WBConfCall 2024.04.04-Agenda and Minutes

Paul and Wen talked to NCBI people about annotating ontology terms for high-throughput datasets. The best option will be NCBI sponsoring the Alliance curators to work on the past datasets and create templates for authors to submit future datasets.
MicroPub successfully gained attention from new researchers via its review session.
- G3 is interested in software publication. MicroPub can publish software papers as well. MicroPub is working with the Caltech library on the requirements for software to be published, like GitHub repository, etc. Many WormBase software like SimpleMine and SoBA Graph can be published.
Karen and Chris joined a Teaching Curation workshop to teach undergraduates about curation. Chris is currently processing the student submissions to remove redundancies.

Eyleen ORourke wants WormBase to take over http://www.wormseq.org/
Paul S: We have no money to take over community software. We may absorb good ideas from them to develop our software.
Wen: There are many softwares about scRNASeq in the community. The Alliance is committed to collaboration with CZI because it is a professional team (better than student software) and we do not need to pay for the developers in CZI.

Hinxton will start the build on 15th April. Caltech curators need to submit data on Tues. April 9.
No schema change

Which release is this targeted for?
- Presumably WS294 since WS293 about to start
Do we want to rename files on FTP site? No.
- e.g. c_elegans.PRJNA13758.WS292.omim_xrefs.txt
Do we need to change the Database name in AceDB? No
- IDs are stored in AceDB without the prefix, but with the Database name OMIM
- Changing this significantly increases the complexity of switching from OMIM to MIM
- Does this database name get prepended to the ID as a prefix in the web code? No.
GitHub ticket related to OMIM and DO changes: https://github.com/WormBase/website/issues/9444

Ticket #9471: User trying to download the results from this search result as a list of genes: https://wormbase.org/search/gene/Stress%20Response?species=c_elegans
- Current message: "Too many results to download. Please use our FTP site." Should we point to a specific file on the download page? There are so many files on the FTP/HTTPs pages.
- Another issue related to this search. When the results are downloadable, all five options (json, csv, HTML, XML, YML) point to the HTML results when users use Chrome. Example: https://wormbase.org/search/gene/Calmodulin/all?species=c_elegans&format=text%2Fcsv
- Wen and Paulo is working on this.

Paul S submitted the proposal to NIH and Worm Board. Will contact PIs and have three town hall meetings.
Among the 1500 worm labs, 500 did not publish in the past 5 years. The rest published 1 - 50 papers.
Paul and Raymond will explore the possibility of a WormBase Foundation for users to make donations. Whenever we help to solve complicated bioinformatics problems for users (like writing a customized script or using TableMaker to create tables for specific requests) we may suggest the users make donations because our efforts save them weeks or months of work.

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