Difference between revisions of "LEGO May 4 2015"

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(Continued Discussion of March Consistency Exercise Paper)
(Continued Discussion of March Consistency Exercise Paper)
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===Specific Questions/Issues===
 
===Specific Questions/Issues===
 
* Here are the links to the models built by David, Kimberley and Rama
 
* Here are the links to the models built by David, Kimberley and Rama
http://go-genkisugi.rhcloud.com/seed/model/gomodel:taxon_559292-5525a0fc0000001
+
http://go-genkisugi.rhcloud.com/seed/model/gomodel:taxon_559292-5525a0fc0000001 <br>
Kimberley- http://go-genkisugi.rhcloud.com/seed/model/gomodel:5525a0fc0000032
+
Kimberley- http://go-genkisugi.rhcloud.com/seed/model/gomodel:5525a0fc0000032 <br>
Rama- http://go-genkisugi.rhcloud.com/seed/model/gomodel:taxon_559292-5525a0fc0000061#
+
Rama- http://go-genkisugi.rhcloud.com/seed/model/gomodel:taxon_559292-5525a0fc0000061#<br>
 
*Use of in_absence_of and in_presence_of annotation extensions.
 
*Use of in_absence_of and in_presence_of annotation extensions.
 
*How to adequately capture the effects of protein binding on subsequent complex formation and resulting molecular functions.
 
*How to adequately capture the effects of protein binding on subsequent complex formation and resulting molecular functions.

Revision as of 11:25, 3 May 2015

Agenda

Continued Discussion of March Consistency Exercise Paper

Specific Questions/Issues

  • Here are the links to the models built by David, Kimberley and Rama

http://go-genkisugi.rhcloud.com/seed/model/gomodel:taxon_559292-5525a0fc0000001
Kimberley- http://go-genkisugi.rhcloud.com/seed/model/gomodel:5525a0fc0000032
Rama- http://go-genkisugi.rhcloud.com/seed/model/gomodel:taxon_559292-5525a0fc0000061#

  • Use of in_absence_of and in_presence_of annotation extensions.
  • How to adequately capture the effects of protein binding on subsequent complex formation and resulting molecular functions.

Begin Discussion of April Consistency Exercise Paper

Specific Questions/Issues

  • Use of occurs_in relation for molecular function annotations
    • What constitutes sufficient evidence for adding this extension, as CC annotations may be from a different experiment than the MF annotation?
    • For example, protein binding based on Y2H or whole cell lysates (IPI) with separate experiments describing localization (IDA).