shawntanzk
commented
2 years ago Points from meetings:
3 main roles that might add/want to add terms:
1) Data Wrangler
- Want a single point of entry (eg for HCAO - term request should be in HCAO repo, and ontology editor redirect)
- Handle terms additions through individual tickets or MIRACL sheets
- Future training with ROBOT template possible -> might however need tooling
- Current single point of entry is a limiting factor as it requires redirects etc., perhaps some tooling to aid that?
2) Researcher/Domain Expert
- Many will not want to use GitHub, so even issue tracker might not work well
- Spreadsheets like MIRACL work well -> maybe we need one for minimal information for PCL
- Perhaps some tooling for simple thing addition of terms that automatically generates a ticket or even populates a template?
3) Ontology Editor
- The only ones who should decided between PCL and CL (they should be the one to move the tickets from CL issue tracker to PCL if it belongs there instead)
- Needs clean data for mass additions
- ROBOT template still limited, might need tooling (perhaps just standard DOSDP templates with minimal information that can be extended? Thinking something similar to BDSO pipeline but simplified)
General notes:
- Google sheets add-ons might be tricky (some unis block them)
- Case: Google sheet Add-On designed by Josef Hardi from Mark Musen’s lab at Stanford, worked with Ellen Quardokus HuBMAP Mapping Component at Indiana University, but some universities have security in place where they will not allow university google accounts to use Add-Ons.
- The tool can be found here: In Google sheet → Extensions→ Add-ons→ Get Add-ons→ search for Reconcile Name Biomedical Term, install, documentation is linked out from the help within the add-on.
CellXGene has many cases of new cell types that are only defined by single cell transcriptomics. We think it would be useful to have a generic template for adding these with:
label; synonyms; parent class; reference; location; marker set
For marker set, it is probably best to use 'marker bags'. We need to look at the best way to generate these. We might need some programmatic step after an initial template table before ROBOT or DOSDP.
I think useful to have this anyway.
Some general issues.
What is the workflow for addition? Do we dump every new cell type here until an editor can review for addition to CL or do we have editors review and decide between PCL and CL?
differences in location relation by cell type, e.g. has_soma_location for neurons. Maybe have a different sheet for these?
CC @BAevermann