docs: Phase I I3 citation template -- APA, BibTeX, CFF, in-text, data-availability formats for consumers of evidence certificates and pipeline outputs

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<VERSION>) [Software].
+GitHub. https://github.com/Open-Problem-Lab/OpenAMP-Foundry
+```
+
+For a specific artifact:
+
+```
+OpenAMP Foundry Contributors. (2026). Evidence certificate <ARTIFACT_ID> from
+OpenAMP Foundry v<VERSION> [Computational artifact]. Retrieved from
+https://github.com/Open-Problem-Lab/OpenAMP-Foundry at commit <COMMIT_SHA>.
+```
+
+### 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      = {<VERSION>},
+  url          = {https://github.com/Open-Problem-Lab/OpenAMP-Foundry},
+  commit       = {<COMMIT_SHA>}
+}
+```
+
+For a specific artifact:
+
+```bibtex
+@misc{openamp_artifact,
+  author       = {OpenAMP Foundry Contributors},
+  title        = {OpenAMP Evidence Artifact {<ARTIFACT_ID>}},
+  year         = 2026,
+  howpublished = {OpenAMP Foundry v<VERSION>, commit \texttt{<COMMIT_SHA>}},
+  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 <ARTIFACT_ID>"
+version: "<VERSION>"
+date-released: "<DATE>"
+authors:
+  - name: "OpenAMP Foundry Contributors"
+repository-code: "https://github.com/Open-Problem-Lab/OpenAMP-Foundry"
+commit: "<COMMIT_SHA>"
+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: <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<VERSION> (OpenAMP Foundry Contributors, 2026),
+artifact ID <ARTIFACT_ID>, commit <COMMIT_SHA[:8]>.
+```
+
+### Data availability statement
+
+When submitting a paper that uses OpenAMP outputs:
+
+```
+Data and code availability: Candidate evidence packages were generated using
+OpenAMP Foundry v<VERSION> (https://github.com/Open-Problem-Lab/OpenAMP-Foundry,
+commit <COMMIT_SHA>). 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 |
+|-------------|--------------|
+| `<VERSION>` | The tagged release, e.g. `v0.8.0` |
+| `<COMMIT_SHA>` | The full git commit SHA, e.g. `3c56621...` |
+| `<COMMIT_SHA[:8]>` | First 8 characters of the commit SHA |
+| `<ARTIFACT_ID>` | The artifact's machine-readable ID, e.g. `CERT-TOY-001` |
+| `<DATE>` | 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.