reactome-curator-workflows

Shared Claude Code workflow skills for Reactome curation and release operations.

What This Is

Reactome is a free, open-source, peer-reviewed pathway database. Human pathways are manually curated at the reaction level and computationally inferred across ~15 other species.

This repository holds the Claude Code skills curators use for that work — markdown instruction files that Claude Code reads directly. Any curator with Claude Code installed can clone this repo and run any skill. There is no build step and no dependency beyond Claude Code itself, plus Python 3 for a few skills.

Skills are added incrementally as we vet repeatable workflows. Each skill's full instructions live in its own .claude/skills/<name>/SKILL.md, which is the authoritative source for how that skill behaves; this file covers what each one is for and what you need to run it. See CLAUDE.md for repo conventions and how to add a skill.

Setup

1. Prerequisites

macOS Ventura (13) or later, or Linux.
Git. Check with git --version. On macOS, if it is missing, run xcode-select --install and click Install.
An Anthropic API key from the Reactome organization. Contact the repo maintainer to be added, then create your own key at console.anthropic.com → API Keys → Create Key. Copy it immediately — it is shown only once.
Repository access. The maintainer must add you as a collaborator; accept the emailed invitation before cloning.
Node.js is not needed for the base install — only for /analysis-graphdb-setup.

Install Claude Code:

curl -fsSL https://claude.ai/install.sh | bash
claude --version

2. Set your API key

echo 'export ANTHROPIC_API_KEY="your-key-here"' >> ~/.zshrc
source ~/.zshrc
echo $ANTHROPIC_API_KEY        # should print your key

Use the organizational key for Reactome work so usage bills to the shared Reactome credit pool; a personal Claude.ai subscription is separate and unaffected. When ANTHROPIC_API_KEY is set, Claude Code prefers it automatically — run /status inside a session to confirm which credentials are active.

Your key lives only in ~/.zshrc on your own machine. Never commit it, paste it into a skill or script, or share it in chat or email. If a key is ever exposed, revoke and rotate it immediately — exposure is the trigger, not misuse.

3. Clone the repository

git clone https://github.com/reactome/reactome-curator-workflows.git \
    ~/Developer/reactome-curator-workflows
cd ~/Developer/reactome-curator-workflows

If Git prompts for a password, use a personal access token with the repo scope — not your GitHub account password.

4. Install Python dependencies

Several skills need Python 3 and a few packages. Versions are pinned in requirements.txt so every curator gets the same set:

pip3 install --user -r requirements.txt

If pip reports externally-managed-environment (PEP 668), use a virtual environment instead — see the notes at the top of requirements.txt. If pip prints a PATH warning, add the directory it names to your shell config:

echo 'export PATH="$HOME/Library/Python/3.x/bin:$PATH"' >> ~/.zshrc
source ~/.zshrc

5. Run Claude Code

cd ~/Developer/reactome-curator-workflows
claude

Always launch from inside the repository folder. Claude Code reads CLAUDE.md and loads all skills from the directory you start it in, and .claude/settings.json in the repo root is what allowlists the external hosts some skills need (eutils.ncbi.nlm.nih.gov, reactome.org). Launched elsewhere, those skills fail.

The Claude for Mac desktop app's </> Claude Code button runs in an OAuth-only context and does not read ANTHROPIC_API_KEY from your shell — launch from Terminal for Reactome work.

6. Keep up to date

cd ~/Developer/reactome-curator-workflows
git pull

New and updated skills are available immediately — no restart needed if Claude Code is already running.

Available Skills

Invoke a skill by typing its name at the Claude Code prompt. Claude will prompt you for anything it needs.

`/review-internal`

Formal structured internal review of a pathway report against Curator Guide V94, producing a prioritized seven-section review DOCX that opens with a Critical Issues table collecting every HIGH-priority finding from all seven sections. Literature references are checked against PubMed via NCBI E-utilities rather than from memory — author, year and journal per PMID, duplicate references, and citations with no matching reference. Upload the pathway report DOCX and the Curator Guide PDF to the conversation before invoking. Every review applies the same standards and covers the full report; disease and drug standards apply automatically where the report carries that annotation.

Pass an optional release version to label the review. The skill asks where to write the DOCX locally, then tells you to upload it to that release's subfolder of the Internal Reviews Drive folder — the destination is also written into the top of the report, so the file carries its own filing instructions.

/review-internal "HHV8 Infection" R-HSA-9521541 "Lisa Matthews" 2026-06-16 V95

`/annotate-pathway-from-reviews-or-topic_name`

AI-assisted pre-curation. From supplied references (Mode A: PMIDs, DOIs, or PDFs) or a biological topic (Mode B), proposes a complete pathway → subpathway → reaction hierarchy and verifies primary literature via a mandatory ten-step PMID verification protocol, applying the species/chimeric framework. Produces a first-pass draft for curator review — it does not touch the database, and ontology/UniProt accessions are left marked PENDING CURATOR VERIFICATION.

/annotate-pathway-from-reviews-or-topic_name

`/extract-reactions`

Extracts a reaction graph for a named pathway from one or more review PDFs. Writes <pathway-slug>_reactions.csv (Title, Input, Output, Catalyst, Regulators, Reviews, Source1–Source5) plus <pathway-slug>_references.html. Each Source cell holds one URL chosen by a PubMed → PMC → DOI → publisher ladder; PMIDs are resolved live against NCBI E-utilities and never recovered from training data. Pre-curation draft.

/extract-reactions "Wnt Signaling Pathway"

`/release-doi-batch`

Generates a CrossRef DOI batch XML file (schema 5.3.1) for a release from DOIs.xlsx.

/release-doi-batch V97

`/release-qa-tracker`

Turns QA comparison output into a multi-sheet curator tracker workbook with per-row Status dropdowns (Not Done / Fixed / Skipped) and a Comments column. Runs compare_dirs.sh against two QA output directories, or starts from an existing Google Sheets URL / .xlsx / .csv. Pauses for curator approval of the included-vs-skipped file list before building the workbook.

/release-qa-tracker

`/curation-build-illustration`

Builds or extends an EHLD-style pathway illustration (1366×768 SVG). The preferred mode is modifying an existing published EHLD fetched by ST_ID (Mode A) — it describes the base diagram back to you for confirmation, then adds new elements and writes <ST_ID>_modified.svg, never overwriting the published diagram. It can also build a new EHLD from a written description (Mode B) or an example image (Mode C).

Every biological image part comes from the Reactome Icon Library — nothing is hand-drawn or invented, and anything the library does not cover is surfaced as a gap. Icons resolve deterministically by accession where you have one (offline, from bundled tables) and by live name search otherwise. The skill stops for approval of the icon map before composing. Outputs go to a per-request project directory (illustrations/<slug>/, git-ignored): the SVG, an icon manifest with CC-BY 4.0 attribution, a gaps file, and the downloaded icons.

/curation-build-illustration

`/admin-drive-readme`

Regenerates the Reactome Team Drive README as a formatted Google Doc from the live folder inventory. Supports --dry-run (preview, no write) and --depth N (inventory depth, default 2).

/admin-drive-readme --dry-run

`/spotlight-article-drafter`

Drafts a candidate Reactome "Research Spotlight" article from a paper that used Reactome data or tools, producing both forms at once: the short one-paragraph homepage teaser and the expanded long-form version. Drafts text only — final HTML/Joomla formatting is a separate step, after a curator approves the wording and publish date.

/spotlight-article-drafter

`/analysis-graphdb-setup`

A one-time setup guide and quarterly update SOP, not a command you invoke during curation. Walks through running a local Reactome Neo4j database connected to Claude Desktop via neo4j-mcp, plus the EBI OLS MCP server for ontology lookups. Once configured, you query the Reactome graph in plain English and get live GO/HP/ChEBI/EFO lookups instead of hallucinated accessions. Follow it once, then use Claude Desktop directly.

Prerequisites by Skill

Skill	Requirements
`/review-internal`	Pathway report DOCX and Curator Guide PDF uploaded to the conversation; Python 3 (stdlib only) and access to `eutils.ncbi.nlm.nih.gov` for PMID verification
`/annotate-pathway-from-reviews-or-topic_name`	claude.ai Pro/Team/Enterprise (Projects) or the Claude API; PubMed and PMC MCP servers recommended; internet access for Mode B
`/extract-reactions`	One or more review-article PDFs; internet access to `eutils.ncbi.nlm.nih.gov`
`/release-doi-batch`	DOIs.xlsx from the Team Drive; Python 3 with `pandas` and `openpyxl`
`/release-qa-tracker`	Python 3 with `openpyxl`; two QA output directories, or an existing comparison file
`/curation-build-illustration`	Python 3 (stdlib only); network access to `reactome.org` for name search and icon/EHLD download (accession lookup works offline); a base-EHLD ST_ID for Mode A, or a sample image for Mode C
`/admin-drive-readme`	Python 3; Google API client libraries (in `requirements.txt`); OAuth credentials at `~/.config/reactome/credentials.json`
`/spotlight-article-drafter`	The candidate paper (PDF, DOI, or URL)
`/analysis-graphdb-setup`	Claude Desktop (Pro plan); Docker Desktop; Node.js; `neo4j-mcp` binary; `uv` package manager

Host allowlisting. In Claude Code launched from the repo root, .claude/settings.json allows WebFetch to eutils.ncbi.nlm.nih.gov and reactome.org, so /extract-reactions resolves PMIDs without a prompt. /curation-build-illustration fetches through its bundled Python helper instead, so it asks for Bash approval on first run — that is expected, not a misconfiguration. In claude.ai (browser), add both hosts manually via Settings → Capabilities → Domain allowlist. Without network access, PMID resolution and icon search fail rather than falling back to fabricated values.

Using Skills Outside Claude Code

To use a skill in the claude.ai desktop app, zip its directory and upload it via Customize → Skills → Upload ZIP:

zip -r review-internal.zip .claude/skills/review-internal/

Quick Reference

What you want to do	Command
Go to the repo	`cd ~/Developer/reactome-curator-workflows`
Start Claude Code	`claude`
Check active credentials	`/status` (inside Claude Code)
Check session token usage	`/cost` (inside Claude Code)
Update the repo	`git pull`
Exit Claude Code	`/exit` or `Control-C`

Troubleshooting

claude: command not found — Claude Code is not on your PATH. Close and reopen Terminal. If it persists, re-run the install command.

Error: Invalid API key — Run echo $ANTHROPIC_API_KEY. If blank, redo Setup step 2. Check for stray spaces or quotation marks inside the key in ~/.zshrc.

Claude Code uses my Claude.ai account instead of the API key — ANTHROPIC_API_KEY is not exported. Check with echo $ANTHROPIC_API_KEY, and run /status inside Claude Code to see the active method.

Python import errors when running a skill — Re-run pip3 install --user -r requirements.txt from the repo root. If pip reports externally-managed-environment, use the virtual-environment route in Setup step 4.

GitHub prompts for a password during clone — Use a personal access token with the repo scope, not your account password.

PMID resolution returns blanks, or icon search fails — You launched Claude Code from outside the repository folder, so the host allowlist in .claude/settings.json never loaded. Restart from ~/Developer/reactome-curator-workflows.

Repository Structure

reactome-curator-workflows/
├── CLAUDE.md                      ← repo conventions + "Adding a New Skill" SOP
├── README.md                      ← this file
├── requirements.txt               ← pinned Python dependencies for all skills
├── .gitignore
├── illustrations/                 ← generated illustration outputs (git-ignored)
└── .claude/
    ├── settings.json              ← host allowlist (eutils.ncbi.nlm.nih.gov, reactome.org)
    └── skills/
        ├── review-internal/                             ← + Curator Guide V94, Data Model
        │                                                  Glossary V95, naming-rule files
        ├── annotate-pathway-from-reviews-or-topic_name/  ← + RLE annotation reference
        ├── extract-reactions/
        ├── release-doi-batch/                           ← + generate_crossref_xml.py
        ├── release-qa-tracker/                          ← + compare_dirs.sh
        ├── curation-build-illustration/                 ← + EHLD/Icon Library specs,
        │                                                  icon_mappings/, reactome_icons.py
        ├── admin-drive-readme/                           ← + update_drive_readme.py
        ├── spotlight-article-drafter/
        └── analysis-graphdb-setup/                       ← + update_reactome.sh

Each skill directory holds its own SKILL.md plus the scripts, templates, and reference documents it needs. Open a skill's directory to see its bundled materials.

Contributing

Skills are added by pull request — see Adding a New Skill in CLAUDE.md for the checklist. Suggestions and bug reports are welcome as GitHub issues. When proposing a change to a curation standard or reference file, cite the specific section of the Curator Guide or Data Model Glossary that supports it, and note the guide version.

Contact

Repo maintainer: Marc Gillespie (SJU) — open a GitHub issue for repo or skill questions
Curation standards questions: consult Curator Guide V94

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reactome-curator-workflows

What This Is

Setup

1. Prerequisites

2. Set your API key

3. Clone the repository

4. Install Python dependencies

5. Run Claude Code

6. Keep up to date

Available Skills

`/review-internal`

`/annotate-pathway-from-reviews-or-topic_name`

`/extract-reactions`

`/release-doi-batch`

`/release-qa-tracker`

`/curation-build-illustration`

`/admin-drive-readme`

`/spotlight-article-drafter`

`/analysis-graphdb-setup`

Prerequisites by Skill

Using Skills Outside Claude Code

Quick Reference

Troubleshooting

Repository Structure

Contributing

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Name		Name	Last commit message	Last commit date
.claude		.claude
.gitignore		.gitignore
CLAUDE.md		CLAUDE.md
README.md		README.md
requirements.txt		requirements.txt

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reactome-curator-workflows

What This Is

Setup

1. Prerequisites

2. Set your API key

3. Clone the repository

4. Install Python dependencies

5. Run Claude Code

6. Keep up to date

Available Skills

/review-internal

/annotate-pathway-from-reviews-or-topic_name

/extract-reactions

/release-doi-batch

/release-qa-tracker

/curation-build-illustration

/admin-drive-readme

/spotlight-article-drafter

/analysis-graphdb-setup

Prerequisites by Skill

Using Skills Outside Claude Code

Quick Reference

Troubleshooting

Repository Structure

Contributing

Contact

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`/review-internal`

`/annotate-pathway-from-reviews-or-topic_name`

`/extract-reactions`

`/release-doi-batch`

`/release-qa-tracker`

`/curation-build-illustration`

`/admin-drive-readme`

`/spotlight-article-drafter`

`/analysis-graphdb-setup`