The PathJam API allows programmers to access PathJam's index in a programmatic way, through a RESTful Web Service. Using this service, the server can be accessed from multiple programming languages, allowing researchers to wire PathJam results to their experiments. At this time, the API offers the pathway retrieval given a list of gene identifiers, genes retrieval given a list of pathways, and some others.
Like any RESTful Web Service, operations are performed via web queries with a well-defined URL structure. The server API is located at http://www.pathjam.org/server/api/
Lists all data sources that the server can access at this moment. The URL is:
http://www.pathjam.org/server/api/sources
Lists all pathways indexed this moment. The URL is:
http://www.pathjam.org/server/api/pathways
You can also filter the listing by data source via:
http://www.pathjam.org/server/api/pathways/{datasource}
For example:
http://www.pathjam.org/server/api/pathways/reactome
This is the main functionality. Retrieves the pathways from a list of identifiers (Ensembl ID, Gene-Symbol (HGNC), Entrez ID uniprot, Affymetrix probeset). It returns one line per gene in the list containing all the pathways where each gene is involved. This is done via:
http://www.pathjam.org/server/api/pathways?genes={comma-separated-gene-ids}
For example, to retrieve pathways where BRCA1 or TP53 are involved:
http://www.pathjam.org/server/api/pathways?genes=BRCA1,TP53
This is the main functionality. Retrieves the genes from a list of pathway identifiers (The identifiers can be obtained previously with the Pathway Listing) or with pathway names (without white spaces). It returns one line per pathway in the list containing all the genes involved in each pathway. This is done via:
http://www.pathjam.org/server/api/genes?pathways={comma-separated-pathway-ids}
For example, to retrieve genes from pathways whose identifiers are path:hsa00010 or REACT_1707
http://www.pathjam.org/server/api/genes?pathways=path:hsa00010,REACT_1707
For example, to retrieve genes from pathway named Pyrimidine metabolism
http://www.pathjam.org/server/api/genes?pathways=pyrimidinemetabolism