INCATools / INCATools/ontology-access-kit
`ProntoImplementation.*_relationship_map()`: no results for subclassed term
- Dominant language
- Python
- Stars
- 198
- Forks
- 35
- Avg merge
- 3d 4h
- Merged PRs (30d)
- 1
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 any term**
I loaded `omim.owl` into `ProntoImplementation`. Then, I got all OMIM terms as CURIEs, and for each of them, I tried getting results from `.incoming_relationship_map()` and `.outgoing_relationship_map()`, but got 0 results in total.
**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. I tried both methods on this explicitly. I would have expected results from at least 1 of these methods (maybe `.outgoing_relationship_map()`?) but got no results:
```owl
...
AAA1
...
```
## Additional info
I tried `[x for x in SqlImplementation(...).relationships()]` and got back 32,926 triples from my `omim.owl`.
Interestingly though, `[x for x in SqlImplementation(...).relationships(subjects=['https://omim.org/entry/100070'])]` returned 0 results. I only tried for this one term though; I wonder if the reason that gave me 0 results has something to do with these pronto methods returning no results. If so, #238 is a related issue.
Note that I do not believe there is a general method in `ProntoImplementation` that returns all relationships in the way that `SqlImplementation.relationships()` does.
Contributor guide
Research direction
Start with ProntoImplementation._relationship_map(), incoming_relationship_map(), and outgoing_relationship_map(), then compare their behavior with SqlImplementation.relationships(), including the subject-filtered example in the issue. Check the related behavior described in issue #238 and determine why subclass relationships are not returned. Done means the relevant Pronto methods return the expected relationships for the OMIM term without breaking existing queries.
Written by the indexing model from the issue text.
Assessment
- Tech stack
- python
- Domain
- backend
- Issue type
- Bug
- Difficulty
- 4/5
- Estimated time
- 3-5 days
- Activity status
- Stale
- Clarity
- Mostly clear
- Newbie friendliness
- 35/100