Difference between revisions of "WBConfCall 2015.10.15-Agenda and Minutes"
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* We need to update the release schedule nb it's over Xmas and SAB | * We need to update the release schedule nb it's over Xmas and SAB | ||
− | ==Pristionchus gene names== | + | === Pristionchus gene names === |
*The issue is: Pristionchus gene names/assembly in the research community drifting away from those in WormBase | *The issue is: Pristionchus gene names/assembly in the research community drifting away from those in WormBase | ||
** Papers being published with Wormbase-style gene names that have not been approved by WormBase (e.g. WBPaper00048552) | ** Papers being published with Wormbase-style gene names that have not been approved by WormBase (e.g. WBPaper00048552) | ||
Line 10: | Line 10: | ||
** Communication / Data flow between pristionchus.org and WormBase could be better. Conversations started. | ** Communication / Data flow between pristionchus.org and WormBase could be better. Conversations started. | ||
*Is there a similar problem with other non-elegans/parasitic species? | *Is there a similar problem with other non-elegans/parasitic species? | ||
+ | |||
+ | ==Minutes== | ||
+ | |||
+ | === WS252 === | ||
+ | * WS251 release scheduled 1st January | ||
+ | * WS252 freeze date start of December | ||
+ | * Build will finish at start of January | ||
+ | * Live on WormBase start of March | ||
+ | * SAB would fall in middle of staging/webdev part of cycle | ||
+ | * Upload after Thanksgiving holiday | ||
+ | |||
+ | === Pristionchus gene names === | ||
+ | * Ralf Sommer has been emailed (awaiting response) | ||
+ | * WormBase has two ways of handling a genome: ownership or importing the data from someone else | ||
+ | * Pristionchus is currently a mixture of these | ||
+ | * Proposed that we should take one direction or the other | ||
+ | * Current gene models in WormBase are >5 years old | ||
+ | * Data in GenBank is 7 years old | ||
+ | * Also a third copy of genome of Pristionchus.org | ||
+ | |||
+ | === Help tickets pending === | ||
+ | <nowiki>#4239</nowiki> | ||
+ | * Web ream to look at | ||
+ | |||
+ | <nowiki>#4259</nowiki> | ||
+ | * Pointing users to the FTP site | ||
+ | * Downloads are not archived | ||
+ | * Will be resolved in WormMine | ||
+ | * Discussion about user documentation: | ||
+ | ** Should there be a widget specific user guide? | ||
+ | ** Can link from widdget to a static page or wiki page. | ||
+ | ** Not sure if all documentation should be rewritten at the present time. | ||
+ | |||
+ | <nowiki>#4264</nowiki> | ||
+ | WormBook nomenclature chapter | ||
+ | * Rather than including species prefixes in chapter, it would be ideal to point to a page on WormBase | ||
+ | * Cannot generate a URL to a specific widget in website | ||
+ | * Discussion about website being a good place to store documentation: | ||
+ | ** MediaWiki is easier to embed into websites | ||
+ | ** Wikis do not have stable URLs as the document name can be changed | ||
+ | ** Wikis (or similar) are generally the easiest for people to edit | ||
+ | ** Can protect document names to keep URL stable | ||
+ | ** Opportunity to address problem of documentation distribution | ||
+ | ** Todd to compile a shortlist of possible solutions and send around the group for everyone to look at | ||
+ | * Current list should go on WormBase wiki and linked to from current WormBase page | ||
+ | * Deprecated nomenclature page already presrnt on the wiki, this can be updated with the latest text | ||
+ | |||
+ | <nowiki>#4278</nowiki> | ||
+ | Links with variation | ||
+ | * Web team will look at next week |
Revision as of 08:28, 16 October 2015
Contents
Agenda
WS252
- We need to update the release schedule nb it's over Xmas and SAB
Pristionchus gene names
- The issue is: Pristionchus gene names/assembly in the research community drifting away from those in WormBase
- Papers being published with Wormbase-style gene names that have not been approved by WormBase (e.g. WBPaper00048552)
- These are linked to anonymous annotations on pristionchus.org that cannot be cross-referenced back to WormBase
- Communication / Data flow between pristionchus.org and WormBase could be better. Conversations started.
- Is there a similar problem with other non-elegans/parasitic species?
Minutes
WS252
- WS251 release scheduled 1st January
- WS252 freeze date start of December
- Build will finish at start of January
- Live on WormBase start of March
- SAB would fall in middle of staging/webdev part of cycle
- Upload after Thanksgiving holiday
Pristionchus gene names
- Ralf Sommer has been emailed (awaiting response)
- WormBase has two ways of handling a genome: ownership or importing the data from someone else
- Pristionchus is currently a mixture of these
- Proposed that we should take one direction or the other
- Current gene models in WormBase are >5 years old
- Data in GenBank is 7 years old
- Also a third copy of genome of Pristionchus.org
Help tickets pending
#4239
- Web ream to look at
#4259
- Pointing users to the FTP site
- Downloads are not archived
- Will be resolved in WormMine
- Discussion about user documentation:
- Should there be a widget specific user guide?
- Can link from widdget to a static page or wiki page.
- Not sure if all documentation should be rewritten at the present time.
#4264 WormBook nomenclature chapter
- Rather than including species prefixes in chapter, it would be ideal to point to a page on WormBase
- Cannot generate a URL to a specific widget in website
- Discussion about website being a good place to store documentation:
- MediaWiki is easier to embed into websites
- Wikis do not have stable URLs as the document name can be changed
- Wikis (or similar) are generally the easiest for people to edit
- Can protect document names to keep URL stable
- Opportunity to address problem of documentation distribution
- Todd to compile a shortlist of possible solutions and send around the group for everyone to look at
- Current list should go on WormBase wiki and linked to from current WormBase page
- Deprecated nomenclature page already presrnt on the wiki, this can be updated with the latest text
#4278 Links with variation
- Web team will look at next week