From 4a9f9e47baedc4daa2f8e37b508e16ede59a6d4b Mon Sep 17 00:00:00 2001
From: ecrum19 <elicrum88@gmail.com>
Date: Thu, 8 Oct 2026 13:18:28 +0200
Subject: [PATCH 1/2] Add Zenodo metadata

.zenodo.json takes precedence over CITATION.cff when Zenodo's GitHub
integration archives a release. It names the creator with ORCID and
affiliations, the licence, keywords, and the VCF Core vocabulary. It
carries no version, so each record takes its version from the release
tag.

Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
---
 .zenodo.json | 34 ++++++++++++++++++++++++++++++++++
 1 file changed, 34 insertions(+)
 create mode 100644 .zenodo.json

diff --git a/.zenodo.json b/.zenodo.json
new file mode 100644
index 0000000..9a6201d
--- /dev/null
+++ b/.zenodo.json
@@ -0,0 +1,34 @@
+{
+  "upload_type": "software",
+  "title": "VCF-RDFizer",
+  "description": "<p>VCF-RDFizer converts Variant Call Format (VCF) files to RDF that uses the VCF Core vocabulary (<a href=\"https://w3id.org/vcf-core/vocab\">https://w3id.org/vcf-core/vocab</a>). It is a Docker-first command-line tool that:</p><ol><li>converts a VCF file to N-Triples with RMLStreamer;</li><li>optionally compresses the graph into the queryable HDT and COTTAS representations;</li><li>validates a converted graph against its source VCF with semantic queries and SHACL shapes;</li><li>links variants to external resources in a separate, provenance-tracked graph;</li><li>attaches ODRL data-use policies to files, regions, and variants, and writes the release views that a requester's policies permit.</li></ol><p>The conversion toolchain runs in one pinned Docker image (<code>ecrum19/vcf-rdfizer</code> on Docker Hub). The command-line tool is also distributed on PyPI and conda-forge (<code>vcf-rdfizer</code>).</p>",
+  "creators": [
+    {
+      "name": "Crum, Elias",
+      "affiliation": "Flemish Institute for Technological Research (VITO); IDLab, Ghent University - imec",
+      "orcid": "0009-0005-3991-754X"
+    }
+  ],
+  "license": "mit",
+  "access_right": "open",
+  "language": "eng",
+  "keywords": [
+    "Variant Call Format",
+    "VCF",
+    "RDF",
+    "RML",
+    "SPARQL",
+    "SHACL",
+    "HDT",
+    "ODRL",
+    "bioinformatics",
+    "genomic variation"
+  ],
+  "related_identifiers": [
+    {
+      "identifier": "https://w3id.org/vcf-core/vocab",
+      "relation": "references",
+      "resource_type": "other"
+    }
+  ]
+}

From 5a53ebf9f2b26843cf5ca7ab2e2c5f1492836c73 Mon Sep 17 00:00:00 2001
From: ecrum19 <elicrum88@gmail.com>
Date: Thu, 8 Oct 2026 13:27:07 +0200
Subject: [PATCH 2/2] Add the Zenodo DOI badge and citation DOI

Releases are now archived on Zenodo. The README badge, the BibTeX entry,
and CITATION.cff give the concept DOI 10.5281/zenodo.23237635, which
resolves to the latest version; v3.3.1 is 10.5281/zenodo.23237636.

Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
---
 CITATION.cff | 1 +
 README.md    | 5 +++++
 2 files changed, 6 insertions(+)

diff --git a/CITATION.cff b/CITATION.cff
index 480b0e8..deaf5d1 100644
--- a/CITATION.cff
+++ b/CITATION.cff
@@ -3,6 +3,7 @@ message: "If you use VCF-RDFizer in your research, please cite it using the meta
 title: "VCF-RDFizer"
 type: software
 version: "3.3.1"
+doi: "10.5281/zenodo.23237635"
 authors:
   - name: "VCF-RDFizer maintainers"
 repository-code: "https://github.com/ecrum19/VCF-RDFizer"
diff --git a/README.md b/README.md
index 525e5eb..5d4e66e 100644
--- a/README.md
+++ b/README.md
@@ -7,6 +7,7 @@
 [![Docker Pulls](https://img.shields.io/docker/pulls/ecrum19/vcf-rdfizer)](https://hub.docker.com/r/ecrum19/vcf-rdfizer)
 [![Conda Version](https://img.shields.io/conda/vn/conda-forge/vcf-rdfizer)](https://anaconda.org/conda-forge/vcf-rdfizer)
 [![License](https://img.shields.io/github/license/ecrum19/VCF-RDFizer)](https://github.com/ecrum19/VCF-RDFizer/blob/main/LICENSE)
+[![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.23237635.svg)](https://doi.org/10.5281/zenodo.23237635)
 
 <p align="center">
   <img src="assets/logo/logo.png" alt="VCF-RDFizer logo" width="220" />
@@ -1135,10 +1136,14 @@ BibTeX:
   year    = {2026},
   version = {3.3.1},
   url     = {https://github.com/ecrum19/VCF-RDFizer},
+  doi     = {10.5281/zenodo.23237635},
   note    = {Computer software}
 }
 ```
 
+Every release is archived on Zenodo. The DOI above, [10.5281/zenodo.23237635](https://doi.org/10.5281/zenodo.23237635), resolves to the latest
+version; each version's own DOI is listed on its Zenodo record.
+
 You can also use the machine-readable citation file: `CITATION.cff`.
 
 ## Contributing