This Python script iterates a list of terms over the Bioportal API's Annotator tool and returns a table with detailed ontology annotations. Each entry on the table also specifies the annotation IRI, its Ontology, and a Completeness value for how complete the annotation was in relation to the term (Complete, Component, Partial). A typical result file should look like this:
| Term | Match | Completeness | Ontology | IRI |
|---|---|---|---|---|
| depression | depression | Complete | HP | http://purl.obolibrary.org/obo/HP_0000716 |
| spasticity | tongue spasticity | Partial | HP | http://purl.obolibrary.org/obo/HP_0001257 |
| hyporeflexia | hyporeflexia | Complete | HP | http://purl.obolibrary.org/obo/HP_0001265 |
| bulbar palsy | progressive bulbar palsy | Component | HP | http://purl.obolibrary.org/obo/HP_0001283 |
You must have the requests and urllib Python modules installed.
Open the script, fill out the variables for:
- apikey - A valid Bioportal user API key (requires a Bioportal account)
- term_path - A path to a .txt file with a list of terms
- result_path - A path to a .csv file to write your results
- ontologies - A list of comma-separated ontologies (must be Bioportal acronyms) you want to use for the annotation process
and run it.
This project has been funded by Portuguese FCT through the LASIGE Research Unit (UID/CEC/00408/2019), and by the SMILAX project Semantic Mining with Linked Data (PTDC/EEI_ESS/4633/2014)