diff --git a/docs/CITATION_TEMPLATE.md b/docs/CITATION_TEMPLATE.md new file mode 100644 index 00000000..5e2cfdf8 --- /dev/null +++ b/docs/CITATION_TEMPLATE.md @@ -0,0 +1,133 @@ +# Citation Template for Data Consumers + +This document provides copy-paste citation formats for teams and tools that use OpenAMP Foundry artifacts — evidence certificates, benchmark results, candidate packages, or pipeline outputs — in their own work. + +Citing the specific artifact (not just the repository) is important because: + +1. OpenAMP artifacts are versioned and may change across releases. +2. A citation that names the artifact ID and commit makes the evidence chain reproducible. +3. Reviewers can check the original dry-lab evidence without contacting the authors. + +## What to cite + +Cite **both** the repository and the specific artifact: + +- **Repository**: cite the version or commit you used. +- **Artifact**: cite the artifact ID (e.g., `CERT-TOY-001`, `RMF-001`, `BCS-001`) and the release version or commit SHA where it appears in `outputs/`. + +If the artifact was received in an external review packet, cite the packet ID (`ERP-`) as well. + +## Citation formats + +### Academic paper (APA-style) + +``` +OpenAMP Foundry Contributors. (2026). OpenAMP Foundry: Verification-first dry-lab +infrastructure for antimicrobial peptide candidate triage (v) [Software]. +GitHub. https://github.com/Open-Problem-Lab/OpenAMP-Foundry +``` + +For a specific artifact: + +``` +OpenAMP Foundry Contributors. (2026). Evidence certificate from +OpenAMP Foundry v [Computational artifact]. Retrieved from +https://github.com/Open-Problem-Lab/OpenAMP-Foundry at commit . +``` + +### BibTeX + +```bibtex +@software{openamp_foundry, + author = {OpenAMP Foundry Contributors}, + title = {{OpenAMP Foundry}: Verification-first dry-lab infrastructure + for antimicrobial peptide candidate triage}, + year = 2026, + publisher = {GitHub}, + version = {}, + url = {https://github.com/Open-Problem-Lab/OpenAMP-Foundry}, + commit = {} +} +``` + +For a specific artifact: + +```bibtex +@misc{openamp_artifact, + author = {OpenAMP Foundry Contributors}, + title = {OpenAMP Evidence Artifact {}}, + year = 2026, + howpublished = {OpenAMP Foundry v, commit \texttt{}}, + note = {Computational dry-lab artifact. No biological activity implied. + Retrieved from \url{https://github.com/Open-Problem-Lab/OpenAMP-Foundry}.} +} +``` + +### CFF (Citation File Format) + +The repository ships a `CITATION.cff` file at the root. Tools that read CFF (e.g., GitHub, Zenodo) will automatically extract this. If you need to override it for a specific artifact, create a local CFF: + +```yaml +cff-version: 1.2.0 +message: "If you use this artifact, please cite both the repository and the artifact ID." +title: "OpenAMP Foundry — Artifact " +version: "" +date-released: "" +authors: + - name: "OpenAMP Foundry Contributors" +repository-code: "https://github.com/Open-Problem-Lab/OpenAMP-Foundry" +commit: "" +type: software +abstract: > + Computational dry-lab artifact produced by OpenAMP Foundry. + This artifact is a nominee from the dry-lab pipeline; no biological + activity is implied. See the accompanying evidence certificate for + the full provenance chain. +notes: + - "Artifact ID: " + - "Proof ladder level: dry_lab_candidate" + - "Dry-lab only: true" +``` + +### Short in-text reference + +For a brief in-text citation when a full reference is in the bibliography: + +``` +... selected using OpenAMP Foundry v (OpenAMP Foundry Contributors, 2026), +artifact ID , commit . +``` + +### Data availability statement + +When submitting a paper that uses OpenAMP outputs: + +``` +Data and code availability: Candidate evidence packages were generated using +OpenAMP Foundry v (https://github.com/Open-Problem-Lab/OpenAMP-Foundry, +commit ). All candidate IDs, evidence certificates, and benchmark +results are available at the repository under outputs/. Computational candidates +are computational nominees only; no biological activity or wet-lab validation +is implied by dry-lab certificate issuance. +``` + +## Placeholder reference + +| Placeholder | Replace with | +|-------------|--------------| +| `` | The tagged release, e.g. `v0.8.0` | +| `` | The full git commit SHA, e.g. `3c56621...` | +| `` | First 8 characters of the commit SHA | +| `` | The artifact's machine-readable ID, e.g. `CERT-TOY-001` | +| `` | ISO 8601 date of the artifact, e.g. `2026-01-01` | + +## What NOT to cite as evidence of biological activity + +OpenAMP artifacts are computational dry-lab outputs. Do not cite them as: + +- Evidence of antimicrobial activity. +- Proof of safety, non-toxicity, or hemolysis resistance. +- A substitute for peer-reviewed wet-lab validation. +- A basis for any therapeutic or clinical claim. + +A proper citation should be accompanied by a statement that the artifact is a computational nominee, not a validated compound.