STATUS - EXPERIMENTAL DO NOT USE

Vasculature Common Coordinate Framework Ontology

Pipeline workflow

This workflow is a work in process.

1. Use a DOSDP to define all vessels available in the datasource. A Python script generates the data for the DOSDP.
   • label, human_label The column 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.
     • TODO: Remove vessels with numbers.
   • parent The column VesselTypeID is used for the vessel classification. Possible values are, as UBERON terms, heart chamber, artery, arteriole, capillary, venule, vein, or sinus.
     • TODO: Add more specific classifications when possible.
     • When 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.
     • TODO: Remove relationship in these cases
     • TODO: Remove heart chamber type terms from data related to vessel DP?.
   • location The column BodyPartID is used as the logical axiom part of to identify the part of the body where the vessel is located.
   • location_label The column 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.
     • TODO: Improve the use of this column in the DOSDP.
   • xrefs The columns 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.
     • TODO: Remove DOI if ReferenceURL is from PMC publication.
     • TODO: Search for DOI in radiopaedia cases
   • fma_xref When available, the column FMA is used as oboInOwl:hasDbXref for the term.
   • synonym, synonym_xref The column 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.
   • taxon The taxon NCBITaxon:9606 (Homo Sapiens) is asserted in all VCCF terms as present in taxon relationship.
2. Robot template to create relationship between vessels defined in the datasource.
   • This uses the column BranchesFrom, which means the “parent” vessel that is one step closer to the heart. For the ontology, we use connecting branch of.
     • Following data source documentation, for veins, it is drains to rather than connecting branch of.
     • TODO: Define relationship by VesselType.
3. Robot template to create relation between vessel and tissue. The data source is the crosswalk table.
   • Vessel The column Vessel contains the VCCF terms created in the DOSDP. The label performs the search.
   • Relationships The template is added for each relationship in the Relationship column.
     • When there isn't a matching UBERON term in the 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.
     • TODO: We still need to discuss what to do in cases where BodyPart is angiosome.
     • TODO: Double-check if there isn't any unmapped Uberon terms in BodySubPart.

Description of columns in datasource (source)

Columns in the pipeline

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).

Columns not in the pipeline, but potentially can be added

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.

Versions

Stable release versions

The latest version of the ontology can always be found at:

vccf.owl

Editors' version

Editors of this ontology should use the edit version, src/ontology/vccf-edit.owl

Contact

Please use this GitHub repository's Issue tracker to request new terms/classes or report errors or specific concerns related to the ontology.

Acknowledgements

This ontology repository was created using the Ontology Development Kit (ODK).