Changes between Version 25 and Version 26 of PreviousCurationMeetings


Ignore:
Timestamp:
Sep 17, 2012, 4:41:05 PM (9 years ago)
Author:
gomidori
Comment:

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  • PreviousCurationMeetings

    v25 v26  
    145145  * relations used in extensions will be reported by  Kim during loading and the we can refine
    146146
    147  * Val went through some Localization examples , e.g  PMID:20298435 egs.
    148     * should the localization only be direct transport, anchoring, chaperoning? what about complex assembly, or part of a complex
     147 * Val went through some localization examples , e.g  PMID:20298435
     148   * should the localization only be direct transport, anchoring, chaperoning? what about complex assembly, or part of a complex
    149149   * decided localizations should be captured with GO if they were clearly "localisation"  (i.e  A- required for B). If possibly "complex dependent" i.e A required for B AND B required for A, should be phenotype only)
    150150
     
    183183== 17th April 2012 ==
    184184
    185  * Revising BioGrid annotation to represent BAIT/HIT
    186   https://sourceforge.net/apps/trac/pombase/wiki/BioGridBaitHitNotationMapping
    187   http://oliver0.sysbiol.cam.ac.uk/pombe/tools/sessions_with_type_list
    188 
    189  * Skype with Kim  to go through allele phenotype workflow
     185 * Revising BioGRID annotation to represent BAIT/HIT
     186  * https://sourceforge.net/apps/trac/pombase/wiki/BioGridBaitHitNotationMapping
     187  * http://oliver0.sysbiol.cam.ac.uk/pombe/tools/sessions_with_type_list
     188
     189 * Skype with Kim to go through allele phenotype workflow
    190190
    191191== 01 May 2012 ==
     
    241241
    242242 == 17th September 2012 ==
    243  * phenotype extensions: how do you distinguish "direct targets" and "downstream targets"?
     243 * phenotype extensions: how do you distinguish effects on binding that does vs. does not directly involve the mutated gene product?
    244244  * To be able to annotate both instances: 'mutation in geneA disrupts proteinB binding to proteinC' & 'mutation in geneA disrupts proteinA binding to proteinC' (see SF item http://sourceforge.net/tracker/?func=detail&atid=2096431&aid=3565516&group_id=65526) 
    245   * Decided to change the term so that all binding partners are specified eg 'decreased protein binding' 'assayed using (geneA, geneC)'. This can also be used to annotate more than 2 interactors ('assayed_using(geneA, geneB, geneC).
     245  * Decided to change the term and extension usage so that all binding partners are specified, e.g. 'decreased protein binding' 'assayed_using(geneA, geneC)'. This can also be used to annotate more than 2 interactors (e.g. assayed_using(geneA, geneB, geneC)).
     246  * [wiki:ProteinBindingPhenotypeExtensions Documentation on wiki]
     247 * dealt with allele disambiguation (https://sourceforge.net/tracker/?func=detail&atid=2525791&aid=3559872&group_id=65526)