Difference between revisions of "MGI Dec 5-March 3"

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(Annotation Progress)
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* 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.
 
* 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.
 
* 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.
+
* 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.

Revision as of 08:13, 5 March 2014

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 -46* -0.18
Total Annotations: 312667 303352 16395 5.70
Total non-IEA Annotation
Total Number of Genes: 24763 24600 50 0.20
Total Annotations: 217975 209013 15925 8.25
Annotation by Direct Experiment
MGI Curated Mouse Genes 11742 11569 465 4.19
MGI Curated Annotations 77459 75555 4940 7.00
GOA Curated Mouse Genes: 4182 4075 600 17.27
GOA Curated Annotations: 23084 22017 3962 21.94
Annotation by Orthology
Total Genes Annotated by Orthology 10583 9827 376 3.98
Total Orthology Annotation 80547 74768 6147 8.96
Genes Annotated by Human Orthology Load (GOA) 9159 8173 417 5.38
Total Annotation by Human Orthology Load 51457 45989 3752 8.88
Genes Annotated by Rat Orthology Load (RGD) 4198 4160 77 1.89
Total Annotations by Rat Orthology Load 25225 24577 1254 5.38
IEA Annotation
Total Genes with IEA Annotations 16808 16784 1254 7.66
Total IEA Annotations 94692 94339 470 0.50
Total Genes with SwissProt to GO Annotations 16454 16414 443 2.77
Total SwissProt to GO Annotations 66182 65799 1066 1.65
Total Genes with Interpro to GO Annotations 10272 10224 432 4.41
Total Interpro to GO Annotations 27382 27375 -429 -1.54
Total Genes with EC to GO Annotations 900 930 -14 -1.48
Total EC to GO Annotations 1128 1165 -178 -13.36
  • 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

  • Hill DP, Adams N, Bada M, Batchelor C, Berardini TZ, Dietze H, Drabkin HJ, Ennis M, Foulger RE, Harris MA, Hastings J, Kale NS, de Matos P, Mungall CJ, Owen G, Roncaglia P, Steinbeck C, Turner S, Lomax J. Dovetailing biology and chemistry: integrating the Gene Ontology with the ChEBI chemical ontology. BMC Genomics. 2013 Jul 29;14:513. doi: 10.1186/1471-2164-14-513.
  • Tripathi S, Christie KR, Balakrishnan R, Huntley R, Hill DP, Thommesen L, Blake JA, Kuiper M, Lægreid A. Gene Ontology annotation of sequence-specific DNA binding transcription factors: setting the stage for a large-scale curation effort. Database (Oxford). 2013 Aug 27;2013:bat062. doi: 10.1093/database/bat062. Print 2013. PubMed PMID: 23981286; PubMed Central PMCID: PMC3753819.
  • Roncaglia P, Martone ME, Hill DP, Berardini TZ, Foulger RE, Imam FT, Drabkin H, Mungall CJ, Lomax J. The Gene Ontology (GO) Cellular Component Ontology: integration with SAO (Subcellular Anatomy Ontology) and other recent developments. J Biomed Semantics. 2013 Oct 7;4(1):20. doi:10.1186/2041-1480-4-20. PubMed PMID: 24093723.


b. Presentations including Talks and Tutorials and Teaching

  • Karen Christie (with Rachael Huntley) - Making Gene Ontology Annotations for Transcription Factors. Workshop at the EBI for the Norwegian University of Science and Technology (NTNU) group annotating transcription factors and their target genes (small group workshop). February 7-8 2013, Hinxton, UK.
  • Drabkin, Harold J; The Jackson Laboratory, USA 2013; Increased expressivity of mouse protein function representation using the gene ontology; Proteomics 2013, July 15-17; Philadelphia PA

c. Poster presentations

  • Ni L, Dolan ME, Blake JA - Assessment of comparative functional annotation propagation in mouse. The 27th International Mammalian Genome Conference, 2013

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.
  • 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.