asctb.yaml

id: https://w3id.org/asctb
name: asctb
description: asctb
imports:
- linkml:types
prefixes:
  linkml: https://w3id.org/linkml/
  asctb: https://w3id.org/asctb
  schema: http://schema.org/
  CL: http://purl.obolibrary.org/obo/CL_
  UBERON: http://purl.obolibrary.org/obo/UBERON_
default_curi_maps:
  - semweb_context
  - obo_context
default_prefix: asctb
types:
  CL identifier:
    typeof: string
  HGNC identifier:
    typeof: string
  identifier:
    typeof: string
  UBERON identifier:
    typeof: string
  FMA identifier:
    typeof: string
  DOI:
    typeof: string
  Anatomical label:
    typeof: string
  Cell type label:
    typeof: string
  CoordinateType:
    typeof: integer
classes:
  VesselClass:
    slots:
    - BranchesFrom
    - Vessel
    - VesselType
    - BodyPart
    - Sex
    - Anastomoses
    - ForBranchesSee
    - MergedVessel
    - CoordX
    - CoordY
    - BranchSequence
    - CellType
    - CellTypeLabel
    - CellTypeID
    - Biomarkers
    - BiomarkersLabel
    - BiomarkersID
    - ReferenceURL
    - Reference
    - ReferenceDOI
    - UBERON
    - FMA
    - BodyPartUberon
    - UBERONLabel
    - FMALabel
    - PathFromHeart
    slot_usage: {}
slots:
  BranchesFrom:
    description: The 'parent' vessel that is one step closer to the heart. For veins it is 'drains to' rather than branches from.
    range: Anatomical label
    examples:
    - value: truncus anterior of right pulmonary artery
  Vessel:
    range: Anatomical label
    description: The name of the blood vessel. The unique item (primary key) in this table.
    identifier: true
    slot_uri: schema:identifier
    examples:
    - value: apical segmental artery of right lung
  VesselType:
    range: VesselType_enum
    description: Either heart chamber, artery, arteriole, capillary, venule, vein, sinusoid, or sinus.
    slot_uri: rdfs:subClassOf
    examples:
    - value: artery
  BodyPart:
    range: Anatomical label
    description: A mapping from vessel to organ or part of the body.
    slot_uri: BFO:0000050
    examples:
    - value: lung
  Sex:
    range: Sex_enum
    description: Indicates whether the vessel is only found in males or females.
    slot_uri: schema:gender
    examples:
    - value: male
  Anastomoses:
    range: Anatomical label
    description: Indicates whether the vessel anastomoses with another vessel.
    examples:
    - value: anterior jugular vein (other side)
    slot_uri: RO:0002378
  ForBranchesSee:
    range: Anatomical label
    description: For some vessels, like the left and right renal arteries, rather than showing all the branches of both arteries, a "virtual" merged vessel is created (e.g., just "renal artery"). The branches are only added once to that virtual vessel. This field indicates the name of the virtual vessel that has the branches. 
    examples:
    - value: segmental pulmonary artery
  MergedVessel:
    range: IsVirtualMergedVessel
    description: This field contains a "1" if it is virtual merged vessel used to show the branches of other vessels. 
    examples:
    - value: '0'
  CoordX:
    range: CoordinateType
    description: The X coordinate for the approximate location of selected vessels. This is more to show relative position (left vs right) rather than the exact location.
    examples:
    - value: '-10'
  CoordY:
    range: CoordinateType
    description: The Y coordinate for the approximate location of selected vessels. This is more to show relative position (above vs below) rather than the exact location. 
    examples:
    - value: '-40'
  BranchSequence:
    range: integer
    description: The order in which vessels branch off of the BranchesFrom vessel. Vessels can have the same value if they branch off the BranchesFrom vessel at the same place. A value of 999 means the branching sequence will be added in a future version of this table. 
    examples:
    - value: '999'
  CellType:
    range: CellType_enum
    description: A type of cell associated with the vessel. 
    examples:
    - value: blood vessel endothelial cell
  CellTypeLabel:
    range: CellTypeLabel_enum
    description: The preferred name of the cell in Cell Ontology. 
    examples:
    - value: blood vessel endothelial cell
  CellTypeID:
    range: CL identifier
    description: The cell type ID in Cell Ontology. 
    examples:
    - value: CL:0000071
  Biomarkers:
#    range: Biomarkers_enum
    description: A biomarker associated with the vessel. 
    examples:
    - value: PECAM1 (CD31)
  BiomarkersLabel:
#    range: BiomarkersLabel_enum
    description: The preferred name of the biomarker in HUGO Gene Nomenclature Committee (HGNC) 
    examples:
    - value: PECAM1
  BiomarkersID:
    range: HGNC identifier
    description: The ID of the biomarker in HUGO Gene Nomenclature Committee (HGNC) 
    examples:
    - value: HGNC:8823
  ReferenceURL:
    range: uri
    description: The website describing the vessel and where it branches from. 
    examples:
    - value: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6039811/
  Reference:
    range: string
    description: A reference for the website. For example, if the ReferenceURL is a journal article, then this field is the reference (authors, title, journal, etc.) of the article. 
    examples:
    - value: Kandathil A, Chamarthy M. Pulmonary vascular anatomy & anatomical variants.
        Cardiovasc Diagn Ther. 2018 Jun;8(3):201-207.
  ReferenceDOI:
    range: DOI
    description: The DOI of the reference if applicable. 
    examples:
    - value: 10.21037/cdt.2018.01.04
  UBERON:
    range: UBERON identifier
    description: The ID of the vessel in the UBERON ontology. 
    examples:
    - value: UBERON:0001651
  FMA:
    range: FMA identifier
    description: The ID of the vessel in the FMA ontology. 
    examples:
    - value: fma8617
  BodyPartUberon:
    range: UBERON identifier
    description: The UBERON ID of the BodyPart. 
    examples:
    - value: UBERON:0002048
  UBERONLabel:
    range: Anatomical label
    description: The preferred name of the vessel in UBERON. 
    examples:
    - value: right pulmonary artery
  FMALabel:
    range: Anatomical label
    description: The preferred name of the vessel in FMA. 
    examples:
    - value: Right apical segmental artery
  PathFromHeart:
    range: Anatomical label
    description: The list of branches leading from a heart chamber to the vessel. 
    examples:
    - value: right ventricle;pulmonary trunk;right pulmonary artery;truncus anterior
        of right pulmonary artery;apical segmental artery of right lung
enums:
  CellTypeLabel_enum:
    permissible_values:
      blood vessel endothelial cell:
        description: blood vessel endothelial cell
        meaning: CL:0000071
      cardiac endothelial cell:
        description: cardiac endothelial cell
        meaning: CL:0010008
  CellType_enum:
    permissible_values:
      blood vessel endothelial cell:
        description: blood vessel endothelial cell
        meaning: CL:0000071
      cardiac endothelial cell:
        description: cardiac endothelial cell
        meaning: CL:0010008
  Sex_enum:
    permissible_values:
      female:
        description: female organism
        meaning: UBERON:0003100
      male:
        description: male organism
        meaning: UBERON:0003101
  VesselType_enum:
    permissible_values:
      arteriole:
        description: arteriole
        meaning: UBERON:0001980
      artery:
        description: artery
        meaning: UBERON:0001637
      capillary:
        description: capillary
        meaning: UBERON:0001982
      heart chamber:
        description: heart
        meaning: UBERON:0000948
      sinus:
        description: sinus
      sinusoid:
        description: sinusoid
        meaning: UBERON:0003909
      vein:
        description: vein
        meaning: UBERON:0001638
      venule:
        description: venule
        meaning: UBERON:0001979
  IsVirtualMergedVessel:
    permissible_values:
      "0": is NOT virtual merged vessel used to show the branches of other vessels. 
      "1": is virtual merged vessel used to show the branches of other vessels.