patrick Masson, Ivo Pedruzzi, Klemens Pichler, Diego Poggioli, Sylvain Poux, Catherine Rivoire, Bernd Roechert, Michel Schneider, Andre Stutz, Shyamala Sundaram, Michael Tognolli

* Funded entirely or partially by GO.

Annotation Progress

Between January 2013 and November 2013, the UniProt-GOA project provided the GO Consortium with 11 annotation file releases, including non-redundant sets of GO annotations to 13 specific proteomes, as well as data releases for annotations of all proteins in UniProtKB.

UniProt incorporates manual annotations from other GO Consortium members and affiliates and displays these annotations in the relevant UniProtKB entries. Currently, the UniProt-GO Annotation project provides GO annotations for 65% of UniProt entries. Altogether, UniProt-GOA now provides almost 208 million GO annotations for almost 32 million proteins in over 437,000 different taxonomic groups. UniProt-GOA provides 269,426 annotations for the 20,730 proteins in the human reference proteome.

UniProt-GOA UniProt gene association file release stats (comparison of January 2013 and November 2013 releases)

Key

*Reduction in WormBase annotation due to cleaning up of data during migration into UniProt-GOA database

**New sources of annotation after January 2013


Methods and strategies for annotation

(TO DO) Literature curation:

Exosome

Apoptosis and necroptosis re-annotation


Computational annotation:

UniProt-GOA provides IEA annotations from the following methods:


  1. UniProt Keyword 2GO (SPKW2GO)1,2
  2. UniProt Subcellular Locations2GO (SPSL2GO)1,2
  3. Unipathway2GO1,2
  4. HAMAP2GO1,2
  5. InterPro2GO
  6. Ensembl Compara (vertebrates)
  7. Ensembl Genomes Compara (plants, fungi)

Key

1: mapping tables created and maintained by UniProt

2: electronic annotations generated by UniProt


UniProt curators supply information to entries that is subsequently used in electronic GO annotation pipelines such as UniProtKB keywords2GO, UniProtKB subcellular location2GO and HAMAP2GO. Altogether, automatic annotation pipelines provide 125 million annotations to almost 19 million proteins.

Priorities for annotation

1. Proteins associated with the exosome (Prudence, Aleksandra)

2. Requests from user community (all curators)

3. Proteins annotated during Swiss-Prot curation duties (all Swiss-Prot/UniProtKB curators at the EBI and SIB)

Presentations and Publications

a. Publications

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

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 large-scale 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

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

The Gene Ontology Consortium. 2013. Gene Ontology Annotations and Resources. Nucleic Acids Research, 41(Database issue), D530-535. PMC3531070


b. Presentations including Talks, Tutorials and Teaching

Prudence Mutowo. Use of Gene Ontology Annotation to understand the peroxisome proteome in humans. Biocuration April 2013, Cambridge, UK. (talk).

Rachael Huntley. The Gene Ontology Resource - Common Misconceptions and Improving Accuracy. Automated Function Prediction SIG at ISMB/ECCB July 20 2013, Berlin, Germany. (talk).

Prudence Mutowo. EBI Bioinformatics Roadshow January 2013 Zimbabwe. (Hands-on tutorial).

Rachael Huntley. Using the Gene Ontology. EMBL-EBI Industry Programme Workshop: "A practical overview of biomedical ontologies". April 17-18 2013, Hinxton, UK. (Hands-on tutorial).


c. Posters

Protein2GO: A curation tool for Gene Ontology. 2013 International Biocuration Conference, Cambridge, UK. Rachael Huntley.

The Gene Ontology Resource - Common Misconceptions and Improving Accuracy. Automated Function Prediction SIG at ISMB/ECCB July 20 2013, Berlin, Germany. Rachael Huntley.

EBI Open Days...

Ontology Development Contributions

TO DO

Annotation Outreach and User Advocacy Efforts

  • Rachael Huntley and Prudence Mutowo-Meullenet trained two new UniProt (EBI) curators in GO annotation
  • Rachael Huntley and Prudence Mutowo-Meullenet trained two GeneDB curators in GO annotation
  • Rachael Huntley and Prudence Mutowo-Meullenet continue to answer queries sent to the GO Consortium helpdesk
  • Rachael Huntley, Prudence Mutowo-Meullenet and Aleksandra Shypitsyna continue to answer user queries sent to the UniProt-GOA project
  • UniProt is continuing to support external annotation groups, such as AgBase, BHF-UCL, DFLAT at Tuft's University, SIB and PIR by providing use of the Protein2GO curation tool.
  • UniProt is continuing to assist GO Consortium groups with migration of their annotations into the UniProt database, as well as providing access and training for the UniProt curation tool Protein2GO. Both WormBase and SGD completed this transition in 2013.
  • As part of the continuing exosome annotation project, Prudence Mutowo-Meullenet is in contact with the ExoCarta database to assist them in providing UniProt with annotations they have for exosome proteins.
  • Together with Rama Balakrishnan from SGD, Rachael Huntley is a manager for the GO Consortium's Annotation Advocacy and Coordination group. The aims of the group are to;
  * educate GO Consortium curators about best annotation practice
  * enforce the annotation rules and policies within the GOC
  * maintain the annotation and evidence code documentation
  * educate and keep all the annotating groups up-to-date with changes in GAF format and ontology development 
  * assist new groups with annotations

Other Highlights

TO DO