MGI December 2012: Difference between revisions
(→Staff:) |
No edit summary |
||
(24 intermediate revisions by 7 users not shown) | |||
Line 1: | Line 1: | ||
= Mouse Genome Informatics Summary, December | [[Category:MGI]] | ||
= Mouse Genome Informatics Summary, December 2012 = | |||
= Overview = | = Overview = | ||
= Staff: = | = Staff: = | ||
Line 6: | Line 7: | ||
Karen R Christie* | Karen R Christie* | ||
Mary Dolan* | Mary E Dolan* | ||
Harold J Drabkin* | Harold J Drabkin* | ||
Line 19: | Line 20: | ||
= Annotation Progress = | = Annotation Progress = | ||
'''''MGI GO STATS as of December 2012''''' | '''''MGI GO STATS as of December 2012''''' | ||
This year our manual annotation effort has focused on obtaining annotations for genes that had no annotations or on obtaining deeper manual annotations to terms that were annotated with IEA or one of the root nodes of GO. | |||
{| style="border-spacing:0;" | {| style="border-spacing:0;" | ||
Line 231: | Line 232: | ||
'''''Priorities for annotation''''' | '''''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. | |||
* Isoform curation (Harold, Protein Ontology project); | |||
* Genes with no GO annotation but with literature (Li and Dmitry) | * Genes with no GO annotation but with literature (Li and Dmitry) | ||
* Genes with only IEA annotation but with literature (Li | * Genes with only IEA annotation but with literature (Li) | ||
* Genes marked as having GO annotation completed, but now having new literature (Dmitry) | * 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 | * Dmitry has been focused on annotation or miRNAs in MGI | ||
= Presentations and Publications = | = Presentations and Publications = | ||
Drabkin HJ, Blake JA; for the Mouse Genome Informatics Database. Manual Gene | |||
Ontology annotation workflow at the Mouse Genome Informatics Database. Database | |||
(Oxford). 2012 Oct 29;2012(0):bas045. Print 2012. PubMed PMID: 23110975; PubMed | |||
Central PMCID: PMC3483533. | |||
Taşan M, Drabkin HJ, Beaver JE, Chua HN, Dunham J, Tian W, Blake JA, Roth FP. | |||
A Resource of Quantitative Functional Annotation for Homo sapiens Genes. G3 | |||
(Bethesda). 2012 Feb;2(2):223-33. Epub 2012 Feb 1. PubMed PMID: 22384401; PubMed | |||
Central PMCID: PMC3284330. | |||
Thomas PD, Wood V, Mungall CJ, Lewis SE, Blake JA; Gene Ontology Consortium. | |||
On the Use of Gene Ontology Annotations to Assess Functional Similarity among | |||
Orthologs and Paralogs: A Short Report. PLoS Comput Biol. 2012;8(2):e1002386. | |||
Epub 2012 Feb 16. PubMed PMID: 22359495; PubMed Central PMCID: PMC3280971. | |||
Bada M, Eckert M, Evans D, Garcia K, Shipley K, Sitnikov D, Baumgartner WA, | |||
Cohen KB, Verspoor K, Blake JA and Hunter LE. Concept annotation in the CRAFT | |||
corpus. BMC Bioinformatics 2012, 13:161 doi:10.1186/1471-2105-13-161. PMID: | |||
22776079 [PubMed - in process] PMCID: PMC3476437. | |||
Dolan ME, Mungall CJ, Dietze H and Blake JA. | |||
A Simplified Method for Creating a Cell Cycle Ontology for the Laboratory Mouse. | |||
Poster presented at CSHALS 2012 http://www.iscb.org/cms_addon/conferences/cshals2012/posters/MDolan_MouseCCO_CSHALS2012.pdf | |||
= Ontology Development Contributions: = | = Ontology Development Contributions: = | ||
* 1. David Hill | * 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. | ||
* 3. 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. | |||
* 3 | * 4. David Hill and Harold Drabkin, have worked with Tanya Berardini, Chris Mungall, Paola Roncaglia, Jane Lomax and ChEBI curators to align GO with ChEBI. GO-CHEBI cross-products are now use. | ||
* 5. David Hill has worked with the GO ontology development and software groups to develop a web-based tool for requesting new terms. | |||
* 6. Harold Drabkin is working on improvement of the the representation of tRNA modification | |||
* | * 7. David Hill has worked with the GO editorial office and the BHF-UCL group to represent cardiac conduction in the ontology. | ||
* 7. David Hill and | |||
= Annotation Outreach and User Advocacy Efforts: = | = 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 | * 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 serves on the GO-help rota. | ||
* | * Judith Blake and Karen Christie are working with Rama Balakrishnan to coordinate with Astrid Laegrid of the Norwegian University of Science and Technology in Trondheim to determine how to incorporate GO annotations for transcription factors made by this group. | ||
= Other Highlights: = | = 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 | * 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. | ||
* Mary Dolan has | * 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. |
Latest revision as of 15:46, 4 June 2014
Mouse Genome Informatics Summary, December 2012
Overview
Staff:
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
MGI GO STATS as of December 2012
This year our manual annotation effort has focused on obtaining annotations for genes that had no annotations or on obtaining deeper manual annotations to terms that were annotated with IEA or one of the root nodes of GO.
Total Genes annotated with at least one GO term of any kind | 25109
|
25452
|
343
|
1.4
|
Total annotations: | 272241
|
286957
|
14716
|
5.4
|
Total Number of Genes | 24029
|
24550
|
521
|
2.2
|
Total Annotations | 178496
|
193088
|
14592
|
8.2
|
MGI Curated Genes | 10332
|
11104
|
772
|
7.5
|
MGI Curated Annotations | 64165
|
70615
|
6450
|
10.1
|
GOA Curated Genes | 2910
|
3475
|
565
|
19.4
|
GOA Curated Annotations | 14048
|
18055
|
4007
|
28.5
|
Genes Annotated by Orthology Total | 8912
|
9451
|
539
|
6.0
|
Total Orthology Annotations | 62606
|
68621
|
6015
|
9.6
|
Genes Annotated by Human Orthology Load (GOA) | 7171
|
7756
|
585
|
8.2
|
Total Annotation by Human Orthology Load | 36796
|
42237
|
5441
|
14.8
|
Genes annotated by Rat Orthology Load (RGD) | 3963
|
4083
|
120
|
3.0
|
Total Annotations by Rat Orthology Load | 22390
|
23323
|
933
|
4.2
|
Total Genes with IEA | 16319
|
16372
|
53
|
0.3
|
Total IEA annotations | 93745
|
93869
|
124
|
0.1
|
Total Genes with SwissProt to GO | 15803
|
15971
|
168
|
1.1
|
Total SwissProt to GO Annotations | 62283
|
64733
|
2450
|
3.9
|
Total Genes with Interpro to GO | 9781
|
9792
|
11
|
0.1
|
Total Interpro to GO Annotations | 29954
|
27804
|
-2150
|
-7.2
|
Total Genes with EC to GO Annotations | 930
|
944
|
14
|
1.5
|
Total EC to GO annotations | 1508
|
1332
|
-176
|
-11.7
|
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
Presentations and Publications
Drabkin HJ, Blake JA; for the Mouse Genome Informatics Database. Manual Gene Ontology annotation workflow at the Mouse Genome Informatics Database. Database (Oxford). 2012 Oct 29;2012(0):bas045. Print 2012. PubMed PMID: 23110975; PubMed Central PMCID: PMC3483533.
Taşan M, Drabkin HJ, Beaver JE, Chua HN, Dunham J, Tian W, Blake JA, Roth FP. A Resource of Quantitative Functional Annotation for Homo sapiens Genes. G3 (Bethesda). 2012 Feb;2(2):223-33. Epub 2012 Feb 1. PubMed PMID: 22384401; PubMed Central PMCID: PMC3284330.
Thomas PD, Wood V, Mungall CJ, Lewis SE, Blake JA; Gene Ontology Consortium. On the Use of Gene Ontology Annotations to Assess Functional Similarity among Orthologs and Paralogs: A Short Report. PLoS Comput Biol. 2012;8(2):e1002386. Epub 2012 Feb 16. PubMed PMID: 22359495; PubMed Central PMCID: PMC3280971.
Bada M, Eckert M, Evans D, Garcia K, Shipley K, Sitnikov D, Baumgartner WA, Cohen KB, Verspoor K, Blake JA and Hunter LE. Concept annotation in the CRAFT corpus. BMC Bioinformatics 2012, 13:161 doi:10.1186/1471-2105-13-161. PMID: 22776079 [PubMed - in process] PMCID: PMC3476437.
Dolan ME, Mungall CJ, Dietze H and Blake JA. A Simplified Method for Creating a Cell Cycle Ontology for the Laboratory Mouse. Poster presented at CSHALS 2012 http://www.iscb.org/cms_addon/conferences/cshals2012/posters/MDolan_MouseCCO_CSHALS2012.pdf
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.
- 3. 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 and Harold Drabkin, have worked with Tanya Berardini, Chris Mungall, Paola Roncaglia, Jane Lomax and ChEBI curators to align GO with ChEBI. GO-CHEBI cross-products are now use.
- 5. David Hill has worked with the GO ontology development and software groups to develop a web-based tool for requesting new terms.
- 6. Harold Drabkin is working on improvement of the the representation of tRNA modification
- 7. David Hill has worked with the GO editorial office and the BHF-UCL group to represent cardiac conduction in the ontology.
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 serves on the GO-help rota.
- Judith Blake and Karen Christie are working with Rama Balakrishnan to coordinate with Astrid Laegrid of the Norwegian University of Science and Technology in Trondheim to determine how to incorporate GO annotations for transcription factors made by this group.
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.
- 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.