Improve pipeline documentation

[pgaudet]

Clarifications requested from Montreal GOC meeting:

• Document the fact that gp2protein files are still being generated for some species that do not provide enough information to make GPI files
  => removed all references to GP2protein files - this is not relevant anymore
• Document internal pipeline (although I was wondering how that differed from http:https://wiki.geneontology.org/index.php/Release_Pipeline? More 'internal' details requested?
• Need guidelines for how to reference GO for dbs that are (1) in sync with GO, (2) behind GO, (3) ahead of GO
• Document how to access organism specific annotation files from GO entire organism set (Seth: several ways, Zenodo with checksum referential file to organism, from GO website, organism file will have doi in metadata)
• Plan for pointing users to a consistent release version, no matter where they get their annotations (MODs vs GO) --- MOD file may be weekly (with own DOI) while GO is monthly (with different DOI)

[cmungall]

Document the fact that gp2protein files are still being generated for some species that do not provide enough information to make GPI files

I don't know what this is, but I don't believe there is anything that to be done here, gp2protein is being replaced by GPI

Document internal pipeline (although I was wondering how that differed from http:https://wiki.geneontology.org/index.php/Release_Pipeline? More 'internal' details requested?

Without more specific details, I do not know what remains to be done here

Need guidelines for how to reference GO for dbs that are (1) in sync with GO, (2) behind GO, (3) ahead of GO

?

Document how to access organism specific annotation files from GO entire organism set (Seth: several ways, Zenodo with checksum referential file to organism, from GO website, organism file will have doi in metadata)
Plan for pointing users to a consistent release version, no matter where they get their annotations (MODs vs GO) --- MOD file may be weekly (with own DOI) while GO is monthly (with different DOI)

I believe our position can be stated as:

• We recommend MODs provide a link to the GO central downloads page for their community
• We realize that some MODs may prefer to offer their own downloads (e.g. ZFIN has a continual release process). While we do not recommend this, ultimately this is a decision of the MOD. For the Alliance subset, there may be further discussions.

I don't think there is any further specific actions here - reopen if I have misinterpreted anything