Dataset Viewer
The dataset viewer is not available for this split.
Cannot load the dataset split (in streaming mode) to extract the first rows.
Error code: StreamingRowsError
Exception: CastError
Message: Couldn't cast
protocol_id: string
protocol_name: string
protocol_scope: struct<applicable_variants: list<item: string>, protocol_version: string>
child 0, applicable_variants: list<item: string>
child 0, item: string
child 1, protocol_version: string
workflows: list<item: struct<final_outputs: list<item: struct<modality: string, state_id: string>>, initial_sta (... 1331 chars omitted)
child 0, item: struct<final_outputs: list<item: struct<modality: string, state_id: string>>, initial_state_ids: lis (... 1319 chars omitted)
child 0, final_outputs: list<item: struct<modality: string, state_id: string>>
child 0, item: struct<modality: string, state_id: string>
child 0, modality: string
child 1, state_id: string
child 1, initial_state_ids: list<item: string>
child 0, item: string
child 2, states: list<item: struct<discontinuities: list<item: null>, molecule_type: string, name: string, paired_reg (... 782 chars omitted)
child 0, item: struct<discontinuities: list<item: null>, molecule_type: string, name: string, paired_regions: list< (... 770 chars omitted)
child 0, discontinuities: list<item: null>
child 0, item: null
child 1, molecule_type: string
child 2, name: string
child 3, paired_regions: list<item: struct<paired_region_id: string, relationship: string, side_1: struct<segment_ids: list<i (... 126 chars omitted)
...
string
child 4, workflow_id: string
libraries: list<item: struct<final_molecule: string, library_sequence: string, modality: string, orientation: s (... 327 chars omitted)
child 0, item: struct<final_molecule: string, library_sequence: string, modality: string, orientation: string, segm (... 315 chars omitted)
child 0, final_molecule: string
child 1, library_sequence: string
child 2, modality: string
child 3, orientation: string
child 4, segments: list<item: struct<kind: string, length: int64, oligo_derivations: list<item: struct<oligo_id: string (... 168 chars omitted)
child 0, item: struct<kind: string, length: int64, oligo_derivations: list<item: struct<oligo_id: string, orientati (... 156 chars omitted)
child 0, kind: string
child 1, length: int64
child 2, oligo_derivations: list<item: struct<oligo_id: string, orientation_to_source: string>>
child 0, item: struct<oligo_id: string, orientation_to_source: string>
child 0, oligo_id: string
child 1, orientation_to_source: string
child 3, orientation: string
child 4, role: string
child 5, segment_id: string
child 6, sequence: string
child 7, support_status: string
child 8, placeholder: string
child 9, notes: string
child 5, strand: string
child 6, support_status: string
to
{'libraries': List({'final_molecule': Value('string'), 'library_sequence': Value('string'), 'modality': Value('string'), 'orientation': Value('string'), 'segments': List({'kind': Value('string'), 'length': Value('int64'), 'oligo_derivations': List({'oligo_id': Value('string'), 'orientation_to_source': Value('string')}), 'orientation': Value('string'), 'role': Value('string'), 'segment_id': Value('string'), 'sequence': Value('string'), 'support_status': Value('string'), 'placeholder': Value('string'), 'notes': Value('string')}), 'strand': Value('string'), 'support_status': Value('string')}), 'protocol_id': Value('string'), 'protocol_name': Value('string'), 'protocol_scope': {'applicable_variants': List(Value('string')), 'protocol_version': Value('string')}}
because column names don't match
Traceback: Traceback (most recent call last):
File "/src/services/worker/src/worker/utils.py", line 147, in get_rows_or_raise
return get_rows(
dataset=dataset,
...<4 lines>...
column_names=column_names,
)
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 127, in get_rows
rows_plus_one = list(itertools.islice(safe_iter(ds, dataset=dataset), rows_max_number + 1))
File "/src/services/worker/src/worker/utils.py", line 483, in safe_iter
yield from ds.decode(False) if ds.features else ds
File "/usr/local/lib/python3.14/site-packages/datasets/iterable_dataset.py", line 2951, in __iter__
for key, example in ex_iterable:
^^^^^^^^^^^
File "/usr/local/lib/python3.14/site-packages/datasets/iterable_dataset.py", line 2461, in __iter__
for key, pa_table in self._iter_arrow():
~~~~~~~~~~~~~~~~^^
File "/usr/local/lib/python3.14/site-packages/datasets/iterable_dataset.py", line 2486, in _iter_arrow
for key, pa_table in self.ex_iterable._iter_arrow():
~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^
File "/usr/local/lib/python3.14/site-packages/datasets/iterable_dataset.py", line 547, in _iter_arrow
for key, pa_table in iterator:
^^^^^^^^
File "/usr/local/lib/python3.14/site-packages/datasets/iterable_dataset.py", line 430, in _iter_arrow
for key, pa_table in self.generate_tables_fn(**gen_kwags):
~~~~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^
File "/usr/local/lib/python3.14/site-packages/datasets/packaged_modules/json/json.py", line 343, in _generate_tables
self._cast_table(pa_table, json_field_paths=json_field_paths),
~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/local/lib/python3.14/site-packages/datasets/packaged_modules/json/json.py", line 132, in _cast_table
pa_table = table_cast(pa_table, self.info.features.arrow_schema)
File "/usr/local/lib/python3.14/site-packages/datasets/table.py", line 2378, in table_cast
return cast_table_to_schema(table, schema)
File "/usr/local/lib/python3.14/site-packages/datasets/table.py", line 2306, in cast_table_to_schema
raise CastError(
...<3 lines>...
)
datasets.table.CastError: Couldn't cast
protocol_id: string
protocol_name: string
protocol_scope: struct<applicable_variants: list<item: string>, protocol_version: string>
child 0, applicable_variants: list<item: string>
child 0, item: string
child 1, protocol_version: string
workflows: list<item: struct<final_outputs: list<item: struct<modality: string, state_id: string>>, initial_sta (... 1331 chars omitted)
child 0, item: struct<final_outputs: list<item: struct<modality: string, state_id: string>>, initial_state_ids: lis (... 1319 chars omitted)
child 0, final_outputs: list<item: struct<modality: string, state_id: string>>
child 0, item: struct<modality: string, state_id: string>
child 0, modality: string
child 1, state_id: string
child 1, initial_state_ids: list<item: string>
child 0, item: string
child 2, states: list<item: struct<discontinuities: list<item: null>, molecule_type: string, name: string, paired_reg (... 782 chars omitted)
child 0, item: struct<discontinuities: list<item: null>, molecule_type: string, name: string, paired_regions: list< (... 770 chars omitted)
child 0, discontinuities: list<item: null>
child 0, item: null
child 1, molecule_type: string
child 2, name: string
child 3, paired_regions: list<item: struct<paired_region_id: string, relationship: string, side_1: struct<segment_ids: list<i (... 126 chars omitted)
...
string
child 4, workflow_id: string
libraries: list<item: struct<final_molecule: string, library_sequence: string, modality: string, orientation: s (... 327 chars omitted)
child 0, item: struct<final_molecule: string, library_sequence: string, modality: string, orientation: string, segm (... 315 chars omitted)
child 0, final_molecule: string
child 1, library_sequence: string
child 2, modality: string
child 3, orientation: string
child 4, segments: list<item: struct<kind: string, length: int64, oligo_derivations: list<item: struct<oligo_id: string (... 168 chars omitted)
child 0, item: struct<kind: string, length: int64, oligo_derivations: list<item: struct<oligo_id: string, orientati (... 156 chars omitted)
child 0, kind: string
child 1, length: int64
child 2, oligo_derivations: list<item: struct<oligo_id: string, orientation_to_source: string>>
child 0, item: struct<oligo_id: string, orientation_to_source: string>
child 0, oligo_id: string
child 1, orientation_to_source: string
child 3, orientation: string
child 4, role: string
child 5, segment_id: string
child 6, sequence: string
child 7, support_status: string
child 8, placeholder: string
child 9, notes: string
child 5, strand: string
child 6, support_status: string
to
{'libraries': List({'final_molecule': Value('string'), 'library_sequence': Value('string'), 'modality': Value('string'), 'orientation': Value('string'), 'segments': List({'kind': Value('string'), 'length': Value('int64'), 'oligo_derivations': List({'oligo_id': Value('string'), 'orientation_to_source': Value('string')}), 'orientation': Value('string'), 'role': Value('string'), 'segment_id': Value('string'), 'sequence': Value('string'), 'support_status': Value('string'), 'placeholder': Value('string'), 'notes': Value('string')}), 'strand': Value('string'), 'support_status': Value('string')}), 'protocol_id': Value('string'), 'protocol_name': Value('string'), 'protocol_scope': {'applicable_variants': List(Value('string')), 'protocol_version': Value('string')}}
because column names don't matchNeed help to make the dataset viewer work? Make sure to review how to configure the dataset viewer, and open a discussion for direct support.
LibStructBench ground truth — 20 protocols
Dataset: https://huggingface.co/datasets/sequencing/scg-protocols-v1-groundtruth
Each protocol folder contains three unchanged ground-truth JSON files:
groundtruth_final_lib_struct.json: Task 1, final library structures.groundtruth_oligos.json: Task 2, oligo inventory and support annotations.groundtruth_library_generation_workflow.json: Task 3, molecular states and transitions.
There are 60 ground-truth files. The 20-protocol subset and full 73-protocol collection have identical JSON for shared protocols. Keep reference labels separate from agent-visible benchmark inputs.
Paper and protocol sources
SOURCE_MANIFEST.json contains source links, recorded revision labels, and hashes of the source copies. Source PDFs, supplements, extracted text, and raw logs are not included. Obtain documents from their original providers under the applicable terms.
The source inventory is still incomplete: 36 of 58 records lack a recorded file-specific URL, and 51 lack an explicit revision label. Candidate DOIs and related protocol links are discovery aids, not verified links to an exact document. Null fields indicate missing metadata. File hashes identify exact copies; auxiliary text hashes do not establish figure/table equivalence.
Attribution and license
These annotations and dataset documentation are prepared for release under CC BY 4.0, covering rights held by the contributing licensors. Preserve attribution, link the license, and indicate changes. This does not grant rights to the linked third-party source documents or imply their authors’ endorsement.
LibStructBench adapted, audited, and extended scg_lib_structs, including molecular workflows and human-adjudicated corrections. Credit both the original curators and the LibStructBench authors when reusing these annotations.
Upstream citation: Xi Chen, Patrick Roelli, Darío Hereñú, Pontus Höjer, and Tim Stuart. Teichlab/scg_lib_structs: Release 26th Oct 2023, version 20231026. DOI: 10.5281/zenodo.10042390. That archived release declares CC BY 4.0. The citation identifies the upstream project, not the exact snapshot used for every record: the local HTML snapshot has no recorded upstream commit. Its file hashes are retained in the source manifest. Descriptive annotation notes have not received comprehensive copyright clearance.
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