Bioportal Adapter

The Bioportal adapter uses ontoportal-client to connect to any OntoPortal endpoint.

Warning

Highly incomplete!

So far this only implements:

• Search Interface

• Text Annotator Interface

• Mapping Provider Interface

API Keys

First you will need to go to BioPortal and get an API key, if you don’t already have one.

You will then need to set it:

runoak set-apikey bioportal YOUR-API-KEY

This stores it in an OS-dependent folder

Command Line Examples

Use the bioportal selector:

runoak -i bioportal: COMMAND [COMMAND-ARGUMENTS-AND-OPTIONS]

Currently ontology sub-selectors are not supported

Search

runoak -i bioportal: search tentacle

Note that bioportal implements relevance-ranked search, so if you search with a multiword term like “octopus brain”, after first returning any exact matches it will return matches to “octopus” and “brain”.

Mappings

runoak -i bioportal: term-mappings UBERON:0002101  -O sssom -o my-mappings.sssom.tsv

Currently mappings may be missing some crucial metadata

Code