The FunCoup API

The FunCoup API allows users to download or access data from the FunCoup database programmatically, without using the graphical interface of the website.

Downloading Networks as TSV Files

To download a full network file for a given species, use the following URL. Replace the text within brackets with the species name.

To download a compact network file for a given species, use the following URL, replacing the text within brackets with the species name.

Obtain Mapping Information for a Gene

The geneQuery API endpoint returns all mapping information included in the FunCoup database for a given gene. It requires a gene name and a species TaxID as input, and it provides a text-based list of all mappings for the queried gene.

The returned list will contain the following headers:

Obtain Species Information

The species API endpoint provides information on all species that have a FunCoup network. The data can be retrieved in either TSV or JSON format, depending on the endpoint used.

The returned list will contain the following headers:

Obtain Network of Query Gene(s)

The network API endpoint retrieves a network of query genes based on various parameters. This data is returned in JSON format. The following URL parameters are required:

• <geneId>: Gene(s) to query (e.g. MYC, or MYC,JUN,FOS).
• <taxid>: NCBI taxonomy ID for genome selection (e.g. 9606).
• <confidenceThreshold>: Link confidence threshold between 0.5 and 1.
• <directionThreshold>: Direction confidence threshold > 0.
• <depth>: Depth of the network expansion should be 0, 1, 2 or 3.
• <nodesPerStep>: Nodes per step in the network expansion > 0.
• <expansionAlgorithm>: Algorithm used for network expansion. It can be: group, local, maxlink or topas.
• <prioritizeNeighbors>: Whether to prioritize neighbors in the network when expansionAlgorithm=group. It can be: on or off
• <comparativeTaxid>: NCBI taxonomy ID for comparative interactomics (e.g. '', or 10090, or 10090,10116).
• <individualEvidenceOnly>: Whether to use individual evidence only. It can be: on or off
• <orthologsOnly>: Whether to include orthologs only. It can be: on or off

FunCoup 6 is using UniProt ID as primary identifiers. If you are using a different gene vocabulary (e.g. Gene Symbol, Ensembl, NCBI), you might want to first resolve query ambiguities using the gene API endpoint, and then use the network API endpoint as previously shown. This data is returned in JSON format. The following URL parameters are required:

• <geneId>: Gene(s) to query (e.g. MYC, or MYC,JUN,FOS).
• <taxid>: NCBI taxonomy ID for genome selection (e.g. 9606).

Cytoscape App Integration

The FunCoup API is used by our Cytoscape app to retrieve and visualize network data. The app is available as a JAR file at our Bitbucket repository and can also be downloaded from the Cytoscape App Store.