ontogpt
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monarch-initiative
LLM-based ontological extraction tools, including SPIRES
I'm interested in using OntoGPT with an OpenAI-compatible base URL. Currently, OntoGPT seems to be designed for use with the official OpenAI API. Could you please consider adding support for...
Haven't been able to reproduce this consistently, but attempts to ground using the Translator endpoint (though OAK) will sometimes fail in an uncontrolled way. Stack trace c/o @enockniyonkuru ``` Traceback...
When missing API keys (and especially the Bioportal one), crashes can happen in the middle of operations. If a template requires Bioportal in its annotators, for example, using that template...
On the page: https://monarch-initiative.github.io/ontogpt/operation/ there are several links to templates, including one specifically to the GO-CAM template. All are 404 - likely because they should actually link to repository locations...
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...
The knowledge engine class includes a `map_identifier` function: https://github.com/monarch-initiative/ontogpt/blob/e3a68ae8391b12559842089657799156c06fd2f0/src/ontogpt/engines/knowledge_engine.py#L418 This calls the NodeNormalizer API through OAK: https://github.com/INCATools/ontology-access-kit/blob/0a734a8383943891173eaf8b1fd95cf4fde1f65e/src/oaklib/implementations/translator/translator_implementation.py This process can take some time, especially when grounding many entities. In some...
The MIRO checklist is for the minimum information in reporting an ontology. Natural fit for an extraction template, as some responses may simply be IRIs, URLs, etc. See https://doi.org/10.1186/s13326-017-0172-7 See...
(related to discussion with @enockniyonkuru re: MAXO extraction on Apr 1 2024) SPIRES extraction does grounding recursively, but still doesn't always catch instances where the term to match is within...
Schemas may currently be annotated with the `owl` slot to denote the OWL equivalent, e.g., in the `recipe` schema: ```yaml FoodItem: is_a: CompoundExpression annotations: owl: IntersectionOf attributes: food: description: the...
Related to the change introduced in #304. For each new YAML output document appended to the `output.txt` file, the `extracted_object` item is correct (only contains information from the current input...
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LLM-based ontological extraction tools, including SPIRES