Freebase: Discussion about patrick

Protein: Proteins & Genes - Mouse & Human

2009-11-05T09:16:17.0006Z

Homologene is supposed to show cross-species gene connections, I think. Here's the entry for the human SRI gene:

http://www.ncbi.nlm.nih.gov/sites/entrez?Db=homologene&Cmd=Retrieve&list_uids=37736&log$=seqview_homolog

At the general level, the proteins produced by these genes have the same name:

Human gene http://www.ncbi.nlm.nih.gov/sites/entrez?Db=gene&Cmd=ShowDetailView&TermToSearch=6717#geneGeneral%20protein%20info Mouse gene http://www.ncbi.nlm.nih.gov/sites/entrez?Db=gene&Cmd=ShowDetailView&TermToSearch=109552#geneGeneral%20protein%20info

but it looks like at the detailed level, even the proteins are tracked separately by species. This link has a cluster of 18 "different" proteins across 11 different species.

http://www.uniprot.org/uniref/?query=member%3aP30626+identity:0.9

I'm not sure what level this stuff needs to be modeled at. Also, the more I look at the various databases that are available, the more I wonder what value Freebase would add to the ecosystem. What gaps need to be filled?

Protein: Proteins & Genes - Mouse & Human

2009-11-05T03:28:30.0013Z

Sounds good to me. (I always prefer starting with the simpler scheme and then building up gradually to the more complex.)

I don't know of any data sources that map between mouse and human (except for Wikipedia!) - I was hoping that the linkage would fall out of the data.

Protein: Proteins & Genes - Mouse & Human

2009-11-04T16:47:45.0006Z

Entrez Gene sounds good. Looks like the NCBI ID that I placed with each gene is the same as Entrez Gene (please correct me if I'm wrong). Can you point me to the online data source you'd like to use which maps between mouse and human?

As for a schema, in the big picture I'd like to eventually include genomic locations of exons, mRNA transcripts, and then their corresponding protein products. But that's longer term. For now we might want to simply create a CVT which links protein entry to gene entry and is annotated as an identity based on Entrez Gene ID. So the CVT would have at one end the gene and at the other end the protein. We could either define a general CVT for linking gene to protein and then a more specific CVT which is an Entrez Gene ID link. Or we could just have a CVT for gene to protein and then a flag within that CVT which explains the link (e.g. some text, like "Entrez Gene ID link").

Other ideas?

Dan

Protein: Proteins & Genes - Mouse & Human

2009-11-04T01:22:22.0013Z

The Entrez Gene database seemed like a good starting point.

If you want to suggest a schema, Dan, that would be great.

Protein: Proteins & Genes - Mouse & Human

2009-11-04T00:53:29.0006Z

Might be best to define a compound value type for this linkage so it is clear how the correspondence between gene and protein was arrived at. I have some experience with this so I'm happy to help with the schema.

What information are you thinking of using to relate protein to gene?

Dan

Protein: Proteins & Genes - Mouse & Human

2009-11-03T23:43:40.0013Z

Why don't we start with adding a property to Gene of "Protein encoded" and the corresponding (reciprocal) property to Protein of "Encoded by"? (I assume that each Gene encodes one Protein but each Protein could be encoded by multiple Genes, e.g. mouse and human.)

I do like the idea of an Orthology type - can we work on that later?