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reactome-curator-workflows

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

What This Is

This repository contains Claude Code skills — markdown-based instruction files that Claude Code reads directly. Any curator with Claude Code installed can clone this repo and immediately run any skill. No build process, no configuration beyond cloning.

Skills are added incrementally as we identify and vet repeatable workflows. See CLAUDE.md for full project context.

Documentation

Full setup and usage instructions are in:

Reactome_CuratorWorkflows_ClaudeCode_Guide_v1_3.docx

This covers one-time prerequisites, cloning the repository, running each skill, and how to add new skills. Start here if you are setting up for the first time.

Setup (Quick Reference)

1. Prerequisites (one-time)

Install Git: https://git-scm.com/downloads

Install Node.js (LTS): https://nodejs.org

Install Claude Code:

mkdir -p ~/.npm-global
npm config set prefix '~/.npm-global'
echo 'export PATH=~/.npm-global/bin:$PATH' >> ~/.zshrc
source ~/.zshrc
npm install -g @anthropic-ai/claude-code

Set your Anthropic API key (add to ~/.zshrc):

export ANTHROPIC_API_KEY=your-key-here

Install Python dependencies (use pip3 on macOS):

pip3 install pandas openpyxl

If you see a PATH warning after installing, add this to ~/.zshrc (replace 3.9 with the version number shown in your warning):

export PATH="/Users/[you]/Library/Python/3.9/bin:$PATH"

2. Clone the repository

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

3. Run Claude Code

cd ~/Developer/reactome-curator-workflows
claude

Claude Code automatically reads CLAUDE.md and loads all skills at session start. The .claude/settings.json file allowlists external hosts (e.g., NCBI E-utilities) required by certain skills.

4. Keep up to date

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

Available Skills

/internal-module-review

Formal structured internal review of a Reactome pathway report against Curator Guide V94 standards. Produces a prioritized review DOCX with seven sections. Upload the pathway report DOCX and Curator Guide PDF to the conversation before invoking. Optional modifiers: disease, drug, large.

Sections:

Section What it covers
1 Reaction connectivity, including Input→Output entity chain verification
2 GO Biological Process assignments
3 Literature references
4 Grammar, clarity, and summation quality
5 General curation quality
6 Prioritized issue summary (consolidated table, all sections)
7 Entity and event name conventions

Section 7 checks every entity and event name against the Reactome controlled vocabulary (Jupe et al. 2014) and associated naming rules. Five subsections cover EWAS/peptide names (gene symbol, coordinates, PTM prefixes), reaction/event names (all 11 CV classes), small molecule names, complex names (colon separator, square bracket hierarchy notation), and set names (comma separator, candidate member notation). Naming convention reference files are automatically loaded — no additional uploads required.

/internal-module-review "HHV8 Infection" R-HSA-9521541 "Lisa Matthews" 2026-04-15

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

AI-assisted pre-curation workflow (v1.3, April 2026). Proposes a complete Reactome pathway hierarchy — pathway names, subpathway names, and reaction names — and verifies primary literature citations using a mandatory ten-step PMID verification protocol.

Requires claude.ai Projects (Pro/Team/Enterprise) or the Claude API. PubMed and PMC MCP servers are recommended for live PMID verification and full-text fetch.

Two entry modes:

  • Mode A — Curator supplies references (PMIDs, DOIs, or uploaded PDFs); assistant reads the papers and proceeds directly to Phase 1.
  • Mode B — Curator supplies a biological topic; assistant performs live web searches for primary literature, presents a ranked candidate reference list, and waits for curator confirmation before proceeding.

Session workflow:

Session opening
    │
    ├── Mode A: Curator supplies references
    │       └── Assistant reads papers → proceeds to Phase 1
    │
    └── Mode B: Curator supplies a topic
            │   Assistant searches → presents ranked reference list
            └── STOP — curator confirms or modifies list
                    └── Curator replies "proceed"

Phase 1 — Hierarchy proposal
    Proposed pathway / subpathway / reaction names
    Evidence species flags (human / non-human / chimeric)
    Non-human and chimeric reactions paired with inferred human reactions
    Proceeds immediately to Phase 2 — no approval gate

Phase 2 — Literature verification
    Ten-step PMID verification protocol per reaction
    PMC full-text fetch and verbatim evidence sentence extraction
    Standard or inferred-human citation blocks
    Subpathway by subpathway — no stops between subpathways

STOP — full output presented for curator review

Citation block formats:

Standard (direct or indirect evidence):

Reaction name:    [name from hierarchy]
Primary PMID:     https://pubmed.ncbi.nlm.nih.gov/[PMID]/
Primary PMC URL:  https://pmc.ncbi.nlm.nih.gov/articles/PMCXXXXXXX/
Authors/Year:     [First author et al., Year, Journal]
Primary evidence: "[verbatim sentence including method, proteins, cell type, figure]"
Evidence type:    DIRECT / INDIRECT / OVEREXP ONLY
Species:          [human / murine / other]
Flags:            [mismatches, gaps, curator actions required]

Inferred human reaction:

Reaction name:    [inferred human reaction name]
Evidence type:    INFERRED FROM NON-HUMAN / INFERRED FROM CHIMERIC
Species:          Homo sapiens (inferred)
inferredFrom:     [paired non-human or chimeric reaction name]
Primary PMID:     https://pubmed.ncbi.nlm.nih.gov/[PMID]/
Authors/Year:     [same as paired evidence reaction]
Flags:            No independent human experimental evidence. Curator should
                  confirm human orthology is supported before submission.

Species and chimeric reaction logic:

Experimental situation Reaction type isChimeric Inferred human required
Human proteins/cells only Human reaction FALSE No
Single non-human species only Non-human reaction FALSE Yes
≥2 species mixed in same assay Chimeric reaction TRUE Yes

Non-human proteins use initial capitalisation (Jak2); human proteins use ALL-CAPS (JAK2).

Evidence classification:

Class Reaction type Examples
DIRECT Reaction co-IP, in vitro reconstitution, SPR/ITC, NMR, crystallography, direct enzymatic assay
INDIRECT BlackBoxEvent (provisional) KO, rescue, overexpression, inhibitor treatment, domain deletion
INSUFFICIENT Do not annotate Microarray alone, bulk proteomics alone, ChIP-seq alone, computational prediction alone

What is out of scope — handled separately by the curator using database tooling: Neo4j/gk_central queries, OLS ontology verification, UniProt REST API verification, GtoPdb drug checks, full annotation table population, disease flag resolution, and pathway diagram drawing. All such fields are marked PENDING CURATOR VERIFICATION.

Key limitations:

  • PMID fabrication risk. The ten-step protocol catches fabricated PMIDs, but curators should independently confirm all PMIDs before database submission.
  • Full-text access. PMC full text fetched for open-access papers only; paywalled papers fall back to web search and are flagged if unavailable.
  • Knowledge cutoff. Mode B performs live searches, but curators should verify that the most recent relevant primary papers have been captured.
  • Ontology accessions. GO, ChEBI, MONDO, and UniProt accessions are not resolved in this workflow — all marked PENDING CURATOR VERIFICATION.

For the full workflow documentation, citation block reference, species/chimeric rules, and version history, see .claude/skills/annotate-pathway-from-reviews-or-topic_name/README.md.

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

/generate-doi-batch

Generates a CrossRef DOI batch XML file for a release using DOIs.xlsx. Requires DOIs.xlsx locally (from Team Drive) and Python 3 + pandas.

/generate-doi-batch V94

/extract-reactions

Extracts a reaction graph for a named pathway from one or more medical/biology review PDFs. Writes two artefacts:

  • <pathway-slug>_reactions.csv — columns: Title, Input, Output, Catalyst, Regulators, Reviews, Source1–Source5
  • <pathway-slug>_references.html — every cited primary reference as a link

Reviews holds pipe-delimited supplied-PDF basenames. Each Source cell holds exactly one URL chosen by a PubMed → PMC → DOI → publisher ladder; any 6th or further sources are dropped. Pre-curation draft, not a curated entry.

/extract-reactions

Prerequisites by Skill

Skill Requirements
/internal-module-review Internet access; pathway report DOCX and Curator Guide PDF uploaded to conversation
/annotate-pathway-from-reviews-or-topic_name claude.ai Pro/Team/Enterprise (Projects) or Claude API; PubMed and PMC MCP servers recommended; internet access for Mode B
/generate-doi-batch DOIs.xlsx from Team Drive; Python 3 with pandas and openpyxl
/extract-reactions One or more review-article PDFs (absolute paths); internet access to eutils.ncbi.nlm.nih.gov

Note on /extract-reactions and NCBI access: In Claude Code, .claude/settings.json allowlists eutils.ncbi.nlm.nih.gov automatically. In claude.ai (browser), add it manually via Settings → Capabilities → Domain allowlist. Without it, PMID resolution falls through to DOI URLs or blanks — PMIDs are never recovered from training data.

Chrome Extensions

pmid-tagger (chrome-extensions/pmid-tagger/)

Automatically prefixes PDF downloads with PMID-<id>_ when initiated from a PubMed or PMC article page. Keeps downloaded papers consistently named with their PMID, making it easier to match PDFs to references during curation.

To install:

  1. Open Chrome → chrome://extensions/
  2. Enable Developer mode (top-right toggle)
  3. Click Load unpacked → select the chrome-extensions/pmid-tagger/ folder
  4. Active immediately — no configuration required

Using Skills in the claude.ai Desktop App

  1. Locate your skill folder: .claude/skills/<skill-name>/
  2. ZIP it: zip -r skill-name.zip skill-name/
  3. Go to Customize → Skills → Upload ZIP in the Desktop app

Contributing a Skill

  1. Create a directory under .claude/skills/ named for your skill
  2. Add SKILL.md with YAML frontmatter (name, description) and instructions
  3. Add any supporting files (templates, scripts, reference docs)
  4. Test it locally with Claude Code
  5. Open a PR with a brief description of what the skill does and when to use it

For detailed instructions on writing and committing a new skill, see the full guide (Reactome_CuratorWorkflows_ClaudeCode_Guide_v1_3.docx).

Suggestions for improving annotate-pathway-from-reviews-or-topic_name — including changes to the system prompt or the RLE annotation reference file — are welcome via GitHub Issues. When proposing changes to the reference file, cite the specific section of the Curator Guide or Data Model Glossary that supports the change, and note the guide version.

Repository Structure

reactome-curator-workflows/
├── CLAUDE.md                                              ← project context for Claude Code
├── README.md                                              ← this file
├── Reactome_CuratorWorkflows_ClaudeCode_Guide_v1_3.docx  ← full setup guide
├── .gitignore
├── chrome-extensions/
│   └── pmid-tagger/                                      ← Chrome extension: PMID-prefix PDF downloads
│       ├── manifest.json
│       ├── background.js
│       └── content.js
└── .claude/
    ├── settings.json                                      ← Claude Code host allowlist
    └── skills/
        ├── internal-module-review/
        │   ├── SKILL.md
        │   ├── Reactome_InternalReview_PROMPT_v1_4.docx
        │   ├── Reactome_InternalReview_TEMPLATE.docx
        │   ├── Claude_ReactomeDataModelGlossary_V95_Final.docx.pdf
        │   ├── Curator_Guide_V94.pdf
        │   ├── EWAS_name_rules.docx                       ← EWAS naming rules (Section 7)
        │   ├── Rules_for_automatic_reaction_typing.docx   ← reaction/event naming rules (Section 7)
        │   ├── bau060.pdf                                 ← Jupe et al. 2014 CV paper (Section 7)
        │   ├── ptm_lookup.xlsx                            ← PSI-MOD → PTM prefix table (source)
        │   ├── ptm_prefixes.md                            ← PTM prefix table, plain text (auto-loaded)
        │   └── Small_molecule_renaming.xlsx               ← canonical small molecule names (Section 7)
        ├── annotate-pathway-from-reviews-or-topic_name/
        │   ├── SKILL.md
        │   ├── README.md
        │   └── Reactome_RLE_Annotation_Reference_V94.md
        ├── extract-reactions/
        │   └── SKILL.md
        └── generate-doi-batch/
            ├── SKILL.md
            └── generate_crossref_xml.py

Contact

Repo maintainer: Marc Gillespie (NYU / SJU) — gillespm@stjohns.edu For curation standards questions: Reactome curator Slack channel For repo/skill questions: open a GitHub issue

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