GO Annotation for the Cardiovascular System
Background
The overall objective of the cardiovascular GO annotation initiative is to provide a unique public resource for the cardiovascular community, both in the UK and internationally, by providing comprehensive functional annotation for genes implicated in heart development and cardiovascular processes and disease. High-throughput genomics and systems biology are particularly powerful tools for the investigation of multi-factorial phenotypes, such as cardiovascular disease. However, at the moment, systems biology approaches to dissect the human cardiovascular system are severely hampered by the lack of functional annotation of many of the key gene products likely to be involved. Consequently this initiative will support a concentrated effort to improve the manual annotation of genes involved in the cardiovascular system using the Gene Ontology (GO). The improved annotation of these genes will ensure that the investment in genome sequencing along with the accumulated knowledge of heart disease and cardiovascular processes can be exploited to the full, for the benefit of researchers seeking to alleviate cardiovascular diseases.
The cardiovascular GO annotation initiative is a collaborative project between the GOA group based at the European Bioinformatics Institute (EBI) [external website] and three research groups at University College London (UCL) [external website].
This project is supported by the British Heart Foundation [external website].
Plan Of Action
- We have created a community annotation wiki for cardiovascular genes that enables cardiovascular scientists and other interested parties to comment on existing GO annotation and guide our continuing GO annotation efforts. Using these wiki pages, missing experimentally established facts about particular genes involved in the cardiovascular system, that are not currently represented by GO annotation, can be submitted to the GO curators.
- We have prepared a gene list of 2538 genes and intend to extend this list by including other cardiovascular gene lists, such as that compiled by Brendan Keating [external website].
- We have started to annotate high priority genes from the cardiovascular relevant gene list in a systematic fashion. There is also documentation on how these genes will be annotated.
- We plan to hold a series of workshops to involve experimental scientists directly in the GO annotation process, to increase the quality and quantity of annotation for cardiovascular associated genes.
How You Can Contribute
You can participate in this effort at many different levels.
- Contribute to the cardiovascular community annotation wiki. We are particularly keen to recruit cardiovascular scientists to review our annotations using the wiki. Users may simply supply us with the PubMed identifier of a key experimental publication for curation or provide more detailed information or commentary, such as pointing out any experimental data that might be controversial (these may be discussed with our international scientific advisory panel). Information regarding genes in any species is welcome. We will review information provided through the wiki on a timely basis, and notify users of how their contributions have resulted in GO annotations.
- Suggest new GO terms related to cardiovascular processes via the cardiovascular community wiki.
- Participate in the GO Consortium's cardiovascular mailing list for discussion of cardiovascular associated genes and GO terms.
- Use the GOA User Survey [external website] to suggest proteins that you would like to see prioritized for manual annotation, to suggest references or GO terms to be included in the GO annotation or to join our expert panel to review a specified set of fully manually-annotated proteins.
All contributions are appreciated.
Data Dissemination
All cardiovascular-associated GO annotations generated from this project will be freely available via the Gene Ontology Consortium website, Ensembl [external website], and UniProtKB [external website] databases, and by the databases of the species-specific projects. These annotations will, de facto, be incorporated into Entrez Gene [external website] by the National Center for Biotechnology Information (NCBI) [external website].
Additional Information
- GO cardiovascular personnel: cardiovascular annotation committee, international scientific advisory panel, GO curators, societies, groups and journals.
- Introduction to GO Annotation: a brief introduction to GO annotation
- Meeting list
- Other relevant and useful links
