Mercurial > repos > mikel-egana-aranguren > oppl

comparison OPPL/README @ 13:7e6604a5ee55

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
New query tool added
author Mikel Egaña Aranguren <mikel-egana-aranguren@toolshed.g2.bx.psu.edu>
date Thu, 29 Mar 2012 14:49:22 +0200
parents 6ca67b155e32
children 622cde484f4c
comparison
equal deleted inserted replaced
12:d0722148cb59 13:7e6604a5ee55
8 8
9 2.- Copy the following files and dirs to 9 2.- Copy the following files and dirs to
10 /galaxy-dist/tool-data/shared/jars/: 10 /galaxy-dist/tool-data/shared/jars/:
11 11
12 oppl_galaxy_tool.jar 12 oppl_galaxy_tool.jar
13 oppl_galax_lib/ 13 inference.jar
14 query.jar
15 oppl_galaxy_lib/
16 inference_lib/
17 query_lib/
14 FaCT++-linux-v1.5.2/ 18 FaCT++-linux-v1.5.2/
15 FaCT++-OSX-v1.5.2/ 19 FaCT++-OSX-v1.5.2/
16 inference.jar 20
17 inference_lib/
18
19 3.- Create directory /galaxy-dist/tools/OPPL/ 21 3.- Create directory /galaxy-dist/tools/OPPL/
20 22
21 4.- Copy oppl.xml and inference.xml to /galaxy-dist/tools/OPPL/ 23 4.- Copy oppl.xml, inference.xml and query.xml to
24 /galaxy-dist/tools/OPPL/
22 25
23 5.- Add the following lines to /galaxy-dist/tool_conf.xml: 26 5.- Add the following lines to /galaxy-dist/tool_conf.xml:
24 27
25 <section name="Ontology Pre Processor Language" id="oppl"> 28 <section name="Ontology Pre Processor Language" id="oppl">
26 <tool file="OPPL/oppl.xml"/> 29 <tool file="OPPL/oppl.xml"/>
27 <tool file="OPPL/inference.xml"/> 30 <tool file="OPPL/inference.xml"/>
31 <tool file="OPPL/query.xml"/>
28 </section> 32 </section>
29 33
30 6.- Start Galaxy. 34 6.- Start Galaxy.
31 35
32 36
33 37
34 FORESEEN FEATURES 38 FORESEEN FEATURES
35 ================= 39 =================
36 40
37 OPPL: 41 General (OPPL, Inference, Query):
38 42
39 - Support for processing ontologies that import other ontologies loaded 43 - Support for processing ontologies that import other ontologies loaded
40 in galaxy. 44 in galaxy.
41 45
42 - Rendering definition (URI fragment, label, etc). 46 - Entities rendering definition (URI fragment, rdfs:label, QName, etc).
47
48 - OWLLink and Racer support.
49
50
51 OPPL:
43 52
44 - Standalone OPPL assertions parsing (e.g. ADD phagocyte subClassOf 53 - Standalone OPPL assertions parsing (e.g. ADD phagocyte subClassOf
45 cell). 54 cell).
46 55
47 - OWLLink and Racer support. 56 - Other output formats apart from RDF/XML.
48 57
49 58
50 Inference: 59 Inference:
51 60
52 - DataPropertyAssertion, DataPropertyHierarchy, DifferentIndividuals, 61 - Support for DataPropertyAssertion, DataPropertyHierarchy,
53 ... 62 DifferentIndividuals, ...
54
55 63
56 64
57 65
58 KNOWN BUGS AND ISSUES 66 KNOWN BUGS AND ISSUES
59 ===================== 67 =====================
85 COPYRIGHT AND LICENSE 93 COPYRIGHT AND LICENSE
86 ===================== 94 =====================
87 95
88 Copyright (c) 2011 Mikel Egaña Aranguren. 96 Copyright (c) 2011 Mikel Egaña Aranguren.
89 97
90 (OPPL|Inference)-Galaxy is free software: you can redistribute it and/or 98 (OPPL|Inference|Query)-Galaxy
91 modify it under the terms of the GNU General Public License as published 99 is free software: you can redistribute it and/or modify it under the
92 by the Free Software Foundation, either version 3 of the License, or (at 100 terms of the GNU General Public License as published by the Free
93 your option) any later version. 101 Software Foundation, either version 3 of the License, or (at your
102 option) any later version.
94 103
95 This program is distributed in the hope that it will be useful, 104 This program is distributed in the hope that it will be useful,
96 but WITHOUT ANY WARRANTY; without even the implied warranty of 105 but WITHOUT ANY WARRANTY; without even the implied warranty of
97 MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the 106 MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
98 GNU General Public License for more details. 107 GNU General Public License for more details.