sssom-py
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mapping-commons
Python toolkit for SSSOM mapping format
## Overview I [noticed recently](https://github.com/monarch-initiative/mondo-ingest/pull/412#discussion_r1493469285) that sometimes warnings are overly verbose. For example, sometimes for a given type of warning, it prints a full warning for each instance of an...
## Overview There are namespace situations that simply cannot be handled by a bimap. For these situations (e.g. prefix or uri_prefix synonyms), we need extended prefix map (EPM) support. ##...
This PR adds methods - parse_sssom_jsonld - from_sssom_jsonld - write_jsonld - to_jsonld - test_parse_sssom_jsonld - test_write_sssom_jsonld Which are exactly analogous to what was there before for JSON. But its actual...
I am 97% sure this is out of scope for sssom-py and this should be either it's own tool or something as part of a general gff package. But this...
version 1.0.0 is scary and scientists can't commit to it so we just never get to 1.0 and use minor versions as major versions. This is called zero versioning, and...
We need a plan for the 0.4 release. Please edit the top note on this issue in place rather than making a long long long thread to read @matentzn preferred...
We need a list of breaking changes since sssom release 0.3.31, to communicate this with stakeholders before the 0.4 release. @cthoyt my assumption is you dont want to do this,...
## Overview I tried `--mapping-predicate-filter omoprel:Mapped_from` and it did not work, but `--mapping-predicate-filter https://w3id.org/cpont/omop/relations/Mapped_from` did. ## Details ### Command Syntax: `f'sssom parse {obograph_path} -I obographs-json -o {outpath_sssom} -m {metadata_path}'` Actual:...
This PR introduces the possibility of rewiring an SSSOM table based on another SSSOM table. This is in scope for sssom-py because of the complex handing of SSSOM mapping set...
Despite some overlap with boomer, I would like to have a function that basically implements https://mapping-commons.github.io/sssom/chaining_rules/ after all. Basically, the method should work just like `invert`, but create new mappings...