MGI December 2014

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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 Dec 5 2014 Dec 5 2013 Change % change
Total Genes annotated with at least one GO term of any kind 24226 25406 *
Total Annotations: 341687 303352 0
Total non-IEA Annotation
Total Number of Genes: 23844 24600
Total Annotations: 242025 209013
Annotation by Direct Experiment
MGI Curated Mouse Genes 12170 11569
MGI Curated Annotations 82573 75555
GOA Curated Mouse Genes: 4565 4075
GOA Curated Annotations: 26002 22017
Annotation by Orthology
Total Genes Annotated by Orthology 11435 9827
Total Orthology Annotation 92787 74768 6
Genes Annotated by Human Orthology Load (GOA) 10207 8173
Total Annotation by Human Orthology Load 61355 45989
Genes Annotated by Rat Orthology Load (RGD) 4415 4160
Total Annotations by Rat Orthology Load 27006 24577
IEA Annotation
Total Genes with IEA Annotations 14602 16784
Total IEA Annotations 99662 94339
Total Genes with SwissProt to GO Annotations 14211 16414 7
Total SwissProt to GO Annotations 55788 65799
Total Genes with Interpro to GO Annotations 10054 10224
Total Interpro to GO Annotations 25511 27375
Total Genes with EC to GO Annotations 1734 930
Total EC to GO Annotations 18363 1165 -
  • 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.
  • 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 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 began a project 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

Other Highlights:

A. Ontology Development Contributions:

  • 1. David Hill continues working with Tanya Berardini, Chris Mungall, Paola Roncaglia and Jane Lomax develop cross-products within and among the three GO namespaces.
  • 2 David Hill and Jane Lomax oversee the biological content development of GO. David now has a regular spot in the rotation to address GO Sourceforge items.
  • 4. David Hill has worked with the GO ontology development and software groups to develop a web-based tool for requesting new terms.

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 are working with Rachael Huntley to coordinate with Astrid Laegrid and Martin Kuiper of the Norwegian University of Science and Technology in Trondheim to determine how to incorporate GO annotations for mammalian (human, mouse, and rat) transcription factors, and their target genes, made by this group.


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.
  • This year, Karen Christie joined Li Ni as an MGI representative on the PAINT curation team. As members of this team, Li and Karen 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.
  • For the reannotation phase of the apoptosis ontology development project, Li Ni and Karen Christie focused on reannotation of mouse genes annotated with a targeted set of very general apoptosis GO terms. At the conclusion of the project, David, Dmitry, and Harold also contributed to the reannotation of mouse genes annotated to high level apoptosis terms.
  • Mary Dolan has begun working with other members of the GO software team on Galaxy for GO. In the past, most groups have used Galaxy for sequence analysis. The focus of the GO Galaxy initiative will be functional analysis, implementing GO tools in Galaxy. Mary also provides various files for the Reference Genome Project, for example, a report to assess the GO annotation status of PANTHER families and subfamilies based on annotations for all reference genome organism genes in the groups.