de.hu.berlin.wbi.objects

Class MutationMention

java.lang.Object

de.hu.berlin.wbi.objects.MutationMention

Direct Known Subclasses:

MutationValidation

public class MutationMention
extends Object

Class to represent a mutation mention found by an NER tool like MutationFinder or SETH

Author:

Philippe Thomas

Nested Class Summary

Nested Classes

Modifier and Type	Class and Description
static class	MutationMention.Tool Enumeration of all named entity recognition components

Field Summary

Fields

Modifier and Type	Field and Description
protected boolean	ambiguous Flag indicating if this SNP is ambiguous.
protected EntityOffset	location Location in the text.
protected String	mutResidue Mutated residue.
protected List<dbSNPNormalized>	normalized List with normalized SNPs
protected boolean	nsm Flag indicating if this SNP is a nucleotide sequence mutation (NSM).
protected int	patternId Which regular expression has been used to extract this SNP from text (MutationFinder only)
protected String	position Location of the mutation wrt residue or nucleotides
protected boolean	psm Flag indicating if this SNP is a protein sequence mutation (PSM).
protected String	ref Used reference sequence (e.g.
protected String	text Text mention in the text.
protected MutationMention.Tool	tool Refers to which tool has been used for extraction (e.g., MutationFinder, SETH, ...)
protected Set<TranscriptNormalized>	transcripts Set of transcripts with which we successfully associated this Element
protected Type	type Type of Mutation (e.g., substitution, insertion, ...)
protected String	wtResidue Wildtype residue.

Constructor Summary

Constructors

Constructor and Description
MutationMention() Empty constructor
MutationMention(EntityOffset location, String mutation)
MutationMention(int start, int end, String text, String ref, String location, String wild, String mutated, Type type, MutationMention.Tool tool)
MutationMention(String mutation) Generates a Mutation object from a String like "A123T".

Method Summary

Modifier and Type	Method and Description
boolean	equals(Object o)
List<dbSNPNormalized>	getBestNormalized() Returns the best dbSNP entries associated with this mutation mention The result is based on the ranking of dbSNPNormalized
int	getEnd() Gets the end-location of the mutation
EntityOffset	getLocation() Gets the location of the mutation
String	getMutResidue() Gets the residues.
List<dbSNPNormalized>	getNormalized() Returns all dbSNP entries associated with this mutation mention
int	getPatternId() Retrieves the pattern ID used for extracting the current Mutation mention
String	getPosition() Gets the position.
String	getRef() Returns reference sequence (e.g.
int	getStart() Gets the start-location of the mutation
String	getText() Returns text-mined text (e.g.
MutationMention.Tool	getTool() Returns MutationMention.Tool used to find mutation (MutationFinder or SETH)
Set<TranscriptNormalized>	getTranscripts() Returns all Transcripts covering this SNP
Type	getType() Returns Mutation Type (e.g.
String	getWtResidue() Gets the residue.
int	hashCode()
boolean	isAmbiguous()
boolean	isNsm()
boolean	isPsm()
void	normalizeSequences(Set<Transcript> candidateTranscripts, List<UniprotFeature> features, boolean append) This method evaluates if some of the Transcript provided in candidateTranscripts equals the text-mined MutationMention.
void	normalizeSNP(int id) Method allows us to "manually" normalize a mutation mention to a dbSNP ID Method is currently not invoked, but might be called for the dbSNPRecognized
void	normalizeSNP(List<dbSNP> candidates, List<UniprotFeature> features, boolean append) This method evaluates if some of the dbSNP provided in candidates actually equals the text-mined MutationMention
static Map<Integer,List<MutationMention>>	readMutations(String file) This method loads Mutations from a file which are in the following format described in data/snps.txt (PMID\tWMutM\tstart\tstop)
void	setAmbiguous(boolean ambiguous)
void	setMutResidue(String mutResidue) Sets the residues.
void	setNsm(boolean nsm)
void	setPatternId(int patternId) Sets pattern ID
void	setPosition(String position) Sets the position.
void	setPsm(boolean psm)
void	setWtResidue(String wtResidue) Sets the residue.
String	toHGVS() Generates a human genome variation nomenclature compliant representation of the mutation mention
String	toNormalized()
String	toString() (non-Javadoc)

Methods inherited from class java.lang.Object

clone, finalize, getClass, notify, notifyAll, wait, wait, wait

Field Detail

type

protected Type type

Type of Mutation (e.g., substitution, insertion, ...)

tool

protected MutationMention.Tool tool

Refers to which tool has been used for extraction (e.g., MutationFinder, SETH, ...)

location

protected EntityOffset location

Location in the text.

text

protected String text

Text mention in the text.

ref

protected String ref

Used reference sequence (e.g. c., g., ...)

wtResidue

protected String wtResidue

Wildtype residue.

mutResidue

protected String mutResidue

Mutated residue.

position

protected String position

Location of the mutation wrt residue or nucleotides

nsm

protected boolean nsm

Flag indicating if this SNP is a nucleotide sequence mutation (NSM).

psm

protected boolean psm

Flag indicating if this SNP is a protein sequence mutation (PSM).

ambiguous

protected boolean ambiguous

Flag indicating if this SNP is ambiguous. I.e., it can be a PSM or NSM

patternId

protected int patternId

Which regular expression has been used to extract this SNP from text (MutationFinder only)

normalized

protected List<dbSNPNormalized> normalized

List with normalized SNPs

transcripts

protected Set<TranscriptNormalized> transcripts

Set of transcripts with which we successfully associated this Element

Constructor Detail

MutationMention

public MutationMention()

Empty constructor

MutationMention

public MutationMention(String mutation)

Generates a Mutation object from a String like "A123T".

Parameters:

mutation - Mutationstring (e.g. A123T)

MutationMention

public MutationMention(EntityOffset location,
                       String mutation)

Parameters:

location - Location in text

mutation - Mutationstring (e.g. A123T)

MutationMention

public MutationMention(int start,
                       int end,
                       String text,
                       String ref,
                       String location,
                       String wild,
                       String mutated,
                       Type type,
                       MutationMention.Tool tool)

Method Detail

normalizeSequences

public void normalizeSequences(Set<Transcript> candidateTranscripts,
                               List<UniprotFeature> features,
                               boolean append)

This method evaluates if some of the Transcript provided in candidateTranscripts equals the text-mined MutationMention. In difference to normalizeSNP(java.util.List, java.util.List, boolean) this method tries to normalize to sequence-ID and not to dbSNP-IDs

Parameters:

candidateTranscripts - List of dbSNP-entries which might actually describe this SNP

features - List of associated uniprot features

append - Sometimes normalization has to be invoked several times (for several genes) Flag indicates if the result is appended or not

normalizeSNP

public void normalizeSNP(int id)

Method allows us to "manually" normalize a mutation mention to a dbSNP ID Method is currently not invoked, but might be called for the dbSNPRecognized

Parameters:

id - dbSNP ID we want to normalize to

normalizeSNP

public void normalizeSNP(List<dbSNP> candidates,
                         List<UniprotFeature> features,
                         boolean append)

This method evaluates if some of the dbSNP provided in candidates actually equals the text-mined MutationMention

Parameters:

candidates - List of dbSNP-entries which might actually describe this SNP

features - List of associated uniprot features

append - Sometimes normalization has to be invoked several times (for several genes) Should we append result or not?

readMutations

public static Map<Integer,List<MutationMention>> readMutations(String file)
                                                        throws IOException

This method loads Mutations from a file which are in the following format described in data/snps.txt (PMID\tWMutM\tstart\tstop)

Parameters:

file - with mutations

Returns:

Mao from pmids to all contained mutations

Throws:

FileNotFoundException

IOException

getLocation

public EntityOffset getLocation()

Gets the location of the mutation

Returns:

the location of the mutation

getStart

public int getStart()

Gets the start-location of the mutation

Returns:

start-location

getEnd

public int getEnd()

Gets the end-location of the mutation

Returns:

end-location

getWtResidue

public String getWtResidue()

Gets the residue.

Returns:

the residue

setWtResidue

public void setWtResidue(String wtResidue)

Sets the residue.

Parameters:

wtResidue - the new residue

getMutResidue

public String getMutResidue()

Gets the residues.

Returns:

the residues

setMutResidue

public void setMutResidue(String mutResidue)

Sets the residues.

Parameters:

mutResidue - the new residues

getPosition

public String getPosition()

Gets the position.

Returns:

the position

setPosition

public void setPosition(String position)

Sets the position.

Parameters:

position - the new position

isNsm

public boolean isNsm()

Returns:

the flag indicating if this SNP is a NSM

setNsm

public void setNsm(boolean nsm)

isPsm

public boolean isPsm()

Returns:

the flag indicating if this SNP is a PSM

setPsm

public void setPsm(boolean psm)

isAmbiguous

public boolean isAmbiguous()

Returns:

the flag indicating if this SNP is ambiguous

setAmbiguous

public void setAmbiguous(boolean ambiguous)

getType

public Type getType()

Returns Mutation Type (e.g. substitution, ...)

Returns:

mutation type

getTool

public MutationMention.Tool getTool()

Returns MutationMention.Tool used to find mutation (MutationFinder or SETH)

Returns:

MutationMention.Tool used to find mutation

getText

public String getText()

Returns text-mined text (e.g. 'substitution of Ala to Pro at 123')

Returns:

text

getRef

public String getRef()

Returns reference sequence (e.g. 'c.' for cDNA)

Returns:

reference sequence

getNormalized

public List<dbSNPNormalized> getNormalized()

Returns all dbSNP entries associated with this mutation mention

Returns:

dbSNP entries

getBestNormalized

public List<dbSNPNormalized> getBestNormalized()

Returns the best dbSNP entries associated with this mutation mention The result is based on the ranking of dbSNPNormalized

Returns:

dbSNP entries

getTranscripts

public Set<TranscriptNormalized> getTranscripts()

Returns all Transcripts covering this SNP

Returns:

Transcripts

getPatternId

public int getPatternId()

Retrieves the pattern ID used for extracting the current Mutation mention

Returns:

pattern Id

setPatternId

public void setPatternId(int patternId)

Sets pattern ID

Parameters:

patternId - pattern ID

equals

public boolean equals(Object o)

Overrides:

equals in class Object

hashCode

public int hashCode()

Overrides:

hashCode in class Object

toHGVS

public String toHGVS()

Generates a human genome variation nomenclature compliant representation of the mutation mention

Returns:

a mutation mention in HGVS

toString

public String toString()

(non-Javadoc)

Overrides:

toString in class Object

See Also:

Object.toString()

toNormalized

public String toNormalized()

Returns:

SNP-description following the nomenclature