Resolve resource versions (UniProt 2026_02, AlphaFold v6, Ensembl 116) + Llama-3.1 license compliance ('Built with Llama')

README.md

@@ -269,7 +269,7 @@ Full guarded report examples and summaries are included in the repository under
 - Missense prediction remains below specialist predictors such as REVEL and AlphaMissense.
 - Broad score model performance is partly driven by easier consequence classes.
 - Structure evidence is only used when transcript/protein/residue mapping can be reconciled.
-- Exact historical versions for some external resources require final manual verification before manuscript submission.
+- External resource versions (resolved 2026-06-19): UniProt release 2026_02, AlphaFold DB v6, Ensembl release 116 (REST API 15.12), all accessed 2026-06-15; exact releases were reconstructed from access dates rather than captured at runtime.
 - The model has not been prospectively validated in clinical settings.
 - Generated text can still contain errors and must be reviewed by domain experts.
 - The uploaded artifact is an adapter, not a standalone full model.
@@ -384,4 +384,12 @@ Suggested acknowledgement:
 
 ## License and Base Model Notes
 
-This repository contains LoRA adapters and project documentation. It does not redistribute full Llama or Qwen base model weights. Use of the root adapter with `meta-llama/Llama-3.1-8B-Instruct` is subject to the Meta Llama 3.1 Community License and Acceptable Use Policy. Use of the `qwen_v0_1/` adapter with `Qwen/Qwen2.5-1.5B-Instruct` is subject to Qwen license terms. Users are responsible for verifying license compatibility for their own use case.
+**Built with Llama.**
+
+This repository contains LoRA adapters and project documentation. It does not redistribute full Llama or Qwen base model weights.
+
+The root adapter is a derivative of `meta-llama/Llama-3.1-8B-Instruct` and its use is governed by the [Meta Llama 3.1 Community License](https://www.llama.com/llama3_1/license/) and the [Acceptable Use Policy](https://www.llama.com/llama3_1/use-policy/). Per that license, derivative models carry the **"Built with Llama"** notice above; note also that the license asks derivative model names to begin with "Llama" — this adapter is published as **KAU-BioMedLLM** for research continuity, and adopters who redistribute should review that naming clause for their own use.
+
+The `qwen_v0_1/` adapter is a derivative of `Qwen/Qwen2.5-1.5B-Instruct` and its use is subject to the [Qwen license terms](https://huggingface.co/Qwen/Qwen2.5-1.5B-Instruct/blob/main/LICENSE).
+
+Users are responsible for verifying license compatibility for their own use case. This research release makes no warranty of fitness for any purpose.

reports/DATA_PROVENANCE.md

@@ -51,7 +51,8 @@ This file records sources actually present or used in the HPC project. Unknown v
 - Evidence file: `/ddn/data/generic/bbabajan/KAUBioMED_LLM/knowledge/kaubiomed_gene_evidence.jsonl`
 - Exists: `True`
 - Size bytes: `253848`
-- Access date/version: version not recorded — verify before submission.
+- Access date: 2026-06-15 (HPC file mtime; queried via rest.uniprot.org/uniprotkb).
+- UniProt release: 2026_02 (released 10-Jun-2026), the release live on the access date. Resolved 2026-06-19 from UniProt relnotes; release was not captured at runtime.
 - Scope: 20-gene evidence panel, not genome-wide.
 
 ## AlphaFold DB
@@ -59,13 +60,15 @@ This file records sources actually present or used in the HPC project. Unknown v
 - Manifest: `/ddn/data/generic/bbabajan/KAUBioMED_LLM/knowledge/alphafold/alphafold_manifest.jsonl`
 - Exists: `True`
 - Size bytes: `12754`
-- Access date/model version: version not recorded — verify before submission.
+- Access date: 2026-06-15 (HPC file mtime).
+- AlphaFold DB model version: v6 (from structure URLs, e.g. AF-P32245-F1-model_v6.cif). Note: an earlier evidence-builder pass fetched model_v4; final structures were refreshed to v6, which the manifest reflects.
 
 ## Ensembl VEP REST
 
 - Mapper script: `/ddn/data/generic/bbabajan/KAUBioMED_LLM/pipeline/vep_residue_mapper.py`
 - Exists: `True`
-- REST service/version/date: version not recorded — verify before submission.
+- Access date: 2026-06-15 (residue-mapping output mtime; rest.ensembl.org/vep/human/region, assembly GRCh38).
+- Ensembl release: 116 (REST API 15.12), the current live release. Resolved 2026-06-19 from rest.ensembl.org/info; release was not captured at runtime.
 - Mapping policy: MANE-preferred, HGVS protein required, UniProt reconciliation required, abstain on mismatch.
 
 ## Base LLM Snapshots