Difference between revisions of "WBConfCall 2013.02.07-Agenda and Minutes"

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**2 provisional
 
**2 provisional
 
***History_gene connections (multiple classes) - Chris
 
***History_gene connections (multiple classes) - Chris
****Needs significant testing, Paul will liaise with Chris.
+
****Chris will discuss with relevant curators and confirm with Paul
 +
****Needs significant testing, Chris will liaise with Paul.
 +
****probably bump to WS238 as there hasn't been any further discussion since call.
 
***Feature_data - Gary
 
***Feature_data - Gary
 
****Mapping to a condition rather than via a method.
 
****Mapping to a condition rather than via a method.
 
****Needs testing as may have implications for acedb.
 
****Needs testing as may have implications for acedb.
 +
****probably bump to WS238 as there hasn't been any further discussion since call.
 
**6 scheduled for inclusion.
 
**6 scheduled for inclusion.
 
***Accession class retirement continues
 
***Accession class retirement continues
****Oligo_set mapping in homol_data
+
***homol_data - Kevin
****Transgene - Karen
+
****Oligo_set mapping as we do for other classes.
 +
***Transgene - Karen
 +
****Construction_summary Text
 
***Transcript - Paul
 
***Transcript - Paul
 
****Add biotype lincRNA.
 
****Add biotype lincRNA.
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***?YH & ?Gene_regulation retirement - Chris
 
***?YH & ?Gene_regulation retirement - Chris
 
****Complicated change as needs interaction adding in lots of classes.
 
****Complicated change as needs interaction adding in lots of classes.
 
 
Will update when back in office.
 
  
 
==David Miller cell specific expression data-tiling arrays==
 
==David Miller cell specific expression data-tiling arrays==
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Have the tiling array data been curated already? if so we can point him to SPELL.
 
Have the tiling array data been curated already? if so we can point him to SPELL.
 +
 +
 +
From discussions:
 +
 +
Daniela will contact David and point him to the expression cluster page. Data will be in in 237.
  
 
==Request from Caltech to expand release notes==
 
==Request from Caltech to expand release notes==
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*Release notes should be aimed at user community, tag names and some numbers may not be interesting for them.
 
*Release notes should be aimed at user community, tag names and some numbers may not be interesting for them.
 
*We could generate a separate list for internal use, with all the statistics that curators want.
 
*We could generate a separate list for internal use, with all the statistics that curators want.
 +
 +
==How to handle predicted interactions==
 +
*Take out all the predicted interactions from the gene page, instead include the link to the external databases that provide these--Gene Orienteer, WormNet etc.
 +
*Data will be kept in acedb for purposes of Cytoscape?
 +
 +
==WormMine==
 +
*There will be priority data sets that will be loaded first
 +
*SGD has ready templates
 +
*JD will give a demo of WormMine, Thursday 14th, at 8.30 PST

Latest revision as of 11:59, 15 February 2013

Models

  • 8 models proposals for WS237 inclusion.
    • 2 provisional
      • History_gene connections (multiple classes) - Chris
        • Chris will discuss with relevant curators and confirm with Paul
        • Needs significant testing, Chris will liaise with Paul.
        • probably bump to WS238 as there hasn't been any further discussion since call.
      • Feature_data - Gary
        • Mapping to a condition rather than via a method.
        • Needs testing as may have implications for acedb.
        • probably bump to WS238 as there hasn't been any further discussion since call.
    • 6 scheduled for inclusion.
      • Accession class retirement continues
      • homol_data - Kevin
        • Oligo_set mapping as we do for other classes.
      • Transgene - Karen
        • Construction_summary Text
      • Transcript - Paul
        • Add biotype lincRNA.
      • Oligo_set & Microarray_result - wen/kev
        • Addition of ?Species
      • ?YH & ?Gene_regulation retirement - Chris
        • Complicated change as needs interaction adding in lots of classes.

David Miller cell specific expression data-tiling arrays

From Daniela: WS235 contains the links to WormViz in the anatomy page under the External links widget. David writes: "Although the link is certainly useful in this location its really buried and will not be noticed by most users. why not include a link to wormviz on the expression page for each gene?"

Have the tiling array data been curated already? if so we can point him to SPELL.


From discussions:

Daniela will contact David and point him to the expression cluster page. Data will be in in 237.

Request from Caltech to expand release notes

Caltech has been making a list of datatypes/objects that we would like numbers for, from each build, to be included in release notes. Is this something that Hinxton could do?

See http://wiki.wormbase.org/index.php/Release_note_requests

From discussions:

  • Release notes should be aimed at user community, tag names and some numbers may not be interesting for them.
  • We could generate a separate list for internal use, with all the statistics that curators want.

How to handle predicted interactions

  • Take out all the predicted interactions from the gene page, instead include the link to the external databases that provide these--Gene Orienteer, WormNet etc.
  • Data will be kept in acedb for purposes of Cytoscape?

WormMine

  • There will be priority data sets that will be loaded first
  • SGD has ready templates
  • JD will give a demo of WormMine, Thursday 14th, at 8.30 PST