Changes between Initial Version and Version 1 of r


Ignore:
Timestamp:
2015-07-21T20:09:31+02:00 (6 years ago)
Author:
Morris Swertz
Comment:

--

Legend:

Unmodified
Added
Removed
Modified
  • r

    v1 v1  
     1== ontoCAT R package==
     2
     3=== Download ===
     4
     5We provide two versions of '''''ontoCAT R package''''':
     6* [http://bioconductor.org/help/bioc-views/2.8/bioc/html/ontoCAT.html Light-weight ontoCAT R package version] is available in [http://bioconductor.org Bioconductor] starting from release 2.7, and includes all single-ontology functionality except for methods to work with multiple ontologies and search in OLS and !BioPortal.
     7* [https://sourceforge.net/projects/ontocat/files/ontoCAT/ontoCAT_R/ontoCAT_1.2.1.tar.gz Full ontoCAT R package version] includes batch methods and due to package-size limitations is available only from the ontoCAT project  [https://sourceforge.net/projects/ontocat sourceforge] page.
     8
     9
     10=== Description ===
     11
     12The R package '''''ontoCAT''''' was created to support basic operations on ontologies: traversal and search,
     13uniform access to ontologies in OWL and OBO formats and to provide R access to major ontology repositories OLS and !BioPortal.
     14
     15Several hundreds of public ontologies and numerous private ontologies for describing biological data exist today.
     16Using ontologies in R is difficult due to the lack of uniform package support.
     17At the same time numerous Java-based ontology projects are available. '''''ontoCAT''''' takes advantage of a standard Java library with the same name "ontoCAT" to implement its functionality.
     18Here are java sources used for our R package: [http://www.ontocat.org/browser/trunk/ontoCAT/src/uk/ac/ebi/ontocat/utils Java sources].
     19
     20The '''''ontoCAT''''' package:
     21 * gives unified, format-independent access to ontology terms and the ontology hierarchy represented in OWL and OBO formats;
     22 * provides basic methods for ontology traversal, such as searching for terms, listing a specific term's relations, showing paths to the term from the root element of the ontology, showing flattened-tree representations of the ontology hierarchy;
     23 * supports working with groups of ontologies and with major public ontology repositories: searching for terms across ontologies, listing available ontologies and loading ontologies for further analysis as necessary.
     24
     25No other package with similar functionality exists at the moment in the R environment.
     26
     27The integration of the above functionality into R allows combining and automating ontology-related tasks.\\
     28Different examples of ontology-related tasks that can be accomplished with the help of the '''''ontoCAT''''' package are given at the [http://www.ontocat.org/wiki/OntocatGuide examples page] of the ontoCAT website: gene enrichment test and grouping of results, search and re-annotation of free-text to ontology.
     29
     30'''''ontoCAT''''' has been included into Bioconductor, the main R open source project in bioinformatics. 
     31==== Reasoning ====
     32Reasoning over ontologies and extracting relationships is supported by using HermiT reasoner.
     33OBO ontologies are translated by OWL API into valid OWL format that can be reasoned over.
     34[wiki:Reasoning More info about reasoning]
     35
     36==== Relationships ====
     37In '''''ontoCAT''''' the subsumption "subclass/superclass" is supported in a user friendly form of "child -- parent" relationship. \\
     38For instance, ontology term "myocardium" is a parent for term "atrial myocardium" since "atrial myocardium" is subclass of "myocardium".
     39No distinction is made between universals (classes) and particulars (instances) as they are both treated as ontology terms. 
     40
     41The advantage of using a reasoner in '''''ontoCAT''''' is the ability to work with different relationships in addition to subsumption.
     42
     43Example of operations with relationships is available here: [http://www.ontocat.org/browser/trunk/ontoCAT/src/uk/ac/ebi/ontocat/examples/R/Example3.R R Example 3].
     44==== Java Heap Size ====
     45
     46Java Heap size needed to reason over GO ontology (more than 20 MB in size) is 512MB.
     47Here are the instructions how to increase Java Heap Size in '''R''':
     48
     49> library(rJava)
     50
     51> options(java.parameters="-Xmx512")
     52
     53> .jinit()
     54
     55#To check the result:
     56> .jcall(.jnew("java/lang/Runtime"), "J", "maxMemory")
     57
     58#Now we can load ontoCAT library and start to work with large ontologies like GO
     59>library(ontoCAT)
     60
     61>go <- getOntology("http://www.geneontology.org/ontology/obo_format_1_2/gene_ontology_ext.obo")
     62=== Methods ===
     63
     64'''Single Ontology Traversal Methods'''
     65
     66* To load an ontology ''getOntology()'' method of the ''Ontology'' class is available. It takes a single argument, specifying the local filesystem path, the full URI for the ontology file, or its OLS/BioPortal accession number. However, if reasoning over ontology is not desirable ''getOntologyNoReasoning()'' method should be used instead of ''getOntology()'' method described above.
     67* ''getAllTermChildren(Ontology, term)'' returns list of term's all children
     68* ''getAllTermChildrenById(Ontology, 'EFO_0000343')'' returns list of term's all children
     69* ''getAllTermIds(Ontology)'' returns list of all term accessions
     70* ''getAllTermParents(Ontology, term)''  returns list of term's all parents
     71* ''getAllTermParentsById(Ontology, 'EFO_0000343')'' returns list of term's all parents
     72* ''getAllTerms(Ontology)'' returns list of all terms
     73* ''getEFOBranchRootIds(Ontology)'' returns set of branch root accessions. Method specific for EFO ontology
     74* ''getOntologyAccession(Ontology)'' returns parsed ontology accession
     75* ''getOntologyDescription(Ontology)'' returns parsed ontology description
     76* ''getRootIds(Ontology)'' returns list of root terms accessions, if there are any
     77* ''getRoots(Ontology)'' returns list of root terms, if there are any
     78* ''getTermAndAllChildren(Ontology, term)''  returns list of accessions of term itself and all its children recursively
     79* ''getTermAndAllChildrenById(Ontology, 'EFO_0000343')'' returns list of accessions of term itself and all its children recursively
     80* ''getTermById(Ontology, 'EFO_0000343')'' fetchs term by accession. returns external term representation if found in ontology, null otherwise
     81* ''getAccession(term)'' returns term's accession
     82* ''getLabel(term)'' returns term's label
     83* ''getTermNameById(Ontology, 'EFO_0000343')'' returns term's label by accession
     84* ''getTermChildren(Ontology, term)''  returns list of term's direct children
     85* ''getTermChildrenById(Ontology, 'EFO_0000343')'' returns list of term's direct children
     86* ''getTermDefinitions(Ontology, term)''  returns set of term's definitions if there are some
     87* ''getTermParents(Ontology, term)'' returns list of term's direct parents
     88* ''getTermParentsById(Ontology, 'EFO_0000343')''  returns list of term's direct parents
     89* ''getTermSynonyms(Ontology, term)''  returns set of term's synonyms  if there are some
     90* ''hasTerm(Ontology, 'EFO_0000343')'' Check if term with specified accession exists in ontology
     91* ''isEFOBranchRoot(Ontology, term)''  returns true if term is branch root of EFO. Method specific for EFO ontology
     92* ''isEFOBranchRootById(Ontology, 'EFO_0000343')'' returns true if term is branch root of EFO. Method specific for EFO ontology
     93* ''isRoot(Ontology, term)''  returns true if term is root of ontology
     94* ''isRootById(Ontology, 'EFO_0000343')'' returns true if term is root of ontology
     95* ''searchTerm(Ontology, 'thymus')'' searches for term in ontology by name
     96* ''searchTermPrefix(Ontology, 'thym')'' searches for prefix in ontology
     97* ''showHierarchyDownToTerm(Ontology, term)'' returns set of terms that represent ontology "opened" down to specified term, hence displaying all its parents first and then a tree level, containing specified term
     98* ''showHierarchyDownToTermById(Ontology, 'EFO_0000343')'' returns set of terms that represent ontology "opened" down to specified term, hence displaying all its parents first and then a tree level, containing specified term
     99* ''showPathsToTerm(Ontology, term)''  returns paths to the specified term from ontology's root term
     100* ''showPathsToTermById(Ontology, 'EFO_0000343')'' returns paths to the specified term from ontology's root term
     101* ''getOntologyRelationNames(Ontology)'' returns list of relations used in ontology
     102* ''getTermRelationNames(Ontology, term)'' returns list of relations that term has
     103* ''getTermRelationNamesById(Ontology, 'EFO_0000343')'' returns list of relations that term under given accession has
     104* ''getTermRelations(Ontology, 'EFO_0000343', 'has_part')'' returns list of terms that are in defined relation with term of interest
     105* ''getTermRelations(Ontology, term, 'has_part')'' returns list of terms that are in defined relation with term of interest
     106
     107'''Operations on Multiple Ontologies'''
     108
     109* To create a local batch of ontologies the ''getOntologyFromBatch()'' method of the ''batch'' class is provided, taking a single argument: the path to the local directory containing ontology files. By default, a call to ''getOntologyFromBatch()'' without any arguments will load the EFO ontology.
     110* Ontologies can be added to an existing batch as needed via the ''addOntology()'' method.
     111* ''searchTerm(batch, 'thymus')'' searches for term in all ontologies in the batch.
     112* ''searchTermInOLS('thymus')'' searches for term in OLS.
     113* ''searchTermInBioPortal('thymus')'' searches for term in !BioPortal.
     114* ''serachTermInAll(batch,'thymus')'' searches for term in all ontologies in the batch as well as in OLS and !BioPortal repositories.
     115* ''listLoadedOntologies(batch)'' returns a list of ontologies from the batch.
     116* ''listOLSOntologies(batch)'' returns a list of ontologies available from OLS.
     117* ''listBioportalOntologies(batch)'' returns a list of ontologies from !BioPortal.
     118* When the sought terms are found and term-specific operations (parent/child retrieval, etc.) are needed, the ''getOntologyFromBatch(batch,accession)'' returns the ontology parser for the concrete ontology with all single-ontology methods as described above.
     119
     120
     121
     122
     123
     124
     125   
     126