Agenda

WormBook chapters

Discussion on making available on WormBase the chapters we wrote for the WormBook.

There are 11 chapters so far -anatomy, genomic data, gene expression, phenotype, GO, Human disease, intermine, nomenclature, Process&Pathway, website, sequence homology.

They could serve as a User guide and are up-to-date. Would be good to have them published. Better to have them on WormBook? Status?

Orthology
- Panther data in WormMine
  - Orthology data in WormMine seems *not* to come from WormBase / AceDB
  - Need clarification on (a) what version of Panther was loaded, and (b) how it was loaded
- Desired update frequency
  - Proposal is to update orthologs once per year. Are we happy with that?
  - Should we adjust our update cycle to accommodate this?
Use case
Disease-phenotype
- We will need to produce a data file that has all of the disease data since disease data is not available from WormMine

Proposal : put chapters up on site now, at the same time trying to get them into WormBook (before it closes down)
Questions:
- How to deal with updates?
  - Micropublications a possible model for citable paragraph updates
- How should we manage the website versions of the articles?
  - Wiki? Perhaps too difficult to maintain consistent format
  - Readthedocs? Content Management System? Web-team to think about this and send round some ideas
- Lots of other discussion around this topic

Orthology
- Established that Panther data in WormMine came directly from Pather (via InterMine loader), rather than AceDB
- TH to supply date/version of Panther that was loaded
Use-case
- In basic search, genes will link back to MODs
- Group now working on more refined use-cases beyond basic search
Disease
- Disease data missing from Mines, so needs to be loaded into AGR via some other means
- Disease Association GAF files? These do not contain the textual curator-written descriptions
- Discussion needed with working group on data exchange mechanisms
Wednesday curator calls
- Curator calls will now include an update from each working group
- Open to suggestions for next topics