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.


Tools and ontologies necessary to create logical definitions

In order to create “logical definitions” via cross products of different ontologies for the WPO, you will need the following:

1) OBO-edit (Version 2.1-beta2 or higher): http://sourceforge.net/projects/geneontology/files/

2) The Gene Ontology (go.obo) http://www.obofoundry.org/cgi-bin/detail.cgi?id=biological_process

3) the PATO ontology (quality.obo) http://www.obofoundry.org/cgi-bin/detail.cgi?id=quality

4) The Worm Phenotype Ontology (wbphenotype.obo) http://www.obofoundry.org/cgi-bin/detail.cgi?id=worm_phenotype

most recent version: http://tazendra.caltech.edu/~azurebrd/cgi-bin/forms/phenotype_ontology_obo.cgi

5) The following 2 .obo files can be obtained from Gary S at WormBase:

  • worm_phenotype_xp_relations.obo
  • Worm_PO_GO_XP.obo

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