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comparison OPPL/README @ 17:c9e01f86b07c draft

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New tool added for merging imported ontologies (GalaxyOWLAPI and README changed and test ontologies added accordingly). Memory settings changed in all the tools XML files
author Mikel Egana Aranguren <mikel-egana-aranguren@toolshed.g2.bx.psu.edu>
date Mon, 20 Aug 2012 11:39:56 +0200
parents 622cde484f4c
children d3616fac4ca5
comparison
equal deleted inserted replaced
16:6c25e717c896 17:c9e01f86b07c
4 INSTALLATION 4 INSTALLATION
5 ============ 5 ============
6 6
7 1.- Stop Galaxy. 7 1.- Stop Galaxy.
8 8
9 2.- Copy the following files and dirs to 9 2.- Copy the following files and directories 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 inference.jar 13 inference.jar
14 query.jar 14 query.jar
15 oppl_query.jar 15 oppl_query.jar
16 merge.jar
16 oppl_galaxy_lib/ 17 oppl_galaxy_lib/
17 inference_lib/ 18 inference_lib/
18 query_lib/ 19 query_lib/
19 oppl_query_lib/ 20 oppl_query_lib/
21 merge_lib/
20 FaCT++-linux-v1.5.2/ 22 FaCT++-linux-v1.5.2/
21 FaCT++-OSX-v1.5.2/ 23 FaCT++-OSX-v1.5.2/
22 24
23 3.- Create directory /galaxy-dist/tools/OPPL/ 25 3.- Create directory /galaxy-dist/tools/OPPL/
24 26
25 4.- Copy oppl.xml, inference.xml and query.xml to 27 4.- Copy oppl.xml, inference.xml, query.xml, oppl_query.xml and
26 /galaxy-dist/tools/OPPL/ 28 merge.xml to /galaxy-dist/tools/OPPL/
27 29
28 5.- Add the following lines to /galaxy-dist/tool_conf.xml: 30 5.- Add the following lines to /galaxy-dist/tool_conf.xml:
29 31
30 <section name="Ontology Pre Processor Language" id="oppl"> 32 <section name="Ontology Pre Processor Language" id="oppl">
31 <tool file="OPPL/oppl.xml"/> 33 <tool file="OPPL/oppl.xml"/>
32 <tool file="OPPL/inference.xml"/> 34 <tool file="OPPL/inference.xml"/>
33 <tool file="OPPL/query.xml"/> 35 <tool file="OPPL/query.xml"/>
34 <tool file="OPPL/oppl_query.xml"/> 36 <tool file="OPPL/oppl_query.xml"/>
37 <tool file="OPPL/merge.xml"/>
35 </section> 38 </section>
36 39
37 6.- Start Galaxy. 40 6.- Start Galaxy.
38 41
39 42
40 43
41 FORESEEN FEATURES 44 FORESEEN FEATURES
42 ================= 45 =================
43 46
44 General (OPPL, Inference, Query, OPPL query):
45
46 - Support for processing ontologies that import other ontologies loaded 47 - Support for processing ontologies that import other ontologies loaded
47 in galaxy. 48 in galaxy (i.e. to resolve imports within galaxy).
48 49
49 - Entities rendering definition (URI fragment, rdfs:label, QName, etc). 50 - Entities rendering definition (URI fragment, rdfs:label, QName, etc).
50 51
51 - OWLLink and Racer support. 52 - OWLLink, Racer and ELK support.
52
53
54 OPPL:
55 53
56 - Standalone OPPL assertions parsing (e.g. ADD phagocyte subClassOf 54 - Standalone OPPL assertions parsing (e.g. ADD phagocyte subClassOf
57 cell). 55 cell).
58 56
59 - Other output formats apart from RDF/XML. 57 - Other output formats apart from RDF/XML.
60 58
61
62 Inference:
63
64 - Support for DataPropertyAssertion, DataPropertyHierarchy, 59 - Support for DataPropertyAssertion, DataPropertyHierarchy,
65 DifferentIndividuals, ... 60 DifferentIndividuals, ...
66
67 OPPL query:
68 61
69 62
70 63
71 KNOWN BUGS AND ISSUES 64 KNOWN BUGS AND ISSUES
72 ===================== 65 =====================
98 COPYRIGHT AND LICENSE 91 COPYRIGHT AND LICENSE
99 ===================== 92 =====================
100 93
101 Copyright (c) 2011 Mikel Egaña Aranguren. 94 Copyright (c) 2011 Mikel Egaña Aranguren.
102 95
103 (OPPL|Inference|Query)-Galaxy 96 (OPPL|Inference|Query|OPPL-Query|Merge)-Galaxy
104 is free software: you can redistribute it and/or modify it under the 97 is free software: you can redistribute it and/or modify it under the
105 terms of the GNU General Public License as published by the Free 98 terms of the GNU General Public License as published by the Free
106 Software Foundation, either version 3 of the License, or (at your 99 Software Foundation, either version 3 of the License, or (at your
107 option) any later version. 100 option) any later version.
108 101
115 along with this program. If not, see <http://www.gnu.org/licenses/>. 108 along with this program. If not, see <http://www.gnu.org/licenses/>.
116 109
117 OPPL API, OWL API, Pellet, HermiT, and FaCT++ have their own licenses. 110 OPPL API, OWL API, Pellet, HermiT, and FaCT++ have their own licenses.
118 111
119 112
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