@bgicli/bgicli 2.1.1 → 2.2.0

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 (1266) hide show
  1. package/data/skills/aav-vector-design-agent/SKILL.md +198 -0
  2. package/data/skills/adaptyv/SKILL.md +112 -0
  3. package/data/skills/adhd-daily-planner/SKILL.md +271 -0
  4. package/data/skills/aeon/SKILL.md +372 -0
  5. package/data/skills/agent-browser/SKILL.md +159 -0
  6. package/data/skills/agentd-drug-discovery/SKILL.md +52 -0
  7. package/data/skills/ai-analyzer/SKILL.md +218 -0
  8. package/data/skills/alphafold/SKILL.md +183 -0
  9. package/data/skills/alphafold-database/SKILL.md +500 -0
  10. package/data/skills/anndata/SKILL.md +394 -0
  11. package/data/skills/antibody-design-agent/SKILL.md +64 -0
  12. package/data/skills/arboreto/SKILL.md +237 -0
  13. package/data/skills/armored-cart-design-agent/SKILL.md +225 -0
  14. package/data/skills/arxiv-search/SKILL.md +224 -0
  15. package/data/skills/autonomous-oncology-agent/SKILL.md +77 -0
  16. package/data/skills/bayesian-optimizer/SKILL.md +60 -0
  17. package/data/skills/benchling-integration/SKILL.md +473 -0
  18. package/data/skills/bgpt-paper-search/SKILL.md +81 -0
  19. package/data/skills/bindcraft/SKILL.md +198 -0
  20. package/data/skills/binder-design/SKILL.md +182 -0
  21. package/data/skills/binding-characterization/SKILL.md +234 -0
  22. package/data/skills/bindingdb-database/SKILL.md +332 -0
  23. package/data/skills/bio-admet-prediction/SKILL.md +224 -0
  24. package/data/skills/bio-alignment-files-bam-statistics/SKILL.md +340 -0
  25. package/data/skills/bio-alignment-filtering/SKILL.md +322 -0
  26. package/data/skills/bio-alignment-indexing/SKILL.md +249 -0
  27. package/data/skills/bio-alignment-io/SKILL.md +301 -0
  28. package/data/skills/bio-alignment-msa-parsing/SKILL.md +366 -0
  29. package/data/skills/bio-alignment-msa-statistics/SKILL.md +375 -0
  30. package/data/skills/bio-alignment-pairwise/SKILL.md +277 -0
  31. package/data/skills/bio-alignment-sorting/SKILL.md +296 -0
  32. package/data/skills/bio-alignment-validation/SKILL.md +374 -0
  33. package/data/skills/bio-atac-seq-atac-peak-calling/SKILL.md +221 -0
  34. package/data/skills/bio-atac-seq-atac-qc/SKILL.md +292 -0
  35. package/data/skills/bio-atac-seq-differential-accessibility/SKILL.md +268 -0
  36. package/data/skills/bio-atac-seq-footprinting/SKILL.md +256 -0
  37. package/data/skills/bio-atac-seq-motif-deviation/SKILL.md +319 -0
  38. package/data/skills/bio-atac-seq-nucleosome-positioning/SKILL.md +321 -0
  39. package/data/skills/bio-basecalling/SKILL.md +368 -0
  40. package/data/skills/bio-batch-downloads/SKILL.md +384 -0
  41. package/data/skills/bio-batch-processing/SKILL.md +303 -0
  42. package/data/skills/bio-bedgraph-handling/SKILL.md +336 -0
  43. package/data/skills/bio-blast-searches/SKILL.md +354 -0
  44. package/data/skills/bio-causal-genomics-colocalization-analysis/SKILL.md +264 -0
  45. package/data/skills/bio-causal-genomics-fine-mapping/SKILL.md +267 -0
  46. package/data/skills/bio-causal-genomics-mediation-analysis/SKILL.md +264 -0
  47. package/data/skills/bio-causal-genomics-mendelian-randomization/SKILL.md +221 -0
  48. package/data/skills/bio-causal-genomics-pleiotropy-detection/SKILL.md +292 -0
  49. package/data/skills/bio-cfdna-preprocessing/SKILL.md +200 -0
  50. package/data/skills/bio-chipseq-differential-binding/SKILL.md +262 -0
  51. package/data/skills/bio-chipseq-motif-analysis/SKILL.md +387 -0
  52. package/data/skills/bio-chipseq-peak-annotation/SKILL.md +239 -0
  53. package/data/skills/bio-chipseq-peak-calling/SKILL.md +277 -0
  54. package/data/skills/bio-chipseq-qc/SKILL.md +391 -0
  55. package/data/skills/bio-chipseq-super-enhancers/SKILL.md +288 -0
  56. package/data/skills/bio-chipseq-visualization/SKILL.md +289 -0
  57. package/data/skills/bio-clinical-databases-clinvar-lookup/SKILL.md +188 -0
  58. package/data/skills/bio-clinical-databases-dbsnp-queries/SKILL.md +171 -0
  59. package/data/skills/bio-clinical-databases-gnomad-frequencies/SKILL.md +205 -0
  60. package/data/skills/bio-clinical-databases-hla-typing/SKILL.md +248 -0
  61. package/data/skills/bio-clinical-databases-myvariant-queries/SKILL.md +174 -0
  62. package/data/skills/bio-clinical-databases-pharmacogenomics/SKILL.md +232 -0
  63. package/data/skills/bio-clinical-databases-polygenic-risk/SKILL.md +276 -0
  64. package/data/skills/bio-clinical-databases-somatic-signatures/SKILL.md +261 -0
  65. package/data/skills/bio-clinical-databases-tumor-mutational-burden/SKILL.md +301 -0
  66. package/data/skills/bio-clinical-databases-variant-prioritization/SKILL.md +225 -0
  67. package/data/skills/bio-clip-seq-binding-site-annotation/SKILL.md +66 -0
  68. package/data/skills/bio-clip-seq-clip-alignment/SKILL.md +70 -0
  69. package/data/skills/bio-clip-seq-clip-motif-analysis/SKILL.md +62 -0
  70. package/data/skills/bio-clip-seq-clip-peak-calling/SKILL.md +282 -0
  71. package/data/skills/bio-clip-seq-clip-preprocessing/SKILL.md +142 -0
  72. package/data/skills/bio-codon-usage/SKILL.md +353 -0
  73. package/data/skills/bio-comparative-genomics-ancestral-reconstruction/SKILL.md +312 -0
  74. package/data/skills/bio-comparative-genomics-hgt-detection/SKILL.md +341 -0
  75. package/data/skills/bio-comparative-genomics-ortholog-inference/SKILL.md +308 -0
  76. package/data/skills/bio-comparative-genomics-positive-selection/SKILL.md +354 -0
  77. package/data/skills/bio-comparative-genomics-synteny-analysis/SKILL.md +315 -0
  78. package/data/skills/bio-compressed-files/SKILL.md +263 -0
  79. package/data/skills/bio-consensus-sequences/SKILL.md +340 -0
  80. package/data/skills/bio-copy-number-cnv-annotation/SKILL.md +307 -0
  81. package/data/skills/bio-copy-number-cnv-visualization/SKILL.md +294 -0
  82. package/data/skills/bio-copy-number-cnvkit-analysis/SKILL.md +290 -0
  83. package/data/skills/bio-copy-number-gatk-cnv/SKILL.md +270 -0
  84. package/data/skills/bio-crispr-screens-base-editing-analysis/SKILL.md +110 -0
  85. package/data/skills/bio-crispr-screens-batch-correction/SKILL.md +316 -0
  86. package/data/skills/bio-crispr-screens-crispresso-editing/SKILL.md +205 -0
  87. package/data/skills/bio-crispr-screens-hit-calling/SKILL.md +264 -0
  88. package/data/skills/bio-crispr-screens-jacks-analysis/SKILL.md +313 -0
  89. package/data/skills/bio-crispr-screens-library-design/SKILL.md +417 -0
  90. package/data/skills/bio-crispr-screens-mageck-analysis/SKILL.md +222 -0
  91. package/data/skills/bio-crispr-screens-screen-qc/SKILL.md +243 -0
  92. package/data/skills/bio-ctdna-mutation-detection/SKILL.md +234 -0
  93. package/data/skills/bio-data-visualization-circos-plots/SKILL.md +405 -0
  94. package/data/skills/bio-data-visualization-color-palettes/SKILL.md +244 -0
  95. package/data/skills/bio-data-visualization-genome-browser-tracks/SKILL.md +328 -0
  96. package/data/skills/bio-data-visualization-genome-tracks/SKILL.md +249 -0
  97. package/data/skills/bio-data-visualization-ggplot2-fundamentals/SKILL.md +313 -0
  98. package/data/skills/bio-data-visualization-heatmaps-clustering/SKILL.md +227 -0
  99. package/data/skills/bio-data-visualization-interactive-visualization/SKILL.md +210 -0
  100. package/data/skills/bio-data-visualization-multipanel-figures/SKILL.md +274 -0
  101. package/data/skills/bio-data-visualization-specialized-omics-plots/SKILL.md +251 -0
  102. package/data/skills/bio-data-visualization-upset-plots/SKILL.md +228 -0
  103. package/data/skills/bio-data-visualization-volcano-customization/SKILL.md +233 -0
  104. package/data/skills/bio-de-deseq2-basics/SKILL.md +376 -0
  105. package/data/skills/bio-de-edger-basics/SKILL.md +418 -0
  106. package/data/skills/bio-de-results/SKILL.md +378 -0
  107. package/data/skills/bio-de-visualization/SKILL.md +408 -0
  108. package/data/skills/bio-differential-expression-batch-correction/SKILL.md +253 -0
  109. package/data/skills/bio-differential-expression-timeseries-de/SKILL.md +370 -0
  110. package/data/skills/bio-differential-splicing/SKILL.md +177 -0
  111. package/data/skills/bio-duplicate-handling/SKILL.md +292 -0
  112. package/data/skills/bio-entrez-fetch/SKILL.md +334 -0
  113. package/data/skills/bio-entrez-link/SKILL.md +325 -0
  114. package/data/skills/bio-entrez-search/SKILL.md +311 -0
  115. package/data/skills/bio-epidemiological-genomics-amr-surveillance/SKILL.md +233 -0
  116. package/data/skills/bio-epidemiological-genomics-pathogen-typing/SKILL.md +202 -0
  117. package/data/skills/bio-epidemiological-genomics-phylodynamics/SKILL.md +207 -0
  118. package/data/skills/bio-epidemiological-genomics-transmission-inference/SKILL.md +237 -0
  119. package/data/skills/bio-epidemiological-genomics-variant-surveillance/SKILL.md +237 -0
  120. package/data/skills/bio-epitranscriptomics-m6a-differential/SKILL.md +88 -0
  121. package/data/skills/bio-epitranscriptomics-m6a-peak-calling/SKILL.md +89 -0
  122. package/data/skills/bio-epitranscriptomics-m6anet-analysis/SKILL.md +101 -0
  123. package/data/skills/bio-epitranscriptomics-merip-preprocessing/SKILL.md +81 -0
  124. package/data/skills/bio-epitranscriptomics-modification-visualization/SKILL.md +98 -0
  125. package/data/skills/bio-experimental-design-batch-design/SKILL.md +110 -0
  126. package/data/skills/bio-experimental-design-multiple-testing/SKILL.md +98 -0
  127. package/data/skills/bio-experimental-design-power-analysis/SKILL.md +84 -0
  128. package/data/skills/bio-experimental-design-sample-size/SKILL.md +93 -0
  129. package/data/skills/bio-expression-matrix-counts-ingest/SKILL.md +220 -0
  130. package/data/skills/bio-expression-matrix-gene-id-mapping/SKILL.md +256 -0
  131. package/data/skills/bio-expression-matrix-metadata-joins/SKILL.md +271 -0
  132. package/data/skills/bio-expression-matrix-sparse-handling/SKILL.md +247 -0
  133. package/data/skills/bio-fastq-quality/SKILL.md +279 -0
  134. package/data/skills/bio-filter-sequences/SKILL.md +265 -0
  135. package/data/skills/bio-flow-cytometry-bead-normalization/SKILL.md +315 -0
  136. package/data/skills/bio-flow-cytometry-clustering-phenotyping/SKILL.md +237 -0
  137. package/data/skills/bio-flow-cytometry-compensation-transformation/SKILL.md +196 -0
  138. package/data/skills/bio-flow-cytometry-cytometry-qc/SKILL.md +382 -0
  139. package/data/skills/bio-flow-cytometry-differential-analysis/SKILL.md +217 -0
  140. package/data/skills/bio-flow-cytometry-doublet-detection/SKILL.md +288 -0
  141. package/data/skills/bio-flow-cytometry-fcs-handling/SKILL.md +221 -0
  142. package/data/skills/bio-flow-cytometry-gating-analysis/SKILL.md +193 -0
  143. package/data/skills/bio-format-conversion/SKILL.md +193 -0
  144. package/data/skills/bio-fragment-analysis/SKILL.md +214 -0
  145. package/data/skills/bio-gatk-variant-calling/SKILL.md +422 -0
  146. package/data/skills/bio-genome-assembly-assembly-polishing/SKILL.md +333 -0
  147. package/data/skills/bio-genome-assembly-assembly-qc/SKILL.md +344 -0
  148. package/data/skills/bio-genome-assembly-contamination-detection/SKILL.md +235 -0
  149. package/data/skills/bio-genome-assembly-hifi-assembly/SKILL.md +178 -0
  150. package/data/skills/bio-genome-assembly-long-read-assembly/SKILL.md +307 -0
  151. package/data/skills/bio-genome-assembly-metagenome-assembly/SKILL.md +227 -0
  152. package/data/skills/bio-genome-assembly-scaffolding/SKILL.md +204 -0
  153. package/data/skills/bio-genome-assembly-short-read-assembly/SKILL.md +319 -0
  154. package/data/skills/bio-genome-engineering-base-editing-design/SKILL.md +277 -0
  155. package/data/skills/bio-genome-engineering-grna-design/SKILL.md +221 -0
  156. package/data/skills/bio-genome-engineering-hdr-template-design/SKILL.md +264 -0
  157. package/data/skills/bio-genome-engineering-off-target-prediction/SKILL.md +232 -0
  158. package/data/skills/bio-genome-engineering-prime-editing-design/SKILL.md +275 -0
  159. package/data/skills/bio-genome-intervals-bed-file-basics/SKILL.md +357 -0
  160. package/data/skills/bio-genome-intervals-bigwig-tracks/SKILL.md +351 -0
  161. package/data/skills/bio-genome-intervals-coverage-analysis/SKILL.md +300 -0
  162. package/data/skills/bio-genome-intervals-gtf-gff-handling/SKILL.md +345 -0
  163. package/data/skills/bio-genome-intervals-interval-arithmetic/SKILL.md +485 -0
  164. package/data/skills/bio-genome-intervals-proximity-operations/SKILL.md +337 -0
  165. package/data/skills/bio-geo-data/SKILL.md +380 -0
  166. package/data/skills/bio-hi-c-analysis-compartment-analysis/SKILL.md +261 -0
  167. package/data/skills/bio-hi-c-analysis-contact-pairs/SKILL.md +278 -0
  168. package/data/skills/bio-hi-c-analysis-hic-data-io/SKILL.md +260 -0
  169. package/data/skills/bio-hi-c-analysis-hic-differential/SKILL.md +328 -0
  170. package/data/skills/bio-hi-c-analysis-hic-visualization/SKILL.md +297 -0
  171. package/data/skills/bio-hi-c-analysis-loop-calling/SKILL.md +284 -0
  172. package/data/skills/bio-hi-c-analysis-matrix-operations/SKILL.md +274 -0
  173. package/data/skills/bio-hi-c-analysis-tad-detection/SKILL.md +239 -0
  174. package/data/skills/bio-imaging-mass-cytometry-cell-segmentation/SKILL.md +241 -0
  175. package/data/skills/bio-imaging-mass-cytometry-data-preprocessing/SKILL.md +279 -0
  176. package/data/skills/bio-imaging-mass-cytometry-interactive-annotation/SKILL.md +304 -0
  177. package/data/skills/bio-imaging-mass-cytometry-phenotyping/SKILL.md +231 -0
  178. package/data/skills/bio-imaging-mass-cytometry-quality-metrics/SKILL.md +316 -0
  179. package/data/skills/bio-imaging-mass-cytometry-spatial-analysis/SKILL.md +246 -0
  180. package/data/skills/bio-immunoinformatics-epitope-prediction/SKILL.md +259 -0
  181. package/data/skills/bio-immunoinformatics-immunogenicity-scoring/SKILL.md +275 -0
  182. package/data/skills/bio-immunoinformatics-mhc-binding-prediction/SKILL.md +260 -0
  183. package/data/skills/bio-immunoinformatics-neoantigen-prediction/SKILL.md +277 -0
  184. package/data/skills/bio-immunoinformatics-tcr-epitope-binding/SKILL.md +257 -0
  185. package/data/skills/bio-isoform-switching/SKILL.md +192 -0
  186. package/data/skills/bio-liquid-biopsy-pipeline/SKILL.md +311 -0
  187. package/data/skills/bio-local-blast/SKILL.md +350 -0
  188. package/data/skills/bio-long-read-sequencing-clair3-variants/SKILL.md +252 -0
  189. package/data/skills/bio-long-read-sequencing-isoseq-analysis/SKILL.md +334 -0
  190. package/data/skills/bio-long-read-sequencing-nanopore-methylation/SKILL.md +110 -0
  191. package/data/skills/bio-longitudinal-monitoring/SKILL.md +271 -0
  192. package/data/skills/bio-longread-alignment/SKILL.md +193 -0
  193. package/data/skills/bio-longread-medaka/SKILL.md +176 -0
  194. package/data/skills/bio-longread-qc/SKILL.md +224 -0
  195. package/data/skills/bio-longread-structural-variants/SKILL.md +201 -0
  196. package/data/skills/bio-machine-learning-atlas-mapping/SKILL.md +139 -0
  197. package/data/skills/bio-machine-learning-biomarker-discovery/SKILL.md +157 -0
  198. package/data/skills/bio-machine-learning-model-validation/SKILL.md +148 -0
  199. package/data/skills/bio-machine-learning-omics-classifiers/SKILL.md +146 -0
  200. package/data/skills/bio-machine-learning-prediction-explanation/SKILL.md +162 -0
  201. package/data/skills/bio-machine-learning-survival-analysis/SKILL.md +176 -0
  202. package/data/skills/bio-metabolomics-lipidomics/SKILL.md +265 -0
  203. package/data/skills/bio-metabolomics-metabolite-annotation/SKILL.md +241 -0
  204. package/data/skills/bio-metabolomics-msdial-preprocessing/SKILL.md +308 -0
  205. package/data/skills/bio-metabolomics-normalization-qc/SKILL.md +283 -0
  206. package/data/skills/bio-metabolomics-pathway-mapping/SKILL.md +237 -0
  207. package/data/skills/bio-metabolomics-statistical-analysis/SKILL.md +276 -0
  208. package/data/skills/bio-metabolomics-targeted-analysis/SKILL.md +314 -0
  209. package/data/skills/bio-metabolomics-xcms-preprocessing/SKILL.md +268 -0
  210. package/data/skills/bio-metagenomics-abundance/SKILL.md +203 -0
  211. package/data/skills/bio-metagenomics-amr-detection/SKILL.md +293 -0
  212. package/data/skills/bio-metagenomics-functional-profiling/SKILL.md +252 -0
  213. package/data/skills/bio-metagenomics-kraken/SKILL.md +204 -0
  214. package/data/skills/bio-metagenomics-metaphlan/SKILL.md +214 -0
  215. package/data/skills/bio-metagenomics-strain-tracking/SKILL.md +292 -0
  216. package/data/skills/bio-metagenomics-visualization/SKILL.md +240 -0
  217. package/data/skills/bio-methylation-based-detection/SKILL.md +223 -0
  218. package/data/skills/bio-methylation-bismark-alignment/SKILL.md +195 -0
  219. package/data/skills/bio-methylation-calling/SKILL.md +200 -0
  220. package/data/skills/bio-methylation-dmr-detection/SKILL.md +211 -0
  221. package/data/skills/bio-methylation-methylkit/SKILL.md +219 -0
  222. package/data/skills/bio-microbiome-amplicon-processing/SKILL.md +137 -0
  223. package/data/skills/bio-microbiome-differential-abundance/SKILL.md +147 -0
  224. package/data/skills/bio-microbiome-diversity-analysis/SKILL.md +188 -0
  225. package/data/skills/bio-microbiome-functional-prediction/SKILL.md +153 -0
  226. package/data/skills/bio-microbiome-qiime2-workflow/SKILL.md +219 -0
  227. package/data/skills/bio-microbiome-taxonomy-assignment/SKILL.md +168 -0
  228. package/data/skills/bio-molecular-descriptors/SKILL.md +200 -0
  229. package/data/skills/bio-molecular-io/SKILL.md +188 -0
  230. package/data/skills/bio-motif-search/SKILL.md +354 -0
  231. package/data/skills/bio-multi-omics-data-harmonization/SKILL.md +228 -0
  232. package/data/skills/bio-multi-omics-mixomics-analysis/SKILL.md +221 -0
  233. package/data/skills/bio-multi-omics-mofa-integration/SKILL.md +225 -0
  234. package/data/skills/bio-multi-omics-similarity-network/SKILL.md +235 -0
  235. package/data/skills/bio-orchestrator/SKILL.md +133 -0
  236. package/data/skills/bio-paired-end-fastq/SKILL.md +334 -0
  237. package/data/skills/bio-pathway-enrichment-visualization/SKILL.md +278 -0
  238. package/data/skills/bio-pathway-go-enrichment/SKILL.md +218 -0
  239. package/data/skills/bio-pathway-gsea/SKILL.md +227 -0
  240. package/data/skills/bio-pathway-kegg-pathways/SKILL.md +234 -0
  241. package/data/skills/bio-pathway-reactome/SKILL.md +215 -0
  242. package/data/skills/bio-pathway-wikipathways/SKILL.md +255 -0
  243. package/data/skills/bio-pdb-geometric-analysis/SKILL.md +475 -0
  244. package/data/skills/bio-pdb-structure-io/SKILL.md +296 -0
  245. package/data/skills/bio-pdb-structure-modification/SKILL.md +448 -0
  246. package/data/skills/bio-pdb-structure-navigation/SKILL.md +335 -0
  247. package/data/skills/bio-phasing-imputation-genotype-imputation/SKILL.md +201 -0
  248. package/data/skills/bio-phasing-imputation-haplotype-phasing/SKILL.md +190 -0
  249. package/data/skills/bio-phasing-imputation-imputation-qc/SKILL.md +265 -0
  250. package/data/skills/bio-phasing-imputation-reference-panels/SKILL.md +203 -0
  251. package/data/skills/bio-phylo-distance-calculations/SKILL.md +307 -0
  252. package/data/skills/bio-phylo-modern-tree-inference/SKILL.md +274 -0
  253. package/data/skills/bio-phylo-tree-io/SKILL.md +252 -0
  254. package/data/skills/bio-phylo-tree-manipulation/SKILL.md +375 -0
  255. package/data/skills/bio-phylo-tree-visualization/SKILL.md +275 -0
  256. package/data/skills/bio-pileup-generation/SKILL.md +314 -0
  257. package/data/skills/bio-population-genetics-association-testing/SKILL.md +293 -0
  258. package/data/skills/bio-population-genetics-linkage-disequilibrium/SKILL.md +260 -0
  259. package/data/skills/bio-population-genetics-plink-basics/SKILL.md +338 -0
  260. package/data/skills/bio-population-genetics-population-structure/SKILL.md +352 -0
  261. package/data/skills/bio-population-genetics-scikit-allel-analysis/SKILL.md +306 -0
  262. package/data/skills/bio-population-genetics-selection-statistics/SKILL.md +251 -0
  263. package/data/skills/bio-primer-design-primer-basics/SKILL.md +289 -0
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@@ -0,0 +1,685 @@
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+ ---
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+ name: wellally-tech
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+ description: Integrate digital health data sources (Apple Health, Fitbit, Oura Ring) and connect to WellAlly.tech knowledge base. Import external health device data, standardize to local format, and recommend relevant WellAlly.tech knowledge base articles based on health data. Support generic CSV/JSON import, provide intelligent article recommendations, and help users better manage personal health data.
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+ allowed-tools: Read, Grep, Glob, Write
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+ ---
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+
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+ # WellAlly Digital Health Integration
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+
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+ Integrate multiple digital health data sources, connect to [WellAlly.tech](https://www.wellally.tech/) knowledge base, providing data import and knowledge reference for personal health management systems.
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+
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+ ## Core Features
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+
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+ ### 1. Digital Health Data Import
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+ - **Apple Health (HealthKit)**: Export XML/ZIP file parsing
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+ - **Fitbit**: OAuth2 API integration and CSV import
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+ - **Oura Ring**: API v2 data synchronization
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+ - **Generic Import**: CSV/JSON file import with field mapping
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+
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+ ### 2. WellAlly.tech Knowledge Base Integration
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+ - **Categorized Article Index**: Nutrition, fitness, sleep, mental health, chronic disease management
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+ - **Intelligent Recommendations**: Recommend relevant articles based on user health data
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+ - **URL References**: Provide direct links to [WellAlly.tech](https://www.wellally.tech/) platform
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+
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+ ### 3. Data Standardization
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+ - **Format Conversion**: Convert external data to local JSON format
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+ - **Field Mapping**: Intelligently map data fields from different platforms
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+ - **Data Validation**: Ensure completeness and accuracy of imported data
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+
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+ ### 4. Intelligent Article Recommendations
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+ - **Health Status Analysis**: Based on user health data analysis
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+ - **Relevance Matching**: Recommend articles most relevant to user health conditions
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+ - **Category Navigation**: Organize knowledge base articles by health topics
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+
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+ ## Usage Instructions
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+
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+ ### Trigger Conditions
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+
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+ Use this skill when users mention the following scenarios:
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+
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+ **Data Import**:
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+ - ✅ "Import my health data from Apple Health"
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+ - ✅ "Connect my Fitbit device"
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+ - ✅ "Sync my Oura Ring data"
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+ - ✅ "Import CSV health data file"
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+ - ✅ "How to import fitness tracker/smartwatch data"
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+
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+ **Knowledge Base Query**:
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+ - ✅ "Articles about hypertension on WellAlly platform"
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+ - ✅ "Recommend some health management reading materials"
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+ - ✅ "Recommend articles based on my health data"
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+ - ✅ "WellAlly knowledge base articles about sleep"
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+ - ✅ "How to improve my blood pressure (check knowledge base)"
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+
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+ **Data Management**:
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+ - ✅ "What health data sources do I have"
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+ - ✅ "Integrate health data from different platforms"
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+ - ✅ "View imported external data"
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+
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+ ### Execution Steps
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+
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+ #### Step 1: Identify User Intent
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+
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+ Determine what the user wants:
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+ 1. **Import Data**: Import data from external health platforms
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+ 2. **Query Knowledge Base**: Find [WellAlly.tech](https://www.wellally.tech/) related articles
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+ 3. **Get Recommendations**: Recommend articles based on health data
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+ 4. **Data Management**: View or manage imported external data
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+
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+ #### Step 2: Data Import Workflow
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+
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+ If user wants to import data:
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+
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+ **2.1 Determine Data Source**
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+ ```javascript
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+ const dataSource = identifySource(userInput);
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+ // Possible returns: "apple-health", "fitbit", "oura", "generic-csv", "generic-json"
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+ ```
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+
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+ **2.2 Read External Data**
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+ Use appropriate import script based on data source type:
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+
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+ ```javascript
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+ // Apple Health
84
+ const appleHealthData = readAppleHealthExport(exportPath);
85
+
86
+ // Fitbit
87
+ const fitbitData = fetchFitbitData(dateRange);
88
+
89
+ // Oura Ring
90
+ const ouraData = fetchOuraData(dateRange);
91
+
92
+ // Generic CSV/JSON
93
+ const genericData = readGenericFile(filePath, mappingConfig);
94
+ ```
95
+
96
+ **2.3 Data Mapping and Conversion**
97
+ Map external data to local format:
98
+
99
+ ```javascript
100
+ // Example: Apple Health steps mapping
101
+ function mapAppleHealthSteps(appleRecord) {
102
+ return {
103
+ date: formatDateTime(appleRecord.startDate),
104
+ steps: parseInt(appleRecord.value),
105
+ source: "Apple Health",
106
+ device: appleRecord.sourceName
107
+ };
108
+ }
109
+
110
+ // Save to local file
111
+ saveToLocalFile("data/fitness/activities.json", mappedData);
112
+ ```
113
+
114
+ **2.4 Data Validation**
115
+ ```javascript
116
+ function validateImportedData(data) {
117
+ // Check required fields
118
+ // Validate data types
119
+ // Check data ranges
120
+ // Ensure correct time format
121
+
122
+ return {
123
+ valid: true,
124
+ errors: [],
125
+ warnings: []
126
+ };
127
+ }
128
+ ```
129
+
130
+ **2.5 Generate Import Report**
131
+ ```javascript
132
+ const importReport = {
133
+ source: dataSource,
134
+ import_date: new Date().toISOString(),
135
+ records_imported: {
136
+ steps: 1234,
137
+ weight: 30,
138
+ heart_rate: 1200,
139
+ sleep: 90
140
+ },
141
+ date_range: {
142
+ start: "2025-01-01",
143
+ end: "2025-01-22"
144
+ },
145
+ validation: validationResults
146
+ };
147
+ ```
148
+
149
+ #### Step 3: Knowledge Base Query Workflow
150
+
151
+ If user wants to query knowledge base:
152
+
153
+ **3.1 Identify Query Topic**
154
+ ```javascript
155
+ const topic = identifyTopic(userInput);
156
+ // Possible returns: "nutrition", "fitness", "sleep", "mental-health", "chronic-disease", "hypertension", "diabetes", etc.
157
+ ```
158
+
159
+ **3.2 Search Relevant Articles**
160
+ Find relevant articles from knowledge base index:
161
+
162
+ ```javascript
163
+ function searchKnowledgeBase(topic) {
164
+ // Read knowledge base index
165
+ const kbIndex = readFile('.claude/skills/wellally-tech/knowledge-base/index.md');
166
+
167
+ // Find matching articles
168
+ const articles = kbIndex.categories.filter(cat =>
169
+ cat.tags.includes(topic) || cat.keywords.includes(topic)
170
+ );
171
+
172
+ return articles;
173
+ }
174
+ ```
175
+
176
+ **3.3 Return Article Links**
177
+ ```javascript
178
+ const results = {
179
+ topic: topic,
180
+ articles: [
181
+ {
182
+ title: "Hypertension Monitoring and Management",
183
+ url: "https://wellally.tech/knowledge-base/chronic-disease/hypertension-monitoring",
184
+ category: "Chronic Disease Management",
185
+ description: "Learn how to effectively monitor and manage blood pressure"
186
+ },
187
+ {
188
+ title: "Blood Pressure Lowering Strategies",
189
+ url: "https://wellally.tech/knowledge-base/chronic-disease/bp-lowering-strategies",
190
+ category: "Chronic Disease Management",
191
+ description: "Improve blood pressure levels through lifestyle changes"
192
+ }
193
+ ],
194
+ total_found: 2
195
+ };
196
+ ```
197
+
198
+ #### Step 4: Intelligent Recommendation Workflow
199
+
200
+ If user wants personalized recommendations:
201
+
202
+ **4.1 Read User Health Data**
203
+ ```javascript
204
+ // Read relevant health data
205
+ const profile = readFile('data/profile.json');
206
+ const bloodPressure = glob('data/blood-pressure/**/*.json');
207
+ const sleepRecords = glob('data/sleep/**/*.json');
208
+ const weightHistory = profile.weight_history || [];
209
+ ```
210
+
211
+ **4.2 Analyze Health Status**
212
+ ```javascript
213
+ function analyzeHealthStatus(data) {
214
+ const status = {
215
+ concerns: [],
216
+ good_patterns: []
217
+ };
218
+
219
+ // Analyze blood pressure
220
+ if (data.blood_pressure?.average > 140/90) {
221
+ status.concerns.push({
222
+ area: "blood_pressure",
223
+ severity: "high",
224
+ condition: "Hypertension",
225
+ value: data.blood_pressure.average
226
+ });
227
+ }
228
+
229
+ // Analyze sleep
230
+ if (data.sleep?.average_duration < 6) {
231
+ status.concerns.push({
232
+ area: "sleep",
233
+ severity: "medium",
234
+ condition: "Sleep Deprivation",
235
+ value: data.sleep.average_duration + " hours"
236
+ });
237
+ }
238
+
239
+ // Analyze weight trend
240
+ if (data.weight?.trend === "increasing") {
241
+ status.concerns.push({
242
+ area: "weight",
243
+ severity: "medium",
244
+ condition: "Weight Gain",
245
+ value: data.weight.change + " kg"
246
+ });
247
+ }
248
+
249
+ // Identify good patterns
250
+ if (data.steps?.average > 8000) {
251
+ status.good_patterns.push({
252
+ area: "activity",
253
+ description: "Daily average steps over 8000",
254
+ value: data.steps.average
255
+ });
256
+ }
257
+
258
+ return status;
259
+ }
260
+ ```
261
+
262
+ **4.3 Recommend Relevant Articles**
263
+ ```javascript
264
+ function recommendArticles(healthStatus) {
265
+ const recommendations = [];
266
+
267
+ for (const concern of healthStatus.concerns) {
268
+ const articles = findArticlesForCondition(concern.condition);
269
+ recommendations.push({
270
+ condition: concern.condition,
271
+ severity: concern.severity,
272
+ articles: articles
273
+ });
274
+ }
275
+
276
+ return recommendations;
277
+ }
278
+ ```
279
+
280
+ **4.4 Generate Recommendation Report**
281
+ ```javascript
282
+ const recommendationReport = {
283
+ generated_at: new Date().toISOString(),
284
+ health_status: healthStatus,
285
+ recommendations: recommendations,
286
+ total_articles: recommendations.reduce((sum, r) => sum + r.articles.length, 0)
287
+ };
288
+ ```
289
+
290
+ ## Output Format
291
+
292
+ ### Data Import Output
293
+
294
+ ```
295
+ ✅ Data Import Successful
296
+
297
+ Data Source: Apple Health
298
+ Import Time: 2025-01-22 14:30:00
299
+
300
+ Import Records Statistics:
301
+ ━━━━━━━━━━━━━━━━━━━━━━━━━━
302
+ 📊 Step Records: 1,234 records
303
+ ⚖️ Weight Records: 30 records
304
+ ❤️ Heart Rate Records: 1,200 records
305
+ 😴 Sleep Records: 90 records
306
+
307
+ Data Time Range: 2025-01-01 to 2025-01-22
308
+ ━━━━━━━━━━━━━━━━━━━━━━━━━━
309
+
310
+ 💾 Data Saved To:
311
+ • data/fitness/activities.json (steps)
312
+ • data/profile.json (weight history)
313
+ • data/fitness/heart-rate.json (heart rate)
314
+ • data/sleep/sleep-records.json (sleep)
315
+
316
+ ⚠️ Validation Warnings:
317
+ • 3 step records missing timestamps, used default values
318
+ • 1 weight record abnormal (<20kg), skipped
319
+
320
+ 💡 Next Steps:
321
+ • Use /health-trend to analyze imported data
322
+ • Use /wellally-tech for personalized article recommendations
323
+ ```
324
+
325
+ ### Knowledge Base Query Output
326
+
327
+ ```
328
+ 📚 WellAlly Knowledge Base Search Results
329
+
330
+ Search Topic: Hypertension Management
331
+ Articles Found: 2
332
+
333
+ ━━━━━━━━━━━━━━━━━━━━━━━━━━
334
+
335
+ 1. Hypertension Monitoring and Management
336
+ Category: Chronic Disease Management
337
+ Link: https://wellally.tech/knowledge-base/chronic-disease/hypertension-monitoring
338
+ Description: Learn how to effectively monitor and manage blood pressure
339
+
340
+ 2. Blood Pressure Lowering Strategies
341
+ Category: Chronic Disease Management
342
+ Link: https://wellally.tech/knowledge-base/chronic-disease/bp-lowering-strategies
343
+ Description: Improve blood pressure levels through lifestyle modifications
344
+
345
+ ━━━━━━━━━━━━━━━━━━━━━━━━━━
346
+
347
+ 🔗 Related Topics:
348
+ • Diabetes Management
349
+ • Cardiovascular Health
350
+ • Medication Adherence
351
+
352
+ 💡 Tips:
353
+ Click links to visit [WellAlly.tech](https://www.wellally.tech/) platform for full articles
354
+ ```
355
+
356
+ ### Intelligent Recommendation Output
357
+
358
+ ```
359
+ 💡 Article Recommendations Based on Your Health Data
360
+
361
+ Generated Time: 2025-01-22 14:30:00
362
+
363
+ ━━━━━━━━━━━━━━━━━━━━━━━━━━
364
+
365
+ 🔴 Attention Needed: Blood Pressure Management
366
+ ━━━━━━━━━━━━━━━━━━━━━━━━━━
367
+ Current Status: Average blood pressure 142/92 mmHg (elevated)
368
+
369
+ Recommended Articles:
370
+ 1. Hypertension Monitoring and Management
371
+ https://wellally.tech/knowledge-base/chronic-disease/hypertension-monitoring
372
+
373
+ 2. Blood Pressure Lowering Strategies
374
+ https://wellally.tech/knowledge-base/chronic-disease/bp-lowering-strategies
375
+
376
+ 3. Antihypertensive Medication Adherence Guide
377
+ https://wellally.tech/knowledge-base/chronic-disease/medication-adherence
378
+
379
+ ━━━━━━━━━━━━━━━━━━━━━━━━━━
380
+
381
+ 🟡 Attention Needed: Sleep Improvement
382
+ ━━━━━━━━━━━━━━━━━━━━━━━━━━
383
+ Current Status: Average sleep duration 5.8 hours (insufficient)
384
+
385
+ Recommended Articles:
386
+ 1. Sleep Hygiene Basics
387
+ https://wellally.tech/knowledge-base/sleep/sleep-hygiene
388
+
389
+ 2. Improve Sleep Quality
390
+ https://wellally.tech/knowledge-base/sleep/sleep-quality-improvement
391
+
392
+ ━━━━━━━━━━━━━━━━━━━━━━━━━━
393
+
394
+ 🟢 Keep Up: Daily Activity
395
+ ━━━━━━━━━━━━━━━━━━━━━━━━━━
396
+ Current Status: Daily average steps 9,234 (good)
397
+
398
+ Related Reading:
399
+ 1. Maintain Active Lifestyle
400
+ https://wellally.tech/knowledge-base/fitness/active-lifestyle
401
+
402
+ ━━━━━━━━━━━━━━━━━━━━━━━━━━
403
+
404
+ Summary: 5 related articles recommended
405
+ Visit [WellAlly.tech](https://www.wellally.tech/) Knowledge Base for full content
406
+ ```
407
+
408
+ ## Data Sources
409
+
410
+ ### External Data Sources
411
+
412
+ | Data Source | Type | Import Method | Data Content |
413
+ |-------------|------|---------------|--------------|
414
+ | Apple Health | File Import | XML/ZIP Parsing | Steps, weight, heart rate, sleep, workouts |
415
+ | Fitbit | API/CSV | OAuth2 or CSV | Activities, heart rate, sleep, weight |
416
+ | Oura Ring | API | OAuth2 | Sleep stages, readiness, heart rate variability |
417
+ | Generic CSV | File Import | Field Mapping | Custom health data |
418
+ | Generic JSON | File Import | Field Mapping | Custom health data |
419
+
420
+ ### Local Data Files
421
+
422
+ | File Path | Data Content | Source Mapping |
423
+ |-----------|--------------|----------------|
424
+ | `data/profile.json` | Profile, weight history | Apple Health, Fitbit, Oura |
425
+ | `data/fitness/activities.json` | Steps, activity data | Apple Health, Fitbit, Oura |
426
+ | `data/fitness/heart-rate.json` | Heart rate records | Apple Health, Fitbit, Oura |
427
+ | `data/sleep/sleep-records.json` | Sleep records | Apple Health, Fitbit, Oura |
428
+ | `data/fitness/recovery.json` | Recovery data | Oura Ring (readiness) |
429
+
430
+ ## WellAlly.tech Knowledge Base
431
+
432
+ ### Knowledge Base Structure
433
+
434
+ **Nutrition & Diet** (`knowledge-base/nutrition.md`)
435
+ - Dietary management guidelines
436
+ - Food nutrition queries
437
+ - Diet recommendations
438
+ - Special dietary needs
439
+
440
+ **Fitness & Exercise** (`knowledge-base/fitness.md`)
441
+ - Exercise tracking best practices
442
+ - Activity recommendations
443
+ - Exercise data interpretation
444
+ - Training plans
445
+
446
+ **Sleep Health** (`knowledge-base/sleep.md`)
447
+ - Sleep quality analysis
448
+ - Sleep improvement strategies
449
+ - Sleep disorders overview
450
+ - Sleep hygiene
451
+
452
+ **Mental Health** (`knowledge-base/mental-health.md`)
453
+ - Stress management techniques
454
+ - Mood tracking interpretation
455
+ - Mental health resources
456
+ - Mindfulness practice
457
+
458
+ **Chronic Disease Management** (`knowledge-base/chronic-disease.md`)
459
+ - Hypertension monitoring
460
+ - Diabetes management
461
+ - COPD care
462
+ - Medication adherence
463
+
464
+ ### Article Recommendation Mapping
465
+
466
+ ```javascript
467
+ const articleMapping = {
468
+ "Hypertension": [
469
+ "chronic-disease/hypertension-monitoring",
470
+ "chronic-disease/bp-lowering-strategies"
471
+ ],
472
+ "Diabetes": [
473
+ "chronic-disease/diabetes-management",
474
+ "nutrition/diabetic-diet"
475
+ ],
476
+ "Sleep Deprivation": [
477
+ "sleep/sleep-hygiene",
478
+ "sleep/sleep-quality-improvement"
479
+ ],
480
+ "Weight Gain": [
481
+ "nutrition/healthy-diet",
482
+ "nutrition/calorie-management"
483
+ ],
484
+ "High Stress": [
485
+ "mental-health/stress-management",
486
+ "mental-health/mindfulness"
487
+ ]
488
+ };
489
+ ```
490
+
491
+ ## Integration Guides
492
+
493
+ ### Apple Health Import
494
+
495
+ **Export Steps**:
496
+ 1. Open "Health" app on iPhone
497
+ 2. Tap profile icon in top right corner
498
+ 3. Scroll to bottom, tap "Export All Health Data"
499
+ 4. Wait for export to complete and choose sharing method
500
+ 5. Save the exported ZIP file
501
+
502
+ **Import Steps**:
503
+ ```bash
504
+ python scripts/import_apple_health.py ~/Downloads/apple_health_export.zip
505
+ ```
506
+
507
+ ### Fitbit Integration
508
+
509
+ **API Integration**:
510
+ 1. Create app on Fitbit Developer Platform
511
+ 2. Get CLIENT_ID and CLIENT_SECRET
512
+ 3. Run OAuth authentication flow
513
+ 4. Store access token
514
+
515
+ **Import Data**:
516
+ ```bash
517
+ python scripts/import_fitbit.py --api --days 30
518
+ ```
519
+
520
+ **CSV Import**:
521
+ ```bash
522
+ python scripts/import_fitbit.py --csv fitbit_export.csv
523
+ ```
524
+
525
+ ### Oura Ring Integration
526
+
527
+ **API Integration**:
528
+ 1. Create app on Oura Developer Platform
529
+ 2. Get Personal Access Token
530
+ 3. Configure token in import script
531
+
532
+ **Import Data**:
533
+ ```bash
534
+ python scripts/import_oura.py --date-range 2025-01-01 2025-01-22
535
+ ```
536
+
537
+ ### Generic CSV/JSON Import
538
+
539
+ **CSV Import**:
540
+ ```bash
541
+ python scripts/import_generic.py health_data.csv --mapping mapping_config.json
542
+ ```
543
+
544
+ **Mapping Configuration Example** (`mapping_config.json`):
545
+ ```json
546
+ {
547
+ "date": "Date",
548
+ "steps": "Step Count",
549
+ "weight": "Weight (kg)",
550
+ "heart_rate": "Resting Heart Rate"
551
+ }
552
+ ```
553
+
554
+ ## Security & Privacy
555
+
556
+ ### Must Follow
557
+
558
+ - ❌ Do not upload data to external servers (except API sync)
559
+ - ❌ Do not hardcode API credentials in code
560
+ - ❌ Do not share user access tokens
561
+ - ✅ All imported data stored locally only
562
+ - ✅ OAuth credentials encrypted storage
563
+ - ✅ Import only after explicit user authorization
564
+
565
+ ### Data Validation
566
+
567
+ - ✅ Validate imported data types and ranges
568
+ - ✅ Filter abnormal values (e.g., negative steps)
569
+ - ✅ Preserve data source information
570
+ - ✅ Handle timezone conversion
571
+
572
+ ### Error Handling
573
+
574
+ **File Read Failure**:
575
+ - Output "Unable to read file, please check file path and format"
576
+ - Provide correct file format examples
577
+ - Suggest re-exporting data
578
+
579
+ **API Call Failure**:
580
+ - Output "API call failed, please check network connection and credentials"
581
+ - Provide OAuth re-authentication guidance
582
+ - Fall back to CSV import method
583
+
584
+ **Data Validation Failure**:
585
+ - Output "Incorrect data format, skipped invalid records"
586
+ - Log number of skipped records
587
+ - Continue processing valid data
588
+
589
+ ## Related Commands
590
+
591
+ - `/health-trend`: Analyze health trends (using imported data)
592
+ - `/sleep`: Record sleep data
593
+ - `/diet`: Record diet data
594
+ - `/fitness`: Record exercise data
595
+ - `/profile`: Manage personal profile
596
+
597
+ ## Technical Implementation
598
+
599
+ ### Tool Limitations
600
+
601
+ This Skill only uses the following tools:
602
+ - **Read**: Read external data files and configurations
603
+ - **Grep**: Search data patterns
604
+ - **Glob**: Find data files
605
+ - **Write**: Save imported data to local JSON files
606
+
607
+ ### Python Dependencies
608
+
609
+ Python packages potentially needed for import scripts:
610
+ ```python
611
+ # Apple Health
612
+ import xml.etree.ElementTree as ET
613
+ import zipfile
614
+
615
+ # Fitbit/Oura
616
+ import requests
617
+
618
+ # Generic Import
619
+ import csv
620
+ import json
621
+ ```
622
+
623
+ ### Performance Optimization
624
+
625
+ - Incremental reading: Only import data within specified time range
626
+ - Data deduplication: Avoid importing duplicate data for same day
627
+ - Batch writing: Save data in batches for better performance
628
+ - Error recovery: Support resume from breakpoint
629
+
630
+ ## Usage Examples
631
+
632
+ ### Example 1: Import Apple Health Data
633
+ **User**: "Import fitness tracker data from Apple Health"
634
+ **Output**: Execute import workflow, generate import report
635
+
636
+ ### Example 2: Query Knowledge Base
637
+ **User**: "WellAlly platform articles about sleep"
638
+ **Output**: Return sleep-related knowledge base article links
639
+
640
+ ### Example 3: Get Personalized Recommendations
641
+ **User**: "Recommend articles based on my health data"
642
+ **Output**: Analyze health data, recommend relevant articles
643
+
644
+ ### Example 4: Import Generic CSV
645
+ **User**: "Import this CSV health data file health.csv"
646
+ **Output**: Parse CSV, map fields, save to local
647
+
648
+ ## Extensibility
649
+
650
+ ### Adding New Data Sources
651
+
652
+ 1. Create new integration guide in `integrations/` directory
653
+ 2. Create new import script in `scripts/` directory
654
+ 3. Update `data-sources.md` documentation
655
+ 4. Add usage instructions in SKILL.md
656
+
657
+ ### Adding New Knowledge Base Categories
658
+
659
+ 1. Create new category file in `knowledge-base/` directory
660
+ 2. Add related article links
661
+ 3. Update `knowledge-base/index.md`
662
+ 4. Update article recommendation mapping
663
+
664
+ ## Reference Resources
665
+
666
+ - **WellAlly.tech**: https://www.wellally.tech/
667
+ - **WellAlly Knowledge Base**: https://wellally.tech/knowledge-base/
668
+ - **WellAlly Blog**: https://wellally.tech/blog/
669
+ - **Apple HealthKit**: https://developer.apple.com/documentation/healthkit
670
+ - **Fitbit API**: https://dev.fitbit.com/
671
+ - **Oura Ring API**: https://cloud.ouraring.com/api/
672
+
673
+ ## FAQ
674
+
675
+ **Q: Will imported data overwrite existing data?**
676
+ A: No. Imported data will be appended to existing data, not overwritten. Duplicate data will be automatically deduplicated.
677
+
678
+ **Q: Can I import data from multiple platforms?**
679
+ A: Yes. You can import data from Apple Health, Fitbit, Oura, and other platforms simultaneously, the system will merge all data.
680
+
681
+ **Q: Are WellAlly.tech knowledge base articles offline?**
682
+ A: No. Knowledge base articles are referenced via URLs, requiring network connection to access the [WellAlly.tech](https://www.wellally.tech/) platform.
683
+
684
+ **Q: Where are API credentials stored?**
685
+ A: API credentials are encrypted and stored in local configuration files, not uploaded to any server.