WBConfCall 2022.07.07-Agenda and Minutes
Contents
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
