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This project is a spin-off from ETH in Switzerland and is a standalone research project turned programming utility.
We used Perl script with NCBI Entrez Programming Utility functions (e-utilities) to query NCBI literature databases.
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Conjointly, we further queried GEO using the eSearch Entrez Programming Utilities (E-utils) service to fetch additional identifiers (IDs), which were not picked up by the previous query (http://www.ncbi.nlm.nih.gov/geo/info/geo_paccess.html).html
UNIX programming utilities are also covered.
These Entrez Programming Utilities, or eUtils, include EInfo, ESearch, EPost, ESummary, EFetch, ELink, EGQuery, ESpell and they are all wrapped into SOAP interface for easier communication.
The Entrez Gene IDs, symbols, and descriptions of genes for all tested transcripts were attained by Entrez Programming Utilities (eUtils) using GI number with the aid of a Perl script.
Connections to PubMed were done using the Entrez Programming Utilities (E-Utilities).
PubMed was queried using the Entrez Programming Utilities (eUtils) [ 36] on 23 April 2015.
All sequences were downloaded with Entrez Programming Utilities and our own PERL scripts (99).
The Entrez Programming Utilities [ 22] was used to retrieve citation information.
The application connects to the MEDLINE/PubMed database using tools from Entrez Programming Utilities (E-Utilities) [ 10].
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