Difference between revisions of "WBConfCall 2013.11.21-Agenda and Minutes"

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WS241 models summary [[WS241 Models.wrm]]
 
WS241 models summary [[WS241 Models.wrm]]
  
Curators to check their model proposals in this file:
+
Curators checked their model proposals in this file:
 
WS241 pre-WS241 tagged models [[http://cvs.sanger.ac.uk/cgi-bin/viewvc.cgi/wormbase/wspec/models.wrm?revision=1.396&root=ensembl&view=markup pre-WS241]]
 
WS241 pre-WS241 tagged models [[http://cvs.sanger.ac.uk/cgi-bin/viewvc.cgi/wormbase/wspec/models.wrm?revision=1.396&root=ensembl&view=markup pre-WS241]]
  
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'''3) ?Movie and Expression_pattern changes'''
 
'''3) ?Movie and Expression_pattern changes'''
 +
 
3.1) Expr_pattern
 
3.1) Expr_pattern
 +
 
3.2) Movie
 
3.2) Movie
  
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'''5.2) ?DO_term - Ranjana'''
 
'''5.2) ?DO_term - Ranjana'''
  
== Outstanding Help Desk issues ==
+
== Outstanding Help Desk issues also known as house keeping ==
 +
 
 +
Wen: These are help desk issues that are still open.
  
Wen: These are help desk issues that are still open, please reply or close them if the issue is resolved.
+
The following are related to GFF3 implementation - no need to discuss individually on the call.  
  
The following are related to GFF3 implement
 
 
* [[https://github.com/WormBase/website/issues/2019 2019]] - gff3 implementation no discussion necessary until gff3 code is ready?
 
* [[https://github.com/WormBase/website/issues/2019 2019]] - gff3 implementation no discussion necessary until gff3 code is ready?
 
* [[https://github.com/WormBase/website/issues/2026 2026]] - gff3 implementation no discussion necessary until gff3 code is ready?
 
* [[https://github.com/WormBase/website/issues/2026 2026]] - gff3 implementation no discussion necessary until gff3 code is ready?
Line 48: Line 51:
 
* [[https://github.com/WormBase/website/issues/1549 1549]] Extra table in Associations widget-Anatomy page
 
* [[https://github.com/WormBase/website/issues/1549 1549]] Extra table in Associations widget-Anatomy page
 
* [[https://github.com/WormBase/website/issues/1890 1890]] original problem fixed but TreeFam image still looks messed up
 
* [[https://github.com/WormBase/website/issues/1890 1890]] original problem fixed but TreeFam image still looks messed up
 +
* [[https://github.com/WormBase/website/issues/2022 2022]] Can we scale TreeFam Image?
 
* [[https://github.com/WormBase/website/issues/1999 1999]] n1774 listed as sequenced but location is not known.
 
* [[https://github.com/WormBase/website/issues/1999 1999]] n1774 listed as sequenced but location is not known.
 
* [[https://github.com/WormBase/website/issues/2009 2009]] Look for wormmine model browser
 
* [[https://github.com/WormBase/website/issues/2009 2009]] Look for wormmine model browser
* [[https://github.com/WormBase/website/issues/2010 2010]] todd is working on it
+
* [[https://github.com/WormBase/website/issues/2012 2012]] Discussion about curation of pers. Comm [Mary Ann: The pers. comm part of this ticket is resolved, but attaching evidence to manual annotation from external curation groups is still under discussion] - '''NOT HELPDESK'''
* [[https://github.com/WormBase/website/issues/2012 2012]] Discussion about curation of pers. Comm [Mary Ann: The pers. comm part of this ticket is resolved, but attaching evidence to manual annotation from external curation groups is still under discussion]
 
 
* [[https://github.com/WormBase/website/issues/2015 2015]] External URL, karen and Abi are working on this  
 
* [[https://github.com/WormBase/website/issues/2015 2015]] External URL, karen and Abi are working on this  
* [[https://github.com/WormBase/website/issues/2016 2016]] External URL, karen is working on this  
+
* [[https://github.com/WormBase/website/issues/2016 2016]] External URL, karen is working on this - '''NOT HELPDESK'''
 
* [[https://github.com/WormBase/website/issues/2017 2017]] slt-1 gene page is still suggesting that the gene hasn't been physically mapped, but clearly has a sequence:
 
* [[https://github.com/WormBase/website/issues/2017 2017]] slt-1 gene page is still suggesting that the gene hasn't been physically mapped, but clearly has a sequence:
* [[https://github.com/WormBase/website/issues/2018 2018]] Molecular Details widget not displaying properly on any variation page on Staging site
+
* [[https://github.com/WormBase/website/issues/2018 2018]] Molecular Details widget not displaying properly on any variation page on Staging site - '''NOT HELPDESK'''
* [[https://github.com/WormBase/website/issues/2021 2021]] WikiPathway images on Topic pages
+
* [[https://github.com/WormBase/website/issues/2021 2021]] WikiPathway images on Topic pages - '''NOT HELPDESK'''
* [[https://github.com/WormBase/website/issues/2022 2022]] Can we scale TreeFam Image?
+
* [[https://github.com/WormBase/website/issues/2027 2027]] 'Associations' widget consistently timing out on the 'nucleus' GO Term page on Staging - '''NOT HELPDESK'''
* [[https://github.com/WormBase/website/issues/2027 2027]] 'Associations' widget consistently timing out on the 'nucleus' GO Term page on Staging
 
 
* [[https://github.com/WormBase/website/issues/2034 2034]] WormMine Qury builder is looking for RNAi data although we have none
 
* [[https://github.com/WormBase/website/issues/2034 2034]] WormMine Qury builder is looking for RNAi data although we have none
 
* [[https://github.com/WormBase/website/issues/2037 2037]] asked for a bunch of tracks got back Bio::GRahics error......
 
* [[https://github.com/WormBase/website/issues/2037 2037]] asked for a bunch of tracks got back Bio::GRahics error......
 
* [[https://github.com/WormBase/website/issues/2041 2041]] Resource Identification in the Literature project
 
* [[https://github.com/WormBase/website/issues/2041 2041]] Resource Identification in the Literature project
* [[https://github.com/WormBase/website/issues/2043 2043]] vab-3 doesnt have a location on the gene page. Please fix.
+
* [[https://github.com/WormBase/website/issues/2043 2043]] vab-3 doesnt have a location on the gene page. Please fix. -- '''closed'''
* [[https://github.com/WormBase/website/issues/2044 2044]] hlh-2 does not have a gene structure either
+
* [[https://github.com/WormBase/website/issues/2044 2044]] hlh-2 does not have a gene structure either -- '''closed'''
* [[https://github.com/WormBase/website/issues/2062 2062]] Wiggle or BEDGraph format on Gbrowse?
+
 
 +
There are lots of other issues in the system not listed here, but will be worked on when time allows.
  
 
== SAB ==
 
== SAB ==
 +
 +
=Minutes=
 +
 +
1. WS241 model changes. All approved by curators.
 +
 +
2. GFF3 implementations will be ready in WS240.
 +
 +
3. Help Desk questions: Chris will reply to questions related to WormMine. Wen will make sure that every user gets response from us.
 +
 +
4. SAB meeting: A small meeting for database should be scheduled in Jan. or Feb. Need to check location availability for SAB, also need to check the schedule of advisors. The meeting should last for 2-3 days to allow extensive discussion. Will need to have a series of video/phone conferences in Dec. and Jan. to brainstorm possible databases to replace ACeDB and then do tests for these ideas.
 +
 +
5. Caltech development environment will need a point person from the web team to guide Caltech people.
 +
 +
6. Human Disese display. Try to get OMIM to link to us like FlyBase. Will need to coordinate with FlyBase.
 +
 +
7. TreeFam graphic display need to to be worked.
 +
 +
8. OthoList -- plan to include it in WormMine.
 +
 +
9. WormMine - Joachim automated the process for building WormMine. WormMine for WS239 is on staging site.
 +
 +
10. Transcription factor class (~700 objects) need to be made more visible. Probably need a static page or create a template for them in WormMine.
 +
 +
11. TSS data will go to WS241 GBrowser. Should also be made available on FTP for download since there are 12 million pieces of data.
 +
 +
12. We need a policy to decide what data for us to provide for public download. Caltech only provide data that they curated, not uncurated raw data. Those data that only exist on Lab websites will need to be archived. Those data from journal websites or GEO should be fine since we already archive them in Caltech.
 +
 +
13. Are there any roadmap on new species that will be added to WormBase? No.
 +
 +
14. WS241 will need to announce additional species. Ranjana will draft a table for basic information that we want to display for all species, then the webteam pull information to fill it in every build.

Latest revision as of 21:56, 21 November 2013

Agenda

Please add your agenda items here.

WS241 models

WS241 models summary WS241 Models.wrm

Curators checked their model proposals in this file: WS241 pre-WS241 tagged models [pre-WS241]

1) ?Person class

2) ?Interaction and ?Feature models

3) ?Movie and Expression_pattern changes

3.1) Expr_pattern

3.2) Movie

4) ?Protein Class

5) Extras from the deadline call

5.1) ?Expression_cluster and ?Analysis class - Wen

5.2) ?DO_term - Ranjana

Outstanding Help Desk issues also known as house keeping

Wen: These are help desk issues that are still open.

The following are related to GFF3 implementation - no need to discuss individually on the call.

  • [2019] - gff3 implementation no discussion necessary until gff3 code is ready?
  • [2026] - gff3 implementation no discussion necessary until gff3 code is ready?
  • [2028] - gff3 implementation no discussion necessary until gff3 code is ready?
  • [2029] - gff3 implementation no discussion necessary until gff3 code is ready?
  • [2030] - gff3 implementation no discussion necessary until gff3 code is ready?
  • [2031] - gff3 implementation no discussion necessary until gff3 code is ready?
  • [2032] - gff3 implementation no discussion necessary until gff3 code is ready?
  • [910] - gff3 implementation no discussion necessary until gff3 code is ready?


Other issues:

  • [1939] Blast tool changes
  • [1549] Extra table in Associations widget-Anatomy page
  • [1890] original problem fixed but TreeFam image still looks messed up
  • [2022] Can we scale TreeFam Image?
  • [1999] n1774 listed as sequenced but location is not known.
  • [2009] Look for wormmine model browser
  • [2012] Discussion about curation of pers. Comm [Mary Ann: The pers. comm part of this ticket is resolved, but attaching evidence to manual annotation from external curation groups is still under discussion] - NOT HELPDESK
  • [2015] External URL, karen and Abi are working on this
  • [2016] External URL, karen is working on this - NOT HELPDESK
  • [2017] slt-1 gene page is still suggesting that the gene hasn't been physically mapped, but clearly has a sequence:
  • [2018] Molecular Details widget not displaying properly on any variation page on Staging site - NOT HELPDESK
  • [2021] WikiPathway images on Topic pages - NOT HELPDESK
  • [2027] 'Associations' widget consistently timing out on the 'nucleus' GO Term page on Staging - NOT HELPDESK
  • [2034] WormMine Qury builder is looking for RNAi data although we have none
  • [2037] asked for a bunch of tracks got back Bio::GRahics error......
  • [2041] Resource Identification in the Literature project
  • [2043] vab-3 doesnt have a location on the gene page. Please fix. -- closed
  • [2044] hlh-2 does not have a gene structure either -- closed

There are lots of other issues in the system not listed here, but will be worked on when time allows.

SAB

Minutes

1. WS241 model changes. All approved by curators.

2. GFF3 implementations will be ready in WS240.

3. Help Desk questions: Chris will reply to questions related to WormMine. Wen will make sure that every user gets response from us.

4. SAB meeting: A small meeting for database should be scheduled in Jan. or Feb. Need to check location availability for SAB, also need to check the schedule of advisors. The meeting should last for 2-3 days to allow extensive discussion. Will need to have a series of video/phone conferences in Dec. and Jan. to brainstorm possible databases to replace ACeDB and then do tests for these ideas.

5. Caltech development environment will need a point person from the web team to guide Caltech people.

6. Human Disese display. Try to get OMIM to link to us like FlyBase. Will need to coordinate with FlyBase.

7. TreeFam graphic display need to to be worked.

8. OthoList -- plan to include it in WormMine.

9. WormMine - Joachim automated the process for building WormMine. WormMine for WS239 is on staging site.

10. Transcription factor class (~700 objects) need to be made more visible. Probably need a static page or create a template for them in WormMine.

11. TSS data will go to WS241 GBrowser. Should also be made available on FTP for download since there are 12 million pieces of data.

12. We need a policy to decide what data for us to provide for public download. Caltech only provide data that they curated, not uncurated raw data. Those data that only exist on Lab websites will need to be archived. Those data from journal websites or GEO should be fine since we already archive them in Caltech.

13. Are there any roadmap on new species that will be added to WormBase? No.

14. WS241 will need to announce additional species. Ranjana will draft a table for basic information that we want to display for all species, then the webteam pull information to fill it in every build.