Aim 1.2.2 Phenotype definition editor

[matentzn]

We currently generate terms from templates using spreadsheets. For example, a term for 'increased blood glucose' generated using the template described in Figure 10a labs, can be specified by a row in a spreadsheet with the columns 'level', 'chemical' and 'substance' filled with ontology terms 'increased', 'glucose' and 'blood' respectively. While spreadsheets are simple enough to make development feasible, maintaining them at scale requires automated QC, syntax validation, and input assistance. We have built a prototype web-based table editor that uses term templates to automatically generate a table with appropriate columns and supports specification of ontology terms using autocompletion [71]. We will further develop this tool to embed it seamlessly into ontology curation workflows and add QC.

[matentzn]

• Contemplate assigning to @pnrobinson team to become a module in his upcoming HPO curation tool?
• Another option a data harmoniser type solution
• A third option is to use ontodev infrastructure

[dosumis]

Possible solution - Jame's Overton's Nanobot (we may adopt this for one of the single cell projects).

[matentzn]

I think the Nanobot idea should be considered. But note that there is no push at all to achieve this task; I think we should probably.

Our curators love the tables; if anything, having autocomplete support and inline validation would be nice. This could be done both with nanobot (20K investment to James Overton as a one-off) and with data-harmoniser (requires @cmungall to make a commitment to get this to work). Another option would be to try and integrate a web service call straight into the google sheet (https://hevodata.com/learn/google-sheets-rest-api-integration/#:~:text=Using%20Google%20Apps%20Script%2C%20we,Numbers%20API%20from%20Google%20Sheets.) - but I am pretty sure there were some limitations.

[pnrobinson]

Honestly I do not think that templated term development for phenotype ontologies is a good idea because (1) the "easy" terms are already in the various phenotype ontologies (e.g., "since E/Q definitions") (2) The kinds of term requests we are now getting for HPO are sometimes exceedingly complicated and require perusal of the medical literature; I would imaging the situation is similar for many of the other ontologies such as MP etc (3) It is super helpful for users to have citations to the original literature to read more. I would suggest doing a requirements analysis first and then decide on the technology

[matentzn]

I think I agree with you @pnrobinson but can we simply say on so many sub aims in a grant: “it turned out to be the wrong way” - we didn't need it after all?

[matentzn]

No updates for current grant period, but we are in active discussions with James Overton still about a web-based tool for developing OBA and VBO, and possibly HPO!