FlyBase December 2014: Difference between revisions
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a. Paper with substantial GO content | a. Paper with substantial GO content | ||
1. Mao Y, Van Auken K, Li D, Arighi CN, McQuilton P, Hayman GT, Tweedie S, Schaeffer ML, Laulederkind SJ, Wang SJ, Gobeill J, Ruch P, Luu AT, Kim JJ, Chiang JH, Chen YD, Yang CJ, Liu H, Zhu D, Li Y, Yu H, Emadzadeh E, Gonzalez G, Chen JM, Dai HJ, Lu Z. Overview of the gene ontology task at BioCreative IV. Database (Oxford). 2014 Aug 25;2014. pii: bau086. doi: 10.1093/database/bau086. PubMed PMID:25157073; PubMed Central PMCID:PMC4142793. | |||
2. Van Auken K, Schaeffer ML, McQuilton P, Laulederkind SJ, Li D, Wang SJ, Hayman GT, Tweedie S, Arighi CN, Done J, Müller HM, Sternberg PW, Mao Y, Wei CH, Lu Z. BC4GO: a full-text corpus for the BioCreative IV GO task. Database (Oxford). 2014 Jul 28;2014. pii: bau074. doi: 10.1093/database/bau074. PubMed PMID:25070993; ; PubMed Central PMC4112614. | |||
3. Alam-Faruque Y, Hill DP, Dimmer EC, Harris MA, Foulger RE, Tweedie S, Attrill H, Howe DG, Thomas SR, Davidson D, Woolf AS, Blake JA, Mungall CJ, O'Donovan C, Apweiler R, Huntley RP. Representing kidney development using the gene ontology. PLoS One. 2014 Jun 18;9(6):e99864. doi: 10.1371/journal.pone.0099864. eCollection 2014. PubMed PMID: 24941002; PubMed Central PMCID: PMC4062467. | |||
4. Rost B; FlyBase Consortium. tagtog: interactive and text-mining-assisted annotation of gene mentions in PLOS full-text articles. Database (Oxford). 2014 Apr 7;2014(0):bau033. doi: 10.1093/database/bau033. PubMed PMID:24715220; PubMed Central PMC3978375. | |||
b. Presentations including Talks and Tutorials and Teaching | b. Presentations including Talks and Tutorials and Teaching | ||
c. Poster presentations | c. Poster presentations | ||
55th Annual Drosophila Research Conference. March 2014: Gene Groups in FlyBase. H. Attrill, S.J. Marygold, S. Tweedie and the FlyBase Consortium. | |||
=== 5. Other Highlights: === | === 5. Other Highlights: === |
Revision as of 09:28, 27 November 2014
1. Staff working on GOC tasks
Susan Tweedie (GO curator) 0.8 FTE
Helen Attrill (GO curator/literature curator) 0.35 FTE
Peter McQuilton (Literature curator)
Steven Marygold (Literature curator)
Gillian Millburn (Literature curator)
Raymund Stefancsik (Literature curator)
Kathleen Falls (Developer)
Andy Schroeder (Developer)
Total number of staff working on GOC tasks approx 1.5 FTE; total funded by NIH GO grant 0.
2. Annotation progress
Table showing progress in annotating Drosophila localized genes Nov 2013 - Nov 2014 (FB2013_06 - FB2014_06)
Nov 13 | Nov 14 | % change | % of total genes | |
---|---|---|---|---|
Total number of localized genes (excluding pseudogenes) | 16457 | 17382 | +5.6% | |
Localized genes with no GO annotation | 4655 | 4692 | +0.8% | 27.0% |
Localized genes with any GO annotation | 11802 | 12690 | +7.5% | 73.0% |
Localized genes with 1 or more term based on experimental evidence | 5786 | 6095 | +18.8% | 35.1% |
Localized genes with other non-IEA, non-ND evidence | 3733 | 3746 | +0.4% | 21.5% |
Localized genes with only IEA evidence | 1270 | 1074 | -15.4% | 6.2% |
Localized genes with only ND evidence | 1013 | 1775 | +75.2% | 10.2% |
Table showing total annotation progress for localized genes Nov 2013 - Nov 2014 (FB2013_06 - FB2014_06)
November 2013 | November 2014 | % change | |
---|---|---|---|
GO Biological Process (BP) annotations (genes annotated for non-ROOT BP term) | 42546 (9183 genes) | 46245 (9471 genes) | +8.7% (+3.1%) |
GO Molecular Function (MF) annotations (genes annotated for non-ROOT MF term) | 26126 (8870 genes) | 27872 (9037 genes) | +6.7% (+1.9%) |
GO Cellular Component (CC) annotations (genes annotated for non-ROOT CC term) | 20294 (7507 genes) | 22911 (7959 genes) | +4.8% (+6.0%) |
Total annotations for localized genes | 88966 | 97028 | +8.6% |
3. Methods and strategies for annotation
a. Literature curation:
b. Computational annotation strategies: GO annotation based on InterPro2GO mappings are updated with every release of FlyBase.
c. Priorities for annotation:
1. Genes that currently lack GO annotation.
2. Reviewing GO annotation for groups of related genes
4. Presentations and publications
a. Paper with substantial GO content
1. Mao Y, Van Auken K, Li D, Arighi CN, McQuilton P, Hayman GT, Tweedie S, Schaeffer ML, Laulederkind SJ, Wang SJ, Gobeill J, Ruch P, Luu AT, Kim JJ, Chiang JH, Chen YD, Yang CJ, Liu H, Zhu D, Li Y, Yu H, Emadzadeh E, Gonzalez G, Chen JM, Dai HJ, Lu Z. Overview of the gene ontology task at BioCreative IV. Database (Oxford). 2014 Aug 25;2014. pii: bau086. doi: 10.1093/database/bau086. PubMed PMID:25157073; PubMed Central PMCID:PMC4142793.
2. Van Auken K, Schaeffer ML, McQuilton P, Laulederkind SJ, Li D, Wang SJ, Hayman GT, Tweedie S, Arighi CN, Done J, Müller HM, Sternberg PW, Mao Y, Wei CH, Lu Z. BC4GO: a full-text corpus for the BioCreative IV GO task. Database (Oxford). 2014 Jul 28;2014. pii: bau074. doi: 10.1093/database/bau074. PubMed PMID:25070993; ; PubMed Central PMC4112614.
3. Alam-Faruque Y, Hill DP, Dimmer EC, Harris MA, Foulger RE, Tweedie S, Attrill H, Howe DG, Thomas SR, Davidson D, Woolf AS, Blake JA, Mungall CJ, O'Donovan C, Apweiler R, Huntley RP. Representing kidney development using the gene ontology. PLoS One. 2014 Jun 18;9(6):e99864. doi: 10.1371/journal.pone.0099864. eCollection 2014. PubMed PMID: 24941002; PubMed Central PMCID: PMC4062467.
4. Rost B; FlyBase Consortium. tagtog: interactive and text-mining-assisted annotation of gene mentions in PLOS full-text articles. Database (Oxford). 2014 Apr 7;2014(0):bau033. doi: 10.1093/database/bau033. PubMed PMID:24715220; PubMed Central PMC3978375.
b. Presentations including Talks and Tutorials and Teaching
c. Poster presentations
55th Annual Drosophila Research Conference. March 2014: Gene Groups in FlyBase. H. Attrill, S.J. Marygold, S. Tweedie and the FlyBase Consortium.
5. Other Highlights:
A. Ontology Development Contributions:
B. Annotation Outreach and User Advocacy Efforts:
- S. Tweedie and H. Attrill attended the GO consortium meeting (Barcelona, 2014)
C. Other:
- S. Tweedie left FlyBase at the end of November 2014