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obophenotype / vccf-ontology

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Document mappings between source files and OWL #13

Closed cmungall closed 4 months ago

cmungall commented 4 months ago

Example

The source has ForBranchesSee

https://github.com/hubmapconsortium/hra-vccf/blob/d9214eea16009264f0423d29845966d77a8925ac/HRA-VCCF_CreateTables.sql#L24

This is not documented in the source repo

But is documented here https://www.nature.com/articles/s41597-023-02018-0

How do we translate this? Does this get dropped?

anitacaron commented 4 months ago

How should it be translated? In the first draft, we used minimal information from the data source.

anitacaron commented 4 months ago

From the paper:

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.

anitacaron commented 4 months ago

I updated the README.

Please open another ticket, if needed, to change parts of the pipeline.

cmungall commented 4 months ago

How should it be translated?

Ideally the source tables would be defined at source, and then this repo would be focused on the transformation; see https://github.com/hubmapconsortium/hra-vccf/pull/5

anitacaron commented 4 months ago

I was asking about the transformation.