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Hi Justin,
I'd like to set up a biolink API instance for Planteome. This provides a wrapper onto golr and the ontologies.
The URL could be http://biolink.planteome.org
the only dependency is…
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Map the generated HCLS metadata to the BioLink model.
BioLink have classes equivalent to dataset, version, distribution:
https://biolink.github.io/biolink-model/docs/DataSet.html
Should we us…
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I would rather receive an NCBI taxonomy identifier in most cases. However, there are many species that aren't in NCBI, so some other source might be needed for those (GBIF or Catalog of Life?). One pr…
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Write generic SPARQL queries to transform OWL BioPax in BioLink
For pathwaycommons for example: http://www.pathwaycommons.org/archives/PC2/v10/PathwayCommons10.All.BIOPAX.owl.gz
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A very common thing users might want to do is to compute the semantic similarity between nodes in a graph and then store that data back in the edges of the graph (to use as edge weights later).
I'v…
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Related with: https://github.com/biolink/biolink-model/issues/1431
Update `https://identifiers.org/ncbigene/` to `http://identifiers.org/ncbigene/`
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When running Pathfinder example 5 [(saved response)](https://github.com/user-attachments/files/17538328/latest-pf5-bug.json.zip), we send sub-queries to automat-robokop with 1 ID. These sub-queries al…
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Nodenormalizer has a few roles:
1. establishing equivalent id sets
2. Assigning types
3. returning labels
One problem is that people rely on it for 3, so if it can't do 1&2 for some chunk of da…
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Some examples here: https://arax.ncats.io/beta/?r=36527
example edge attribute list containing the attribute of interest:
```
--
attribute_type_id: | biolink:aggregator_knowledge_source
value_t…
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### Describe the bug
See https://github.com/monarch-initiative/monarch-ingest/issues/468#issuecomment-1564660130
Biolink imports linkml types (see https://github.com/biolink/biolink-model/blob/m…