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.
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