INCATools / INCATools/ontology-access-kit
`SqlImplementation.relationships()`: no results when filtering by `subjects`
- Dominant language
- Python
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- 198
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Description
## Overview
I am using OAK to query OMIM. I want to get CURIEs for parent classes of a given term CURIE.
**No results for specific term**
Here's a truncated example of an a term that I know is subclassed in the `omim.owl`. It doesn't have any subclasses of its own.
```owl
...
AAA1
...
```
I did `[x for x in SqlImplementation(...).relationships()]`, and got back 32,926 results. Among those results, this term `https://omim.org/entry/100070` appeared in 2 triples:
```py
[('', 'RO:0002525', 'obo:CHR_9606chr19q13'),
('', 'rdfs:subClassOf', '')]
```
However, I tried querying for this term using the `subjects` filter, but got no results: `[x for x in ontology_sql.relationships(subjects=['https://omim.org/entry/100070'])]`.
I am assuming that this problem for filtering `.relationships()` by `subjects` might also apply to `predicates` and `objects`, but I haven't tried.
I also haven't tried doing this operation for all terms in my `omim.owl`. I only tried it on that 1 term (`100070`) that I knew to have relationships.
## Additional info
Potentially related issue: #237
Contributor guide
Research direction
Start at SqlImplementation.relationships(), comparing the unfiltered relationship tuples with the subjects=['https://omim.org/entry/100070'] call; review related issue #237 for context. Done means subject filtering returns the matching triples shown in the report, with predicate and object filtering checked if the same path handles them.
Written by the indexing model from the issue text.
Assessment
- Tech stack
- python, sql
- Domain
- database
- Issue type
- Bug
- Difficulty
- 3/5
- Estimated time
- 1-2 days
- Activity status
- Stale
- Clarity
- Mostly clear
- Newbie friendliness
- 42/100