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Initialize FlyBase knowledge graph data product
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‎.gitattributes‎

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* text=auto eol=lf
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*.png binary
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*.jpg binary
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*.jpeg binary
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*.pdf binary
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*.parquet binary
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*.gz binary
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*.zst binary

‎.github/ISSUE_TEMPLATE/config.yml‎

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blank_issues_enabled: true
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contact_links:
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- name: FlyBase contact
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url: https://flybase.org/contact/email
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about: Contact FlyBase about records or topics outside this dataset project.

‎.github/ISSUE_TEMPLATE/schema-question.yml‎

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name: Schema or biological-model question
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description: Ask about a graph concept or propose a source-backed correction.
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title: "[Schema]: "
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labels:
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- schema
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body:
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- type: markdown
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attributes:
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value: >-
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Please do not include credentials, private infrastructure details, or
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unpublished/restricted data.
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- type: input
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id: release
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attributes:
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label: FlyBase/graph release
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description: Identify the release if the question concerns published data.
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placeholder: FB2026_02 / schema-v1.0.0
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- type: textarea
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id: concept
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attributes:
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label: Biological concept or graph member
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description: Name the entity, assertion, relationship, or property.
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validations:
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required: true
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- type: textarea
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id: source
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attributes:
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label: Source evidence
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description: Link or cite the relevant FlyBase field, identifier, ontology, or publication.
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- type: textarea
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id: expected
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attributes:
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label: Expected interpretation
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description: Explain the scientific meaning you expected in plain language.
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validations:
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required: true

‎.github/workflows/secret-scan.yml‎

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name: Secret scan
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on:
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pull_request:
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push:
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branches:
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- main
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workflow_dispatch:
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permissions:
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contents: read
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jobs:
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gitleaks:
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runs-on: ubuntu-latest
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steps:
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- name: Check out repository
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uses: actions/checkout@11d5960a326750d5838078e36cf38b85af677262 # v4
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with:
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fetch-depth: 0
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- name: Scan Git history and changes
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uses: gitleaks/gitleaks-action@ff98106e4c7b2bc287b24eaf42907196329070c7 # v2
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env:
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GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}

‎.gitignore‎

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.DS_Store
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.env
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.env.*
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!.env.example
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.venv/
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__pycache__/
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*.py[cod]
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*.log
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# Full graph releases and local database state belong in object storage.
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artifacts/
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downloads/
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neo4j-data/
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*.dump
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*.dump.gz
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*.parquet
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*.csv.gz
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*.tsv.gz
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*.tar
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*.tar.gz
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*.tar.zst
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# Notebook and local-tool state.
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.ipynb_checkpoints/
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.duckdb/
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*.duckdb

‎CITATION.cff‎

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cff-version: 1.2.0
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message: >-
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Please cite FlyBase and identify the exact FlyBase Knowledge Graph release
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used in your work.
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title: FlyBase Knowledge Graph
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type: dataset
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authors:
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- name: FlyBase Consortium
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license: CC-BY-4.0
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repository-code: https://github.com/FlyBase/knowledge-graph
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url: https://flybase.org/
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version: 0.1.0-dev
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keywords:
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- Drosophila
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- FlyBase
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- knowledge graph
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- genetics
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- genomics
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preferred-citation:
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type: article
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title: "FlyBase: updates to the Drosophila genes and genomes database"
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authors:
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- family-names: Öztürk-Çolak
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given-names: Ayça
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- name: FlyBase Consortium
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journal: Genetics
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year: 2024
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volume: 227
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issue: 1
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doi: 10.1093/genetics/iyad211

‎CONTRIBUTING.md‎

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# Contributing
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FlyBase welcomes corrections, scientist use cases, documentation improvements,
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and reproducible examples.
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## Before opening a change
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- Search existing issues for the same biological concept or source field.
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- Use official FlyBase identifiers, ontology identifiers, and source vocabulary.
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- Cite the public FlyBase file, report field, ontology, or publication that
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supports the proposal.
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- Explain whether a proposal changes biological identity, an evidence-bearing
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assertion, provenance, release metadata, or display/navigation metadata.
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- Never submit credentials, private hosts, Chat logs, account data, unpublished
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curator notes, or restricted third-party data.
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## Schema proposals
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A schema proposal should include:
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1. the affected entity, assertion, relationship, or property;
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2. the exact source field and release;
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3. domain, range, direction, cardinality, and null behavior;
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4. evidence, qualifier, and provenance behavior;
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5. licensing/redistribution status; and
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6. at least one source-backed example and one relevant negative boundary.
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Do not introduce replacement identifiers, hardcoded biological answer lists,
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or generated links as evidence. Approximate interoperability mappings must be
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identified as broader, narrower, partial, or unmapped rather than described as
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exact.
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## Pull requests
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- Keep changes focused and explain their scientific effect in plain language.
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- Run the repository validation and secret-scanning checks.
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- Do not commit generated full-release artifacts, database dumps, or large
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downloads.
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- Schema changes require regenerated documentation and a compatibility note.
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Biological corrections may require verification against the current FlyBase
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release before merge.

‎GOVERNANCE.md‎

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# Governance
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The FlyBase Consortium maintains the FlyBase Knowledge Graph as a public,
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release-keyed scientific data product.
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## Decision principles
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- FlyBase source fields, identifiers, controlled vocabularies, ontologies, and
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curation semantics are authoritative.
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- Evidence-bearing assertions remain distinct from search terms, generated
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descriptions, navigation URLs, and other planning or display context.
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- One canonical biological model feeds all public formats.
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- Changes are evaluated for scientific meaning, evidence/provenance retention,
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source coverage, licensing, compatibility, and usability by scientists.
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- Unresolved or unlicensed content is excluded from a release rather than
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guessed or silently simplified.
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## Change process
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- Documentation-only corrections may be reviewed through an ordinary pull
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request.
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- Additive compatible schema changes require source evidence, regenerated
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documentation, and release notes.
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- Breaking changes require a schema major-version change and migration guide.
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- Published release objects are immutable. Corrections produce a new release
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revision.
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The public issue tracker records proposals and user questions. FlyBase
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maintainers make release decisions and may request curator or domain-expert
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review when source semantics are disputed.

‎LICENSE‎

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MIT License
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Copyright (c) 2026 FlyBase Consortium
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Permission is hereby granted, free of charge, to any person obtaining a copy
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of this software and associated documentation files (the "Software"), to deal
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in the Software without restriction, including without limitation the rights
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to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
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copies of the Software, and to permit persons to whom the Software is
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furnished to do so, subject to the following conditions:
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The above copyright notice and this permission notice shall be included in all
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copies or substantial portions of the Software.
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THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
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IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
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FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
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AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
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LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
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OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
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SOFTWARE.

‎LICENSE-DATA.md‎

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# Data license
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FlyBase-produced data and annotations in an explicitly published FlyBase
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Knowledge Graph release are made available under the
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[Creative Commons Attribution 4.0 International License](https://creativecommons.org/licenses/by/4.0/)
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(CC BY 4.0).
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The required attribution is to the FlyBase Consortium. Publications and
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derived products should identify the exact FlyBase data release and the exact
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knowledge-graph dataset/schema version. See `CITATION.cff` and the release's
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machine-readable manifest for the preferred citation.
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## Third-party content
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FlyBase incorporates information from external resources. CC BY 4.0 does not
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automatically override a third party's copyright or license. Every published
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graph release must include a field/data-family source and license inventory.
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Material with unknown or incompatible redistribution terms must be excluded or
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distributed separately under its applicable terms.
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The authoritative FlyBase licensing statement is maintained on the
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[FlyBase About page](https://wiki.flybase.org/wiki/FlyBase%3AAbout). The
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manifest accompanying a release controls the included-source and attribution
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details for that release.
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## No stable dataset yet
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This repository is pre-release. The presence of a schema draft, example, or
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mapping in Git does not by itself designate a stable data release.

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