Constant Field Values

Contents

• owltools.*

owltools.*

owltools.InferenceBuilder

Modifier and Type	Constant Field	Value
public static final String	REASONER_ELK	"elk"
public static final String	REASONER_HERMIT	"hermit"
public static final String	REASONER_JCEL	"jcel"
public static final String	REASONER_JFACT	"jfact"
public static final String	REASONER_MORE	"more"
public static final String	REASONER_MORE_HERMIT	"more-hermit"
public static final String	REASONER_MORE_JFACT	"more-jfact"

owltools.gaf.*

owltools.gaf.EcoTools

Modifier and Type	Constant Field	Value
public static final String	ECO_PURL	"http://purl.obolibrary.org/obo/eco.owl"

owltools.gaf.GeneAnnotation

Modifier and Type	Constant Field	Value
public static final int	COLOCATES_WITH_MASK	2
public static final int	CONTRIBUTES_TO_MASK	1
public static final int	CUT_MASK	16
public static final int	INTEGRAL_TO_MASK	4
public static final int	NOT_MASK	8

owltools.gaf.TaxonTools

Modifier and Type	Constant Field	Value
public static final String	NCBI	"NCBITaxon:"
public static final String	TAXON_PREFIX	"taxon:"
public static final String	TAXON_PURL	"http://purl.obolibrary.org/obo/ncbitaxon/subsets/taxslim.owl"

owltools.gaf.eco.EcoMapper

Modifier and Type	Constant Field	Value
public static final String	ECO_MAPPING_PURL	"http://purl.obolibrary.org/obo/eco/gaf-eco-mapping.txt"
public static final String	ECO_PURL	"http://purl.obolibrary.org/obo/eco.owl"

owltools.gaf.parser.GAFParser

Modifier and Type	Constant Field	Value
public static final int	ANNOTATION_XP	15
public static final int	ASPECT	8
public static final int	ASSIGNED_BY	14
public static final int	DATE	13
public static final int	DB	0
public static final int	DB_OBJECT_ID	1
public static final int	DB_OBJECT_NAME	9
public static final int	DB_OBJECT_SYMBOL	2
public static final int	DB_OBJECT_SYNONYM	10
public static final int	DB_OBJECT_TYPE	11
public static final int	EVIDENCE	6
public static final int	GENE_PRODUCT_ISOFORM	16
public static final int	GOID	4
public static final int	QUALIFIER	3
public static final int	REFERENCE	5
public static final int	TAXON	12
public static final int	WITH	7

owltools.gaf.rules.GenericReasonerValidationCheck

Modifier and Type	Constant Field	Value
public static final String	PERMANENT_JAVA_ID	"org.geneontology.gold.rules.GenericReasonerValidationCheck"

owltools.gaf.rules.go.BasicChecksRule

Modifier and Type	Constant Field	Value
public static final String	PERMANENT_JAVA_ID	"org.geneontology.gold.rules.BasicChecksRule"

owltools.gaf.rules.go.GoAnnotationExperimentalPredictionRule

Modifier and Type	Constant Field	Value
public static final String	PERMANENT_JAVA_ID	"org.geneontology.gold.rules.GoAnnotationExperimentalPredictionRule"

owltools.gaf.rules.go.GoAnnotationPredictionRule

Modifier and Type	Constant Field	Value
public static final String	PERMANENT_JAVA_ID	"org.geneontology.gold.rules.GoAnnotationPredictionRule"

owltools.gaf.rules.go.GoAnnotationTaxonRule

Modifier and Type	Constant Field	Value
public static final String	PERMANENT_JAVA_ID	"org.geneontology.gold.rules.AnnotationTaxonRule"

owltools.gaf.rules.go.GoBindingCheckWithFieldRule

Modifier and Type	Constant Field	Value
public static final String	PERMANENT_JAVA_ID	"org.geneontology.rules.GO_AR_0000003"

owltools.gaf.rules.go.GoClassReferenceAnnotationRule

Modifier and Type	Constant Field	Value
public static final String	PERMANENT_JAVA_ID	"org.geneontology.gold.rules.GoClassReferenceAnnotationRule"

owltools.gaf.rules.go.GoICAnnotationRule

Modifier and Type	Constant Field	Value
public static final String	PERMANENT_JAVA_ID	"org.geneontology.rules.GO_AR_0000016"

owltools.gaf.rules.go.GoIDAAnnotationRule

Modifier and Type	Constant Field	Value
public static final String	PERMANENT_JAVA_ID	"org.geneontology.rules.GO_AR_0000017"

owltools.gaf.rules.go.GoIEPRestrictionsRule

Modifier and Type	Constant Field	Value
public static final String	PERMANENT_JAVA_ID	"org.geneontology.rules.GO_AR_0000006"

owltools.gaf.rules.go.GoIPIAnnotationRule

Modifier and Type	Constant Field	Value
public static final String	PERMANENT_JAVA_ID	"org.geneontology.rules.GO_AR_0000018"

owltools.gaf.rules.go.GoIPICatalyticActivityRestrictionsRule

Modifier and Type	Constant Field	Value
public static final String	PERMANENT_JAVA_ID	"org.geneontology.rules.GO_AR_0000007"

owltools.gaf.rules.go.GoMultipleTaxonRule

Modifier and Type	Constant Field	Value
public static final String	PERMANENT_JAVA_ID	"org.geneontology.rules.GO_AR_0000015"

owltools.gaf.rules.go.GoNDAnnotationRule

Modifier and Type	Constant Field	Value
public static final String	PERMANENT_JAVA_ID	"org.geneontology.rules.GO_AR_0000011"

owltools.gaf.rules.go.GoNoHighLevelTermAnnotationRule

Modifier and Type	Constant Field	Value
public static final String	PERMANENT_JAVA_ID	"org.geneontology.rules.GO_AR_0000008"

owltools.gaf.rules.go.GoNoISSProteinBindingRule

Modifier and Type	Constant Field	Value
public static final String	PERMANENT_JAVA_ID	"org.geneontology.rules.GO_AR_0000005"

owltools.gaf.rules.go.GOReciprocalAnnotationRule

Modifier and Type	Constant Field	Value
public static final String	PERMANENT_JAVA_ID	"org.geneontology.rules.GO_AR_0000004"

owltools.gfx.*

owltools.gfx.HierarchyImage

Modifier and Type	Constant Field	Value
public static final int	bottomMargin	16
public static final int	keyMargin	50
public static final int	minWidth	250
public static final int	rightMargin	10

owltools.graph.*

owltools.graph.OWLGraphWrapper

Modifier and Type	Constant Field	Value
public static final String	DEFAULT_IRI_PREFIX	"http://purl.obolibrary.org/obo/"

owltools.graph.RelationSets

Modifier and Type	Constant Field	Value
public static final String	COMMON	"regulates/is_a/part_of/occurs_in"
public static final String	ISA_PARTOF	"is_a/part_of"
public static final String	REGULATES	"regulates/is_a/part_of"

owltools.ncbi.*

owltools.ncbi.OWLConverter

Modifier and Type	Constant Field	Value
protected static final String	IAO	"http://purl.obolibrary.org/obo/IAO_"
protected static final String	NCBI	"http://purl.obolibrary.org/obo/NCBITaxon_"
protected static final String	OBO	"http://purl.obolibrary.org/obo/"
protected static final String	OIO	"http://www.geneontology.org/formats/oboInOwl#"

owltools.ontologyrelease.*

owltools.ontologyrelease.ReleaseRunnerFileTools

Modifier and Type	Constant Field	Value
public static final String	STAGING_DIRECTORY_NAME	"staging"

owltools.ontologyverification.*

owltools.ontologyverification.impl.AltIdInSignature

Modifier and Type	Constant Field	Value
public static final String	SHORT_HAND	"altid-in-signature"

owltools.ontologyverification.impl.CycleCheck

Modifier and Type	Constant Field	Value
public static final String	SHORT_HAND	"is_a-cycle"

owltools.ontologyverification.impl.DanglingReferenceCheck

Modifier and Type	Constant Field	Value
public static final String	SHORT_HAND	"dangling-ref"

owltools.ontologyverification.impl.NameRedundancyCheck

Modifier and Type	Constant Field	Value
public static final String	SHORT_HAND	"name-redundancy"

owltools.ontologyverification.impl.ObsoleteClassInSignature

Modifier and Type	Constant Field	Value
public static final String	SHORT_HAND	"obsolete-in-signature"

owltools.ontologyverification.impl.SelfReferenceInDefinition

Modifier and Type	Constant Field	Value
public static final String	SHORT_HAND	"self-reference-in-def"

owltools.sim2.*

owltools.sim2.AbstractOwlSim

Modifier and Type	Constant Field	Value
public final String	icIRIString	"http://owlsim.org/ontology/ic"

owltools.vocab.*

owltools.vocab.OBOUpperVocabulary

Modifier and Type	Constant Field	Value
public static final String	OBO	"http://purl.obolibrary.org/obo/"