Mercurial > repos > mikel-egana-aranguren > oppl
annotate OPPL/README @ 6:3740505b579c
Added reasoner option: Pellet or HermiT
| author | Mikel Egaña Aranguren <mikel-egana-aranguren@toolshed.g2.bx.psu.edu> |
|---|---|
| date | Sun, 18 Sep 2011 12:35:18 +0200 |
| parents | 68935f90c2db |
| children | 40adbcb2a7cc |
| rev | line source |
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| 0 | 1 |
| 2 | |
| 3 | |
| 4 =========== | |
| 5 OPPL-GALAXY | |
| 6 =========== | |
| 7 | |
| 8 | |
| 9 | |
| 10 INSTALLATION | |
| 11 ============ | |
| 12 | |
| 13 1.- Stop galaxy. | |
| 14 | |
| 15 2.- Copy oppl_galaxy_tool.jar and oppl_galaxy_tool_lib/ to | |
| 16 /galaxy-dist/tool-data/shared/jars/. | |
| 17 | |
| 18 3.- Create directory /galaxy-dist/tools/OPPL/. | |
| 19 | |
| 20 4.- Copy oppl.xml to /galaxy-dist/tools/OPPL/. | |
| 21 | |
| 22 5.- Add the following lines to /galaxy-dist/tool_conf.xml: | |
| 23 | |
| 24 <section name="Ontology Pre Processor Language" id="oppl"> | |
| 25 <tool file="OPPL/oppl.xml"/> | |
| 26 </section> | |
| 27 | |
| 28 6.- Start galaxy. | |
| 29 | |
| 30 | |
| 31 | |
| 32 USAGE | |
| 33 ===== | |
| 34 | |
| 35 An ontology and an OPPL file are needed (test.owl and test.oppl can be | |
| 36 used as samples). Load both: | |
| 37 | |
| 38 Get Data | |
| 39 >> Upload File from your computer | |
| 40 | |
| 41 Then execute the OPPL file against the OWL file: | |
| 42 | |
| 43 Ontology Pre Processor Language | |
| 44 >> Execute an OPPL file against an OWL file | |
| 45 | |
| 46 | |
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5
68935f90c2db
Added OWL imports closure
Mikel Egaña Aranguren <mikel-egana-aranguren@toolshed.g2.bx.psu.edu>
parents:
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47 |
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4f60202c58d9
Added option to push inferred subsumption axioms into output ontology
Mikel Egaña Aranguren <mikel-egana-aranguren@toolshed.g2.bx.psu.edu>
parents:
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48 FORESEEN FEATURES |
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4f60202c58d9
Added option to push inferred subsumption axioms into output ontology
Mikel Egaña Aranguren <mikel-egana-aranguren@toolshed.g2.bx.psu.edu>
parents:
3
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49 ================= |
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4f60202c58d9
Added option to push inferred subsumption axioms into output ontology
Mikel Egaña Aranguren <mikel-egana-aranguren@toolshed.g2.bx.psu.edu>
parents:
3
diff
changeset
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50 |
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4f60202c58d9
Added option to push inferred subsumption axioms into output ontology
Mikel Egaña Aranguren <mikel-egana-aranguren@toolshed.g2.bx.psu.edu>
parents:
3
diff
changeset
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51 Choose which inferred axioms to add to the output ontology (Right now |
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4f60202c58d9
Added option to push inferred subsumption axioms into output ontology
Mikel Egaña Aranguren <mikel-egana-aranguren@toolshed.g2.bx.psu.edu>
parents:
3
diff
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52 only subsumption is available). |
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4f60202c58d9
Added option to push inferred subsumption axioms into output ontology
Mikel Egaña Aranguren <mikel-egana-aranguren@toolshed.g2.bx.psu.edu>
parents:
3
diff
changeset
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53 |
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6
3740505b579c
Added reasoner option: Pellet or HermiT
Mikel Egaña Aranguren <mikel-egana-aranguren@toolshed.g2.bx.psu.edu>
parents:
5
diff
changeset
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54 FaCT++ and OWLLink support. |
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4f60202c58d9
Added option to push inferred subsumption axioms into output ontology
Mikel Egaña Aranguren <mikel-egana-aranguren@toolshed.g2.bx.psu.edu>
parents:
3
diff
changeset
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55 |
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4f60202c58d9
Added option to push inferred subsumption axioms into output ontology
Mikel Egaña Aranguren <mikel-egana-aranguren@toolshed.g2.bx.psu.edu>
parents:
3
diff
changeset
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56 |
| 0 | 57 |
| 58 TESTS | |
| 59 ===== | |
| 60 | |
| 61 To run the functional test, first complete installation and then: | |
| 62 | |
| 63 1.- Copy test.owl and test.oppl to /galaxy-dist/test-data/ | |
| 64 | |
| 65 2.- Add the following lines to /galaxy-dist/tool_conf.xml.sample | |
| 66 | |
| 67 <section name="Ontology Pre Processor Language" id="oppl"> | |
| 68 <tool file="OPPL/oppl.xml"/> | |
| 69 </section> | |
| 70 | |
| 71 3.- Execute /galaxy-dist/run_functional_tests.sh -id oppl | |
| 72 | |
| 73 | |
| 74 | |
| 75 CONTACT | |
| 76 ======= | |
| 77 | |
| 78 Please send any request or comment to mikel.egana.aranguren@gmail.com. | |
| 79 | |
| 80 | |
| 81 | |
| 82 ACKNOWLEDGEMENTS | |
| 83 ================ | |
| 84 | |
| 85 This work is funded by the Marie Curie Cofund program of the EU, FP7. | |
| 86 | |
| 87 | |
| 88 | |
| 89 COPYRIGHT AND LICENSE | |
| 90 ===================== | |
| 91 | |
| 92 Copyright (c) 2011 Mikel Egaña Aranguren. | |
| 93 | |
| 94 OPPL-Galaxy is free software: you can redistribute it and/or modify | |
| 95 it under the terms of the GNU General Public License as published by | |
| 96 the Free Software Foundation, either version 3 of the License, or | |
| 97 (at your option) any later version. | |
| 98 | |
| 99 This program is distributed in the hope that it will be useful, | |
| 100 but WITHOUT ANY WARRANTY; without even the implied warranty of | |
| 101 MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the | |
| 102 GNU General Public License for more details. | |
| 103 | |
| 104 You should have received a copy of the GNU General Public License | |
| 105 along with this program. If not, see <http://www.gnu.org/licenses/>. | |
| 106 | |
| 107 OPPL, OWL API and Pellet have their own licenses. | |
| 108 | |
| 109 Galaxy is distributed as open source under the conditions of the | |
| 110 Academic Free License (http://www.opensource.org/licenses/academic.php). | |
| 111 | |
| 112 | |
| 113 | |
| 114 | |
| 115 | |
| 116 | |
| 117 | |
| 118 |