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Developer Documents
NeXO datasets are fully accessible through simple RESTful API. Current NeXO web app is using this API as its backend. This means that developers can use NeXO datasets via REST API and they can use them in their workflows/applications.
This is a beta release of API, and some of the method may change in the final version.
Our current API server is http://chardonnay.ucsd.edu/
- BASE_URL/ID
ID is a unique identifier for a term/gene. For terms, ID always starts with namespace, and then ID for the ontology. For genes, SGD IDs are used as unique identifier.
A JSON Object
- http://chardonnay.ucsd.edu/NEXO:9818
- http://chardonnay.ucsd.edu/GO:0000502
- http://chardonnay.ucsd.edu/S000004466
- BASE_URL/ID/path
This return array of paths. First element is always the shortest path to the root term, and others are the first neighbour of the term. These first neighbours are hidden in the visualization, and if you want to get those, you need to access this API to get all neighbour terms.
Array of arrays
- http://chardonnay.ucsd.edu/NEXO:9818/path
- http://chardonnay.ucsd.edu/GO:0000502/path
- http://chardonnay.ucsd.edu/S000004466/path
- BASE_URL/NEXO_ID/interactions
NeXO ontology terms are always associated with raw interaction data. This method returns raw interaction data for the given NeXO term as Cytoscape.js graph object.
Cytoscape.js style graph object.
- BASE_URL/search/NAMESPACE/QUERY
This method provides simple keyword search for the database. NAMESPACE is NEXO or GO, and query is a keywords for search.
Array of JSON objects. First entry is always the original keywords.
- BASE_URL/search/genes/GENE_IDS
where GENE_ISD is list of gene names/IDs for search.
Array of JSON objects.
- BASE_URL/enrich
You need to post the following parameters as a object:
- type - Ontology Type (NeXO or GO)
- genes - List of genes to be tested
- alpha - Cut-off threshold
Array of JSON objects.