1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219
220
221
222
223
224
225
226
227
228
229
230
231
232
233
234
235
236
237
238
239
240
241
242
243
244
245
246
247
248
249
250
251
252
253
254
255
256
257
258
259
260
261
262
263
264
265
266
267
268
269
270
271
272
273
274
275
276
277
278
279
280
281
282
283
284
285
286
287
288
289
290
291
292
293
294
295
296
297
298
299
300
301
302
|
edamhasinput
Wiki
The master copies of EMBOSS documentation are available at
http://emboss.open-bio.org/wiki/Appdocs on the EMBOSS Wiki.
Please help by correcting and extending the Wiki pages.
Function
Find EDAM ontology terms by has_input relation
Description
edamhasinput searches the has_input relations of EDAM terms and returns
matching terms. The input is read from the installed EDAM database. The
ontology term output can be written to screen, to file, or passed to
another program. A wide range of standard ontology term formats may be
specified for input and output.
Optionally the search can be restricted to specified EDAM namespaces.
Usage
Here is a sample session with edamhasinput
% edamhasinput sequence
Find EDAM ontology terms by has_input relation
Obo output file [edamhasinput.obo]:
Go to the output files for this example
Command line arguments
Find EDAM ontology terms by has_input relation
Version: EMBOSS:6.6.0.0
Standard (Mandatory) qualifiers:
[-identifier] string Identifier(s) to search for in ontology (Any
string)
[-outfile] outobo [*.edamhasinput] Output ontology term file
name
Additional (Optional) qualifiers:
-namespace menu [*] By default all terms are returned.
Searches can be limited to one or a few
namespaces. (Values: data (Data entity);
entity (Biological entity); format (Data
format); identifier (Identifier); operation
(Bioinformatics operation); resource (Data
resource); topic (Field of bioinformatics
study))
Advanced (Unprompted) qualifiers:
-sensitive boolean [N] By default, the query keywords are
matched against the EDAM term names (and
synonyms) only. This option also matches the
keywords against the EDAM term definitions
and will therefore (typically) report more
matches.
-subclasses boolean [N] Extend the query matches to include all
terms which are specialisations (EDAM
sub-classes) of the matched type.
-obsolete boolean [N] The default behaviour is to not use or
return obsolete terms. This option if set
will include all terms.
Associated qualifiers:
"-outfile" associated qualifiers
-odirectory2 string Output directory
-oformat2 string Ontology term output format
General qualifiers:
-auto boolean Turn off prompts
-stdout boolean Write first file to standard output
-filter boolean Read first file from standard input, write
first file to standard output
-options boolean Prompt for standard and additional values
-debug boolean Write debug output to program.dbg
-verbose boolean Report some/full command line options
-help boolean Report command line options and exit. More
information on associated and general
qualifiers can be found with -help -verbose
-warning boolean Report warnings
-error boolean Report errors
-fatal boolean Report fatal errors
-die boolean Report dying program messages
-version boolean Report version number and exit
Input file format
edamhasinput queries the EDAM ontology.
Output file format
The output is a standard EMBOSS ontology term file.
The results can be output in one of several styles by using the
command-line qualifier -oformat xxx, where 'xxx' is replaced by the
name of the required format. The available format names are: obo,
brief, list, html, xml, json, excel.
See: http://emboss.sf.net/docs/themes/OntologyFormats.html for further
information on ontology formats.
Output files for usage example
File: edamhasinput.obo
[Term]
id: EDAM_operation:1780
name: Sequence submission
namespace: operation
def: Submit a molecular sequence to a database.
subset: bioinformatics
subset: edam
subset: operations
created_in: "beta12orEarlier"
is_a: EDAM_operation:2446 ! Sequence processing
relationship: has_input EDAM_data:2044 ! Sequence
relationship: has_topic EDAM_topic:3077 ! Data acquisition and deposition
[Term]
id: EDAM_operation:0564
name: Sequence rendering
namespace: operation
def: Visualise, format or render a molecular sequence, possibly with sequence fe
atures or properties shown.
subset: bioinformatics
subset: edam
subset: operations
created_in: "beta12orEarlier"
is_a: EDAM_operation:0337 ! Plotting and rendering
is_a: EDAM_operation:2446 ! Sequence processing
relationship: has_input EDAM_data:2044 ! Sequence
relationship: has_output EDAM_data:2969 ! Sequence image
[Term]
id: EDAM_operation:2451
name: Sequence comparison
namespace: operation
def: Compare two or more molecular sequences.
subset: bioinformatics
subset: edam
subset: operations
created_in: "beta12orEarlier"
is_a: EDAM_operation:2403 ! Sequence analysis
is_a: EDAM_operation:2424 ! Comparison
relationship: has_input EDAM_data:2044 ! Sequence
relationship: has_output EDAM_data:2955 ! Sequence report
relationship: has_topic EDAM_topic:0159 ! Sequence comparison
[Term]
id: EDAM_operation:0292
name: Sequence alignment construction
namespace: operation
def: Align (identify equivalent sites within) molecular sequences.
subset: bioinformatics
subset: edam
subset: operations
[Part of this file has been deleted for brevity]
subset: bioinformatics
subset: edam
subset: operations
created_in: "beta12orEarlier"
is_a: EDAM_operation:0338 ! Sequence database search
relationship: has_input EDAM_data:1267 ! Amino acid frequencies
relationship: has_topic EDAM_topic:0157 ! Sequence composition analysis
[Term]
id: EDAM_operation:0566
name: Sequence cluster rendering
namespace: operation
def: Visualise, format or render sequence clusters.
subset: bioinformatics
subset: edam
subset: operations
created_in: "beta12orEarlier"
is_a: EDAM_operation:0337 ! Plotting and rendering
is_a: EDAM_operation:2452 ! Sequence cluster processing
relationship: has_input EDAM_data:1235 ! Sequence cluster
[Term]
id: EDAM_operation:2507
name: Sequence alignment analysis (nucleic acid)
namespace: operation
def: Analyse a protein sequence alignment, typically to detect features or make
predictions.
subset: bioinformatics
subset: edam
subset: operations
created_in: "beta12orEarlier"
is_a: EDAM_operation:0258 ! Sequence alignment analysis
is_a: EDAM_operation:2501 ! Nucleic acid data processing
is_a: EDAM_operation:3024 ! Prediction, detection and recognition (nucleic acid)
relationship: has_input EDAM_data:1383 ! Sequence alignment (nucleic acid)
relationship: has_topic EDAM_topic:0740 ! Nucleic acid sequence alignment
[Term]
id: EDAM_operation:2479
name: Protein sequence analysis
namespace: operation
def: Analyse a protein sequence (using methods that are only applicable to prote
in sequences).
subset: bioinformatics
subset: edam
subset: operations
synonym: "Sequence analysis (protein)" EXACT []
created_in: "beta12orEarlier"
is_a: EDAM_operation:2403 ! Sequence analysis
is_a: EDAM_operation:2447 ! Sequence processing (protein)
relationship: has_input EDAM_data:2976 ! Protein sequence
relationship: has_topic EDAM_topic:0639 ! Protein sequence analysis
Data files
The EDAM Ontology is included in EMBOSS as local database edam.
Notes
None.
References
None.
Warnings
None.
Diagnostic Error Messages
None.
Exit status
It always exits with status 0.
Known bugs
None.
See also
Program name Description
drfinddata Find public databases by data type
drfindformat Find public databases by format
drfindid Find public databases by identifier
drfindresource Find public databases by resource
edamdef Find EDAM ontology terms by definition
edamhasoutput Find EDAM ontology terms by has_output relation
edamisformat Find EDAM ontology terms by is_format_of relation
edamisid Find EDAM ontology terms by is_identifier_of relation
edamname Find EDAM ontology terms by name
godef Find GO ontology terms by definition
goname Find GO ontology terms by name
ontoget Get ontology term(s)
ontogetcommon Get common ancestor for terms
ontogetdown Get ontology term(s) by parent id
ontogetobsolete Get ontology ontology terms
ontogetroot Get ontology root terms by child identifier
ontogetsibs Get ontology term(s) by id with common parent
ontogetup Get ontology term(s) by id of child
ontoisobsolete Report whether an ontology term id is obsolete
ontotext Get ontology term(s) original full text
wossdata Find programs by EDAM data
wossinput Find programs by EDAM input data
wossoperation Find programs by EDAM operation
wossoutput Find programs by EDAM output data
wossparam Find programs by EDAM parameter
wosstopic Find programs by EDAM topic
Author(s)
Peter Rice
European Bioinformatics Institute, Wellcome Trust Genome Campus,
Hinxton, Cambridge CB10 1SD, UK
Please report all bugs to the EMBOSS bug team
(emboss-bug (c) emboss.open-bio.org) not to the original author.
History
Target users
This program is intended to be used by everyone and everything, from
naive users to embedded scripts.
Comments
None
|
