Phenotype Ontology Development

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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.

Current PATO mappings to WPO

One WPO => One Pato

variant =>PATO:0001227 ! variant

resistant => PATO:0001552 ! decreased sensitivity of a process

inefficient => PATO:0001677 ! inefficient

protracted => PATO:0000304 ! decreased speed

asynchronous => PATO:0000688 ! asynchronous

erratic => PATO:0001584 ! increased variability

Reversed => PATO:0000625 ! inverted

uncoordinated => PATO:0000770 ! uncoordinated

ectopic => PATO:0000460 ! abnormal --- but there exists id: PATO:0000628 => mislocalized with ectopic as an exact synonym

rate variant = PATO:0001586 ! variability of rate

Inhibited => PATO:0001624 ! decreased functionality

Exaggerated => PATO:0000463 ! conspicuous


One Pato => Many WPO

PATO:0001511 ! non-functional

defective

deficient

depleted

attenuated

failure

lethal

Note: Can replace some with - PATO:0001624 ! decreased functionality or other terms


PATO:0000502 ! delayed

delayed

retarded


PATO:0000297 ! arrested

arrested

incomplete

abolished


PATO:0001551 ! increased sensitivity of a process

hypersensitive

enhanced

NOTE: PATO also has more specific “increase sensitivity” terms, for example PATO:0001808 ! increased sensitivity to irradiation


PATO:0000380 ! increased frequency

Constitutive

Hyperactive

Increased


PATO:0000911 ! decreased rate

reduced

slow


PATO:0000498 ! increased duration

Extended

Slow


PATO:0000694 ! premature

premature

precocious

early


PATO:0000462 ! absent

absent

fails to occur

fails

constitutive (with a GO entity of “loss of negative regulation” )


PATO:0000499 ! decreased duration

shortened

brief


One WPO => Many Pato

Irregular

PATO:0001845 ! irregular rhythm

PATO:0001584 ! increased variability


slow

PATO:0000911 ! decreased rate

PATO:0000304 ! decreased speed

PATO:0000498 ! increased duration


reduced

PATO:0000911 ! decreased rate

PATO:0001783 ! decreased intensity

PATO:0000381 ! decreased frequency

PATO:0001562 ! decreased mass

PATO:0002052 ! decreased occurrence


Increased

PATO:0000912 ! increased rate

PATO:0001563 ! increased mass

PATO:0000380 ! increased frequency

PATO:0001551 ! increased sensitivity of a process

PATO:0001782 ! increased intensity (used with high gene expression)


constitutive

PATO:0000380 ! increased frequency

PATO:0000462 ! absent (with a GO entity of “loss of negative regulation” )


Hyperactive

PATO:0000912 ! increased rate

PATO:0000380 ! increased frequency