Web services API

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REST API

Please read carefully the documentation, citation and disclaimer before using this service. In order to query the web service, an HTTP request has to be sent to a specific URL. This URL is composed by a base URL followed by key-value pairs, the latter defining the input parameters of the queried service. The resulting file is a table of genes or diseases as tab-separated values. Please use this service moderately, letting reasonable time between consecutive queries. Upon heavy or unexpected use of the service, its access may be blocked to specific IP ranges without notice.

Base URL

  • http://cbdm-01.zdv.uni-mainz.de/~jfontain/cgi-bin/genes2diseases.pl

Template full URL

Please note the question mark (?) to separate the Base URL to the rest, symbols & to separate key-value pairs, and symbols = to separate keys and values.
  • BaseURL?key1=value1&key2=value2&key3=value3 ...

Parameters and corresponding key-value pairs

Please see the documentation for a definition of each parameter: Documentation page.
  • Type of Analysis*
    • key: analysis_type
    • possible values:
      • geneset: gene set to disease
      • gene: gene to disease / disease to gene
  • List of human protein-coding genes or diseases*
    • key: items
    • value: pipe separated list of official gene symbols, Entrez Gene IDs or MeSH C disease terms
  • Min number of disease-related citations for a gene (min=3)
    • key: min_citations_for_gene
    • value: integer number (default is 5)
  • For a gene set, min number of genes significantly associated with a disease
    • key: min_genes_for_geneset
    • value: integer number (default is 2)
  • Max False Discovery Rate (FDR)
    • key: fdr_cutoff
    • value: number between 0 and 1 (default is 0.05)
  • Type of output*:
    • key: output_type
    • value: text
* mandatory

Output file

Please see the documentation for a description of the output as tab-separated values: Documentation page.

Examples

The key-value pairs below are required for the query "Get diseases enriched for a gene set of 5 genes (APP, BACE1, PSEN1, MAPT, and APOE), each gene must be involved with a disease in at least 10 citations, at least 3 genes of the gene set must be associated with a disease, FDR<0.1, output as text TSV file"
  • analysis_type=geneset
  • items=APP|BACE1|PSEN1|MAPT|APOE
  • min_citations_for_gene=10
  • min_genes_for_geneset=3
  • fdr_cutoff=0.1
  • output_type=text
Then the full URL to query is the following: The same query with default parameters is the following (only the 3 mandatory key-value pairs are provided): In order to get for each input gene and disease all individual gene-disease associations, "analysis_type=geneset" has to be changed to "analysis_type=gene" as follows (using the previous example): Input diseases must be given as exact Mesh terms as in the following example:

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