valuesets 0.3.1__py3-none-any.whl
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- valuesets/__init__.py +7 -0
- valuesets/_version.py +8 -0
- valuesets/datamodel/valuesets.py +13796 -0
- valuesets/datamodel/valuesets_dataclass.py +24503 -0
- valuesets/datamodel/valuesets_pydantic.py +13796 -0
- valuesets/enums/__init__.py +590 -0
- valuesets/enums/academic/__init__.py +1 -0
- valuesets/enums/academic/research.py +559 -0
- valuesets/enums/analytical_chemistry/__init__.py +1 -0
- valuesets/enums/analytical_chemistry/mass_spectrometry.py +198 -0
- valuesets/enums/bio/__init__.py +1 -0
- valuesets/enums/bio/biological_colors.py +238 -0
- valuesets/enums/bio/cell_cycle.py +180 -0
- valuesets/enums/bio/currency_chemicals.py +52 -0
- valuesets/enums/bio/developmental_stages.py +103 -0
- valuesets/enums/bio/genome_features.py +182 -0
- valuesets/enums/bio/genomics.py +91 -0
- valuesets/enums/bio/go_aspect.py +32 -0
- valuesets/enums/bio/go_causality.py +58 -0
- valuesets/enums/bio/go_evidence.py +129 -0
- valuesets/enums/bio/human_developmental_stages.py +62 -0
- valuesets/enums/bio/insdc_geographic_locations.py +591 -0
- valuesets/enums/bio/insdc_missing_values.py +49 -0
- valuesets/enums/bio/lipid_categories.py +67 -0
- valuesets/enums/bio/mouse_developmental_stages.py +62 -0
- valuesets/enums/bio/plant_biology.py +86 -0
- valuesets/enums/bio/plant_developmental_stages.py +54 -0
- valuesets/enums/bio/plant_sex.py +81 -0
- valuesets/enums/bio/protein_evidence.py +61 -0
- valuesets/enums/bio/proteomics_standards.py +123 -0
- valuesets/enums/bio/psi_mi.py +306 -0
- valuesets/enums/bio/relationship_to_oxygen.py +37 -0
- valuesets/enums/bio/sequence_alphabets.py +449 -0
- valuesets/enums/bio/sequence_chemistry.py +357 -0
- valuesets/enums/bio/sequencing_platforms.py +302 -0
- valuesets/enums/bio/structural_biology.py +320 -0
- valuesets/enums/bio/taxonomy.py +238 -0
- valuesets/enums/bio/trophic_levels.py +85 -0
- valuesets/enums/bio/uniprot_species.py +344 -0
- valuesets/enums/bio/viral_genome_types.py +47 -0
- valuesets/enums/bioprocessing/__init__.py +1 -0
- valuesets/enums/bioprocessing/scale_up.py +249 -0
- valuesets/enums/business/__init__.py +1 -0
- valuesets/enums/business/human_resources.py +275 -0
- valuesets/enums/business/industry_classifications.py +181 -0
- valuesets/enums/business/management_operations.py +228 -0
- valuesets/enums/business/organizational_structures.py +236 -0
- valuesets/enums/business/quality_management.py +181 -0
- valuesets/enums/business/supply_chain.py +232 -0
- valuesets/enums/chemistry/__init__.py +1 -0
- valuesets/enums/chemistry/chemical_entities.py +315 -0
- valuesets/enums/chemistry/reaction_directionality.py +65 -0
- valuesets/enums/chemistry/reactions.py +256 -0
- valuesets/enums/clinical/__init__.py +1 -0
- valuesets/enums/clinical/nih_demographics.py +177 -0
- valuesets/enums/clinical/phenopackets.py +254 -0
- valuesets/enums/common_value_sets.py +8791 -0
- valuesets/enums/computing/__init__.py +1 -0
- valuesets/enums/computing/file_formats.py +294 -0
- valuesets/enums/computing/maturity_levels.py +196 -0
- valuesets/enums/computing/mime_types.py +227 -0
- valuesets/enums/confidence_levels.py +168 -0
- valuesets/enums/contributor.py +30 -0
- valuesets/enums/core.py +42 -0
- valuesets/enums/data/__init__.py +1 -0
- valuesets/enums/data/data_absent_reason.py +53 -0
- valuesets/enums/data_science/__init__.py +1 -0
- valuesets/enums/data_science/binary_classification.py +87 -0
- valuesets/enums/data_science/emotion_classification.py +66 -0
- valuesets/enums/data_science/priority_severity.py +73 -0
- valuesets/enums/data_science/quality_control.py +46 -0
- valuesets/enums/data_science/sentiment_analysis.py +50 -0
- valuesets/enums/data_science/text_classification.py +97 -0
- valuesets/enums/demographics.py +206 -0
- valuesets/enums/ecological_interactions.py +151 -0
- valuesets/enums/energy/__init__.py +1 -0
- valuesets/enums/energy/energy.py +343 -0
- valuesets/enums/energy/fossil_fuels.py +29 -0
- valuesets/enums/energy/nuclear/__init__.py +1 -0
- valuesets/enums/energy/nuclear/nuclear_facilities.py +195 -0
- valuesets/enums/energy/nuclear/nuclear_fuel_cycle.py +96 -0
- valuesets/enums/energy/nuclear/nuclear_fuels.py +175 -0
- valuesets/enums/energy/nuclear/nuclear_operations.py +191 -0
- valuesets/enums/energy/nuclear/nuclear_regulatory.py +188 -0
- valuesets/enums/energy/nuclear/nuclear_safety.py +164 -0
- valuesets/enums/energy/nuclear/nuclear_waste.py +158 -0
- valuesets/enums/energy/nuclear/reactor_types.py +163 -0
- valuesets/enums/environmental_health/__init__.py +1 -0
- valuesets/enums/environmental_health/exposures.py +265 -0
- valuesets/enums/geography/__init__.py +1 -0
- valuesets/enums/geography/geographic_codes.py +741 -0
- valuesets/enums/health/__init__.py +12 -0
- valuesets/enums/health/vaccination.py +98 -0
- valuesets/enums/health.py +36 -0
- valuesets/enums/health_base.py +36 -0
- valuesets/enums/healthcare.py +45 -0
- valuesets/enums/industry/__init__.py +1 -0
- valuesets/enums/industry/extractive_industry.py +94 -0
- valuesets/enums/industry/mining.py +388 -0
- valuesets/enums/industry/safety_colors.py +201 -0
- valuesets/enums/investigation.py +27 -0
- valuesets/enums/materials_science/__init__.py +1 -0
- valuesets/enums/materials_science/characterization_methods.py +112 -0
- valuesets/enums/materials_science/crystal_structures.py +76 -0
- valuesets/enums/materials_science/material_properties.py +119 -0
- valuesets/enums/materials_science/material_types.py +104 -0
- valuesets/enums/materials_science/pigments_dyes.py +198 -0
- valuesets/enums/materials_science/synthesis_methods.py +109 -0
- valuesets/enums/medical/__init__.py +1 -0
- valuesets/enums/medical/clinical.py +277 -0
- valuesets/enums/medical/neuroimaging.py +119 -0
- valuesets/enums/mining_processing.py +302 -0
- valuesets/enums/physics/__init__.py +1 -0
- valuesets/enums/physics/states_of_matter.py +46 -0
- valuesets/enums/social/__init__.py +1 -0
- valuesets/enums/social/person_status.py +29 -0
- valuesets/enums/spatial/__init__.py +1 -0
- valuesets/enums/spatial/spatial_qualifiers.py +246 -0
- valuesets/enums/statistics/__init__.py +5 -0
- valuesets/enums/statistics/prediction_outcomes.py +31 -0
- valuesets/enums/statistics.py +31 -0
- valuesets/enums/time/__init__.py +1 -0
- valuesets/enums/time/temporal.py +254 -0
- valuesets/enums/units/__init__.py +1 -0
- valuesets/enums/units/measurements.py +310 -0
- valuesets/enums/visual/__init__.py +1 -0
- valuesets/enums/visual/colors.py +376 -0
- valuesets/generators/__init__.py +19 -0
- valuesets/generators/auto_slot_injector.py +280 -0
- valuesets/generators/enhanced_pydantic_generator.py +100 -0
- valuesets/generators/enum_slot_generator.py +201 -0
- valuesets/generators/modular_rich_generator.py +353 -0
- valuesets/generators/prefix_standardizer.py +198 -0
- valuesets/generators/rich_enum.py +127 -0
- valuesets/generators/rich_pydantic_generator.py +310 -0
- valuesets/generators/smart_slot_syncer.py +428 -0
- valuesets/generators/sssom_generator.py +394 -0
- valuesets/merged/merged_hierarchy.yaml +21649 -0
- valuesets/schema/README.md +3 -0
- valuesets/schema/academic/research.yaml +911 -0
- valuesets/schema/analytical_chemistry/mass_spectrometry.yaml +206 -0
- valuesets/schema/bio/bio_entities.yaml +364 -0
- valuesets/schema/bio/biological_colors.yaml +434 -0
- valuesets/schema/bio/cell_cycle.yaml +309 -0
- valuesets/schema/bio/currency_chemicals.yaml +70 -0
- valuesets/schema/bio/developmental_stages.yaml +226 -0
- valuesets/schema/bio/genome_features.yaml +342 -0
- valuesets/schema/bio/genomics.yaml +101 -0
- valuesets/schema/bio/go_aspect.yaml +39 -0
- valuesets/schema/bio/go_causality.yaml +119 -0
- valuesets/schema/bio/go_evidence.yaml +215 -0
- valuesets/schema/bio/insdc_geographic_locations.yaml +911 -0
- valuesets/schema/bio/insdc_missing_values.yaml +85 -0
- valuesets/schema/bio/lipid_categories.yaml +72 -0
- valuesets/schema/bio/plant_biology.yaml +125 -0
- valuesets/schema/bio/plant_developmental_stages.yaml +77 -0
- valuesets/schema/bio/plant_sex.yaml +108 -0
- valuesets/schema/bio/protein_evidence.yaml +63 -0
- valuesets/schema/bio/proteomics_standards.yaml +116 -0
- valuesets/schema/bio/psi_mi.yaml +400 -0
- valuesets/schema/bio/relationship_to_oxygen.yaml +46 -0
- valuesets/schema/bio/sequence_alphabets.yaml +1168 -0
- valuesets/schema/bio/sequence_chemistry.yaml +477 -0
- valuesets/schema/bio/sequencing_platforms.yaml +515 -0
- valuesets/schema/bio/structural_biology.yaml +428 -0
- valuesets/schema/bio/taxonomy.yaml +453 -0
- valuesets/schema/bio/trophic_levels.yaml +118 -0
- valuesets/schema/bio/uniprot_species.yaml +1209 -0
- valuesets/schema/bio/viral_genome_types.yaml +99 -0
- valuesets/schema/bioprocessing/scale_up.yaml +458 -0
- valuesets/schema/business/human_resources.yaml +752 -0
- valuesets/schema/business/industry_classifications.yaml +448 -0
- valuesets/schema/business/management_operations.yaml +602 -0
- valuesets/schema/business/organizational_structures.yaml +645 -0
- valuesets/schema/business/quality_management.yaml +502 -0
- valuesets/schema/business/supply_chain.yaml +688 -0
- valuesets/schema/chemistry/chemical_entities.yaml +639 -0
- valuesets/schema/chemistry/reaction_directionality.yaml +60 -0
- valuesets/schema/chemistry/reactions.yaml +442 -0
- valuesets/schema/clinical/nih_demographics.yaml +285 -0
- valuesets/schema/clinical/phenopackets.yaml +429 -0
- valuesets/schema/computing/file_formats.yaml +631 -0
- valuesets/schema/computing/maturity_levels.yaml +229 -0
- valuesets/schema/computing/mime_types.yaml +266 -0
- valuesets/schema/confidence_levels.yaml +206 -0
- valuesets/schema/contributor.yaml +30 -0
- valuesets/schema/core.yaml +55 -0
- valuesets/schema/data/data_absent_reason.yaml +82 -0
- valuesets/schema/data_science/binary_classification.yaml +125 -0
- valuesets/schema/data_science/emotion_classification.yaml +109 -0
- valuesets/schema/data_science/priority_severity.yaml +122 -0
- valuesets/schema/data_science/quality_control.yaml +68 -0
- valuesets/schema/data_science/sentiment_analysis.yaml +81 -0
- valuesets/schema/data_science/text_classification.yaml +135 -0
- valuesets/schema/demographics.yaml +238 -0
- valuesets/schema/ecological_interactions.yaml +298 -0
- valuesets/schema/energy/energy.yaml +595 -0
- valuesets/schema/energy/fossil_fuels.yaml +28 -0
- valuesets/schema/energy/nuclear/nuclear_facilities.yaml +463 -0
- valuesets/schema/energy/nuclear/nuclear_fuel_cycle.yaml +82 -0
- valuesets/schema/energy/nuclear/nuclear_fuels.yaml +421 -0
- valuesets/schema/energy/nuclear/nuclear_operations.yaml +480 -0
- valuesets/schema/energy/nuclear/nuclear_regulatory.yaml +200 -0
- valuesets/schema/energy/nuclear/nuclear_safety.yaml +352 -0
- valuesets/schema/energy/nuclear/nuclear_waste.yaml +332 -0
- valuesets/schema/energy/nuclear/reactor_types.yaml +394 -0
- valuesets/schema/environmental_health/exposures.yaml +355 -0
- valuesets/schema/generated_slots.yaml +1828 -0
- valuesets/schema/geography/geographic_codes.yaml +1018 -0
- valuesets/schema/health/vaccination.yaml +102 -0
- valuesets/schema/health.yaml +38 -0
- valuesets/schema/healthcare.yaml +53 -0
- valuesets/schema/industry/extractive_industry.yaml +89 -0
- valuesets/schema/industry/mining.yaml +888 -0
- valuesets/schema/industry/safety_colors.yaml +375 -0
- valuesets/schema/investigation.yaml +64 -0
- valuesets/schema/materials_science/characterization_methods.yaml +193 -0
- valuesets/schema/materials_science/crystal_structures.yaml +138 -0
- valuesets/schema/materials_science/material_properties.yaml +135 -0
- valuesets/schema/materials_science/material_types.yaml +151 -0
- valuesets/schema/materials_science/pigments_dyes.yaml +465 -0
- valuesets/schema/materials_science/synthesis_methods.yaml +186 -0
- valuesets/schema/medical/clinical.yaml +610 -0
- valuesets/schema/medical/neuroimaging.yaml +325 -0
- valuesets/schema/mining_processing.yaml +295 -0
- valuesets/schema/physics/states_of_matter.yaml +46 -0
- valuesets/schema/slot_mixins.yaml +143 -0
- valuesets/schema/social/person_status.yaml +28 -0
- valuesets/schema/spatial/spatial_qualifiers.yaml +466 -0
- valuesets/schema/statistics/prediction_outcomes.yaml +26 -0
- valuesets/schema/statistics.yaml +34 -0
- valuesets/schema/time/temporal.yaml +435 -0
- valuesets/schema/types.yaml +15 -0
- valuesets/schema/units/measurements.yaml +675 -0
- valuesets/schema/valuesets.yaml +100 -0
- valuesets/schema/visual/colors.yaml +778 -0
- valuesets/utils/__init__.py +6 -0
- valuesets/utils/comparison.py +102 -0
- valuesets/utils/expand_dynamic_enums.py +414 -0
- valuesets/utils/mapping_utils.py +236 -0
- valuesets/validators/__init__.py +11 -0
- valuesets/validators/enum_evaluator.py +669 -0
- valuesets/validators/oak_config.yaml +70 -0
- valuesets/validators/validate_with_ols.py +241 -0
- valuesets-0.3.1.dist-info/METADATA +395 -0
- valuesets-0.3.1.dist-info/RECORD +248 -0
- valuesets-0.3.1.dist-info/WHEEL +4 -0
- valuesets-0.3.1.dist-info/licenses/LICENSE +201 -0
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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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description: Political news and government affairs
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title: Politics
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description: Business, finance, and economic news
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title: Business
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- finance
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- economy
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description: Technology and computing news
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title: Technology
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- tech
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- IT
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description: Sports news and events
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title: Sports
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description: Entertainment and celebrity news
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aliases:
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- showbiz
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description: Scientific discoveries and research
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title: Science
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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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description: International news and events
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title: World
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- international
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description: Text is appropriate and non-harmful
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meaning: SIO:001010
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- clean
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- '0'
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title: Toxic
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title: Severe Toxic
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title: Help
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title: Information
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title: Complaint
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title: Feedback
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description: User intent to buy or purchase
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title: Purchase
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title: Cancel
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name: valuesets-demographics
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2
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title: valuesets-demographics
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3
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description: Demographic and social determinant value sets from NIH CDE and HL7 standards
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4
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id: https://w3id.org/valuesets/demographics
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5
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prefixes:
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# linkml_common: https://w3id.org/valuesets/
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7
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linkml: https://w3id.org/linkml/
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8
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biolink: https://w3id.org/biolink/
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9
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schema: http://schema.org/
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10
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HL7: http://terminology.hl7.org/CodeSystem/
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11
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SNOMED: http://snomed.info/id/
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12
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valuesets: https://w3id.org/valuesets/
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13
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default_prefix: valuesets
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14
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slots:
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15
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education_level:
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16
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description: Years of education that a person has completed
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17
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range: EducationLevel
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18
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marital_status:
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description: The domestic partnership status of a person
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20
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range: MaritalStatus
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employment_status:
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22
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description: Employment status of a person
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23
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range: EmploymentStatus
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24
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housing_status:
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25
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description: Housing status of patients per UDS Plus HRSA standards
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range: HousingStatus
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gender_identity:
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description: Gender identity codes indicating an individual's personal sense of gender
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29
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range: GenderIdentity
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30
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omb_race_category:
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31
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description: Office of Management and Budget (OMB) race category codes
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32
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range: OmbRaceCategory
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33
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omb_ethnicity_category:
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description: Office of Management and Budget (OMB) ethnicity category codes
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range: OmbEthnicityCategory
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enums:
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37
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EducationLevel:
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description: Years of education that a person has completed
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39
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source: https://terminology.hl7.org/CodeSystem-v3-EducationLevel.html
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40
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permissible_values:
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41
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ELEM:
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42
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description: Elementary School
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43
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meaning: HL7:v3-EducationLevel#ELEM
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44
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SEC:
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45
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description: Some secondary or high school education
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46
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meaning: HL7:v3-EducationLevel#SEC
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HS:
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48
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description: High School or secondary school degree complete
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49
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meaning: HL7:v3-EducationLevel#HS
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50
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SCOL:
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51
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description: Some College education
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52
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meaning: HL7:v3-EducationLevel#SCOL
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ASSOC:
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54
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description: Associate's or technical degree complete
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55
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meaning: HL7:v3-EducationLevel#ASSOC
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BD:
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57
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description: College or baccalaureate degree complete
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meaning: HL7:v3-EducationLevel#BD
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59
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PB:
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60
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description: Some post-baccalaureate education
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61
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meaning: HL7:v3-EducationLevel#PB
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GD:
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63
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description: Graduate or professional Degree complete
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64
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meaning: HL7:v3-EducationLevel#GD
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65
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+
POSTG:
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66
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description: Doctoral or post graduate education
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67
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+
meaning: HL7:v3-EducationLevel#POSTG
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68
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+
MaritalStatus:
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69
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description: The domestic partnership status of a person
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70
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+
source: https://www.hl7.org/fhir/valueset-marital-status.html
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71
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+
permissible_values:
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72
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ANNULLED:
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73
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+
description: Marriage contract has been declared null and to not have existed
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74
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+
meaning: HL7:marital-status#A
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75
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+
DIVORCED:
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76
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+
description: Marriage contract has been declared dissolved and inactive
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77
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+
meaning: HL7:marital-status#D
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78
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+
INTERLOCUTORY:
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79
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+
description: Subject to an Interlocutory Decree
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80
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+
meaning: HL7:marital-status#I
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81
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+
LEGALLY_SEPARATED:
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82
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+
description: Legally Separated
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83
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+
meaning: HL7:marital-status#L
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84
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+
MARRIED:
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85
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+
description: A current marriage contract is active
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86
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+
meaning: HL7:marital-status#M
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87
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+
COMMON_LAW:
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88
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+
description: Marriage recognized in some jurisdictions based on parties' agreement
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89
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+
meaning: HL7:marital-status#C
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90
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+
POLYGAMOUS:
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91
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+
description: More than 1 current spouse
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92
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+
meaning: HL7:marital-status#P
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93
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+
DOMESTIC_PARTNER:
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94
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+
description: Person declares that a domestic partner relationship exists
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|
95
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+
meaning: HL7:marital-status#T
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|
96
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+
UNMARRIED:
|
|
97
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+
description: Currently not in a marriage contract
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|
98
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+
meaning: HL7:marital-status#U
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99
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+
NEVER_MARRIED:
|
|
100
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+
description: No marriage contract has ever been entered
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101
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+
meaning: HL7:marital-status#S
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|
102
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+
WIDOWED:
|
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103
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+
description: The spouse has died
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104
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+
meaning: HL7:marital-status#W
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105
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+
UNKNOWN:
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106
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+
description: A proper value is applicable, but not known
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107
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+
meaning: HL7:marital-status#UNK
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108
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+
EmploymentStatus:
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109
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+
description: Employment status of a person
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110
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+
source: https://terminology.hl7.org/CodeSystem-v2-0066.html
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111
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+
permissible_values:
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112
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+
FULL_TIME_EMPLOYED:
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113
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+
description: Full time employed
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114
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+
meaning: HL7:v2-0066#1
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115
|
+
PART_TIME_EMPLOYED:
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116
|
+
description: Part time employed
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117
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+
meaning: HL7:v2-0066#2
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118
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+
UNEMPLOYED:
|
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119
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+
description: Unemployed
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120
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+
meaning: HL7:v2-0066#3
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121
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+
SELF_EMPLOYED:
|
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122
|
+
description: Self-employed
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123
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+
meaning: HL7:v2-0066#4
|
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124
|
+
RETIRED:
|
|
125
|
+
description: Retired
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126
|
+
meaning: HL7:v2-0066#5
|
|
127
|
+
ACTIVE_MILITARY:
|
|
128
|
+
description: On active military duty
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|
129
|
+
meaning: HL7:v2-0066#6
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|
130
|
+
CONTRACT:
|
|
131
|
+
description: Contract, per diem
|
|
132
|
+
meaning: HL7:v2-0066#C
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|
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
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|
144
|
+
meaning: HL7:v2-0066#T
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|
145
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+
UNKNOWN:
|
|
146
|
+
description: Unknown
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|
147
|
+
meaning: HL7:v2-0066#9
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|
148
|
+
HousingStatus:
|
|
149
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+
description: Housing status of patients per UDS Plus HRSA standards
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|
150
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+
source: https://www.fhir.org/guides/hrsa/uds-plus/CodeSystem-udsplus-housing-status-codes.html
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|
151
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+
permissible_values:
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|
152
|
+
HOMELESS_SHELTER:
|
|
153
|
+
description: Patients who are living in a homeless shelter
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|
154
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+
meaning: HL7:udsplus-housing-status-codes#homeless-shelter
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155
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+
TRANSITIONAL:
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|
156
|
+
description: Patients who do not have a house and are in a transitional state
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|
157
|
+
meaning: HL7:udsplus-housing-status-codes#transitional
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158
|
+
DOUBLING_UP:
|
|
159
|
+
description: Patients who are doubling up with others
|
|
160
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+
meaning: HL7:udsplus-housing-status-codes#doubling-up
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|
161
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+
STREET:
|
|
162
|
+
description: Patients who do not have a house and are living on the streets
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|
163
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+
meaning: HL7:udsplus-housing-status-codes#street
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|
164
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+
PERMANENT_SUPPORTIVE_HOUSING:
|
|
165
|
+
description: Patients who are living in a permanent supportive housing
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|
166
|
+
meaning: HL7:udsplus-housing-status-codes#permanent-supportive-housing
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|
167
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+
OTHER:
|
|
168
|
+
description: Patients who have other kinds of accommodation
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|
169
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+
meaning: HL7:udsplus-housing-status-codes#other
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|
170
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+
UNKNOWN:
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|
171
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+
description: Patients with Unknown accommodation
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|
172
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+
meaning: HL7:udsplus-housing-status-codes#unknown
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173
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+
GenderIdentity:
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174
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+
description: Gender identity codes indicating an individual's personal sense of gender
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|
175
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+
source: https://terminology.hl7.org/ValueSet-gender-identity.html
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176
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+
permissible_values:
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177
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+
FEMALE:
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178
|
+
description: Identifies as female gender (finding)
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|
179
|
+
meaning: SNOMED:446141000124107
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180
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+
MALE:
|
|
181
|
+
description: Identifies as male gender (finding)
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|
182
|
+
meaning: SNOMED:446151000124109
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183
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+
NON_BINARY:
|
|
184
|
+
description: Identifies as gender nonbinary
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|
185
|
+
meaning: SNOMED:33791000087105
|
|
186
|
+
ASKED_DECLINED:
|
|
187
|
+
description: Asked But Declined
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188
|
+
meaning: HL7:asked-declined
|
|
189
|
+
UNKNOWN:
|
|
190
|
+
description: A proper value is applicable, but not known
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|
191
|
+
meaning: HL7:UNK
|
|
192
|
+
OmbRaceCategory:
|
|
193
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+
description: Office of Management and Budget (OMB) race category codes
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|
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
|
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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)
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|
213
|
+
meaning: HL7:CDCREC#2131-1
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214
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+
ASKED_BUT_UNKNOWN:
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|
215
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+
description: asked but unknown
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216
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+
meaning: HL7:ASKU
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217
|
+
UNKNOWN:
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|
218
|
+
description: unknown
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219
|
+
meaning: HL7:UNK
|
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220
|
+
OmbEthnicityCategory:
|
|
221
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+
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
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|
229
|
+
meaning: HL7:CDCREC#2186-5
|
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230
|
+
ASKED_BUT_UNKNOWN:
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231
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+
description: asked but unknown
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232
|
+
meaning: HL7:ASKU
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233
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+
UNKNOWN:
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234
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+
description: unknown
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235
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+
meaning: HL7:UNK
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236
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+
license: MIT
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237
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+
see_also:
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238
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+
- https://linkml.github.io/valuesets
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|
@@ -0,0 +1,298 @@
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|
|
1
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+
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.
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|
5
|
+
|
|
6
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+
'
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|
7
|
+
id: https://w3id.org/valuesets/ecological-interactions
|
|
8
|
+
version: 1.0.0
|
|
9
|
+
status: release
|
|
10
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+
imports:
|
|
11
|
+
- linkml:types
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|
12
|
+
- ./core
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|
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:
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|
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
|