Data Dissemination

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About this group

To provide help to groups who are incorporating external annotations into their Gene Association files. These pages will outline a suggested set of filters for incorporating data from other model organism databases and the status of each groups progress.

Why are we doing this?

Currently we filter FTP files by taxon ID so that only the MOD for that particular species can publish data. However many groups do cross-species annotations that we need to get into the dataset of the relevant MODs gene association file/database.

Overview of current status

Here contact information is taken from gene_association.[dbname]_conf file. Please change if incorrect.

Status of shared data between MODs
Contact Implemented? Integrates data from Update Frequency
cgd candida-curator@genome.stanford.edu n none  ?
ddb dictybase@northwestern.edu  ?  ?  ?
fb ma11@gen.cam.ac.uk,s.tweedie@gen.cam.ac.uk y GOA  ?
GeneDB_Lmajor mb4@sanger.ac.uk,maa@sanger.ac.uk n none occasional/irregular
GeneDB_Pfalciparum mb4@sanger.ac.uk,maa@sanger.ac.uk n none occasional/irregular
GeneDB_Spombe val@sanger.ac.uk,maa@sanger.ac.uk y GOA (non-redundantly with manual annotations) bimonthly
GeneDB_Tbrucei mb4@sanger.ac.uk,maa@sanger.ac.uk n none occasional/irregular
GeneDB_tsetse mb4@sanger.ac.uk,maa@sanger.ac.uk n none occasional/irregular
goa_arabidopsis dbarrell@ebi.ac.uk  ? tair intact monthly
goa_chicken dbarrell@ebi.ac.uk  ? mgi intact monthly
goa_cow dbarrell@ebi.ac.uk  ? mgi intact monthly
goa_human dbarrell@ebi.ac.uk  ? mgi gdb reactome intact lifedb monthly
goa_mouse dbarrell@ebi.ac.uk  ? mgi rgd intact monthly
goa_pdb dbarrell@ebi.ac.uk  ? * monthly
goa_rat dbarrell@ebi.ac.uk  ? rgd mgi monthly
goa_uniprot dbarrell@ebi.ac.uk  ? mgi sgd fb spombe rgd tair gdb reactome intact mgi_nonmouse tigr gramene wb lifedb ddb monthly
goa_zebrafish dbarrell@ebi.ac.uk  ? zfin monthly
gramene_oryza pj37@cornell.edu  ?  ?  ?
mgi hjd@informatics.jax.org Y GOA weekly
pseudocap pseudocap-mail@sfu.ca  ?  ?
rgd shimoyma@mcw.edu,simont@mcw.edu,VPetri@hmgc.mcw.edu Y GOA  ?
sgd go-curator@genome.stanford.edu Y GOA (IEA and non-IEA)  ?
tair curator@arabidopsis.org,tberardi@acoma.stanford.edu y TIGR, GOA will be weekly
tigr_Aphagocytophilum mlgwinn@tigr.org partial screened GOA for nonIEA,nonISS, nonND; found none irregular
tigr_Banthracis mlgwinn@tigr.org partial screened GOA for nonIEA,nonISS, nonND; found none irregular
tigr_Cburnetii mlgwinn@tigr.org partial screened GOA for nonIEA,nonISS, nonND; found none irregular
tigr_Chydrogenoformans mlgwinn@tigr.org partial screened GOA for nonIEA,nonISS, nonND; found none irregular
tigr_Cjejuni mlgwinn@tigr.org partial screened GOA for nonIEA,nonISS, nonND; found none irregular
tigr_Dethenogenes mlgwinn@tigr.org partial screened GOA for nonIEA,nonISS, nonND; found none irregular
tigr_Echaffeensis mlgwinn@tigr.org partial screened GOA for nonIEA,nonISS, nonND; found none irregular
tigr_gene_index lhannick@tigr.org  ?  ?  ?
tigr_Gsulfurreducens mlgwinn@tigr.org partial screened GOA for nonIEA,nonISS, nonND; found none irregular
tigr_Lmonocytogenes mlgwinn@tigr.org partial screened GOA for nonIEA,nonISS, nonND; found none irregular
tigr_Mcapsulatus mlgwinn@tigr.org partial screened GOA for nonIEA,nonISS, nonND; found none irregular
tigr_Nsennetsu mlgwinn@tigr.org partial screened GOA for nonIEA,nonISS, nonND; found none irregular
tigr_Psyringae mlgwinn@tigr.org partial screened GOA for nonIEA,nonISS, nonND; found none irregular
tigr_Soneidensis mlgwinn@tigr.org partial screened GOA for nonIEA,nonISS, nonND; found none irregular
tigr_Spomeroyi mlgwinn@tigr.org partial screened GOA for nonIEA,nonISS, nonND; found none irregular
tigr_Tbrucei_chr2 lhannick@tigr.org  ?  ?  ?
tigr_Vcholerae mlgwinn@tigr.org partial screened GOA for nonIEA,nonISS, nonND; found none irregular
wb ranjana@its.caltech.edu,emsch@its.caltech.edu,vanauken@caltech.edu Y GOA  ?
zfin dhowe@cs.uoregon.edu y GOA weekly

Integration guidelines

For the GOA project we filter GA files from MODs for the following:

  • Ignore if we cannot map MOD ID to UniProt accession
  • Ignore if no PUBMED ID for annotation or we cannot map an internal publication identifier to a PUBMED ID.
  • Ignore unless attribution column refers to the MOD who submitted the file. i.e. gene_association.mgi attribution column must equal 'MGI'. This is important to remove cyclic redundancy.
  • Ignore IEA
  • Ignore ISS
  • Ignore ND