Comments (1)
caufieldjh
commented on August 12, 2024
For BioPortal purposes, many of the ontologies can just have namespace mapped to a single Biolink cat, so that can just be a big two-column TSV at its most simple. This should be kept in this repo but parsed with universalizer so the provenance can still be tracked along with other category assignments.
from bioportal-to-kgx.
Related Issues (20)
- Aim 2.3.a. Evaluate extent of expected integration between BioPortal ontologies.
- Omit biolink:OntologyClass when assigning new node category
- ValueError: mapping_justification must be supplied HOT 1
- Transform for `ISSVA` fails HOT 1
- Transform for `RDL` fails HOT 4
- General transformation failures for the July 20 2022 data HOT 3
- HGNC type maps incorrect
- UMLS semantic types not being applied HOT 1
- Some prefixes need updates as of Jul 20 2022 BP dump
- Missing IRIs and metadata from many transforms HOT 7
- Convert prefix conversion to use `curies` package HOT 2
- Fix prefixes for OBO:[external resource] HOT 1
- Collision between ATO and ATOL, potentially others of similar names HOT 1
- Produce stats yaml with status and node/edge count of each ontology source HOT 1
- Error in relaxing Cell Cycle Ontology, BERO, and PR HOT 5
- validate() got an unexpected keyword argument 'stream'
- UnboundLocalError: local variable 'nodecount' referenced before assignment
- Transform from most recent BioPortal data
- Source metadata is missing in new transforms
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from bioportal-to-kgx.