This workflow is a work in process.
VesselBaseName
is used for the VCCF term label and for oio:obo_foundry_uniquename
annotation, adding "(Human)". We use this column as a label because it's the vessel name without the “#N” at the end. This applies to vessels with more than one BranchesFrom
. However, in cases with a specific number of vessels in the body, the VesselBaseName
includes a number for each vessel. In UBERON, these cases should be added only one term.
VesselTypeID
is used for the vessel classification. Possible values are, as UBERON terms, heart chamber, artery, arteriole, capillary, venule, vein, or sinus.
VesselTypeID
is heart chamber,
the values in BranchesFrom
and Vessel
are the same, which are not vessels, and should not add the BranchesFrom
relationship because it's the same as in Vessel
, which is false. It should include only the VesselTypeID
as a parent and link to the matching UBERON term.BodyPartID
is used as the logical axiom part of
to identify the part of the body where the vessel is located.BodyPart
generates a simplified definition. In some cases, this can be redundant with data available in the crosswalk table, which defines the specific relationship between the vessel and the tissue.
ReferenceURL
and ReferenceDOI
are used as xref for the definition in the pattern. Some values in ReferenceURL
are the URLs for the UBERON matching term. In these cases, the reference is empty. When the ReferenceURL
is a PMC publication URL, it's transformed into PMID.
ReferenceURL
is from PMC publication.FMA
is used as oboInOwl:hasDbXref
for the term.FMALabel
and FMA
are used as exact synonym and synonym xref, respectively, when the label
is different than the FMALabel
. The synonym is added as lowercase.present in taxon
relationship.BranchesFrom
, which means the “parent” vessel that is one step closer to the heart. For the ontology, we use connecting branch of
.
drains to
rather than connecting branch of
.VesselType
.Vessel
contains the VCCF terms created in the DOSDP. The label performs the search.Relationship
column.
BodySubPartID
, a VCCF ID is created and the label from BodySubPart
are added to the template. Then the new VCCF ID is used for the relationship. This process creates 76 terms.BodyPart
is angiosome.BodySubPart
.BranchesFrom: The “parent” vessel that is one step closer to the heart. For veins it is “drains to” rather than branches from.
Vessel: The name of the blood vessel. The unique item (primary key) in this table. If a vessel has more than one BranchesFrom, the vessel is listed on multiple rows, but with “ #2”, “ #3”, etc. added to the end of its name.
VesselBaseName: The vessel name without the “#N” at the end. This applies to vessels with more than one BranchesFrom.
BodyPart: A mapping from vessel to organ or part of the body.
BodyPartID: The UBERON or FMA ID of the BodyPart (imported from UBERON or FMA).
UBERON: The ID of the vessel in the UBERON ontology.
(Not directly used; UBERON import via OD) UBERONLabel: The main label of the vessel in UBERON (imported from UBERON).
FMA: The ID of the vessel in the FMA ontology.
FMALabel: The main label of the vessel in FMA (imported from FMA).
ReferenceURL: The website describing the vessel and where it branches from.
ReferenceDOI: The DOI of the reference if applicable.
VesselType: Either heart chamber, artery, arteriole, capillary, venule, vein, or sinus.
VesselTypeID: The UBERON or FMA ID of the VesselType (imported from UBERON or FMA).
VesselSubType: For capillaries: continuous, fenestrated, sinusoid.
VesselSubTypeID: The UBERON or FMA ID of the VesselSubType (imported from UBERON or FMA).
BodySubPart: The specific anatomical structure the vessel supplies or drains.
BodySubPartID. The UBERON or FMA ID of the BodySubPart (imported from UBERON or FMA).
PortalSystem: Indicates if the vessel is part of a portal system (e.g., hepatic portal system, hypophyseal portal system, etc.).
Sex: Indicates whether the vessel is only found in males or females.
Anastomoses: Indicates whether the vessel anastomoses with another vessel.
ArteryVeinConnects: Indicates if an end branch (“leaf” vessel) in one vessel tree connects to a vessel in a different tree leading back to the heart (e.g., hepatic arteriole ->liver sinusoid).
ArteryVeinPair: Indicates if another vessel has the same name, but with the words artery/arteriole swapped with vein/venule. Later this field will be used to match vessels with similar supplies/drains regions.
ForBranchesSee: 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.
VirtualVessel: This field contains a “1” if it is virtual merged vessel used to show the branches of other vessels; a negative value also indicates a virtual vessel, but the merged vessels are not yet explicitly defined in this table; zero for all other vessels.
BranchSequence: 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.
VirtualVesselOfList: The list (separated by semicolons) of vessels that are merged to form a virtual vessel.
VirtualVesselOfCount: The number of vessels that are merged to form a virtual vessel.
VirtualInstances: The number of times this vessel would be listed if virtual vessels were not used along the path back to the heart.
VirtualPath: The list of vessels that have been merged along the path back to the heart.
PathFromHeart: The list of branches leading from a heart chamber to the vessel. This field is useful for sorting the table.
PathFromHeartWithIDs: Same as PathFromHeart, but the ASLabel and ASID are listed next to each vessel in the path.
The latest version of the ontology can always be found at:
Editors of this ontology should use the edit version, src/ontology/vccf-edit.owl
Please use this GitHub repository's Issue tracker to request new terms/classes or report errors or specific concerns related to the ontology.
This ontology repository was created using the Ontology Development Kit (ODK).