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comparison GEMBASSY-1.0.3/doc/text/gentrez.txt @ 0:8300eb051bea draft

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1 gentrez
2 Function
3
4 Search NCBI Entrez
5
6 Description
7
8 gentrez searches NCBI Entrez with keyword through EUtilities.
9 This is intended for quick lookup through the command line
10 so only top ten hits are reported.
11
12 G-language SOAP service is provided by the
13 Institute for Advanced Biosciences, Keio University.
14 The original web service is located at the following URL:
15
16 http://www.g-language.org/wiki/soap
17
18 WSDL(RPC/Encoded) file is located at:
19
20 http://soap.g-language.org/g-language.wsdl
21
22 Documentation on G-language Genome Analysis Environment methods are
23 provided at the Document Center
24
25 http://ws.g-language.org/gdoc/
26
27 Usage
28
29 Here is a sample session with gentrez
30
31 % gentrez genome 'Escherichia coli'
32 Search NCBI Entrez
33 ASCII text output file [genome.Escherichia coli.gentrez]:
34
35 Go to the input files for this example
36 Go to the output files for this example
37
38 Command line arguments
39
40 Standard (Mandatory) qualifiers:
41 [-database] string [pubmed] NCBI database to search (Any
42 string)
43 [-query] string Query to search (Any string)
44 [-outfile] outfile [$(database).$(query).gentrez] ASCII text
45 output file
46
47 Additional (Optional) qualifiers: (none)
48 Advanced (Unprompted) qualifiers: (none)
49 Associated qualifiers:
50
51 "-outfile" associated qualifiers
52 -odirectory3 string Output directory
53
54 General qualifiers:
55 -auto boolean Turn off prompts
56 -stdout boolean Write first file to standard output
57 -filter boolean Read first file from standard input, write
58 first file to standard output
59 -options boolean Prompt for standard and additional values
60 -debug boolean Write debug output to program.dbg
61 -verbose boolean Report some/full command line options
62 -help boolean Report command line options and exit. More
63 information on associated and general
64 qualifiers can be found with -help -verbose
65 -warning boolean Report warnings
66 -error boolean Report errors
67 -fatal boolean Report fatal errors
68 -die boolean Report dying program messages
69 -version boolean Report version number and exit
70
71 Input file format
72
73 The database definitions for following commands are available at
74 http://soap.g-language.org/kbws/embossrc
75
76 gentrez reads no file input.
77
78 Output file format
79
80 The output from gentrez is to a plain text file.
81
82 File: genome.Escherichia coli.gentrez
83
84 53 entries found in NUCLEOTIDE: (Showing up to 10 hits)
85
86 1. Accession Number: NZ_AKBV01000001
87 Escherichia coli str. K-12 substr. MG1655 strain K-12 cont1.1 chromosome, whole genome shotgun sequence, complete genome
88
89 2. Accession Number: NC_018658
90 Escherichia coli O104:H4 str. 2011C-3493 chromosome, complete genome
91
92 3. Accession Number: NC_012971
93 Escherichia coli BL21(DE3) chromosome, complete genome
94
95 4. Accession Number: NC_017635
96 Escherichia coli W chromosome, complete genome
97
98 5. Accession Number: NC_018650
99 Escherichia coli O104:H4 str. 2009EL-2050 chromosome, complete genome
100
101 6. Accession Number: NC_018661
102 Escherichia coli O104:H4 str. 2009EL-2071 chromosome, complete genome
103
104 7. Accession Number: NC_017906
105 Escherichia coli Xuzhou21 chromosome, complete genome
106
107 8. Accession Number: NC_017634
108 Escherichia coli O83:H1 str. NRG 857C chromosome, complete genome
109
110 9. Accession Number: NC_017656
111 Escherichia coli O55:H7 str. RM12579 chromosome, complete genome
112
113 10. Accession Number: NC_017664
114 Escherichia coli W chromosome, complete genome
115
116
117 Data files
118
119 None.
120
121 Notes
122
123 None.
124
125 References
126
127 Arakawa, K., Mori, K., Ikeda, K., Matsuzaki, T., Konayashi, Y., and
128 Tomita, M. (2003) G-language Genome Analysis Environment: A Workbench
129 for Nucleotide Sequence Data Mining, Bioinformatics, 19, 305-306.
130
131 Arakawa, K. and Tomita, M. (2006) G-language System as a Platform for
132 large-scale analysis of high-throughput omics data, J. Pest Sci.,
133 31, 7.
134
135 Arakawa, K., Kido, N., Oshita, K., Tomita, M. (2010) G-language Genome
136 Analysis Environment with REST and SOAP Web Service Interfaces,
137 Nucleic Acids Res., 38, W700-W705.
138
139 Warnings
140
141 None.
142
143 Diagnostic Error Messages
144
145 None.
146
147 Exit status
148
149 It always exits with a status of 0.
150
151 Known bugs
152
153 None.
154
155 See also
156
157 None.
158
159 Author(s)
160
161 Hidetoshi Itaya (celery@g-language.org)
162 Institute for Advanced Biosciences, Keio University
163 252-0882 Japan
164
165 Kazuharu Arakawa (gaou@sfc.keio.ac.jp)
166 Institute for Advanced Biosciences, Keio University
167 252-0882 Japan
168
169 History
170
171 2012 - Written by Hidetoshi Itaya
172 2013 - Fixed by Hidetoshi Itaya
173
174 Target users
175
176 This program is intended to be used by everyone and everything, from
177 naive users to embedded scripts.
178
179 Comments
180
181 None.
182