FlyBase to supply file of PMID, genes, alleles

[ValWood]

File of PMID, genes, alleles
PomBase has a JSON file that we export each night.
Make the same format with minimal info about genes and alleles.

@kimrutherford will supply a snippet of our JSON output

[ValWood]

Notes:

• Will probably proceed by loading all alleles as type “other” (alleles are already described in FB)
  • “Name” and “description are available
• Expression part not required (creation, editing or display)

[kimrutherford]

I've made a separate issue about the file format: #1779

As a first step, I've add a new flag to the canto_add.pl script: --sessions-from-json. So far the code will:

• parse a JSON file
• lookup the PubMed ID(s) using the PubMed web service
• store the publication details (title, abstract, authors)
• create an empty session for the pub
• add genes to the session using their systematic ID / uniquename

It can only parse files that look like this:

{
   "PMID:2120045": {
       "genes": ["FBgn0004107", "FBgn0016131"]
    },
    "PMID:1234567": {
       "genes": [...]
    }
}

I haven't done any work on loading alleles or genotypes. I wait until after the next Skype call since there are still many things to decide.

The changes are on a branch for now: https://github.com/pombase/canto/tree/fly-canto-dev

[kimrutherford]

PMID, genes, alleles

We can support genes, alleles and aberrations now. Is there anything else from FlyBase that needs be loaded into Canto?

[gm119]

We can support genes, alleles and aberrations now. Is there anything else from FlyBase that needs be loaded into Canto?

well thats exciting !

I will double check with @vmt25 if we need any other type of object (I don't think we do,but will be good to double check !)

[vmt25]

Yes, that is all we need to go forward

[kimrutherford]

I'll close this issue because I think we're done. If changes or additions are needed we can open new issues.