Remove NDFRT and add MEDRT to umls.conf before the next import (2018AB)

[mdorf]

According to this NIH document, https://evs.nci.nih.gov/ftp1/MED-RT/Introduction%20to%20MED-RT.pdf, NDFRT terminology has been retired and replaced with MEDRT. The original version of MEDRT had been included in UMLS 2018AA release, but we had not pulled it because it had been missing from the configuration file, https://github.com/ncbo/umls2rdf/blob/master/umls.conf.

[rwynne]

There will likely be more issues. MED-RT is a hybrid terminology-mapping, and the first of its kind inverted into UMLS. The source has RELs to SNOMEDCT_US, RxNORM, and MeSH sourced CUIs. Extracting just MED-RT will not contain these referenced CUIs, and will not yield a "conservation of mass". What this means is the umls2rdf conversion will probably need to allow more than one SAB in umls.conf before conversion to TTL. It is also likely IRIs in the expected output could be from any of the four sources.

EVS is attempting to create RRF files manually from the four-sourced extraction by collecting CUIs from MED-RT sourced rows in MRREL, and then "pruning" all other RRF files. We are working towards an automated process with the help of UMLS, though this has not been a simple task.

[jvendetti]

As @rwynne mentions above, it doesn't appear that our import process handled MED-RT appropriately. The roots endpoint (http://data.bioontology.org/ontologies/MEDRT/classes/roots) returns an empty set, which results in an inability to view a class tree in the BioPortal UI. Also, the classes endpoint only returns 127 classes.

[graybeal]

We have to defer this until we have the expertise (or an alternative source for the "pre-inverted into UMLS" version of it) to turn it into a fair working ontology representations.

In the meantime, we will delete it from the config file for UMLS uploads, and remove it from BioPortal.

[jvendetti]

Deleted the MEDRT ontology entry from BioPortal.

[Jorge-Hernansanz]

Hi

Is it possible to obtain a csv file of 2018AA NDFRT ontology from BioPortal? The entry is deleted and I don't find anywhere else to download it.