Map template to formal ontologies

[lwaldron]

We need maps between terms in the template and formal ontologies. Preferred ontologies for:

• body_site & body_subsite -> Uberon Ontology
• disease & disease_subsite -> Experimental Factor Ontology
• antibiotics_family -> ?

Also see:

• The Ontology Lookup Service
• The Bioconductor ontoProc package

[lwaldron]

@ftzohra22 would you do this? It would just be a two-column spreadsheet of mappings different grammar.

[lwaldron]

Add ontology map to inst/extdata on GitHub

[lwaldron]

@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.

[lwaldron]

@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

[QuanWan89]

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

— Reply to this email directly, view it on GitHub https://github.com/waldronlab/curatedMetagenomicDataCuration/issues/26#issuecomment-1080713646, or unsubscribe https://github.com/notifications/unsubscribe-auth/ALAKTLAHQDK4JJX3QAC5HBTVCG5TTANCNFSM4FMBMEWA . You are receiving this because you were mentioned.Message ID: @.*** com>

[schifferl]

@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

[lwaldron]

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.

[lwaldron]

Direct link to files in GitHub repo for convenience: https://github.com/waldronlab/curatedMetagenomicDataCuration/tree/3e7fba1bcacbc65cb3ef3a5b36c7feb9bcae6acc/inst/extdata