MGI Dec 5-March 3

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Overview:

Staff:

[please include FTEs working on GOC tasks designating as well how many FTEs funding by GOC NIHGRI grant]

Judith Blake*

Karen R Christie*

Mary E Dolan*

Harold J Drabkin*

David Hill*

Li Ni*

Dmitry Sitnikov

* Funded entirely or partially by GO

Annotation Progress

Annotation Type Mar 3 2014 Dec 5 2013 Change % change
Total Genes annotated with at least one GO term of any kind 25413 25406 7 0.03
Total Annotations: 312667 303352 9315 3.1
Total non-IEA Annotation
Total Number of Genes: 24763 24600 163 0.66
Total Annotations: 217975 209013 8962 4.29
Annotation by Direct Experiment
MGI Curated Mouse Genes 11742 11569 173 1.50
MGI Curated Annotations 77459 75555 1904 2.52
GOA Curated Mouse Genes: 4182 4075 107 2.63
GOA Curated Annotations: 23084 22017 1067 4.85
Annotation by Orthology
Total Genes Annotated by Orthology 10583 9827 756 7.698
Total Orthology Annotation 80547 74768 6147 8.96
Genes Annotated by Human Orthology Load (GOA) 9159 8173 986 12.06
Total Annotation by Human Orthology Load 51457 45989 5468 11.89
Genes Annotated by Rat Orthology Load (RGD) 4198 4160 38 0.91
Total Annotations by Rat Orthology Load 25225 24577 648 2.64
IEA Annotation
Total Genes with IEA Annotations 16808 16784 24 0.14
Total IEA Annotations 94692 94339 353 0.37
Total Genes with SwissProt to GO Annotations 16454 16414 40 0.24
Total SwissProt to GO Annotations 66182 65799 383 0.58
Total Genes with Interpro to GO Annotations 10272 10224 48 0.47
Total Interpro to GO Annotations 27382 27375 7 0.03
Total Genes with EC to GO Annotations 900 930 -30 -3.23
Total EC to GO Annotations 1128 1165 -37 -3.16
  • Loses due to gene merges, withdrawals, or marker type changes (gene to pseudogene).

Methods and strategies for annotation

Literature curation:

Literature curation continues to be the major focus of our annotation efforts.

Computational annotation strategies:

As always, current strategies involve use of translation table to mine SwissProt keywords, InterPro domains, and EC numbers for IEA annotation. These are performed automatically on a nightly basis and require little human intervention.

Priorities for annotation

  • Isoform curation (Harold, Karen, Protein Ontology project); focusing on genes that have isoforms or whose products are modified, and co-ordinate with the Protein Ontology Protein Complex project. Also is working on changing all isoform ids entered in MGI to PRO ids to create better presence in AMIGO.
  • Genes with no GO annotation but with literature (Li and Dmitry)
  • Genes with only IEA annotation but with literature (Li)
  • Genes marked as having GO annotation completed, but now having new literature (Dmitry)
  • Genes that have an annotation to one or more of the three root nodes of GO, but have new literature (David, Karen, Dmitry)
  • Dmitry has been focused on annotation or miRNAs in MGI
  • Karen has been focusing on annotation of ciliary genes

Presentations and Publications

a. Papers with substantial GO content

  • 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.


b. Presentations including Talks and Tutorials and Teaching


c. Poster presentations

  • Christie KR and Blake JA. Comprehensive Gene Ontology annotation of ciliary genes in the mouse, Mus musculus. Keystone: Cilia, Development, and Human Disease. Tahoe City, CA. March 2-7, 2014.

Other Highlights:

A. Ontology Development Contributions:

  • 1. David Hill continues working with the ontology group to develop cross-products within and among the three GO namespaces.
  • 2 David Hill and Jane Lomax oversee the biological content development of GO. David has a regular spot in the rotation to address GO Sourceforge items.
  • 3. David Hill has worked to link molecular function with glycolytic and molybdopterin-based cofactor biosynthetic pathways.


B. Annotation Outreach and User Advocacy Efforts:

  • The Protein Ontology project continues to provide a web interface (http/pir.georgetown.edu/cgi-bin/pro/race_pro) whereby functional annotation using the GO can be applied to PRO submissions.
  • Harold Drabkin continues to serve on the GO-help rota.
  • Judith Blake and Karen Christie continue to work with Rachael Huntley to coordinate with Astrid Laegrid and Martin Kuiper of the Norwegian University of Science and Technology in Trondheim on the incorporation of GO annotations for mammalian (human, mouse, and rat) transcription factors, and their target genes, made by this group. Karen reviewed some proposed annotations and participated in a call with Astrid and Martin as ongoing training in the requirements and format for GO annotations.


C. Other Highlights:

  • As the designated coordinator of the MGI/GO project with the GO Reference Genome project, Li Ni participates in annotations of genes assigned by the Reference Genome Project, oversees the curation of Reference Genome Genes for the mouse group. Li responds and resolves questions about MGI GO annotations for the reference genome annotation project genes, and especially responds and resolves questions from the lead PAINT curator (see Reference Genome Project report for a description of PAINT). Li is also part of the PAINT curation team.
  • As members of the PAINT curation team, Li Ni and Karen Christie curate Panther families in PAINT to propagate annotations based on evolutionary relationships. They also file bug reports on PAINT and contribute to the improvement of the PAINT software.
  • Based on the work of Joao A Ascensao, a student at Rice University, in the 2013 Jackson Laboratory Summer Student Program, we are submitting a paper "Methodology for the Inference of Gene Function from Phenotype Data" with co-authors Mary Dolan, David Hill, and Judith Blake. Joao presented the work at the Bar Harbor GOC meeting October 2013.