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@Scigantic

Scigantic

README.md

Scigantic

Scigantic builds a platform for working with public scientific data: a searchable catalog of thousands of archives, notebooks that mount them directly with no download step, an in-notebook AI assistant with schema-aware context, and fine-tuning pipelines for biological sequence models. scigantic.com

The packages in this org are the query layer underneath that platform, released standalone. Each one is a permissively licensed Python client for a specific public archive or file format, self-contained and usable with no dependency on the rest of Scigantic. Together they're a library of libraries: point-lookups, search, and streaming access over public scientific data, without mirroring a database yourself or downloading more than you need. Using one on its own is a preview of the access layer that Scigantic's contextualized archives and fine-tuning infrastructure are built on top of.

Structural biology & cryo-EM

Package What it does
scigantic-empiar Stream any of ~3,000 EMPIAR cryo-EM datasets (8.9 PiB) over parallel HTTP range reads, nothing downloaded
scigantic-emdb Search all 60,895 EMDB structures by protein, organism, resolution, molecular weight, or PDB cross-reference
scigantic-wwpdb Fetch any of ~45,000 wwPDB Chemical Component Dictionary ligands and monomers by id, no download
scigantic-cryoet Search ~370 CZ CryoET Data Portal tomography datasets by organism, sample type, disease, or annotation coverage

Chemistry & bioactivity

Package What it does
scigantic-chembl Query ChEMBL directly from a public S3 mirror with DuckDB, no local database
scigantic-bindingdb Query BindingDB the same way, including a live cross-reference bridge into ChEMBL
scigantic-pubchem Live PubChem client with throttle-aware retry, BioAssay/gene/protein/Tox21 coverage, and caching PubChemPy doesn't have
scigantic-comptox Query EPA's ToxCast bioactivity data from a public S3 mirror, plus live Chemical/Hazard/Exposure lookups over EPA's own CCTE API
scigantic-deeppk Client for Deep-PK's small-molecule ADMET/toxicity prediction API, plus a mirrored CYP450 inhibitor/substrate reference dataset
scigantic-surechembl SureChEMBL patent chemistry: 31M compounds and 45M patents by id, name, SMILES, InChIKey or structure search, the patents for any ChEMBL or PubChem compound, full patent text, EBI's bulk parquet read in place with DuckDB, and joins into scigantic-chembl and scigantic-bindingdb

Microscopy & neuroscience

Package What it does
scigantic-bil Search all 14,000+ Brain Image Library datasets (6 PB of BICCN brain microscopy) and read light-sheet, fMOST and STPT volumes over HTTP: one slice, one thumbnail, or an OME-Zarr level, nothing downloaded

File formats & agent tooling

Package What it does
scigantic-headers Decode scientific file headers (cryo-EM, imaging, flow cytometry, mass spec, sequencing, structural biology) into typed fields. Zero dependencies.
scigantic-mcp MCP server for the Scigantic archive catalog: search thousands of datasets and get LLM-ready schema cards without downloading anything 
pip install scigantic-empiar scigantic-emdb scigantic-wwpdb scigantic-cryoet \
            scigantic-chembl scigantic-bindingdb scigantic-pubchem scigantic-comptox \
            scigantic-deeppk scigantic-surechembl scigantic-bil scigantic-headers scigantic-mcp

Every package here is MIT or MIT-0 licensed, with its own README, tests, and CI. Issues and PRs welcome.

Popular repositories Loading

  1. scigantic-chembl scigantic-chembl Public

    Query ChEMBL directly from a public S3 mirror with DuckDB. No download, no local database.

    Python 8 1

  2. scigantic-pubchem scigantic-pubchem Public

    A PubChemPy-inspired PUG REST client with throttle-aware retry, caching, BioAssay/gene/protein/Tox21 data, live cross-references into ChEMBL, BindingDB and the PDB, and a local parquet mirror for b…

    Python 4

  3. scigantic-empiar scigantic-empiar Public

    Explore the EMPIAR cryo-EM archive from Python — stream any of ~3,000 datasets (8.9 PiB) over parallel HTTP range reads, nothing downloaded.

    Python 1

  4. scigantic-emdb scigantic-emdb Public

    Search every structure in EMDB from Python — 60,895 cryo-EM maps by protein, organism, resolution, molecular weight and PDB cross-reference.

    Python 1

  5. scigantic-bindingdb scigantic-bindingdb Public

    Query BindingDB directly from a public S3 mirror with DuckDB, including a ChEMBL cross-reference bridge table.

    Python 1

  6. scigantic-comptox scigantic-comptox Public

    Query EPA's CompTox Chemicals Dashboard: ToxCast bioactivity from a public S3 mirror, plus live Chemical/Hazard/Exposure lookups via EPA's CCTE API.

    Python 1

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