valuesets 0.3.1__py3-none-any.whl

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  1. valuesets/__init__.py +7 -0
  2. valuesets/_version.py +8 -0
  3. valuesets/datamodel/valuesets.py +13796 -0
  4. valuesets/datamodel/valuesets_dataclass.py +24503 -0
  5. valuesets/datamodel/valuesets_pydantic.py +13796 -0
  6. valuesets/enums/__init__.py +590 -0
  7. valuesets/enums/academic/__init__.py +1 -0
  8. valuesets/enums/academic/research.py +559 -0
  9. valuesets/enums/analytical_chemistry/__init__.py +1 -0
  10. valuesets/enums/analytical_chemistry/mass_spectrometry.py +198 -0
  11. valuesets/enums/bio/__init__.py +1 -0
  12. valuesets/enums/bio/biological_colors.py +238 -0
  13. valuesets/enums/bio/cell_cycle.py +180 -0
  14. valuesets/enums/bio/currency_chemicals.py +52 -0
  15. valuesets/enums/bio/developmental_stages.py +103 -0
  16. valuesets/enums/bio/genome_features.py +182 -0
  17. valuesets/enums/bio/genomics.py +91 -0
  18. valuesets/enums/bio/go_aspect.py +32 -0
  19. valuesets/enums/bio/go_causality.py +58 -0
  20. valuesets/enums/bio/go_evidence.py +129 -0
  21. valuesets/enums/bio/human_developmental_stages.py +62 -0
  22. valuesets/enums/bio/insdc_geographic_locations.py +591 -0
  23. valuesets/enums/bio/insdc_missing_values.py +49 -0
  24. valuesets/enums/bio/lipid_categories.py +67 -0
  25. valuesets/enums/bio/mouse_developmental_stages.py +62 -0
  26. valuesets/enums/bio/plant_biology.py +86 -0
  27. valuesets/enums/bio/plant_developmental_stages.py +54 -0
  28. valuesets/enums/bio/plant_sex.py +81 -0
  29. valuesets/enums/bio/protein_evidence.py +61 -0
  30. valuesets/enums/bio/proteomics_standards.py +123 -0
  31. valuesets/enums/bio/psi_mi.py +306 -0
  32. valuesets/enums/bio/relationship_to_oxygen.py +37 -0
  33. valuesets/enums/bio/sequence_alphabets.py +449 -0
  34. valuesets/enums/bio/sequence_chemistry.py +357 -0
  35. valuesets/enums/bio/sequencing_platforms.py +302 -0
  36. valuesets/enums/bio/structural_biology.py +320 -0
  37. valuesets/enums/bio/taxonomy.py +238 -0
  38. valuesets/enums/bio/trophic_levels.py +85 -0
  39. valuesets/enums/bio/uniprot_species.py +344 -0
  40. valuesets/enums/bio/viral_genome_types.py +47 -0
  41. valuesets/enums/bioprocessing/__init__.py +1 -0
  42. valuesets/enums/bioprocessing/scale_up.py +249 -0
  43. valuesets/enums/business/__init__.py +1 -0
  44. valuesets/enums/business/human_resources.py +275 -0
  45. valuesets/enums/business/industry_classifications.py +181 -0
  46. valuesets/enums/business/management_operations.py +228 -0
  47. valuesets/enums/business/organizational_structures.py +236 -0
  48. valuesets/enums/business/quality_management.py +181 -0
  49. valuesets/enums/business/supply_chain.py +232 -0
  50. valuesets/enums/chemistry/__init__.py +1 -0
  51. valuesets/enums/chemistry/chemical_entities.py +315 -0
  52. valuesets/enums/chemistry/reaction_directionality.py +65 -0
  53. valuesets/enums/chemistry/reactions.py +256 -0
  54. valuesets/enums/clinical/__init__.py +1 -0
  55. valuesets/enums/clinical/nih_demographics.py +177 -0
  56. valuesets/enums/clinical/phenopackets.py +254 -0
  57. valuesets/enums/common_value_sets.py +8791 -0
  58. valuesets/enums/computing/__init__.py +1 -0
  59. valuesets/enums/computing/file_formats.py +294 -0
  60. valuesets/enums/computing/maturity_levels.py +196 -0
  61. valuesets/enums/computing/mime_types.py +227 -0
  62. valuesets/enums/confidence_levels.py +168 -0
  63. valuesets/enums/contributor.py +30 -0
  64. valuesets/enums/core.py +42 -0
  65. valuesets/enums/data/__init__.py +1 -0
  66. valuesets/enums/data/data_absent_reason.py +53 -0
  67. valuesets/enums/data_science/__init__.py +1 -0
  68. valuesets/enums/data_science/binary_classification.py +87 -0
  69. valuesets/enums/data_science/emotion_classification.py +66 -0
  70. valuesets/enums/data_science/priority_severity.py +73 -0
  71. valuesets/enums/data_science/quality_control.py +46 -0
  72. valuesets/enums/data_science/sentiment_analysis.py +50 -0
  73. valuesets/enums/data_science/text_classification.py +97 -0
  74. valuesets/enums/demographics.py +206 -0
  75. valuesets/enums/ecological_interactions.py +151 -0
  76. valuesets/enums/energy/__init__.py +1 -0
  77. valuesets/enums/energy/energy.py +343 -0
  78. valuesets/enums/energy/fossil_fuels.py +29 -0
  79. valuesets/enums/energy/nuclear/__init__.py +1 -0
  80. valuesets/enums/energy/nuclear/nuclear_facilities.py +195 -0
  81. valuesets/enums/energy/nuclear/nuclear_fuel_cycle.py +96 -0
  82. valuesets/enums/energy/nuclear/nuclear_fuels.py +175 -0
  83. valuesets/enums/energy/nuclear/nuclear_operations.py +191 -0
  84. valuesets/enums/energy/nuclear/nuclear_regulatory.py +188 -0
  85. valuesets/enums/energy/nuclear/nuclear_safety.py +164 -0
  86. valuesets/enums/energy/nuclear/nuclear_waste.py +158 -0
  87. valuesets/enums/energy/nuclear/reactor_types.py +163 -0
  88. valuesets/enums/environmental_health/__init__.py +1 -0
  89. valuesets/enums/environmental_health/exposures.py +265 -0
  90. valuesets/enums/geography/__init__.py +1 -0
  91. valuesets/enums/geography/geographic_codes.py +741 -0
  92. valuesets/enums/health/__init__.py +12 -0
  93. valuesets/enums/health/vaccination.py +98 -0
  94. valuesets/enums/health.py +36 -0
  95. valuesets/enums/health_base.py +36 -0
  96. valuesets/enums/healthcare.py +45 -0
  97. valuesets/enums/industry/__init__.py +1 -0
  98. valuesets/enums/industry/extractive_industry.py +94 -0
  99. valuesets/enums/industry/mining.py +388 -0
  100. valuesets/enums/industry/safety_colors.py +201 -0
  101. valuesets/enums/investigation.py +27 -0
  102. valuesets/enums/materials_science/__init__.py +1 -0
  103. valuesets/enums/materials_science/characterization_methods.py +112 -0
  104. valuesets/enums/materials_science/crystal_structures.py +76 -0
  105. valuesets/enums/materials_science/material_properties.py +119 -0
  106. valuesets/enums/materials_science/material_types.py +104 -0
  107. valuesets/enums/materials_science/pigments_dyes.py +198 -0
  108. valuesets/enums/materials_science/synthesis_methods.py +109 -0
  109. valuesets/enums/medical/__init__.py +1 -0
  110. valuesets/enums/medical/clinical.py +277 -0
  111. valuesets/enums/medical/neuroimaging.py +119 -0
  112. valuesets/enums/mining_processing.py +302 -0
  113. valuesets/enums/physics/__init__.py +1 -0
  114. valuesets/enums/physics/states_of_matter.py +46 -0
  115. valuesets/enums/social/__init__.py +1 -0
  116. valuesets/enums/social/person_status.py +29 -0
  117. valuesets/enums/spatial/__init__.py +1 -0
  118. valuesets/enums/spatial/spatial_qualifiers.py +246 -0
  119. valuesets/enums/statistics/__init__.py +5 -0
  120. valuesets/enums/statistics/prediction_outcomes.py +31 -0
  121. valuesets/enums/statistics.py +31 -0
  122. valuesets/enums/time/__init__.py +1 -0
  123. valuesets/enums/time/temporal.py +254 -0
  124. valuesets/enums/units/__init__.py +1 -0
  125. valuesets/enums/units/measurements.py +310 -0
  126. valuesets/enums/visual/__init__.py +1 -0
  127. valuesets/enums/visual/colors.py +376 -0
  128. valuesets/generators/__init__.py +19 -0
  129. valuesets/generators/auto_slot_injector.py +280 -0
  130. valuesets/generators/enhanced_pydantic_generator.py +100 -0
  131. valuesets/generators/enum_slot_generator.py +201 -0
  132. valuesets/generators/modular_rich_generator.py +353 -0
  133. valuesets/generators/prefix_standardizer.py +198 -0
  134. valuesets/generators/rich_enum.py +127 -0
  135. valuesets/generators/rich_pydantic_generator.py +310 -0
  136. valuesets/generators/smart_slot_syncer.py +428 -0
  137. valuesets/generators/sssom_generator.py +394 -0
  138. valuesets/merged/merged_hierarchy.yaml +21649 -0
  139. valuesets/schema/README.md +3 -0
  140. valuesets/schema/academic/research.yaml +911 -0
  141. valuesets/schema/analytical_chemistry/mass_spectrometry.yaml +206 -0
  142. valuesets/schema/bio/bio_entities.yaml +364 -0
  143. valuesets/schema/bio/biological_colors.yaml +434 -0
  144. valuesets/schema/bio/cell_cycle.yaml +309 -0
  145. valuesets/schema/bio/currency_chemicals.yaml +70 -0
  146. valuesets/schema/bio/developmental_stages.yaml +226 -0
  147. valuesets/schema/bio/genome_features.yaml +342 -0
  148. valuesets/schema/bio/genomics.yaml +101 -0
  149. valuesets/schema/bio/go_aspect.yaml +39 -0
  150. valuesets/schema/bio/go_causality.yaml +119 -0
  151. valuesets/schema/bio/go_evidence.yaml +215 -0
  152. valuesets/schema/bio/insdc_geographic_locations.yaml +911 -0
  153. valuesets/schema/bio/insdc_missing_values.yaml +85 -0
  154. valuesets/schema/bio/lipid_categories.yaml +72 -0
  155. valuesets/schema/bio/plant_biology.yaml +125 -0
  156. valuesets/schema/bio/plant_developmental_stages.yaml +77 -0
  157. valuesets/schema/bio/plant_sex.yaml +108 -0
  158. valuesets/schema/bio/protein_evidence.yaml +63 -0
  159. valuesets/schema/bio/proteomics_standards.yaml +116 -0
  160. valuesets/schema/bio/psi_mi.yaml +400 -0
  161. valuesets/schema/bio/relationship_to_oxygen.yaml +46 -0
  162. valuesets/schema/bio/sequence_alphabets.yaml +1168 -0
  163. valuesets/schema/bio/sequence_chemistry.yaml +477 -0
  164. valuesets/schema/bio/sequencing_platforms.yaml +515 -0
  165. valuesets/schema/bio/structural_biology.yaml +428 -0
  166. valuesets/schema/bio/taxonomy.yaml +453 -0
  167. valuesets/schema/bio/trophic_levels.yaml +118 -0
  168. valuesets/schema/bio/uniprot_species.yaml +1209 -0
  169. valuesets/schema/bio/viral_genome_types.yaml +99 -0
  170. valuesets/schema/bioprocessing/scale_up.yaml +458 -0
  171. valuesets/schema/business/human_resources.yaml +752 -0
  172. valuesets/schema/business/industry_classifications.yaml +448 -0
  173. valuesets/schema/business/management_operations.yaml +602 -0
  174. valuesets/schema/business/organizational_structures.yaml +645 -0
  175. valuesets/schema/business/quality_management.yaml +502 -0
  176. valuesets/schema/business/supply_chain.yaml +688 -0
  177. valuesets/schema/chemistry/chemical_entities.yaml +639 -0
  178. valuesets/schema/chemistry/reaction_directionality.yaml +60 -0
  179. valuesets/schema/chemistry/reactions.yaml +442 -0
  180. valuesets/schema/clinical/nih_demographics.yaml +285 -0
  181. valuesets/schema/clinical/phenopackets.yaml +429 -0
  182. valuesets/schema/computing/file_formats.yaml +631 -0
  183. valuesets/schema/computing/maturity_levels.yaml +229 -0
  184. valuesets/schema/computing/mime_types.yaml +266 -0
  185. valuesets/schema/confidence_levels.yaml +206 -0
  186. valuesets/schema/contributor.yaml +30 -0
  187. valuesets/schema/core.yaml +55 -0
  188. valuesets/schema/data/data_absent_reason.yaml +82 -0
  189. valuesets/schema/data_science/binary_classification.yaml +125 -0
  190. valuesets/schema/data_science/emotion_classification.yaml +109 -0
  191. valuesets/schema/data_science/priority_severity.yaml +122 -0
  192. valuesets/schema/data_science/quality_control.yaml +68 -0
  193. valuesets/schema/data_science/sentiment_analysis.yaml +81 -0
  194. valuesets/schema/data_science/text_classification.yaml +135 -0
  195. valuesets/schema/demographics.yaml +238 -0
  196. valuesets/schema/ecological_interactions.yaml +298 -0
  197. valuesets/schema/energy/energy.yaml +595 -0
  198. valuesets/schema/energy/fossil_fuels.yaml +28 -0
  199. valuesets/schema/energy/nuclear/nuclear_facilities.yaml +463 -0
  200. valuesets/schema/energy/nuclear/nuclear_fuel_cycle.yaml +82 -0
  201. valuesets/schema/energy/nuclear/nuclear_fuels.yaml +421 -0
  202. valuesets/schema/energy/nuclear/nuclear_operations.yaml +480 -0
  203. valuesets/schema/energy/nuclear/nuclear_regulatory.yaml +200 -0
  204. valuesets/schema/energy/nuclear/nuclear_safety.yaml +352 -0
  205. valuesets/schema/energy/nuclear/nuclear_waste.yaml +332 -0
  206. valuesets/schema/energy/nuclear/reactor_types.yaml +394 -0
  207. valuesets/schema/environmental_health/exposures.yaml +355 -0
  208. valuesets/schema/generated_slots.yaml +1828 -0
  209. valuesets/schema/geography/geographic_codes.yaml +1018 -0
  210. valuesets/schema/health/vaccination.yaml +102 -0
  211. valuesets/schema/health.yaml +38 -0
  212. valuesets/schema/healthcare.yaml +53 -0
  213. valuesets/schema/industry/extractive_industry.yaml +89 -0
  214. valuesets/schema/industry/mining.yaml +888 -0
  215. valuesets/schema/industry/safety_colors.yaml +375 -0
  216. valuesets/schema/investigation.yaml +64 -0
  217. valuesets/schema/materials_science/characterization_methods.yaml +193 -0
  218. valuesets/schema/materials_science/crystal_structures.yaml +138 -0
  219. valuesets/schema/materials_science/material_properties.yaml +135 -0
  220. valuesets/schema/materials_science/material_types.yaml +151 -0
  221. valuesets/schema/materials_science/pigments_dyes.yaml +465 -0
  222. valuesets/schema/materials_science/synthesis_methods.yaml +186 -0
  223. valuesets/schema/medical/clinical.yaml +610 -0
  224. valuesets/schema/medical/neuroimaging.yaml +325 -0
  225. valuesets/schema/mining_processing.yaml +295 -0
  226. valuesets/schema/physics/states_of_matter.yaml +46 -0
  227. valuesets/schema/slot_mixins.yaml +143 -0
  228. valuesets/schema/social/person_status.yaml +28 -0
  229. valuesets/schema/spatial/spatial_qualifiers.yaml +466 -0
  230. valuesets/schema/statistics/prediction_outcomes.yaml +26 -0
  231. valuesets/schema/statistics.yaml +34 -0
  232. valuesets/schema/time/temporal.yaml +435 -0
  233. valuesets/schema/types.yaml +15 -0
  234. valuesets/schema/units/measurements.yaml +675 -0
  235. valuesets/schema/valuesets.yaml +100 -0
  236. valuesets/schema/visual/colors.yaml +778 -0
  237. valuesets/utils/__init__.py +6 -0
  238. valuesets/utils/comparison.py +102 -0
  239. valuesets/utils/expand_dynamic_enums.py +414 -0
  240. valuesets/utils/mapping_utils.py +236 -0
  241. valuesets/validators/__init__.py +11 -0
  242. valuesets/validators/enum_evaluator.py +669 -0
  243. valuesets/validators/oak_config.yaml +70 -0
  244. valuesets/validators/validate_with_ols.py +241 -0
  245. valuesets-0.3.1.dist-info/METADATA +395 -0
  246. valuesets-0.3.1.dist-info/RECORD +248 -0
  247. valuesets-0.3.1.dist-info/WHEEL +4 -0
  248. valuesets-0.3.1.dist-info/licenses/LICENSE +201 -0
@@ -0,0 +1,135 @@
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+ name: text_classification
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+ id: https://w3id.org/linkml/valuesets/data_science/text_classification
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+ prefixes:
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+ # linkml_common: https://w3id.org/linkml-common/
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+ NCIT: http://purl.obolibrary.org/obo/NCIT_
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+ SIO: http://semanticscience.org/resource/SIO_
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+ valuesets: https://w3id.org/valuesets/
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+ default_prefix: valuesets
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+ slots:
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+ news_topic_category:
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+ description: Common news article topic categories
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+ range: NewsTopicCategoryEnum
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+ toxicity_classification:
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+ description: Text toxicity classification labels
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+ range: ToxicityClassificationEnum
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+ intent_classification:
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+ description: Common chatbot/NLU intent categories
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+ range: IntentClassificationEnum
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+ enums:
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+ NewsTopicCategoryEnum:
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+ description: Common news article topic categories
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+ permissible_values:
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+ POLITICS:
24
+ description: Political news and government affairs
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+ title: Politics
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+ BUSINESS:
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+ description: Business, finance, and economic news
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+ title: Business
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+ aliases:
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+ - finance
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+ - economy
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+ TECHNOLOGY:
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+ description: Technology and computing news
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+ title: Technology
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+ aliases:
36
+ - tech
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+ - IT
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+ SPORTS:
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+ description: Sports news and events
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+ title: Sports
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+ ENTERTAINMENT:
42
+ description: Entertainment and celebrity news
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+ title: Entertainment
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+ aliases:
45
+ - showbiz
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+ SCIENCE:
47
+ description: Scientific discoveries and research
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+ title: Science
49
+ HEALTH:
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+ description: Health, medicine, and wellness news
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+ title: Health
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+ aliases:
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+ - medical
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+ WORLD:
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+ description: International news and events
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+ title: World
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+ aliases:
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+ - international
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+ - global
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+ LOCAL:
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+ description: Local and regional news
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+ title: Local
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+ aliases:
64
+ - regional
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+ ToxicityClassificationEnum:
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+ description: Text toxicity classification labels
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+ permissible_values:
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+ NON_TOXIC:
69
+ description: Text is appropriate and non-harmful
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+ title: Non-Toxic
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+ meaning: SIO:001010
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+ aliases:
73
+ - safe
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+ - clean
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+ - '0'
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+ TOXIC:
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+ description: Text contains harmful or inappropriate content
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+ title: Toxic
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+ aliases:
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+ - harmful
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+ - inappropriate
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+ - '1'
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+ SEVERE_TOXIC:
84
+ description: Text contains severely harmful content
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+ title: Severe Toxic
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+ is_a: TOXIC
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+ OBSCENE:
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+ description: Text contains obscene content
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+ title: Obscene
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+ is_a: TOXIC
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+ THREAT:
92
+ description: Text contains threatening content
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+ title: Threat
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+ is_a: TOXIC
95
+ INSULT:
96
+ description: Text contains insulting content
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+ title: Insult
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+ is_a: TOXIC
99
+ IDENTITY_HATE:
100
+ description: Text contains identity-based hate
101
+ title: Identity Hate
102
+ is_a: TOXIC
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+ IntentClassificationEnum:
104
+ description: Common chatbot/NLU intent categories
105
+ permissible_values:
106
+ GREETING:
107
+ description: User greeting or hello
108
+ title: Greeting
109
+ GOODBYE:
110
+ description: User saying goodbye
111
+ title: Goodbye
112
+ THANKS:
113
+ description: User expressing gratitude
114
+ title: Thanks
115
+ HELP:
116
+ description: User requesting help or assistance
117
+ title: Help
118
+ INFORMATION:
119
+ description: User requesting information
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+ title: Information
121
+ COMPLAINT:
122
+ description: User expressing dissatisfaction
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+ title: Complaint
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+ FEEDBACK:
125
+ description: User providing feedback
126
+ title: Feedback
127
+ PURCHASE:
128
+ description: User intent to buy or purchase
129
+ title: Purchase
130
+ CANCEL:
131
+ description: User intent to cancel
132
+ title: Cancel
133
+ REFUND:
134
+ description: User requesting refund
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+ title: Refund
@@ -0,0 +1,238 @@
1
+ name: valuesets-demographics
2
+ title: valuesets-demographics
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+ description: Demographic and social determinant value sets from NIH CDE and HL7 standards
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+ id: https://w3id.org/valuesets/demographics
5
+ prefixes:
6
+ # linkml_common: https://w3id.org/valuesets/
7
+ linkml: https://w3id.org/linkml/
8
+ biolink: https://w3id.org/biolink/
9
+ schema: http://schema.org/
10
+ HL7: http://terminology.hl7.org/CodeSystem/
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+ SNOMED: http://snomed.info/id/
12
+ valuesets: https://w3id.org/valuesets/
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+ default_prefix: valuesets
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+ slots:
15
+ education_level:
16
+ description: Years of education that a person has completed
17
+ range: EducationLevel
18
+ marital_status:
19
+ description: The domestic partnership status of a person
20
+ range: MaritalStatus
21
+ employment_status:
22
+ description: Employment status of a person
23
+ range: EmploymentStatus
24
+ housing_status:
25
+ description: Housing status of patients per UDS Plus HRSA standards
26
+ range: HousingStatus
27
+ gender_identity:
28
+ description: Gender identity codes indicating an individual's personal sense of gender
29
+ range: GenderIdentity
30
+ omb_race_category:
31
+ description: Office of Management and Budget (OMB) race category codes
32
+ range: OmbRaceCategory
33
+ omb_ethnicity_category:
34
+ description: Office of Management and Budget (OMB) ethnicity category codes
35
+ range: OmbEthnicityCategory
36
+ enums:
37
+ EducationLevel:
38
+ description: Years of education that a person has completed
39
+ source: https://terminology.hl7.org/CodeSystem-v3-EducationLevel.html
40
+ permissible_values:
41
+ ELEM:
42
+ description: Elementary School
43
+ meaning: HL7:v3-EducationLevel#ELEM
44
+ SEC:
45
+ description: Some secondary or high school education
46
+ meaning: HL7:v3-EducationLevel#SEC
47
+ HS:
48
+ description: High School or secondary school degree complete
49
+ meaning: HL7:v3-EducationLevel#HS
50
+ SCOL:
51
+ description: Some College education
52
+ meaning: HL7:v3-EducationLevel#SCOL
53
+ ASSOC:
54
+ description: Associate's or technical degree complete
55
+ meaning: HL7:v3-EducationLevel#ASSOC
56
+ BD:
57
+ description: College or baccalaureate degree complete
58
+ meaning: HL7:v3-EducationLevel#BD
59
+ PB:
60
+ description: Some post-baccalaureate education
61
+ meaning: HL7:v3-EducationLevel#PB
62
+ GD:
63
+ description: Graduate or professional Degree complete
64
+ meaning: HL7:v3-EducationLevel#GD
65
+ POSTG:
66
+ description: Doctoral or post graduate education
67
+ meaning: HL7:v3-EducationLevel#POSTG
68
+ MaritalStatus:
69
+ description: The domestic partnership status of a person
70
+ source: https://www.hl7.org/fhir/valueset-marital-status.html
71
+ permissible_values:
72
+ ANNULLED:
73
+ description: Marriage contract has been declared null and to not have existed
74
+ meaning: HL7:marital-status#A
75
+ DIVORCED:
76
+ description: Marriage contract has been declared dissolved and inactive
77
+ meaning: HL7:marital-status#D
78
+ INTERLOCUTORY:
79
+ description: Subject to an Interlocutory Decree
80
+ meaning: HL7:marital-status#I
81
+ LEGALLY_SEPARATED:
82
+ description: Legally Separated
83
+ meaning: HL7:marital-status#L
84
+ MARRIED:
85
+ description: A current marriage contract is active
86
+ meaning: HL7:marital-status#M
87
+ COMMON_LAW:
88
+ description: Marriage recognized in some jurisdictions based on parties' agreement
89
+ meaning: HL7:marital-status#C
90
+ POLYGAMOUS:
91
+ description: More than 1 current spouse
92
+ meaning: HL7:marital-status#P
93
+ DOMESTIC_PARTNER:
94
+ description: Person declares that a domestic partner relationship exists
95
+ meaning: HL7:marital-status#T
96
+ UNMARRIED:
97
+ description: Currently not in a marriage contract
98
+ meaning: HL7:marital-status#U
99
+ NEVER_MARRIED:
100
+ description: No marriage contract has ever been entered
101
+ meaning: HL7:marital-status#S
102
+ WIDOWED:
103
+ description: The spouse has died
104
+ meaning: HL7:marital-status#W
105
+ UNKNOWN:
106
+ description: A proper value is applicable, but not known
107
+ meaning: HL7:marital-status#UNK
108
+ EmploymentStatus:
109
+ description: Employment status of a person
110
+ source: https://terminology.hl7.org/CodeSystem-v2-0066.html
111
+ permissible_values:
112
+ FULL_TIME_EMPLOYED:
113
+ description: Full time employed
114
+ meaning: HL7:v2-0066#1
115
+ PART_TIME_EMPLOYED:
116
+ description: Part time employed
117
+ meaning: HL7:v2-0066#2
118
+ UNEMPLOYED:
119
+ description: Unemployed
120
+ meaning: HL7:v2-0066#3
121
+ SELF_EMPLOYED:
122
+ description: Self-employed
123
+ meaning: HL7:v2-0066#4
124
+ RETIRED:
125
+ description: Retired
126
+ meaning: HL7:v2-0066#5
127
+ ACTIVE_MILITARY:
128
+ description: On active military duty
129
+ meaning: HL7:v2-0066#6
130
+ CONTRACT:
131
+ description: Contract, per diem
132
+ meaning: HL7:v2-0066#C
133
+ PER_DIEM:
134
+ description: Per Diem
135
+ meaning: HL7:v2-0066#D
136
+ LEAVE_OF_ABSENCE:
137
+ description: Leave of absence
138
+ meaning: HL7:v2-0066#L
139
+ OTHER:
140
+ description: Other
141
+ meaning: HL7:v2-0066#O
142
+ TEMPORARILY_UNEMPLOYED:
143
+ description: Temporarily unemployed
144
+ meaning: HL7:v2-0066#T
145
+ UNKNOWN:
146
+ description: Unknown
147
+ meaning: HL7:v2-0066#9
148
+ HousingStatus:
149
+ description: Housing status of patients per UDS Plus HRSA standards
150
+ source: https://www.fhir.org/guides/hrsa/uds-plus/CodeSystem-udsplus-housing-status-codes.html
151
+ permissible_values:
152
+ HOMELESS_SHELTER:
153
+ description: Patients who are living in a homeless shelter
154
+ meaning: HL7:udsplus-housing-status-codes#homeless-shelter
155
+ TRANSITIONAL:
156
+ description: Patients who do not have a house and are in a transitional state
157
+ meaning: HL7:udsplus-housing-status-codes#transitional
158
+ DOUBLING_UP:
159
+ description: Patients who are doubling up with others
160
+ meaning: HL7:udsplus-housing-status-codes#doubling-up
161
+ STREET:
162
+ description: Patients who do not have a house and are living on the streets
163
+ meaning: HL7:udsplus-housing-status-codes#street
164
+ PERMANENT_SUPPORTIVE_HOUSING:
165
+ description: Patients who are living in a permanent supportive housing
166
+ meaning: HL7:udsplus-housing-status-codes#permanent-supportive-housing
167
+ OTHER:
168
+ description: Patients who have other kinds of accommodation
169
+ meaning: HL7:udsplus-housing-status-codes#other
170
+ UNKNOWN:
171
+ description: Patients with Unknown accommodation
172
+ meaning: HL7:udsplus-housing-status-codes#unknown
173
+ GenderIdentity:
174
+ description: Gender identity codes indicating an individual's personal sense of gender
175
+ source: https://terminology.hl7.org/ValueSet-gender-identity.html
176
+ permissible_values:
177
+ FEMALE:
178
+ description: Identifies as female gender (finding)
179
+ meaning: SNOMED:446141000124107
180
+ MALE:
181
+ description: Identifies as male gender (finding)
182
+ meaning: SNOMED:446151000124109
183
+ NON_BINARY:
184
+ description: Identifies as gender nonbinary
185
+ meaning: SNOMED:33791000087105
186
+ ASKED_DECLINED:
187
+ description: Asked But Declined
188
+ meaning: HL7:asked-declined
189
+ UNKNOWN:
190
+ description: A proper value is applicable, but not known
191
+ meaning: HL7:UNK
192
+ OmbRaceCategory:
193
+ description: Office of Management and Budget (OMB) race category codes
194
+ source: https://www.hl7.org/fhir/us/core/ValueSet-omb-race-category.html
195
+ permissible_values:
196
+ AMERICAN_INDIAN_OR_ALASKA_NATIVE:
197
+ description: American Indian or Alaska Native
198
+ meaning: HL7:CDCREC#1002-5
199
+ ASIAN:
200
+ description: Asian
201
+ meaning: HL7:CDCREC#2028-9
202
+ BLACK_OR_AFRICAN_AMERICAN:
203
+ description: Black or African American
204
+ meaning: HL7:CDCREC#2054-5
205
+ NATIVE_HAWAIIAN_OR_OTHER_PACIFIC_ISLANDER:
206
+ description: Native Hawaiian or Other Pacific Islander
207
+ meaning: HL7:CDCREC#2076-8
208
+ WHITE:
209
+ description: White
210
+ meaning: HL7:CDCREC#2106-3
211
+ OTHER_RACE:
212
+ description: Other Race (discouraged for statistical analysis)
213
+ meaning: HL7:CDCREC#2131-1
214
+ ASKED_BUT_UNKNOWN:
215
+ description: asked but unknown
216
+ meaning: HL7:ASKU
217
+ UNKNOWN:
218
+ description: unknown
219
+ meaning: HL7:UNK
220
+ OmbEthnicityCategory:
221
+ description: Office of Management and Budget (OMB) ethnicity category codes
222
+ source: https://www.hl7.org/fhir/us/core/ValueSet-omb-ethnicity-category.html
223
+ permissible_values:
224
+ HISPANIC_OR_LATINO:
225
+ description: Hispanic or Latino
226
+ meaning: HL7:CDCREC#2135-2
227
+ NOT_HISPANIC_OR_LATINO:
228
+ description: Not Hispanic or Latino
229
+ meaning: HL7:CDCREC#2186-5
230
+ ASKED_BUT_UNKNOWN:
231
+ description: asked but unknown
232
+ meaning: HL7:ASKU
233
+ UNKNOWN:
234
+ description: unknown
235
+ meaning: HL7:UNK
236
+ license: MIT
237
+ see_also:
238
+ - https://linkml.github.io/valuesets
@@ -0,0 +1,298 @@
1
+ name: ecological_interactions
2
+ title: Ecological Interactions Value Sets
3
+ description: 'Value sets for ecological and biological interactions, based on the Relations Ontology (RO) biotically interacts
4
+ with (RO:0002437) hierarchy.
5
+
6
+ '
7
+ id: https://w3id.org/valuesets/ecological-interactions
8
+ version: 1.0.0
9
+ status: release
10
+ imports:
11
+ - linkml:types
12
+ - ./core
13
+ prefixes:
14
+ linkml: https://w3id.org/linkml/
15
+ # cval: https://w3id.org/linkml-common/
16
+ RO: http://purl.obolibrary.org/obo/RO_
17
+ valuesets: https://w3id.org/valuesets/
18
+ default_prefix: valuesets
19
+ default_curi_maps:
20
+ - semweb_context
21
+ slots:
22
+ biotic_interaction:
23
+ description: Types of biotic interactions between organisms, based on RO:0002437 (biotically interacts with)
24
+ range: BioticInteractionType
25
+ enums:
26
+ BioticInteractionType:
27
+ description: 'Types of biotic interactions between organisms, based on RO:0002437 (biotically interacts with). These represent
28
+ ecological relationships where at least one partner is an organism.
29
+
30
+ '
31
+ permissible_values:
32
+ BIOTICALLY_INTERACTS_WITH:
33
+ description: 'An interaction relationship in which at least one of the partners is an organism and the other is either
34
+ an organism or an abiotic entity with which the organism interacts.
35
+
36
+ '
37
+ meaning: RO:0002437
38
+ TROPHICALLY_INTERACTS_WITH:
39
+ description: An interaction relationship in which the partners are related via a feeding relationship.
40
+ meaning: RO:0002438
41
+ is_a: BIOTICALLY_INTERACTS_WITH
42
+ PREYS_ON:
43
+ description: 'An interaction relationship involving a predation process, where the subject kills the target in order
44
+ to eat it or to feed to siblings, offspring or group members.
45
+
46
+ '
47
+ meaning: RO:0002439
48
+ is_a: TROPHICALLY_INTERACTS_WITH
49
+ PREYED_UPON_BY:
50
+ description: Inverse of preys on
51
+ meaning: RO:0002458
52
+ is_a: TROPHICALLY_INTERACTS_WITH
53
+ EATS:
54
+ description: 'A biotic interaction where one organism consumes a material entity through a type of mouth or other
55
+ oral opening.
56
+
57
+ '
58
+ meaning: RO:0002470
59
+ is_a: BIOTICALLY_INTERACTS_WITH
60
+ IS_EATEN_BY:
61
+ description: Inverse of eats
62
+ meaning: RO:0002471
63
+ is_a: BIOTICALLY_INTERACTS_WITH
64
+ ACQUIRES_NUTRIENTS_FROM:
65
+ description: Inverse of provides nutrients for
66
+ meaning: RO:0002457
67
+ is_a: BIOTICALLY_INTERACTS_WITH
68
+ PROVIDES_NUTRIENTS_FOR:
69
+ description: A biotic interaction where a material entity provides nutrition for an organism.
70
+ meaning: RO:0002469
71
+ is_a: BIOTICALLY_INTERACTS_WITH
72
+ SYMBIOTICALLY_INTERACTS_WITH:
73
+ description: 'A biotic interaction in which the two organisms live together in more or less intimate association.
74
+
75
+ '
76
+ meaning: RO:0002440
77
+ is_a: BIOTICALLY_INTERACTS_WITH
78
+ COMMENSUALLY_INTERACTS_WITH:
79
+ description: 'An interaction relationship between two organisms living together in more or less intimate association
80
+ in a relationship in which one benefits and the other is unaffected.
81
+
82
+ '
83
+ meaning: RO:0002441
84
+ is_a: SYMBIOTICALLY_INTERACTS_WITH
85
+ MUTUALISTICALLY_INTERACTS_WITH:
86
+ description: 'An interaction relationship between two organisms living together in more or less intimate association
87
+ in a relationship in which both organisms benefit from each other.
88
+
89
+ '
90
+ meaning: RO:0002442
91
+ is_a: SYMBIOTICALLY_INTERACTS_WITH
92
+ INTERACTS_VIA_PARASITE_HOST:
93
+ title: interacts with via parasite-host interaction
94
+ description: 'An interaction relationship between two organisms living together in more or less intimate association
95
+ in a relationship in which association is disadvantageous or destructive to one of the organisms.
96
+
97
+ '
98
+ meaning: RO:0002443
99
+ is_a: SYMBIOTICALLY_INTERACTS_WITH
100
+ SYMBIOTROPHICALLY_INTERACTS_WITH:
101
+ description: 'A trophic interaction in which one organism acquires nutrients through a symbiotic relationship with
102
+ another organism.
103
+
104
+ '
105
+ meaning: RO:0008510
106
+ is_a: SYMBIOTICALLY_INTERACTS_WITH
107
+ PARASITE_OF:
108
+ description: A parasite-host relationship where an organism benefits at the expense of another.
109
+ meaning: RO:0002444
110
+ is_a: INTERACTS_VIA_PARASITE_HOST
111
+ HOST_OF:
112
+ description: Inverse of has host
113
+ meaning: RO:0002453
114
+ is_a: INTERACTS_VIA_PARASITE_HOST
115
+ HAS_HOST:
116
+ description: 'X ''has host'' y if and only if: x is an organism, y is an organism, and x can live on the surface of
117
+ or within the body of y.
118
+
119
+ '
120
+ meaning: RO:0002454
121
+ is_a: INTERACTS_VIA_PARASITE_HOST
122
+ PARASITOID_OF:
123
+ description: A parasite that kills or sterilizes its host
124
+ meaning: RO:0002208
125
+ is_a: PARASITE_OF
126
+ ECTOPARASITE_OF:
127
+ description: 'A sub-relation of parasite-of in which the parasite lives on or in the integumental system of the host.
128
+
129
+ '
130
+ meaning: RO:0002632
131
+ is_a: PARASITE_OF
132
+ ENDOPARASITE_OF:
133
+ description: A parasite that lives inside its host
134
+ meaning: RO:0002634
135
+ is_a: PARASITE_OF
136
+ INTRACELLULAR_ENDOPARASITE_OF:
137
+ description: A sub-relation of endoparasite-of in which the parasite inhabits host cells.
138
+ meaning: RO:0002640
139
+ is_a: ENDOPARASITE_OF
140
+ INTERCELLULAR_ENDOPARASITE_OF:
141
+ description: 'A sub-relation of endoparasite-of in which the parasite inhabits the spaces between host cells.
142
+
143
+ '
144
+ meaning: RO:0002638
145
+ is_a: ENDOPARASITE_OF
146
+ HEMIPARASITE_OF:
147
+ description: 'A sub-relation of parasite-of in which the parasite is a plant, and the parasite is parasitic under
148
+ natural conditions and is also photosynthetic to some degree.
149
+
150
+ '
151
+ meaning: RO:0002237
152
+ is_a: PARASITE_OF
153
+ STEM_PARASITE_OF:
154
+ description: 'A parasite-of relationship in which the host is a plant and the parasite that attaches to the host stem.
155
+
156
+ '
157
+ meaning: RO:0002235
158
+ is_a: PARASITE_OF
159
+ ROOT_PARASITE_OF:
160
+ description: 'A parasite-of relationship in which the host is a plant and the parasite that attaches to the host root.
161
+
162
+ '
163
+ meaning: RO:0002236
164
+ is_a: PARASITE_OF
165
+ OBLIGATE_PARASITE_OF:
166
+ description: 'A sub-relation of parasite-of in which the parasite that cannot complete its life cycle without a host.
167
+
168
+ '
169
+ meaning: RO:0002227
170
+ is_a: PARASITE_OF
171
+ FACULTATIVE_PARASITE_OF:
172
+ description: 'A sub-relations of parasite-of in which the parasite that can complete its life cycle independent of
173
+ a host.
174
+
175
+ '
176
+ meaning: RO:0002228
177
+ is_a: PARASITE_OF
178
+ TROPHIC_PARASITE_OF:
179
+ description: 'A symbiotrophic interaction in which one organism acquires nutrients through a parasitic relationship
180
+ with another organism.
181
+
182
+ '
183
+ meaning: RO:0008511
184
+ is_a: PARASITE_OF
185
+ PATHOGEN_OF:
186
+ description: Inverse of has pathogen
187
+ meaning: RO:0002556
188
+ is_a: BIOTICALLY_INTERACTS_WITH
189
+ HAS_PATHOGEN:
190
+ description: 'A host interaction where the smaller of the two members of a symbiosis causes a disease in the larger
191
+ member.
192
+
193
+ '
194
+ meaning: RO:0002557
195
+ is_a: BIOTICALLY_INTERACTS_WITH
196
+ RESERVOIR_HOST_OF:
197
+ description: 'A relation between a host organism and a hosted organism in which the hosted organism naturally occurs
198
+ in an indefinitely maintained reservoir provided by the host.
199
+
200
+ '
201
+ meaning: RO:0002802
202
+ is_a: HOST_OF
203
+ HAS_RESERVOIR_HOST:
204
+ description: Inverse of reservoir host of
205
+ meaning: RO:0002803
206
+ is_a: HAS_HOST
207
+ IS_VECTOR_FOR:
208
+ description: Organism acts as a vector for transmitting another organism
209
+ meaning: RO:0002459
210
+ is_a: BIOTICALLY_INTERACTS_WITH
211
+ POLLINATES:
212
+ description: An interaction where an organism transfers pollen to a plant
213
+ meaning: RO:0002455
214
+ is_a: BIOTICALLY_INTERACTS_WITH
215
+ PARTICIPATES_IN_ABIOTIC_BIOTIC_INTERACTION_WITH:
216
+ title: participates in a abiotic-biotic interaction with
217
+ description: 'A biotic interaction relationship in which one partner is an organism and the other partner is inorganic.
218
+ For example, the relationship between a sponge and the substrate to which is it anchored.
219
+
220
+ '
221
+ meaning: RO:0002446
222
+ is_a: BIOTICALLY_INTERACTS_WITH
223
+ ECOLOGICALLY_CO_OCCURS_WITH:
224
+ description: 'An interaction relationship describing organisms that often occur together at the same time and space
225
+ or in the same environment.
226
+
227
+ '
228
+ meaning: RO:0008506
229
+ is_a: BIOTICALLY_INTERACTS_WITH
230
+ HYPERPARASITE_OF:
231
+ description: x is a hyperparasite of y iff x is a parasite of a parasite of the target organism y
232
+ meaning: RO:0002553
233
+ is_a: PARASITE_OF
234
+ MESOPARASITE_OF:
235
+ description: 'A sub-relation of parasite-of in which the parasite is partially an endoparasite and partially an ectoparasite.
236
+
237
+ '
238
+ meaning: RO:0002636
239
+ is_a: PARASITE_OF
240
+ KLEPTOPARASITE_OF:
241
+ description: 'A sub-relation of parasite of in which a parasite steals resources from another organism, usually food
242
+ or nest material.
243
+
244
+ '
245
+ meaning: RO:0008503
246
+ is_a: PARASITE_OF
247
+ EPIPHYTE_OF:
248
+ description: 'An interaction relationship wherein a plant or algae is living on the outside surface of another plant.
249
+
250
+ '
251
+ meaning: RO:0008501
252
+ is_a: BIOTICALLY_INTERACTS_WITH
253
+ ALLELOPATH_OF:
254
+ description: 'A relationship between organisms where one organism is influenced by the biochemicals produced by another.
255
+ Allelopathy is a phenomenon in which one organism releases chemicals to positively or negatively influence the growth,
256
+ survival or reproduction of other organisms in its vicinity.
257
+
258
+ '
259
+ meaning: RO:0002555
260
+ is_a: BIOTICALLY_INTERACTS_WITH
261
+ VISITS:
262
+ description: An interaction where an organism visits another organism or location
263
+ meaning: RO:0002618
264
+ is_a: BIOTICALLY_INTERACTS_WITH
265
+ VISITS_FLOWERS_OF:
266
+ description: An interaction where an organism visits the flowers of a plant
267
+ meaning: RO:0002622
268
+ is_a: VISITS
269
+ HAS_FLOWERS_VISITED_BY:
270
+ description: Inverse of visits flowers of
271
+ meaning: RO:0002623
272
+ is_a: BIOTICALLY_INTERACTS_WITH
273
+ LAYS_EGGS_IN:
274
+ description: An interaction where an organism deposits eggs inside another organism
275
+ meaning: RO:0002624
276
+ is_a: BIOTICALLY_INTERACTS_WITH
277
+ HAS_EGGS_LAID_IN_BY:
278
+ description: Inverse of lays eggs in
279
+ meaning: RO:0002625
280
+ is_a: BIOTICALLY_INTERACTS_WITH
281
+ LAYS_EGGS_ON:
282
+ description: 'An interaction relationship in which organism a lays eggs on the outside surface of organism b. Organism
283
+ b is neither helped nor harmed in the process of egg laying or incubation.
284
+
285
+ '
286
+ meaning: RO:0008507
287
+ is_a: BIOTICALLY_INTERACTS_WITH
288
+ HAS_EGGS_LAID_ON_BY:
289
+ description: Inverse of lays eggs on
290
+ meaning: RO:0008508
291
+ is_a: BIOTICALLY_INTERACTS_WITH
292
+ CREATES_HABITAT_FOR:
293
+ description: 'An interaction relationship wherein one organism creates a structure or environment that is lived in
294
+ by another organism.
295
+
296
+ '
297
+ meaning: RO:0008505
298
+ is_a: BIOTICALLY_INTERACTS_WITH