ZFIN December 2012

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Zebrafish Model Organism Database Summary, December 2012

Overview

Staff:

Name Position Type FTE for GO
Doug Howe Data Curation Manager
Principle GO contact at ZFIN
0.3
7 Curators Curatorial ~0.1 each; 0.7 in aggregate
4 Technical 3 Developers, 1 DBA Variable; ~0.1 in aggregate


No direct funding from GO.

Annotation Progress

ZFIN GO STATS as of December 2012

Count of Annotations
Annotation Type Annotations Dec. 29 2011 Annotations Dec. 16 2012 Change
  MF BP CC Total MF BP CC Total MF BP CC Total
All Evidence Codes 47938 45412 28219 121569 55622 47465 31593 134680 7684 (16.0%) 2053 (4.5%) 3374 (11.96%) 13111 (10.78%)
Non-IEA/Non-ND 2799 12518 2162 17479 3004 14167 2364 19535 205 (7.3%) 1649 (13.2%) 202 (9.3%) 2056 (11.8%)
IEA 41577 29236 21567 92380 49330 29913 25009 104252 7753 (18.7%) 677 (2.3%) 3442 (16.0%) 11872 (12.9%)
ND 3562 3658 4490 11710 3288 3385 4220 10893 -274 (-7.7%) -273 (-7.5%) -270 (-6.0%) -817 (-7.0%)
Via PAINT 691 1333 523 2547 685 1303 564 2552 -6 (-0.9%) -30 (-2.3%) 41 (7.8%) 5 (0.2%)
Via GOA 1364 7548 4353 13264 1500 3207 3957 8664 136 (10%) -4341 (-57.5%) -396 (-9.1%) -4600 (-34.7%)



Count of Genes with Annotation
Annotation Type Annotations Dec. 29 2011 Annotations Dec. 16 2012 Change
  MF BP CC Total MF BP CC Total MF BP CC Total
All Evidence Codes 13889 13595 12454 15753 15730 14477 13767 18101 1841 (13.3%) 882 (6.5%) 1313 (10.5%) 2348 (14.9%)
Non-IEA/Non-ND 1440 3044 1249 3482 1550 3386 1360 3846 110 (7.6%) 342 (11.2%) 111 (8.9%) 364 (10.5%)
IEA 10056 8913 7607 12024 12124 9854 9184 14660 2068 (20.6%) 941 (10.6%) 1577 (20.7%) 2636 (21.9%)
ND 3562 3658 4490 5797 3288 3385 4220 5566 -274 (-7.7%) -273 (-7.5%) -270 (-6.0%) -231 (-4.0%)
Via PAINT 304 263 269 315 300 272 281 310 -4 (-1.3%) 9 (3.4%) 12 (4.5%) -5 (1.6%)
Via GOA 683 2931 2881 4860 747 966 2586 2779 64 (9.4%) -1965 (-67%) -295 (-10.2%) -2081 (-42.8%)





Methods and strategies for annotation

ZFIN does not have curators dedicated exclusively to GO curation. Our curators work on a prioritized set of the current literature focusing first on new mutants, phenotypes, expression, and Human disease models. Any GO that is found in those papers gets added to ZFIN in the course of curating those papers.

Literature curation:

We curate many data types, including GO, as a routine part of our curation effort focused on the most current publications. The only real exception to that is when we participate in a focused annotation effort spearheaded by members of the GO consortium. During those efforts, Doug curates GO from any papers associated with genes in the set of genes being focused on for the project.


Computational annotation strategies:

We continue to align our gene records with UniProt protein records on an approximately monthly basis. At that time, we also apply current versions of the GO translation tables interpro2go, UniProtKW2go, and ec2go to generate electronic annotations in our system. On a monthly basis we also load GO annotations from GOA, PAINT, and computationally inferred GO annotations provided by the GOC. In some cases the resulting new annotations in ZFIN are electronic in origin, particularly from GOA (sub cellular location for example) and the inferred annotations.


Priorities for annotation:

Our curation priority remains focused on keeping up with the current zebrafish literature generally, focusing first on papers with new mutants, phenotypes, expression, and Human disease models. We consider this to be "paper-centric" curation. Though many of these papers do contain GO annotations, we do not currently prioritize our curation on the basis of their potential GO content. When GOC members ask us to participate in a focused annotation effort we do make an effort to participate as fully as possible in the required "gene-centric" GO curation.

Presentations and Publications

Ontology Development Contributions

Annotation Outreach and User Advocacy Efforts

Other Highlights