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x-atlas-consortia / ubkg-etl

A framework that combines data from the UMLS with assertions from other data sources into a set of CSV files that can be imported into neo4j to build a Unified Biomedical Knowledge Graph (UBKG)
MIT License
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Ingest CCF 2D Reference Functional Tissue Unit (FTU) Library ASCT+B 2D FTU mappings into UBKG #110

Open AlanSimmons opened 9 months ago

AlanSimmons commented 9 months ago

FYI @lchoy

Request

Ingest (ASCTB 2D FTU mappings)[https://hubmapconsortium.github.io/ccf-releases/v1.2/docs/2d-ftu/asctb-2d-ftu-mapping.html].

Based on a review of CSV downloaded from (this page)[https://hubmapconsortium.github.io/ccf-releases/v1.2/docs/2d-ftu/asctb-2d-ftu-mapping.html], this involves mapping FTUs to sets of CL or UBERON codes.

e.g., anatomical_structure_of source_spatial_entity node_name label OntologyID
#FTUAlveolus #2DRefObjects Type_1_Pneumocyte_1 type I pneumocyte CL:0002062
#FTUAlveolus #2DRefObjects Type_1_Pneumocyte_2 type I pneumocyte CL:0002062
#FTUAlveolus #2DRefObjects Type_1_Pneumocyte_3 type I pneumocyte CL:0002062
#FTUAlveolus #2DRefObjects Type_1_Pneumocyte_4 type I pneumocyte CL:0002062
#FTUAlveolus #2DRefObjects Type_1_Pneumocyte_5 type I pneumocyte CL:0002062
#FTUAlveolus #2DRefObjects Type_1_Pneumocyte_6 type I pneumocyte CL:0002062
#FTUAlveolus #2DRefObjects Type_1_Pneumocyte_7 type I pneumocyte CL:0002062
#FTUAlveolus #2DRefObjects Type_1_Pneumocyte_8 type I pneumocyte CL:0002062

...

bherr2 commented 9 months ago

MC-IU is in the process of ontologizing all FTUs and their crosswalk for the December release of the HRA. An in process version of the data as we have parsed it is here: https://github.com/hubmapconsortium/hra-ui/blob/develop/apps/ftu-ui/src/assets/TEMP/2d-ftu-illustrations.jsonld (note some structure subject to change, but pretty close). Once we get it in the HRA-KG we can add exports to the hra-ubkg-export project to extract relationships for UBGK if that's desired.

AlanSimmons commented 9 months ago

Thanks, @bherr2. I'm not sure at this point what's needed. Lisa and Nick mentioned that the UI would need FTU information for something that they are working on, and I built this issue to track the request.