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WIP: Add LOINC PART mappings #35

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WIP: Add LOINC PART mappings #35

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@matentzn matentzn commented Nov 14, 2023 •
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@drseb this is work in progress, I will give you some rounds of feedback on these.

Dont change the skos:exactMatches yet.

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matentzn commented Nov 14, 2023
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If you were to drop the suffix (everything after the ^ ), would the mapping be exact by all standards and in all cases?

mappings/loinc-part-obo/loinc2cl.tsv Outdated Show resolved Hide resolved
mappings/loinc-part-obo/loinc2cl.tsv Outdated Show resolved Hide resolved
mappings/loinc-part-obo/loinc2cl.tsv Outdated Show resolved Hide resolved
mappings/loinc-part-obo/loinc2ncit.tsv Outdated Show resolved Hide resolved
mappings/loinc-part-obo/loinc2chebi_tim.tsv Outdated Show resolved Hide resolved
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drseb commented Jan 27, 2024

@matentzn please give another round of feedback and help with the open issues. thanks a lot

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matentzn commented Jan 30, 2024
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@matentzn matentzn left a comment •
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Awesome THANKS!

Here my review

  • All SSSOM files should be directly in mappings/ not sub directories.
  • Filenames are important, so I would prefer 1 and 2 over seb and tim, e.g loinc2chebi_2.sssom.tsv. Use the filenames that correspond the the "mapping_set_id" suggestions I made.
  • Add link to issue_tracker to all of them. I made an example of this in loinc2uberon.sssom.tsv
  • Add author_id (your orcid) to all of them

You can apply all my change suggestions at once by clicking on "Ass suggestion to batch" on all of them, and then "commit changes".

mappings/loinc-part-obo/loinc2ncbitaxon.sssom.tsv Outdated Show resolved Hide resolved
mappings/loinc-part-obo/loinc2go.sssom.tsv Outdated Show resolved Hide resolved
mappings/loinc-part-obo/loinc2go.sssom.tsv Outdated Show resolved Hide resolved
mappings/loinc-part-obo/loinc2go.sssom.tsv Outdated Show resolved Hide resolved
mappings/loinc-part-obo/loinc2chebi_seb.sssom.tsv Outdated Show resolved Hide resolved
mappings/loinc-part-obo/loinc2ncit.sssom.tsv Outdated Show resolved Hide resolved
mappings/loinc-part-obo/loinc2pr.sssom.tsv Outdated Show resolved Hide resolved
mappings/loinc-part-obo/loinc2uberon.sssom.tsv Outdated Show resolved Hide resolved
mappings/loinc-part-obo/loinc2uberon.sssom.tsv Outdated Show resolved Hide resolved
mappings/loinc-part-obo/loinc2pr.sssom.tsv Outdated Show resolved Hide resolved
drseb and others added 20 commits March 8, 2024 10:49
@drseb @matentzn
Update mappings/loinc-part-obo/loinc2ncbitaxon.sssom.tsv
6e555de 
Co-authored-by: Nico Matentzoglu <nicolas.matentzoglu@gmail.com>
@drseb @matentzn
Update mappings/loinc-part-obo/loinc2go.sssom.tsv
b1aaf96 
Co-authored-by: Nico Matentzoglu <nicolas.matentzoglu@gmail.com>
@drseb @matentzn
Update mappings/loinc-part-obo/loinc2go.sssom.tsv
12384a5 
Co-authored-by: Nico Matentzoglu <nicolas.matentzoglu@gmail.com>
@drseb @matentzn
Update mappings/loinc-part-obo/loinc2go.sssom.tsv
760287c 
Co-authored-by: Nico Matentzoglu <nicolas.matentzoglu@gmail.com>
@drseb @matentzn
Update mappings/loinc-part-obo/loinc2chebi_seb.sssom.tsv
19ce01e 
Co-authored-by: Nico Matentzoglu <nicolas.matentzoglu@gmail.com>
@drseb @matentzn
Update mappings/loinc-part-obo/loinc2ncit.sssom.tsv
331c048 
Co-authored-by: Nico Matentzoglu <nicolas.matentzoglu@gmail.com>
@drseb @matentzn
Update mappings/loinc-part-obo/loinc2pr.sssom.tsv
a68241e 
Co-authored-by: Nico Matentzoglu <nicolas.matentzoglu@gmail.com>
@drseb @matentzn
Update mappings/loinc-part-obo/loinc2uberon.sssom.tsv
2a9afc6 
Co-authored-by: Nico Matentzoglu <nicolas.matentzoglu@gmail.com>
@drseb @matentzn
Update mappings/loinc-part-obo/loinc2uberon.sssom.tsv
eb2eb5a 
Co-authored-by: Nico Matentzoglu <nicolas.matentzoglu@gmail.com>
@drseb @matentzn
Update mappings/loinc-part-obo/loinc2pr.sssom.tsv
4ee0846 
Co-authored-by: Nico Matentzoglu <nicolas.matentzoglu@gmail.com>
@drseb
move files to correct folder as requested by Nico
4b35266
@drseb
rename files as requested by Nico
fc164b1
@drseb
change mapping set id and remove mapping tool as requested by Nico
4728824
@drseb
add author-id to all but one file (not the one from tim) as requested…
1d5726a 
… by Nico
@drseb
fix formatting error in loinc-chebi meeting
a7421b3
@drseb
fix formatting error in loinc-chebi mapping ( remove one header item)
a51666d
@drseb
fix formatting error in one line - please god let the qc now pass
bfbcb9c
@drseb
fix formatting errors in sssom: please any of you gods - let the qc n…
06f302e 
…ow pass
@drseb
Merge branch 'main' into upload-loinc-part-mappings
23cbfcf
@drseb
add orcid in curie map - dear gh-actions, I give you 10 dollars if yo…
caaf453 
…u let this pass now
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drseb commented Mar 8, 2024

I hope it looks better now

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matentzn commented Mar 9, 2024

@drseb can you confirm:

You personally curated all of these mapping sets manually? Can you write two sentences here (in a comment on the PR) on how you created the mapping sets exactly (methodology), and what mapping rules you applied (using exact in case where units were mentioned, etc).

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drseb commented Mar 10, 2024

All mappings except loinc2chebi_1.sssom.tsv were created using a semi-manual approach, in which software suggested mappings based on string comparisons, but a human would always review and possibly refine the mapping. loinc2chebi_1.sssom.tsv was obtained from compLoinc (Tim etc.)

matentzn
matentzn commented Mar 10, 2024
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mappings/loinc2chebi_1.sssom.tsv
# license: https://github.com/mapping-commons/mapping-commons.github.io/blob/main/docs/original_license_applies.md
# mapping_date: '2022-02-23'
# mapping_set_id: http://w3id.org/mapping_commons/monarch/loinc2chebi_1.sssom.tsv
# issue_tracker: https://github.com/monarch-initiative/monarch-mapping-commons/issues
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Missing author_id and creator_id. What is the provenance for this one?

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i got this from compLoinc

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Can you describe in a bit more detail the mapping rules you used, for example:

In cases where the LOINC part reflected a measurement like protein^3rd tube we used skos:exactMatch to map to PR:protein to reflect the fact that the entity described by the LOINC part is identical to the PR ontology concept.

but a human would always review and possibly refine the mapping.

So so the statement would be correct that all mappings aside from Tims were manually reviewed by you right?

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