Alkemio SOAP API (Beta1!)

This page describes an implementation of Alkemio SOAP API (beta 1 version). Please do NOT run many queries in a short time.

Connection data

  • WSDL descriptor: http://cbdm-01.zdv.uni-mainz.de/~jfontain/soap/wsdl/AlkemioSOAPbeta1.wsdl

Functions and parameters

The main function is called 'rank_chemicals' and accepts the following parameters:
  • Training set type = {pubmed|list|allmesh}
    • pubmed: for a query to PubMed (recommended)
    • allmesh: a list of MeSH terms
    • list: a list of PubMed identifiers (PMIDs)

  • Training set query = a text defining the training set as a PubMed query, a semicolumn-separated list of MeSH terms or PMIDs (1000 items max).

  • Background set type = {subset|medline|list}
    • medline: the all MEDLINE (default)
    • subset: 10 000 random PMIDs
    • list: a list of PMIDs

  • Background set query = a text defining the background set as a semicolumn-separated list of PMIDs (1000 PMIDs max) if the background set type is equal to 'list', an empty string otherwise.

  • Test set type = {chemid_list|all|all_1year}
    • all_1year: process all chemicals from the recent literature (<1 year).
    • all: process all chemicals from the recent literature (<3 years).
    • chemid_list: use a list of Chemical names from the MeSH vocabulary.

  • Test set query = a text defining the test set as a semicolumn-separated list of chemical names if the test set type is equal to 'chemid_list', an empty string otherwise.

  • Cutoff type = {custom|goodPPV|maxPPV|goodF|maxF}
    • custom: User must specify a cutoff p-value (default).
    • goodPPV: High precision / Positive Predicted Value.
    • maxPPV: Best precision / Positive Predicted Value.
    • goodF: High F score.
    • maxF: Best F score.

  • Abstracts cutoff = P-value cutoff if the custom cutoff type is selected. If empty string, the default is equal to 0.01.

  • FDR cutoff = False discovery rate cutoff for chemicals selection. If empty string, the default is equal to 0.001.

  • Debugging options = An empty string.

Examples in PERL

  • Initialization:
    use SOAP::Lite;
    my $soap = SOAP::Lite
    ->readable(1)
    ->service("http://cbdm-01.zdv.uni-mainz.de/~jfontain/soap/wsdl/AlkemioSOAPbeta1.wsdl");
    
  • Rank chemicals related to Alzheimer's disease using 1 year old abstracts, abstract cutoff equal to 0.01, and FDR cutoff equal to 0.001:
     print $soap->rank_chemicals('pubmed', 'Alzheimer Disease', '', '', 'all_1year', '', 'custom', '0.01', '0.001', '')-> result; 
  • Rank 3 given chemicals related to Alzheimer's disease using abstract cutoff equal to 0.01, and FDR cutoff equal to 0.001:
     print $soap->rank_chemicals('pubmed', 'Alzheimer Disease', '', '', 'chemid_list', 'Ascorbic Acid;Nicotine;Glycerol', 'custom', '0.01', '0.001', '')-> result; 
  • Rank 3 given chemicals related to phosphorylation and protein binding using the automatic cutoff that maximizes the precision (positive predictive value), and FDR cutoff equal to 0.01:
     print $soap->rank_chemicals('allmesh', 'Phosphorylation;Protein Binding', '', '', 'chemid_list', 'Ascorbic Acid;Nicotine;Glycerol', 'maxPPV', '', '0.01', '')-> result; 

Output format

The 'rank_chemicals' function returns a single string containing the XML ouput of Alkemio that follows this document type definition: DTD. Example output for chemicals related to Alzheimer disease: AD example.

Perl script client for Alkemio SOAP webservice (beta 1!)

Installation

The command-line Perl script was developped with Perl 5.10.1 under a linux OS and depends on the following Perl modules that must be installed on your system: Download the script file to your working directory: AlkemioSOAPclientBeta1.pl.

Documentation

Follow this link to read the full documentation: link to documentation. You could also run in a terminal the following command to display the documentation on the standard output:
perl AlkemioSOAPclientBeta1.pl --help

Some examples

Differently from to the parameters of the SOAP function, the command line client accepts comma-separated lists to define the training set or the test set, and multi-words MeSH terms must be quoted by single quotes.

  • Query a MeSH term to rank chemicals in the recent literature (3 years max.):
    perl AlkemioSOAPclientBeta1.pl --trset-type allmesh --trset 'Alzheimer Disease' --testset-type all
  • Query using PubMed to rank 2 given chemicals:
    perl AlkemioSOAPclientBeta1.pl --trset-type pubmed --trset 'Vinification' --testset-type chemid_list --testset  Nicotine,'Vitamin A'
  • Query a PMIDs list to rank chemicals in the recent literature (1 years max.):
    perl AlkemioSOAPclientBeta1.pl --trset-type list --trset 991,6996,4896 --testset-type all_1year
  • Query by PubMed to rank 2 given chemicals using a p-value cutoff equal to 0.001 and FDR cutoff equal to 0.05:
    perl AlkemioSOAPclientBeta1.pl --trset-type pubmed --trset 'Vinification' --testset-type chemid_list --testset Glycerol,'Vitamin A' --cutoff-type custom --pvalue 0.001 --fdr 0.05

Licence

THIS SERVICE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SERVICE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.

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