Merge pull request #334 from monarch-initiative/clarify-evidence-source-docs

Clarify evidence_source documents publication evidence type, not curation method

Author: cmungall

.claude/skills/initiate-new-disorder-creation/SKILL.md

@@ -114,10 +114,13 @@ phenotypes:
   evidence:
   - reference: PMID:XXXXXXXX
     supports: <SUPPORT | REFUTE | PARTIAL>
+    evidence_source: <HUMAN_CLINICAL | MODEL_ORGANISM | IN_VITRO | COMPUTATIONAL>
     snippet: "<Exact quote from abstract>"
     explanation: "<Why this supports the phenotype>"
 ```
 
+**IMPORTANT**: The `evidence_source` field classifies **the type of evidence in the cited publication** (human study, animal model, cell culture, computational simulation), NOT whether the curation was performed by an AI agent. Always classify based on what the paper reports, regardless of who or what is doing the curation.
+
 The same generic `evidence` list schema is used for most types.
 
 ### Step 5: Add term objects
@@ -216,9 +219,12 @@ All evidence items MUST:
 1. Use real PMIDs from the research query results
 2. Have snippets that are exact quotes from abstracts
 3. Include explanations linking evidence to claims
+4. Set `evidence_source` based on the **publication's evidence type** (human clinical, animal model, in vitro, computational), NOT based on whether an AI agent performed the curation
 
 **NEVER fabricate PMIDs or paraphrase snippets.**
 
+**Evidence Source Classification**: When adding `evidence_source`, ask "What kind of study does this paper report?" not "How was this entry curated?" A computational fluid dynamics study gets `COMPUTATIONAL`, a mouse model study gets `MODEL_ORGANISM`, a human clinical trial gets `HUMAN_CLINICAL` - regardless of whether the curation was done by a human or an AI agent.
+
 ## Validation Errors and Fixes
 
 ### "Term not found in ontology"

CLAUDE.md

@@ -96,11 +96,13 @@ evidence:
     explanation: "Why this evidence supports/refutes the claim"
 ```
 
-Set `evidence_source` to clarify provenance:
+**IMPORTANT**: The `evidence_source` field classifies **the type of evidence presented in the cited publication**, NOT how the curation was performed. Even if an AI agent is curating the entry, `evidence_source` describes what kind of study the paper reports (human clinical trial, animal model, cell culture, computational simulation, etc.).
+
+Set `evidence_source` to clarify the publication's evidence type:
 - HUMAN_CLINICAL for direct human observations (default when not specified)
 - MODEL_ORGANISM when citing animal model recapitulation
 - IN_VITRO for cell-based experiments
-- COMPUTATIONAL for in silico predictions
+- COMPUTATIONAL for in silico predictions/simulations reported in the paper
 - OTHER for evidence types that do not fit the above categories
 Model organism evidence should not be the only support for human phenotypes; keep it distinct via `evidence_source`.