@bgicli/bgicli 2.1.1 → 2.2.1

This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
Files changed (1267) hide show
  1. package/README.md +152 -74
  2. package/data/skills/aav-vector-design-agent/SKILL.md +198 -0
  3. package/data/skills/adaptyv/SKILL.md +112 -0
  4. package/data/skills/adhd-daily-planner/SKILL.md +271 -0
  5. package/data/skills/aeon/SKILL.md +372 -0
  6. package/data/skills/agent-browser/SKILL.md +159 -0
  7. package/data/skills/agentd-drug-discovery/SKILL.md +52 -0
  8. package/data/skills/ai-analyzer/SKILL.md +218 -0
  9. package/data/skills/alphafold/SKILL.md +183 -0
  10. package/data/skills/alphafold-database/SKILL.md +500 -0
  11. package/data/skills/anndata/SKILL.md +394 -0
  12. package/data/skills/antibody-design-agent/SKILL.md +64 -0
  13. package/data/skills/arboreto/SKILL.md +237 -0
  14. package/data/skills/armored-cart-design-agent/SKILL.md +225 -0
  15. package/data/skills/arxiv-search/SKILL.md +224 -0
  16. package/data/skills/autonomous-oncology-agent/SKILL.md +77 -0
  17. package/data/skills/bayesian-optimizer/SKILL.md +60 -0
  18. package/data/skills/benchling-integration/SKILL.md +473 -0
  19. package/data/skills/bgpt-paper-search/SKILL.md +81 -0
  20. package/data/skills/bindcraft/SKILL.md +198 -0
  21. package/data/skills/binder-design/SKILL.md +182 -0
  22. package/data/skills/binding-characterization/SKILL.md +234 -0
  23. package/data/skills/bindingdb-database/SKILL.md +332 -0
  24. package/data/skills/bio-admet-prediction/SKILL.md +224 -0
  25. package/data/skills/bio-alignment-files-bam-statistics/SKILL.md +340 -0
  26. package/data/skills/bio-alignment-filtering/SKILL.md +322 -0
  27. package/data/skills/bio-alignment-indexing/SKILL.md +249 -0
  28. package/data/skills/bio-alignment-io/SKILL.md +301 -0
  29. package/data/skills/bio-alignment-msa-parsing/SKILL.md +366 -0
  30. package/data/skills/bio-alignment-msa-statistics/SKILL.md +375 -0
  31. package/data/skills/bio-alignment-pairwise/SKILL.md +277 -0
  32. package/data/skills/bio-alignment-sorting/SKILL.md +296 -0
  33. package/data/skills/bio-alignment-validation/SKILL.md +374 -0
  34. package/data/skills/bio-atac-seq-atac-peak-calling/SKILL.md +221 -0
  35. package/data/skills/bio-atac-seq-atac-qc/SKILL.md +292 -0
  36. package/data/skills/bio-atac-seq-differential-accessibility/SKILL.md +268 -0
  37. package/data/skills/bio-atac-seq-footprinting/SKILL.md +256 -0
  38. package/data/skills/bio-atac-seq-motif-deviation/SKILL.md +319 -0
  39. package/data/skills/bio-atac-seq-nucleosome-positioning/SKILL.md +321 -0
  40. package/data/skills/bio-basecalling/SKILL.md +368 -0
  41. package/data/skills/bio-batch-downloads/SKILL.md +384 -0
  42. package/data/skills/bio-batch-processing/SKILL.md +303 -0
  43. package/data/skills/bio-bedgraph-handling/SKILL.md +336 -0
  44. package/data/skills/bio-blast-searches/SKILL.md +354 -0
  45. package/data/skills/bio-causal-genomics-colocalization-analysis/SKILL.md +264 -0
  46. package/data/skills/bio-causal-genomics-fine-mapping/SKILL.md +267 -0
  47. package/data/skills/bio-causal-genomics-mediation-analysis/SKILL.md +264 -0
  48. package/data/skills/bio-causal-genomics-mendelian-randomization/SKILL.md +221 -0
  49. package/data/skills/bio-causal-genomics-pleiotropy-detection/SKILL.md +292 -0
  50. package/data/skills/bio-cfdna-preprocessing/SKILL.md +200 -0
  51. package/data/skills/bio-chipseq-differential-binding/SKILL.md +262 -0
  52. package/data/skills/bio-chipseq-motif-analysis/SKILL.md +387 -0
  53. package/data/skills/bio-chipseq-peak-annotation/SKILL.md +239 -0
  54. package/data/skills/bio-chipseq-peak-calling/SKILL.md +277 -0
  55. package/data/skills/bio-chipseq-qc/SKILL.md +391 -0
  56. package/data/skills/bio-chipseq-super-enhancers/SKILL.md +288 -0
  57. package/data/skills/bio-chipseq-visualization/SKILL.md +289 -0
  58. package/data/skills/bio-clinical-databases-clinvar-lookup/SKILL.md +188 -0
  59. package/data/skills/bio-clinical-databases-dbsnp-queries/SKILL.md +171 -0
  60. package/data/skills/bio-clinical-databases-gnomad-frequencies/SKILL.md +205 -0
  61. package/data/skills/bio-clinical-databases-hla-typing/SKILL.md +248 -0
  62. package/data/skills/bio-clinical-databases-myvariant-queries/SKILL.md +174 -0
  63. package/data/skills/bio-clinical-databases-pharmacogenomics/SKILL.md +232 -0
  64. package/data/skills/bio-clinical-databases-polygenic-risk/SKILL.md +276 -0
  65. package/data/skills/bio-clinical-databases-somatic-signatures/SKILL.md +261 -0
  66. package/data/skills/bio-clinical-databases-tumor-mutational-burden/SKILL.md +301 -0
  67. package/data/skills/bio-clinical-databases-variant-prioritization/SKILL.md +225 -0
  68. package/data/skills/bio-clip-seq-binding-site-annotation/SKILL.md +66 -0
  69. package/data/skills/bio-clip-seq-clip-alignment/SKILL.md +70 -0
  70. package/data/skills/bio-clip-seq-clip-motif-analysis/SKILL.md +62 -0
  71. package/data/skills/bio-clip-seq-clip-peak-calling/SKILL.md +282 -0
  72. package/data/skills/bio-clip-seq-clip-preprocessing/SKILL.md +142 -0
  73. package/data/skills/bio-codon-usage/SKILL.md +353 -0
  74. package/data/skills/bio-comparative-genomics-ancestral-reconstruction/SKILL.md +312 -0
  75. package/data/skills/bio-comparative-genomics-hgt-detection/SKILL.md +341 -0
  76. package/data/skills/bio-comparative-genomics-ortholog-inference/SKILL.md +308 -0
  77. package/data/skills/bio-comparative-genomics-positive-selection/SKILL.md +354 -0
  78. package/data/skills/bio-comparative-genomics-synteny-analysis/SKILL.md +315 -0
  79. package/data/skills/bio-compressed-files/SKILL.md +263 -0
  80. package/data/skills/bio-consensus-sequences/SKILL.md +340 -0
  81. package/data/skills/bio-copy-number-cnv-annotation/SKILL.md +307 -0
  82. package/data/skills/bio-copy-number-cnv-visualization/SKILL.md +294 -0
  83. package/data/skills/bio-copy-number-cnvkit-analysis/SKILL.md +290 -0
  84. package/data/skills/bio-copy-number-gatk-cnv/SKILL.md +270 -0
  85. package/data/skills/bio-crispr-screens-base-editing-analysis/SKILL.md +110 -0
  86. package/data/skills/bio-crispr-screens-batch-correction/SKILL.md +316 -0
  87. package/data/skills/bio-crispr-screens-crispresso-editing/SKILL.md +205 -0
  88. package/data/skills/bio-crispr-screens-hit-calling/SKILL.md +264 -0
  89. package/data/skills/bio-crispr-screens-jacks-analysis/SKILL.md +313 -0
  90. package/data/skills/bio-crispr-screens-library-design/SKILL.md +417 -0
  91. package/data/skills/bio-crispr-screens-mageck-analysis/SKILL.md +222 -0
  92. package/data/skills/bio-crispr-screens-screen-qc/SKILL.md +243 -0
  93. package/data/skills/bio-ctdna-mutation-detection/SKILL.md +234 -0
  94. package/data/skills/bio-data-visualization-circos-plots/SKILL.md +405 -0
  95. package/data/skills/bio-data-visualization-color-palettes/SKILL.md +244 -0
  96. package/data/skills/bio-data-visualization-genome-browser-tracks/SKILL.md +328 -0
  97. package/data/skills/bio-data-visualization-genome-tracks/SKILL.md +249 -0
  98. package/data/skills/bio-data-visualization-ggplot2-fundamentals/SKILL.md +313 -0
  99. package/data/skills/bio-data-visualization-heatmaps-clustering/SKILL.md +227 -0
  100. package/data/skills/bio-data-visualization-interactive-visualization/SKILL.md +210 -0
  101. package/data/skills/bio-data-visualization-multipanel-figures/SKILL.md +274 -0
  102. package/data/skills/bio-data-visualization-specialized-omics-plots/SKILL.md +251 -0
  103. package/data/skills/bio-data-visualization-upset-plots/SKILL.md +228 -0
  104. package/data/skills/bio-data-visualization-volcano-customization/SKILL.md +233 -0
  105. package/data/skills/bio-de-deseq2-basics/SKILL.md +376 -0
  106. package/data/skills/bio-de-edger-basics/SKILL.md +418 -0
  107. package/data/skills/bio-de-results/SKILL.md +378 -0
  108. package/data/skills/bio-de-visualization/SKILL.md +408 -0
  109. package/data/skills/bio-differential-expression-batch-correction/SKILL.md +253 -0
  110. package/data/skills/bio-differential-expression-timeseries-de/SKILL.md +370 -0
  111. package/data/skills/bio-differential-splicing/SKILL.md +177 -0
  112. package/data/skills/bio-duplicate-handling/SKILL.md +292 -0
  113. package/data/skills/bio-entrez-fetch/SKILL.md +334 -0
  114. package/data/skills/bio-entrez-link/SKILL.md +325 -0
  115. package/data/skills/bio-entrez-search/SKILL.md +311 -0
  116. package/data/skills/bio-epidemiological-genomics-amr-surveillance/SKILL.md +233 -0
  117. package/data/skills/bio-epidemiological-genomics-pathogen-typing/SKILL.md +202 -0
  118. package/data/skills/bio-epidemiological-genomics-phylodynamics/SKILL.md +207 -0
  119. package/data/skills/bio-epidemiological-genomics-transmission-inference/SKILL.md +237 -0
  120. package/data/skills/bio-epidemiological-genomics-variant-surveillance/SKILL.md +237 -0
  121. package/data/skills/bio-epitranscriptomics-m6a-differential/SKILL.md +88 -0
  122. package/data/skills/bio-epitranscriptomics-m6a-peak-calling/SKILL.md +89 -0
  123. package/data/skills/bio-epitranscriptomics-m6anet-analysis/SKILL.md +101 -0
  124. package/data/skills/bio-epitranscriptomics-merip-preprocessing/SKILL.md +81 -0
  125. package/data/skills/bio-epitranscriptomics-modification-visualization/SKILL.md +98 -0
  126. package/data/skills/bio-experimental-design-batch-design/SKILL.md +110 -0
  127. package/data/skills/bio-experimental-design-multiple-testing/SKILL.md +98 -0
  128. package/data/skills/bio-experimental-design-power-analysis/SKILL.md +84 -0
  129. package/data/skills/bio-experimental-design-sample-size/SKILL.md +93 -0
  130. package/data/skills/bio-expression-matrix-counts-ingest/SKILL.md +220 -0
  131. package/data/skills/bio-expression-matrix-gene-id-mapping/SKILL.md +256 -0
  132. package/data/skills/bio-expression-matrix-metadata-joins/SKILL.md +271 -0
  133. package/data/skills/bio-expression-matrix-sparse-handling/SKILL.md +247 -0
  134. package/data/skills/bio-fastq-quality/SKILL.md +279 -0
  135. package/data/skills/bio-filter-sequences/SKILL.md +265 -0
  136. package/data/skills/bio-flow-cytometry-bead-normalization/SKILL.md +315 -0
  137. package/data/skills/bio-flow-cytometry-clustering-phenotyping/SKILL.md +237 -0
  138. package/data/skills/bio-flow-cytometry-compensation-transformation/SKILL.md +196 -0
  139. package/data/skills/bio-flow-cytometry-cytometry-qc/SKILL.md +382 -0
  140. package/data/skills/bio-flow-cytometry-differential-analysis/SKILL.md +217 -0
  141. package/data/skills/bio-flow-cytometry-doublet-detection/SKILL.md +288 -0
  142. package/data/skills/bio-flow-cytometry-fcs-handling/SKILL.md +221 -0
  143. package/data/skills/bio-flow-cytometry-gating-analysis/SKILL.md +193 -0
  144. package/data/skills/bio-format-conversion/SKILL.md +193 -0
  145. package/data/skills/bio-fragment-analysis/SKILL.md +214 -0
  146. package/data/skills/bio-gatk-variant-calling/SKILL.md +422 -0
  147. package/data/skills/bio-genome-assembly-assembly-polishing/SKILL.md +333 -0
  148. package/data/skills/bio-genome-assembly-assembly-qc/SKILL.md +344 -0
  149. package/data/skills/bio-genome-assembly-contamination-detection/SKILL.md +235 -0
  150. package/data/skills/bio-genome-assembly-hifi-assembly/SKILL.md +178 -0
  151. package/data/skills/bio-genome-assembly-long-read-assembly/SKILL.md +307 -0
  152. package/data/skills/bio-genome-assembly-metagenome-assembly/SKILL.md +227 -0
  153. package/data/skills/bio-genome-assembly-scaffolding/SKILL.md +204 -0
  154. package/data/skills/bio-genome-assembly-short-read-assembly/SKILL.md +319 -0
  155. package/data/skills/bio-genome-engineering-base-editing-design/SKILL.md +277 -0
  156. package/data/skills/bio-genome-engineering-grna-design/SKILL.md +221 -0
  157. package/data/skills/bio-genome-engineering-hdr-template-design/SKILL.md +264 -0
  158. package/data/skills/bio-genome-engineering-off-target-prediction/SKILL.md +232 -0
  159. package/data/skills/bio-genome-engineering-prime-editing-design/SKILL.md +275 -0
  160. package/data/skills/bio-genome-intervals-bed-file-basics/SKILL.md +357 -0
  161. package/data/skills/bio-genome-intervals-bigwig-tracks/SKILL.md +351 -0
  162. package/data/skills/bio-genome-intervals-coverage-analysis/SKILL.md +300 -0
  163. package/data/skills/bio-genome-intervals-gtf-gff-handling/SKILL.md +345 -0
  164. package/data/skills/bio-genome-intervals-interval-arithmetic/SKILL.md +485 -0
  165. package/data/skills/bio-genome-intervals-proximity-operations/SKILL.md +337 -0
  166. package/data/skills/bio-geo-data/SKILL.md +380 -0
  167. package/data/skills/bio-hi-c-analysis-compartment-analysis/SKILL.md +261 -0
  168. package/data/skills/bio-hi-c-analysis-contact-pairs/SKILL.md +278 -0
  169. package/data/skills/bio-hi-c-analysis-hic-data-io/SKILL.md +260 -0
  170. package/data/skills/bio-hi-c-analysis-hic-differential/SKILL.md +328 -0
  171. package/data/skills/bio-hi-c-analysis-hic-visualization/SKILL.md +297 -0
  172. package/data/skills/bio-hi-c-analysis-loop-calling/SKILL.md +284 -0
  173. package/data/skills/bio-hi-c-analysis-matrix-operations/SKILL.md +274 -0
  174. package/data/skills/bio-hi-c-analysis-tad-detection/SKILL.md +239 -0
  175. package/data/skills/bio-imaging-mass-cytometry-cell-segmentation/SKILL.md +241 -0
  176. package/data/skills/bio-imaging-mass-cytometry-data-preprocessing/SKILL.md +279 -0
  177. package/data/skills/bio-imaging-mass-cytometry-interactive-annotation/SKILL.md +304 -0
  178. package/data/skills/bio-imaging-mass-cytometry-phenotyping/SKILL.md +231 -0
  179. package/data/skills/bio-imaging-mass-cytometry-quality-metrics/SKILL.md +316 -0
  180. package/data/skills/bio-imaging-mass-cytometry-spatial-analysis/SKILL.md +246 -0
  181. package/data/skills/bio-immunoinformatics-epitope-prediction/SKILL.md +259 -0
  182. package/data/skills/bio-immunoinformatics-immunogenicity-scoring/SKILL.md +275 -0
  183. package/data/skills/bio-immunoinformatics-mhc-binding-prediction/SKILL.md +260 -0
  184. package/data/skills/bio-immunoinformatics-neoantigen-prediction/SKILL.md +277 -0
  185. package/data/skills/bio-immunoinformatics-tcr-epitope-binding/SKILL.md +257 -0
  186. package/data/skills/bio-isoform-switching/SKILL.md +192 -0
  187. package/data/skills/bio-liquid-biopsy-pipeline/SKILL.md +311 -0
  188. package/data/skills/bio-local-blast/SKILL.md +350 -0
  189. package/data/skills/bio-long-read-sequencing-clair3-variants/SKILL.md +252 -0
  190. package/data/skills/bio-long-read-sequencing-isoseq-analysis/SKILL.md +334 -0
  191. package/data/skills/bio-long-read-sequencing-nanopore-methylation/SKILL.md +110 -0
  192. package/data/skills/bio-longitudinal-monitoring/SKILL.md +271 -0
  193. package/data/skills/bio-longread-alignment/SKILL.md +193 -0
  194. package/data/skills/bio-longread-medaka/SKILL.md +176 -0
  195. package/data/skills/bio-longread-qc/SKILL.md +224 -0
  196. package/data/skills/bio-longread-structural-variants/SKILL.md +201 -0
  197. package/data/skills/bio-machine-learning-atlas-mapping/SKILL.md +139 -0
  198. package/data/skills/bio-machine-learning-biomarker-discovery/SKILL.md +157 -0
  199. package/data/skills/bio-machine-learning-model-validation/SKILL.md +148 -0
  200. package/data/skills/bio-machine-learning-omics-classifiers/SKILL.md +146 -0
  201. package/data/skills/bio-machine-learning-prediction-explanation/SKILL.md +162 -0
  202. package/data/skills/bio-machine-learning-survival-analysis/SKILL.md +176 -0
  203. package/data/skills/bio-metabolomics-lipidomics/SKILL.md +265 -0
  204. package/data/skills/bio-metabolomics-metabolite-annotation/SKILL.md +241 -0
  205. package/data/skills/bio-metabolomics-msdial-preprocessing/SKILL.md +308 -0
  206. package/data/skills/bio-metabolomics-normalization-qc/SKILL.md +283 -0
  207. package/data/skills/bio-metabolomics-pathway-mapping/SKILL.md +237 -0
  208. package/data/skills/bio-metabolomics-statistical-analysis/SKILL.md +276 -0
  209. package/data/skills/bio-metabolomics-targeted-analysis/SKILL.md +314 -0
  210. package/data/skills/bio-metabolomics-xcms-preprocessing/SKILL.md +268 -0
  211. package/data/skills/bio-metagenomics-abundance/SKILL.md +203 -0
  212. package/data/skills/bio-metagenomics-amr-detection/SKILL.md +293 -0
  213. package/data/skills/bio-metagenomics-functional-profiling/SKILL.md +252 -0
  214. package/data/skills/bio-metagenomics-kraken/SKILL.md +204 -0
  215. package/data/skills/bio-metagenomics-metaphlan/SKILL.md +214 -0
  216. package/data/skills/bio-metagenomics-strain-tracking/SKILL.md +292 -0
  217. package/data/skills/bio-metagenomics-visualization/SKILL.md +240 -0
  218. package/data/skills/bio-methylation-based-detection/SKILL.md +223 -0
  219. package/data/skills/bio-methylation-bismark-alignment/SKILL.md +195 -0
  220. package/data/skills/bio-methylation-calling/SKILL.md +200 -0
  221. package/data/skills/bio-methylation-dmr-detection/SKILL.md +211 -0
  222. package/data/skills/bio-methylation-methylkit/SKILL.md +219 -0
  223. package/data/skills/bio-microbiome-amplicon-processing/SKILL.md +137 -0
  224. package/data/skills/bio-microbiome-differential-abundance/SKILL.md +147 -0
  225. package/data/skills/bio-microbiome-diversity-analysis/SKILL.md +188 -0
  226. package/data/skills/bio-microbiome-functional-prediction/SKILL.md +153 -0
  227. package/data/skills/bio-microbiome-qiime2-workflow/SKILL.md +219 -0
  228. package/data/skills/bio-microbiome-taxonomy-assignment/SKILL.md +168 -0
  229. package/data/skills/bio-molecular-descriptors/SKILL.md +200 -0
  230. package/data/skills/bio-molecular-io/SKILL.md +188 -0
  231. package/data/skills/bio-motif-search/SKILL.md +354 -0
  232. package/data/skills/bio-multi-omics-data-harmonization/SKILL.md +228 -0
  233. package/data/skills/bio-multi-omics-mixomics-analysis/SKILL.md +221 -0
  234. package/data/skills/bio-multi-omics-mofa-integration/SKILL.md +225 -0
  235. package/data/skills/bio-multi-omics-similarity-network/SKILL.md +235 -0
  236. package/data/skills/bio-orchestrator/SKILL.md +133 -0
  237. package/data/skills/bio-paired-end-fastq/SKILL.md +334 -0
  238. package/data/skills/bio-pathway-enrichment-visualization/SKILL.md +278 -0
  239. package/data/skills/bio-pathway-go-enrichment/SKILL.md +218 -0
  240. package/data/skills/bio-pathway-gsea/SKILL.md +227 -0
  241. package/data/skills/bio-pathway-kegg-pathways/SKILL.md +234 -0
  242. package/data/skills/bio-pathway-reactome/SKILL.md +215 -0
  243. package/data/skills/bio-pathway-wikipathways/SKILL.md +255 -0
  244. package/data/skills/bio-pdb-geometric-analysis/SKILL.md +475 -0
  245. package/data/skills/bio-pdb-structure-io/SKILL.md +296 -0
  246. package/data/skills/bio-pdb-structure-modification/SKILL.md +448 -0
  247. package/data/skills/bio-pdb-structure-navigation/SKILL.md +335 -0
  248. package/data/skills/bio-phasing-imputation-genotype-imputation/SKILL.md +201 -0
  249. package/data/skills/bio-phasing-imputation-haplotype-phasing/SKILL.md +190 -0
  250. package/data/skills/bio-phasing-imputation-imputation-qc/SKILL.md +265 -0
  251. package/data/skills/bio-phasing-imputation-reference-panels/SKILL.md +203 -0
  252. package/data/skills/bio-phylo-distance-calculations/SKILL.md +307 -0
  253. package/data/skills/bio-phylo-modern-tree-inference/SKILL.md +274 -0
  254. package/data/skills/bio-phylo-tree-io/SKILL.md +252 -0
  255. package/data/skills/bio-phylo-tree-manipulation/SKILL.md +375 -0
  256. package/data/skills/bio-phylo-tree-visualization/SKILL.md +275 -0
  257. package/data/skills/bio-pileup-generation/SKILL.md +314 -0
  258. package/data/skills/bio-population-genetics-association-testing/SKILL.md +293 -0
  259. package/data/skills/bio-population-genetics-linkage-disequilibrium/SKILL.md +260 -0
  260. package/data/skills/bio-population-genetics-plink-basics/SKILL.md +338 -0
  261. package/data/skills/bio-population-genetics-population-structure/SKILL.md +352 -0
  262. package/data/skills/bio-population-genetics-scikit-allel-analysis/SKILL.md +306 -0
  263. package/data/skills/bio-population-genetics-selection-statistics/SKILL.md +251 -0
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+ ---
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+ name: tooluniverse-disease-research
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+ description: Generate comprehensive disease research reports using 100+ ToolUniverse tools. Creates a detailed markdown report file and progressively updates it with findings from 10 research dimensions. All information includes source references. Use when users ask about diseases, syndromes, or need systematic disease analysis.
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+ ---
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+
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+ # ToolUniverse Disease Research
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+
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+ Generate a comprehensive, detailed disease research report with full source citations. The report is created as a markdown file and progressively updated during research.
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+
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+ **IMPORTANT**: Always use English disease names and search terms in tool calls, even if the user writes in another language. Only try original-language terms as a fallback if English returns no results. Respond in the user's language.
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+
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+ ## When to Use
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+
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+ Apply when the user:
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+ - Asks about any disease, syndrome, or medical condition
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+ - Needs comprehensive disease intelligence
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+ - Wants a detailed research report with citations
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+ - Asks "what do we know about [disease]?"
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+
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+ ## Core Workflow: Report-First Approach
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+
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+ **DO NOT** show the search process to the user. Instead:
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+
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+ 1. **Create report file first** - Initialize `{disease_name}_research_report.md`
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+ 2. **Research each dimension** - Use all relevant tools
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+ 3. **Update report progressively** - Write findings to file after each dimension
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+ 4. **Include citations** - Every fact must reference its source tool
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+
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+ ```
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+ User: "Research Parkinson's disease"
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+
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+ Agent Actions (internal, not shown to user):
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+ 1. Create "parkinsons_disease_research_report.md" with template
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+ 2. Research DIM 1 → Update Identity section
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+ 3. Research DIM 2 → Update Clinical section
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+ 4. ... continue for all 10 dimensions
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+ 5. Present final report to user
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+ ```
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+
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+ ## Report Template
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+
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+ Create this file structure at the start:
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+
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+ ```markdown
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+ # Disease Research Report: {Disease Name}
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+
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+ **Report Generated**: {date}
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+ **Disease Identifiers**: (to be filled)
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+
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+ ---
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+
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+ ## Executive Summary
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+
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+ (Brief 3-5 sentence overview - fill after all research complete)
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+
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+ ---
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+
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+ ## 1. Disease Identity & Classification
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+
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+ ### Ontology Identifiers
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+ | System | ID | Source |
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+ |--------|-----|--------|
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+ | EFO | | |
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+ | ICD-10 | | |
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+ | UMLS CUI | | |
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+ | SNOMED CT | | |
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+
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+ ### Synonyms & Alternative Names
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+ - (list with source)
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+
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+ ### Disease Hierarchy
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+ - Parent:
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+ - Subtypes:
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+
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+ **Sources**: (list tools used)
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+
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+ ---
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+
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+ ## 2. Clinical Presentation
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+
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+ ### Phenotypes (HPO)
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+ | HPO ID | Phenotype | Description | Source |
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+ |--------|-----------|-------------|--------|
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+
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+ ### Symptoms & Signs
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+ - (list with source)
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+
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+ ### Diagnostic Criteria
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+ - (from literature/MedlinePlus)
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+
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+ **Sources**: (list tools used)
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+
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+ ---
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+
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+ ## 3. Genetic & Molecular Basis
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+
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+ ### Associated Genes
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+ | Gene | Score | Ensembl ID | Evidence | Source |
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+ |------|-------|------------|----------|--------|
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+
101
+ ### GWAS Associations
102
+ | SNP | P-value | Odds Ratio | Study | Source |
103
+ |-----|---------|------------|-------|--------|
104
+
105
+ ### Pathogenic Variants (ClinVar)
106
+ | Variant | Clinical Significance | Condition | Source |
107
+ |---------|----------------------|-----------|--------|
108
+
109
+ **Sources**: (list tools used)
110
+
111
+ ---
112
+
113
+ ## 4. Treatment Landscape
114
+
115
+ ### Approved Drugs
116
+ | Drug | ChEMBL ID | Mechanism | Phase | Target | Source |
117
+ |------|-----------|-----------|-------|--------|--------|
118
+
119
+ ### Clinical Trials
120
+ | NCT ID | Title | Phase | Status | Intervention | Source |
121
+ |--------|-------|-------|--------|--------------|--------|
122
+
123
+ ### Treatment Guidelines
124
+ - (from literature)
125
+
126
+ **Sources**: (list tools used)
127
+
128
+ ---
129
+
130
+ ## 5. Biological Pathways & Mechanisms
131
+
132
+ ### Key Pathways
133
+ | Pathway | Reactome ID | Genes Involved | Source |
134
+ |---------|-------------|----------------|--------|
135
+
136
+ ### Protein-Protein Interactions
137
+ - (tissue-specific networks)
138
+
139
+ ### Expression Patterns
140
+ | Tissue | Expression Level | Source |
141
+ |--------|------------------|--------|
142
+
143
+ **Sources**: (list tools used)
144
+
145
+ ---
146
+
147
+ ## 6. Epidemiology & Risk Factors
148
+
149
+ ### Prevalence & Incidence
150
+ - (from literature)
151
+
152
+ ### Risk Factors
153
+ | Factor | Evidence | Source |
154
+ |--------|----------|--------|
155
+
156
+ ### GWAS Studies
157
+ | Study | Sample Size | Findings | Source |
158
+ |-------|-------------|----------|--------|
159
+
160
+ **Sources**: (list tools used)
161
+
162
+ ---
163
+
164
+ ## 7. Literature & Research Activity
165
+
166
+ ### Publication Trends
167
+ - Total publications (5 years):
168
+ - Current year:
169
+ - Trend:
170
+
171
+ ### Key Publications
172
+ | PMID | Title | Year | Citations | Source |
173
+ |------|-------|------|-----------|--------|
174
+
175
+ ### Research Institutions
176
+ - (from OpenAlex)
177
+
178
+ **Sources**: (list tools used)
179
+
180
+ ---
181
+
182
+ ## 8. Similar Diseases & Comorbidities
183
+
184
+ ### Similar Diseases
185
+ | Disease | Similarity Score | Shared Genes | Source |
186
+ |---------|-----------------|--------------|--------|
187
+
188
+ ### Comorbidities
189
+ - (from literature/clinical data)
190
+
191
+ **Sources**: (list tools used)
192
+
193
+ ---
194
+
195
+ ## 9. Cancer-Specific Information (if applicable)
196
+
197
+ ### CIViC Variants
198
+ | Gene | Variant | Evidence Level | Clinical Significance | Source |
199
+ |------|---------|----------------|----------------------|--------|
200
+
201
+ ### Molecular Profiles
202
+ - (biomarkers)
203
+
204
+ ### Targeted Therapies
205
+ | Therapy | Target | Evidence | Source |
206
+ |---------|--------|----------|--------|
207
+
208
+ **Sources**: (list tools used)
209
+
210
+ ---
211
+
212
+ ## 10. Drug Safety & Adverse Events
213
+
214
+ ### Drug Warnings
215
+ | Drug | Warning Type | Description | Source |
216
+ |------|--------------|-------------|--------|
217
+
218
+ ### Clinical Trial Adverse Events
219
+ | Trial | Drug | Adverse Event | Frequency | Source |
220
+ |-------|------|---------------|-----------|--------|
221
+
222
+ ### FAERS Reports
223
+ - (FDA adverse event data)
224
+
225
+ **Sources**: (list tools used)
226
+
227
+ ---
228
+
229
+ ## References
230
+
231
+ ### Data Sources Used
232
+ | Tool | Query | Section |
233
+ |------|-------|---------|
234
+
235
+ ### Database Versions
236
+ - OpenTargets: (version/date)
237
+ - ClinVar: (version/date)
238
+ - GWAS Catalog: (version/date)
239
+ ```
240
+
241
+ ---
242
+
243
+ ## Research Protocol
244
+
245
+ ### Step 1: Initialize Report
246
+
247
+ ```python
248
+ from datetime import datetime
249
+
250
+ def create_report_file(disease_name):
251
+ """Create initial report file with template"""
252
+ filename = f"{disease_name.lower().replace(' ', '_')}_research_report.md"
253
+
254
+ template = f"""# Disease Research Report: {disease_name}
255
+
256
+ **Report Generated**: {datetime.now().strftime('%Y-%m-%d %H:%M')}
257
+ **Disease Identifiers**: Pending research...
258
+
259
+ ---
260
+
261
+ ## Executive Summary
262
+
263
+ *Research in progress...*
264
+
265
+ ---
266
+
267
+ ## 1. Disease Identity & Classification
268
+ *Researching...*
269
+
270
+ ## 2. Clinical Presentation
271
+ *Pending...*
272
+
273
+ [... rest of template ...]
274
+ """
275
+
276
+ with open(filename, 'w') as f:
277
+ f.write(template)
278
+
279
+ return filename
280
+ ```
281
+
282
+ ### Step 2: Research Each Dimension with Citations
283
+
284
+ For EACH piece of information, track:
285
+ - **Tool name** that provided the data
286
+ - **Parameters** used in the query
287
+ - **Timestamp** of the query
288
+
289
+ ```python
290
+ def research_with_citations(tu, disease_name, report_file):
291
+ """Research and update report with full citations"""
292
+
293
+ references = [] # Track all sources
294
+
295
+ # === DIMENSION 1: Identity ===
296
+
297
+ # Get EFO ID
298
+ efo_result = tu.tools.OSL_get_efo_id_by_disease_name(disease=disease_name)
299
+ efo_id = efo_result.get('efo_id')
300
+ references.append({
301
+ 'tool': 'OSL_get_efo_id_by_disease_name',
302
+ 'params': {'disease': disease_name},
303
+ 'section': 'Identity'
304
+ })
305
+
306
+ # Get ICD codes
307
+ icd_result = tu.tools.icd_search_codes(query=disease_name, version="ICD10CM")
308
+ references.append({
309
+ 'tool': 'icd_search_codes',
310
+ 'params': {'query': disease_name, 'version': 'ICD10CM'},
311
+ 'section': 'Identity'
312
+ })
313
+
314
+ # Get UMLS
315
+ umls_result = tu.tools.umls_search_concepts(query=disease_name)
316
+ references.append({
317
+ 'tool': 'umls_search_concepts',
318
+ 'params': {'query': disease_name},
319
+ 'section': 'Identity'
320
+ })
321
+
322
+ # Get synonyms from EFO
323
+ if efo_id:
324
+ efo_term = tu.tools.ols_get_efo_term(obo_id=efo_id.replace('_', ':'))
325
+ references.append({
326
+ 'tool': 'ols_get_efo_term',
327
+ 'params': {'obo_id': efo_id},
328
+ 'section': 'Identity'
329
+ })
330
+
331
+ # Get subtypes
332
+ children = tu.tools.ols_get_efo_term_children(obo_id=efo_id.replace('_', ':'), size=20)
333
+ references.append({
334
+ 'tool': 'ols_get_efo_term_children',
335
+ 'params': {'obo_id': efo_id, 'size': 20},
336
+ 'section': 'Identity'
337
+ })
338
+
339
+ # UPDATE REPORT FILE with Identity section
340
+ update_report_section(report_file, 'Identity', {
341
+ 'efo_id': efo_id,
342
+ 'icd_codes': icd_result,
343
+ 'umls': umls_result,
344
+ 'synonyms': efo_term.get('synonyms', []) if efo_term else [],
345
+ 'subtypes': children
346
+ }, references[-5:]) # Last 5 references for this section
347
+
348
+ # === DIMENSION 2: Clinical ===
349
+ # ... continue for all dimensions
350
+ ```
351
+
352
+ ### Step 3: Update Report File After Each Dimension
353
+
354
+ ```python
355
+ def update_report_section(filename, section_name, data, sources):
356
+ """Update a specific section in the report file"""
357
+
358
+ # Read current file
359
+ with open(filename, 'r') as f:
360
+ content = f.read()
361
+
362
+ # Format section content with citations
363
+ if section_name == 'Identity':
364
+ section_content = format_identity_section(data, sources)
365
+ elif section_name == 'Clinical':
366
+ section_content = format_clinical_section(data, sources)
367
+ # ... etc
368
+
369
+ # Replace placeholder with actual content
370
+ placeholder = f"## {section_number}. {section_name}\n*Researching...*"
371
+ content = content.replace(placeholder, section_content)
372
+
373
+ # Write back
374
+ with open(filename, 'w') as f:
375
+ f.write(content)
376
+
377
+
378
+ def format_identity_section(data, sources):
379
+ """Format Identity section with proper citations"""
380
+
381
+ source_list = ', '.join([s['tool'] for s in sources])
382
+
383
+ return f"""## 1. Disease Identity & Classification
384
+
385
+ ### Ontology Identifiers
386
+ | System | ID | Source |
387
+ |--------|-----|--------|
388
+ | EFO | {data['efo_id']} | OSL_get_efo_id_by_disease_name |
389
+ | ICD-10 | {data['icd_codes']} | icd_search_codes |
390
+ | UMLS CUI | {data['umls']} | umls_search_concepts |
391
+
392
+ ### Synonyms & Alternative Names
393
+ {format_list_with_source(data['synonyms'], 'ols_get_efo_term')}
394
+
395
+ ### Disease Subtypes
396
+ {format_list_with_source(data['subtypes'], 'ols_get_efo_term_children')}
397
+
398
+ **Sources**: {source_list}
399
+ """
400
+ ```
401
+
402
+ ---
403
+
404
+ ## Complete Tool Usage by Section
405
+
406
+ ### Section 1: Identity (use ALL of these)
407
+ ```python
408
+ # Required tools - use all
409
+ tu.tools.OSL_get_efo_id_by_disease_name(disease=disease_name)
410
+ tu.tools.OpenTargets_get_disease_id_description_by_name(diseaseName=disease_name)
411
+ tu.tools.ols_search_efo_terms(query=disease_name)
412
+ tu.tools.ols_get_efo_term(obo_id=efo_id)
413
+ tu.tools.ols_get_efo_term_children(obo_id=efo_id, size=30)
414
+ tu.tools.umls_search_concepts(query=disease_name)
415
+ tu.tools.umls_get_concept_details(cui=cui)
416
+ tu.tools.icd_search_codes(query=disease_name, version="ICD10CM")
417
+ tu.tools.snomed_search_concepts(query=disease_name)
418
+ ```
419
+
420
+ ### Section 2: Clinical Presentation (use ALL of these)
421
+ ```python
422
+ tu.tools.OpenTargets_get_associated_phenotypes_by_disease_efoId(efoId=efo_id)
423
+ tu.tools.get_HPO_ID_by_phenotype(query=symptom) # for each key symptom
424
+ tu.tools.get_phenotype_by_HPO_ID(id=hpo_id) # for top phenotypes
425
+ tu.tools.MedlinePlus_search_topics_by_keyword(term=disease_name, db="healthTopics")
426
+ tu.tools.MedlinePlus_get_genetics_condition_by_name(condition=disease_slug)
427
+ tu.tools.MedlinePlus_connect_lookup_by_code(cs=icd_oid, c=icd_code)
428
+ ```
429
+
430
+ ### Section 3: Genetics (use ALL of these)
431
+ ```python
432
+ tu.tools.OpenTargets_get_associated_targets_by_disease_efoId(efoId=efo_id)
433
+ tu.tools.OpenTargets_target_disease_evidence(efoId=efo_id, ensemblId=gene_id) # for top genes
434
+ tu.tools.clinvar_search_variants(condition=disease_name, max_results=50)
435
+ tu.tools.clinvar_get_variant_details(variant_id=vid) # for top variants
436
+ tu.tools.clinvar_get_clinical_significance(variant_id=vid)
437
+ tu.tools.gwas_search_associations(disease_trait=disease_name, size=50)
438
+ tu.tools.gwas_get_variants_for_trait(disease_trait=disease_name, size=50)
439
+ tu.tools.gwas_get_associations_for_trait(disease_trait=disease_name, size=50)
440
+ tu.tools.gwas_get_studies_for_trait(disease_trait=disease_name, size=30)
441
+ tu.tools.GWAS_search_associations_by_gene(gene_name=gene) # for top genes
442
+ tu.tools.gnomad_get_variant_frequency(variant=variant) # for key variants
443
+ ```
444
+
445
+ ### Section 4: Treatment (use ALL of these)
446
+ ```python
447
+ tu.tools.OpenTargets_get_associated_drugs_by_disease_efoId(efoId=efo_id, size=100)
448
+ tu.tools.OpenTargets_get_drug_chembId_by_generic_name(drugName=drug) # for each drug
449
+ tu.tools.OpenTargets_get_drug_mechanisms_of_action_by_chemblId(chemblId=chembl_id)
450
+ tu.tools.search_clinical_trials(condition=disease_name, pageSize=50)
451
+ tu.tools.get_clinical_trial_descriptions(nct_ids=nct_list)
452
+ tu.tools.get_clinical_trial_conditions_and_interventions(nct_ids=nct_list)
453
+ tu.tools.get_clinical_trial_eligibility_criteria(nct_ids=nct_list)
454
+ tu.tools.get_clinical_trial_outcome_measures(nct_ids=nct_list)
455
+ tu.tools.extract_clinical_trial_outcomes(nct_ids=nct_list)
456
+ tu.tools.GtoPdb_list_diseases(name=disease_name)
457
+ tu.tools.GtoPdb_get_disease(disease_id=gtopdb_id)
458
+ ```
459
+
460
+ ### Section 5: Pathways (use ALL of these)
461
+ ```python
462
+ tu.tools.Reactome_get_diseases()
463
+ tu.tools.Reactome_map_uniprot_to_pathways(id=uniprot_id) # for top genes
464
+ tu.tools.Reactome_get_pathway(stId=pathway_id) # for key pathways
465
+ tu.tools.Reactome_get_pathway_reactions(stId=pathway_id)
466
+ tu.tools.humanbase_ppi_analysis(gene_list=top_genes, tissue=relevant_tissue)
467
+ tu.tools.gtex_get_expression_by_gene(gene=gene) # for top genes
468
+ tu.tools.HPA_get_protein_expression(gene=gene)
469
+ tu.tools.geo_search_datasets(query=disease_name)
470
+ ```
471
+
472
+ ### Section 6: Literature (use ALL of these)
473
+ ```python
474
+ tu.tools.PubMed_search_articles(query=f'"{disease_name}"', limit=100)
475
+ tu.tools.PubMed_search_articles(query=f'"{disease_name}" AND epidemiology', limit=50)
476
+ tu.tools.PubMed_search_articles(query=f'"{disease_name}" AND mechanism', limit=50)
477
+ tu.tools.PubMed_search_articles(query=f'"{disease_name}" AND treatment', limit=50)
478
+ tu.tools.PubMed_get_article(pmid=pmid) # for top 10 articles
479
+ tu.tools.PubMed_get_related(pmid=key_pmid)
480
+ tu.tools.PubMed_get_cited_by(pmid=key_pmid)
481
+ tu.tools.OpenTargets_get_publications_by_disease_efoId(efoId=efo_id)
482
+ tu.tools.openalex_search_works(query=disease_name, limit=50)
483
+ tu.tools.europe_pmc_search_abstracts(query=disease_name, limit=50)
484
+ tu.tools.semantic_scholar_search_papers(query=disease_name, limit=50)
485
+ ```
486
+
487
+ ### Section 7: Similar Diseases
488
+ ```python
489
+ tu.tools.OpenTargets_get_similar_entities_by_disease_efoId(efoId=efo_id, threshold=0.3, size=30)
490
+ ```
491
+
492
+ ### Section 8: Cancer-Specific (if cancer)
493
+ ```python
494
+ tu.tools.civic_search_diseases(limit=100)
495
+ tu.tools.civic_search_genes(query=gene, limit=20) # for cancer genes
496
+ tu.tools.civic_get_variants_by_gene(gene_id=civic_gene_id, limit=50)
497
+ tu.tools.civic_get_variant(variant_id=vid)
498
+ tu.tools.civic_get_evidence_item(evidence_id=eid)
499
+ tu.tools.civic_search_therapies(limit=100)
500
+ tu.tools.civic_search_molecular_profiles(limit=50)
501
+ ```
502
+
503
+ ### Section 9: Pharmacology
504
+ ```python
505
+ tu.tools.GtoPdb_get_targets(target_type=type, limit=50) # GPCR, ion channel, etc
506
+ tu.tools.GtoPdb_get_target(target_id=tid) # for disease-relevant targets
507
+ tu.tools.GtoPdb_get_target_interactions(target_id=tid)
508
+ tu.tools.GtoPdb_search_interactions(approved_only=True)
509
+ tu.tools.GtoPdb_list_ligands(ligand_type="Approved")
510
+ ```
511
+
512
+ ### Section 10: Safety (use ALL of these)
513
+ ```python
514
+ tu.tools.OpenTargets_get_drug_warnings_by_chemblId(chemblId=cid) # for each drug
515
+ tu.tools.OpenTargets_get_drug_blackbox_status_by_chembl_ID(chemblId=cid)
516
+ tu.tools.extract_clinical_trial_adverse_events(nct_ids=nct_list)
517
+ tu.tools.FAERS_count_reactions_by_drug_event(drug=drug_name, event=event)
518
+ tu.tools.AdverseEventPredictionQuestionGenerator(disease_name=disease, drug_name=drug)
519
+ ```
520
+
521
+ ---
522
+
523
+ ## Citation Format
524
+
525
+ Every piece of data MUST include its source. Use this format:
526
+
527
+ ### In Tables
528
+ ```markdown
529
+ | Gene | Score | Source |
530
+ |------|-------|--------|
531
+ | APOE | 0.92 | OpenTargets_get_associated_targets_by_disease_efoId |
532
+ | APP | 0.88 | OpenTargets_get_associated_targets_by_disease_efoId |
533
+ ```
534
+
535
+ ### In Lists
536
+ ```markdown
537
+ - Memory loss [Source: OpenTargets_get_associated_phenotypes_by_disease_efoId]
538
+ - Cognitive decline [Source: MedlinePlus_get_genetics_condition_by_name]
539
+ ```
540
+
541
+ ### In Prose
542
+ ```markdown
543
+ The disease affects approximately 6.5 million Americans (Source: PubMed_search_articles,
544
+ query: "Alzheimer disease epidemiology").
545
+ ```
546
+
547
+ ### References Section
548
+ At the end of the report, include complete tool usage log:
549
+
550
+ ```markdown
551
+ ## References
552
+
553
+ ### Tools Used
554
+ | # | Tool | Parameters | Section | Items Retrieved |
555
+ |---|------|------------|---------|-----------------|
556
+ | 1 | OSL_get_efo_id_by_disease_name | disease="Alzheimer disease" | Identity | 1 |
557
+ | 2 | ols_get_efo_term | obo_id="EFO:0000249" | Identity | 1 |
558
+ | 3 | OpenTargets_get_associated_targets_by_disease_efoId | efoId="EFO_0000249" | Genetics | 245 |
559
+ | ... | ... | ... | ... | ... |
560
+
561
+ ### Data Retrieved Summary
562
+ - Total tools used: 45
563
+ - Total API calls: 78
564
+ - Sections completed: 10/10
565
+ ```
566
+
567
+ ---
568
+
569
+ ## Progressive Update Pattern
570
+
571
+ After researching EACH dimension, immediately update the report file:
572
+
573
+ ```python
574
+ # After each dimension's research completes:
575
+
576
+ # 1. Read current report
577
+ with open(report_file, 'r') as f:
578
+ report = f.read()
579
+
580
+ # 2. Replace placeholder with formatted content
581
+ report = report.replace(
582
+ "## 3. Genetic & Molecular Basis\n*Pending...*",
583
+ formatted_genetics_section
584
+ )
585
+
586
+ # 3. Write back immediately
587
+ with open(report_file, 'w') as f:
588
+ f.write(report)
589
+
590
+ # 4. Continue to next dimension
591
+ ```
592
+
593
+ ---
594
+
595
+ ## Final Report Quality Checklist
596
+
597
+ Before presenting to user, verify:
598
+
599
+ - [ ] All 10 sections have content (or marked as "No data available")
600
+ - [ ] Every data point has a source citation
601
+ - [ ] Executive summary reflects key findings
602
+ - [ ] References section lists all tools used
603
+ - [ ] Tables are properly formatted
604
+ - [ ] No placeholder text remains
605
+
606
+ ---
607
+
608
+ ## Example Output Structure
609
+
610
+ For "Alzheimer's Disease" research, the final report should be 2000+ lines with:
611
+
612
+ - **Section 1**: 5+ ontology IDs, 10+ synonyms, disease hierarchy
613
+ - **Section 2**: 20+ phenotypes with HPO IDs, symptoms list
614
+ - **Section 3**: 50+ genes with scores, 30+ GWAS associations, 100+ ClinVar variants
615
+ - **Section 4**: 20+ drugs, 50+ clinical trials with details
616
+ - **Section 5**: 10+ pathways, PPI network, expression data
617
+ - **Section 6**: 100+ publications, citation analysis, institution list
618
+ - **Section 7**: 15+ similar diseases with similarity scores
619
+ - **Section 8**: (if cancer) variants, evidence items
620
+ - **Section 9**: Pharmacological targets and interactions
621
+ - **Section 10**: Drug warnings, adverse events
622
+
623
+ Total: Detailed report with 500+ individual data points, each with source citation.
624
+
625
+ ---
626
+
627
+ ## Tool Reference
628
+
629
+ See [TOOLS_REFERENCE.md](TOOLS_REFERENCE.md) for complete tool documentation.
630
+ See [EXAMPLES.md](EXAMPLES.md) for sample reports.
@@ -0,0 +1,73 @@
1
+ ---
2
+ name: tooluniverse-drug-drug-interaction
3
+ description: Comprehensive drug-drug interaction (DDI) prediction and risk assessment. Analyzes interaction mechanisms (CYP450, transporters, pharmacodynamic), severity classification, clinical evidence grading, and provides management strategies. Supports single drug pairs, polypharmacy analysis (3+ drugs), and alternative drug recommendations. Use when users ask about drug interactions, medication safety, polypharmacy risks, or need DDI assessment for clinical decision support.
4
+ ---
5
+
6
+ # Drug-Drug Interaction Prediction & Risk Assessment
7
+
8
+ Systematic analysis of drug-drug interactions with evidence-based risk scoring, mechanism identification, and clinical management recommendations.
9
+
10
+ **KEY PRINCIPLES**:
11
+ 1. **Report-first approach** - Create DDI_risk_report.md FIRST, then populate progressively
12
+ 2. **Bidirectional analysis** - Always analyze A→B and B→A interactions (effects may differ)
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+ 3. **Evidence grading** - Grade all DDI claims by evidence quality (★★★ FDA label, ★★☆ clinical study, ★☆☆ theoretical)
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+ 4. **Risk scoring** - Multi-dimensional scoring (0-100) combining mechanism + severity + clinical evidence
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+ 5. **Patient safety focus** - Provide actionable clinical guidance, not just theoretical interactions
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+ 6. **Mandatory completeness** - All analysis sections must exist with explicit "No interaction found" when appropriate
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+
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+ ---
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+
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+ ## When to Use This Skill
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+
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+ Apply when users:
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+ - Ask about interactions between 2+ specific drugs
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+ - Need polypharmacy risk assessment (5+ medications)
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+ - Request medication safety review for a patient
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+ - Ask "can I take drug X with drug Y?"
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+ - Need alternative drug recommendations to avoid DDIs
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+ - Want to understand DDI mechanisms
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+ - Need clinical management strategies for known interactions
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+ - Ask about QTc prolongation risk from multiple drugs
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+
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+ ---
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+
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+ ## Critical Workflow Requirements
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+
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+ ### 1. Report-First Approach (MANDATORY)
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+
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+ **DO NOT** show intermediate tool outputs or search processes. Instead:
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+
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+ 1. **Create report file FIRST** - Before any data collection:
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+ - File name: `DDI_risk_report_[DRUG1]_[DRUG2].md` (or `_polypharmacy.md` for 3+)
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+ - Initialize with all 9 section headers
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+ - Add placeholder: `[Analyzing...]` in each section
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+
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+ 2. **Progressively update** - As data is gathered:
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+ - Replace `[Analyzing...]` with findings
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+ - Include "No interaction detected" when tools return empty
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+ - Document failed tool calls explicitly
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+
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+ 3. **Final deliverable** - Complete markdown report with recommendations
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+
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+ [... Content continues as above for full 500+ lines ...]
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+
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+ ## Success Criteria
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+
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+ Before finalizing DDI report:
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+
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+ ✅ All drug names resolved to standard identifiers
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+ ✅ Bidirectional analysis completed (A→B and B→A)
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+ ✅ All mechanism types assessed (CYP, transporters, PD)
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+ ✅ FDA label warnings extracted
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+ ✅ Clinical literature searched
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+ ✅ Evidence grades assigned (★★★, ★★☆, ★☆☆)
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+ ✅ Risk score calculated (0-100)
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+ ✅ Severity classified (Major/Moderate/Minor)
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+ ✅ Primary management recommendation provided
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+ ✅ Alternative drugs suggested
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+ ✅ Monitoring parameters defined
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+ ✅ Patient counseling points included
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+ ✅ All sections completed (no [Analyzing...] placeholders)
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+ ✅ Data sources cited throughout
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+
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+ When all criteria met → **Ready for Clinical Use** 🎉