WBConfCall 2021.02.04-Agenda and Minutes

Help Desk

• ePCR "position" function broken - https://github.com/WormBase/website/issues/8081

There is already an ongoing discussion

• Typo in gene WBGene00019747 name - https://github.com/WormBase/website/issues/8080

Already taken care of

• New JBrowse polyA Atlas tracks - https://github.com/WormBase/website/issues/8070

There is already an ongoing discussion

• Paper upload directly from authors - https://github.com/WormBase/website/issues/8068

Kimberly is looking into it. We need to decide if that specific patent can be included. We don't have a paper type for patents and they are not peer reviewed (at least the experiments are not). It can be added as a meeting abstract.

• Paper anatomy function links - https://github.com/WormBase/website/issues/8065

Raymond is thinking about an easy to display solution. Maybe adding more info to the reference page with some sort of concise description of anatomy function. Another option would be to have a separate widget for anatomy function.

• Miller CeNGEN data links brainstorm - https://github.com/WormBase/website/issues/8075

Raymond, Daniela, Eduardo and Wen are planning to start working on this in late February

Agenda and Minutes

GAF files

• Are GAF files C. elegans specific? We have 39 expression annotations to other species (remanei, brenneri, brugia). ok to leave them out? If not, make sure that those Expression_objects don't make it to the GAF.
• Chris has written up a Wiki page to point to GAF specifications as well as describe the format details and suggest a new header for each GAF in our FTP "ONTOLOGY" directory
  • To resolve GitHub ticket: https://github.com/WormBase/website/issues/7900
  • Current "ONTOLOGY" directory on FTP: ftp://ftp.wormbase.org/pub/wormbase/releases/current-production-release/ONTOLOGY/
  • New Wiki page: https://wiki.wormbase.org/index.php/WormBase_gene_association_file
  • We would like to push ahead with modifying the headers of these association files

Do we need to remove annotations to other species? For GO, we have separate files, but till now we had C. elegans only GAF files for all other data types. Is it worth to create new species specific GAF anatomy files if we have only a handful of annotations? New GO GAF specifications have taxonID, so a single file with multiple species would be ok.

The FTP folder contains duplicate species specific files in the overall folder and in the species specific folders. Kevin is proposing to remove species specific files from the overall folder and leave them in species folders only. Hinxton is also thinking about adding empty files for species without annotations. We'll leave symlinks in the main folder for now and we'll completely remove the redundant files for WS281.

AOB: Dates for WS281 build?

Proposed quarterly release cycle: April-July-October-January. We could release the last day of the months in the cycle.