Developer Documents

Keiichiro Ono edited this page Oct 21, 2013 · 12 revisions

NeXO RESTful API Version 1 Beta

Introduction

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.

Base URL

Our current API server is http://chardonnay.ucsd.edu/

Basic Entry Retrieval (GET methods)

Get details

Syntax
  • 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.

Return Value

A JSON Object

Example

Get path to the root term

Syntax
  • 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.

Return value

Array of arrays

Example

Get raw interactions (NeXO only)

Syntax
  • 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.

Return Value

Cytoscape.js style graph object.

Example

Search by keywords

Syntax
  • 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.

Return Value

Array of JSON objects. First entry is always the original keywords.

Example

Search by gene names

Syntax
  • BASE_URL/search/genes/GENE_IDS

where GENE_ISD is list of gene names/IDs for search.

Return Value

Array of JSON objects.

Example

Advanced Features (POST methods)

Term Enrichment

Syntax
  • 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
Return Value

Array of JSON objects.

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