| 1 | # Copyright (c) 2010 - 2011 European Molecular Biology Laboratory |
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| 2 | # |
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| 3 | # Licensed under the Apache License, Version 2.0 (the "License"); |
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| 4 | # you may not use this file except in compliance with the License. |
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| 5 | # You may obtain a copy of the License at |
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| 6 | # |
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| 7 | # http://www.apache.org/licenses/LICENSE-2.0 |
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| 8 | # |
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| 9 | # Unless required by applicable law or agreed to in writing, software |
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| 10 | # distributed under the License is distributed on an "AS IS" BASIS, |
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| 11 | # WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. |
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| 12 | # See the License for the specific language governing permissions and |
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| 13 | # limitations under the License. |
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| 14 | |
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| 15 | ########################################################## |
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| 16 | # Operations with relationships |
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| 17 | # Please use the full version of ontoCAT R package: https://sourceforge.net/projects/ontocat/files/ontoCAT/ontoCAT_R/ontoCAT_1.2.1.tar.gz |
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| 18 | ########################################################## |
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| 19 | |
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| 20 | #Java Heap size needed to reason over GO ontology (more than 20 MB in size) is 512MB. |
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| 21 | #Here are the instructions how to increase Java Heap Size in R: |
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| 22 | |
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| 23 | library(rJava) |
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| 24 | options(java.parameters="-Xmx512") |
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| 25 | .jinit() |
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| 26 | |
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| 27 | #To check the result: |
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| 28 | .jcall(.jnew("java/lang/Runtime"), "J", "maxMemory") |
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| 29 | #Now it is possible to work with large ontologies like GO |
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| 30 | |
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| 31 | library(ontoCAT) |
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| 32 | |
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| 33 | #Example with OBO ontology |
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| 34 | |
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| 35 | # Obtain GO ontology without reasoning over it |
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| 36 | go_wr <- getOntologyNoReasoning("http://www.geneontology.org/ontology/obo_format_1_2/gene_ontology_ext.obo") |
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| 37 | |
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| 38 | getOntologyRelationNames(go_wr) |
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| 39 | |
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| 40 | # Obtain GO ontology with reasoning over it |
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| 41 | go <- getOntology("http://www.geneontology.org/ontology/obo_format_1_2/gene_ontology_ext.obo") |
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| 42 | |
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| 43 | getOntologyRelationNames(go) |
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| 44 | |
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| 45 | |
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| 46 | #Example with OWL ontology |
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| 47 | |
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| 48 | # Obtain EFO ontology with reasoning over it |
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| 49 | |
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| 50 | efo_wr <- getOntologyNoReasoning("http://rest.bioontology.org/bioportal/ontologies/download/45781?applicationid=4ea81d74-8960-4525-810b-fa1baab576ff"); |
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| 51 | |
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| 52 | getOntologyRelationNames(efo_wr) |
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| 53 | |
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| 54 | # Obtain EFO ontology with reasoning over it |
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| 55 | efo <- getOntology("http://rest.bioontology.org/bioportal/ontologies/download/45781?applicationid=4ea81d74-8960-4525-810b-fa1baab576ff") |
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| 56 | |
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| 57 | getOntologyRelationNames(efo) |
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| 58 | |
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| 59 | term <- getTermById(efo,"EFO_0000815") |
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| 60 | getTermRelations(efo,term,"has_part") |
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