sssom-py
sssom-py copied to clipboard
mapping-commons
Python toolkit for SSSOM mapping format
Partially addresses: - https://github.com/timsbiomed/issues/issues/85 ## Overview - Minor bug fixes - Dev updates (comments, etc) - Added test(s) ## Updates `7b91d57da9a5143c5ce8335897ad2542424797c6` ``` - Add: _test_to_fhir_json() ``` `157ae226921891feeaa38b4329c98b762b2b8727` ``` - Refactored...
More readable output for validate and a few smaller bugfixes - Alignment API parser correctly parses purls as entity references now - tbd
- [ ] We need less verbose output. For example, when hitting an error like: ``` Failed validating 'additionalProperties' in schema: ``` hundreds of rows are printed. - [ ]...
### About related https://github.com/agroportal/project-management/issues/265 ### How to use ```bash python -m sssom convert basic.tsv -o basic-ontoportal.json -O ontoportal_json ```
@hrshdhgd This mapping file should fail because it is missing prefixes, but it does not. It produces some default output and I don't understand at a cursory glance how. Can...
The Biomappings (https://github.com/biopragmatics/biomappings) project exports its curated mappings into SSSOM, however the code hasn't been updated since before the SSSOM standard to have the "mapping justification" (see https://github.com/mapping-commons/sssom/pull/117) and therefore...
Fixes #208 New Feature: SNOMED::ICD10CM Mapping Support - Added feature to allow for conversion of these premade mappings provided by SNOMED into SSSOM format. General updates - `utils.py`: Reorganized `SSSOM_READ_FORMATS`:...
- what are the distinct prefixes used - aggregate counts by - prefix - subj-obj prefix pairs - subj-obj prefix pairs broken down by predicate
It will cause a lot of errors at first, but overall, it will lead to better mapping data. The suggestion is that whenever we call `write_table()`, the final part of...
- curie maps where missing - subject and object labels (see Gaurav suggestion [here](https://github.com/mapping-commons/sssom/discussions/207)) What would be a name for such a method. Should this be folded into another method...