MGI Mar 3 to June 5

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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 June 5 2014 Change % change
Total Genes annotated with at least one GO term of any kind 25413 25425 12 0.05
Total Annotations: 312667 317308 4641 1.5
Total non-IEA Annotation
Total Number of Genes: 24763 24835 72 0.30
Total Annotations: 223433 5458 2.51
Annotation by Direct Experiment
MGI Curated Mouse Genes 11742 11937 195 1.66
MGI Curated Annotations 77459 79422 1963 2.53
GOA Curated Mouse Genes: 4182 4265 83 1.98
GOA Curated Annotations: 23084 23814 730 3.15
Annotation by Orthology
Total Genes Annotated by Orthology 10583 10748 165 1.56
Total Orthology Annotation 80547 83195 2648 3.29
Genes Annotated by Human Orthology Load (GOA) 9159 9279 120 1.31
Total Annotation by Human Orthology Load 51457 53044 1587 3.08
Genes Annotated by Rat Orthology Load (RGD) 4198 4326 128 3.05
Total Annotations by Rat Orthology Load 25225 26177 952 3.77
IEA Annotation
Total Genes with IEA Annotations 16808 16819 11 0.0.07
Total IEA Annotations 94692 110685 15993 16.89
Total Genes with SwissProt to GO Annotations 16454 16463 9 0.05
Total SwissProt to GO Annotations 66182 66054 -128 -0.19
Total Genes with Interpro to GO Annotations 10272 10207 -65 -0.63
Total Interpro to GO Annotations 27382 26943 -439 -1.60
Total Genes with EC to GO Annotations 900 1755 855 95.00
Total EC to GO Annotations 1128 17688 16560 1468
  • 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

  • Huntley RP, Harris MA, Alam-Faruque Y, Blake JA, Carbon SJ, Dietze H, Dimmer E, Foulger R, Hill DP, Khodiyar V, Lock A, Lomax J, Lovering RC, Mutowo-Meullenet P, Sawford T, Van Auken K, Wood V, Mungall, CJ. 2014. A Method for Increasing the Expressivity of Gene Ontology Annotations using a Compositional Approach. BMC Bioinformatics 15:155.

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.
  • Sitnikov D, Zhu S, McAndrews M, Bult C, Eppig J, Blake J. Cellular Localization, Functional, and Biological Process Curation of microRNA Literature. microRNA as Biomarkers and Diagnostics, Boston, MA, March 17-18.

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 and submitted TermGenie terms.
  3. David Hill completed the formal representation of 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 attend monthly teleconferences led by Astrid Laegrid and Martin Kuiper of the Norwegian University of Science and Technology in Trondheim to organize an international Gene Regulation Consortium (GRECO) focused on comprehensive annotation of mammalian (human, mouse, and rat) transcription factors and their target genes using a variety of existing controlled vocabularies for annotation, including GO.

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.