INCATools / INCATools/ontology-access-kit

Lexmatch: inconsistent behaviour in `sqlite` and `default` mode

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Dominant language
Python
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Description

According to documentation, I should be able to use `lexmatch` with other ontology interfaces. However, while this here works fine:

```
runoak -i sqlite:foodon_wd.owl lexmatch -o foodon_wd_lexmatch.tsv
```

This here:

```
runoak -i foodon_wd.owl lexmatch -o foodon_wd_lexmatch.tsv
```

results in an empty mapping set data frame (with curie map and all, just no mappings).

The following warnings are printed:

```
WARNING:root:Using rdflib rdf/xml parser; this behavior may change in future
WARNING:root:Not a curie: foodon.owl
WARNING:root:Not a curie: foodon.owl
```

One idiosyncrasy of the ontology in question is that contains entities with no OWL typing in it:

```

cashew apple juice

```

Contributor guide

Open the contributing guide

Research direction

Start by running the two documented runoak lexmatch commands and compare their mapping sets and warnings. Trace how the sqlite and default ontology interfaces handle the RDF/XML input, including the untyped rdf:Description entity. Done means default mode produces the expected mappings consistently with sqlite mode.

Written by the indexing model from the issue text.

Assessment

Tech stack
python, sqlite
Domain
cli, search
Issue type
Bug
Difficulty
3/5
Estimated time
1-2 days
Activity status
Stale
Clarity
Mostly clear
Newbie friendliness
35/100

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