Converter: OWL to FHIR CodeSystem #320

joeflack4 · 2022-10-18T22:19:34Z

Updates

OWL to FHIR
- Add: New converter for OWL to FHIR CodeSystem JON (WIP)
- Add: Tests for new converter (WIP)

Misc
- Update: .gitignore: added: .DS_Store

Commenting on the draft is good. The input is useful and it could take a long time to complete this PR if I get pulled in other directions.

This is a sound suggestion. I've added it to the list of "todo's minor" at the top of the file. My primary objective is to complete this issue for TIMS so that I can continue working on other issues, but if I can improve the typing at all in a quick way, I will do that earlier on.

joeflack4 · 2022-10-19T01:31:41Z

pyproject.toml

@@ -27,8 +27,9 @@ kgcl-rdflib = "^0.3.0"
 pystow = "^0.4.4"
 class-resolver = "^0.3.10"
 ontoportal-client = "0.0.3"
-curies = "^0.1.5"


Update: curies = "^0.1.5" --> curies = "^0.3.0"

Add: bioontologies = "^0.2.0"

For now I'm using bioontologies until I can fix issues I'm having with getting OAK to do the conversion.
The curies bit changed because, for some reason, even though semver syntax should support download of 0.3.0 via ^0.1.5, it would simply not install unless I made this change. Error messages and discussion of that in are in this slack thread.

it's best to do these in separate PRs, you will have conflicts now

No worries. This change probably won't be included anyway. Also, Damien explained to me why semver was not doing as I expected here.

src/oaklib/converters/owl_to_fhir.py

joeflack4 · 2022-10-19T01:37:14Z

src/oaklib/converters/owl_to_fhir.py

+    """Convert
+
+    Side effects:
+    - Writes file at `outpath`"""


Commenting on the draft is good. The input is useful and it could take a long time to complete this PR if I get pulled in other directions.

This is a sound suggestion. I've added it to the list of "todo's minor" at the top of the file. My primary objective is to complete this issue for TIMS so that I can continue working on other issues, but if I can improve the typing at all in a quick way, I will do that earlier on.

joeflack4 · 2022-10-19T01:38:58Z

src/oaklib/converters/owl_to_fhir.py

+
+# todo: This is for development purposes. can delete after or modify if needed
+# todo: would be nice if faster to load pickle https://stackoverflow.com/questions/66348333/speed-up-reading-multiple-pickle-files
+def _load_obograph(inpath: str, cache_dir=CACHE_DIR, save_cache=False, load_cache=True):


FYI: Caching. May or may not keep some variation of this, turned off by default, in the final PR. This is especially useful for me right now since simply loading the bioontologies.robot module is taking me about ~24 seconds right now.

cmungall · 2022-10-27T23:43:04Z

src/oaklib/converters/owl_to_fhir_codesystem.py

+        }
+        for syn in node.meta.synonyms:
+            # todo: will each Synonym realistically only have 1 xref? It supports a list. But could it be 0 or >1?
+            for xref in syn.xrefs:


Note that synonym.xrefs is for the provenance of the synonym - it's not the code system of the synonym.

E.g.

meta: synonyms: val: "foo disease type 2" xrefs: - PMID:1234 ### a publications - ORCID:4567-897 ### Nicole's/curators orcid - ...

Ah, thanks for pointing that out. I might have ended up making a mistake here.

cmungall · 2022-10-27T23:43:40Z

pyproject.toml

 bioregistry = "^0.5.64"
+bioontologies = "^0.2.0"


shouldn't be necessary

Yeah, I agree. I'll remove this. I think I only added this here temporarily because I was using an interface and not an implementation and having issues because of that.

cmungall · 2022-10-27T23:44:09Z

src/oaklib/converters/owl_to_fhir_codesystem.py

+
+TODO's
+  * Move this into GitHub issue (and link here) so I can get input on some of these more difficult parts / parts I don't yet understand
+  1. Write converter MVP


you could also look at pyrophen as a model of how to do this

Just FYI, I checked how Pyrophen does a couple days ago. It is simple enough to understand. My intuition is still leaning towards Obographs being faster and easier to do.

cmungall · 2022-10-27T23:44:46Z

src/oaklib/converters/owl_to_fhir_codesystem.py

+  4.3. Obograph Node stuff
+  4.3.1. See what all I can include from:
+    - alternative_ids[], created_by, creation_date, definition, definition_provenance, id, lbl (label), synonyms[],
+    - xrefs[] (I see the CURIE, but nothing else... does it not parse other xref info? or is it in axioms?),


this is the mappings - think of what we are doing with mondo, omim, ...

I think you are explicitly comparing this mapping case (xrefs between ontologies) with this mapping case (data models). I agree with you hear that this is the higher priority for using a mapping standard. In this case, if I do do that (and I'm not sure I will yet), I would reach for SSSOM.

src/oaklib/converters/owl_to_fhir_codesystem.py

- Add: New converter for OWL to FHIR CodeSystem JON (WIP) - Add: Tests for new converter (WIP) Misc - Update: .gitignore: added: .DS_Store

…edges

Fixes #367 May replace #320

cmungall · 2022-11-30T21:30:44Z

Hi @joeflack4 - I had a shot at a simplified version of this here:

Converter: OWL to FHIR CodeSystem #320

@joeflack4

* Adding FHIR CodeSystem dumping. Fixes #367 May replace #320 * making logical def retrieval more efficient * Hacking with @joeflack4 * lint

joeflack4 marked this pull request as draft October 18, 2022 22:19

joeflack4 commented Oct 18, 2022

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joeflack4 force-pushed the fhir branch 2 times, most recently from 33d5aad to 51cbd17 Compare October 18, 2022 23:34

cmungall reviewed Oct 19, 2022

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joeflack4 force-pushed the fhir branch from 51cbd17 to 9a32070 Compare October 19, 2022 01:26

joeflack4 commented Oct 19, 2022

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joeflack4 force-pushed the fhir branch 3 times, most recently from aa2f64a to 41b50e5 Compare October 19, 2022 02:53

cmungall reviewed Oct 27, 2022

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src/oaklib/converters/owl_to_fhir_codesystem.py Show resolved Hide resolved

joeflack4 force-pushed the fhir branch 11 times, most recently from 25442c7 to 064bd0d Compare November 4, 2022 22:19

joeflack4 force-pushed the fhir branch 2 times, most recently from 581bb2e to 0e9b94a Compare November 6, 2022 21:43

OWL to FHIR

2a0a324

- Add: New converter for OWL to FHIR CodeSystem JON (WIP) - Add: Tests for new converter (WIP) Misc - Update: .gitignore: added: .DS_Store

joeflack4 force-pushed the fhir branch from 0e9b94a to 2a0a324 Compare November 6, 2022 22:25

- Add: TODO related to some bugs, mostly related to concept property …

408af17

…edges

cmungall mentioned this pull request Nov 11, 2022

Add a HAPI FHIR adapter #351

Open

- Add: CompLOINC as test case. This is very ad-hoc and temporary

aea3dff

joeflack4 force-pushed the fhir branch from 6fc3310 to aea3dff Compare November 11, 2022 16:25

joeflack4 mentioned this pull request Nov 30, 2022

CodeSystems: OWL/OBO Ontologies timsbiomed/issues#41

Open

11 tasks

cmungall mentioned this pull request Nov 30, 2022

Add a FHIR CodeSystem dumper #367

Closed

cmungall added a commit that referenced this pull request Nov 30, 2022

Adding FHIR CodeSystem dumping.

217ce43

Fixes #367 May replace #320

cmungall mentioned this pull request Nov 30, 2022

Adding FHIR CodeSystem dumping. #368

Merged

cmungall added a commit that referenced this pull request Nov 30, 2022

Adding FHIR CodeSystem dumping. (#368)

b8fd5ad

* Adding FHIR CodeSystem dumping. Fixes #367 May replace #320 * making logical def retrieval more efficient * Hacking with @joeflack4 * lint

joeflack4 closed this Dec 1, 2022

               notebooks/api-key.txt
               .template.db
               .venv
               .tox/
               .coverage.*
+              .DS_Store

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Converter: OWL to FHIR CodeSystem #320

Converter: OWL to FHIR CodeSystem #320

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cmungall commented Nov 30, 2022

		@@ -0,0 +1,20 @@
		"""Convert OWL to FHIR CodeSystem JSON

		TODO's

		"""


		def convert(inpath: str):

Converter: OWL to FHIR CodeSystem #320

Converter: OWL to FHIR CodeSystem #320

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