Dataset Viewer
The dataset viewer is not available for this split.
Cannot extract the features (columns) for the split 'train' of the config 'default' of the dataset.
Error code: FeaturesError
Exception: FileNotFoundError
Message: [Errno 2] No such file or directory: '<datasets.utils.file_utils.FilesIterable object at 0x7f722084da90>'
Traceback: Traceback (most recent call last):
File "/src/services/worker/src/worker/job_runners/split/first_rows.py", line 246, in compute_first_rows_from_streaming_response
iterable_dataset = iterable_dataset._resolve_features()
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/local/lib/python3.12/site-packages/datasets/iterable_dataset.py", line 4196, in _resolve_features
features = _infer_features_from_batch(self.with_format(None)._head())
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/local/lib/python3.12/site-packages/datasets/iterable_dataset.py", line 2533, in _head
return next(iter(self.iter(batch_size=n)))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/local/lib/python3.12/site-packages/datasets/iterable_dataset.py", line 2711, in iter
for key, pa_table in ex_iterable.iter_arrow():
^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/local/lib/python3.12/site-packages/datasets/iterable_dataset.py", line 2249, in _iter_arrow
yield from self.ex_iterable._iter_arrow()
File "/usr/local/lib/python3.12/site-packages/datasets/iterable_dataset.py", line 494, in _iter_arrow
for key, pa_table in iterator:
^^^^^^^^
File "/usr/local/lib/python3.12/site-packages/datasets/iterable_dataset.py", line 384, 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/xml/xml.py", line 67, in _generate_tables
with open(file, encoding=self.config.encoding, errors=self.config.encoding_errors) as f:
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/local/lib/python3.12/site-packages/datasets/streaming.py", line 73, in wrapper
return function(*args, download_config=download_config, **kwargs)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/local/lib/python3.12/site-packages/datasets/utils/file_utils.py", line 967, in xopen
return open(main_hop, mode, *args, **kwargs)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
FileNotFoundError: [Errno 2] No such file or directory: '<datasets.utils.file_utils.FilesIterable object at 0x7f722084da90>'Need help to make the dataset viewer work? Make sure to review how to configure the dataset viewer, and open a discussion for direct support.
Open-Rosalind Knowledge Base Standard
This dataset contains the Open-Rosalind Standard local knowledge-base bundle used for local-first biomedical agent retrieval.
Contents
raw/: downloaded public source files from UniProt, NCBI Gene, HGNC, Gene Ontology, Reactome, ClinVar, Ensembl, PubMed baseline, and Swiss-Prot BLAST FASTA.index/: first-pass local indexes for MVP5.index/open_rosalind_standard.sqlite: SQLite FTS5 text index.index/blast/swissprot.*: local Swiss-Prot BLAST protein database.index/manifest.json: build metadata and source counts.logs/: source download logs.
Current Index Counts
- HGNC genes: 44,986
- Reactome human pathways: 2,870
- GO terms: 5,000
- ClinVar gene summaries: 5,000
- Swiss-Prot BLAST sequences: 574,627
Size
- Raw source bundle: about 60 GB
- Index bundle: about 646 MB
Usage
huggingface-cli download dnagpt/open-rosalind-kb-standard --repo-type dataset --local-dir /autodl-fs/data/open-rosalind-kb/standard
Then point Open-Rosalind local KB code at /autodl-fs/data/open-rosalind-kb/standard/index.
Provenance
All source files are public biomedical data downloads. Open-Rosalind stores local indexes and manifests to make agent retrieval faster, auditable, and reproducible.
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