@wentorai/research-plugins 1.0.0 → 1.2.0

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 (415) hide show
  1. package/README.md +22 -22
  2. package/curated/analysis/README.md +82 -56
  3. package/curated/domains/README.md +225 -69
  4. package/curated/literature/README.md +115 -46
  5. package/curated/research/README.md +106 -58
  6. package/curated/tools/README.md +107 -87
  7. package/curated/writing/README.md +92 -45
  8. package/mcp-configs/academic-db/alphafold-mcp.json +20 -0
  9. package/mcp-configs/academic-db/brightspace-mcp.json +21 -0
  10. package/mcp-configs/academic-db/climatiq-mcp.json +20 -0
  11. package/mcp-configs/academic-db/gibs-mcp.json +20 -0
  12. package/mcp-configs/academic-db/gis-mcp-server.json +22 -0
  13. package/mcp-configs/academic-db/google-earth-engine-mcp.json +21 -0
  14. package/mcp-configs/academic-db/m4-clinical-mcp.json +21 -0
  15. package/mcp-configs/academic-db/medical-mcp.json +21 -0
  16. package/mcp-configs/academic-db/nexonco-mcp.json +20 -0
  17. package/mcp-configs/academic-db/omop-mcp.json +20 -0
  18. package/mcp-configs/academic-db/onekgpd-mcp.json +20 -0
  19. package/mcp-configs/academic-db/openedu-mcp.json +20 -0
  20. package/mcp-configs/academic-db/opengenes-mcp.json +20 -0
  21. package/mcp-configs/academic-db/openstax-mcp.json +21 -0
  22. package/mcp-configs/academic-db/openstreetmap-mcp.json +21 -0
  23. package/mcp-configs/academic-db/opentargets-mcp.json +21 -0
  24. package/mcp-configs/academic-db/pdb-mcp.json +21 -0
  25. package/mcp-configs/academic-db/smithsonian-mcp.json +20 -0
  26. package/mcp-configs/ai-platform/magi-researchers.json +21 -0
  27. package/mcp-configs/ai-platform/mcp-academic-researcher.json +22 -0
  28. package/mcp-configs/ai-platform/open-paper-machine.json +21 -0
  29. package/mcp-configs/ai-platform/paper-intelligence.json +21 -0
  30. package/mcp-configs/ai-platform/paper-reader.json +21 -0
  31. package/mcp-configs/ai-platform/paperdebugger.json +21 -0
  32. package/mcp-configs/browser/exa-mcp.json +20 -0
  33. package/mcp-configs/browser/mcp-searxng.json +21 -0
  34. package/mcp-configs/browser/mcp-webresearch.json +20 -0
  35. package/mcp-configs/cloud-docs/confluence-mcp.json +37 -0
  36. package/mcp-configs/cloud-docs/google-drive-mcp.json +35 -0
  37. package/mcp-configs/cloud-docs/notion-mcp.json +29 -0
  38. package/mcp-configs/communication/discord-mcp.json +29 -0
  39. package/mcp-configs/communication/discourse-mcp.json +21 -0
  40. package/mcp-configs/communication/slack-mcp.json +29 -0
  41. package/mcp-configs/communication/telegram-mcp.json +28 -0
  42. package/mcp-configs/data-platform/automl-stat-mcp.json +21 -0
  43. package/mcp-configs/data-platform/jefferson-stats-mcp.json +22 -0
  44. package/mcp-configs/data-platform/mcp-excel-server.json +21 -0
  45. package/mcp-configs/data-platform/mcp-stata.json +21 -0
  46. package/mcp-configs/data-platform/mcpstack-jupyter.json +21 -0
  47. package/mcp-configs/data-platform/ml-mcp.json +21 -0
  48. package/mcp-configs/data-platform/nasdaq-data-link-mcp.json +20 -0
  49. package/mcp-configs/data-platform/numpy-mcp.json +21 -0
  50. package/mcp-configs/database/neo4j-mcp.json +37 -0
  51. package/mcp-configs/database/postgres-mcp.json +28 -0
  52. package/mcp-configs/database/sqlite-mcp.json +29 -0
  53. package/mcp-configs/dev-platform/geogebra-mcp.json +21 -0
  54. package/mcp-configs/dev-platform/github-mcp.json +31 -0
  55. package/mcp-configs/dev-platform/gitlab-mcp.json +34 -0
  56. package/mcp-configs/dev-platform/latex-mcp-server.json +21 -0
  57. package/mcp-configs/dev-platform/manim-mcp.json +20 -0
  58. package/mcp-configs/dev-platform/mcp-echarts.json +20 -0
  59. package/mcp-configs/dev-platform/panel-viz-mcp.json +20 -0
  60. package/mcp-configs/dev-platform/paperbanana.json +20 -0
  61. package/mcp-configs/dev-platform/texflow-mcp.json +20 -0
  62. package/mcp-configs/dev-platform/texmcp.json +20 -0
  63. package/mcp-configs/dev-platform/typst-mcp.json +21 -0
  64. package/mcp-configs/dev-platform/vizro-mcp.json +20 -0
  65. package/mcp-configs/email/email-mcp.json +40 -0
  66. package/mcp-configs/email/gmail-mcp.json +37 -0
  67. package/mcp-configs/note-knowledge/local-faiss-mcp.json +21 -0
  68. package/mcp-configs/note-knowledge/mcp-memory-service.json +21 -0
  69. package/mcp-configs/note-knowledge/mcp-obsidian.json +23 -0
  70. package/mcp-configs/note-knowledge/mcp-ragdocs.json +20 -0
  71. package/mcp-configs/note-knowledge/mcp-summarizer.json +21 -0
  72. package/mcp-configs/note-knowledge/mediawiki-mcp.json +21 -0
  73. package/mcp-configs/note-knowledge/openzim-mcp.json +20 -0
  74. package/mcp-configs/note-knowledge/zettelkasten-mcp.json +21 -0
  75. package/mcp-configs/reference-mgr/academic-paper-mcp-http.json +20 -0
  76. package/mcp-configs/reference-mgr/academix.json +20 -0
  77. package/mcp-configs/reference-mgr/arxiv-research-mcp.json +21 -0
  78. package/mcp-configs/reference-mgr/google-scholar-abstract-mcp.json +19 -0
  79. package/mcp-configs/reference-mgr/google-scholar-mcp.json +20 -0
  80. package/mcp-configs/reference-mgr/mcp-paperswithcode.json +21 -0
  81. package/mcp-configs/reference-mgr/mcp-scholarly.json +20 -0
  82. package/mcp-configs/reference-mgr/mcp-simple-arxiv.json +20 -0
  83. package/mcp-configs/reference-mgr/mcp-simple-pubmed.json +20 -0
  84. package/mcp-configs/reference-mgr/mcp-zotero.json +21 -0
  85. package/mcp-configs/reference-mgr/mendeley-mcp.json +20 -0
  86. package/mcp-configs/reference-mgr/ncbi-mcp-server.json +22 -0
  87. package/mcp-configs/reference-mgr/onecite.json +21 -0
  88. package/mcp-configs/reference-mgr/paper-search-mcp.json +21 -0
  89. package/mcp-configs/reference-mgr/pubmed-search-mcp.json +21 -0
  90. package/mcp-configs/reference-mgr/scholar-mcp.json +21 -0
  91. package/mcp-configs/reference-mgr/scholar-multi-mcp.json +21 -0
  92. package/mcp-configs/reference-mgr/seerai.json +21 -0
  93. package/mcp-configs/reference-mgr/semantic-scholar-fastmcp.json +21 -0
  94. package/mcp-configs/reference-mgr/sourcelibrary.json +20 -0
  95. package/mcp-configs/registry.json +178 -149
  96. package/mcp-configs/repository/dataverse-mcp.json +33 -0
  97. package/mcp-configs/repository/huggingface-mcp.json +29 -0
  98. package/openclaw.plugin.json +2 -2
  99. package/package.json +2 -2
  100. package/skills/analysis/dataviz/algorithm-visualizer-guide/SKILL.md +259 -0
  101. package/skills/analysis/dataviz/bokeh-visualization-guide/SKILL.md +270 -0
  102. package/skills/analysis/dataviz/chart-image-generator/SKILL.md +229 -0
  103. package/skills/analysis/dataviz/citation-map-guide/SKILL.md +184 -0
  104. package/skills/analysis/dataviz/d3-visualization-guide/SKILL.md +281 -0
  105. package/skills/analysis/dataviz/data-visualization-principles/SKILL.md +171 -0
  106. package/skills/analysis/dataviz/echarts-visualization-guide/SKILL.md +250 -0
  107. package/skills/analysis/dataviz/metabase-analytics-guide/SKILL.md +242 -0
  108. package/skills/analysis/dataviz/plotly-interactive-guide/SKILL.md +266 -0
  109. package/skills/analysis/dataviz/redash-analytics-guide/SKILL.md +284 -0
  110. package/skills/analysis/econometrics/econml-causal-guide/SKILL.md +163 -0
  111. package/skills/analysis/econometrics/empirical-paper-analysis/SKILL.md +192 -0
  112. package/skills/analysis/econometrics/mostly-harmless-guide/SKILL.md +139 -0
  113. package/skills/analysis/econometrics/panel-data-analyst/SKILL.md +259 -0
  114. package/skills/analysis/econometrics/panel-data-regression-workflow/SKILL.md +267 -0
  115. package/skills/analysis/econometrics/python-causality-guide/SKILL.md +134 -0
  116. package/skills/analysis/econometrics/stata-accounting-guide/SKILL.md +269 -0
  117. package/skills/analysis/econometrics/stata-analyst-guide/SKILL.md +245 -0
  118. package/skills/analysis/econometrics/stata-reference-guide/SKILL.md +293 -0
  119. package/skills/analysis/statistics/data-anomaly-detection/SKILL.md +157 -0
  120. package/skills/analysis/statistics/general-statistics-guide/SKILL.md +226 -0
  121. package/skills/analysis/statistics/infiagent-benchmark-guide/SKILL.md +106 -0
  122. package/skills/analysis/statistics/ml-experiment-tracker/SKILL.md +212 -0
  123. package/skills/analysis/statistics/pywayne-statistics-guide/SKILL.md +192 -0
  124. package/skills/analysis/statistics/quantitative-methods-guide/SKILL.md +193 -0
  125. package/skills/analysis/statistics/senior-data-scientist-guide/SKILL.md +223 -0
  126. package/skills/analysis/wrangling/claude-data-analysis-guide/SKILL.md +100 -0
  127. package/skills/analysis/wrangling/csv-data-analyzer/SKILL.md +170 -0
  128. package/skills/analysis/wrangling/data-cleaning-pipeline/SKILL.md +266 -0
  129. package/skills/analysis/wrangling/data-cog-guide/SKILL.md +178 -0
  130. package/skills/analysis/wrangling/open-data-scientist-guide/SKILL.md +197 -0
  131. package/skills/analysis/wrangling/stata-data-cleaning/SKILL.md +276 -0
  132. package/skills/analysis/wrangling/streamline-analyst-guide/SKILL.md +119 -0
  133. package/skills/analysis/wrangling/survey-data-processing/SKILL.md +298 -0
  134. package/skills/domains/ai-ml/ai-agent-papers-guide/SKILL.md +146 -0
  135. package/skills/domains/ai-ml/ai-model-benchmarking/SKILL.md +209 -0
  136. package/skills/domains/ai-ml/annotated-dl-papers-guide/SKILL.md +159 -0
  137. package/skills/domains/ai-ml/anomaly-detection-papers-guide/SKILL.md +167 -0
  138. package/skills/domains/ai-ml/autonomous-agents-papers-guide/SKILL.md +178 -0
  139. package/skills/domains/ai-ml/dl-transformer-finetune/SKILL.md +239 -0
  140. package/skills/domains/ai-ml/domain-adaptation-papers-guide/SKILL.md +173 -0
  141. package/skills/domains/ai-ml/generative-ai-guide/SKILL.md +146 -0
  142. package/skills/domains/ai-ml/graph-learning-papers-guide/SKILL.md +125 -0
  143. package/skills/domains/ai-ml/huggingface-inference-guide/SKILL.md +196 -0
  144. package/skills/domains/ai-ml/keras-deep-learning/SKILL.md +210 -0
  145. package/skills/domains/ai-ml/kolmogorov-arnold-networks-guide/SKILL.md +185 -0
  146. package/skills/domains/ai-ml/llm-from-scratch-guide/SKILL.md +124 -0
  147. package/skills/domains/ai-ml/ml-pipeline-guide/SKILL.md +295 -0
  148. package/skills/domains/ai-ml/nlp-toolkit-guide/SKILL.md +247 -0
  149. package/skills/domains/ai-ml/npcpy-research-guide/SKILL.md +137 -0
  150. package/skills/domains/ai-ml/pytorch-guide/SKILL.md +281 -0
  151. package/skills/domains/ai-ml/pytorch-lightning-guide/SKILL.md +244 -0
  152. package/skills/domains/ai-ml/responsible-ai-guide/SKILL.md +126 -0
  153. package/skills/domains/ai-ml/tensorflow-guide/SKILL.md +241 -0
  154. package/skills/domains/ai-ml/vmas-simulator-guide/SKILL.md +129 -0
  155. package/skills/domains/biomedical/bioagents-guide/SKILL.md +308 -0
  156. package/skills/domains/biomedical/clawbio-guide/SKILL.md +167 -0
  157. package/skills/domains/biomedical/clinical-dialogue-agents-guide/SKILL.md +145 -0
  158. package/skills/domains/biomedical/ena-sequence-api/SKILL.md +175 -0
  159. package/skills/domains/biomedical/genomas-guide/SKILL.md +126 -0
  160. package/skills/domains/biomedical/genotex-benchmark-guide/SKILL.md +125 -0
  161. package/skills/domains/biomedical/med-researcher-guide/SKILL.md +161 -0
  162. package/skills/domains/biomedical/med-researcher-r1-guide/SKILL.md +146 -0
  163. package/skills/domains/biomedical/medgeclaw-guide/SKILL.md +345 -0
  164. package/skills/domains/biomedical/medical-imaging-guide/SKILL.md +305 -0
  165. package/skills/domains/biomedical/ncbi-blast-api/SKILL.md +195 -0
  166. package/skills/domains/biomedical/ncbi-datasets-api/SKILL.md +220 -0
  167. package/skills/domains/biomedical/quickgo-api/SKILL.md +181 -0
  168. package/skills/domains/business/architecture-design-guide/SKILL.md +279 -0
  169. package/skills/domains/business/innovation-management-guide/SKILL.md +257 -0
  170. package/skills/domains/business/operations-research-guide/SKILL.md +258 -0
  171. package/skills/domains/business/xpert-bi-guide/SKILL.md +84 -0
  172. package/skills/domains/chemistry/cactus-cheminformatics-guide/SKILL.md +89 -0
  173. package/skills/domains/chemistry/chemeagle-guide/SKILL.md +147 -0
  174. package/skills/domains/chemistry/chemgraph-agent-guide/SKILL.md +120 -0
  175. package/skills/domains/chemistry/molecular-dynamics-guide/SKILL.md +237 -0
  176. package/skills/domains/chemistry/pubchem-api-guide/SKILL.md +180 -0
  177. package/skills/domains/chemistry/spectroscopy-analysis-guide/SKILL.md +290 -0
  178. package/skills/domains/cs/ai-security-papers-guide/SKILL.md +103 -0
  179. package/skills/domains/cs/code-llm-papers-guide/SKILL.md +131 -0
  180. package/skills/domains/cs/distributed-systems-guide/SKILL.md +268 -0
  181. package/skills/domains/cs/formal-verification-guide/SKILL.md +298 -0
  182. package/skills/domains/cs/gaussian-splatting-papers-guide/SKILL.md +158 -0
  183. package/skills/domains/cs/llm-aiops-guide/SKILL.md +70 -0
  184. package/skills/domains/cs/software-heritage-api/SKILL.md +200 -0
  185. package/skills/domains/ecology/species-distribution-guide/SKILL.md +343 -0
  186. package/skills/domains/economics/imf-data-api-guide/SKILL.md +174 -0
  187. package/skills/domains/economics/nber-working-papers-api/SKILL.md +177 -0
  188. package/skills/domains/economics/post-labor-economics/SKILL.md +254 -0
  189. package/skills/domains/economics/pricing-psychology-guide/SKILL.md +273 -0
  190. package/skills/domains/economics/repec-economics-api/SKILL.md +188 -0
  191. package/skills/domains/economics/world-bank-data-guide/SKILL.md +179 -0
  192. package/skills/domains/education/academic-study-methods/SKILL.md +228 -0
  193. package/skills/domains/education/assessment-design-guide/SKILL.md +213 -0
  194. package/skills/domains/education/educational-research-methods/SKILL.md +179 -0
  195. package/skills/domains/education/edumcp-guide/SKILL.md +74 -0
  196. package/skills/domains/education/mooc-analytics-guide/SKILL.md +206 -0
  197. package/skills/domains/education/open-syllabus-api/SKILL.md +171 -0
  198. package/skills/domains/finance/akshare-finance-data/SKILL.md +207 -0
  199. package/skills/domains/finance/finsight-research-guide/SKILL.md +113 -0
  200. package/skills/domains/finance/options-analytics-agent-guide/SKILL.md +117 -0
  201. package/skills/domains/finance/portfolio-optimization-guide/SKILL.md +279 -0
  202. package/skills/domains/finance/risk-modeling-guide/SKILL.md +260 -0
  203. package/skills/domains/finance/stata-accounting-research/SKILL.md +372 -0
  204. package/skills/domains/geoscience/climate-modeling-guide/SKILL.md +215 -0
  205. package/skills/domains/geoscience/pangaea-data-api/SKILL.md +197 -0
  206. package/skills/domains/geoscience/satellite-remote-sensing/SKILL.md +193 -0
  207. package/skills/domains/geoscience/seismology-data-guide/SKILL.md +208 -0
  208. package/skills/domains/humanities/digital-humanities-methods/SKILL.md +232 -0
  209. package/skills/domains/humanities/ethical-philosophy-guide/SKILL.md +244 -0
  210. package/skills/domains/humanities/history-research-guide/SKILL.md +260 -0
  211. package/skills/domains/humanities/political-history-guide/SKILL.md +241 -0
  212. package/skills/domains/law/caselaw-access-api/SKILL.md +149 -0
  213. package/skills/domains/law/legal-agent-skills-guide/SKILL.md +132 -0
  214. package/skills/domains/law/legal-nlp-guide/SKILL.md +236 -0
  215. package/skills/domains/law/legal-research-methods/SKILL.md +190 -0
  216. package/skills/domains/law/opencontracts-guide/SKILL.md +168 -0
  217. package/skills/domains/law/patent-analysis-guide/SKILL.md +257 -0
  218. package/skills/domains/law/regulatory-compliance-guide/SKILL.md +267 -0
  219. package/skills/domains/math/lean-theorem-proving-guide/SKILL.md +140 -0
  220. package/skills/domains/math/symbolic-computation-guide/SKILL.md +263 -0
  221. package/skills/domains/math/topology-data-analysis/SKILL.md +305 -0
  222. package/skills/domains/pharma/clinical-trial-design-guide/SKILL.md +271 -0
  223. package/skills/domains/pharma/drug-target-interaction/SKILL.md +242 -0
  224. package/skills/domains/pharma/madd-drug-discovery-guide/SKILL.md +153 -0
  225. package/skills/domains/pharma/pharmacovigilance-guide/SKILL.md +216 -0
  226. package/skills/domains/physics/astrophysics-data-guide/SKILL.md +305 -0
  227. package/skills/domains/physics/particle-physics-guide/SKILL.md +287 -0
  228. package/skills/domains/social-science/ipums-microdata-api/SKILL.md +211 -0
  229. package/skills/domains/social-science/network-analysis-guide/SKILL.md +310 -0
  230. package/skills/domains/social-science/psychology-research-guide/SKILL.md +270 -0
  231. package/skills/domains/social-science/sociology-research-guide/SKILL.md +238 -0
  232. package/skills/domains/social-science/sociology-research-methods/SKILL.md +181 -0
  233. package/skills/literature/discovery/arxiv-paper-monitoring/SKILL.md +233 -0
  234. package/skills/literature/discovery/paper-recommendation-guide/SKILL.md +120 -0
  235. package/skills/literature/discovery/papers-we-love-guide/SKILL.md +169 -0
  236. package/skills/literature/discovery/semantic-paper-radar/SKILL.md +144 -0
  237. package/skills/literature/discovery/zotero-arxiv-daily-guide/SKILL.md +94 -0
  238. package/skills/literature/fulltext/bioc-pmc-api/SKILL.md +146 -0
  239. package/skills/literature/fulltext/core-api-guide/SKILL.md +144 -0
  240. package/skills/literature/fulltext/dataverse-api/SKILL.md +215 -0
  241. package/skills/literature/fulltext/hal-archive-api/SKILL.md +218 -0
  242. package/skills/literature/fulltext/institutional-repository-guide/SKILL.md +212 -0
  243. package/skills/literature/fulltext/open-access-mining-guide/SKILL.md +341 -0
  244. package/skills/literature/fulltext/osf-api/SKILL.md +212 -0
  245. package/skills/literature/fulltext/pmc-ftp-bulk-download/SKILL.md +182 -0
  246. package/skills/literature/fulltext/zotero-ai-butler-guide/SKILL.md +166 -0
  247. package/skills/literature/fulltext/zotero-scihub-guide/SKILL.md +168 -0
  248. package/skills/literature/metadata/academic-paper-summarizer/SKILL.md +101 -0
  249. package/skills/literature/metadata/bibliometrix-guide/SKILL.md +164 -0
  250. package/skills/literature/metadata/crossref-event-data-api/SKILL.md +183 -0
  251. package/skills/literature/metadata/doi-content-negotiation/SKILL.md +202 -0
  252. package/skills/literature/metadata/orkg-api/SKILL.md +153 -0
  253. package/skills/literature/metadata/plumx-metrics-api/SKILL.md +188 -0
  254. package/skills/literature/metadata/ror-organization-api/SKILL.md +208 -0
  255. package/skills/literature/metadata/sophosia-reference-guide/SKILL.md +110 -0
  256. package/skills/literature/metadata/viaf-authority-api/SKILL.md +209 -0
  257. package/skills/literature/metadata/wikidata-api-guide/SKILL.md +156 -0
  258. package/skills/literature/metadata/zoplicate-dedup-guide/SKILL.md +147 -0
  259. package/skills/literature/metadata/zotero-actions-tags-guide/SKILL.md +212 -0
  260. package/skills/literature/metadata/zotmoov-guide/SKILL.md +120 -0
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  262. package/skills/literature/search/arxiv-batch-reporting/SKILL.md +133 -0
  263. package/skills/literature/search/arxiv-cli-tools/SKILL.md +172 -0
  264. package/skills/literature/search/arxiv-osiris/SKILL.md +199 -0
  265. package/skills/literature/search/arxiv-paper-processor/SKILL.md +141 -0
  266. package/skills/literature/search/baidu-scholar-guide/SKILL.md +110 -0
  267. package/skills/literature/search/base-academic-search/SKILL.md +196 -0
  268. package/skills/literature/search/chatpaper-guide/SKILL.md +122 -0
  269. package/skills/literature/search/citeseerx-api/SKILL.md +183 -0
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@@ -0,0 +1,132 @@
1
+ ---
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+ name: papersgpt-zotero-guide
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+ description: "AI plugin for Zotero with ChatGPT, Claude, and DeepSeek support"
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+ version: 1.0.0
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+ author: wentor-community
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+ source: https://github.com/papersgpt/papersgpt-for-zotero
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+ metadata:
8
+ openclaw:
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+ category: "writing"
10
+ subcategory: "citation"
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+ keywords:
12
+ - zotero
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+ - ai-assistant
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+ - paper-summarization
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+ - chatgpt
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+ - claude
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+ - research-reading
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+ ---
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+
20
+ # PapersGPT for Zotero Guide
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+
22
+ A skill for using the PapersGPT plugin to integrate AI assistants (ChatGPT, Claude, DeepSeek) directly into the Zotero reference management workflow for paper summarization, question-answering, and research analysis. Based on papersgpt-for-zotero (2K stars), this skill transforms Zotero from a passive reference store into an active research intelligence tool.
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+
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+ ## Overview
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+
26
+ Researchers accumulate large Zotero libraries but often lack time to deeply read every paper. PapersGPT addresses this by bringing AI analysis capabilities directly into the Zotero interface. Without leaving the reference manager, researchers can generate summaries, ask specific questions about paper content, compare papers, extract key findings, and get AI-assisted insights that accelerate the literature review process.
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+
28
+ The plugin supports multiple AI backends, allowing researchers to choose based on quality, cost, and privacy preferences. All interactions happen in context of the selected paper's full text, ensuring responses are grounded in the actual document rather than the model's general knowledge.
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+
30
+ ## Setup and Configuration
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+
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+ **Installation**
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+ - Download the plugin from the project's releases page
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+ - Install in Zotero via Tools then Add-ons then Install from File
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+ - Restart Zotero to activate the plugin
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+ - Open plugin preferences to configure the AI backend
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+
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+ **Backend Configuration**
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+ - Select the AI provider: OpenAI (ChatGPT), Anthropic (Claude), or DeepSeek
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+ - Enter the API credentials for your chosen provider
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+ - Set the model version (e.g., GPT-4, Claude Sonnet, DeepSeek-V3)
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+ - Configure context window size and response length preferences
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+ - Set language preferences for AI responses (supports multilingual output)
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+
45
+ **Privacy Considerations**
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+ - Paper text is sent to the selected AI provider's API for processing
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+ - Consider using local or self-hosted models for sensitive pre-publication work
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+ - Review your institution's data handling policies before processing restricted materials
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+ - The plugin does not store conversation history on external servers
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+ - API credentials are stored locally in Zotero's configuration
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+
52
+ ## Core Capabilities
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+
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+ **Paper Summarization**
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+ - Generate concise summaries of any paper in your library
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+ - Customize summary length (tweet, abstract, detailed, comprehensive)
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+ - Focus summaries on specific aspects (methodology, results, contributions)
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+ - Generate bullet-point key takeaways for quick scanning
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+ - Produce structured summaries with standardized sections
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+
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+ **Question-Answering**
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+ - Ask specific questions about a selected paper's content
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+ - The AI grounds its answers in the paper's actual text, citing specific sections
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+ - Follow up with clarifying questions in a conversational format
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+ - Ask for explanations of technical concepts in the paper's context
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+ - Request comparisons between the paper's approach and alternatives
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+
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+ **Critical Analysis**
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+ - Request an evaluation of the paper's methodology strengths and weaknesses
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+ - Ask about potential limitations not acknowledged by the authors
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+ - Get an assessment of the evidence quality for specific claims
72
+ - Request identification of assumptions underlying the paper's conclusions
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+ - Compare the paper's findings with known results in the field
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+
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+ ## Workflow Patterns
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+
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+ **Triage Workflow**
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+ - When adding a batch of new papers to your library, use AI summaries to quickly assess relevance
79
+ - Generate one-paragraph summaries for each new paper
80
+ - Based on summaries, sort papers into "read now," "read later," and "archive" categories
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+ - Save AI-generated tags to Zotero items for future filtering
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+ - This approach handles 10-20 papers in the time it would take to manually skim 2-3
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+
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+ **Deep Reading Workflow**
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+ - Before reading a paper, generate a structured summary to preview its content
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+ - While reading, ask questions about confusing passages or technical details
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+ - After reading, use the AI to verify your understanding of key claims
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+ - Generate a literature note combining your annotations with AI analysis
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+ - Store the analysis alongside the paper in Zotero for future reference
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+
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+ **Literature Review Workflow**
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+ - Select a collection of papers for review
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+ - Generate comparative summaries highlighting similarities and differences
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+ - Ask the AI to identify common themes across the collection
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+ - Request a synthesis of findings organized by research question
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+ - Use the AI to draft literature review paragraphs grounded in the selected papers
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+
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+ **Writing Support Workflow**
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+ - When drafting a paper, ask the AI to find relevant quotes from your library
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+ - Request context about how a reference supports your argument
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+ - Generate citation context paragraphs that integrate multiple sources
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+ - Ask for suggestions on which papers in your library are most relevant to a specific claim
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+ - Verify that your characterization of a cited paper's findings is accurate
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+
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+ ## Multi-Model Strategy
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+
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+ Different AI models have different strengths:
108
+
109
+ **ChatGPT (GPT-4)** - Strong general comprehension, good at structured output, broad knowledge base
110
+ **Claude** - Strong analytical reasoning, careful about uncertainty, detailed explanations
111
+ **DeepSeek** - Cost-effective for batch processing, strong multilingual capabilities
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+
113
+ Consider using different models for different tasks: a cost-effective model for initial triage summaries and a more capable model for deep analysis of key papers.
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+
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+ ## Integration with Research-Claw
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+
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+ This skill enhances the Research-Claw reading and analysis pipeline:
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+
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+ - Use AI-generated summaries as input for literature search expansion
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+ - Feed paper analyses to writing skills for literature review drafting
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+ - Connect with other Zotero skills for a comprehensive reference management workflow
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+ - Store AI analyses in the Research-Claw knowledge base for cross-session access
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+ - Combine with paper-to-agent skills for even deeper interactive exploration
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+
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+ ## Best Practices
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+
127
+ - Always verify AI-generated summaries against the original paper for accuracy
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+ - Use AI analysis as a complement to, not a replacement for, close reading of key papers
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+ - Be aware that AI models may hallucinate details not present in the paper
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+ - For systematic reviews, document that AI tools were used and how in your methods section
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+ - Monitor API costs when processing large collections of papers
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+ - Periodically review and update AI-generated notes as your understanding evolves
@@ -0,0 +1,213 @@
1
+ ---
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+ name: papis-cli-guide
3
+ description: "Guide to Papis command-line document and bibliography manager for researchers"
4
+ metadata:
5
+ openclaw:
6
+ emoji: "💻"
7
+ category: "writing"
8
+ subcategory: "citation"
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+ keywords: ["papis", "cli", "bibliography", "document-manager", "terminal", "command-line"]
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+ source: "https://github.com/papis/papis"
11
+ ---
12
+
13
+ # Papis CLI Document Manager Guide
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+
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+ ## Overview
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+
17
+ Papis is a powerful command-line document and bibliography manager with over 2,000 GitHub stars, designed for researchers who prefer terminal-based workflows. Written in Python, it provides a fast, scriptable, and highly customizable alternative to GUI-based reference managers like Zotero or Mendeley.
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+
19
+ The philosophy behind Papis is that bibliographic data should be stored in simple, human-readable files organized in a plain directory structure. Each document in a Papis library is a folder containing a YAML metadata file (`info.yaml`) and associated files (PDFs, supplementary materials, notes). This approach means your library is inherently portable, versionable with Git, and accessible through any tool that can read files and directories.
20
+
21
+ For researchers who spend most of their time in terminals, use Vim or Emacs for writing, and prefer scriptable tools over graphical interfaces, Papis offers a natural fit. It integrates with academic databases for metadata retrieval, supports BibTeX and BibLaTeX export, and provides an extensible plugin system for custom workflows. Despite its command-line interface, Papis also includes optional GUI pickers and a web interface for when visual browsing is helpful.
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+
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+ ## Installation and Setup
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+
25
+ Install Papis using pip or your system package manager:
26
+
27
+ **Via pip (recommended)**:
28
+ ```bash
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+ pip install papis
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+ ```
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+
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+ **Via system package managers**:
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+ - macOS: `brew install papis`
34
+ - Arch Linux: `pacman -S papis`
35
+ - Nix: `nix-env -i papis`
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+
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+ **Initial configuration**: Papis stores its configuration in `~/.config/papis/config`. Create a minimal configuration:
38
+
39
+ ```ini
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+ [settings]
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+ default-library = research
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+
43
+ [research]
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+ dir = ~/Documents/papers
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+ ```
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+
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+ This tells Papis to manage a library called "research" stored in `~/Documents/papers`. Each document you add will create a subdirectory within this path containing the document file and metadata.
48
+
49
+ **Additional configuration options**:
50
+ ```ini
51
+ [settings]
52
+ default-library = research
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+ editor = vim
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+ file-browser = open
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+ picktool = papis.pick
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+ database-backend = papis
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+
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+ [research]
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+ dir = ~/Documents/papers
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+ use-cache = True
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+
62
+ [books]
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+ dir = ~/Documents/books
64
+ ```
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+
66
+ You can define multiple libraries (research papers, books, technical reports) each with their own directory and configuration.
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+
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+ ## Core Features
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+
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+ **Adding Documents**: Add papers to your library from multiple sources:
71
+
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+ ```bash
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+ # Add a PDF with automatic metadata retrieval via DOI
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+ papis add paper.pdf --from doi 10.1038/s41586-024-07487-w
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+
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+ # Add from arXiv identifier
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+ papis add --from arxiv 2401.12345
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+
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+ # Add from a BibTeX file
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+ papis add paper.pdf --from bibtex reference.bib
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+
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+ # Add with manual metadata
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+ papis add paper.pdf --set author "Smith, John" --set title "Deep Learning" --set year 2024
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+
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+ # Add from ISBN (for books)
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+ papis add book.pdf --from isbn 978-0-13-468599-1
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+ ```
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+
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+ **Searching and Browsing**: Query your library with flexible search:
90
+
91
+ ```bash
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+ # Search by any field
93
+ papis open "author:smith AND year:2024"
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+
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+ # List matching documents
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+ papis list "machine learning"
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+
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+ # Browse with an interactive picker
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+ papis browse "neural networks"
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+
101
+ # Export search results as BibTeX
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+ papis export --format bibtex "deep learning 2024"
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+ ```
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+
105
+ **Document Operations**:
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+
107
+ ```bash
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+ # Open the PDF of a document
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+ papis open "smith 2024"
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+
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+ # Edit metadata in your configured editor
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+ papis edit "smith 2024"
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+
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+ # Rename and organize files
115
+ papis rename "smith 2024"
116
+
117
+ # Remove a document
118
+ papis rm "old paper 2015"
119
+
120
+ # Move between libraries
121
+ papis mv --lib books "programming textbook"
122
+ ```
123
+
124
+ **BibTeX Export**: Generate BibTeX files for LaTeX projects:
125
+
126
+ ```bash
127
+ # Export entire library
128
+ papis export --all --format bibtex > references.bib
129
+
130
+ # Export specific entries
131
+ papis export --format bibtex "author:smith" >> project.bib
132
+
133
+ # Export in BibLaTeX format
134
+ papis export --format biblatex "machine learning" > ml-refs.bib
135
+ ```
136
+
137
+ **Metadata Retrieval**: Fetch or update metadata from online sources:
138
+
139
+ ```bash
140
+ # Update metadata from DOI
141
+ papis update --from doi "smith 2024"
142
+
143
+ # Fetch metadata from CrossRef
144
+ papis update --from crossref "incomplete entry"
145
+
146
+ # Bulk update metadata for all items missing DOIs
147
+ papis update --from crossref --all
148
+ ```
149
+
150
+ ## Academic Workflow Integration
151
+
152
+ **Terminal-Centric Research Workflow**:
153
+
154
+ 1. **Discovery**: Find a paper, download the PDF
155
+ 2. **Import**: `papis add paper.pdf --from doi 10.xxxx/xxxxx`
156
+ 3. **Read**: `papis open "paper title"` to open in your PDF viewer
157
+ 4. **Annotate**: Add notes directly to the info.yaml or in a separate notes file
158
+ 5. **Cite**: `papis export --format bibtex "paper title" >> thesis.bib`
159
+ 6. **Write**: Reference in your LaTeX/Markdown document
160
+
161
+ **Version Control Integration**: Since Papis stores everything as files and directories, you can version your entire library with Git:
162
+
163
+ ```bash
164
+ cd ~/Documents/papers
165
+ git init
166
+ git add .
167
+ git commit -m "Initial library snapshot"
168
+ ```
169
+
170
+ This gives you full history of metadata changes, the ability to sync across machines, and collaborative library management through Git workflows.
171
+
172
+ **Scripting and Automation**: Papis exposes a Python API for custom scripts:
173
+
174
+ ```python
175
+ import papis.api
176
+
177
+ # Search the library programmatically
178
+ docs = papis.api.get_documents_in_lib("research")
179
+ ml_papers = [d for d in docs if "machine learning" in d.get("tags", "")]
180
+
181
+ # Export filtered results
182
+ for doc in ml_papers:
183
+ print(f"{doc['author']} ({doc['year']}). {doc['title']}")
184
+ ```
185
+
186
+ **Integration with Text Editors**:
187
+ - **Vim**: Use `papis.vim` plugin for searching and inserting citations without leaving the editor
188
+ - **Emacs**: Use `papis.el` for Org-mode and LaTeX integration
189
+ - **FZF**: Pipe Papis output to fzf for fuzzy finding: `papis list --all | fzf`
190
+
191
+ **Syncing Across Machines**: Use any file synchronization tool (Syncthing, rsync, cloud storage) or Git to keep your Papis library consistent across workstations. The plain-file storage format ensures compatibility regardless of platform.
192
+
193
+ ## Plugin Ecosystem
194
+
195
+ Papis supports plugins for extended functionality:
196
+
197
+ - **papis-rofi**: Rofi-based document picker for Linux desktop users
198
+ - **papis-zotero**: Import your existing Zotero library into Papis
199
+ - **papis-firefox**: Browser extension for adding papers from web pages
200
+ - **papis-libgen**: Search and download from Library Genesis (for open-access content)
201
+
202
+ Install plugins via pip:
203
+ ```bash
204
+ pip install papis-zotero
205
+ papis zotero import --from-bibtex zotero-export.bib
206
+ ```
207
+
208
+ ## References
209
+
210
+ - GitHub Repository: https://github.com/papis/papis
211
+ - Papis Documentation: https://papis.readthedocs.io
212
+ - Papis Wiki: https://github.com/papis/papis/wiki
213
+ - PyPI Package: https://pypi.org/project/papis
@@ -0,0 +1,107 @@
1
+ ---
2
+ name: zotero-better-bibtex-guide
3
+ description: "Guide to Better BibTeX for Zotero for LaTeX and BibTeX workflows"
4
+ metadata:
5
+ openclaw:
6
+ emoji: "📚"
7
+ category: "writing"
8
+ subcategory: "citation"
9
+ keywords: ["zotero", "bibtex", "latex", "citation-keys", "better-bibtex", "bibliography"]
10
+ source: "https://github.com/retorquere/zotero-better-bibtex"
11
+ ---
12
+
13
+ # Better BibTeX for Zotero Guide
14
+
15
+ ## Overview
16
+
17
+ Better BibTeX (BBT) is an essential Zotero plugin for any researcher who uses LaTeX, BibTeX, or BibLaTeX for academic writing. With over 6,000 GitHub stars, it bridges the gap between Zotero's powerful reference management and the precise citation requirements of LaTeX-based document preparation systems.
18
+
19
+ The core problem BBT solves is citation key management. Standard Zotero export generates citation keys that can change unpredictably when library items are modified, breaking references in LaTeX documents. Better BibTeX provides stable, customizable citation keys that remain consistent across exports, ensuring your LaTeX documents always compile correctly with up-to-date bibliographic data.
20
+
21
+ Beyond citation keys, BBT offers superior BibTeX and BibLaTeX export with fine-grained control over field mapping, character encoding, and format compliance. It supports automatic export that keeps your `.bib` files synchronized with your Zotero library in real time, eliminating the manual export step from the writing workflow entirely.
22
+
23
+ ## Installation and Setup
24
+
25
+ Install Better BibTeX through Zotero's add-on mechanism:
26
+
27
+ 1. Download the latest `.xpi` file from https://github.com/retorquere/zotero-better-bibtex/releases
28
+ 2. In Zotero, go to Tools > Add-ons > gear icon > Install Add-on From File
29
+ 3. Select the downloaded `.xpi` file and restart Zotero
30
+ 4. On first launch after installation, BBT will scan your library and generate citation keys
31
+
32
+ Configure citation key generation:
33
+
34
+ - Open Zotero Preferences > Better BibTeX > Citation Keys
35
+ - Set the citation key formula (default is `auth.lower + year`):
36
+ - `auth.lower + year` produces keys like `smith2024`
37
+ - `authEtal2.lower + year` produces `smithjones2024` or `smithetal2024`
38
+ - `auth.lower + shorttitle(3,3) + year` produces `smith.wor.thr.2024`
39
+ - Enable "Keep citation keys unique" to automatically resolve conflicts
40
+ - Choose conflict resolution strategy (postfix with letter, number, etc.)
41
+
42
+ Configure export settings:
43
+
44
+ - Go to Preferences > Better BibTeX > Export
45
+ - Select your preferred export format (BibLaTeX recommended for modern setups)
46
+ - Configure field mapping for custom fields
47
+ - Set Unicode handling (recommended: convert to LaTeX commands for maximum compatibility)
48
+ - Enable "Automatic export" to keep `.bib` files synchronized
49
+
50
+ ## Core Features
51
+
52
+ **Stable Citation Keys**: BBT generates predictable citation keys based on configurable patterns. Once a key is assigned, it remains stable even when you edit item metadata. You can also pin specific citation keys to override the automatic generation when needed.
53
+
54
+ **Citation Key Formulas**: The formula system is highly flexible:
55
+
56
+ | Formula | Example Output | Use Case |
57
+ |---------|---------------|----------|
58
+ | `auth.lower + year` | `smith2024` | Simple, common convention |
59
+ | `auth.lower + journal.abbr + year` | `smithnature2024` | Disambiguate by journal |
60
+ | `auth.lower + shorttitle(1,1) + year` | `smith.deep.2024` | Include title fragment |
61
+ | `auth(2).lower + year` | `smjo2024` | Short keys, multiple authors |
62
+
63
+ **Automatic Export**: Set up a Zotero collection or your entire library to automatically export to a `.bib` file whenever changes are made. This means your LaTeX project always has access to the latest bibliography data without manual intervention.
64
+
65
+ To set up automatic export:
66
+ 1. Right-click a collection in Zotero
67
+ 2. Select "Export Collection"
68
+ 3. Choose "Better BibTeX" or "Better BibLaTeX" format
69
+ 4. Check "Keep updated" to enable auto-sync
70
+ 5. Choose the target file path (typically in your LaTeX project directory)
71
+
72
+ **Pull Export via HTTP**: BBT runs a local HTTP server that serves your bibliography on demand. Configure your LaTeX build system to pull the latest `.bib` file from `http://127.0.0.1:23119/better-bibtex/export/collection?...` before each compilation.
73
+
74
+ **Quality Reports**: BBT checks your bibliography entries for common issues such as missing fields, encoding problems, and duplicate entries. Review the quality report to ensure your bibliography meets journal submission standards.
75
+
76
+ **Drag-and-Drop Citations**: Drag items from Zotero into your text editor to insert formatted citation commands. BBT supports multiple formats including `\cite{key}`, `\autocite{key}`, `\textcite{key}`, and Pandoc-style `[@key]`.
77
+
78
+ ## LaTeX Integration Workflow
79
+
80
+ **Project Setup**:
81
+ 1. Create a Zotero collection for your paper or project
82
+ 2. Set up automatic export to a `.bib` file in your LaTeX project directory
83
+ 3. Add `\bibliography{references}` or `\addbibresource{references.bib}` to your LaTeX document
84
+ 4. Use `\cite{citekey}` commands throughout your document
85
+
86
+ **Working with Overleaf**: If using Overleaf, set up a periodic manual export or use the pull export feature with a build script that fetches the latest bibliography before uploading. Some researchers maintain a Git repository that includes both the LaTeX source and the auto-exported `.bib` file.
87
+
88
+ **Multi-Author Projects**: For collaborative projects, establish a shared Zotero group library with BBT configured consistently across all collaborators. Agree on a citation key formula so that keys are predictable regardless of who adds the reference.
89
+
90
+ **Handling Key Conflicts**: When two papers produce the same citation key (e.g., two Smith 2024 papers), BBT automatically appends a disambiguation suffix. You can manually pin a specific key by right-clicking an item and selecting "Better BibTeX > Pin citation key."
91
+
92
+ **Integration with Reference Checkers**: Use BBT's quality reports alongside tools like `biber --validate-datamodel` to ensure your bibliography is complete and well-formed before journal submission.
93
+
94
+ ## Troubleshooting
95
+
96
+ **Export File Not Updating**: Verify that automatic export is enabled for the collection. Check the BBT debug log (Help > Better BibTeX Debug Log) for export errors. Ensure the target directory is writable.
97
+
98
+ **Unicode Characters in Keys**: If citation keys contain unexpected characters, review your key formula. Use `.fold` in the formula to transliterate Unicode characters to ASCII equivalents.
99
+
100
+ **Large Library Performance**: For libraries with thousands of items, the initial citation key generation may take several minutes. Subsequent operations are incremental and fast. Consider disabling automatic export for very large collections and using scheduled exports instead.
101
+
102
+ ## References
103
+
104
+ - GitHub Repository: https://github.com/retorquere/zotero-better-bibtex
105
+ - BBT Documentation: https://retorque.re/zotero-better-bibtex/
106
+ - Citation Key Formulas: https://retorque.re/zotero-better-bibtex/citing/
107
+ - Zotero Plugin Directory: https://www.zotero.org/support/plugins
@@ -0,0 +1,121 @@
1
+ ---
2
+ name: zotero-better-notes-guide
3
+ description: "Guide to Zotero Better Notes for comprehensive note-taking in research"
4
+ metadata:
5
+ openclaw:
6
+ emoji: "📝"
7
+ category: "writing"
8
+ subcategory: "citation"
9
+ keywords: ["zotero", "note-taking", "better-notes", "research-notes", "knowledge-management"]
10
+ source: "https://github.com/windingwind/zotero-better-notes"
11
+ ---
12
+
13
+ # Zotero Better Notes Guide
14
+
15
+ ## Overview
16
+
17
+ Zotero Better Notes transforms Zotero from a reference manager into a full-featured research knowledge management system. With over 7,000 GitHub stars, it is one of the most popular Zotero plugins, addressing a critical gap in the academic workflow: the connection between reading papers and building structured knowledge.
18
+
19
+ The plugin introduces a powerful note editor with bidirectional linking, templates, and syncing capabilities directly within Zotero. Instead of jumping between Zotero and external note-taking applications like Obsidian or Notion, researchers can maintain their notes alongside the papers they reference, preserving the tight coupling between sources and ideas.
20
+
21
+ Better Notes supports Markdown editing, note templates, outline views, and export to external systems. It integrates with Zotero's annotation system so that highlights and comments made while reading PDFs can flow directly into structured notes. This creates a seamless pipeline from reading to writing that significantly reduces friction in the research process.
22
+
23
+ ## Installation and Setup
24
+
25
+ Install Better Notes through the standard Zotero add-on mechanism:
26
+
27
+ 1. Download the latest `.xpi` release from https://github.com/windingwind/zotero-better-notes/releases
28
+ 2. In Zotero, go to Tools > Add-ons > gear icon > Install Add-on From File
29
+ 3. Select the `.xpi` file and restart Zotero
30
+
31
+ Initial configuration steps:
32
+
33
+ - Open Zotero Preferences > Better Notes
34
+ - Set your preferred note template directory (a local folder for custom templates)
35
+ - Configure the default note template for new notes
36
+ - Enable or disable auto-insert of annotations into linked notes
37
+ - Set up sync preferences if you want notes to export to an external folder
38
+ - Choose your preferred Markdown editor behavior and keyboard shortcuts
39
+
40
+ For researchers using external knowledge bases, configure the sync feature:
41
+
42
+ - Set a sync target directory (e.g., your Obsidian vault or a shared folder)
43
+ - Choose the sync format (Markdown with YAML frontmatter recommended)
44
+ - Configure auto-sync frequency or use manual sync triggers
45
+ - Map Zotero fields to frontmatter keys for consistent metadata
46
+
47
+ ## Core Features
48
+
49
+ **Enhanced Note Editor**: Better Notes replaces the default Zotero note editor with a Markdown-capable editor that supports rich formatting, code blocks, mathematical notation, tables, and more. The editor provides a live preview mode and an outline panel for navigating long notes.
50
+
51
+ **Note Templates**: Create and manage reusable note templates for different types of research activities:
52
+ - Paper reading templates with sections for summary, methods, findings, and critique
53
+ - Literature review templates that aggregate information across multiple papers
54
+ - Meeting notes templates for lab meetings and conference sessions
55
+ - Project planning templates with task tracking and milestone sections
56
+
57
+ Templates support dynamic variables that auto-populate with item metadata:
58
+
59
+ ```
60
+ # ${title}
61
+ **Authors**: ${authors}
62
+ **Year**: ${year}
63
+ **Journal**: ${publicationTitle}
64
+
65
+ ## Summary
66
+
67
+ ## Methods
68
+
69
+ ## Key Findings
70
+
71
+ ## Relevance to My Research
72
+ ```
73
+
74
+ **Bidirectional Linking**: Create links between notes using a wiki-style `[[note title]]` syntax. This builds a knowledge graph within your Zotero library, allowing you to trace connections between concepts, papers, and ideas. The backlinks panel shows all notes that reference the current note.
75
+
76
+ **Annotation Integration**: When you highlight text or add comments in the Zotero PDF reader, Better Notes can automatically insert these annotations into a designated note for that item. Annotations are formatted with citation links back to the exact page and location in the PDF.
77
+
78
+ **Outline View**: A dedicated outline panel displays the heading structure of your current note, providing quick navigation for long documents. This is especially useful for literature review notes that may span dozens of pages.
79
+
80
+ **Note Export and Sync**: Export notes as Markdown files to any directory on your system. The sync feature can automatically keep an external folder up to date with your Zotero notes, enabling integration with tools like Obsidian, Logseq, or any Markdown-based system.
81
+
82
+ ## Research Workflow Integration
83
+
84
+ **Phase 1 - Paper Reading**: When you begin reading a paper, create a new note from your reading template. As you read in the Zotero PDF reader, your highlights and annotations automatically flow into the note. Add your own commentary and analysis in the appropriate template sections.
85
+
86
+ **Phase 2 - Knowledge Synthesis**: After reading multiple papers on a topic, create a synthesis note that links to individual paper notes using bidirectional links. Use the template system to structure your synthesis with sections for themes, contradictions, gaps, and your own contributions.
87
+
88
+ **Phase 3 - Writing Preparation**: When preparing to write, use the outline view to organize your synthesis notes into a logical argument structure. Export relevant notes to your writing environment, maintaining citation links that can be converted to formal references.
89
+
90
+ **Phase 4 - Collaboration**: Share exported notes with collaborators through synced folders. The Markdown format ensures compatibility across different tools and platforms, while Zotero citation keys maintain the connection to the original sources.
91
+
92
+ **Best Practices for Note Organization**:
93
+ - Use a consistent naming convention for notes (e.g., `@citekey - title`)
94
+ - Create index notes for major research themes that link to related paper notes
95
+ - Review and update your knowledge graph regularly to maintain connections
96
+ - Use tags in notes to create cross-cutting categories beyond the folder structure
97
+ - Periodically export and backup your notes to guard against data loss
98
+
99
+ ## Advanced Template Customization
100
+
101
+ Better Notes templates support JavaScript expressions for dynamic content generation:
102
+
103
+ ```
104
+ # Reading Notes: ${title}
105
+
106
+ **Date Read**: ${new Date().toISOString().split('T')[0]}
107
+ **Item Type**: ${itemType}
108
+ **DOI**: ${DOI}
109
+
110
+ ## Quick Reference
111
+ - **Citation**: ${authors} (${year}). ${title}. *${publicationTitle}*.
112
+ ```
113
+
114
+ You can create template collections for different research activities and switch between them from the note creation dialog. Templates can also include conditional sections that only appear when certain metadata fields are present.
115
+
116
+ ## References
117
+
118
+ - GitHub Repository: https://github.com/windingwind/zotero-better-notes
119
+ - Better Notes Documentation: https://github.com/windingwind/zotero-better-notes/wiki
120
+ - Zotero Plugin Directory: https://www.zotero.org/support/plugins
121
+ - Zettelkasten Method for Researchers: https://zettelkasten.de/introduction