Difference between revisions of "Phenotype Ontology Development"

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(Created page with "=Phenotype Working Group --- Team Phene!= __TOC__ ==Logical Definitions== *Create cross-product logical definitions for all terms (see below) *Which ontologies to use? Curre...")
 
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==Website Display==
 
==Website Display==
*Immediate changes we want to implement (for 12/10/14)
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*Immediate changes we want to implement (for 12/1-2/14)
*after 12/10/14
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*after 12/1-2/14
  
 
==Community Annotation==
 
==Community Annotation==

Revision as of 19:53, 20 November 2014

Phenotype Working Group --- Team Phene!

Logical Definitions

  • Create cross-product logical definitions for all terms (see below)
  • Which ontologies to use? Currently WPO / GO / PATO
  • Monarch initiative


Updating Slim Terms

  • Figure out terms to include
  • Make sure cross-product logical definitions exist for these terms

Terms and branches to fix/revisit

  • Keep list

Example ; Ionizing radiation terms : I want to change gamma to ionizing for a number of terms…in particular 1391…..then make old name with “gamma” a syn

OA changes necessary

  • Not “piecemeal” – wait to we have a solid plan before asking JC

Website Display

  • Immediate changes we want to implement (for 12/1-2/14)
  • after 12/1-2/14

Community Annotation

  • Branches to fix/revisit
    • Ionizing radiation terms : I want to change gamma to ionizing for a number of terms…in particular 1391…..then make old name with “gamma” a syn
    • Epigenetics terms


WPO: Logical definitions

  • Find examples from Jolene and I of terms that can't be made into crossproducts:

**Just using PATO (quality) and GO

  • Can be made*
egg laying defective
intersection_of: PATO:0001511 ! non-functional
intersection_of: inheres_in GO:0018991 ! oviposition
			hyperactive egg laying
intersection_of: PATO:0000694 ! premature
intersection_of: inheres_in GO:0046662 ! regulation of oviposition

Roller
intersection_of: PATO:0001227 ! variant
intersection_of: inheres_in GO:0040002 ! collagen and cuticulin-based cuticle development
  • Can't be made
bloated - egg retention 
inactive phase long
egg laying phases variant
dead eggs laid
Kinker
coiler

Agenda/minutes

11/20/14

  • Who would like to tackle which branch for the next two weeks
  • List of “commonly used” PATO terms
  • How to track changes

I can CVS, but will affect WPO as well

  • BROAD syn….3 and 4 letter names-> short name tag
  • Website changes

action items for todd…in order of priority.