Add bulk NTR ROBOT template generation workflow

.claude/agents/ontology-term-lookup.md

@@ -0,0 +1,102 @@
+---
+name: ontology-term-lookup
+description: Use this agent when you need to find ontology terms by their textual labels or descriptions using the OLS4 MCP. This includes:\n\n<example>\nContext: User is populating a DOSDP template and needs to find the correct ontology term for 'hepatic artery'.\nuser: "I need to find the ontology term for 'hepatic artery' in UBERON"\nassistant: "I'll use the ontology-term-lookup agent to search for this term in UBERON."\n<agent call to ontology-term-lookup with text='hepatic artery' and ontology='UBERON'>\n</example>\n\n<example>\nContext: Agent is filling in missing ontology terms in a template and encounters text describing an anatomical structure.\nassistant: "I need to find the ontology term for 'renal vein' to complete this template entry. Let me use the ontology-term-lookup agent."\n<agent call to ontology-term-lookup with text='renal vein' and ontology='UBERON'>\n</example>\n\n<example>\nContext: User provides alternative phrasings that need to be searched.\nuser: "Check if there's a term for either 'artery of kidney' or 'kidney artery'"\nassistant: "I'll use the ontology-term-lookup agent to search for both phrasings."\n<agent call to ontology-term-lookup with text='artery of kidney' and ontology='UBERON'>\n<agent call to ontology-term-lookup with text='kidney artery' and ontology='UBERON'>\n</example>
+model: sonnet
+---
+
+You are an expert ontology term matcher specializing in using the OLS4 (Ontology Lookup Service 4) MCP to find precise ontology term matches for textual descriptions.
+
+Your core responsibility is to take textual input describing an anatomical or biological concept and find the best matching ontology term(s) from a specified ontology using the ols4-mcp tool.
+
+## Input Processing
+
+You will receive:
+1. **text**: The term or phrase to look up (e.g., 'hepatic artery', 'blood vessel', 'artery of liver')
+2. **ontology**: The target ontology to search within (e.g., 'UBERON', 'CL', 'GO')
+
+## Search Strategy
+
+Execute searches systematically:
+
+1. **Primary Search**: Search for the exact text as provided in the specified ontology using ols4-mcp, looking for matches in labels and synonyms.
+
+2. **Alternative Phrasing**: If no high-confidence match is found, automatically generate and search alternative phrasings:
+   - Convert "X artery" to "artery of X" and vice versa
+   - Try singular/plural variations
+   - Substitute common synonyms (e.g., 'vessel' for 'blood vessel', 'hepatic' for 'liver')
+   - Consider anatomical term variations (e.g., 'renal' for 'kidney', 'cardiac' for 'heart')
+
+3. **Iterative Refinement**: If initial searches yield poor results, progressively broaden or narrow the search terms based on the domain.
+
+## Match Quality Assessment
+
+Evaluate matches based on:
+- **Exact label match**: Highest confidence
+- **Exact synonym match**: High confidence
+- **Partial label/synonym match**: Medium confidence (note the differences)
+- **Related term**: Low confidence (clearly indicate this is not a direct match)
+
+## Output Format
+
+Return results in this structured format:
+
+**For single high-confidence match:**
+```
+Best Match Found:
+- Input Text: [original input]
+- Matched Term: [term label]
+- Ontology ID: [full IRI or CURIE]
+- Match Type: [exact label | exact synonym | partial match]
+- Definition: [term definition if available]
+- Confidence: High
+```
+
+**For multiple high-confidence matches:**
+```
+Multiple Matches Found (ranked by relevance):
+
+Input Text: [original input]
+
+1. [Match rank]
+   - Matched Term: [term label]
+   - Ontology ID: [full IRI or CURIE]
+   - Match Type: [exact label | exact synonym | partial match]
+   - Definition: [term definition if available]
+   - Confidence: High/Medium
+   - Reason for ranking: [brief explanation]
+
+2. [Match rank]
+   - Matched Term: [term label]
+   - Ontology ID: [full IRI or CURIE]
+   - Match Type: [exact label | exact synonym | partial match]
+   - Definition: [term definition if available]
+   - Confidence: High/Medium
+   - Reason for ranking: [brief explanation]
+
+[Continue for all relevant matches]
+```
+
+**For no matches:**
+```
+No Match Found:
+- Input Text: [original input]
+- Ontology Searched: [ontology name]
+- Alternative phrasings tried: [list attempted variations]
+- Recommendation: [suggest manual review, broader ontology search, or term creation]
+```
+
+## Quality Control
+
+- Always verify that the matched term's definition aligns semantically with the input text
+- Flag cases where the match seems questionable despite technical similarity
+- When ranking multiple matches, prioritize based on: definition alignment > match type > term specificity
+- Never return matches with low confidence without clearly labeling them as such
+- If the ontology parameter seems inappropriate for the term type, note this in your response
+
+## Error Handling
+
+- If the ols4-mcp tool is unavailable, clearly state this and suggest alternative approaches
+- If the specified ontology doesn't exist or is inaccessible, report this explicitly
+- If the input text is ambiguous, note this and explain what additional context would help
+
+Remember: Precision is paramount. It's better to return no match or multiple candidates than to return a single incorrect high-confidence match.

.claude/skills/fetch-wiki-info/SKILL.md

@@ -0,0 +1,145 @@
+---
+name: fetch-wiki-info
+description: Fetch structured and descriptive information from Wikidata and Wikipedia for any topic
+argument-hint: "[search term]"
+allowed-tools: mcp__playwright__browser_run_code
+---
+
+# Fetch Wiki Info Skill
+
+Retrieve information from Wikidata and Wikipedia for any topic. This skill uses a hybrid approach to get both structured data and descriptive text.
+
+## Search Term
+Topic to search for: **$ARGUMENTS**
+
+## Instructions
+
+Use the Playwright MCP to fetch information using the following two-step approach:
+
+### Step 1: Search Wikidata
+
+First, search for the topic in Wikidata to get the entity ID:
+
+```javascript
+async (page) => {
+  const searchTerm = "$ARGUMENTS";
+  await page.goto(`https://www.wikidata.org/w/api.php?action=wbsearchentities&search=${encodeURIComponent(searchTerm)}&language=en&format=json`);
+  const searchData = await page.evaluate(() => JSON.parse(document.body.textContent));
+
+  if (searchData.search && searchData.search.length > 0) {
+    return searchData.search.slice(0, 5).map(item => ({
+      id: item.id,
+      label: item.label,
+      description: item.description || 'N/A'
+    }));
+  }
+  return [];
+}
+```
+
+### Step 2: Fetch Wikidata Entity Details
+
+Once you have the most relevant entity ID (usually the first result), fetch its full details:
+
+```javascript
+async (page) => {
+  const entityId = "Q1234567"; // Replace with actual ID from step 1
+  await page.goto(`https://www.wikidata.org/wiki/Special:EntityData/${entityId}.json`);
+  const jsonData = await page.evaluate(() => JSON.parse(document.body.textContent));
+  const entity = jsonData.entities[entityId];
+
+  let result = {};
+
+  // Basic info
+  if (entity.labels?.en) result.label = entity.labels.en.value;
+  if (entity.descriptions?.en) result.description = entity.descriptions.en.value;
+  if (entity.aliases?.en) result.aliases = entity.aliases.en.map(a => a.value);
+
+  // Properties - extract common ones
+  result.properties = {};
+  if (entity.claims) {
+    // Instance of (P31)
+    if (entity.claims.P31) {
+      result.properties.instanceOf = entity.claims.P31.map(c => c.mainsnak.datavalue?.value?.id).filter(Boolean);
+    }
+    // Part of (P361)
+    if (entity.claims.P361) {
+      result.properties.partOf = entity.claims.P361.map(c => c.mainsnak.datavalue?.value?.id).filter(Boolean);
+    }
+    // Subclass of (P279)
+    if (entity.claims.P279) {
+      result.properties.subclassOf = entity.claims.P279.map(c => c.mainsnak.datavalue?.value?.id).filter(Boolean);
+    }
+    // Add any other relevant properties based on the topic
+  }
+
+  return result;
+}
+```
+
+### Step 3: Fetch Wikipedia Content (if needed)
+
+If Wikidata doesn't have enough descriptive text, fetch from Wikipedia:
+
+```javascript
+async (page) => {
+  const searchTerm = "$ARGUMENTS";
+  const wikipediaUrl = `https://en.wikipedia.org/wiki/${encodeURIComponent(searchTerm.replace(/ /g, '_'))}`;
+
+  await page.goto(wikipediaUrl);
+
+  const content = await page.evaluate(() => {
+    let text = '';
+
+    // Get the first paragraph (main definition)
+    const firstPara = document.querySelector('#mw-content-text .mw-parser-output > p:first-of-type');
+    if (firstPara) {
+      text += firstPara.textContent.trim() + '\n\n';
+    }
+
+    // Get subsequent paragraphs until first heading
+    const paras = document.querySelectorAll('#mw-content-text .mw-parser-output > p');
+    for (let i = 1; i < Math.min(paras.length, 5); i++) {
+      const paraText = paras[i].textContent.trim();
+      if (paraText && paraText.length > 20) {
+        text += paraText + '\n\n';
+      }
+    }
+
+    return text.trim();
+  });
+
+  return content;
+}
+```
+
+## Output Format
+
+Present the information in a clear, structured format:
+
+```
+# $ARGUMENTS
+
+## Wikidata (Q#######)
+- **Label**: [label]
+- **Description**: [description]
+- **Aliases**: [aliases]
+- **Instance of**: [Q-IDs with labels if available]
+- **Part of**: [Q-IDs with labels if available]
+- [Other relevant properties]
+
+## Wikipedia Summary
+[Descriptive text from Wikipedia]
+
+## Source URLs
+- Wikidata: https://www.wikidata.org/wiki/Q#######
+- Wikipedia: https://en.wikipedia.org/wiki/[page]
+```
+
+## Notes
+
+- Always check if search results are relevant before fetching full details
+- If multiple Wikidata entities match, list them and ask the user which one to fetch
+- Wikipedia article names are case-sensitive and use underscores instead of spaces
+- Some topics may only be in Wikidata or Wikipedia, not both
+- For topics not in English, you can modify the language code in the API calls

.mcp.json

@@ -0,0 +1,21 @@
+{
+  "mcpServers": {
+    "artl-mcp": {
+      "command": "uvx",
+      "args": ["artl-mcp"],
+      "tools": ["*"]
+    },
+    "ols4": {
+      "type": "http",
+      "url": "http://www.ebi.ac.uk/ols4/api/mcp",
+      "tools": ["*"]
+    },
+    "playwright": {
+      "command": "npx",
+      "args": [
+        "@playwright/mcp@latest"
+      ],
+     "tools": ["*"]
+    }
+  }
+}