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MGI gene product associations

Harold Drabkin hjd at informatics.jax.org
Wed Jan 2 06:45:50 PST 2002


The duplicate GO terms are there because they originate from 
different reference sources which may have different levels of 
confidence:

This is what you see on the marker detail page at MGI

Type: Gene
Symbol: Blk
Name: B lymphoid kinase
Chromosome: 14
cM Position: 28.0
MGI Accession ID: MGI:88169
------------------------------------------------------------------------
Additional Information:

*	Mammalian Homology
*	Marker Mapping Data (5)
*	Phenotype (MLC)
*	RFLP/PCR Polymorphism (2)
*	GXD Index Data (1)
*	Molecular Probes and Segments (22)
*	References(22)
------------------------------------------------------------------------
Gene Classifications: (You can browse the Gene Ontology (GO) Classifications)

Category	Classification Term	Evidence	Reference
Biological Process	intracellular signaling cascade	electronic 
annotation	J:72247
Biological Process	protein amino acid phosphorylation 
	electronic annotation	J:72247
Molecular Function	ATP binding	electronic annotation	J:60000
Molecular Function	protein tyrosine kinase	electronic annotation	J:60000
Molecular Function	protein tyrosine kinase	electronic annotation	J:72245
Molecular Function	ATP binding	electronic annotation	J:72247
Molecular Function	protein kinase	electronic annotation	J:72247
Molecular Function	protein tyrosine kinase	electronic annotation	J:72247
------------------------------------------------------------------------

Both J:72247 and J:60000 are electronic annotations;

The J:72247 refers to interpro domain to GO assignments; therefore 
these are predicted functions based solely on the putative domain 
structures contained in the proteins.

J:60000 refers to Swissprot to GO assignments; The SwissProt Keywords 
are assigned to the proteins based on human curration at SwissProt.

At present, Blk has no hand currated literature based assignments by 
MGD currators (we need to catch up).
If two different papers can be used to assign the same GO term, there 
may be two references, or if two papers can be used to assign the GO 
terms using different evidence, then there would be two references.

The column next to the GO terms is the MGI accession number for the 
reference that supports that code. Because we use several MGI 
specific references (like the J:72247 and J:60000), we don't put 
PMIDs in this field (there would be no PMID for the two references 
just cited).

The field order for the gene_association files is:


DB	DB_Object_ID	DB_Object_Symbol	[NOT]	GOid 
	DB:Reference(|DB:Reference)	Evidence	With 
	Aspect	DB_Object_Name(|Name)	DB_Object_Synonym(|Synonym) 
	DB_Object_Type	taxon(|taxon)	Date

This is doucmented in http://www.geneontology.org/GO.annotation.html#file


>
>i would appreciate some help with the mgi gene association file, because
>when looking for terms i found some "redundancy" for some gene products,
>i.e. for Blk(MGI:88169) with GO:0004713,GO:0005524. and i may miss some
>data, but what is the column next to go terms referring to?.
>Thanks and happy new year!!,
>					JC.
>
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-- 
Harold J. Drabkin, Ph.D.
Scientific Curator
Mouse Genome Informatics
The Jackson Laboratory
600 Main Street
Bar Harbor, ME 04609
207-288-6650 (voice)
207-288-6131 (fax)
hjd at informatics.jax.org
http://www.informatics.jax.org/


--
This message is from the GOFriends moderated mailing list.  A list of public
announcements and discussion of the Gene Ontology (GO) project.
Problems with the list?           E-mail: owner-gofriends at geneontology.org
Subscribing   send   "subscribe"   to   gofriends-request at geneontology.org
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