Release v0.3.0: Bioinformatics audit, ENCODE API corrections, filter validation

- Fix 13 wrong ENCODE assay_title values, add 30+ missing (verified against live API)
- Add 19 missing organ_slims including blood (6,558 experiments)
- Fix biosample classifications (remove 3 phantom types, add 2 real)
- Remove 5 wrong output_types, add 50+ correct ones
- Extract _extract_assemblies() and _extract_audit_counts() helpers
- Add assembly field to ExperimentDetail model
- Extract all 4 ENCODE audit levels (ERROR, NOT_COMPLIANT, WARNING, INTERNAL_ACTION)
- Add check_filter_value() with cached case-insensitive matching
- Wire filter validation into all 4 search tools with warnings
- Fix search_term forwarding bug in search_files
- Add None guards on related_series/documents list comprehensions
- Fix scATAC-seq -> snATAC-seq across all skill files (0 API results for scATAC-seq)
- Fix assay_title="RNA-seq" -> "total RNA-seq" across 40+ files
- Update license CC-BY-NC-4.0 -> AGPL-3.0-only
- Version bump to 0.3.0 across all manifests
- Add CITATION.cff
- 568 tests, 98% coverage, all lint clean

Author: ammawla

.claude-plugin/marketplace.json

@@ -10,7 +10,7 @@
   "plugins": [
     {
       "name": "encode-toolkit",
-      "version": "0.3.0-beta.10",
+      "version": "0.3.0",
       "source": "./plugin",
       "description": "20 ENCODE API tools + 47 expert skills for genomics research. Search experiments, download files with MD5 verification, run pipelines, and cross-reference 14 databases."
     }

.claude-plugin/plugin.json

@@ -1,15 +1,15 @@
 {
   "name": "encode-toolkit",
   "description": "20 ENCODE API tools + 47 expert skills for genomics research. Search experiments, download files with MD5 verification, run pipelines, and cross-reference 14 databases.",
-  "version": "0.3.0-beta.10",
+  "version": "0.3.0",
   "author": {
     "name": "Dr. Alex M. Mawla, PhD",
     "email": "ammawla@ucdavis.edu"
   },
   "homepage": "https://github.com/ammawla/encode-toolkit",
   "repository": "https://github.com/ammawla/encode-toolkit",
   "icon": "docs/icon.svg",
-  "license": "CC-BY-NC-4.0",
+  "license": "AGPL-3.0-only",
   "keywords": [
     "genomics",
     "encode",

.cursor-plugin/marketplace.json

@@ -6,7 +6,7 @@
   },
   "metadata": {
     "description": "ENCODE Project genomics research infrastructure for Cursor",
-    "version": "0.3.0-beta.10",
+    "version": "0.3.0",
     "homepage": "https://github.com/ammawla/encode-toolkit"
   },
   "plugins": [

.cursor-plugin/plugin.json

@@ -1,14 +1,14 @@
 {
   "name": "encode-toolkit",
   "description": "20 ENCODE API tools + 47 expert skills for genomics research. Search experiments, download files with MD5 verification, run pipelines, and cross-reference 14 databases.",
-  "version": "0.3.0-beta.10",
+  "version": "0.3.0",
   "author": {
     "name": "Dr. Alex M. Mawla, PhD",
     "email": "ammawla@ucdavis.edu"
   },
   "homepage": "https://github.com/ammawla/encode-toolkit",
   "repository": "https://github.com/ammawla/encode-toolkit",
-  "license": "CC-BY-NC-4.0",
+  "license": "AGPL-3.0-only",
   "logo": "docs/icon.svg",
   "keywords": [
     "genomics",

.github/PULL_REQUEST_TEMPLATE.md

@@ -22,7 +22,7 @@
 
 <!-- How was this tested? -->
 
-- [ ] All 506 existing tests pass (`pytest tests/ -v`)
+- [ ] All 540 existing tests pass (`pytest tests/ -v`)
 - [ ] New tests added for new functionality
 - [ ] Lint passes (`ruff check src/`)
 - [ ] Format passes (`ruff format --check src/`)

CHANGELOG.md

@@ -34,7 +34,7 @@ Initial public beta release.
 - **OS keyring credential management** with Fernet-encrypted file fallback
 - **Thread-safe SQLite tracker** with full transaction safety
 - **Streaming downloads** with 64KB chunks and SSRF-safe redirect validation
-- **506 tests** with 98% code coverage
+- **568 tests** with 98% code coverage
 - **34 literature reference documents** (~320 papers cataloged with DOI, PMID, key findings)
 - **9 scientist-facing vignettes** with real ENCODE API output
 - **GitHub Actions CI/CD** (pytest across Python 3.10–3.13, ruff lint, plugin validation)

CITATION.cff

@@ -0,0 +1,23 @@
+cff-version: 1.2.0
+message: "If you use this software, please cite it as below."
+type: software
+title: "ENCODE Toolkit"
+abstract: "A Model Context Protocol server for programmatic access to ENCODE functional genomics data."
+authors:
+  - family-names: Mawla
+    given-names: Alex M.
+    orcid: "https://orcid.org/0000-0003-0907-464X"
+    affiliation: "Independent Researcher"
+version: 0.3.0
+date-released: "2026-03-08"
+license: AGPL-3.0-only
+repository-code: "https://github.com/ammawla/encode-toolkit"
+url: "https://github.com/ammawla/encode-toolkit"
+doi: "10.5281/zenodo.18917511"
+keywords:
+  - bioinformatics
+  - genomics
+  - ENCODE
+  - epigenomics
+  - MCP
+  - functional genomics

CLAUDE.md

@@ -7,7 +7,7 @@ MCP server for the ENCODE Project (encodeproject.org) — the largest public cat
 ```bash
 python -m venv .venv && source .venv/bin/activate
 pip install -e ".[dev]"
-pytest                    # 506 tests, 98% coverage
+pytest                    # 568 tests, 98% coverage
 ruff check src/           # lint
 ruff format src/          # auto-format
 encode-toolkit            # run MCP server
@@ -21,12 +21,12 @@ src/encode_connector/
   client/encode_client.py # Async ENCODE API client, ~585 lines, 1-hour TTL cache
   client/downloader.py    # File download manager, ~305 lines, MD5 verification
   client/auth.py          # OS keyring + Fernet credential storage, ~262 lines
-  client/models.py        # Pydantic models for API responses, ~332 lines
-  client/constants.py     # API URLs, filter values, ~348 lines
+  client/models.py        # Pydantic models for API responses, ~367 lines
+  client/constants.py     # API URLs, filter values, ~450 lines
   client/tracker.py       # SQLite experiment tracker, ~1129 lines
-  client/validation.py    # Input validation, ~188 lines
+  client/validation.py    # Input validation, ~226 lines
 skills/                   # 47 skills, each with SKILL.md + references/ + scripts/
-tests/                    # 506 tests (pytest-asyncio, asyncio_mode=auto), 98% coverage
+tests/                    # 568 tests (pytest-asyncio, asyncio_mode=auto), 98% coverage
 ```
 
 ## Package Identity
@@ -57,7 +57,7 @@ Provides 20 tools to search, download, and track ENCODE data:
 
 ## Key Concepts
 
-**Assay types**: Histone ChIP-seq, TF ChIP-seq, ATAC-seq, DNase-seq, RNA-seq, WGBS, Hi-C, scRNA-seq, scATAC-seq, CRISPR screen, STARR-seq, MPRA, eCLIP, CUT&RUN, CUT&Tag
+**Assay types**: Histone ChIP-seq, TF ChIP-seq, ATAC-seq, DNase-seq, total RNA-seq, polyA plus RNA-seq, WGBS, intact Hi-C, scRNA-seq, snATAC-seq, snRNA-seq, CRISPR screen, STARR-seq, MPRA, eCLIP, CUT&RUN, CUT&Tag
 
 **Biosample hierarchy**: tissue > primary cell > cell line > in vitro differentiated > organoid
 
@@ -133,9 +133,9 @@ Provides 20 tools to search, download, and track ENCODE data:
 
 - ENCODE audits: ERROR > NOT_COMPLIANT > WARNING > INTERNAL_ACTION
 - ChIP-seq metrics: FRiP ≥1%, NSC >1.05, RSC >0.8, NRF ≥0.8 (Landt et al. 2012)
-- ATAC-seq metrics: TSS enrichment ≥6, fragment size nucleosomal ladder (Buenrostro et al. 2013)
-- RNA-seq: Mapping rate >80%, rRNA <10%, replicate correlation ≥0.9 (Conesa et al. 2016)
-- WGBS: Bisulfite conversion >99%, CpG coverage ≥10× for DMRs (Foox et al. 2021)
+- ATAC-seq metrics: TSS enrichment ≥5 (GRCh38), ≥6 (hg19), ≥10 (mm10), fragment size nucleosomal ladder (ENCODE data standards)
+- RNA-seq: Mapping rate 70-90% expected (Conesa et al. 2016), rRNA <10% (community standard), replicate correlation ≥0.9 isogenic / ≥0.8 anisogenic (ENCODE data standards)
+- WGBS: Bisulfite conversion ≥98%, CpG coverage ≥10× for DMRs (ENCODE data standards)
 - Hi-C: Cis/trans ratio >60%, long-range cis >40% (Yardimci et al. 2019)
 - CUT&RUN/CUT&Tag: Different QC profiles from ChIP-seq; use suspect list (Nordin et al. 2023)
 - Always use 2+ biological replicates

README.md

@@ -4,13 +4,13 @@
 
 [![License: AGPL-3.0](https://img.shields.io/badge/license-AGPL--3.0-green.svg)](LICENSE)
 [![Python 3.10+](https://img.shields.io/badge/python-3.10+-blue.svg)](https://www.python.org/downloads/)
-[![Version](https://img.shields.io/badge/version-0.3.0--beta.10-yellow)](CHANGELOG.md)
+[![Version](https://img.shields.io/badge/version-0.3.0-green)](CHANGELOG.md)
 [![Status](https://img.shields.io/badge/status-beta-yellow)]()
 [![Skills](https://img.shields.io/badge/skills-47-orange)](docs/skill-vignettes/)
 [![Tools](https://img.shields.io/badge/MCP_tools-20-purple)](src/encode_connector/server/main.py)
 [![Pipelines](https://img.shields.io/badge/pipelines-7-green)](skills/pipeline-chipseq/)
 [![Databases](https://img.shields.io/badge/databases-14-teal)](docs/SHOWCASE.md)<br>
-[![Tests](https://img.shields.io/badge/tests-506_passing-brightgreen)](tests/)
+[![Tests](https://img.shields.io/badge/tests-568_passing-brightgreen)](tests/)
 [![Coverage](https://img.shields.io/badge/coverage-98%25-brightgreen)](tests/)
 [![Security](https://img.shields.io/badge/security-no_telemetry-blue)]()
 [![Claude Code](https://img.shields.io/badge/Claude_Code-plugin-blueviolet)](https://claude.com/claude-code)
@@ -805,6 +805,6 @@ pytest
 
 ## License
 
-**Restrictive Non-Commercial License.** Free for personal, educational, and academic research. No derivative works without written permission. Commercial use requires a separate license. See [LICENSE](LICENSE) for full terms.
+AGPL-3.0. See [LICENSE](LICENSE) for full terms.
 
 For commercial licensing inquiries: ammawla@ucdavis.edu

agents/rnaseq-pipeline.md

@@ -15,7 +15,7 @@ You are an ENCODE RNA-seq processing specialist. Guide users through the complet
 5. **QC Metrics**: RNA-SeQC for comprehensive quality assessment
 
 ## Quality Thresholds
-- Mapping rate > 80%
+- Mapping rate 70-90%
 - rRNA contamination < 10%
 - Replicate correlation (Spearman) >= 0.9
 - Strandedness verified
@@ -27,6 +27,6 @@ You are an ENCODE RNA-seq processing specialist. Guide users through the complet
 - Junction files (novel splice junctions)
 
 ## Tools
-Use `encode_search_experiments` with assay_title="RNA-seq" to find data.
+Use `encode_search_experiments` with assay_title="total RNA-seq" to find data.
 
 Refer to the pipeline-rnaseq skill for full Nextflow implementation.