WBConfCall 2022.07.07-Agenda and Minutes

Agenda

• Quick demo of JBrowse 2 features we'll be beta testing in WS286. Scain (talk) 16:46, 6 July 2022 (UTC)
• WormBase ParaSite's new release 17 with genome updates, browsable AlphaFold models and more is out now! Please share, share, share! (Tweet)

Global Core Biodata Resource application https://docs.google.com/document/d/1juJ4mm1evay32lNt3OOsbKL36RY4_3cW/edit#heading=h.gjdgxs

2b. Usage in research as measured through biodata resource citation in the scientific literature

Resource-specific accession numbers or unique identifiers mentioned in PubMed/EuropePMC/Google Scholar (citation of specific entities from the biodata resource)

2d. Connections to other data resources

Please include a url link to pre-existing documentation on this topic, if relevant.

3e i. Data Curation

Does the resource provide documentation of the data curation process/deposition workflow? Please describe, with a url link to public documentation, where relevant.

3e ii. Provenance and Evidence Does the resource link to the primary scientific literature for provenance of/evidence for data statements or biological context?

Please provide examples, with a url link to public documentation, where relevant.

Help desk issues

• Thanks to people for self-assigning themselves, most/all issues helped or under progress
• Next help-desk officer is Kimberly (from July 11th)

Minutes

JBrowse 2 demo

• JBrowse 2 instance added on gene pages (WS284), fully functional browser
• zoomin, Zoom out features
• Can add other tracks that are available
• Can add own personal data as tracks
• Dotplot tool added, available to access from the Tools drop down menu, right now it's a beta version, will go in for WS286

Global Core Biodata Resource application

• Questions discussed in this meeting:

2b. Usage in research as measured through biodata resource citation in the scientific literature

Resource-specific accession numbers or unique identifiers mentioned in PubMed/EuropePMC/Google Scholar (citation of specific entities from the biodata resource)

2d. Connections to other data resources

Please include a url link to pre-existing documentation on this topic, if relevant.

3e i. Data Curation

Does the resource provide documentation of the data curation process/deposition workflow? Please describe, with a url link to public documentation, where relevant.

3e ii. Provenance and Evidence Does the resource link to the primary scientific literature for provenance of/evidence for data statements or biological context?

Please provide examples, with a url link to public documentation, where relevant.

• Suggestion was to write a high level summary for these questions and perhaps put it in the wiki and point to this in the application
• WB Parasite has already put in their part, so WB needs to put in relevant parts, please mark as WB
• Deadline is late August ...?

Reference Genome Metadata File Specification

• Adam has been working on this as a side project with David Molik (USDA)
• https://github.com/FFRGS/FFRGS-Specification/
• Added the ability to Jbrowse2 to have metadata file for the reference sequence
  • Is in the current release of JBrowse
  • The user is able to see the metadata on the track by going to "About Track" for the reference sequence
• The specification is to make it so that the files are consistent between projects
• This is another way to increase FAIRness / TRUSTworthiness across resources and requires minimal effort
  • We have already gained some interest from other genome repositories including the i5k.
  • Hoping to gain some interest from within the Alliance / WormBase