Expand node properties

[kevinschaper]

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]

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]

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]

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]

Yes, we should not use xrefs for any reason.