@synsci/cli-darwin-x64-baseline 1.1.76 → 1.1.78

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 (830) hide show
  1. package/bin/skills/adaptyv/SKILL.md +114 -0
  2. package/bin/skills/adaptyv/reference/api_reference.md +308 -0
  3. package/bin/skills/adaptyv/reference/examples.md +913 -0
  4. package/bin/skills/adaptyv/reference/experiments.md +360 -0
  5. package/bin/skills/adaptyv/reference/protein_optimization.md +637 -0
  6. package/bin/skills/aeon/SKILL.md +374 -0
  7. package/bin/skills/aeon/references/anomaly_detection.md +154 -0
  8. package/bin/skills/aeon/references/classification.md +144 -0
  9. package/bin/skills/aeon/references/clustering.md +123 -0
  10. package/bin/skills/aeon/references/datasets_benchmarking.md +387 -0
  11. package/bin/skills/aeon/references/distances.md +256 -0
  12. package/bin/skills/aeon/references/forecasting.md +140 -0
  13. package/bin/skills/aeon/references/networks.md +289 -0
  14. package/bin/skills/aeon/references/regression.md +118 -0
  15. package/bin/skills/aeon/references/segmentation.md +163 -0
  16. package/bin/skills/aeon/references/similarity_search.md +187 -0
  17. package/bin/skills/aeon/references/transformations.md +246 -0
  18. package/bin/skills/alphafold-database/SKILL.md +513 -0
  19. package/bin/skills/alphafold-database/references/api_reference.md +423 -0
  20. package/bin/skills/anndata/SKILL.md +400 -0
  21. package/bin/skills/anndata/references/best_practices.md +525 -0
  22. package/bin/skills/anndata/references/concatenation.md +396 -0
  23. package/bin/skills/anndata/references/data_structure.md +314 -0
  24. package/bin/skills/anndata/references/io_operations.md +404 -0
  25. package/bin/skills/anndata/references/manipulation.md +516 -0
  26. package/bin/skills/arboreto/SKILL.md +243 -0
  27. package/bin/skills/arboreto/references/algorithms.md +138 -0
  28. package/bin/skills/arboreto/references/basic_inference.md +151 -0
  29. package/bin/skills/arboreto/references/distributed_computing.md +242 -0
  30. package/bin/skills/arboreto/scripts/basic_grn_inference.py +97 -0
  31. package/bin/skills/astropy/SKILL.md +331 -0
  32. package/bin/skills/astropy/references/coordinates.md +273 -0
  33. package/bin/skills/astropy/references/cosmology.md +307 -0
  34. package/bin/skills/astropy/references/fits.md +396 -0
  35. package/bin/skills/astropy/references/tables.md +489 -0
  36. package/bin/skills/astropy/references/time.md +404 -0
  37. package/bin/skills/astropy/references/units.md +178 -0
  38. package/bin/skills/astropy/references/wcs_and_other_modules.md +373 -0
  39. package/bin/skills/benchling-integration/SKILL.md +480 -0
  40. package/bin/skills/benchling-integration/references/api_endpoints.md +883 -0
  41. package/bin/skills/benchling-integration/references/authentication.md +379 -0
  42. package/bin/skills/benchling-integration/references/sdk_reference.md +774 -0
  43. package/bin/skills/biopython/SKILL.md +443 -0
  44. package/bin/skills/biopython/references/advanced.md +577 -0
  45. package/bin/skills/biopython/references/alignment.md +362 -0
  46. package/bin/skills/biopython/references/blast.md +455 -0
  47. package/bin/skills/biopython/references/databases.md +484 -0
  48. package/bin/skills/biopython/references/phylogenetics.md +566 -0
  49. package/bin/skills/biopython/references/sequence_io.md +285 -0
  50. package/bin/skills/biopython/references/structure.md +564 -0
  51. package/bin/skills/biorxiv-database/SKILL.md +483 -0
  52. package/bin/skills/biorxiv-database/references/api_reference.md +280 -0
  53. package/bin/skills/biorxiv-database/scripts/biorxiv_search.py +445 -0
  54. package/bin/skills/bioservices/SKILL.md +361 -0
  55. package/bin/skills/bioservices/references/identifier_mapping.md +685 -0
  56. package/bin/skills/bioservices/references/services_reference.md +636 -0
  57. package/bin/skills/bioservices/references/workflow_patterns.md +811 -0
  58. package/bin/skills/bioservices/scripts/batch_id_converter.py +347 -0
  59. package/bin/skills/bioservices/scripts/compound_cross_reference.py +378 -0
  60. package/bin/skills/bioservices/scripts/pathway_analysis.py +309 -0
  61. package/bin/skills/bioservices/scripts/protein_analysis_workflow.py +408 -0
  62. package/bin/skills/brenda-database/SKILL.md +719 -0
  63. package/bin/skills/brenda-database/references/api_reference.md +537 -0
  64. package/bin/skills/brenda-database/scripts/brenda_queries.py +844 -0
  65. package/bin/skills/brenda-database/scripts/brenda_visualization.py +772 -0
  66. package/bin/skills/brenda-database/scripts/enzyme_pathway_builder.py +1053 -0
  67. package/bin/skills/cellxgene-census/SKILL.md +511 -0
  68. package/bin/skills/cellxgene-census/references/census_schema.md +182 -0
  69. package/bin/skills/cellxgene-census/references/common_patterns.md +351 -0
  70. package/bin/skills/chembl-database/SKILL.md +389 -0
  71. package/bin/skills/chembl-database/references/api_reference.md +272 -0
  72. package/bin/skills/chembl-database/scripts/example_queries.py +278 -0
  73. package/bin/skills/cirq/SKILL.md +346 -0
  74. package/bin/skills/cirq/references/building.md +307 -0
  75. package/bin/skills/cirq/references/experiments.md +572 -0
  76. package/bin/skills/cirq/references/hardware.md +515 -0
  77. package/bin/skills/cirq/references/noise.md +515 -0
  78. package/bin/skills/cirq/references/simulation.md +350 -0
  79. package/bin/skills/cirq/references/transformation.md +416 -0
  80. package/bin/skills/clinicaltrials-database/SKILL.md +507 -0
  81. package/bin/skills/clinicaltrials-database/references/api_reference.md +358 -0
  82. package/bin/skills/clinicaltrials-database/scripts/query_clinicaltrials.py +215 -0
  83. package/bin/skills/clinpgx-database/SKILL.md +638 -0
  84. package/bin/skills/clinpgx-database/references/api_reference.md +757 -0
  85. package/bin/skills/clinpgx-database/scripts/query_clinpgx.py +518 -0
  86. package/bin/skills/clinvar-database/SKILL.md +362 -0
  87. package/bin/skills/clinvar-database/references/api_reference.md +227 -0
  88. package/bin/skills/clinvar-database/references/clinical_significance.md +218 -0
  89. package/bin/skills/clinvar-database/references/data_formats.md +358 -0
  90. package/bin/skills/cobrapy/SKILL.md +463 -0
  91. package/bin/skills/cobrapy/references/api_quick_reference.md +655 -0
  92. package/bin/skills/cobrapy/references/workflows.md +593 -0
  93. package/bin/skills/cosmic-database/SKILL.md +336 -0
  94. package/bin/skills/cosmic-database/references/cosmic_data_reference.md +220 -0
  95. package/bin/skills/cosmic-database/scripts/download_cosmic.py +231 -0
  96. package/bin/skills/dask/SKILL.md +456 -0
  97. package/bin/skills/dask/references/arrays.md +497 -0
  98. package/bin/skills/dask/references/bags.md +468 -0
  99. package/bin/skills/dask/references/best-practices.md +277 -0
  100. package/bin/skills/dask/references/dataframes.md +368 -0
  101. package/bin/skills/dask/references/futures.md +541 -0
  102. package/bin/skills/dask/references/schedulers.md +504 -0
  103. package/bin/skills/datacommons-client/SKILL.md +255 -0
  104. package/bin/skills/datacommons-client/references/getting_started.md +417 -0
  105. package/bin/skills/datacommons-client/references/node.md +250 -0
  106. package/bin/skills/datacommons-client/references/observation.md +185 -0
  107. package/bin/skills/datacommons-client/references/resolve.md +246 -0
  108. package/bin/skills/datamol/SKILL.md +706 -0
  109. package/bin/skills/datamol/references/conformers_module.md +131 -0
  110. package/bin/skills/datamol/references/core_api.md +130 -0
  111. package/bin/skills/datamol/references/descriptors_viz.md +195 -0
  112. package/bin/skills/datamol/references/fragments_scaffolds.md +174 -0
  113. package/bin/skills/datamol/references/io_module.md +109 -0
  114. package/bin/skills/datamol/references/reactions_data.md +218 -0
  115. package/bin/skills/deepchem/SKILL.md +597 -0
  116. package/bin/skills/deepchem/references/api_reference.md +303 -0
  117. package/bin/skills/deepchem/references/workflows.md +491 -0
  118. package/bin/skills/deepchem/scripts/graph_neural_network.py +338 -0
  119. package/bin/skills/deepchem/scripts/predict_solubility.py +224 -0
  120. package/bin/skills/deepchem/scripts/transfer_learning.py +375 -0
  121. package/bin/skills/deeptools/SKILL.md +531 -0
  122. package/bin/skills/deeptools/assets/quick_reference.md +58 -0
  123. package/bin/skills/deeptools/references/effective_genome_sizes.md +116 -0
  124. package/bin/skills/deeptools/references/normalization_methods.md +410 -0
  125. package/bin/skills/deeptools/references/tools_reference.md +533 -0
  126. package/bin/skills/deeptools/references/workflows.md +474 -0
  127. package/bin/skills/deeptools/scripts/validate_files.py +195 -0
  128. package/bin/skills/deeptools/scripts/workflow_generator.py +454 -0
  129. package/bin/skills/denario/SKILL.md +215 -0
  130. package/bin/skills/denario/references/examples.md +494 -0
  131. package/bin/skills/denario/references/installation.md +213 -0
  132. package/bin/skills/denario/references/llm_configuration.md +265 -0
  133. package/bin/skills/denario/references/research_pipeline.md +471 -0
  134. package/bin/skills/diffdock/SKILL.md +483 -0
  135. package/bin/skills/diffdock/assets/batch_template.csv +4 -0
  136. package/bin/skills/diffdock/assets/custom_inference_config.yaml +90 -0
  137. package/bin/skills/diffdock/references/confidence_and_limitations.md +182 -0
  138. package/bin/skills/diffdock/references/parameters_reference.md +163 -0
  139. package/bin/skills/diffdock/references/workflows_examples.md +392 -0
  140. package/bin/skills/diffdock/scripts/analyze_results.py +334 -0
  141. package/bin/skills/diffdock/scripts/prepare_batch_csv.py +254 -0
  142. package/bin/skills/diffdock/scripts/setup_check.py +278 -0
  143. package/bin/skills/dnanexus-integration/SKILL.md +383 -0
  144. package/bin/skills/dnanexus-integration/references/app-development.md +247 -0
  145. package/bin/skills/dnanexus-integration/references/configuration.md +646 -0
  146. package/bin/skills/dnanexus-integration/references/data-operations.md +400 -0
  147. package/bin/skills/dnanexus-integration/references/job-execution.md +412 -0
  148. package/bin/skills/dnanexus-integration/references/python-sdk.md +523 -0
  149. package/bin/skills/document-skills/docx/LICENSE.txt +30 -0
  150. package/bin/skills/document-skills/docx/SKILL.md +233 -0
  151. package/bin/skills/document-skills/docx/docx-js.md +350 -0
  152. package/bin/skills/document-skills/docx/ooxml/schemas/ISO-IEC29500-4_2016/dml-chart.xsd +1499 -0
  153. package/bin/skills/document-skills/docx/ooxml/schemas/ISO-IEC29500-4_2016/dml-chartDrawing.xsd +146 -0
  154. package/bin/skills/document-skills/docx/ooxml/schemas/ISO-IEC29500-4_2016/dml-diagram.xsd +1085 -0
  155. package/bin/skills/document-skills/docx/ooxml/schemas/ISO-IEC29500-4_2016/dml-lockedCanvas.xsd +11 -0
  156. package/bin/skills/document-skills/docx/ooxml/schemas/ISO-IEC29500-4_2016/dml-main.xsd +3081 -0
  157. package/bin/skills/document-skills/docx/ooxml/schemas/ISO-IEC29500-4_2016/dml-picture.xsd +23 -0
  158. package/bin/skills/document-skills/docx/ooxml/schemas/ISO-IEC29500-4_2016/dml-spreadsheetDrawing.xsd +185 -0
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  160. package/bin/skills/document-skills/docx/ooxml/schemas/ISO-IEC29500-4_2016/pml.xsd +1676 -0
  161. package/bin/skills/document-skills/docx/ooxml/schemas/ISO-IEC29500-4_2016/shared-additionalCharacteristics.xsd +28 -0
  162. package/bin/skills/document-skills/docx/ooxml/schemas/ISO-IEC29500-4_2016/shared-bibliography.xsd +144 -0
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  193. package/bin/skills/document-skills/docx/ooxml/scripts/validate.py +69 -0
  194. package/bin/skills/document-skills/docx/ooxml/scripts/validation/__init__.py +15 -0
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1
+ # Additional USPTO APIs Reference
2
+
3
+ ## Overview
4
+
5
+ Beyond patent search, PEDS, and trademarks, USPTO provides specialized APIs for citations, office actions, assignments, litigation, and other patent data.
6
+
7
+ ## 1. Enriched Citation API
8
+
9
+ ### Overview
10
+
11
+ Provides insights into patent evaluation processes and cited references for the IP5 (USPTO, EPO, JPO, KIPO, CNIPA) and public use.
12
+
13
+ **Versions:** v3, v2, v1
14
+
15
+ **Base URL:** Access through USPTO Open Data Portal
16
+
17
+ ### Purpose
18
+
19
+ Analyze which references examiners cite during patent examination and how patents cite prior art.
20
+
21
+ ### Key Features
22
+
23
+ - **Forward citations** - Patents that cite a given patent
24
+ - **Backward citations** - References cited by a patent
25
+ - **Examiner citations** - References cited by examiner vs. applicant
26
+ - **Citation context** - How and why references are cited
27
+
28
+ ### Use Cases
29
+
30
+ - Prior art analysis
31
+ - Patent landscape analysis
32
+ - Identifying related technologies
33
+ - Assessing patent strength based on citations
34
+
35
+ ## 2. Office Action APIs
36
+
37
+ ### 2.1 Office Action Text Retrieval API
38
+
39
+ **Version:** v1
40
+
41
+ ### Purpose
42
+
43
+ Retrieves complete full-text office action correspondence documents for patent applications.
44
+
45
+ ### Features
46
+
47
+ - Full text of office actions
48
+ - Restrictions, rejections, objections
49
+ - Examiner amendments
50
+ - Search information
51
+
52
+ ### Example Use
53
+
54
+ ```python
55
+ # Retrieve office action text by application number
56
+ def get_office_action_text(app_number, api_key):
57
+ """
58
+ Fetch full text of office actions for an application.
59
+ Note: Integrate with PEDS to identify which office actions exist.
60
+ """
61
+ # API implementation
62
+ pass
63
+ ```
64
+
65
+ ### 2.2 Office Action Citations API
66
+
67
+ **Versions:** v2, beta v1
68
+
69
+ ### Purpose
70
+
71
+ Provides patent citation data extracted from office actions, showing which references examiners used during examination.
72
+
73
+ ### Key Data
74
+
75
+ - Patent and non-patent literature citations
76
+ - Citation context (rejection, information, etc.)
77
+ - Examiner search strategies
78
+ - Prosecution research dataset
79
+
80
+ ### 2.3 Office Action Rejection API
81
+
82
+ **Versions:** v2, beta v1
83
+
84
+ ### Purpose
85
+
86
+ Details rejection reasons and examination outcomes with bulk rejection data through March 2025.
87
+
88
+ ### Rejection Types
89
+
90
+ - **35 U.S.C. § 102** - Anticipation (lack of novelty)
91
+ - **35 U.S.C. § 103** - Obviousness
92
+ - **35 U.S.C. § 112** - Enablement, written description, indefiniteness
93
+ - **35 U.S.C. § 101** - Subject matter eligibility
94
+
95
+ ### Use Cases
96
+
97
+ - Analyze common rejection reasons
98
+ - Identify problematic claim language
99
+ - Prepare responses based on historical data
100
+ - Portfolio analysis of rejection patterns
101
+
102
+ ### 2.4 Office Action Weekly Zips API
103
+
104
+ **Version:** v1
105
+
106
+ ### Purpose
107
+
108
+ Delivers bulk downloads of full-text office action documents organized by weekly release schedules.
109
+
110
+ ### Features
111
+
112
+ - Weekly archive downloads
113
+ - Complete office action text
114
+ - Bulk access for large-scale analysis
115
+
116
+ ## 3. Patent Assignment Search API
117
+
118
+ ### Overview
119
+
120
+ **Version:** v1.4
121
+
122
+ Accesses USPTO patent assignment database for ownership records and transfers.
123
+
124
+ **Base URL:** `https://assignment-api.uspto.gov/patent/`
125
+
126
+ ### Purpose
127
+
128
+ Track patent ownership, assignments, security interests, and corporate transactions.
129
+
130
+ ### Search Methods
131
+
132
+ #### By Patent Number
133
+
134
+ ```
135
+ GET /v1.4/assignment/patent/{patent_number}
136
+ ```
137
+
138
+ #### By Application Number
139
+
140
+ ```
141
+ GET /v1.4/assignment/application/{application_number}
142
+ ```
143
+
144
+ #### By Assignee Name
145
+
146
+ ```
147
+ POST /v1.4/assignment/search
148
+ {
149
+ "criteria": {
150
+ "assigneeName": "Company Name"
151
+ }
152
+ }
153
+ ```
154
+
155
+ ### Response Format
156
+
157
+ Returns XML with assignment records similar to trademark assignments:
158
+
159
+ - Reel/frame numbers
160
+ - Conveyance type
161
+ - Dates (execution and recorded)
162
+ - Assignors and assignees
163
+ - Affected patents/applications
164
+
165
+ ### Common Uses
166
+
167
+ ```python
168
+ def track_patent_ownership(patent_number, api_key):
169
+ """Track ownership history of a patent."""
170
+ url = f"https://assignment-api.uspto.gov/patent/v1.4/assignment/patent/{patent_number}"
171
+ headers = {"X-Api-Key": api_key}
172
+
173
+ response = requests.get(url, headers=headers)
174
+ if response.status_code == 200:
175
+ # Parse XML to extract assignment history
176
+ return response.text
177
+ return None
178
+
179
+ def find_company_patents(company_name, api_key):
180
+ """Find patents assigned to a company."""
181
+ url = "https://assignment-api.uspto.gov/patent/v1.4/assignment/search"
182
+ headers = {"X-Api-Key": api_key}
183
+ data = {"criteria": {"assigneeName": company_name}}
184
+
185
+ response = requests.post(url, headers=headers, json=data)
186
+ return response.text
187
+ ```
188
+
189
+ ## 4. PTAB API (Patent Trial and Appeal Board)
190
+
191
+ ### Overview
192
+
193
+ **Version:** v2
194
+
195
+ Access to Patent Trial and Appeal Board proceedings data.
196
+
197
+ ### Purpose
198
+
199
+ Retrieve information about:
200
+ - Inter partes review (IPR)
201
+ - Post-grant review (PGR)
202
+ - Covered business method (CBM) review
203
+ - Ex parte appeals
204
+
205
+ ### Data Available
206
+
207
+ - Petition information
208
+ - Trial decisions
209
+ - Final written decisions
210
+ - Petitioner and patent owner information
211
+ - Claims challenged
212
+ - Trial outcomes
213
+
214
+ ### Note
215
+
216
+ Currently migrating to new Open Data Portal. Check current documentation for access details.
217
+
218
+ ## 5. Patent Litigation Cases API
219
+
220
+ ### Overview
221
+
222
+ **Version:** v1
223
+
224
+ Contains 74,623+ district court litigation records covering patent litigation data.
225
+
226
+ ### Purpose
227
+
228
+ Access federal district court patent infringement cases.
229
+
230
+ ### Key Data
231
+
232
+ - Case numbers and filing dates
233
+ - Patents asserted
234
+ - Parties (plaintiffs and defendants)
235
+ - Venues
236
+ - Case outcomes
237
+
238
+ ### Use Cases
239
+
240
+ - Litigation risk analysis
241
+ - Identify frequently litigated patents
242
+ - Track litigation trends
243
+ - Analyze venue preferences
244
+ - Assess patent enforcement patterns
245
+
246
+ ## 6. Cancer Moonshot Patent Data Set API
247
+
248
+ ### Overview
249
+
250
+ **Version:** v1.0.1
251
+
252
+ Specialized dataset for cancer-related patent discoveries.
253
+
254
+ ### Purpose
255
+
256
+ Search and download patents related to cancer research, treatment, and diagnostics.
257
+
258
+ ### Features
259
+
260
+ - Curated cancer-related patents
261
+ - Bulk data download
262
+ - Classification by cancer type
263
+ - Treatment modality categorization
264
+
265
+ ### Use Cases
266
+
267
+ - Cancer research prior art
268
+ - Technology landscape analysis
269
+ - Identify research trends
270
+ - Licensing opportunities
271
+
272
+ ## 7. OCE Patent Examination Status/Event Codes APIs
273
+
274
+ ### Overview
275
+
276
+ **Version:** v1
277
+
278
+ Provides official descriptions of USPTO status and event codes used in patent examination.
279
+
280
+ ### Purpose
281
+
282
+ Decode transaction codes and status codes found in PEDS and other examination data.
283
+
284
+ ### Data Provided
285
+
286
+ - **Status codes** - Application status descriptions
287
+ - **Event codes** - Transaction/event descriptions
288
+ - **Code definitions** - Official meanings
289
+
290
+ ### Integration
291
+
292
+ Use with PEDS data to interpret transaction codes:
293
+
294
+ ```python
295
+ def get_code_description(code, api_key):
296
+ """Get human-readable description of USPTO code."""
297
+ # Fetch from OCE API
298
+ pass
299
+
300
+ def enrich_peds_data(peds_transactions, api_key):
301
+ """Add descriptions to PEDS transaction codes."""
302
+ for trans in peds_transactions:
303
+ trans['description'] = get_code_description(trans['code'], api_key)
304
+ return peds_transactions
305
+ ```
306
+
307
+ ## API Integration Patterns
308
+
309
+ ### Combined Workflow Example
310
+
311
+ ```python
312
+ def comprehensive_patent_analysis(patent_number, api_key):
313
+ """
314
+ Comprehensive analysis combining multiple APIs.
315
+ """
316
+ results = {}
317
+
318
+ # 1. Get patent details from PatentSearch
319
+ results['patent_data'] = search_patent(patent_number, api_key)
320
+
321
+ # 2. Get examination history from PEDS
322
+ results['prosecution'] = get_peds_data(patent_number, api_key)
323
+
324
+ # 3. Get assignment history
325
+ results['assignments'] = get_assignments(patent_number, api_key)
326
+
327
+ # 4. Get citation data
328
+ results['citations'] = get_citations(patent_number, api_key)
329
+
330
+ # 5. Check litigation history
331
+ results['litigation'] = get_litigation(patent_number, api_key)
332
+
333
+ # 6. Get PTAB challenges
334
+ results['ptab'] = get_ptab_proceedings(patent_number, api_key)
335
+
336
+ return results
337
+ ```
338
+
339
+ ### Portfolio Analysis Example
340
+
341
+ ```python
342
+ def analyze_company_portfolio(company_name, api_key):
343
+ """
344
+ Analyze a company's patent portfolio using multiple APIs.
345
+ """
346
+ # 1. Find all assigned patents
347
+ assignments = find_company_patents(company_name, api_key)
348
+ patent_numbers = extract_patent_numbers(assignments)
349
+
350
+ # 2. Get details for each patent
351
+ portfolio = []
352
+ for patent_num in patent_numbers:
353
+ patent_data = {
354
+ 'number': patent_num,
355
+ 'details': search_patent(patent_num, api_key),
356
+ 'citations': get_citations(patent_num, api_key),
357
+ 'litigation': get_litigation(patent_num, api_key)
358
+ }
359
+ portfolio.append(patent_data)
360
+
361
+ # 3. Aggregate statistics
362
+ stats = {
363
+ 'total_patents': len(portfolio),
364
+ 'cited_by_count': sum(len(p['citations']) for p in portfolio),
365
+ 'litigated_count': sum(1 for p in portfolio if p['litigation']),
366
+ 'technology_areas': aggregate_tech_areas(portfolio)
367
+ }
368
+
369
+ return {'portfolio': portfolio, 'statistics': stats}
370
+ ```
371
+
372
+ ## Best Practices
373
+
374
+ 1. **API Key Management** - Use environment variables, never hardcode
375
+ 2. **Rate Limiting** - Implement exponential backoff for all APIs
376
+ 3. **Caching** - Cache API responses to minimize redundant calls
377
+ 4. **Error Handling** - Gracefully handle API errors and missing data
378
+ 5. **Data Validation** - Validate input formats before API calls
379
+ 6. **Combining APIs** - Use appropriate APIs together for comprehensive analysis
380
+ 7. **Documentation** - Keep track of API versions and changes
381
+
382
+ ## API Key Registration
383
+
384
+ All APIs require registration at:
385
+ **https://account.uspto.gov/api-manager/**
386
+
387
+ Single API key works across most USPTO APIs.
388
+
389
+ ## Resources
390
+
391
+ - **Developer Portal**: https://developer.uspto.gov/
392
+ - **Open Data Portal**: https://data.uspto.gov/
393
+ - **API Catalog**: https://developer.uspto.gov/api-catalog
394
+ - **Swagger Docs**: Available for individual APIs
@@ -0,0 +1,266 @@
1
+ # PatentSearch API Reference
2
+
3
+ ## Overview
4
+
5
+ The PatentSearch API is USPTO's modern ElasticSearch-based patent search system that replaced the legacy PatentsView API in May 2025. It provides access to patent data through June 30, 2025, with regular updates.
6
+
7
+ **Base URL:** `https://search.patentsview.org/api/v1/`
8
+
9
+ ## Authentication
10
+
11
+ All API requests require authentication using an API key in the request header:
12
+
13
+ ```
14
+ X-Api-Key: YOUR_API_KEY
15
+ ```
16
+
17
+ Register for an API key at: https://account.uspto.gov/api-manager/
18
+
19
+ ## Rate Limits
20
+
21
+ - **45 requests per minute** per API key
22
+ - Exceeding rate limits results in HTTP 429 errors
23
+
24
+ ## Available Endpoints
25
+
26
+ ### Core Patent & Publication Endpoints
27
+
28
+ - **`/patent`** - General patent data (granted patents)
29
+ - **`/publication`** - Pregrant publication data
30
+ - **`/publication/rel_app_text`** - Related application data for publications
31
+
32
+ ### Entity Endpoints
33
+
34
+ - **`/inventor`** - Inventor information with location and gender code fields
35
+ - **`/assignee`** - Assignee details with location identifiers
36
+ - **`/location`** - Geographic data including latitude/longitude coordinates
37
+ - **`/attorney`** - Legal representative information
38
+
39
+ ### Classification Endpoints
40
+
41
+ - **`/cpc_subclass`** - Cooperative Patent Classification at subclass level
42
+ - **`/cpc_at_issue`** - CPC classification as of patent issue date
43
+ - **`/uspc`** - US Patent Classification data
44
+ - **`/wipo`** - World Intellectual Property Organization classifications
45
+ - **`/ipc`** - International Patent Classification
46
+
47
+ ### Text Data Endpoints (Beta)
48
+
49
+ - **`/brief_summary_text`** - Patent brief summaries (granted and pre-grant)
50
+ - **`/claims`** - Patent claims text
51
+ - **`/drawing_description_text`** - Drawing descriptions
52
+ - **`/detail_description_text`** - Detailed description text
53
+
54
+ *Note: Text endpoints are in beta with data primarily from 2023 onward. Historical backfilling is in progress.*
55
+
56
+ ### Supporting Endpoints
57
+
58
+ - **`/other_reference`** - Patent reference materials
59
+ - **`/related_document`** - Cross-references between patents
60
+
61
+ ## Query Parameters
62
+
63
+ All endpoints support four main parameters:
64
+
65
+ ### 1. Query String (`q`)
66
+
67
+ Filters data using JSON query objects. **Required parameter.**
68
+
69
+ **Query Operators:**
70
+
71
+ - **Equality**: `{"field": "value"}` or `{"field": {"_eq": "value"}}`
72
+ - **Not equal**: `{"field": {"_neq": "value"}}`
73
+ - **Comparison**: `_gt`, `_gte`, `_lt`, `_lte`
74
+ - **String matching**:
75
+ - `_begins` - starts with
76
+ - `_contains` - substring match
77
+ - **Full-text search** (recommended for text fields):
78
+ - `_text_all` - all terms must match
79
+ - `_text_any` - any term matches
80
+ - `_text_phrase` - exact phrase match
81
+ - **Logical operators**: `_and`, `_or`, `_not`
82
+ - **Array matching**: Use arrays for OR conditions
83
+
84
+ **Examples:**
85
+
86
+ ```json
87
+ // Simple equality
88
+ {"patent_number": "11234567"}
89
+
90
+ // Date range
91
+ {"patent_date": {"_gte": "2020-01-01", "_lte": "2020-12-31"}}
92
+
93
+ // Text search (preferred for text fields)
94
+ {"patent_abstract": {"_text_all": ["machine", "learning"]}}
95
+
96
+ // Inventor name
97
+ {"inventor_name": {"_text_phrase": "John Smith"}}
98
+
99
+ // Complex query with logical operators
100
+ {
101
+ "_and": [
102
+ {"patent_date": {"_gte": "2020-01-01"}},
103
+ {"assignee_organization": {"_text_any": ["Google", "Alphabet"]}}
104
+ ]
105
+ }
106
+
107
+ // Array for OR conditions
108
+ {"cpc_subclass_id": ["H04N", "H04L"]}
109
+ ```
110
+
111
+ ### 2. Field List (`f`)
112
+
113
+ Specifies which fields to return in the response. Optional - each endpoint has default fields.
114
+
115
+ **Format:** JSON array of field names
116
+
117
+ ```json
118
+ ["patent_number", "patent_title", "patent_date", "inventor_name"]
119
+ ```
120
+
121
+ ### 3. Sorting (`s`)
122
+
123
+ Orders results by specified fields. Optional.
124
+
125
+ **Format:** JSON array with field name and direction
126
+
127
+ ```json
128
+ [{"patent_date": "desc"}]
129
+ ```
130
+
131
+ ### 4. Options (`o`)
132
+
133
+ Controls pagination and additional settings. Optional.
134
+
135
+ **Available options:**
136
+
137
+ - `page` - Page number (default: 1)
138
+ - `per_page` - Records per page (default: 100, max: 1,000)
139
+ - `pad_patent_id` - Pad patent IDs with leading zeros (default: false)
140
+ - `exclude_withdrawn` - Exclude withdrawn patents (default: true)
141
+
142
+ **Format:** JSON object
143
+
144
+ ```json
145
+ {
146
+ "page": 1,
147
+ "per_page": 500,
148
+ "exclude_withdrawn": false
149
+ }
150
+ ```
151
+
152
+ ## Response Format
153
+
154
+ All responses follow this structure:
155
+
156
+ ```json
157
+ {
158
+ "error": false,
159
+ "count": 100,
160
+ "total_hits": 5432,
161
+ "patents": [...],
162
+ // or "inventors": [...], "assignees": [...], etc.
163
+ }
164
+ ```
165
+
166
+ - `error` - Boolean indicating if an error occurred
167
+ - `count` - Number of records in current response
168
+ - `total_hits` - Total number of matching records
169
+ - Endpoint-specific data array (e.g., `patents`, `inventors`)
170
+
171
+ ## Complete Request Example
172
+
173
+ ### Using curl
174
+
175
+ ```bash
176
+ curl -X POST "https://search.patentsview.org/api/v1/patent" \
177
+ -H "X-Api-Key: YOUR_API_KEY" \
178
+ -H "Content-Type: application/json" \
179
+ -d '{
180
+ "q": {
181
+ "_and": [
182
+ {"patent_date": {"_gte": "2024-01-01"}},
183
+ {"patent_abstract": {"_text_all": ["artificial", "intelligence"]}}
184
+ ]
185
+ },
186
+ "f": ["patent_number", "patent_title", "patent_date", "assignee_organization"],
187
+ "s": [{"patent_date": "desc"}],
188
+ "o": {"per_page": 100}
189
+ }'
190
+ ```
191
+
192
+ ### Using Python
193
+
194
+ ```python
195
+ import requests
196
+
197
+ url = "https://search.patentsview.org/api/v1/patent"
198
+ headers = {
199
+ "X-Api-Key": "YOUR_API_KEY",
200
+ "Content-Type": "application/json"
201
+ }
202
+ data = {
203
+ "q": {
204
+ "_and": [
205
+ {"patent_date": {"_gte": "2024-01-01"}},
206
+ {"patent_abstract": {"_text_all": ["artificial", "intelligence"]}}
207
+ ]
208
+ },
209
+ "f": ["patent_number", "patent_title", "patent_date", "assignee_organization"],
210
+ "s": [{"patent_date": "desc"}],
211
+ "o": {"per_page": 100}
212
+ }
213
+
214
+ response = requests.post(url, headers=headers, json=data)
215
+ results = response.json()
216
+ ```
217
+
218
+ ## Common Field Names
219
+
220
+ ### Patent Endpoint Fields
221
+
222
+ - `patent_number` - Patent number
223
+ - `patent_title` - Title of the patent
224
+ - `patent_date` - Grant date
225
+ - `patent_abstract` - Abstract text
226
+ - `patent_type` - Type of patent
227
+ - `inventor_name` - Inventor names (array)
228
+ - `assignee_organization` - Assignee company names (array)
229
+ - `cpc_subclass_id` - CPC classification codes
230
+ - `uspc_class` - US classification codes
231
+ - `cited_patent_number` - Citations to other patents
232
+ - `citedby_patent_number` - Patents citing this patent
233
+
234
+ Refer to the full field dictionary at: https://search.patentsview.org/docs/
235
+
236
+ ## Best Practices
237
+
238
+ 1. **Use `_text*` operators for text fields** - More performant than `_contains` or `_begins`
239
+ 2. **Request only needed fields** - Reduces response size and improves performance
240
+ 3. **Implement pagination** - Handle large result sets efficiently
241
+ 4. **Respect rate limits** - Implement backoff/retry logic for 429 errors
242
+ 5. **Cache results** - Reduce redundant API calls
243
+ 6. **Use date ranges** - Narrow searches to improve performance
244
+
245
+ ## Error Handling
246
+
247
+ Common HTTP status codes:
248
+
249
+ - **200** - Success
250
+ - **400** - Bad request (invalid query syntax)
251
+ - **401** - Unauthorized (missing or invalid API key)
252
+ - **429** - Too many requests (rate limit exceeded)
253
+ - **500** - Server error
254
+
255
+ ## Recent Updates (February 2025)
256
+
257
+ - Data updated through December 31, 2024
258
+ - New `pad_patent_id` option for formatting patent IDs
259
+ - New `exclude_withdrawn` option to show withdrawn patents
260
+ - Text endpoints continue beta backfilling
261
+
262
+ ## Resources
263
+
264
+ - **Official Documentation**: https://search.patentsview.org/docs/
265
+ - **API Key Registration**: https://account.uspto.gov/api-manager/
266
+ - **Legacy API Notice**: The old PatentsView API was discontinued May 1, 2025