StaticProteinKBLookup

Instance Constructors

new StaticProteinKBLookup()

Value Members

final def !=(arg0: Any): Boolean

Definition Classes
AnyRef → Any
final def ##(): Int

Definition Classes
AnyRef → Any
final def ==(arg0: Any): Boolean

Definition Classes
AnyRef → Any
val AllKeysStopSuffixes: Set[String]

The set of words to remove from all keys to create a lookup key.
The set of words to remove from all keys to create a lookup key.

Definition Classes
KnowledgeBaseConstants
val AuxBioProcessFilename: String

Filename of the auxiliary biological processes file.
Filename of the auxiliary biological processes file.

Definition Classes
KnowledgeBaseConstants
val AuxCellLocationFilename: String

Filename of the auxiliary cellular location file.
Filename of the auxiliary cellular location file.

Definition Classes
KnowledgeBaseConstants
val AuxChemicalFilename: String

Filename of the auxiliary small molecule (chemical) file.
Filename of the auxiliary small molecule (chemical) file.

Definition Classes
KnowledgeBaseConstants
val AuxMetaboliteFilename: String

Filename of the auxiliary small molecule (metabolite) file.
Filename of the auxiliary small molecule (metabolite) file.

Definition Classes
KnowledgeBaseConstants
val AuxProteinFamilyFilename: String

Filename of the auxiliary protein family file.
Filename of the auxiliary protein family file.

Definition Classes
KnowledgeBaseConstants
val AuxProteinFilename: String

Filename of the auxiliary protein file.
Filename of the auxiliary protein file.

Definition Classes
KnowledgeBaseConstants
val AuxTissueTypeFilename: String

Filename of the auxiliary protein file.
Filename of the auxiliary protein file.

Definition Classes
KnowledgeBaseConstants
val FamilyStopSuffixes: Set[String]

The set of words to remove from a key to create a protein family lookup key.
The set of words to remove from a key to create a protein family lookup key.

Definition Classes
KnowledgeBaseConstants
val GendCellLocationFilename: String

Filename of the cellular location file generated by the entity checker.
Filename of the cellular location file generated by the entity checker.

Definition Classes
KnowledgeBaseConstants
val GendCellLocationPrefix: String

Prefix string for cellular location IDs generated by the entity checker.
Prefix string for cellular location IDs generated by the entity checker.

Definition Classes
KnowledgeBaseConstants
val GendChemicalFilename: String

Filename of the small molecule file generated by the entity checker.
Filename of the small molecule file generated by the entity checker.

Definition Classes
KnowledgeBaseConstants
val GendChemicalPrefix: String

Prefix string for small molecule IDs generated by the entity checker.
Prefix string for small molecule IDs generated by the entity checker.

Definition Classes
KnowledgeBaseConstants
val GendProteinFilename: String

Filename of the protein/family file generated by the entity checker.
Filename of the protein/family file generated by the entity checker.

Definition Classes
KnowledgeBaseConstants
val GendProteinPrefix: String

Prefix string for protein/family IDs generated by the entity checker.
Prefix string for protein/family IDs generated by the entity checker.

Definition Classes
KnowledgeBaseConstants
val HumanLabels: Set[String]

The set of words to remove from the text to create a lookup key.
The set of words to remove from the text to create a lookup key.

Definition Classes
KnowledgeBaseConstants
val KBDirFilePath: String

File Path to the directory which holds the entity knowledge bases.
File Path to the directory which holds the entity knowledge bases.

Definition Classes
KnowledgeBaseConstants
val KBDirResourcePath: String

Resource Path to the directory which holds the entity knowledge bases.
Resource Path to the directory which holds the entity knowledge bases.

Definition Classes
KnowledgeBaseConstants
val KeyCharactersToRemove: Set[Char]

The set of characters to remove from the text to create a lookup key.
The set of characters to remove from the text to create a lookup key.

Definition Classes
KnowledgeBaseConstants
val ManualCellLocationFilename: String

Filename of the manually maintained cellular location file.
Filename of the manually maintained cellular location file.

Definition Classes
KnowledgeBaseConstants
val ManualChemicalFilename: String

Filename of the manually maintained small molecule file.
Filename of the manually maintained small molecule file.

Definition Classes
KnowledgeBaseConstants
val ManualProteinFamilyFilename: String

Filename of the manually maintained protein family file.
Filename of the manually maintained protein family file.

Definition Classes
KnowledgeBaseConstants
val ManualProteinFilename: String

Filename of the manually maintained protein file.
Filename of the manually maintained protein file.

Definition Classes
KnowledgeBaseConstants
val ProteinStopSuffixes: Set[String]

The set of words to remove from a key to create a protein lookup key.
The set of words to remove from a key to create a protein lookup key.

Definition Classes
KnowledgeBaseConstants
val StaticCellLocationFilename: String

Filename of the static cellular location file.
Filename of the static cellular location file.

Definition Classes
KnowledgeBaseConstants
val StaticChemicalFilename: String

Filename of the static small molecule (chemical) file.
Filename of the static small molecule (chemical) file.

Definition Classes
KnowledgeBaseConstants
val StaticMetaboliteFilename: String

Filename of the static small molecule (chemical) file.
Filename of the static small molecule (chemical) file.

Definition Classes
KnowledgeBaseConstants
val StaticProteinFamilyFilename: String

Filename of the static protein family file.
Filename of the static protein family file.

Definition Classes
KnowledgeBaseConstants
val StaticProteinFilename: String

Filename of the static protein file.
Filename of the static protein file.

Definition Classes
KnowledgeBaseConstants
val StaticTissueTypeFilename: String

Filename of the static tissue type file.
Filename of the static tissue type file.

Definition Classes
KnowledgeBaseConstants
final def asInstanceOf[T0]: T0

Definition Classes
Any
def baseURI: String

The primary URI of the external KB (e.g., http://identifiers.org/uniprot/).
The primary URI of the external KB (e.g., http://identifiers.org/uniprot/).

Definition Classes
StaticProteinKBLookup → LocalKBLookup → ExternalKBAccessor
def clone(): AnyRef

Attributes
protected[java.lang]
Definition Classes
AnyRef
Annotations
@throws( ... )
final def eq(arg0: AnyRef): Boolean

Definition Classes
AnyRef
def equals(arg0: Any): Boolean

Definition Classes
AnyRef → Any
def finalize(): Unit

Attributes
protected[java.lang]
Definition Classes
AnyRef
Annotations
@throws( classOf[java.lang.Throwable] )
final def getClass(): Class[_]

Definition Classes
AnyRef → Any
def getLookupKey(key: String): String

Definition Classes
LocalKBLookup
def getLookupKey(mention: Mention): String

Extract and return a key string, from the given Mention, which can be used to access an external knowledge base or a local object cache.
Extract and return a key string, from the given Mention, which can be used to access an external knowledge base or a local object cache.

Definition Classes
ExternalKBAccessor
def hashCode(): Int

Definition Classes
AnyRef → Any
final def isInstanceOf[T0]: Boolean

Definition Classes
Any
def namespace: String

The namespace of the external KB (e.g., uniprot).
The namespace of the external KB (e.g., uniprot).

Definition Classes
StaticProteinKBLookup → LocalKBLookup → ExternalKBAccessor
final def ne(arg0: AnyRef): Boolean

Definition Classes
AnyRef
final def notify(): Unit

Definition Classes
AnyRef
final def notifyAll(): Unit

Definition Classes
AnyRef
def readAndFillKB(kbResourcePath: String): Unit

Attributes
protected
Definition Classes
LocalKBLookup
def referenceURI(mention: Mention): String

Using the given Mention, generate a URI which references an entry in the namespace of external knowledge base.
Using the given Mention, generate a URI which references an entry in the namespace of external knowledge base.

Definition Classes
ExternalKBAccessor
def referenceURI(id: String): String

Using the given ID string, generate a URI which references an entry in the namespace of external knowledge base (e.g., given "P2345" => "http://identifiers.org/uniprot/P2345").
Using the given ID string, generate a URI which references an entry in the namespace of external knowledge base (e.g., given "P2345" => "http://identifiers.org/uniprot/P2345").

Definition Classes
ExternalKBAccessor
def resolve(key: String): Option[String]

Resolve the given string to a optional string value in an external knowledge base.
Resolve the given string to a optional string value in an external knowledge base. Default method to be overridden by each child knowledge base accessor.

Definition Classes
LocalKBLookup → SpeciatedKBLookup
def resolve(mention: Mention): Map[String, String]

Resolve the given Mention to an entry in an external knowledge base and return a map of keys and property values from that entry.
Resolve the given Mention to an entry in an external knowledge base and return a map of keys and property values from that entry. Default method to be overridden by each child knowledge base accessor.

Definition Classes
ExternalKBAccessor
def resolveBySpecies(key: String, species: Set[String]): Option[String]

Resolve the given string to a optional string value in an external knowledge base, for any of the species name strings in the given set.
Resolve the given string to a optional string value in an external knowledge base, for any of the species name strings in the given set. NB: Default method ignores species argument and resolves to any species.

Definition Classes
LocalKBLookup → SpeciatedKBLookup
def resolveHuman(key: String): Option[String]

Resolve the given string to a optional string value in an external knowledge base, failing if the KB entry is not for humans, NB: Default method ignores species argument and resolves to any species.
Resolve the given string to a optional string value in an external knowledge base, failing if the KB entry is not for humans, NB: Default method ignores species argument and resolves to any species.

Definition Classes
SpeciatedKBLookup
def resourceID: String

The Resource Identifier for the primary resource location for this knowledge base (e.g., MIR:00100164).
The Resource Identifier for the primary resource location for this knowledge base (e.g., MIR:00100164). NB: This is MIRIAM registration ID of the external knowledge base, NOT an entity ID.

Definition Classes
StaticProteinKBLookup → LocalKBLookup → ExternalKBAccessor
final def synchronized[T0](arg0: ⇒ T0): T0

Definition Classes
AnyRef
val theKB: Map[String, Map[String, String]]

Attributes
protected
Definition Classes
LocalKBLookup
def toString(): String

Definition Classes
AnyRef → Any
def validateFields(fields: Seq[String]): Boolean

Attributes
protected
Definition Classes
LocalKBLookup
final def wait(): Unit

Definition Classes
AnyRef
Annotations
@throws( ... )
final def wait(arg0: Long, arg1: Int): Unit

Definition Classes
AnyRef
Annotations
@throws( ... )
final def wait(arg0: Long): Unit

Definition Classes
AnyRef
Annotations
@throws( ... )

Related Doc: package grounding

class StaticProteinKBLookup extends LocalKBLookup

Instance Constructors

new StaticProteinKBLookup()

Value Members

final def !=(arg0: Any): Boolean

final def ##(): Int

final def ==(arg0: Any): Boolean

val AllKeysStopSuffixes: Set[String]

val AuxBioProcessFilename: String

val AuxCellLocationFilename: String

val AuxChemicalFilename: String

val AuxMetaboliteFilename: String

val AuxProteinFamilyFilename: String

val AuxProteinFilename: String

val AuxTissueTypeFilename: String

val FamilyStopSuffixes: Set[String]

val GendCellLocationFilename: String

val GendCellLocationPrefix: String

val GendChemicalFilename: String

val GendChemicalPrefix: String

val GendProteinFilename: String

val GendProteinPrefix: String

val HumanLabels: Set[String]

val KBDirFilePath: String

val KBDirResourcePath: String

val KeyCharactersToRemove: Set[Char]

val ManualCellLocationFilename: String

val ManualChemicalFilename: String

val ManualProteinFamilyFilename: String

val ManualProteinFilename: String

val ProteinStopSuffixes: Set[String]

val StaticCellLocationFilename: String

val StaticChemicalFilename: String

val StaticMetaboliteFilename: String

val StaticProteinFamilyFilename: String

val StaticProteinFilename: String

val StaticTissueTypeFilename: String

final def asInstanceOf[T0]: T0

def baseURI: String

def clone(): AnyRef

final def eq(arg0: AnyRef): Boolean

def equals(arg0: Any): Boolean

def finalize(): Unit

final def getClass(): Class[_]

def getLookupKey(key: String): String

def getLookupKey(mention: Mention): String

def hashCode(): Int

final def isInstanceOf[T0]: Boolean

def namespace: String

final def ne(arg0: AnyRef): Boolean

final def notify(): Unit

final def notifyAll(): Unit

def readAndFillKB(kbResourcePath: String): Unit

def referenceURI(mention: Mention): String

def referenceURI(id: String): String

def resolve(key: String): Option[String]

def resolve(mention: Mention): Map[String, String]

def resolveBySpecies(key: String, species: Set[String]): Option[String]

def resolveHuman(key: String): Option[String]

def resourceID: String

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

val theKB: Map[String, Map[String, String]]

def toString(): String

def validateFields(fields: Seq[String]): Boolean

final def wait(): Unit

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

final def wait(arg0: Long): Unit

Inherited from LocalKBLookup

Inherited from KnowledgeBaseConstants

Inherited from SpeciatedKBLookup

Inherited from ExternalKBAccessor

Inherited from AnyRef

Inherited from Any

Ungrouped