inst/sql/postprocess/umls_class/README.md

In meerapatelmd/setupMetathesaurus: Setup UMLS Metathesaurus

/*********** Derive entire hierarchies from UMLS Metathesaurus MRHIER Table Authors: Meera Patel Date: 2021-10-27 https://lucid.app/lucidchart/b7e40e42-ea80-43be-baf5-7f92cbfb6d6f/edit?viewport_loc=-185%2C997%2C1560%2C929%2C0_0&invitationId=inv_61a38c21-37a1-49fa-a857-d7585471e5f1 | MRHIER | --> | MRHIER | ptr_id is added to the source table. ptr_id is the source MRHIER's row number. It is added as an identifier for each unique AUI-RELA-PTR (ptr: Path To Root). Note that unlike the identifiers provided by the UMLS, this one cannot be used across different Metathesaurus versions. | MRHIER | --> | MRHIER_STR | + | MRHIER_STR_EXCL | MRHIER is then processed to replace the decimal-separated ptr string into individual atoms (aui) and mapped to the atom's str value. Any missing ptr values in MRHIER_STR are accounted for in the MRHIER_STR_EXCL table. To Do: [X] Cleanup scripts with functions from 1387 onward, including logging to the progress log and annotations [ ] After 2021AB update, see how the lookup and results tables can be renamed with a degree of provenance. [ ] Add the sab field back to final MRHIER_STR table by doing a join to the MRCONSO table at this stage [X] Some log entries do not have target table row counts [ ] Log entries from ext_ to pivot_ do not have sab value [X] Re-imagine the RxClass log so that it is a 1-row entry per incidence (mimic setup_umls_class_log) [X] Change sort order of final tables in RxClass [ ] Change sort order of final tables in UMLS Class [ ] Add indexes to final UMLS Class tables [X] Add indexes to final RxClass tables ************/

meerapatelmd/setupMetathesaurus documentation built on May 25, 2022, 6:19 a.m.