DiseaseOntology / HumanDiseaseOntology

Repository for the Human Disease Ontology.
Creative Commons Zero v1.0 Universal
331 stars 109 forks source link

Support British English aliases #787

Closed kkrysiak closed 4 years ago

kkrysiak commented 4 years ago

A few examples that would be useful for searching: Pediatric == Paediatric Hematopoietic == Haematopoietic Estrogen == Oestrogen Fiber == Fibre Behavoir == Behaviour

I've made a similar request of HPO. There are likely relevant terms that I am missing.

https://github.com/obophenotype/human-phenotype-ontology/issues/5103

kkrysiak commented 4 years ago

tumor == tumour edema == oedema etiology == aetiology anemia == anaemia hemoglobin == haemoglobin

A few more

lschriml commented 4 years ago

Agreed !! Will look into getting these added !! Cheers, Lynn

Sent from my iPhone

On Jan 9, 2020, at 4:07 PM, Kilannin Krysiak notifications@github.com wrote:

 tumor == tumour edema == oedema etiology == aetiology anemia == anaemia hemoglobin == haemoglobin

A few more

— You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub, or unsubscribe.

lschriml commented 4 years ago

We will put together a plan on how to do this programmatically. Looking in the DO, we have both US and British english versions of terms and synonyms. My overall plan thus far, would be to set up a sprawl query, to identify all of the cases: query first: DO terms : US spellings, British Spellings, then treat them as two groups of updates -- if US spelling, do we have a British spelling synonym, if yes, then add flag in DO that the synonym is British spelling -- if we don't have the British spelling synonym, we will add it.

DO term -- if UK spelling, same as above

Look at DO synonyms, same steps as above. Cheers, Lynn

lschriml commented 4 years ago

To be systematic, we will compile a list of terms to review from: http://translation-clinic.com/spelling-medical-terms-british-american-english/ or a similar source.

matentzn commented 4 years ago

I wrote a little ROBOT pipeline to do automatically create british language synonyms for HPO, maybe @beckyjackson can "steal" it an adopt it for your case. Seems to work well. It takes all labels and existing synonyms (using ROBOT query) then creates british english translations using some dictionary (that you can maintain yourself), and then creates a ROBOT template with only those BE synonyms that are not yet in the ontology.

matentzn commented 4 years ago

Oops forget the link: https://github.com/obophenotype/human-phenotype-ontology/pull/5109

beckyjackson commented 4 years ago

Thanks @matentzn ! I will take a look next week when I'm back from vacation 🙂

lschriml commented 4 years ago

This would be great !! Very useful.

May I suggest you submit an abstract for Biocuration for this work ? Deadline January 24th.

I think there would be a lot of interest in the community.

Thank you Nico !!

Cheers, Lynn

Sent from my iPhone

On Jan 16, 2020, at 5:26 PM, Nico Matentzoglu notifications@github.com wrote:

 I wrote a little ROBOT pipeline to do automatically create british language synonyms for HPO, maybe @beckyjackson can "steal" it an adopt it for your case. Seems to work well. It takes all labels and existing synonyms (using ROBOT query) then creates british english translations using some dictionary (that you can maintain yourself), and then creates a ROBOT template with only those BE synonyms that are not yet in the ontology.

— You are receiving this because you were assigned. Reply to this email directly, view it on GitHub, or unsubscribe.

matentzn commented 4 years ago

Thanks Lynn! This is just a little script I wrote in two hours :) not worth to be mentioned I think! Let me know if you need help adopting it to your case.

lschriml commented 4 years ago

Thank you Nico !!

Sent from my iPhone

On Jan 16, 2020, at 6:55 PM, Nico Matentzoglu notifications@github.com wrote:

 Thanks Lynn! This is just a little script I wrote in two hours :) not worth to be mentioned I think! Let me know if you need help adopting it to your case.

— You are receiving this because you were assigned. Reply to this email directly, view it on GitHub, or unsubscribe.

lschriml commented 4 years ago

Hello @beckyjackson --- did we need to discuss further ? Cheers, Lynn

beckyjackson commented 4 years ago

I was just curious if you wanted this to be a one-time process, or run every time you build a release in the Makefile?

lschriml commented 4 years ago

Good point. I think we want to incorporate this into our release process. So that we keep the synonyms up to date.

Cheers, Lynn

lschriml commented 4 years ago

Thank you Becky !! I've reviewed the British synonym spreadsheet, in google docs, --> No problems. It is very helpful to look through the changes, I appreciate the extra step for QC.

Becky - please go ahead and implement for all of the British spellings

Cheers, Lynn

beckyjackson commented 4 years ago

Alright, I'll do that now.

It looks like almost all of those are in the HPO British-American dictionary already, but a few are missing. @matentzn - could we add these to the dict? I can make a PR if that's easiest.

American British
celiac coeliac
cesarian caesarian
dyslipidemia dyslipidaemia
dyspnea dyspnoea
glycemic glycaemic
ischemic ischaemic
matentzn commented 4 years ago

Gladly!

matentzn commented 4 years ago

(If you can make a PR perfect), and assign to me

lschriml commented 4 years ago

Done

lschriml commented 4 years ago

Hello @beckyjackson -- what do we need to update in Protege, so that when entering a synonym manually, we have the "British" language option. Noticed this today, while added a new synonym.

Cheers, Lynn

lschriml commented 4 years ago

Decided to not add British option.