ZFIN December 2012: Difference between revisions

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|+'''Count of Annotations'''
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! style="background:lightgray; width:100px;" | Evidence Type
! colspan="4" style="background:lightgray;" | Annotations Dec. 29 2011
! colspan="4" style="background:lightgray;" | Annotations Dec. 16 2012
! colspan="4" style="background:lightgray;" | Change
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! style="background:lightgray; width:60px;" |MF
! style="background:lightgray; width:60px;" |BP
! style="background:lightgray; width:60px;" |CC
! style="background:lightgray; width:60px;" |Total
! style="background:lightgray; width:60px;" |MF
! style="background:lightgray; width:60px;" |BP
! style="background:lightgray; width:60px;" |CC
! style="background:lightgray; width:60px;" |Total
! style="background:lightgray; width:80px;" |MF
! style="background:lightgray; width:80px;" |BP
! style="background:lightgray; width:80px;" |CC
! style="background:lightgray; width:60px;" |Total
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|style="border-bottom:1px solid lightgray;"  valign="top" |All Evidence Codes
|style="border-bottom:1px solid lightgray;"  valign="top" |47938
|style="border-bottom:1px solid lightgray;"  valign="top" |45412
|style="border-bottom:1px solid lightgray;"  valign="top" |28219
|style="border-bottom:1px solid lightgray;"  valign="top" |121569
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|style="border-bottom:1px solid lightgray;"  valign="top" |Non-IEA/Non-ND
|style="border-bottom:1px solid lightgray;"  valign="top" |2799
|style="border-bottom:1px solid lightgray;"  valign="top" |12518
|style="border-bottom:1px solid lightgray;"  valign="top" |2162
|style="border-bottom:1px solid lightgray;"  valign="top" |17479
|style="border-bottom:1px solid lightgray;"  valign="top" |3004
|style="border-bottom:1px solid lightgray;"  valign="top" |14167
|style="border-bottom:1px solid lightgray;"  valign="top" |2364
|style="border-bottom:1px solid lightgray;"  valign="top" |19535
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|style="border-bottom:1px solid lightgray;"  valign="top" |IEA
|style="border-bottom:1px solid lightgray;"  valign="top" |41577
|style="border-bottom:1px solid lightgray;"  valign="top" |29236
|style="border-bottom:1px solid lightgray;"  valign="top" |21567
|style="border-bottom:1px solid lightgray;"  valign="top" |92380
|style="border-bottom:1px solid lightgray;"  valign="top" |49330
|style="border-bottom:1px solid lightgray;"  valign="top" |29913
|style="border-bottom:1px solid lightgray;"  valign="top" |25009
|style="border-bottom:1px solid lightgray;"  valign="top" |104252
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|style="border-bottom:1px solid lightgray;"  valign="top" |ND
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|style="border-bottom:1px solid lightgray;"  valign="top" |Via PAINT
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|style="border-bottom:1px solid lightgray;"  valign="top" |Via GOA
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{|  cellspacing="0" cellpadding="4" align="left"
|+'''Count of Genes Annotated'''
! style="background:lightgray; width:100px;" | Evidence Type
! style="background:lightgray; width:100px;" | Evidence Type
! colspan="3" style="background:lightgray;" | Annotations Dec. 29 2011
! colspan="3" style="background:lightgray;" | Annotations Dec. 29 2011

Revision as of 14:32, 20 December 2012

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
Evidence 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
Non-IEA/Non-ND 2799 12518 2162 17479 3004 14167 2364 19535
IEA 41577 29236 21567 92380 49330 29913 25009 104252
ND
Via PAINT
Via GOA



Count of Genes Annotated
Evidence Type Annotations Dec. 29 2011 Annotations Dec. 16 2012 Change
  MF BP CC MF BP CC MF BP CC
Non-IEA/Non-ND
IEA
ND



Count of Genes Annotated
Evidence Type Annotations Dec. 29 2011 Annotations Dec. 16 2012 Change
  MF BP CC MF BP CC MF BP CC
Non-IEA/Non-ND
IEA
ND




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: