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I'm curious as to the difference between the ambitions of these two tools? Are they converging or going off in different directions? I can't quite tell from the descriptions. (https://github.com/mona…
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I'm trying to follow the example provided in [Strategy 1: Knowledge extraction using SPIRES](https://github.com/monarch-initiative/ontogpt#strategy-1-knowledge-extraction-using-spires)
in command l…
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##### Project link
https://github.com/orgs/geneontology/projects/TBD
##### Project description
Lorem ipsum
##### PI
Chris
##### Product owner (PO)
Chris?
##### Technical lead (TL)
TBD…
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Originally seen in #346.
Using a Bioportal ontology (like bioportal:SNOMEDCT) as an annotator works fine on its own.
If used in a value set expansion, e.g., with a `reachable_from`, it tries to down…
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Running the following command:
```
$ ontogpt -vvv pubmed-annotate -t gocam --get-pmc --limit 1 "27849154"
```
results in an error:
```
...
INFO:ontogpt.engines.knowledge_engine:GROUNDING HSN us…
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I have a corpus of ~75,000 abstracts that I want to make a KG out of using OntoGPT. After 4 hours, it only got through 50 documents -- not super promising!
I took a look through the docs to see if …
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Calls to the `recipe-extract` command fail with the following:
```
Traceback (most recent call last):
File "/home/harry/ontogpt/.venv/bin/ontogpt", line 6, in
sys.exit(main())
File "/hom…
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Hi, I tried to use the BioLink model as base to run the SPIRES engine (as it was recommended in the readme!), but faced some issue.
Generating the `.py` file from the `biolink_model.yaml` put in `…
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Hello @cmungall, I was able to install ontogpt after adjusting dependencies using poetry. I was trying to run the example your readme, i.e.
```
kih1pal@SYV-C-0001Y:~/ontogpt$ poetry run ontogpt ext…