Fixes #3288 Add blood vasculature design pattern and 55 blood terms from VCCF #3289
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…rom VCCF Fixes #3288 Add blood vasculature design pattern and 55 blood terms from VCCF
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| defined_class label parent part_of_vccf definition xref_vccf synonym synonym_xrefs connecting_branch_of tributary_of vessel_supplies_blood_to vessel_drains_blood_from creator | |||
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label will not be used, check docs. I think it must be defined_class_name
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Same as definition - are they too irregular to automatically generate them with dosdp?
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The big advantage of DOSDPs over ROBOT is text generation. This can use optionals too. If really need to add labels and defs manually, then maybe ROBOT is more appropriate.
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In this case I prefer to not automatically generate them, since they have different structures. I can use ROBOT then, thank you!
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IMO the main advantage of DOSDPs is that they are a specification here, independent of whether you want to use the spec to generate or validate. We are desperately in need of specifications of all the patterns in Uberon
| hasDbXref: "oboInOwl:hasDbXref" | ||
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| parent: "" |
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Why not typing these? Why "" instead of, say, "anatomical entity"?
parent is not a name for a slot in a dosdp pattern. Sounds again like a ROBOT template to me.
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You can call your slots whatever you want, but it is good practice to specify a range.
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I was adapting the design pattern that we have for the VCCF ontology, but yes, I should have added a range.
Thank you, I have split the pattern in two patterns, one for veins/venules and one for arteries/arterioles. I will create a DOSDP for capillaries in the future.
Apologies, the column was supposed to be relabeled and it will be fix in the next commit. |
Changes in the DOSDP: - Split in two DOSDP for venous and arterial blood vessels - Add proper description - Add range to variables - Logical axioms that might have more than one variable, use list_vars and multi_clause Changes in the table: - Fix column labels - Due a problem on the range of vessel supplies/drains blood to/from, all anatomical spaces or cavities had to be substituted
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Changes in the DOSDPs:
Changes in the tables:
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Once the object properties are fixed, needs to be reversed
…type/uberon into 3288_vccf_DOSDP_vessels
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#gogoeditdiff |
Here's a diff of how these changes impact the classified ontology (on -base file):Ontology comparisonLeft
Right
Ontology importsOntology annotationsRO_0020101
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Here's a diff of your edit file (unreasoned)Ontologies are identical |
- Change column name part_of for location - Add FMA_xref - All radiopedia URL are substituted by doi - Add more specific ranges
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LGTM to me, but I didnt do a deep dive.
@aleixpuigb I absolutely love it you took the time to carefully craft these patterns. This is super essential for Uberon moving forward!
Thanks a lot!
I will leave the deep dive review to @rays22 and @anitacaron
Co-authored-by: Ray Stefancsik <ray@ebi.ac.uk>
This commit fixes: - Unnecessary indentation - Add new empty line at the end of the yaml files - Change the range of date to xsd:dateTime - Fix typo in atrioventricular nodal artery
Fixes #3288 Add blood vasculature design pattern and 55 blood terms from VCCF