Update: Outputs: New updated outputs based on inclusion of updated list of Mondo::GARD mappings, and also sorting.
Update: Added sorting of outputs
Update: Mondo::GARD mappings: Now from official mondo.sssom.tsv GARD mappings derivative rather than a grep and manual ETL operation as was previously found in gard_in_mondo.txt.
Add: Output for gard.sssom.tsv: This is the new way of determining proxy mappings. Not strictly SSSOM, though, as I've included mondo_id and some other columns.
This is different than the previous, more simplistic gard_terms_mapping_status.csv. It includes predicates, and has more mappings.
Bugfix: gard_terms_mapping_status.csv erronesouly had some references to Orphanet mappings that were actually OMIM mappings.
Update: Output for gard_terms_mapping_status.csv: Several columns dropped and moved to gard.sssom.tsv. Now, the purpose of this CSV is as a simple reference to the current explicit GARD mappings in Mondo. Proxy mapping information via OMIM/Orphanet removed.
Update: Added additional mappings. Not only are predicates now clarified, but the ParentOrphaCode from the GARD data source is now utilized, and those are considered broad mappings. Meanwhile, the OmimMember column is ignored when redundant, and otherwise, those terms are considered narrow mappings. Finally, for rows where DataSource == GARD, OmimMember is considered related instead of narrow, even though there was only 1 OmimMember listed, since GARD disclosed that these mappings were tentative.
Update: tmp/ now has subdirectories tmp/input/ and tmp/output/
Updates: Minor: Reduced number of JetBrains 'noinspection' comments.
Add: Mapping analysis output files to data/analysis_outputs/
First update
Add: gard_unmapped_terms.txt
Update: gard_terms_mapping_status.tsv: Added SSSOM fields for predicate and object mappings info.
Third update
Second update
First update
gard_unmapped_terms.txtgard_terms_mapping_status.tsv: Added SSSOM fields for predicate and object mappings info.