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lactate as an extension #2834

Closed ValWood closed 5 months ago

ValWood commented 6 months ago

error log has warning in 9d56e0cfc18f0d09: can't find term with ID: CHEBI:24996 warning in 9d56e0cfc18f0d09: can't find term with ID: CHEBI:24996

but we can't work out why because lactate is in the extension options. Does it need to be added to some config? I can't remember

ValWood commented 6 months ago

CC @PCarme

kimrutherford commented 6 months ago

Hi Val.

The message is because that term isn't in Chado. It's not in the mini ontology: pombe-embl/mini-ontologies/chebi.obo

I've just added it. The warning should be gone in the morning.

ValWood commented 6 months ago

So how was it recognized, this part confuses me? I thought things only showed up in the autocomplete if they were already in the mini-ontology?

kimrutherford commented 6 months ago

I thought things only showed up in the autocomplete if they were already in the mini-ontology?

Yep, good point. Which extension were you auto-completing?

kimrutherford commented 6 months ago

Which extension were you auto-completing?

It's OK, I found it in the session: increased_in_presence_of lactate

kimrutherford commented 6 months ago

It turns out that it comes from loading the GO OBO file. I think this has confused us before. We load all the terms in the GO OBO file because that's simpler. But it means we get some bonus terms in Canto.

The GO files we load into Canto and Chado are different. For Chado we load the standard go-basic.obo from the snapshot: http://purl.obolibrary.org/obo/go/snapshot/go-basic.obo

For Canto we process go-plus.owl from the snapshot to generate a taxon restricted OBO file. Unfortunately that has extra terms and I've never got around to investigating how we can remove them. The lactate ChEBI term is in go-plus.owl because it's used in the logical definition of lactate metabolic process (GO:0006089)

ValWood commented 6 months ago

So why do we still need to add it to our chebi.obo? Cant we just automatically include anything which comes via GO?

kimrutherford commented 6 months ago

Cant we just automatically include anything which comes via GO?

The GO OBO file we load into Chado doesn't have the ChEBI terms needed for logical definitions. We load go-basic.obo which doesn't have the logical definitions.

The taxon restricted OBO we load into Canto is generated from go-plus.owl by OWLTools and includes the logical definitions and the terms (like ChEBI term) that are needed for the logical definitions.