valuesets 0.3.1__py3-none-any.whl

valuesets/schema/analytical_chemistry/mass_spectrometry.yaml

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+id: https://w3id.org/valuesets/analytical_chemistry/mass_spectrometry
+name: mass_spectrometry
+title: Mass Spectrometry Value Sets
+description: |-
+  Value sets for mass spectrometry and analytical chemistry, derived from MS and MSIO ontologies.
+license: https://creativecommons.org/publicdomain/zero/1.0/
+version: 0.1.0
+prefixes:
+  valuesets: https://w3id.org/valuesets/
+  linkml: https://w3id.org/linkml/
+  MS: http://purl.obolibrary.org/obo/MS_
+  MSIO: http://purl.obolibrary.org/obo/MSIO_
+  CHMO: http://purl.obolibrary.org/obo/CHMO_
+default_prefix: valuesets
+imports:
+  - linkml:types
+  - ../core
+
+enums:
+  MassSpectrometerFileFormat:
+    description: Standard file formats used in mass spectrometry
+    permissible_values:
+      MZML:
+        title: mzML format
+        description: mzML format - PSI standard for mass spectrometry data
+        meaning: MS:1000584
+      MZXML:
+        title: ISB mzXML format
+        description: ISB mzXML format
+        meaning: MS:1000566
+      MGF:
+        title: Mascot MGF format
+        description: Mascot Generic Format
+        meaning: MS:1001062
+      THERMO_RAW:
+        title: Thermo RAW format
+        description: Thermo RAW format
+        meaning: MS:1000563
+      WATERS_RAW:
+        title: Waters raw format
+        description: Waters raw format
+        meaning: MS:1000526
+      WIFF:
+        title: ABI WIFF format
+        description: ABI WIFF format
+        meaning: MS:1000562
+      MZDATA:
+        title: PSI mzData format
+        description: PSI mzData format
+        meaning: MS:1000564
+      PKL:
+        title: Micromass PKL format
+        description: Micromass PKL format
+        meaning: MS:1000565
+      DTA:
+        title: DTA format
+        description: DTA format
+        meaning: MS:1000613
+      MS2:
+        title: MS2 format
+        description: MS2 format
+        meaning: MS:1001466
+      BRUKER_BAF:
+        title: Bruker BAF format
+        description: Bruker BAF format
+        meaning: MS:1000815
+      BRUKER_TDF:
+        title: Bruker TDF format
+        description: Bruker TDF format
+        meaning: MS:1002817
+      BRUKER_TSF:
+        title: Bruker TSF format
+        description: Bruker TSF format
+        meaning: MS:1003282
+      MZ5:
+        title: mz5 format
+        description: mz5 format
+        meaning: MS:1001881
+      MZMLB:
+        title: mzMLb format
+        description: mzMLb format
+        meaning: MS:1002838
+      UIMF:
+        title: UIMF format
+        description: UIMF format
+        meaning: MS:1002531
+
+  MassSpectrometerVendor:
+    description: Major mass spectrometer manufacturers
+    permissible_values:
+      THERMO_FISHER_SCIENTIFIC:
+        title: Thermo Fisher Scientific instrument model
+        description: Thermo Fisher Scientific
+        meaning: MS:1000483
+      WATERS:
+        title: Waters instrument model
+        description: Waters Corporation
+        meaning: MS:1000126
+      BRUKER_DALTONICS:
+        title: Bruker Daltonics instrument model
+        description: Bruker Daltonics
+        meaning: MS:1000122
+      SCIEX:
+        title: SCIEX instrument model
+        description: SCIEX (formerly Applied Biosystems)
+        meaning: MS:1000121
+      AGILENT:
+        title: Agilent instrument model
+        description: Agilent Technologies
+        meaning: MS:1000490
+      SHIMADZU:
+        title: Shimadzu instrument model
+        description: Shimadzu Corporation
+        meaning: MS:1000124
+      LECO:
+        title: LECO instrument model
+        description: LECO Corporation
+        meaning: MS:1001800
+
+  ChromatographyType:
+    description: Types of chromatographic separation methods
+    permissible_values:
+      GAS_CHROMATOGRAPHY:
+        description: Gas chromatography
+        meaning: MSIO:0000147
+      HIGH_PERFORMANCE_LIQUID_CHROMATOGRAPHY:
+        description: High performance liquid chromatography
+        meaning: MSIO:0000148
+      LIQUID_CHROMATOGRAPHY_MASS_SPECTROMETRY:
+        description: Liquid chromatography-mass spectrometry
+        meaning: CHMO:0000524
+      GAS_CHROMATOGRAPHY_MASS_SPECTROMETRY:
+        description: Gas chromatography-mass spectrometry
+        meaning: CHMO:0000497
+      TANDEM_MASS_SPECTROMETRY:
+        description: Tandem mass spectrometry
+        meaning: CHMO:0000575
+      ISOTOPE_RATIO_MASS_SPECTROMETRY:
+        description: Isotope ratio mass spectrometry
+        meaning: CHMO:0000506
+
+  DerivatizationMethod:
+    description: Chemical derivatization methods for sample preparation
+    permissible_values:
+      SILYLATION:
+        description: Addition of silyl groups for improved volatility
+        meaning: MSIO:0000117
+      METHYLATION:
+        description: Addition of methyl groups
+        meaning: MSIO:0000115
+      ACETYLATION:
+        description: Addition of acetyl groups
+        meaning: MSIO:0000112
+      TRIFLUOROACETYLATION:
+        description: Addition of trifluoroacetyl groups
+        meaning: MSIO:0000113
+      ALKYLATION:
+        description: Addition of alkyl groups
+        meaning: MSIO:0000114
+      OXIMATION:
+        description: Addition of oxime groups
+        meaning: MSIO:0000116
+
+  MetabolomicsAssayType:
+    description: Types of metabolomics assays and profiling approaches
+    permissible_values:
+      TARGETED_METABOLITE_PROFILING:
+        title: targeted metabolite profiling
+        description: Assay targeting specific known metabolites
+        meaning: MSIO:0000100
+      UNTARGETED_METABOLITE_PROFILING:
+        title: untargeted metabolite profiling
+        description: Assay profiling all detectable metabolites
+        meaning: MSIO:0000101
+      METABOLITE_QUANTITATION_HPLC:
+        title: metabolite quantitation using high performance liquid chromatography
+        description: Metabolite quantitation using HPLC
+        meaning: MSIO:0000099
+
+  AnalyticalControlType:
+    description: Types of control samples used in analytical chemistry
+    permissible_values:
+      INTERNAL_STANDARD:
+        title: internal standard role
+        description: Known amount of standard added to analytical sample
+        meaning: MSIO:0000005
+      EXTERNAL_STANDARD:
+        title: external standard role
+        description: Reference standard used as external reference point
+        meaning: MSIO:0000004
+      POSITIVE_CONTROL:
+        title: positive control role
+        description: Control providing known positive signal
+        meaning: MSIO:0000008
+      NEGATIVE_CONTROL:
+        title: negative control role
+        description: Control providing baseline/no signal reference
+        meaning: MSIO:0000007
+      LONG_TERM_REFERENCE:
+        title: long term reference role
+        description: Stable reference for cross-batch comparisons
+        meaning: MSIO:0000006
+      BLANK:
+        description: Sample containing only solvent/matrix without analyte
+      QUALITY_CONTROL:
+        description: Sample with known composition for system performance monitoring

valuesets/schema/bio/bio_entities.yaml

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+name: bio_entities
+title: Biological Entity Value Sets
+description: 'Dynamic enumerations for biological entities including anatomical structures,
+
+  cell types, diseases, and chemical entities. These enums are populated
+
+  dynamically from ontologies.'
+id: https://w3id.org/linkml/valuesets/bio/bio_entities
+imports:
+- linkml:types
+prefixes:
+  valuesets: https://w3id.org/valuesets/
+  UBERON: http://purl.obolibrary.org/obo/UBERON_
+  CL: http://purl.obolibrary.org/obo/CL_
+  MONDO: http://purl.obolibrary.org/obo/MONDO_
+  CHEBI: http://purl.obolibrary.org/obo/CHEBI_
+  HP: http://purl.obolibrary.org/obo/HP_
+  GO: http://purl.obolibrary.org/obo/GO_
+  DOID: http://purl.obolibrary.org/obo/DOID_
+  NCBITaxon: http://purl.obolibrary.org/obo/NCBITaxon_
+  ENVO: http://purl.obolibrary.org/obo/ENVO_
+  PO: http://purl.obolibrary.org/obo/PO_
+  PR: http://purl.obolibrary.org/obo/PR_
+  SO: http://purl.obolibrary.org/obo/SO_
+  PATO: http://purl.obolibrary.org/obo/PATO_
+  RO: http://purl.obolibrary.org/obo/RO_
+default_prefix: valuesets
+slots:
+  metazoan_anatomical_structure:
+    description: Any anatomical structure found in metazoan organisms, including organs, tissues, and body parts
+    range: MetazoanAnatomicalStructure
+  human_anatomical_structure:
+    description: Anatomical structures specific to humans (Homo sapiens)
+    range: HumanAnatomicalStructure
+  plant_anatomical_structure:
+    description: Any anatomical structure found in plant organisms
+    range: PlantAnatomicalStructure
+  cell:
+    description: Any cell type from the Cell Ontology (CL), including native and experimentally modified cells
+    range: CellType
+  neuron:
+    description: Neuron cell types from the Cell Ontology
+    range: NeuronType
+  immune_cell:
+    description: Immune system cell types (leukocytes and their subtypes)
+    range: ImmuneCell
+  stem_cell:
+    description: Stem cell types and progenitor cells
+    range: StemCell
+  disease:
+    description: Human diseases from the Mondo Disease Ontology
+    range: Disease
+  infectious_disease:
+    description: Infectious diseases caused by pathogenic organisms
+    range: InfectiousDisease
+  cancer:
+    description: Neoplastic and cancerous diseases
+    range: Cancer
+  genetic_disease:
+    description: Hereditary and genetic diseases
+    range: GeneticDisease
+  chemical_entity:
+    description: Any chemical entity from ChEBI ontology
+    range: ChemicalEntity
+  drug:
+    description: Pharmaceutical drugs and medications
+    range: Drug
+  metabolite:
+    description: Metabolites and metabolic intermediates
+    range: Metabolite
+  protein:
+    description: Proteins and protein complexes
+    range: Protein
+  phenotype:
+    description: Phenotypic abnormalities from Human Phenotype Ontology
+    range: Phenotype
+  clinical_finding:
+    description: Clinical findings and observations
+    range: ClinicalFinding
+  biological_process:
+    description: Biological processes from Gene Ontology
+    range: BiologicalProcess
+  metabolic_process:
+    description: Metabolic processes and pathways
+    range: MetabolicProcess
+  molecular_function:
+    description: Molecular functions from Gene Ontology
+    range: MolecularFunction
+  cellular_component:
+    description: Cellular components and locations from Gene Ontology
+    range: CellularComponent
+  sequence_feature:
+    description: Sequence features from the Sequence Ontology
+    range: SequenceFeature
+    multivalued: true
+  gene_feature:
+    description: Gene-related sequence features
+    range: GeneFeature
+    multivalued: true
+  environment:
+    description: Environmental systems and biomes
+    range: Environment
+  environmental_material:
+    description: Environmental materials and substances
+    range: EnvironmentalMaterial
+  quality:
+    description: Phenotypic qualities and attributes from PATO
+    range: Quality
+  physical_quality:
+    description: Physical qualities like size, shape, color
+    range: PhysicalQuality
+enums:
+  MetazoanAnatomicalStructure:
+    description: 'Any anatomical structure found in metazoan organisms,
+
+      including organs, tissues, and body parts'
+    reachable_from:
+      source_ontology: obo:uberon
+      source_nodes:
+      - UBERON:0000061
+      include_self: true
+      relationship_types:
+      - rdfs:subClassOf
+  HumanAnatomicalStructure:
+    description: Anatomical structures specific to humans (Homo sapiens)
+    reachable_from:
+      source_ontology: obo:uberon
+      source_nodes:
+      - UBERON:0000061
+      include_self: false
+      relationship_types:
+      - rdfs:subClassOf
+  PlantAnatomicalStructure:
+    description: Any anatomical structure found in plant organisms
+    reachable_from:
+      source_ontology: obo:po
+      source_nodes:
+      - PO:0025131
+      include_self: true
+      relationship_types:
+      - rdfs:subClassOf
+  CellType:
+    description: 'Any cell type from the Cell Ontology (CL),
+
+      including native and experimentally modified cells'
+    reachable_from:
+      source_ontology: obo:cl
+      source_nodes:
+      - CL:0000000
+      include_self: true
+      relationship_types:
+      - rdfs:subClassOf
+  NeuronType:
+    description: Neuron cell types from the Cell Ontology
+    reachable_from:
+      source_ontology: obo:cl
+      source_nodes:
+      - CL:0000540
+      include_self: true
+      relationship_types:
+      - rdfs:subClassOf
+  ImmuneCell:
+    description: Immune system cell types (leukocytes and their subtypes)
+    reachable_from:
+      source_ontology: obo:cl
+      source_nodes:
+      - CL:0000988
+      include_self: true
+      relationship_types:
+      - rdfs:subClassOf
+  StemCell:
+    description: Stem cell types and progenitor cells
+    reachable_from:
+      source_ontology: obo:cl
+      source_nodes:
+      - CL:0000034
+      - CL:0000055
+      include_self: true
+      relationship_types:
+      - rdfs:subClassOf
+  Disease:
+    description: Human diseases from the Mondo Disease Ontology
+    reachable_from:
+      source_ontology: obo:mondo
+      source_nodes:
+      - MONDO:0000001
+      include_self: true
+      relationship_types:
+      - rdfs:subClassOf
+  InfectiousDisease:
+    description: Infectious diseases caused by pathogenic organisms
+    reachable_from:
+      source_ontology: obo:mondo
+      source_nodes:
+      - MONDO:0005550
+      include_self: true
+      relationship_types:
+      - rdfs:subClassOf
+  Cancer:
+    description: Neoplastic and cancerous diseases
+    reachable_from:
+      source_ontology: obo:mondo
+      source_nodes:
+      - MONDO:0004992
+      - MONDO:0005070
+      include_self: true
+      relationship_types:
+      - rdfs:subClassOf
+  GeneticDisease:
+    description: Hereditary and genetic diseases
+    reachable_from:
+      source_ontology: obo:mondo
+      source_nodes:
+      - MONDO:0003847
+      - MONDO:0021198
+      include_self: true
+      relationship_types:
+      - rdfs:subClassOf
+  ChemicalEntity:
+    description: Any chemical entity from ChEBI ontology
+    reachable_from:
+      source_ontology: obo:chebi
+      source_nodes:
+      - CHEBI:24431
+      include_self: true
+      relationship_types:
+      - rdfs:subClassOf
+  Drug:
+    description: Pharmaceutical drugs and medications
+    reachable_from:
+      source_ontology: obo:chebi
+      source_nodes:
+      - CHEBI:23888
+      include_self: true
+      relationship_types:
+      - rdfs:subClassOf
+      - RO:0000087
+  Metabolite:
+    description: Metabolites and metabolic intermediates
+    reachable_from:
+      source_ontology: obo:chebi
+      source_nodes:
+      - CHEBI:25212
+      include_self: true
+      relationship_types:
+      - rdfs:subClassOf
+  Protein:
+    description: Proteins and protein complexes
+    reachable_from:
+      source_ontology: obo:pr
+      source_nodes:
+      - PR:000000001
+      include_self: true
+      relationship_types:
+      - rdfs:subClassOf
+  Phenotype:
+    description: Phenotypic abnormalities from Human Phenotype Ontology
+    reachable_from:
+      source_ontology: obo:hp
+      source_nodes:
+      - HP:0000118
+      include_self: true
+      relationship_types:
+      - rdfs:subClassOf
+  ClinicalFinding:
+    description: Clinical findings and observations
+    reachable_from:
+      source_ontology: obo:hp
+      source_nodes:
+      - HP:0000118
+      include_self: false
+      relationship_types:
+      - rdfs:subClassOf
+  BiologicalProcess:
+    description: Biological processes from Gene Ontology
+    reachable_from:
+      source_ontology: obo:go
+      source_nodes:
+      - GO:0008150
+      include_self: true
+      relationship_types:
+      - rdfs:subClassOf
+  MetabolicProcess:
+    description: Metabolic processes and pathways
+    reachable_from:
+      source_ontology: obo:go
+      source_nodes:
+      - GO:0008152
+      include_self: true
+      relationship_types:
+      - rdfs:subClassOf
+  MolecularFunction:
+    description: Molecular functions from Gene Ontology
+    reachable_from:
+      source_ontology: obo:go
+      source_nodes:
+      - GO:0003674
+      include_self: true
+      relationship_types:
+      - rdfs:subClassOf
+  CellularComponent:
+    description: Cellular components and locations from Gene Ontology
+    reachable_from:
+      source_ontology: obo:go
+      source_nodes:
+      - GO:0005575
+      include_self: true
+      relationship_types:
+      - rdfs:subClassOf
+  SequenceFeature:
+    description: Sequence features from the Sequence Ontology
+    reachable_from:
+      source_ontology: obo:so
+      source_nodes:
+      - SO:0000110
+      include_self: true
+      relationship_types:
+      - rdfs:subClassOf
+  GeneFeature:
+    description: Gene-related sequence features
+    reachable_from:
+      source_ontology: obo:so
+      source_nodes:
+      - SO:0000704
+      include_self: true
+      relationship_types:
+      - rdfs:subClassOf
+  Environment:
+    description: Environmental systems and biomes
+    reachable_from:
+      source_ontology: obo:envo
+      source_nodes:
+      - ENVO:00000428
+      - ENVO:01000254
+      include_self: true
+      relationship_types:
+      - rdfs:subClassOf
+  EnvironmentalMaterial:
+    description: Environmental materials and substances
+    reachable_from:
+      source_ontology: obo:envo
+      source_nodes:
+      - ENVO:00010483
+      include_self: true
+      relationship_types:
+      - rdfs:subClassOf
+  Quality:
+    description: Phenotypic qualities and attributes from PATO
+    reachable_from:
+      source_ontology: obo:pato
+      source_nodes:
+      - PATO:0000001
+      include_self: true
+      relationship_types:
+      - rdfs:subClassOf
+  PhysicalQuality:
+    description: Physical qualities like size, shape, color
+    reachable_from:
+      source_ontology: obo:pato
+      source_nodes:
+      - PATO:0001241
+      include_self: true
+      relationship_types:
+      - rdfs:subClassOf