Phenotype Ontology Development
Phenotype Working Group --- Team Phene!
Contents
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