MGI December 2016: Difference between revisions

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(Created page with "Category:MGI Overview: = Staff: = [please include FTEs working on GOC tasks designating as well how many FTEs funding by GOC NIHGRI grant] Judith Blake* Karen R Christ...")
 
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= Annotation Progress =
= Annotation Progress =


{| style="border-spacing:0;"
| colspan="2"  style="border:0.0069in solid #00000a;padding:0.0694in;"| <center>'''Annotation Type '''</center>
| style="border:0.0069in solid #00000a;padding:0.0694in;"| <center>'''Dec 5 2016 '''</center>
| style="border:0.0069in solid #00000a;padding:0.0694in;"| <center>'''Dec 5, 2015 '''</center>
| style="border:0.0069in solid #00000a;padding:0.0694in;"| <center>'''Change '''</center>
| style="border:0.0069in solid #00000a;padding:0.0694in;"| <center>'''% change '''</center>


{| class="wikitable" cellpadding="5"
!Annotation Type !! Dec 5 2014  !! Dec 5, 2015 !! Change !!% change
|-
|-
|Total Genes annotated with at least one GO term of any kind || 24226  ||24224 ||-2*||0.01
| colspan="2"  style="border:0.0069in solid #00000a;padding:0.0694in;"| Total Genes annotated with at least one GO term of any kind  
| style="border:0.0069in solid #00000a;padding:0.0694in;"| 24213
| style="border:0.0069in solid #00000a;padding:0.0694in;"| 24224  
| style="border:0.0069in solid #00000a;padding:0.0694in;"| -11*
| style="border:0.0069in solid #00000a;padding:0.0694in;"| -0.05
 
|-
|-
| Total Annotations: || 341687 || 362727 || 21040 || 6.2
| colspan="2"  style="border:0.0069in solid #00000a;padding:0.0694in;"| Total Annotations:  
| style="border:0.0069in solid #00000a;padding:0.0694in;"| 360758
| style="border:0.0069in solid #00000a;padding:0.0694in;"| 362727  
| style="border:0.0069in solid #00000a;padding:0.0694in;"| -1969
| style="border:0.0069in solid #00000a;padding:0.0694in;"| -0.54
 
|-
|-
| colspan=5 align=center bgcolor=white| '''Total non-IEA Annotation'''  
| colspan="6"  style="border:0.0069in solid #00000a;padding:0.0694in;"| '''Total non-IEA Annotation '''
 
|-
|-
|  Total Number of Genes: || 23844 || 23979 ||135  || 0.5
| colspan="2" style="border:0.0069in solid #00000a;padding:0.0694in;"| Total Number of Genes:  
| style="border:0.0069in solid #00000a;padding:0.0694in;"| 24032
| style="border:0.0069in solid #00000a;padding:0.0694in;"| 23979  
| style="border:0.0069in solid #00000a;padding:0.0694in;"| 53
| style="border:0.0069in solid #00000a;padding:0.0694in;"| 0.22
 
|-
|-
|Total Annotations: ||242025 ||262218 || 20193||7.7 ||
| colspan="2"  style="border:0.0069in solid #00000a;padding:0.0694in;"| Total Annotations:  
| style="border:0.0069in solid #00000a;padding:0.0694in;"| 278277
| style="border:0.0069in solid #00000a;padding:0.0694in;"| 262218  
| style="border:0.0069in solid #00000a;padding:0.0694in;"| 16059
| style="border:0.0069in solid #00000a;padding:0.0694in;"| 6.12
 
|-
|-
|colspan=5 align=center bgcolor=white| '''Annotation by Direct Experiment'''
| colspan="6"  style="border:0.0069in solid #00000a;padding:0.0694in;"| '''Annotation by Direct Experiment '''
 
|-
|-
|MGI Curated Mouse Genes ||12170 ||12433 ||263||2.2 ||
| colspan="2"  style="border:0.0069in solid #00000a;padding:0.0694in;"| MGI Curated Mouse Genes  
| style="border:0.0069in solid #00000a;padding:0.0694in;"| 12624
| style="border:0.0069in solid #00000a;padding:0.0694in;"| 12433  
| style="border:0.0069in solid #00000a;padding:0.0694in;"| 191
| style="border:0.0069in solid #00000a;padding:0.0694in;"| 1.54
 
|-
|-
|MGI Curated Annotations ||82573 ||87159 ||4586 || 5.6||
| colspan="2"  style="border:0.0069in solid #00000a;padding:0.0694in;"| MGI Curated Annotations  
| style="border:0.0069in solid #00000a;padding:0.0694in;"| 89907
| style="border:0.0069in solid #00000a;padding:0.0694in;"| 87159  
| style="border:0.0069in solid #00000a;padding:0.0694in;"| 2748
| style="border:0.0069in solid #00000a;padding:0.0694in;"| 3.15
 
|-
|-
|GOA Curated Mouse Genes: ||4565 ||5075 ||510 ||11.2 ||
| colspan="2"  style="border:0.0069in solid #00000a;padding:0.0694in;"| GOA Curated Mouse Genes:  
| style="border:0.0069in solid #00000a;padding:0.0694in;"| 5424
| style="border:0.0069in solid #00000a;padding:0.0694in;"| 5075  
| style="border:0.0069in solid #00000a;padding:0.0694in;"| 349
| style="border:0.0069in solid #00000a;padding:0.0694in;"| 6.88
 
|-
| colspan="2"  style="border:0.0069in solid #00000a;padding:0.0694in;"| GOA Curated Annotations:
| style="border:0.0069in solid #00000a;padding:0.0694in;"| 33530
| style="border:0.0069in solid #00000a;padding:0.0694in;"| 30177
| style="border:0.0069in solid #00000a;padding:0.0694in;"| 3353
| style="border:0.0069in solid #00000a;padding:0.0694in;"| 11.11
 
|-
|-
|GOA Curated Annotations: ||26002 ||30177 ||4175 ||16.1 ||
| colspan="6"  style="border:0.0069in solid #00000a;padding:0.0694in;"| '''Annotation by Orthology '''
 
|-
|-
|colspan=5 align=center bgcolor=white| '''Annotation by Orthology'''
| style="border:0.0069in solid #00000a;padding:0.0694in;"| Total Genes Annotated by Orthology
| colspan="2"  style="border:0.0069in solid #00000a;padding:0.0694in;"| 12067
| style="border:0.0069in solid #00000a;padding:0.0694in;"| 11866
| style="border:0.0069in solid #00000a;padding:0.0694in;"| 201
| style="border:0.0069in solid #00000a;padding:0.0694in;"| 1.69
 
|-
| style="border:0.0069in solid #00000a;padding:0.0694in;"| Total Orthology Annotation  
| colspan="2"  style="border:0.0069in solid #00000a;padding:0.0694in;"| 106607
| style="border:0.0069in solid #00000a;padding:0.0694in;"| 102212
| style="border:0.0069in solid #00000a;padding:0.0694in;"| 4395
| style="border:0.0069in solid #00000a;padding:0.0694in;"| 4.30
 
|-
|-
|Total Genes Annotated by Orthology ||11435
| style="border:0.0069in solid #00000a;padding:0.0694in;"| Genes Annotated by Human Orthology Load (GOA)
| colspan="2"  style="border:0.0069in solid #00000a;padding:0.0694in;"| 10942
||11866 ||431 ||3.8 ||
| style="border:0.0069in solid #00000a;padding:0.0694in;"| 10701
| style="border:0.0069in solid #00000a;padding:0.0694in;"| 241
| style="border:0.0069in solid #00000a;padding:0.0694in;"| 2.25
 
|-
|-
|Total Orthology Annotation ||92787
| style="border:0.0069in solid #00000a;padding:0.0694in;"| Total Annotation by Human Orthology Load
| colspan="2"  style="border:0.0069in solid #00000a;padding:0.0694in;"| 71680
||102212 ||9425 ||10.2 ||
| style="border:0.0069in solid #00000a;padding:0.0694in;"| 68129
| style="border:0.0069in solid #00000a;padding:0.0694in;"| 3551
| style="border:0.0069in solid #00000a;padding:0.0694in;"| 5.21
 
|-
|-
|Genes Annotated by Human Orthology Load (GOA) ||10207 ||10701 || 494 ||4.8 ||
| style="border:0.0069in solid #00000a;padding:0.0694in;"| Genes Annotated by Rat Orthology Load (RGD)  
| colspan="2"  style="border:0.0069in solid #00000a;padding:0.0694in;"| 4849
| style="border:0.0069in solid #00000a;padding:0.0694in;"| 4696
| style="border:0.0069in solid #00000a;padding:0.0694in;"| 153
| style="border:0.0069in solid #00000a;padding:0.0694in;"| 3.26
 
|-
|-
|Total Annotation by Human Orthology Load ||61355 ||68129 || 6774|| 11.0||
| style="border:0.0069in solid #00000a;padding:0.0694in;"| Total Annotations by Rat Orthology Load  
| colspan="2"  style="border:0.0069in solid #00000a;padding:0.0694in;"| 31405
| style="border:0.0069in solid #00000a;padding:0.0694in;"| 30769
| style="border:0.0069in solid #00000a;padding:0.0694in;"| 636
| style="border:0.0069in solid #00000a;padding:0.0694in;"| 2.07
 
|-
|-
|Genes Annotated by Rat Orthology Load (RGD) ||4415 ||4696 ||281 ||6.4 ||
| style="border:0.0069in solid #00000a;padding:0.0694in;"| Genes Annotated by Phylogeny
| colspan="2"  style="border:0.0069in solid #00000a;padding:0.0694in;"| 8153
| style="border:0.0069in solid #00000a;padding:0.0694in;"| 6400
| style="border:0.0069in solid #00000a;padding:0.0694in;"| 1753
| style="border:0.0069in solid #00000a;padding:0.0694in;"| 27.39
 
|-
|-
|Total Annotations by Rat Orthology Load || 27006||30769 || 3763|| 13.9||
| style="border:0.0069in solid #00000a;padding:0.0694in;"| Total Annotations by Phylogeny
| colspan="2"  style="border:0.0069in solid #00000a;padding:0.0694in;"| 29434
| style="border:0.0069in solid #00000a;padding:0.0694in;"| 22522
| style="border:0.0069in solid #00000a;padding:0.0694in;"| 6912
| style="border:0.0069in solid #00000a;padding:0.0694in;"| 30.69
 
|-
|-
|colspan=5 align=center bgcolor=white| '''IEA Annotation'''
| colspan="6"  style="border:0.0069in solid #00000a;padding:0.0694in;"| '''IEA Annotation '''
 
|-
|-
|Total Genes with IEA Annotations ||14602 ||14724 || 122|| 0.8 ||
| colspan="2"  style="border:0.0069in solid #00000a;padding:0.0694in;"| Total Genes with IEA Annotations  
| style="border:0.0069in solid #00000a;padding:0.0694in;"| 14815
| style="border:0.0069in solid #00000a;padding:0.0694in;"| 14724  
| style="border:0.0069in solid #00000a;padding:0.0694in;"| 91
| style="border:0.0069in solid #00000a;padding:0.0694in;"| 0.62
 
|-
|-
|Total IEA Annotations ||99662 ||100509 || 847||0.8 ||  
| colspan="2"  style="border:0.0069in solid #00000a;padding:0.0694in;"| Total IEA Annotations  
| style="border:0.0069in solid #00000a;padding:0.0694in;"| 82481
| style="border:0.0069in solid #00000a;padding:0.0694in;"| 100509  
| style="border:0.0069in solid #00000a;padding:0.0694in;"| -18028
| style="border:0.0069in solid #00000a;padding:0.0694in;"| -17.94
 
|-
|-
|Total Genes with SwissProt to GO Annotations ||14211
| colspan="2"  style="border:0.0069in solid #00000a;padding:0.0694in;"| Total Genes with SwissProt to GO Annotations  
| style="border:0.0069in solid #00000a;padding:0.0694in;"| 14440
||14337 ||126||0.9 ||
| style="border:0.0069in solid #00000a;padding:0.0694in;"| 14337  
| style="border:0.0069in solid #00000a;padding:0.0694in;"| 103
| style="border:0.0069in solid #00000a;padding:0.0694in;"| 0.72
 
|-
|-
|Total SwissProt to GO Annotations ||55788 || 56888 || 1100||2.0 ||
| colspan="2"  style="border:0.0069in solid #00000a;padding:0.0694in;"| Total SwissProt to GO Annotations  
| style="border:0.0069in solid #00000a;padding:0.0694in;"| 57420
| style="border:0.0069in solid #00000a;padding:0.0694in;"| 56888  
| style="border:0.0069in solid #00000a;padding:0.0694in;"| 532
| style="border:0.0069in solid #00000a;padding:0.0694in;"| 0.94
 
|-
|-
|Total Genes with Interpro to GO Annotations ||10054
| colspan="2"  style="border:0.0069in solid #00000a;padding:0.0694in;"| Total Genes with Interpro to GO Annotations  
| style="border:0.0069in solid #00000a;padding:0.0694in;"| 10d103
||9966 ||-88 || -0.9||  
| style="border:0.0069in solid #00000a;padding:0.0694in;"| 9966  
| style="border:0.0069in solid #00000a;padding:0.0694in;"| 137
| style="border:0.0069in solid #00000a;padding:0.0694in;"| 1.37
 
|-
|-
|Total Interpro to GO Annotations ||25511
| colspan="2"  style="border:0.0069in solid #00000a;padding:0.0694in;"| Total Interpro to GO Annotations  
| style="border:0.0069in solid #00000a;padding:0.0694in;"| 24074
||24408 ||-1103 ||-4.3||
| style="border:0.0069in solid #00000a;padding:0.0694in;"| 24408  
| style="border:0.0069in solid #00000a;padding:0.0694in;"| -334
| style="border:0.0069in solid #00000a;padding:0.0694in;"| -1.37
 
|-
|-
|Total Genes with EC to GO Annotations ||1734 ||1709 ||25 || 1.5||
| colspan="2"  style="border:0.0069in solid #00000a;padding:0.0694in;"| Total Genes with EC to GO Annotations*
| style="border:0.0069in solid #00000a;padding:0.0694in;"| 817
| style="border:0.0069in solid #00000a;padding:0.0694in;"| 1709  
| style="border:0.0069in solid #00000a;padding:0.0694in;"| -892
| style="border:0.0069in solid #00000a;padding:0.0694in;"| -52.19
 
|-
|-
|Total EC to GO Annotations ||18363 ||19213 ||850 ||4.6 ||
| colspan="2"  style="border:0.0069in solid #00000a;padding:0.0694in;"| Total EC to GO Annotations *
| style="border:0.0069in solid #00000a;padding:0.0694in;"| 987
| style="border:0.0069in solid #00000a;padding:0.0694in;"| 19213  
| style="border:0.0069in solid #00000a;padding:0.0694in;"| -18226
| style="border:0.0069in solid #00000a;padding:0.0694in;"| -94.96


|}
|}
 
'''<nowiki>* Loss due to EC2GO refactoring (no annotations to EC root terms).</nowiki>'''
* Loses due to gene merges, withdrawals, or marker type changes (gene to pseudogene).


= Methods and strategies for annotation =
= Methods and strategies for annotation =

Revision as of 14:12, 6 December 2016

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, 2015
Change
% change
Total Genes annotated with at least one GO term of any kind 24213 24224 -11* -0.05
Total Annotations: 360758 362727 -1969 -0.54
Total non-IEA Annotation
Total Number of Genes: 24032 23979 53 0.22
Total Annotations: 278277 262218 16059 6.12
Annotation by Direct Experiment
MGI Curated Mouse Genes 12624 12433 191 1.54
MGI Curated Annotations 89907 87159 2748 3.15
GOA Curated Mouse Genes: 5424 5075 349 6.88
GOA Curated Annotations: 33530 30177 3353 11.11
Annotation by Orthology
Total Genes Annotated by Orthology 12067 11866 201 1.69
Total Orthology Annotation 106607 102212 4395 4.30
Genes Annotated by Human Orthology Load (GOA) 10942 10701 241 2.25
Total Annotation by Human Orthology Load 71680 68129 3551 5.21
Genes Annotated by Rat Orthology Load (RGD) 4849 4696 153 3.26
Total Annotations by Rat Orthology Load 31405 30769 636 2.07
Genes Annotated by Phylogeny 8153 6400 1753 27.39
Total Annotations by Phylogeny 29434 22522 6912 30.69
IEA Annotation
Total Genes with IEA Annotations 14815 14724 91 0.62
Total IEA Annotations 82481 100509 -18028 -17.94
Total Genes with SwissProt to GO Annotations 14440 14337 103 0.72
Total SwissProt to GO Annotations 57420 56888 532 0.94
Total Genes with Interpro to GO Annotations 10d103 9966 137 1.37
Total Interpro to GO Annotations 24074 24408 -334 -1.37
Total Genes with EC to GO Annotations* 817 1709 -892 -52.19
Total EC to GO Annotations * 987 19213 -18226 -94.96

* Loss due to EC2GO refactoring (no annotations to EC root terms).

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.

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

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)
  • 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

Presentations and Publications

a. Papers with substantial GO content

  • Drabkin HJ, Christie KR, Dolan ME, Hill DP, Ni L, Sitnikov D, Blake JA. Application of comparative biology in GO functional annotation: the mouse model. Mamm Genome. 2015 26, Issue 9, pp 574-58, PubMed PMID: 26141960.
  • Dolan ME, Baldarelli RM, Bello SM, Ni L, McAndrews MS, Bult CJ, Kadin JA, Richardson JE, Ringwald M, Eppig JT, Blake JA. Orthology for comparative genomics in the mouse genome database. Mamm Genome. 2015 Aug;26(7-8):305-13. doi: 10.1007/s00335-015-9588-5. Epub 2015 Jul 30. PubMed PMID:26223881; PubMed Central PMCID: PMC4534493
  • Gene Ontology Consortium. Gene Ontology Consortium: going forward. Nucleic Acids Res. 2015 Jan;43(Database issue):D1049-56. doi: 10.1093/nar/gku1179. Epub 2014 Nov 26. PubMed PMID: 25428369; PubMed Central PMCID: PMC4383973.

b. Presentations including Talks and Tutorials and Teaching

  • to be filled in

c. Poster presentations

  • David Hill, Peter D' Eustachio, Nikolai Renedo, Judith Blake. Linking GO Pathways to the Bigger Picture. July 2015. ISMB/ECCB, Dublin Ireland (audience: Computational Biologists)
  • Karen Christie and Judith Blake. Comprehensive Gene Ontology annotation of ciliary genes in the laboratory mouse. July 2015. FASEB Biology of Cilia & Flagella, Snowmass, CO (audience: Cilia researchers)

Other Highlights:

A. Ontology Development Contributions:

  • David Hill continues working with the ontology development group to implement logical definitions for GO terms.
  • David Hill is in the rotation to address GO-ontology GITHUB items.
  • David Hill has completed an overhaul of carbohydrate catabolic processes to the TCA cycle.
  • David Hill has been working with a focus group on representing autophagy in the ontology.


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 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.
  • Karen Christie reviewed and finalized annotations for human ciliary genes made using UniProt's Protein2GO tool by Lora Nacheva, who was a student in Tony Gibson's group at the EMBL in Germany.
  • David Hill is now co-managing the annotation group with Kimberly Van Auken (WormBase).


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.

  • 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 works with other members (particularly Seth Carbon) of the GO software team to develop automated unit tests for AmiGO2 in order to facilitate releases.