sssom-py
sssom-py copied to clipboard
mapping-commons
Python toolkit for SSSOM mapping format
We need to figure out why that is first of all, i.e. which functions are so inefficient, and then working on improving efficiency. First goal: - [ ] A small...
The default order on mapping set metadata is currently alphabetical. I think it would be better to do it like this: 1. Sort by SSSOM metadata model slot order 1....
- https://mapping-commons.github.io/sssom-py/installation.html * [ ] end-users should not have to install from git. use pypi * [ ] change cmungall to mapping-commons * [ ] consider consolidating docs aimed at...
``` sssom validate mappings/mgi_alzheimer_mp_hpo.sssom.tsv ``` We should not print stack traces _ever_ unless unhandled exception. This is the output of the above. ``` /Users/matentzn/opt/anaconda3/lib/python3.8/site-packages/rdflib_jsonld/__init__.py:9: DeprecationWarning: The rdflib-jsonld package has been...
Would be great if we could get this to work: ``` sssom parse https://raw.githubusercontent.com/mapping-commons/sssom/master/examples/external/example1.sssom.tsv -m https://raw.githubusercontent.com/mapping-commons/sssom/master/examples/external/example1.sssom.yml -o ex.sssom.tsv ``` The first part already works, but the yml file at this...
If we see a biolink:category annotation (keep this configurable to extend to other "category" annotations) we should be able to automatically extract "subject_category" and "object_category" during sssom parse.
While exporting a SSSOM TSV, currently we are exporting only columns that have data. - Q. Should we export all slots regardless of it having data or not? - If...
From @cthoyt an example (thank you): ```python import re import bioregistry def main(): obo_context = bioregistry.get_context("obo") reverse_remapping = { custom_prefix: bioregistry_prefix for bioregistry_prefix, custom_prefix in (obo_context.prefix_remapping or {}).items() } #...
@DaveraGabriel has been working on a mapping between SSSOM and ConceptMap2. From the perspective of SSSOM, it would be great to have an importer for ConceptMap2 datasets based on her...