INCATools / INCATools/ontology-access-kit

`ProntoImplementation` Obograph takes ~8 minutes to load

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#338 2 comments 0 reactions 0 assignees View on GitHub
Dominant language
Python
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Merged PRs (30d)
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Description

## Overview
I'm trying to use OAK to get an Obograph, but `ProntoImplementation` took me 467 seconds to load it, where the `bioontologies` package took 48 seconds.

## Example
**ProntoImplementation**
```py
from datetime import datetime
from oaklib.resource import OntologyResource
from oaklib.implementations.pronto.pronto_implementation import ProntoImplementation
resource = OntologyResource(slug=inpath, local=True)
t1 = datetime.now()
oi = ProntoImplementation(resource)
graph = oi.as_obograph()
t2 = datetime.now()
print(f'Loaded obograph using ProntoImplementation in {(t2-t1).seconds} seconds')
```
> `Loaded obograph using ProntoImplementation in 467 seconds`

**bioontologies & robot**
```py
from datetime import datetime
t1 = datetime.now()
from bioontologies import robot
parse_results: robot.ParseResults = robot.convert_to_obograph_local(inpath)
graph = parse_results.graph_document.graphs[0]
t2 = datetime.now()
print(f'Loaded obograph using robot through bioontologies in {(t2-t1).seconds} seconds')
```
> `Loaded obograph using robot through bioontologies in 48 seconds`

## Additional info
I was looking around and wasn't quite sure which implementation was best to use for Obographs. I tried `OboGraphImplementation`, but I [got an error](https://github.com/INCATools/ontology-access-kit/issues/337). I was searching through the `implementations/` dir, but it was difficult for me to tell whether or not Obographs were fully implemented in each implementation. If there's a better implementation to use, I'm open to trying.

## Related
- #339

Contributor guide

Open the contributing guide

Research direction

Start with oaklib.implementations.pronto.pronto_implementation.ProntoImplementation and compare its Obograph loading path with bioontologies.robot.convert_to_obograph_local. Review the implementations/ directory and related issue #339; done means identifying the cause of the loading gap and either improving the implementation or documenting the better choice.

Written by the indexing model from the issue text.

Assessment

Tech stack
python
Domain
backend, performance
Issue type
Bug
Difficulty
4/5
Estimated time
3-5 days
Activity status
Stale
Clarity
Needs clarification
Newbie friendliness
30/100

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