gentrez

 

Function

Search NCBI Entrez

Description

gentrez searches NCBI Entrez with keyword through EUtilities.
This is intended for quick lookup through the command line
so only top ten hits are reported.

G-language SOAP service is provided by the
Institute for Advanced Biosciences, Keio University.
The original web service is located at the following URL:

http://www.g-language.org/wiki/soap

WSDL(RPC/Encoded) file is located at:

http://soap.g-language.org/g-language.wsdl

Documentation on G-language Genome Analysis Environment methods are
provided at the Document Center

http://ws.g-language.org/gdoc/

Usage

Here is a sample session with gentrez

% gentrez genome 'Escherichia coli'
Search NCBI Entrez
ASCII text output file [genome.Escherichia coli.gentrez]: 

Go to the input files for this example
Go to the output files for this example

Command line arguments

Qualifier Type Description Allowed values Default
Standard (Mandatory) qualifiers
[-database]
(Parameter 1)
string NCBI database to search Any string pubmed
[-query]
(Parameter 2)
string Query to search Any string  
[-outfile]
(Parameter 3)
outfile ASCII text output file Output file $(database).$(query).gentrez
Additional (Optional) qualifiers
(none)
Advanced (Unprompted) qualifiers
(none)

Input file format

The database definitions for following commands are available at
http://soap.g-language.org/kbws/embossrc

gentrez reads no file input.

Output file format

The output from gentrez is to a plain text file.

File: genome.Escherichia coli.gentrez

53 entries found in NUCLEOTIDE: (Showing up to 10 hits)

1. Accession Number: NZ_AKBV01000001
Escherichia coli str. K-12 substr. MG1655 strain K-12 cont1.1 chromosome, whole genome shotgun sequence, complete genome

2. Accession Number: NC_018658
Escherichia coli O104:H4 str. 2011C-3493 chromosome, complete genome

3. Accession Number: NC_012971
Escherichia coli BL21(DE3) chromosome, complete genome

4. Accession Number: NC_017635
Escherichia coli W chromosome, complete genome

5. Accession Number: NC_018650
Escherichia coli O104:H4 str. 2009EL-2050 chromosome, complete genome

6. Accession Number: NC_018661
Escherichia coli O104:H4 str. 2009EL-2071 chromosome, complete genome

7. Accession Number: NC_017906
Escherichia coli Xuzhou21 chromosome, complete genome

8. Accession Number: NC_017634
Escherichia coli O83:H1 str. NRG 857C chromosome, complete genome

9. Accession Number: NC_017656
Escherichia coli O55:H7 str. RM12579 chromosome, complete genome

10. Accession Number: NC_017664
Escherichia coli W chromosome, complete genome

Data files

None.

Notes

None.

References

   Arakawa, K., Mori, K., Ikeda, K., Matsuzaki, T., Konayashi, Y., and
      Tomita, M. (2003) G-language Genome Analysis Environment: A Workbench
      for Nucleotide Sequence Data Mining, Bioinformatics, 19, 305-306.

   Arakawa, K. and Tomita, M. (2006) G-language System as a Platform for
      large-scale analysis of high-throughput omics data, J. Pest Sci.,
      31, 7.

   Arakawa, K., Kido, N., Oshita, K., Tomita, M. (2010) G-language Genome
      Analysis Environment with REST and SOAP Web Service Interfaces,
      Nucleic Acids Res., 38, W700-W705.

Warnings

None.

Diagnostic Error Messages

None.

Exit status

It always exits with a status of 0.

Known bugs

None.

See also

Program name Description

Author(s)

Hidetoshi Itaya (celery@g-language.org)
  Institute for Advanced Biosciences, Keio University
  252-0882 Japan

Kazuharu Arakawa (gaou@sfc.keio.ac.jp)
  Institute for Advanced Biosciences, Keio University
  252-0882 Japan

History

2012 - Written by Hidetoshi Itaya

Target users

This program is intended to be used by everyone and everything, from naive users to embedded scrips.

Comments

None.