Annotation Call July 8, 2014: Difference between revisions
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==Agenda== | ==Agenda== | ||
SGD: Rama, Edith, Stacia <br> | |||
WB: Kimberley<br> | |||
Pombase: Midori<br> | |||
MGI: David, Judy, Li, Mary<br> | |||
Berkeley: Suzi, Chris, Mono, Heiko<br> | |||
EBI: Rachael, Paola, Prudence, Jane<br> | |||
Dicty: Pascale<br> | |||
===New QC checks=== | ===New QC checks=== | ||
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Help page on how to edit/format: | Help page on how to edit/format: | ||
http://wiki.geneontology.org/index.php/Editing_GO_Site | http://wiki.geneontology.org/index.php/Editing_GO_Site | ||
==Discussion== | |||
===Reference Field=== | |||
It is difficult to track references if just the MOD internal reference is used (if there are typos then the reference did not mean anything). Many groups use abstracts to annotate which do not have a PMID or GO_Ref. Rachael will check to see how many of these are there in the annotations. (Post meeting she sent the breakdown of reference #s for various groups) | |||
[[Category:Meetings]] | [[Category:Meetings]] |
Revision as of 13:31, 11 July 2014
Agenda
SGD: Rama, Edith, Stacia
WB: Kimberley
Pombase: Midori
MGI: David, Judy, Li, Mary
Berkeley: Suzi, Chris, Mono, Heiko
EBI: Rachael, Paola, Prudence, Jane
Dicty: Pascale
New QC checks
- Reference field
For each annotation, should there be either a PMID or a GO_REF as reference, with option to have an internal MOD reference in addition? i.e. it shouldn't be allowed to have an internal reference alone. There doesn't appear to be a hard check on this.
E.g. Gramene have thousands of annotations using an RCA evidence code and an internal Gramene reference, e.g.
GR_protein B8A749 OsI_01599 GO:0005739 GR_REF:7047 RCA C Putative uncharacterized protein protein taxon:39946 20090810 GR
The reference is detailed here; http://archive.gramene.org/db/literature/pub_search?ref_id=7047
GR_protein Q947Z9 OSJNBa0050M22.8 GO:0004252 GR_REF:8030 RCA InterPro:IPR000209 F Putative retroelement protein taxon:39947 20090212 GR
http://archive.gramene.org/db/literature/pub_search?ref_id=8030
- RCA evidence
1 year shelf life for Annotations made with RCA. Groups should update the date or remove the annotations after the one year limit.
Source #_of_old_RCA_annotations gramene_oryza 120035 tair 95741 dictyBase 2513 aspgd 1538 pombase 484 GeneDB_Pfalciparum 7003 PAMGO_Mgrisea 21560 ecocyc 171 goa_pdb 141 mgi 105 GeneDB_Lmajor 50 goa_human 35 goa_ref_human 35 fb 19 GeneDB_Tbrucei 14 wb 10 goa_chicken 6 goa_ref_chicken 4 rgd 3 sgd 1
New Website
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URL to edit:
http://www.geneontology.org/user/login
Help page on how to edit/format: http://wiki.geneontology.org/index.php/Editing_GO_Site
Discussion
Reference Field
It is difficult to track references if just the MOD internal reference is used (if there are typos then the reference did not mean anything). Many groups use abstracts to annotate which do not have a PMID or GO_Ref. Rachael will check to see how many of these are there in the annotations. (Post meeting she sent the breakdown of reference #s for various groups)