search

geneontology / go-site

A collection of metadata, tools, and files associated with the Gene Ontology public web presence.
http://geneontology.org
BSD 3-Clause "New" or "Revised" License
46 stars 89 forks source link

Request for report to help populate group-contacts.csv #807

Closed ValWood closed 6 years ago

ValWood commented 6 years ago

Could we get a list of every group in the "assigned by" field that we can use to populate

https://github.com/geneontology/go-site/blob/master/metadata/group-contacts.csv

some are missing currently (will be useful to invite people to proposed GO workshops etc)

kltm commented 6 years ago 
$ zgrep -v '^!'  *.gaf.gz | cut -f 15 | sort | uniq -c | sort -n > /tmp/val-report.txt
$ cat /tmp/val-report.txt
      2 FLYBASE
      3 AGBASE
      3 GO_CENTRAL
      6 Eurofung
     47 GO_Noctua
     52 GDB
     71 Roslin_Institute
    126 PAMGO_VMD
    140 SynGO-UCL
    162 SYSCILIA_CCNET
    202 MENGO
    250 PAMGO_GAT
    271 COLLECTF
    286 WormBase
    309 ASAP
    330 Alzheimers_University_of_Toronto
    453 LIFEdb
    454 YuBioLab
    624 DFLAT
    795 PAMGO
    963 ComplexPortal
   1150 GONUTS
   1456 SGN
   2278 EcoliWiki
   3275 SynGO
   4210 PseudoCAP
   4319 ARUK-UCL
   4698 NTNU_SB
   4837 HGNC
   5148 CACAO
   5320 CollecTF
   7100 ParkinsonsUK-UCL
   7555 CAFA
   8587 PINC
  11007 EnsemblProtists
  13630 EcoCyc
  13832 MTBBASE
  16316 HPA
  18262 dictyBase
  37707 PomBase
  40320 WB
  43517 BHF-UCL
  44290 GeneDB
  50029 GR
  53587 JCVI
  54873 UniProtKB
  55056 PAMGO_MGG
  55698 SGD
  74152 FlyBase
 104708 AgBase
 104852 IntAct
 111891 TAIR
 154070 ZFIN
 157008 TIGR
 202891 Reactome
 221642 RGD
 235909 MGI
 275188 EnsemblPlants
 325395 EnsemblMetazoa
 349826 CGD
 762365 AspGD
1432616 EnsemblFungi
3426234 GO_Central
5157560 Ensembl
10764686 RNAcentral
22626969 GOC
205301636 InterPro
296778494 UniProt
ValWood commented 6 years ago

Thanks Seth!

pgaudet commented 6 years ago

@kltm (or anyone else) Do you know why we still have 'redundant' sources:

How can we track where these are coming from? @tonysawfordebi I dont suppose these are not coming from UniProt?

Thanks, Pascale

tonysawfordebi commented 6 years ago

No, they're not coming from us.

pgaudet commented 6 years ago

This is moved to to #2071

kltm commented 6 years ago

@pgaudet If it's in a different tracker, you have to mark it differently: geneontology/go-annotation#2071