Medline Ranker SOAP API (beta2!)

This page describes an implementation of MedlineRanker SOAP API (beta 2 version). Please do NOT run many queries in a short time. Known bug: connection to the web service may be terminated after several minutes for time consuming queries (e.g. to rank 10-year old abstracts). For such queries, you may use the beta REST API instead.

Connection data

  • WSDL descriptor: http://cbdm-01.zdv.uni-mainz.de/~jfontain/soap/wsdl/MedlineRankerSOAPbeta2.wsdl

Functions and parameters

The main function is called 'rank' 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 semi-column-separated list of terms or PMIDs (1000 items max).

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

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

  • Test set type = {trset|bgset|recent|last_months|list}
    • trset: the training set
    • bgset: the background set
    • recent: 10 000 random PMIDs
    • last_months: Articles published during the last N months (Default). N is defined by --month.
    • list: a list of PMIDs (1000 PMIDs max).

  • Test set query = a text defining the test set as a semi-column-separated list of PMIDs if the test set type is equal to 'list', an integer value representing the maximal age of the articles to be ranked from MEDLINE if the test set type is equal to 'last_months', or an empty string otherwise.

Examples in PERL

  • Initialization:
        my $soap = SOAP::Lite
        ->readable(1)
        ->service("http://cbdm-01.zdv.uni-mainz.de/~jfontain/soap/wsdl/MedlineRankerSOAPbeta2.wsdl");
    
  • Retrieve and display Alzheimer disease articles published during the last 3 months:
        print $soap->rank('pubmed', 'Alzheimer Disease', 'medline', '', 'last_months', '3'); 
  • Query two MeSH terms to rank 6 months old abstracts:
        print $soap->rank('allmesh', 'Phosphorylation;Protein Binding', 'medline', '', 'last_months', '6'); 
  • Rank a given list of PMIDs:
        print $soap->rank('allmesh', 'Phosphorylation;Protein Binding', 'medline', '', 'list', '8702572;7852332;8845306;8524942'); 

Output format

The 'rank' function returns a single string containing the XML ouput of Medline Ranker that follows this document type definition: DTD.

Example output for the query of Alzheimer disease articles in the last 3 months of Medline: AD example.

Perl script client for MedlineRanker SOAP webservice (beta 2!)

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: MedlineRankerSOAPclientBeta2.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 MedlineRankerSOAPclientBeta2.pl --help

Some examples

Query the last 2 months of PubMed abstracts for Phosphorylation through a PubMed query:

perl MedlineRankerSOAPclientBeta2.pl --trset Phosphorylation

Query a MeSH term to rank abstracts in the training set:

perl MedlineRankerSOAPclientBeta2.pl --trset-type allmesh --trset "Alzheimer Disease" --testset-type trset

Query two MeSH terms to rank 6 months old abstracts:

perl MedlineRankerSOAPclientBeta2.pl --trset-type allmesh --trset "Phosphorylation;Protein Binding" --testset 6

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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