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Method for creating a list of unique gene sequences matching a specified publication criterion for a gene expression experiment, using a WebService

IP.com Disclosure Number: IPCOM000016196D
Original Publication Date: 2002-Nov-23
Included in the Prior Art Database: 2003-Jun-21
Document File: 1 page(s) / 87K

Publishing Venue

IBM

Abstract

This publication describes a method for creating a list of unique gene sequences matching a specified publication criterion for a gene expression experiment, using a WebService This method is designed to automate generation of sequences from a list of PubMed publications to be used as probes in a Micro array gene expression using WebServices. Currently researchers spend days to identify various proteins involved in a particular disease. They search PubMed and other in-house clinical text to identify various proteins that he could use for the micro array experiments. This involves manual querying using various search terms. The manual procedure consists of finding relevant articles using PubMed with relevant search criteria, and then requesting for gene sequences in the FASTA format for each article found satisfying the various search criterion. The procedure described in this disclosure automates this manual querying process, which is at best tedious and error prone. Web Services Used:

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  Method for creating a list of unique gene sequences matching a specified publication criterion for a gene expression experiment, using a WebService

    This publication describes a method for creating a list of unique gene sequences matching a specified publication criterion for a gene expression experiment, using a WebService

This method is designed to automate generation of sequences from a list of PubMed publications to be used as probes in a Micro array gene expression using WebServices.

Currently researchers spend days to identify various proteins involved in a particular disease. They search PubMed and other in-house clinical text to identify various proteins that he could use for the micro array experiments. This involves manual querying using various search terms. The manual procedure consists of finding relevant articles using PubMed with relevant search criteria, and then requesting for gene sequences in the FASTA format for each article found satisfying the various search criterion. The procedure described in this disclosure automates this manual querying process, which is at best tedious and error prone.

Web Services Used:
1. PubMed WebService

Description: This web service would find the list of publications; extract the accession number from the Medline document of each publication and retrieves the gene sequences identified in the publication in a FASTA format.

Inputs: A set of terms, which define the search criterion normally MeSH terms, text terms used...