Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Expand node properties #90

Open
kevinschaper opened this issue Feb 1, 2023 · 4 comments
Open

Expand node properties #90

kevinschaper opened this issue Feb 1, 2023 · 4 comments

Comments

@kevinschaper
Copy link
Collaborator

I created this issue over in monarch-ingest when I realized that I didn't have synonyms for ontology terms.

I know that we also need to know if nodes are obsolete, and there's #79 for xrefs. I have no idea whether to use xrefs as provided or SSSOM mappings in place of them! I wonder the same thing about our gene mapping vs provided xrefs, but this issue has even shown up in the new UI where the interface currently has a spot for both xrefs and equivalent relationships.

@kevinschaper
Copy link
Collaborator Author

The synonym & xref columns aren't empty anymore, but I'm not so sure about the quantities.

For synonym, somehow we're only getting 65 records with the field synonym field populated, that's definitely a bug. For xref, we're getting 71k, which isn't as obviously broken, but does seem a bit low.

@caufieldjh
Copy link
Contributor

Strange! Do you have an idea about how many you'd expect to see? Perhaps not for all of PHENIO, but for a given namespace?

The other question here is how many of those synonyms/xrefs are in the phenio.json. I see ~103K unique "xrefs" fields across all of phenio.json, and some of those involve namespaces we don't really use anywhere or the occasional http URL.

I think synonyms aren't getting parsed correctly at all - there are > 274K hasExactSynonym predicates used across all of phenio.json.

@kevinschaper
Copy link
Collaborator Author

I don't have any sense of xrefs, but given that we probably eventually want to use SSSOM instead, it probably makes more sense to chase after those 274K synonyms

@matentzn
Copy link

matentzn commented Jul 7, 2023

Yes, we should not use xrefs for any reason.

Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Labels
None yet
Projects
None yet
Development

No branches or pull requests

3 participants