Closed kkrysiak closed 4 years ago
tumor == tumour edema == oedema etiology == aetiology anemia == anaemia hemoglobin == haemoglobin
A few more
Agreed !! Will look into getting these added !! Cheers, Lynn
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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
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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
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.
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.
Oops forget the link: https://github.com/obophenotype/human-phenotype-ontology/pull/5109
Thanks @matentzn ! I will take a look next week when I'm back from vacation 🙂
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
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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.
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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.
Thank you Nico !!
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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.
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Hello @beckyjackson --- did we need to discuss further ? Cheers, Lynn
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
?
Good point. I think we want to incorporate this into our release process. So that we keep the synonyms up to date.
Cheers, Lynn
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
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 |
Gladly!
(If you can make a PR perfect), and assign to me
Done
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
Decided to not add British option.
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