BHF-UCL, Sept 2010

From GO Wiki
Jump to: navigation, search

Meeting Progress Reports, September 2010

Overview

The aim of the Cardiovascular GO Annotation Initiative (BHF-UCL, British Heart Foundation – University College London) is to provide GO annotation to human cardiovascular-associated genes. This project represents a successful collaboration between University College London (UCL) and the European Bioinformatics Institute (EBI); the annotations created by the UCL-based curators are made directly into the GOA database at the EBI. 4000 human genes have been identified as associated with cardiovascular processes and annotation priorities are agreed on an annual basis in consultation with the Co-Grant holders, the International Scientific Advisory Committee and the UCL-based GO curators. The Initiative aims to comprehensively annotate 2500 genes in 5 years. BHF-UCL has been a GOC member since July 2008.

Staff

  • Dr Ruth Lovering, 1 FTE – Curator, BHF grant to November 2012
  • Dr Varsha Khodiyar, 0.8 FTE – Curator, BHF grant to May 2013

No funding by GOC NIHGRI grant

Annotation Progress

The annotation progress reflects the priority of this project to annotate human genes, with 5882 GO terms associated to 827 human proteins (1st November 2007 to 1st September 2010). Across all species BHF-UCL have annotated 1,947 proteins with over 14,000 GO terms.

BHF-UCL GO STATS as of 1st September, 2010

Annotation Type 01_Sept_09 01_Sept_10 Change % Change
Total proteins annotated (with at least one GO term of any kind):
1333
1947
614
46
Total associations
10256
14068
3812
37
Total human proteins annotated (with at least one GO term of any kind):
827
1336
509
62
Total associations to human proteins
5882
11314
5432
92
Number of different species annotated
29


Methods and strategies for annotation

(please note % effort on literature curation vs. computational annotation methods)

Literature curation:

100%

The aim of this Initiative is to provide complete and deep annotation of 300 human proteins per year. This is achieved through both protein-centric and process-centric targeting of proteins to annotate. The process-centric annotation enables the curators to gain a better understanding of the targeted a process and using the GONUTs table ensure that relevant terms are associated with all proteins involved in a particular process. The protein-centric annotation is undertaken when annotating proteins on the reference genome list. The following approaches are taken to achieve this:

  • To ensure a rapid improvement in the annotations available for a large number of cardiovascular associated proteins the curators spend a maximum of one day researching the literature associated with each protein.
  • The protein will be marked as ‘complete’ if the curator feels there are no further terms to add.
  • If complete annotation cannot be achieved in a day, the protein record is marked as first pass complete. The intention is to revisit these first pass proteins, hopefully with some expert scientist input, in the following year.
  • The approved gene symbol (and relevant gene and protein aliases) are used to query a variety of biomedical search engines, including NCBI PubMed, iHOP and GOPubMed, to identify suitable papers for the GO annotation of each target protein (with highly researched genes the search is usually limited to human entries only).
  • The curators will usually associate GO terms to all of the human proteins mentioned in each paper read, depending on the experimental evidence available (occasionally GO terms are associated with non-human proteins too).
  • Preference is given to the use of experimental-based evidence codes, however these are only used when the curator is completely confident of the identity of the protein and its derivative species.
  • Reviews are also used to provide an overview of the characteristics of a protein and an insight into the complete set of GO terms required.
  • Experimental data relating to model organism proteins maybe included in our GO annotation process, through the direct annotation of the model organism protein and the use of the ‘inferred by sequence similarity’ evidence code to transfer the information to the orthologous human protein.
  • When experimentally supported literature is unobtainable, due to insufficient information about the species the protein is derived from, the lack of access to a referenced paper, or simply because the knowledge is considered so well accepted that references are not supplied, author statements are used.
  • When possible we associate the chronologically first paper that provides experimental evidence for the characteristic features of a given human protein.
  • We aim to capture the knowledge about each protein using a limited number of papers, with experimental evidence.
  • We do not annotate all relevant papers, if this will lead to repeated duplication of GO terms associated to the protein.
  • GO terms are chosen by querying the GO files with QuickGO or AmiGO.
  • Before assigning a GO term, its definition and position within the ontology are checked to ensure its suitability.
  • The GO editorial office is contacted, via SourceForge, when a new GO term is required, or modifications are needed to an existing GO term.

Computational annotation strategies:

None used.

Priorities for annotation:

Human genes involved in cardiovascular-related processes, as agreed by the International Scientific Advisory.

Presentations and Publications

Papers with substantial GO content:

  • Fundamentals of gene ontology functional annotation, Varsha K Khodiyar, Emily C Dimmer, Rachael P Huntley, Ruth C Lovering in Knowledge-based Bioinformatics: From analysis to interpretation Book editors Gill Alterovitz and Marco Ramoni; 2010, Wiley: Boston, Massachusetts. p. 171-208
  • The Gene Ontology in 2010: extensions and refinements Gene Ontology Consortium. Nucleic Acids Research 2010 Jan;38(Database issue):D331-5. PMID: 19920128.

Presentations including Talks and Tutorials and Teaching:

  • Invited presentation (20 min) entitled: Heart Development and Gene Ontology, at the 8th London Heart Development Meeting, December 2009 London, UK.
  • The BHF-UCL team taught a 10 week module on a new UCL MSc course, Genetics of Human Diseases, UCL Genetics of Human Disease MSc, and will be teaching this module to the 2010 MSc students.
  • The BHF-UCL team will be running a 2 day GO annotation workshop in September 2010

Poster presentations:

  • Gene Ontology - A Way Forwards, Ruth Lovering, Varsha Khodiyar, Pete Scambler, Mike Hubank, Rolf Apweiler, Philippa Talmud. Institute of Stroke Research - Scientific Meeting UCL, October 2009, London, UK.
  • Gene Ontology - A Way Forwards, Ruth Lovering, Varsha Khodiyar, Pete Scambler, Mike Hubank, Rolf Apweiler, Philippa Talmud. UCL Genetics Institute - Public launch, November 2009, London, UK.

Other Highlights

Ontology Development Contributions:

Since 01 Sept 2009 the BHF-UCL team have submitted 185 Source Forge request (to 01 Sept 2010) which have led to the creation of 156 new GO terms.

The BHF-UCL team hosted a Heart Development Ontology Workshop at UCL in September 2009. This was the first ontology workshop hosted by the BHF-UCL team and proved to be highly successful. Varsha had identified a lack of ontology terms in the heart development earlier in the year, while annotating genes involved in this process. Consequently, she invited 4 heart development experts, Peter Scambler, Paul Riley, Shoumo Bhattacharya and Ross Breckenridge as well as several GO curators from Cambridge and the US. This workhsop led to the creation of 250 new GO terms.

Varsha and Ruth are regular contributors to the following working groups: Binding, Signaling, Regulation, Downstream effects, Response to.

Annotation Outreach and User Advocacy Efforts:

The UCL GO curators are closely associated with the Cardiovascular Genetics group at UCL and have given 6 presentations at their group meetings.

Other Highlights:

This year the Initiative has circulated four newsletters, in October, January, April, July, by direct email to the International Advisory Committee and individuals who have expressed an interest in this project; by indirect email, though the mailing lists of several cardiovascular related societies, as hardcopies at meetings and through our web site.