Category:Data dissemination group

From GO Public

Contents 1 About this group 2 Why are we doing this? 3 Overview of current status 4 Integration guidelines

[edit] 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.

[edit] 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.

[edit] 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

[edit] 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