search

PHI-base / phipo

Pathogen-Host Interaction Phenotype Ontology
Other
5 stars 5 forks source link

PHIPO terms with missing text definitions #337

Closed jseager7 closed 3 years ago

jseager7 commented 3 years ago

The ODK is reporting that 18 terms in PHIPO do not have text definitions. It would help if definitions could be added for all these terms. Fixing these will remove most of the warnings in the ODK report and the OBO Dashboard.

term label Definition
PHIPO:0000038 mutualism phenotype A phenotype which affects the balance of symbiotic mutualism, mutualism describes an interaction between two symbionts (where the larger is usually the host), results in positive (beneficial) effects on reproduction and/or survival of both species. (simplify children terms)
PHIPO:0000041 normal motility phenotype obsolete
PHIPO:0000042 abnormal motility phenotype obsolete
PHIPO:0000100 increased motility obsolete
PHIPO:0000101 decreased motility obsolete
PHIPO:0000102 loss of motility obsolete
PHIPO:0000157 motility phenotype obsolete
PHIPO:0000166 chlorosis phenotype obsolete
PHIPO:0000169 chlorosis absent obsolete
PHIPO:0000170 chlorosis present obsolete
PHIPO:0000200 host chlorosis phenotype in presence of pathogen A pathogen-host interaction phenotype in which leaves produce insufficient chlorophyll.
PHIPO:0000213 host chlorosis absent ~with pathogen~ in presence of pathogen A pathogen-host interaction phenotype in which host chlorosis is absent
PHIPO:0000215 host chlorosis present ~with pathogen~ in presence of pathogen A pathogen-host interaction phenotype in which host chlorosis is present
PHIPO:0000216 pathogen host interaction disease symptom phenotype obsolete. Consider adding 'disease symptom' as a related synonym of any disease symptom?
PHIPO:0000279 systemic phenotype obsolete
PHIPO:0000411 molecular function phenotype A phenotype that affects a molecular function such as binding or catalytic activity
PHIPO:0000950 pathogen spore germination on host phenotype obsolete
CuzickA commented 3 years ago

@jseager7 please could you let us know which terms have been used in annotations

jseager7 commented 3 years ago

@CuzickA See below for a list of which terms are used and where.

Note that this list is current as of 4 May 2021, so please let me know if you think you've used any of these terms later than that, because I'll need to re-export the curation sessions if so.

ValWood commented 3 years ago

tissue phenotype term def add HOST. PHIPO:0000512 A pathogen host interaction phenotype that is observed at the level of a HOST tissue (eg leaf, inflorescence, ear or kidney).

CuzickA commented 3 years ago

Edit def and term label for PHIPO:0000512 pathogen host interaction host tissue phenotype ce3a5c0

Edit PHIPO:0000200, PHIPO:0000213 and PHIPO:0000215 a89e9c2

Edit PHIPO:0000411 738654f

Edit PHIPO:0000038 fb8b115

Still to do 1) obsolete terms 2) simplify defs for child terms of mutualism phenotype

CuzickA commented 3 years ago

Obsolete 6 motility phenotypes f1552f5 image image

Obsolete 3 chlorosis terms 97d0a0e image image

obsolete e3ed863 PHIPO:0000279 | systemic phenotype

obsolete 1456e5c PHIPO:0000950 | pathogen spore germination on host phenotype

Above 11 terms now obsoleted

CuzickA commented 3 years ago

Hopefully all PHIPO terms now have a text definition. Is there a way to check this please @jseager7

jseager7 commented 3 years ago

Yes, I can run the same query on the phipo-edit.owl file to confirm. I'll close this issue if I don't notice any problems, and I'll make a full release so that the OBO Dashboard gets updated and hopefully removes the warning about missing definitions.

CuzickA commented 3 years ago

Sound good, thanks.

jseager7 commented 3 years ago

@CuzickA The only term that the query reports as missing a definition is 'pathogen host interaction disease symptom phenotype' (PHIPO:0000216). In your notes above, it seems the intended action was to:

obsolete. Consider adding 'disease symptom' as a related synonym of any disease symptom?

I've noticed that this term has some host chlorosis terms as its children, so they'll probably need to be moved if the parent term is obsoleted.

CuzickA commented 3 years ago

Thanks @jseager7, I missed this one due to the extra text!

image Move host chlorosis terms directly under 'pathogen host interaction host tissue phenotype' e36f581

obsolete 4c47ff5 PHIPO:0000216 | pathogen host interaction disease symptom phenotype

Now looks like image

jseager7 commented 3 years ago

The query doesn't report any more terms, so it looks like that's all of them. Thanks for all your work fixing this. When I have time I'll make a full release so that the definitions show on external services like OLS, Ontobee, and the OBO Dashboard.