@yeyuan98/opencode-bioresearcher-plugin 1.5.2 → 1.5.3

package/dist/skills/bioresearcher-core/patterns/citations.md

@@ -1,234 +1,234 @@
-# Citations Pattern
-
-Standardized citation format for biomedical research with automatic bibliography generation.
-
-## Overview
-
-Use this pattern to maintain consistent citations throughout research outputs. All findings must be backed by sources with proper citations.
-
-## Citation Style
-
-Use **numbered citations** for biomedical research:
-
-- In-text: [1], [2], [3]
-- Bibliography: Numbered list at end of document
-
-## In-Text Citation Format
-
-### Single Source
-```
-BRAF V600E mutations are found in approximately 50% of melanomas [1].
-```
-
-### Multiple Sources
-```
-Several studies have confirmed this association [1, 2, 3].
-```
-
-### Range of Sources
-```
-This has been extensively documented [1-5].
-```
-
-### Specific Claims
-```
-The drug was approved in 2011 [1] and has since become standard of care [2, 3].
-```
-
-## Bibliography Format
-
-### PubMed Articles
-
-```
-[1] Author1 AB, Author2 CD, Author3 EF. Article Title. Journal Name. Year;Volume(Issue):Pages. PMID: XXXXXXXX.
-```
-
-**Example:**
-```
-[1] Chapman PB, Hauschild A, Robert C, et al. Improved survival with vemurafenib in melanoma with BRAF V600E mutation. N Engl J Med. 2011;364(26):2507-2516. PMID: 21639808.
-```
-
-### Clinical Trials
-
-```
-[N] NCT ID: Trial Title. Phase X. Sponsor: Company/Institution. Status: Recruiting/Completed. URL: https://clinicaltrials.gov/ct2/show/NCTXXXXXXX
-```
-
-**Example:**
-```
-[2] NCT04280705: A Study of Encorafenib Plus Cetuximab With or Without Nivolumab in Metastatic Colorectal Cancer. Phase 2. Sponsor: Pfizer. Status: Completed. https://clinicaltrials.gov/ct2/show/NCT04280705
-```
-
-### Web Sources
-
-```
-[N] Page Title. Website Name. Published/Updated Date. URL. Accessed: YYYY-MM-DD.
-```
-
-**Example:**
-```
-[3] BRAF Gene. National Cancer Institute. Updated 2024. https://www.cancer.gov/about-cancer/causes-prevention/genetics/brca-genes. Accessed: 2024-01-15.
-```
-
-### Drug/Chemical Information
-
-```
-[N] Drug Name. DrugBank ID: DBXXXXX. ChEMBL ID: CHEMBLXXXXX. Indication: Disease.
-```
-
-**Example:**
-```
-[4] Vemurafenib. DrugBank ID: DB08881. ChEMBL ID: CHEMBL1229511. Indication: Melanoma.
-```
-
-### Gene Information
-
-```
-[N] Gene Symbol: Gene Name. Entrez ID: XXXXXX. HGNC ID: HGNC:XXXX.
-```
-
-**Example:**
-```
-[5] BRAF: B-Raf proto-oncogene, serine/threonine kinase. Entrez ID: 673. HGNC ID: HGNC:1097.
-```
-
-## Source-Specific Citation Workflows
-
-### From BioMCP Article Results
-
-When using `biomcp_search` or `biomcp_article_searcher`:
-
-```
-1. Extract from result:
-   - Authors (first author + "et al." if many)
-   - Title
-   - Journal
-   - Year
-   - PMID (from result.id or result.metadata)
-
-2. Use biomcp_article_getter(pmid="XXXXXXXX") for full metadata if needed
-
-3. Format citation
-```
-
-### From Clinical Trials
-
-When using `biomcp_trial_searcher` or `biomcp_trial_getter`:
-
-```
-1. Extract from result:
-   - NCT ID (result.id)
-   - Official title
-   - Phase
-   - Sponsor
-   - Status
-
-2. Format citation with ClinicalTrials.gov URL
-```
-
-### From Gene/Drug/Variant Information
-
-When using gene_getter, drug_getter, or variant_getter:
-
-```
-1. Extract identifiers:
-   - Gene: Symbol, Entrez ID, HGNC ID
-   - Drug: Name, DrugBank ID, ChEMBL ID
-   - Variant: HGVS notation, rsID, ClinVar significance
-
-2. Format as database citation
-```
-
-## Bibliography Section Format
-
-Place bibliography at the end of your document:
-
-```markdown
-## References
-
-[1] Chapman PB, Hauschild A, Robert C, et al. Improved survival with vemurafenib in melanoma with BRAF V600E mutation. N Engl J Med. 2011;364(26):2507-2516. PMID: 21639808.
-
-[2] NCT04280705: A Study of Encorafenib Plus Cetuximab With or Without Nivolumab in Metastatic Colorectal Cancer. Phase 2. Sponsor: Pfizer. Status: Completed. https://clinicaltrials.gov/ct2/show/NCT04280705
-
-[3] BRAF Gene. National Cancer Institute. Updated 2024. https://www.cancer.gov/about-cancer/causes-prevention/genetics/brca-genes. Accessed: 2024-01-15.
-```
-
-## Example: Research Report with Citations
-
-```markdown
-# BRAF Mutations in Melanoma
-
-## Overview
-
-BRAF V600E is the most common mutation in cutaneous melanoma, occurring in approximately 50% of cases [1]. This mutation leads to constitutive activation of the MAPK signaling pathway [2].
-
-## Treatment Landscape
-
-Targeted therapies against BRAF V600E have significantly improved outcomes:
-
-- **Vemurafenib**: First FDA-approved BRAF inhibitor (2011) [3]
-- **Dabrafenib**: Second-generation BRAF inhibitor [4]
-- **Combination therapy**: BRAF + MEK inhibition improves survival [5]
-
-## Clinical Trials
-
-Several ongoing trials are exploring combination approaches:
-
-- NCT04280705: Encorafenib + cetuximab ± nivolumab in colorectal cancer [6]
-- NCT04511078: Adjuvant dabrafenib + trametinib in melanoma [7]
-
-## References
-
-[1] Davies H, Bignell GR, Cox C, et al. Mutations of the BRAF gene in human cancer. Nature. 2002;417(6892):949-954. PMID: 12068308.
-
-[2] Wan PT, Garnett MJ, Roe SM, et al. Mechanism of activation of RAF-ERK signaling by oncogenic mutations of B-RAF. Cell. 2004;116(6):855-867. PMID: 15035987.
-
-[3] Chapman PB, Hauschild A, Robert C, et al. Improved survival with vemurafenib in melanoma with BRAF V600E mutation. N Engl J Med. 2011;364(26):2507-2516. PMID: 21639808.
-
-[4] Hauschild A, Grob JJ, Demidov LV, et al. Dabrafenib in BRAF-mutated metastatic melanoma: a multicentre, open-label, phase 3 randomised controlled trial. Lancet. 2012;380(9839):358-365. PMID: 22735384.
-
-[5] Robert C, Karaszewska B, Schachter J, et al. Improved overall survival in melanoma with combined dabrafenib and trametinib. N Engl J Med. 2015;372(1):30-39. PMID: 25399551.
-
-[6] NCT04280705: A Study of Encorafenib Plus Cetuximab With or Without Nivolumab in Metastatic Colorectal Cancer. Phase 2. Sponsor: Pfizer. Status: Completed. https://clinicaltrials.gov/ct2/show/NCT04280705
-
-[7] NCT04511078: Adjuvant Dabrafenib Plus Trametinib in Resected BRAF V600-Mutant Melanoma. Phase 3. Sponsor: Novartis. Status: Recruiting. https://clinicaltrials.gov/ct2/show/NCT04511078
-```
-
-## Citation Quality Standards
-
-### What to Cite
-
-| Source Type | Citation Required |
-|-------------|-------------------|
-| Published research | Yes |
-| Clinical trial data | Yes |
-| Drug approval info | Yes |
-| Gene/variant annotations | Yes |
-| Statistical claims | Yes |
-| Direct quotes | Yes |
-| General knowledge | No (e.g., "DNA has 4 bases") |
-
-### Citation Integrity
-
-1. **Verify source exists**: Always confirm PMID, NCT ID, URL is valid
-2. **Quote accurately**: Don't misrepresent findings
-3. **Cite primary sources**: Prefer original papers over reviews
-4. **Update outdated citations**: Use latest evidence when available
-
-## Tools for Citation Generation
-
-| Tool | Use Case |
-|------|----------|
-| `biomcp_article_getter` | Get full article metadata from PMID |
-| `biomcp_trial_getter` | Get trial details from NCT ID |
-| `biomcp_gene_getter` | Get gene identifiers |
-| `biomcp_drug_getter` | Get drug identifiers |
-
-## Best Practices
-
-1. **Cite as you write**: Add citations immediately when making claims
-2. **Number sequentially**: [1], [2], [3] in order of appearance
-3. **Include access dates**: For web sources, always include when accessed
-4. **Verify PMIDs**: Double-check PMID matches the article
-5. **Keep bibliography alphabetical by number**: Not by author
-6. **Format consistently**: Same style throughout document
+# Citations Pattern
+
+Standardized citation format for biomedical research with automatic bibliography generation.
+
+## Overview
+
+Use this pattern to maintain consistent citations throughout research outputs. All findings must be backed by sources with proper citations.
+
+## Citation Style
+
+Use **numbered citations** for biomedical research:
+
+- In-text: [1], [2], [3]
+- Bibliography: Numbered list at end of document
+
+## In-Text Citation Format
+
+### Single Source
+```
+BRAF V600E mutations are found in approximately 50% of melanomas [1].
+```
+
+### Multiple Sources
+```
+Several studies have confirmed this association [1, 2, 3].
+```
+
+### Range of Sources
+```
+This has been extensively documented [1-5].
+```
+
+### Specific Claims
+```
+The drug was approved in 2011 [1] and has since become standard of care [2, 3].
+```
+
+## Bibliography Format
+
+### PubMed Articles
+
+```
+[1] Author1 AB, Author2 CD, Author3 EF. Article Title. Journal Name. Year;Volume(Issue):Pages. PMID: XXXXXXXX.
+```
+
+**Example:**
+```
+[1] Chapman PB, Hauschild A, Robert C, et al. Improved survival with vemurafenib in melanoma with BRAF V600E mutation. N Engl J Med. 2011;364(26):2507-2516. PMID: 21639808.
+```
+
+### Clinical Trials
+
+```
+[N] NCT ID: Trial Title. Phase X. Sponsor: Company/Institution. Status: Recruiting/Completed. URL: https://clinicaltrials.gov/ct2/show/NCTXXXXXXX
+```
+
+**Example:**
+```
+[2] NCT04280705: A Study of Encorafenib Plus Cetuximab With or Without Nivolumab in Metastatic Colorectal Cancer. Phase 2. Sponsor: Pfizer. Status: Completed. https://clinicaltrials.gov/ct2/show/NCT04280705
+```
+
+### Web Sources
+
+```
+[N] Page Title. Website Name. Published/Updated Date. URL. Accessed: YYYY-MM-DD.
+```
+
+**Example:**
+```
+[3] BRAF Gene. National Cancer Institute. Updated 2024. https://www.cancer.gov/about-cancer/causes-prevention/genetics/brca-genes. Accessed: 2024-01-15.
+```
+
+### Drug/Chemical Information
+
+```
+[N] Drug Name. DrugBank ID: DBXXXXX. ChEMBL ID: CHEMBLXXXXX. Indication: Disease.
+```
+
+**Example:**
+```
+[4] Vemurafenib. DrugBank ID: DB08881. ChEMBL ID: CHEMBL1229511. Indication: Melanoma.
+```
+
+### Gene Information
+
+```
+[N] Gene Symbol: Gene Name. Entrez ID: XXXXXX. HGNC ID: HGNC:XXXX.
+```
+
+**Example:**
+```
+[5] BRAF: B-Raf proto-oncogene, serine/threonine kinase. Entrez ID: 673. HGNC ID: HGNC:1097.
+```
+
+## Source-Specific Citation Workflows
+
+### From BioMCP Article Results
+
+When using `biomcp_search` or `biomcp_article_searcher`:
+
+```
+1. Extract from result:
+   - Authors (first author + "et al." if many)
+   - Title
+   - Journal
+   - Year
+   - PMID (from result.id or result.metadata)
+
+2. Use biomcp_article_getter(pmid="XXXXXXXX") for full metadata if needed
+
+3. Format citation
+```
+
+### From Clinical Trials
+
+When using `biomcp_trial_searcher` or `biomcp_trial_getter`:
+
+```
+1. Extract from result:
+   - NCT ID (result.id)
+   - Official title
+   - Phase
+   - Sponsor
+   - Status
+
+2. Format citation with ClinicalTrials.gov URL
+```
+
+### From Gene/Drug/Variant Information
+
+When using gene_getter, drug_getter, or variant_getter:
+
+```
+1. Extract identifiers:
+   - Gene: Symbol, Entrez ID, HGNC ID
+   - Drug: Name, DrugBank ID, ChEMBL ID
+   - Variant: HGVS notation, rsID, ClinVar significance
+
+2. Format as database citation
+```
+
+## Bibliography Section Format
+
+Place bibliography at the end of your document:
+
+```markdown
+## References
+
+[1] Chapman PB, Hauschild A, Robert C, et al. Improved survival with vemurafenib in melanoma with BRAF V600E mutation. N Engl J Med. 2011;364(26):2507-2516. PMID: 21639808.
+
+[2] NCT04280705: A Study of Encorafenib Plus Cetuximab With or Without Nivolumab in Metastatic Colorectal Cancer. Phase 2. Sponsor: Pfizer. Status: Completed. https://clinicaltrials.gov/ct2/show/NCT04280705
+
+[3] BRAF Gene. National Cancer Institute. Updated 2024. https://www.cancer.gov/about-cancer/causes-prevention/genetics/brca-genes. Accessed: 2024-01-15.
+```
+
+## Example: Research Report with Citations
+
+```markdown
+# BRAF Mutations in Melanoma
+
+## Overview
+
+BRAF V600E is the most common mutation in cutaneous melanoma, occurring in approximately 50% of cases [1]. This mutation leads to constitutive activation of the MAPK signaling pathway [2].
+
+## Treatment Landscape
+
+Targeted therapies against BRAF V600E have significantly improved outcomes:
+
+- **Vemurafenib**: First FDA-approved BRAF inhibitor (2011) [3]
+- **Dabrafenib**: Second-generation BRAF inhibitor [4]
+- **Combination therapy**: BRAF + MEK inhibition improves survival [5]
+
+## Clinical Trials
+
+Several ongoing trials are exploring combination approaches:
+
+- NCT04280705: Encorafenib + cetuximab ± nivolumab in colorectal cancer [6]
+- NCT04511078: Adjuvant dabrafenib + trametinib in melanoma [7]
+
+## References
+
+[1] Davies H, Bignell GR, Cox C, et al. Mutations of the BRAF gene in human cancer. Nature. 2002;417(6892):949-954. PMID: 12068308.
+
+[2] Wan PT, Garnett MJ, Roe SM, et al. Mechanism of activation of RAF-ERK signaling by oncogenic mutations of B-RAF. Cell. 2004;116(6):855-867. PMID: 15035987.
+
+[3] Chapman PB, Hauschild A, Robert C, et al. Improved survival with vemurafenib in melanoma with BRAF V600E mutation. N Engl J Med. 2011;364(26):2507-2516. PMID: 21639808.
+
+[4] Hauschild A, Grob JJ, Demidov LV, et al. Dabrafenib in BRAF-mutated metastatic melanoma: a multicentre, open-label, phase 3 randomised controlled trial. Lancet. 2012;380(9839):358-365. PMID: 22735384.
+
+[5] Robert C, Karaszewska B, Schachter J, et al. Improved overall survival in melanoma with combined dabrafenib and trametinib. N Engl J Med. 2015;372(1):30-39. PMID: 25399551.
+
+[6] NCT04280705: A Study of Encorafenib Plus Cetuximab With or Without Nivolumab in Metastatic Colorectal Cancer. Phase 2. Sponsor: Pfizer. Status: Completed. https://clinicaltrials.gov/ct2/show/NCT04280705
+
+[7] NCT04511078: Adjuvant Dabrafenib Plus Trametinib in Resected BRAF V600-Mutant Melanoma. Phase 3. Sponsor: Novartis. Status: Recruiting. https://clinicaltrials.gov/ct2/show/NCT04511078
+```
+
+## Citation Quality Standards
+
+### What to Cite
+
+| Source Type | Citation Required |
+|-------------|-------------------|
+| Published research | Yes |
+| Clinical trial data | Yes |
+| Drug approval info | Yes |
+| Gene/variant annotations | Yes |
+| Statistical claims | Yes |
+| Direct quotes | Yes |
+| General knowledge | No (e.g., "DNA has 4 bases") |
+
+### Citation Integrity
+
+1. **Verify source exists**: Always confirm PMID, NCT ID, URL is valid
+2. **Quote accurately**: Don't misrepresent findings
+3. **Cite primary sources**: Prefer original papers over reviews
+4. **Update outdated citations**: Use latest evidence when available
+
+## Tools for Citation Generation
+
+| Tool | Use Case |
+|------|----------|
+| `biomcp_article_getter` | Get full article metadata from PMID |
+| `biomcp_trial_getter` | Get trial details from NCT ID |
+| `biomcp_gene_getter` | Get gene identifiers |
+| `biomcp_drug_getter` | Get drug identifiers |
+
+## Best Practices
+
+1. **Cite as you write**: Add citations immediately when making claims
+2. **Number sequentially**: [1], [2], [3] in order of appearance
+3. **Include access dates**: For web sources, always include when accessed
+4. **Verify PMIDs**: Double-check PMID matches the article
+5. **Keep bibliography alphabetical by number**: Not by author
+6. **Format consistently**: Same style throughout document