explain dp and templates creation

README.md

@@ -3,19 +3,31 @@
 # STATUS - EXPERIMENTAL DO NOT USE
 # Vasculature Common Coordinate Framework Ontology
 
-Description: None
-
-More information can be found at http://obofoundry.org/ontology/vccf
+## Pipeline workflow
+
+1. Use a [DOSDP](src/patterns/dosdp-patterns/vessel.yaml) to define all vessels available in the [datasource](https://github.com/hubmapconsortium/hra-vccf/blob/main/Vessel.csv). A python script is used to generate the [data](src/patterns/data/default/vessel.tsv) for the DOSDP.
+   - [label, human_label] The colum `VesselBaseName` is used for the VCCF term label and for  `oio:obo_foundry_uniquename` annotation, adding "(Human)". We use this column as 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 where there is a specific number of vessels in the body, the `VesselBaseName` includes a number for each different 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 term, heart chamber, artery, arteriole, capillary, venule, vein, or sinus. In the cases there isn't a matching UBERON term for the vessel, defined in the column `UBERON`. In other words, when the vessel exists in FMA or no matching term is available. **TODO: add `VesselTypeID` for all cases**. 
+     - When `VesselTypeID` is `heart chamber` the values in `BranchesFrom` and `Vessel` are the same, which in fact are not vessels. e should not add the `BranchesFrom` relationship because it's the same as in `Vessel` which is not true. It should include only the `VesselTypeID` as 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 `BodyPart` is used for a simplified definition generation. In some cases, this can be redundant with data available in the [crosswalk table](https://github.com/hubmapconsortium/hra-vccf/blob/main/VesselOrganCrosswalk.csv) which defines 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 URL for the UBERON matching term. These cases the reference is empty. When the `ReferenceURL` is a PMC publication url, it's transformed to PMID. **TODO: Remove DOI if `ReferenceURL` is from PMC publication**. **TODO: Search for DOI in radiopaedia cases**
+   -  [synonym, synonym_xref] The column `FMALabel` and `FMA` are used as exact synonym and synonym xref, respectively, when available.
+   -  [taxon] The taxon NCBITaxon:9606 (Homo Sapiens) is asserted in all VCCF terms as `present in taxon` relationship.
+1. [Robot template](src/templates/vessel_relation.tsv) to create relationship between vessels defined in the [datasource](https://github.com/hubmapconsortium/hra-vccf/blob/main/Vessel.csv).
+   - 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`**.
+1. [Robot template](src/templates/vessel_organ_crosswalk.tsv) to create relation between vessel and tissue. The data source is the [crosswalk table](https://github.com/hubmapconsortium/hra-vccf/blob/main/VesselOrganCrosswalk.csv). 
+   - [Vessel] The column `Vessel` is the VCCF terms created in the DOSDP. The search is done by the label.
+   - [relationships] For each relationship in the `Relationship` column, is added in the template. **TODO: When there isn't a matching UBERON term in the column `BodySubPartID`, use `BodyPartID` which is the organ. However, we need to discuss what to do in cases `BodyPart` is angiosome**.
 
 ## Versions
 
 ### Stable release versions
 
 The latest version of the ontology can always be found at:
 
-http://purl.obolibrary.org/obo/vccf.owl
+[vccf.owl](vccf.owl)
 
-(note this will not show up until the request has been approved by obofoundry.org)
 
 ### Editors' version