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org.phenoscape.kb.ingest.zfin

ZFINExpressionToOWL

Related Doc: package zfin

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object ZFINExpressionToOWL

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  1. final def !=(arg0: Any): Boolean

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  2. final def ##(): Int

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  3. final def ==(arg0: Any): Boolean

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  4. final def asInstanceOf[T0]: T0

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  5. def clone(): AnyRef

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  6. def convert(expressionData: Source): Set[OWLAxiom]

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    expressionData

    tab-delimited input from http://zfin.org/downloads/wildtype-expression_fish.txt Each line (an annotation) is translated into a set of OWL axioms

  7. final def eq(arg0: AnyRef): Boolean

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  8. def equals(arg0: Any): Boolean

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  9. def finalize(): Unit

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  10. final def getClass(): Class[_]

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  11. def hashCode(): Int

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  12. final def isInstanceOf[T0]: Boolean

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  13. final def ne(arg0: AnyRef): Boolean

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  14. final def notify(): Unit

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  15. final def notifyAll(): Unit

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  16. final def synchronized[T0](arg0: ⇒ T0): T0

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  17. def toString(): String

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  18. def translate(expressionLine: String): Set[OWLAxiom]

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    expressionLine

    Example line: ZDB-GENE-000125-4 dlc AB/TU ZFA:0000107 eye \ \ Pharyngula:Prim-15 Pharyngula:Prim-25 mRNA in situ hybridization ZDB-PUB-051025-1 ZDB-EST-051107-52 ZDB-FISH-150901-29084 Should generate OWL: Prefix: GO: <http://purl.obolibrary.org/obo/GO_> Prefix: NCBITaxon: <http://purl.obolibrary.org/obo/NCBITaxon_> Prefix: ZFA: <http://purl.obolibrary.org/obo/ZFA_> Prefix: BFO: <http://purl.obolibrary.org/obo/BFO_> Prefix: dc: <http://purl.org/dc/terms/> Prefix: ps: <http://purl.org/phenoscape/vocab.owl#> Prefix: zfin: <http://zfin.org/> Prefix: uuid: <http://purl.org/phenoscape/uuid/> Individual: zfin:ZDB-GENE-000125-4 # dlc Individual: uuid:3e1ad895-56b2-4b54-a3f8-c99e7b42f646 Types: GO:0010467 # gene expression Facts: ps:associated_with_taxon NCBITaxon:7955, # Danio rerio dc:source zfin:ZDB-PUB-051025-1, BFO:0000066 ZFA:0000107, # occurs_in eye (punned) ps:associated_with_gene zfin:ZDB-GENE-000125-4 # dlc

  19. final def wait(): Unit

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  20. final def wait(arg0: Long, arg1: Int): Unit

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  21. final def wait(arg0: Long): Unit

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