The FlyBase Knowledge Graph is a versioned, evidence-grounded representation of public FlyBase data for scientists, educators, and software developers.
This repository is the public home for the graph's biological schema, data dictionary, provenance model, examples, release metadata, and user-facing download/load/query guidance. Full release artifacts will be distributed through FlyBase's existing AWS Open Data resource rather than stored in Git.
Important
This project is currently pre-release. No stable knowledge-graph dataset has
been published from this repository yet. Files under schema/, docs/, and
samples/ will be added only after their source, biological meaning,
provenance, and redistribution status have been validated.
The first stable release is expected to provide:
- compressed Neo4j bulk-import tables;
- Parquet tables suitable for DuckDB and other analytical tools;
- a native artifact for a pinned Neo4j version; and
- a small, explicitly licensed example dataset.
RDF or Biolink-compatible exports will be included only if a field-by-field crosswalk preserves FlyBase semantics and provenance.
This is a public data-product repository. It will contain:
- the canonical public schema and generated documentation;
- public source-to-graph mapping documentation;
- release manifests and checksums;
- scientist-oriented queries, notebooks, and examples; and
- minimal utilities needed to download, verify, load, or query public releases.
Private extraction, transformation, validation, deployment, and publishing automation does not belong here. Production credentials, private hosts, Chat logs, account data, unpublished curator material, and internal infrastructure configuration must never be committed.
Repository software is licensed under the MIT License. FlyBase- produced data and annotations are licensed under CC BY 4.0. A release manifest will identify source and license information for each included data family; third-party material is not automatically covered by the FlyBase data license.
When using a release, cite both FlyBase and the exact graph release identifier. See CITATION.cff and FlyBase's citation guidance.
The current milestone is schema-v1.0.0-rc1: a source-backed schema candidate
and human-readable review package. Stable download and loading instructions
will appear only after the candidate passes scientific, licensing, format, and
anonymous-download validation.
Questions from biologists and corrections to definitions or examples are welcome. Please read CONTRIBUTING.md and GOVERNANCE.md. Report suspected credential or repository security problems using SECURITY.md, not a public issue.