Open lwaldron opened 6 years ago
@ftzohra22 would you do this? It would just be a two-column spreadsheet of mappings different grammar.
Add ontology map to inst/extdata
on GitHub
@schifferl I think you've made some changes here, can you provide rationale & keep the issue updated? 422dfd9535e809739949f88790c0eb5b81a1a78c
The goal is to begin curating entirely based on ontology terms instead of the ad-hoc terms we have used previously. The map can be used to correct previously curated files, and provide a "legacy" option for code using the originally curated terms.
@QuanWan89 can you think of how to include ontology terms and the "informal" terms as synonyms in the metadata database? See the work on maps at https://github.com/waldronlab/curatedMetagenomicDataCuration/commit/422dfd9535e809739949f88790c0eb5b81a1a78c
Hi Levi,
Let me add this topic in tomorrow's meeting agenda. I am sorry that I am really busy until next Wednesday. I am sorry that I cannot reply to you immediately yesterday. But I have several topics to discuss tomorrow. I will update the notes tonight.
Best regards, Quan
On Mon, Mar 28, 2022 at 10:18 AM Levi Waldron @.***> wrote:
@QuanWan89 https://github.com/QuanWan89 can you think of how to include ontology terms and the "informal" terms as synonyms in the metadata database? See the work on maps at 422dfd9 https://github.com/waldronlab/curatedMetagenomicDataCuration/commit/422dfd9535e809739949f88790c0eb5b81a1a78c
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@lwaldron and @QuanWan89, I went a little overboard in 422dfd9 knowing that we could revive the maps if needed. I will bring them back now, sorry about that.
body-site-ontology.csv updated-disease-ontology.csv updated-template.csv
No worries - my only concern is that it wasn't mentioned in this issue, and I don't want to lose track of the work done. It's not a bad place to keep them until we can complete this issue. It points to the need to update a central project management space for all the moving parts of cMD.
Direct link to files in GitHub repo for convenience: https://github.com/waldronlab/curatedMetagenomicDataCuration/tree/3e7fba1bcacbc65cb3ef3a5b36c7feb9bcae6acc/inst/extdata
We need maps between terms in the template and formal ontologies. Preferred ontologies for:
Also see: