nicolevasilevsky
commented
5 years ago Some additional potential patterns:
higher priority
Label: aplasia (hypoplasia would be similar, and HP also has aplasia/hypoplasia terms) Logical def: 'has part' some (aplastic and ('inheres in' some %s) and ('has modifier' some abnormal)) var: anatomical entity example: HP_0009238 'Aplasia of the 5th finger'
Label: premature process Logical def: 'has part' some (premature and ('inheres in' some %s) and ('has modifier' some abnormal)) var: biological process example: HP_0001622 'Premature birth'
Label: abnormalVolume Logical def: 'has part' some (volume and ('inheres in' some %s) and ('has modifier' some abnormal)) var: entity (anatomical entity or cell) example: HP_0012684 'Abnormal pineal volume'
Label: ectoptic Logical def: 'has part' some (mislocalised and ('inheres in' %s) and ('has modifier' some abnormal)) var: anatomical entity example: HP_0001083 'Ectopia lentis'
Label: obstructed Logical def: 'has part' some (obstructed and ('inheres in part of' some %s) and ('has modifier' some abnormal)) var: anatomical entity example: HP_0004796 'Gastrointestinal obstruction'
lower priority
Label: recurrent process in a location Logical def: 'has part' some ('having extra processual parts' and (towards some (%s and ('part of' some %s))) and ('has modifier' some recurrent) and ('has modifier' some abnormal)) var: biological process var: anatomical entity example: HP_0006535 'Recurrent intrapulmonary hemorrhage'
Label: vacuolatedEntity Logical def: 'has part' some (vacuolated and ('inheres in' some %s) and ('has modifier' some abnormal)) var: entity (or cell) example: HP_0001922 'Vacuolated lymphocytes'
Label: abnormalNumber Logical def: 'has part' some ('altered number of' and ('inheres in' some %s) and ('has modifier' some abnormal)) var: entity example: HP_0011873 'Abnormal platelet count' note: not sure when we'd want to use this though vs using the quality amount, like in HP_0011064 'Abnormal number of incisors' logical def: 'has part' some (amount and ('inheres in' some 'incisor tooth') and ('has modifier' some abnormal))
Label: malformed Logical def: 'has part' some (malformed and ('inheres in' some %s) and ('has modifier' some abnormal)) var: anatomical entity example: HP_0002438 'Cerebellar malformation'
Label: decreased depth Logical def: 'has part' some ('decreased depth' and ('inheres in' some '%s') and ('has modifier' some abnormal)) var: anatomical entity example: HP_0000586 'Shallow orbits'
matentzn
The past months we were busy getting a bit more used to implementing and discussing new patterns. Making sure our definitions adhere to standard patterns is getting us 60% of the way to reconciliation. Making sure our reference ontologies (GO, UBERON) are aligned a further 20% (this is most relevant for species that use their own, species-specific anatomy ontologies). We have kickstarted both of these, and we will continue to work on them over the year(s). The remaining 20% will be to make sure that, given two phenotypes we believe should be reconciled, we actually pick the same pattern. As we discussed during the POTATO workshop, this will require us to identity reconciliation candidates. While there is some prototype tooling in the making to assist with candidate identification across species (and within!), we should start with identifying larger groups (themes) of related items that can be covered by a handful of patterns, for example: abnormal morphology, abnormal behaviour, inflammation, neoplasm, abnormally sized anatomical entity (including decreased, increased etc), etc, and then identify the branches in the species-specific ontologies that should correspond to those (example classes).
Please use this issue to collect such themes (just throw them in), including some examples from across species that you think should confirm to the same patterns, and indicate how impactfull you believe reconciling those branches might be. Over the year, we will implement better workflows to do this, but for now, I think it is best we just started in the good old manual way, just to actually get started.