Skip to main page content
Access keys NCBI Homepage MyNCBI Homepage Main Content Main Navigation
Filters applied. Clear all
. 2011;6(12):e27541.
doi: 10.1371/journal.pone.0027541. Epub 2011 Dec 9.

The Impact of Focused Gene Ontology Curation of Specific Mammalian Systems

Free PMC article

The Impact of Focused Gene Ontology Curation of Specific Mammalian Systems

Yasmin Alam-Faruque et al. PLoS One. .
Free PMC article


The Gene Ontology (GO) resource provides dynamic controlled vocabularies to provide an information-rich resource to aid in the consistent description of the functional attributes and subcellular locations of gene products from all taxonomic groups ( System-focused projects, such as the Renal and Cardiovascular GO Annotation Initiatives, aim to provide detailed GO data for proteins implicated in specific organ development and function. Such projects support the rapid evaluation of new experimental data and aid in the generation of novel biological insights to help alleviate human disease. This paper describes the improvement of GO data for renal and cardiovascular research communities and demonstrates that the cardiovascular-focused GO annotations, created over the past three years, have led to an evident improvement of microarray interpretation. The reanalysis of cardiovascular microarray datasets confirms the need to continue to improve the annotation of the human proteome.


Conflict of interest statement

Competing Interests: The authors have declared that no competing interests exist.


Figure 1
Figure 1. Distribution of GO term specificity by annotation source.
Accumulative frequency of the distribution of GO terms applied in human annotations. Manual annotations created by the Cardiovascular and Renal Initiative, compared to those created by annotation groups without a system focused approach. Mann Whitney U confirms that the median granularity of GO terms used in human protein annotation by the Cardiovascular and Renal Initiatives is 8.0 (inter quartile range 6–10), compared to a median granularity of 7.0 (inter quartile range 5–9), for the GO terms used by other groups manually annotating to the human proteome (P<0.0001).
Figure 2
Figure 2. AmiGO ‘Tree View’ image of part of the kidney developmental process ontology.
The ‘tree view’ in AmiGO ( showing the GO term parents of GO:0003337 ‘mesenchymal to epithelial transition involved in metanephros morphogenesis’. The most specific twelve GO terms (shaded) were amongst the 470 new terms created following the kidney development ontology workshop. The numbers in brackets indicate the number of human proteins annotated to the GO term, or one of its child terms (07th October 2011). [I] is_a parent-child relationship, ‘P’ part_of parent-child relationship.
Figure 3
Figure 3. QuickGO term display.
QuickGO ( ancestor chart showing information for GO:0006935 ‘chemotaxis’ and its ‘is_a’ parent relationships within the hierarchical directed acyclic graph. The GO terms ‘chemotaxis’, ‘locomotion’ and ‘response to stimulus’ are highlighted to illustrate their parent-child relationships. The child term details are displayed for the GO term ‘chemotaxis’.

Similar articles

  • The Renal Gene Ontology Annotation Initiative.
    Alam-Faruque Y, Dimmer EC, Huntley RP, O'Donovan C, Scambler P, Apweiler R. Alam-Faruque Y, et al. Organogenesis. 2010 Apr-Jun;6(2):71-5. doi: 10.4161/org.6.2.11294. Organogenesis. 2010. PMID: 20885853 Free PMC article. Review.
  • Representing kidney development using the gene ontology.
    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. Alam-Faruque Y, et al. PLoS One. 2014 Jun 18;9(6):e99864. doi: 10.1371/journal.pone.0099864. eCollection 2014. PLoS One. 2014. PMID: 24941002 Free PMC article.
  • The Gene Ontology: enhancements for 2011.
    Gene Ontology Consortium. Gene Ontology Consortium. Nucleic Acids Res. 2012 Jan;40(Database issue):D559-64. doi: 10.1093/nar/gkr1028. Epub 2011 Nov 18. Nucleic Acids Res. 2012. PMID: 22102568 Free PMC article.
  • Manual Gene Ontology annotation workflow at the Mouse Genome Informatics Database.
    Drabkin HJ, Blake JA; Mouse Genome Informatics Database. Drabkin HJ, et al. Database (Oxford). 2012 Oct 29;2012:bas045. doi: 10.1093/database/bas045. Print 2012. Database (Oxford). 2012. PMID: 23110975 Free PMC article.
  • Gene Ontology annotation of the rice blast fungus, Magnaporthe oryzae.
    Meng S, Brown DE, Ebbole DJ, Torto-Alalibo T, Oh YY, Deng J, Mitchell TK, Dean RA. Meng S, et al. BMC Microbiol. 2009 Feb 19;9 Suppl 1(Suppl 1):S8. doi: 10.1186/1471-2180-9-S1-S8. BMC Microbiol. 2009. PMID: 19278556 Free PMC article. Review.
See all similar articles

Cited by 17 articles

See all "Cited by" articles


    1. Gene Ontology Consortium. Creating the gene ontology resource: Design and implementation. Genome Res. 2001;11(8):1425–1433. 10.1101/gr.180801. - PMC - PubMed
    1. Hill DP, Smith B, McAndrews-Hill MS, Blake JA. Gene ontology annotations: What they mean and where they come from. BMC Bioinformatics. 2008;9(Suppl 5):S2. 10.1186/1471-2105-9-S5-S2. - PMC - PubMed
    1. Blake JA, Harris MA. The gene ontology (GO) project: Structured vocabularies for molecular biology and their application to genome and expression analysis. Curr Protoc Bioinformatics. 2008;Chapter 7:Unit 7.2. 10.1002/0471250953.bi0702s23. - PubMed
    1. Gene Ontology Consortium. The gene ontology in 2010: Extensions and refinements. Nucleic Acids Res. 2010;38(Database issue):D331–5. 10.1093/nar/gkp1018. - PMC - PubMed
    1. Huntley RP, Binns D, Dimmer E, Barrell D, O'Donovan C, et al. QuickGO: A user tutorial for the web-based gene ontology browser. Database (Oxford) 2009;2009:bap010. 10.1093/database/bap010. - PMC - PubMed

Publication types