Bump version to 0.3.0-beta.4

- Add mcpName to package.json for MCP Registry verification
- Update server.json to official MCP Registry schema
- Add .mcpregistry_* tokens to .gitignore

Author: ammawla

.claude-plugin/plugin.json

@@ -1,7 +1,7 @@
 {
   "name": "encode-toolkit",
   "description": "20 ENCODE API tools + 48 expert skills for genomics research. Search experiments, download files with MD5 verification, run pipelines, and cross-reference 14 databases.",
-  "version": "0.3.0-beta.3",
+  "version": "0.3.0-beta.4",
   "author": {
     "name": "Dr. Alex M. Mawla, PhD",
     "email": "ammawla@ucdavis.edu"

.gitignore

@@ -48,6 +48,9 @@ node_modules/
 credentials*
 data/
 
+# MCP Registry tokens
+.mcpregistry_*
+
 # OS
 .DS_Store
 Thumbs.db

README.md

@@ -1,5 +1,7 @@
 # ENCODE Toolkit — Genomics Research Infrastructure for Claude
 
+<!-- mcp-name: io.github.ammawla/encode-toolkit -->
+
 [![License: CC BY-NC-ND 4.0](https://img.shields.io/badge/License-CC_BY--NC--ND_4.0-red.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-yellow)](CHANGELOG.md)

package.json

@@ -1,6 +1,7 @@
 {
   "name": "encode-toolkit",
-  "version": "0.3.0-beta.3",
+  "version": "0.3.0-beta.4",
+  "mcpName": "io.github.ammawla/encode-toolkit",
   "description": "ENCODE Toolkit — Genomics research infrastructure with 20 MCP tools, 47 skills, 14 database integrations, and 7 pipelines for Claude Code",
   "main": "index.js",
   "bin": {

pyproject.toml

@@ -4,7 +4,7 @@ build-backend = "hatchling.build"
 
 [project]
 name = "encode-toolkit"
-version = "0.3.0b3"
+version = "0.3.0b4"
 description = "MCP server for querying and downloading ENCODE Project genomics data directly from Claude"
 readme = "README.md"
 license = "CC-BY-NC-ND-4.0"

server.json

@@ -1,123 +1,29 @@
 {
-  "$schema": "https://raw.githubusercontent.com/modelcontextprotocol/servers/main/registry/schema.json",
-  "name": "encode-toolkit",
-  "display_name": "ENCODE Project",
-  "description": "Query, download, and track ENCODE Project genomics data. Search 8,000+ experiments across ChIP-seq, ATAC-seq, RNA-seq, Hi-C, and 50+ assay types. Download BED, FASTQ, BAM, bigWig files with MD5 verification. Track experiments, publications, and data provenance locally.",
-  "icon": "https://www.encodeproject.org/favicon.ico",
+  "$schema": "https://static.modelcontextprotocol.io/schemas/2025-12-11/server.schema.json",
+  "name": "io.github.ammawla/encode-toolkit",
+  "title": "ENCODE Toolkit",
+  "description": "20 MCP tools + 48 skills for ENCODE Project genomics — search, download, pipelines",
   "repository": {
-    "type": "git",
-    "url": "https://github.com/ammawla/encode-toolkit"
+    "url": "https://github.com/ammawla/encode-toolkit",
+    "source": "github"
   },
-  "license": "LicenseRef-Noncommercial",
-  "homepage": "https://github.com/ammawla/encode-toolkit",
-  "author": {
-    "name": "Dr. Alex M. Mawla, PhD"
-  },
-  "categories": [
-    "science",
-    "data",
-    "research"
-  ],
-  "tags": [
-    "encode",
-    "genomics",
-    "bioinformatics",
-    "chip-seq",
-    "atac-seq",
-    "rna-seq",
-    "epigenomics",
-    "biology"
-  ],
-  "installations": {
-    "uvx": {
-      "type": "uvx",
-      "package": "encode-toolkit"
-    },
-    "pip": {
-      "type": "pip",
-      "package": "encode-toolkit"
-    }
-  },
-  "tools": [
-    {
-      "name": "encode_search_experiments",
-      "description": "Search ENCODE experiments with 20+ filters including assay type, organism, organ, biosample, target, and more."
-    },
-    {
-      "name": "encode_get_experiment",
-      "description": "Get full details for a specific experiment including all files, quality metrics, and audit info."
-    },
-    {
-      "name": "encode_list_files",
-      "description": "List files for a specific experiment with format/type filters."
-    },
-    {
-      "name": "encode_search_files",
-      "description": "Search files across all experiments with combined experiment + file filters."
-    },
-    {
-      "name": "encode_download_files",
-      "description": "Download specific files by accession to a local directory with MD5 verification."
-    },
-    {
-      "name": "encode_get_metadata",
-      "description": "List valid filter values for any search parameter."
-    },
-    {
-      "name": "encode_batch_download",
-      "description": "Search + download files in one step with preview mode."
-    },
-    {
-      "name": "encode_manage_credentials",
-      "description": "Store, check, or clear ENCODE credentials for restricted data access."
-    },
-    {
-      "name": "encode_get_facets",
-      "description": "Get live counts from ENCODE showing what data exists for given filters."
-    },
-    {
-      "name": "encode_get_file_info",
-      "description": "Get detailed metadata for a single file."
-    },
-    {
-      "name": "encode_track_experiment",
-      "description": "Track an experiment locally with publications, methods, and pipeline info."
-    },
-    {
-      "name": "encode_list_tracked",
-      "description": "List all tracked experiments with metadata and publication counts."
-    },
-    {
-      "name": "encode_get_citations",
-      "description": "Get publications for tracked experiments. Export as BibTeX or RIS."
-    },
-    {
-      "name": "encode_compare_experiments",
-      "description": "Analyze whether two experiments are compatible for combined analysis."
-    },
-    {
-      "name": "encode_log_derived_file",
-      "description": "Log derived files for provenance tracking back to ENCODE source data."
-    },
-    {
-      "name": "encode_get_provenance",
-      "description": "View provenance chains from derived files to source ENCODE data."
-    },
-    {
-      "name": "encode_export_data",
-      "description": "Export tracked experiments as CSV, TSV, or JSON with PMIDs for cross-referencing."
-    },
-    {
-      "name": "encode_summarize_collection",
-      "description": "Get grouped statistics of your tracked experiment collection."
-    },
-    {
-      "name": "encode_link_reference",
-      "description": "Link external references (PubMed, bioRxiv, ClinicalTrials, GEO) to experiments."
-    },
-    {
-      "name": "encode_get_references",
-      "description": "Get external references linked to experiments for cross-server workflows."
+  "version": "0.3.0-beta.4",
+  "packages": [
+    {
+      "registryType": "npm",
+      "identifier": "encode-toolkit",
+      "version": "0.3.0-beta.4",
+      "transport": {
+        "type": "stdio"
+      }
+    },
+    {
+      "registryType": "pypi",
+      "identifier": "encode-toolkit",
+      "version": "0.3.0b4",
+      "transport": {
+        "type": "stdio"
+      }
     }
   ]
 }