The dataset viewer is not available for this split.
Error code: StreamingRowsError
Exception: ValueError
Message: Trailing data
Traceback: Traceback (most recent call last):
File "/src/services/worker/src/worker/utils.py", line 99, in get_rows_or_raise
return get_rows(
^^^^^^^^^
File "/src/libs/libcommon/src/libcommon/utils.py", line 272, in decorator
return func(*args, **kwargs)
^^^^^^^^^^^^^^^^^^^^^
File "/src/services/worker/src/worker/utils.py", line 77, in get_rows
rows_plus_one = list(itertools.islice(ds, rows_max_number + 1))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/local/lib/python3.12/site-packages/datasets/iterable_dataset.py", line 2567, in __iter__
for key, example in ex_iterable:
^^^^^^^^^^^
File "/usr/local/lib/python3.12/site-packages/datasets/iterable_dataset.py", line 2102, in __iter__
for key, pa_table in self._iter_arrow():
^^^^^^^^^^^^^^^^^^
File "/usr/local/lib/python3.12/site-packages/datasets/iterable_dataset.py", line 2125, in _iter_arrow
for key, pa_table in self.ex_iterable._iter_arrow():
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/local/lib/python3.12/site-packages/datasets/iterable_dataset.py", line 479, in _iter_arrow
for key, pa_table in iterator:
^^^^^^^^
File "/usr/local/lib/python3.12/site-packages/datasets/iterable_dataset.py", line 380, in _iter_arrow
for key, pa_table in self.generate_tables_fn(**gen_kwags):
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/local/lib/python3.12/site-packages/datasets/packaged_modules/json/json.py", line 176, in _generate_tables
ujson_dumps({"text": x}) for x in ujson_loads(full_data)
^^^^^^^^^^^^^^^^^^^^^^
File "/usr/local/lib/python3.12/site-packages/datasets/utils/json.py", line 20, in ujson_loads
return pd.io.json.ujson_loads(*args, **kwargs)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
ValueError: Trailing dataNeed help to make the dataset viewer work? Make sure to review how to configure the dataset viewer, and open a discussion for direct support.
Ontology & Embedding Database
This repository provides the local ontology database to be used by StructSense (in general can be used for any other purpose), including both structured ontological data and precomputed vector embeddings for efficient semantic search.
Overview
- 3,925,124 classes
- 2,683,756 synonyms
- Data storage:
- SQLite → structured ontology data (
bioportal.db) - Embeddings → vector embeddings (to be uploaded)
- SQLite → structured ontology data (
Vector embeddings (includes preferred label + definition + synonyms + alternative labels + parent labels + ontology context) are generated using the BAAI/bge-small-en-v1.5 model to enable high-quality semantic similarity search.
Database Schema (Main Tables)
If you plan to extend or enrich the database, the primary tables include:
ontologiesclassessynonymslabelsparents
🔎 Search & Query
You can explore the ontology, perform semantic search, and run database queries via the Hugging Face Space:
👉 https://huggingface.co/spaces/sensein/demo-ontology-search
Data Source
The original ontology data is sourced from BioPortal, which aggregates biomedical ontologies from multiple authoritative providers.
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