| name | gocam-claims-pipeline |
| description | Run the full GO-CAM literature-backed annotation pipeline. Reads GO-CAM models (OWL/TTL), verifies all claims against primary research PDFs, and produces expert validation documents. Use when starting or continuing a GO-CAM curation project folder. |
| argument-hint | [PROCESS_FOLDER_NAME e.g. ampar-endocytosis] |
GO-CAM Claims Pipeline
The annotation instructions are split across section files in workflow/. Read on demand — do not read all files at once.
| File | Read when |
|---|
workflow/annotate_gocam.md | Index — read first for navigation |
workflow/annotate_gocam_rules.md | Session start — always |
workflow/annotate_gocam_setup.md | Session start — always |
workflow/annotate_gocam_phases_0_2.md | Before Phases 0–2 |
workflow/annotate_gocam_phases_3_6.md | Before Phase 3 |
workflow/annotate_gocam_outputs.md | Before Phase 7 |
Context Budget Rules — Read Before Proceeding
Always save agent-output/protein_inventory.md at the end of Phase 1. This file is your working protein list and is updated in Phase 4 with confirmed UniProt IDs and MF terms. It serves as a checkpoint, a process monitor, and a backup if the session is interrupted.
The pipeline can run in a single session (Phases 0–7, excluding drawio and the post-pipeline review skills) or be split at Phase 2. Both modes are supported:
- Single session: proceed continuously; the protein_inventory.md is always there as a reference
- Split at Phase 2: end the session after Phase 2 with
protein_inventory.md saved; resume Phases 3–7 in a later session by reading agent-output/protein_inventory.md as your starting inventory
When resuming Phases 3–7 from a saved inventory: read protein_inventory.md first, then proceed directly to Phase 3 without repeating Phase 1 or Phase 2.
Never read PDF files directly. Each PDF is 2–15 MB in context. Always delegate to a subagent:
Agent(subagent_type="Explore", prompt="Read gocam_models/<process>/literature/<PMID>.pdf. Extract: [structured questions]")
See annotate_gocam_phases_0_2.md for the full subagent patterns for inventory (Phase 1) and targeted verification (Phase 2).
Never Read datamine files. Use Grep to extract PMIDs only:
grep -oE 'PMID:[0-9]+' gocam_models/<process>/datamine/claims_nodes*.md | sort -u
Never Read noctua TTL/OWL files whole. Use barista export-model -f gocam-yaml for inventory. Use Grep for PMID/evidence extraction.
Do not pre-load skills. Only invoke a skill when you first need it. /noctua is never needed for Stage 1. /drawio is only needed in Phase 7. /pubmed, /amigo, /eco-validator are on-demand — invoke only when the specific situation arises.
Two-Stage Workflow
Stage 1 — Literature only (no Noctua model yet)
PDFs + expert material → Agent → claims doc + comments + draw.io → Expert review
Then after agreement: curator builds GO-CAM in Noctua.
Stage 2 — Model exists (extending/revising)
Noctua model (barista export) + PDFs → Agent → updated claims + corrected comments + errors report
Detect which stage applies: does noctua/ exist with a TTL/OWL file?
You NEVER write to Noctua. You NEVER rely on biological knowledge from prior sessions.
Tools to Load
| When | Tool |
|---|
| Always | /gocam-curator skill — gocam search for UniProt IDs, GO MF/BP/CC terms |
| Stage 2 only | /noctua skill — barista for model export (read-only); skip entirely for Stage 1 |
| Phase 3 on demand | /eco-validator skill — live OLS4 query; only invoke when assay not in quick-reference table |
| Phase 7 only | /drawio skill — pathway diagram; do not load before Phase 7 |
| New model | /go-cam-user-guide skill — Noctua model creation workflow (curator action) |
| Phase 4 on demand | WebFetch OLS4 — CHEBI term verification: https://www.ebi.ac.uk/ols4/api/v2/entities?search=CHEBI:<id>&ontologyId=chebi&size=3 |
| Missing PDFs only | /pubmed skill — full text (PMC) or abstract; only invoke when a PDF is absent from literature/ |
| On demand | /amigo skill — only invoke when an MGI/MOD ID is encountered or gocam search fails |
| After Phase 7 | /gemini-dual-review skill — optional dual-perspective Gemini review; can run in same or fresh session |
| After Phase 7 | /blind-review-claude skill — optional fully independent blind quality review using Claude; run in a separate session |
| After Phase 7 | /blind-review-gemini skill — optional fully independent blind quality review using Gemini; run in a separate session |
Phases
Phase 0 — Determine Stage and Collect Inputs
Stage 1 (no noctua/ model):
- Check
noctua/ — if empty or absent, proceed as Stage 1
- Check for existing GO-CAM in store anyway:
barista list-models --title / --gp
- Collect all inputs: PDFs in
literature/, expert_claims.docx, slides, tables, figures
- If no PDFs yet: use
/pubmed to build reading list → give curator PMID list for download
- Orient yourself from expert material (slides, tables, diagrams) — these are hypotheses, not evidence
Stage 2 (noctua/ model exists):
- Export model:
barista export-model --model <id> -f gocam-yaml
- Find model ID via
barista list-models --title if not known
- Collect PDFs in
literature/; read expert_claims.docx if present
Phase 1 — Inventory
Stage 1: Build the protein/activity list from PDFs and expert material directly. There is no model to export. Delegate each PDF to an Explore subagent (see annotate_gocam_phases_0_2.md for the subagent pattern). Collect structured summaries. Extract: gene products, molecular activities, causal relationships, evidence (PMIDs + figures). This becomes your node/edge inventory.
Stage 2: Export model via barista. Detect evidence format (rdfs:comment vs owl:Axiom). List all nodes, edges, gene product IRIs, and PMIDs via Grep. Cross-reference PMIDs against PDFs in literature/; flag gaps. Read expert_claims.docx if present — use as starting framework.
Save agent-output/protein_inventory.md at the end of this phase (gene symbol, role from text, PMIDs). Updated in Phase 4 with UniProt IDs and MF terms.
Phase 2 — PDF Verification (batched by PDF)
- Group all claims/nodes/edges citing the same PMID into one subagent call — never one subagent per claim
- Verify every PMID, figure reference, assay description, and quantitative claim
- Stage 2 only: confirm existing UniProt IDs via
gocam search — Stage 1 UniProt IDs are assigned in Phase 4
- See
annotate_gocam_phases_0_2.md for subagent patterns and batching instructions
- Process-specific PMID errors and known UniProt corrections: check
gocam_models/<process>/ANNOTATION_NOTES.md
Phase 3 — ECO Code Verification
- Re-derive every ECO code from the paper — never trust input
- Use
/eco-validator for any assay not in the annotate_gocam_phases_3_6.md reference table
- Multiple ECO codes per edge when a paper uses multiple assay types
Phase 4 — Molecular Function Verification
- Read
protein_inventory.md first; run gocam search for every gene; update inventory with confirmed UniProt ID and MF
- See
annotate_gocam_phases_3_6.md for strict MF rules (no binding, no substrate names) and ANNOTATION_NOTES.md for process-specific corrections
- Verify CHEBI IDs via WebFetch OLS4
Phase 4b — BP and CC Annotation
- Every node needs
part_of (BP) and occurs_in (CC)
- Use
gocam search to find the most specific terms with IDA/IMP/IEP evidence
Phase 5 — RO Relation Verification
- Verify each causal edge uses the correct RO relation
- See
annotate_gocam_phases_3_6.md for the relation selection table
Phase 6 — Confidence Assessment
- HIGH / MEDIUM / LOW per edge — see
annotate_gocam_phases_3_6.md for criteria
Phase 7 — Output Generation
All outputs to agent-output/. Read workflow/comments_template.md and workflow/claims_template.md before generating.
| Output | File | Stage 1 | Stage 2 |
|---|
| 1 | comments.md | Proposed comments for future Noctua nodes | Corrected rdfs:comment blocks, paste-ready |
| 2 | expert_validation_claims.md | Primary output — goes to expert reviewers | Updated claims after model review |
| 3 | errors_report.md | Not applicable (no existing model to correct) | Every correction with before/after |
| 4 | network_topology.md | Text-based pathway diagram (separate file — not embedded in claims doc) | Text-based pathway diagram |
| 5 | protein_inventory.md | Created Phase 1, updated Phase 4 — protein list with UniProt IDs and MF terms | Same |
| 6 | pathway_sketch.drawio | Use /drawio skill — run separately, not part of main pipeline session | Use /drawio skill |
For Output 2: write Markdown directly. Do not generate a .docx. When the curator is ready to distribute the document to expert reviewers, they will explicitly ask for a Word export — only then convert via python-docx.
For Output 6: the template is at workflow/network_template_draw.drawio — read it before running /drawio.
After Phase 7: stop. Do not invoke /blind-review-claude, /blind-review-gemini, /gemini-dual-review, or /validate-claims automatically. Tell the curator the outputs are ready and that these skills require a separate invocation.
Critical Rules
- Never write to Noctua — curator builds the GO-CAM after expert sign-off
- Never read PDF files directly — always delegate to Explore subagent
- Never Read datamine files — use Grep to extract PMIDs only
- Never Read noctua TTL/OWL files whole — use barista export + Grep
- Every PMID must be verified against the actual PDF (via subagent)
- Every figure reference must exist in the cited paper
- Every ECO code must be re-derived from the paper
- UniProt IDs must be confirmed via
gocam search — never assumed
- MF must never contain "binding" or a substrate name
- CHEBI IDs must be verified against OLS
- Do not invent biology — absent evidence gets flagged, not fabricated
- Distinguish direct enzymatic evidence from pharmacological/indirect
- Every correction must be recorded in
errors_report.md
/blind-review-claude and /blind-review-gemini must run in a separate session — never in the same session as the pipeline
