MGI December 2017

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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 2016
Dec 5 2017
Change
% change
Total Genes annotated with at least one GO term of any kind 24213 24529 316 1.3
Total Annotations: 360758 375767 15009 4.2
Total non-IEA Annotation
Total Number of Genes: 24032 24344 312 1.3
Total Annotations: 278277 295718 17441 6.3
Annotation by Direct Experiment
MGI Curated Mouse Genes 12624 12836 212 1.7
MGI Curated Annotations 89907 91935 2028 2.3
GOA Curated Mouse Genes: 5424 5996 572 10.5
GOA Curated Annotations: 33530 38212 4682 14.0
Annotation by Orthology
Total Genes Annotated by Orthology 12067 12654 587 4.9
Total Orthology Annotation 106607 117460 10853 10.2
Genes Annotated by Human Orthology Load (GOA) 10942 11653 711 6.5
Total Annotation by Human Orthology Load 71680 80897 9217 12.9
Genes Annotated by Rat Orthology Load (RGD) 4849 4980 131 2.7
Total Annotations by Rat Orthology Load 31405 33117 1712 5.5
Genes Annotated by Phylogeny 8153 8447 294 3.6
Total Annotations by Phylogeny 29434 30476 1042 3.5
IEA Annotation
Total Genes with IEA Annotations 14815 14975 160 1.1
Total IEA Annotations 82481 80049 -2432 -2.9
Total Genes with SwissProt to GO Annotations 14440 14606 166 1.1
Total SwissProt to GO Annotations 57420 56515 -905 -1.6
Total Genes with Interpro to GO Annotations 10103 9879 -224 -2.2
Total Interpro to GO Annotations 24074 22564 -1510 -6.3
Total Genes with EC to GO Annotations* 817 789 -28 -3.4
Total EC to GO Annotations * 987 970 -17 --1.7

Methods and strategies for annotation

Priorities for annotation

  • Isoform curation (Harold, Li, 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 (Karen, David)
  • Dmitry has been focused on annotation or miRNAs in MGI
  • Annotation of ciliary genes (Karen)
  • Annotation of metabolic genes, glycolysis,pyruvate metabolism, and carbohydrate catabolism in general (David)
  • Autophagy genes

Literature curation:

Literature curation continues to be the major focus of our annotation efforts. Recently the MGI team implemented new literature mining and curation support mechanisms to improve efficiency of the identification of relevant literature and to mark-up and track data curation efforts. Evaluation of literature used across MGI shows that althrough the number of papers in PubMed associated with 'mouse' as the experimental organism, the number of papers relevant to genetics and genomics research has remained roughly steady. That said, however, the number of papers reported on in papers has increased, leading to increased curation effort per paper overall.

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.

Harold Drabkin monitors weekly QC reports on manual and automatic annotation stats, and responds to questions about specific annotations as required.

Presentations and Publications

a. Papers with substantial GO content

  • Roncaglia P, van Dam TJP, Christie KR, Nacheva L, Toedt G, Huynen MA, Huntley RP, Gibson TJ, Lomax J. The Gene Ontology of eukaryotic cilia and flagella. Cilia. 2017 Nov 16;6:10. doi: 10.1186/s13630-017-0054-8. eCollection 2017. PMID:29177046

c. Poster presentations

  • Christie KR, Roncaglia P, van Dam TJP, Gibson TJ, Lomax J, Blake JA. Comprehensive Gene Ontology annotation of ciliary genes in the laboratory mouse. Biocuration 2017, Stanford, March 26-29, 2017
  • Dolan, ME and Blake, JA. Constructing a multi-species GO Slim. GOC October 2-4, 2017.
  • Ni L, Drabkin HJ, Christie KR, Arighi CN, Wu CH and Blake JA. Functional annotation of proteoforms in the Mouse Genome Database using the Protein Ontology. ISMB 2017, Prague, Czech Republic, July 21 - July 25, 2017

Other Highlights:

A. Ontology Development Contributions:

  • David Hill led the ontology development group with help from Kimberly VanAuken. There is now a much closer association with the ontology developers and the annotation group. David and Kimberly meet at least once a week.
  • Harold Drabkin is adding new molecular function terms to aid in mapping Metacyc identifiers to GO terms for plant metabolic enzymes.
  • David Hill, Karen Christie and Harold Drabkin are core members of the GitHub ontology ticket rota. They are joined by Pascale Gaudet and Kimberly Van Auken.
  • David Hill, Karen Christie and Harold Drabkin attended ontology developers' training workshops twice this calendar year. Those workshops resulted in the ontology group switching over to GitHub and Protege-based maintenance of the ontology.
  • Karen Christie, as part of the cilia ontology working group, completed work (now published) on the cilia ontology development project.
  • David Hill completed work on the autophagy annotation-ontology development project.
  • David Hill attended the Protein Ontology workshop as a GO representative.


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.


C. Noctua annotation tool.

  • David Hill, Karen Christie, and Harold Drabkin attend bimonthly meetings on the development of the Noctua tool to improve its functionality to become a production level tool for curation of GO annotations throughout the GO Consortium.
  • All MGI curators continue to test the new Noctua tool for GO-CAM modeling in GO, including development and design of standards for modeling and began creating production GO-CAM models.


D. Other Highlights:

  • Karen Christie serves as the MGI representative on the PAINT curation team. As a member of this team, Karen curates Panther families in PAINT to propagate annotations based on evolutionary relationships. She also files bug reports on PAINT and contribute to the improvement of the PAINT software.
  • Mary Dolan: Data analysis and visualization for the MGI GO group. QC for GO-related projects: PRO to MGI mapping (attended PRO meeting October 2017), resolving mouse reference proteome (ongoing work as part of MGI-AGR).
  • Mary Dolan applied the MGI GOSlim methodology for use by the AGR. Poster "Constructing a multi-species GO Slim" presented at GOC Meeting October 2017.