JSON API for WikiPathways

This set of JSON files contain all the information needed to replace the prior, deprecated web services. This new approach supports bulk actions with better performance, providing results for all pathways with a single query. The client libraries, such as rWikiPathways, now use these files instead of the deprecated web services while maintaining (and even adding to) the same functionality. These JSON files are generated from the WikiPathways database and are updated in real time with every change.

List

Comprehensive lists of key data types in WikiPathwys with minimal information for each.

listOrganisms.json

A list of all organisms in WikiPathways as an array of latin genus species values all under the `organisms` key.

listPathways.json

A list of all pathways in WikiPathways organized by organism. The `organisms` key has an array of arrays containing each organism's `latin`, `two-letter-code` and `common` key-value pairs, plus a `pathways` key that has an array of arrays containing each pathway's `id`, `url`, `name`, `species`, `revision` key-value pairs.

listCommunities.json

A list of all communities in WikiPathways as an array of arrays containing descriptive keys for each community, plus a `pathways` key that has an array of arrays containing each pathway's `id`, `url`, `name`, `species`, and `revision` key-value pairs, all under the `communities` key.

Get

While getCounts.json provides summary statistics for WikiPathways, getPathwayInfo.json provides key metadata for every pathway, and getPathwaysByOntologyTerm.json and getOntologyTermsByPathway.json provide lists of pathways and ontology terms associated with each other, respectively.

getCounts.json

Summary statistics for the WikiPathways database, including the number of `organisms`, `pathways`, `authors`, and `communities` as key-value pairs.

getPathwayInfo.json

Key metadata for every pathway in WikiPathways. The `pathwayInfo` key contains an array of arrays containing each pathway's `id`, `url`, `name`, `species`, `revision`, `authors`, `description` and `citedin` key-value pairs.

getPathwaysByOntologyTerm.json

A listing of all pathways associated with each top-level ontology term in WikiPathways. The `terms` key contains an array of arrays containing each term's `id`, `name`, and `ontology` key-value pairs, plus a `pathways` key that has an array of arrays containing each pathway's `id`, `url`, `name`, `species`, and `revision` key-value pairs.

getOntologyTermsByPathway.json

A listing of all ontology terms associated with each pathway in WikiPathways. The `pathways` key contains an array of arrays containing each pathway's `id`, plus a `terms` key that has an array of arrays containing each term's `id`, `name`, `ontology` and `parent` key-value pairs.

Find

These files are particularly useful to consume into your own application or script when wanting to implement custom search functionality. Client libraries are available in specific languages that implement search based on these files. Note: these files have the same basic struture as the getPathwayInfo.json file, but with additional key-value pairs (in bold).

findPathwaysByText.json

Relevant text metadata for every pathway in WikiPathways. The `pathwayInfo` key contains an array of arrays containing each pathway's `id`, `url`, `name`, `species`, `revision`, `authors`, `description`, `citedin`, `datanodes`, and `annotations` key-value pairs.

findPathwaysByXref.json

Relevant metadata plus external references (Xrefs) for the genes, proteins and metabolites for every pathway in WikiPathways. The `pathwayInfo` key contains an array of arrays containing each pathway's `id`, `url`, `name`, `species`, `revision`, `authors`, `description`, and a series of Xref key-value pairs, e.g., `ncbigene`, `uniprot` and `chebi`.

findPathwaysByLiterature.json

Relevant metadata plus citation IDs and text for every pathway in WikiPathways. The `pathwayInfo` key contains an array of arrays containing each pathway's `id`, `url`, `name`, `species`, `revision`, `authors`, `description`, `refs` and `citations` key-value pairs.

findPathwaysByOrcid.json

Relevant metadata plus author ORCIDs for every pathway in WikiPathways. The `pathwayInfo` key contains an array of arrays containing each pathway's `id`, `url`, `name`, `species`, `revision`, `authors`, `description`, and `orcids` key-value pairs.