StructSense Pipeline Upgrade: Specialized Tools, Robust Chunking, and BioPortal Integration#62
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tekrajchhetri wants to merge 143 commits intomainfrom
Open
StructSense Pipeline Upgrade: Specialized Tools, Robust Chunking, and BioPortal Integration#62tekrajchhetri wants to merge 143 commits intomainfrom
tekrajchhetri wants to merge 143 commits intomainfrom
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Note: to disable traces run "crewai traces disable"
…han just spacy NER
sample output
{
"text": "photopic spectral sensitivity curves",
"label": "CONCEPT",
"occurrences": [
{
"start": 51,
"end": 87,
"global_start": 1127,
"global_end": 1163,
"sentence": "Recently, electroretinogram (ERG) responses of the photopic spectral sensitivity curves of photoreceptors of rats and mice were measured throughout the UV-visible spectrum (300-700 nm) (Rocha et al., 2016)."
}
]
},
{
"text": "photoreceptors",
"label": "ANATOMICAL-CONCEPT",
"occurrences": [
{
"start": 91,
"end": 105,
"global_start": 1167,
"global_end": 1181,
"sentence": "Recently, electroretinogram (ERG) responses of the photopic spectral sensitivity curves of photoreceptors of rats and mice were measured throughout the UV-visible spectrum (300-700 nm) (Rocha et al., 2016)."
}
]
},
{
"text": "rats and mice",
"label": "ORGANISM",
"occurrences": [
{
"start": 109,
"end": 122,
"global_start": 1185,
"global_end": 1198,
"sentence": "Recently, electroretinogram (ERG) responses of the photopic spectral sensitivity curves of photoreceptors of rats and mice were measured throughout the UV-visible spectrum (300-700 nm) (Rocha et al., 2016)."
}
]
},
…loading of models.
Collaborator
Author
|
WIP: search and reranking for ontology alignment. |
Move usage documentation (CLI, Python API, known issues) from tutorial/readme.md into the root README.md and delete the tutorial copy. Closes task 1 of #69.
removed link to brainkb documentation and moved `tutorials` section further down
Separate symptom and resolution into distinct sections for the pip resolution-too-deep and Python version known issues.
The 'Python version' issue section is unclear because the resolution is listed as if it were part of the symptom. To make it easier for users to understand and solve the problem, I recommend separating the symptom and resolution and formatting the error message as a code block for better readability. Co-authored-by: gemini-code-assist[bot] <176961590+gemini-code-assist[bot]@users.noreply.github.com>
This reverts commit 4b320c6.
…ssed properly; removing src/tests from gitignore
Added link to original dataset in the readme.
Added a link to the original dataset for reference.
…runs these tests only when openrouter is available
NER Benchmarking Dataset
…ate directory in readme
Merge tutorial README into root README
adding source checks and source_text option
adding option to set task_type + tests
Add NER tests
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This pull request introduces major improvements to StructSense, including the addition of specialized tools, fixes to the chunking mechanism, and integration with BioPortal as the ontology database.
What’s Included
Issues this PR addresses