A B C D E F G H I L M N O P Q R S T U V W

A

aaPosition - Variable in class de.hu.berlin.wbi.objects.dbSNP

location of the mutation in terms of amino acids

addFN() - Method in class seth.seth.eval.Performance

addFN(int) - Method in class seth.seth.eval.Performance

addFP() - Method in class seth.seth.eval.Performance

addFP(int) - Method in class seth.seth.eval.Performance

addHgvs(String) - Method in class de.hu.berlin.wbi.stuff.xml.SNP

addMutation(String) - Method in class de.hu.berlin.wbi.stuff.xml.PSM

addMutations(Set<String>) - Method in class de.hu.berlin.wbi.stuff.xml.PSM

addPSM(PSM) - Method in class de.hu.berlin.wbi.stuff.xml.SNP

addTN() - Method in class seth.seth.eval.Performance

addTN(int) - Method in class seth.seth.eval.Performance

addTP() - Method in class seth.seth.eval.Performance

addTP(int) - Method in class seth.seth.eval.Performance

ambiguous - Variable in class de.hu.berlin.wbi.objects.MutationMention

Flag indicating if this SNP is ambiguous.

ambiguous - Static variable in class edu.uchsc.ccp.nlp.ei.mutation.MutationFinder

AminoAcidHelper - Class in de.hu.berlin.wbi.objects

Helper class to transform a one letter amino-acid into a three letter representation

AminoAcidHelper() - Constructor for class de.hu.berlin.wbi.objects.AminoAcidHelper

ApplyNER - Class in seth.seth.eval

Created with IntelliJ IDEA.

ApplyNER() - Constructor for class seth.seth.eval.ApplyNER

ApplyNerToVerspoor - Class in seth.seth.eval

Created with IntelliJ IDEA.

ApplyNerToVerspoor() - Constructor for class seth.seth.eval.ApplyNerToVerspoor

ApplyNERToWei - Class in seth.seth.eval

Created with IntelliJ IDEA.

ApplyNERToWei() - Constructor for class seth.seth.eval.ApplyNERToWei

B

begin - Variable in class cnveth.RegionMention

start position in text

C

calculate() - Method in class seth.seth.eval.Performance

Calculates precision recall and so on

CDC_sequence - Variable in class de.hu.berlin.wbi.objects.Transcript

Coding Sequence

characters(char[], int, int) - Method in class de.hu.berlin.wbi.stuff.xml.ParseXMLToFile

CheckOsiris - Class in de.hu.berlin.wbi.process.osiris

CheckOsiris() - Constructor for class de.hu.berlin.wbi.process.osiris.CheckOsiris

closeQuery() - Method in class de.hu.berlin.wbi.objects.DatabaseConnection

Close resultset

cnveth - package cnveth

Package for copy number variation detection of genes (e.g., Aplification of BRCA1) Currently, this package is not used by SETH

CNVETH - Class in cnveth

this class allows to detect possible mentions of copy number variations

CNVETH() - Constructor for class cnveth.CNVETH

CNVRecognizer - Class in cnveth

CNVRecognizer() - Constructor for class cnveth.CNVRecognizer

compareTo(dbSNPNormalized) - Method in class de.hu.berlin.wbi.objects.dbSNPNormalized

compareTo(TranscriptNormalized) - Method in class de.hu.berlin.wbi.objects.TranscriptNormalized

conn - Variable in class de.hu.berlin.wbi.objects.DatabaseConnection

connect() - Method in class de.hu.berlin.wbi.objects.DatabaseConnection

Connects with database

createPointMutationFrom_wNm(String) - Static method in class edu.uchsc.ccp.nlp.ei.mutation.PointMutation

Create PointMutation from wNm-format, single-letter abbreviated mention.

D

DatabaseConnection - Class in de.hu.berlin.wbi.objects

Convenience class for database communication

DatabaseConnection(String, String, String, String, String) - Constructor for class de.hu.berlin.wbi.objects.DatabaseConnection

Set up a database connection by providing all reelevant connection information

DatabaseConnection(Properties) - Constructor for class de.hu.berlin.wbi.objects.DatabaseConnection

Set up a database connection, by using a java-property object

dbSNP - Class in de.hu.berlin.wbi.objects

Represents a dbSNP entry; loaded from a local database.

dbSNP() - Constructor for class de.hu.berlin.wbi.objects.dbSNP

Simple constructor

dbSNP(int, int, Set<String>, int, String) - Constructor for class de.hu.berlin.wbi.objects.dbSNP

Constructor

dbSNPNormalized - Class in de.hu.berlin.wbi.objects

Represents a MutationMention mention which has been successfully normalized to a dbSNP .

dbSNPNormalized(dbSNP, EnumSet<MatchOptions>, UniprotFeature) - Constructor for class de.hu.berlin.wbi.objects.dbSNPNormalized

dbSNPRecognizer - Class in seth

Detect dnSNP mentions in text (e.g., rs2345)

dbSNPRecognizer() - Constructor for class seth.dbSNPRecognizer

de.hu.berlin.wbi.objects - package de.hu.berlin.wbi.objects

Package with the main data objects.

de.hu.berlin.wbi.process - package de.hu.berlin.wbi.process

Various common work-flows based on SNP normalization.

de.hu.berlin.wbi.process.osiris - package de.hu.berlin.wbi.process.osiris

Package to evaluate performance of SETH on the osiris dataset

de.hu.berlin.wbi.stuff.xml - package de.hu.berlin.wbi.stuff.xml

This package is relevant to rebuild the MySQL-Database for SNP normalization purposes

disconnect() - Method in class de.hu.berlin.wbi.objects.DatabaseConnection

Disconnects from database

E

edu.uchsc.ccp.nlp.ei.mutation - package edu.uchsc.ccp.nlp.ei.mutation

Contains the modified MutationFinder code Adaptations include the recognition of ambiguous mutations, non-synonymous mutations, and DNA mutations For the original code we refer to http://mutationfinder.sourceforge.net/

end - Variable in class cnveth.RegionMention

end position in text

endElement(String, String, String) - Method in class de.hu.berlin.wbi.stuff.xml.ParseXMLToFile

ensg - Variable in class de.hu.berlin.wbi.objects.Transcript

Ensemble gene ID.

ensp - Variable in class de.hu.berlin.wbi.objects.Transcript

Ensemble protein ID.

enst - Variable in class de.hu.berlin.wbi.objects.Transcript

Ensemble transcript ID.

Entity - Class in seth.seth.eval

Created with IntelliJ IDEA.

Entity(String, String, int, int, String, String) - Constructor for class seth.seth.eval.Entity

EntityOffset - Class in de.hu.berlin.wbi.objects

Represents the text span of entity mentions (MutationMention, Gene, etc.).

EntityOffset(int, int) - Constructor for class de.hu.berlin.wbi.objects.EntityOffset

Constructor with start and end offset based on text

entrez - Variable in class de.hu.berlin.wbi.objects.Transcript

Gene-ID (Entrez in our case).

equals(Object) - Method in class de.hu.berlin.wbi.objects.dbSNP

(non-Javadoc)

equals(Object) - Method in class de.hu.berlin.wbi.objects.EntityOffset

(non-Javadoc)

equals(Object) - Method in class de.hu.berlin.wbi.objects.Gene

(non-Javadoc)

equals(Object) - Method in class de.hu.berlin.wbi.objects.HGVS

(non-Javadoc)

equals(Object) - Method in class de.hu.berlin.wbi.objects.MutationMention

equals(Object) - Method in class de.hu.berlin.wbi.objects.Transcript

equals(Object) - Method in class edu.uchsc.ccp.nlp.ei.mutation.Mutation

To be overridden by subclasses

equals(Object) - Method in class edu.uchsc.ccp.nlp.ei.mutation.PointMutation

Two PointMutation objects are equal if their Position, WtResidue, and MutResidue values are all equal.

equals(Object) - Method in class seth.seth.eval.Entity

error(String) - Method in class edu.uchsc.ccp.nlp.ei.mutation.Mutation

error(String) - Method in class edu.uchsc.ccp.nlp.ei.mutation.MutationExtractor

Evaluate - Class in de.hu.berlin.wbi.process

Class is used to evaluate snp-normalizer; Corpus is not provided due to licence restrictions but a link is provided in the paper..

Evaluate() - Constructor for class de.hu.berlin.wbi.process.Evaluate

EvaluateNER - Class in seth.seth.eval

Created with IntelliJ IDEA.

EvaluateNER() - Constructor for class seth.seth.eval.EvaluateNER

EvaluateNoGeneNER - Class in de.hu.berlin.wbi.process

Class is used to evaluate snp-normalizer; Corpus is not provided due to licence restrictions but a link is provided in the paper..

EvaluateNoGeneNER() - Constructor for class de.hu.berlin.wbi.process.EvaluateNoGeneNER

EvaluateOsiris - Class in de.hu.berlin.wbi.process.osiris

EvaluateOsiris() - Constructor for class de.hu.berlin.wbi.process.osiris.EvaluateOsiris

EvaluateVerspoor - Class in seth.seth.eval

Created with IntelliJ IDEA.

EvaluateVerspoor() - Constructor for class seth.seth.eval.EvaluateVerspoor

EvaluateWei - Class in seth.seth.eval

Created with IntelliJ IDEA.

EvaluateWei() - Constructor for class seth.seth.eval.EvaluateWei

extractMappingsFromPythonRegex(String) - Static method in class edu.uchsc.ccp.nlp.ei.mutation.MutationFinder

extractMutations(String) - Method in class cnveth.CNVRecognizer

extractMutations(String) - Method in class edu.uchsc.ccp.nlp.ei.mutation.MutationExtractor

Extract point mutations mentions from raw_text and return them in a map.

extractMutations(String) - Method in class edu.uchsc.ccp.nlp.ei.mutation.MutationFinder

Extract point mutations mentions from raw_text and return them in a map.

extractMutations(String) - Method in class seth.dbSNPRecognizer

FInd dbSNP mentions in a text

extractMutations(String) - Method in class seth.ner.wrapper.SETHNER

Extracts mentions of mutations written in the HGVS nomenclature from natural language text

extractMutations(String) - Method in class seth.OldNomenclature

Extracts mentions of mutations from natural language text written in deprecated nomenclature

extractRegion(String) - Method in class cnveth.RegionRecognizer

F

findMutations(String) - Method in class cnveth.CNVETH

Extract mentions of CNV keywords and assigns Type CNV

findMutations(String) - Method in class seth.SETH

Searches for mutation mentions in applied text and returns them

fn - Variable in class seth.seth.eval.Performance

fp - Variable in class seth.seth.eval.Performance

G

Gene - Class in de.hu.berlin.wbi.objects

Represents a gene mention found by any Named Enttiy Recognition and Normalization tool.

Gene() - Constructor for class de.hu.berlin.wbi.objects.Gene

Empty constructor

Gene(int, int, int) - Constructor for class de.hu.berlin.wbi.objects.Gene

geneID - Variable in class de.hu.berlin.wbi.objects.dbSNP

gene associated with this dbSNP entry.

genes - Variable in class cnveth.RegionMention

possible genes from this region with entrez ID

getAaLoc() - Method in class de.hu.berlin.wbi.stuff.xml.PSM

getAaPosition() - Method in class de.hu.berlin.wbi.objects.dbSNP

getAll() - Method in class seth.seth.eval.Performance

getBegin() - Method in class cnveth.RegionMention

getBestNormalized() - Method in class de.hu.berlin.wbi.objects.MutationMention

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

getCDC_sequence() - Method in class de.hu.berlin.wbi.objects.Transcript

getConfidence() - Method in class de.hu.berlin.wbi.objects.dbSNPNormalized

getConfidence() - Method in class de.hu.berlin.wbi.objects.Gene

Gets the confidence for this gene.

getConfidence() - Method in class de.hu.berlin.wbi.objects.TranscriptNormalized

getConn() - Method in class de.hu.berlin.wbi.objects.DatabaseConnection

getDbSNP() - Method in class de.hu.berlin.wbi.objects.MutationValidation

Gets the associated dbSNP entry.

getEnd() - Method in class cnveth.RegionMention

getEnd() - Method in class de.hu.berlin.wbi.objects.MutationMention

Gets the end-location of the mutation

getEnd() - Method in class seth.seth.eval.Entity

getEndLoc() - Method in class de.hu.berlin.wbi.objects.UniprotFeature

Returns end location of the modification on the peptide

getEnsg() - Method in class de.hu.berlin.wbi.objects.Transcript

getEnsp() - Method in class de.hu.berlin.wbi.objects.Transcript

getEnst() - Method in class de.hu.berlin.wbi.objects.Transcript

getEntity() - Method in class de.hu.berlin.wbi.objects.Gene

Gets the string in the text.

getEntity() - Method in class de.hu.berlin.wbi.objects.MutationValidation

Gets the actual entity mention

getEntity() - Method in class seth.seth.eval.Entity

getEntrez() - Method in class de.hu.berlin.wbi.objects.Transcript

getEntrez() - Method in class de.hu.berlin.wbi.stuff.xml.PSM

getF1() - Method in class seth.seth.eval.Performance

getFeature() - Method in class de.hu.berlin.wbi.objects.dbSNPNormalized

getFeature() - Method in class de.hu.berlin.wbi.objects.TranscriptNormalized

getFeatures(int) - Static method in class de.hu.berlin.wbi.objects.UniprotFeature

Returns all UniProt features for one specific Entrez-Gene Identifier

getFN() - Method in class seth.seth.eval.Performance

getFP() - Method in class seth.seth.eval.Performance

getGeneID() - Method in class de.hu.berlin.wbi.objects.dbSNP

Get the associated entrez gene identifier

getGeneID() - Method in class de.hu.berlin.wbi.objects.Gene

Gets the gene-ID (Entrez in our case).

getGeneId() - Method in class de.hu.berlin.wbi.objects.UniprotFeature

Returns associated Enzrez Gene ID

getGenes() - Method in class cnveth.RegionMention

getHgvs() - Method in class de.hu.berlin.wbi.objects.dbSNP

getHgvs() - Method in class de.hu.berlin.wbi.stuff.xml.SNP

getId() - Method in class edu.uchsc.ccp.nlp.ei.mutation.Mutation

Retrieves the pattern id

getId() - Method in class edu.uchsc.ccp.nlp.ei.mutation.MyPattern

getId() - Method in class seth.seth.eval.Entity

getLocation() - Method in class de.hu.berlin.wbi.objects.Gene

Gets the found at which position.

getLocation() - Method in class de.hu.berlin.wbi.objects.HGVS

Gets the location.

getLocation() - Method in class de.hu.berlin.wbi.objects.MutationMention

Gets the location of the mutation

getMatchType() - Method in class de.hu.berlin.wbi.objects.dbSNPNormalized

getMatchType() - Method in class de.hu.berlin.wbi.objects.TranscriptNormalized

getModificationType() - Method in class de.hu.berlin.wbi.objects.UniprotFeature

Returns modification type (e.g.

getMutation() - Method in class de.hu.berlin.wbi.objects.HGVS

Gets the mutation.

getMutations() - Method in class de.hu.berlin.wbi.stuff.xml.PSM

getMutationType() - Method in class de.hu.berlin.wbi.objects.MutationValidation

Gets the either NSM or PSM.

getMutResidue() - Method in class de.hu.berlin.wbi.objects.MutationMention

Gets the residues.

getMutResidue() - Method in class edu.uchsc.ccp.nlp.ei.mutation.PointMutation

Return the mutant residue for this point mutation.

getNormalized() - Method in class de.hu.berlin.wbi.objects.MutationMention

Returns all dbSNP entries associated with this mutation mention

getPattern() - Method in class edu.uchsc.ccp.nlp.ei.mutation.MyPattern

getPatternId() - Method in class de.hu.berlin.wbi.objects.MutationMention

Retrieves the pattern ID used for extracting the current Mutation mention

getPmid() - Method in class de.hu.berlin.wbi.objects.Gene

Gets the article ID.

getPosition() - Method in class de.hu.berlin.wbi.objects.MutationMention

Gets the position.

getPosition() - Method in class edu.uchsc.ccp.nlp.ei.mutation.Mutation

Retrieves the mutation sequence position

getPrecision() - Method in class seth.seth.eval.Performance

getProtein_sequence() - Method in class de.hu.berlin.wbi.objects.Transcript

getPsms() - Method in class de.hu.berlin.wbi.stuff.xml.SNP

getRecall() - Method in class seth.seth.eval.Performance

getRef() - Method in class de.hu.berlin.wbi.objects.MutationMention

Returns reference sequence (e.g.

getRegex() - Method in class edu.uchsc.ccp.nlp.ei.mutation.MyPattern

getRegion() - Method in class cnveth.RegionMention

getResidues() - Method in class de.hu.berlin.wbi.objects.dbSNP

getRs() - Method in class de.hu.berlin.wbi.objects.DatabaseConnection

getRsID() - Method in class de.hu.berlin.wbi.objects.dbSNP

Get dbSNP identifier (rs-id)

getRsId() - Method in class de.hu.berlin.wbi.stuff.xml.SNP

getSNP(int) - Static method in class de.hu.berlin.wbi.objects.dbSNP

Retrieves a list of dbSNP entries associated with a specific entrez-gene ID

getSpecies() - Method in class de.hu.berlin.wbi.objects.Gene

Gets the species.

getStart() - Method in class de.hu.berlin.wbi.objects.EntityOffset

Get start character

getStart() - Method in class de.hu.berlin.wbi.objects.MutationMention

Gets the start-location of the mutation

getStart() - Method in class seth.seth.eval.Entity

getStartLoc() - Method in class de.hu.berlin.wbi.objects.UniprotFeature

Returns start location of the modification on the peptide

getStop() - Method in class de.hu.berlin.wbi.objects.EntityOffset

Get end character position

getText() - Method in class de.hu.berlin.wbi.objects.MutationMention

Returns text-mined text (e.g.

getThreeLetter(String) - Static method in class de.hu.berlin.wbi.objects.AminoAcidHelper

Takes as input a string of length one and returns the three letter code for it

getTN() - Method in class seth.seth.eval.Performance

getTool() - Method in class de.hu.berlin.wbi.objects.MutationMention

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

getTool() - Method in class seth.seth.eval.Entity

getTP() - Method in class seth.seth.eval.Performance

getTranscripts() - Method in class de.hu.berlin.wbi.objects.MutationMention

Returns all Transcripts covering this SNP

getTranscripts(int) - Static method in class de.hu.berlin.wbi.objects.Transcript

getType() - Method in class de.hu.berlin.wbi.objects.HGVS

Gets the mutation type (e.g.

getType() - Method in class de.hu.berlin.wbi.objects.MutationMention

Returns Mutation Type (e.g.

getType() - Method in class seth.seth.eval.Entity

getUniprot() - Method in class de.hu.berlin.wbi.objects.Transcript

getWildtype() - Method in class de.hu.berlin.wbi.objects.dbSNP

getWildtype() - Method in class de.hu.berlin.wbi.objects.HGVS

Gets the wild-type.

getWildtype() - Method in class de.hu.berlin.wbi.stuff.xml.PSM

getWtResidue() - Method in class de.hu.berlin.wbi.objects.MutationMention

Gets the residue.

getWtResidue() - Method in class edu.uchsc.ccp.nlp.ei.mutation.PointMutation

Return the wild-type residue for this point mutation.

H

hashCode() - Method in class de.hu.berlin.wbi.objects.dbSNP

(non-Javadoc)

hashCode() - Method in class de.hu.berlin.wbi.objects.EntityOffset

(non-Javadoc)

hashCode() - Method in class de.hu.berlin.wbi.objects.Gene

(non-Javadoc)

hashCode() - Method in class de.hu.berlin.wbi.objects.HGVS

(non-Javadoc)

hashCode() - Method in class de.hu.berlin.wbi.objects.MutationMention

hashCode() - Method in class de.hu.berlin.wbi.objects.Transcript

hashCode() - Method in class edu.uchsc.ccp.nlp.ei.mutation.Mutation

To be overridden by subclasses

hashCode() - Method in class edu.uchsc.ccp.nlp.ei.mutation.PointMutation

hashCode() - Method in class seth.seth.eval.Entity

hgvs - Variable in class de.hu.berlin.wbi.objects.dbSNP

Different Strings describing the variations in nomenclature

HGVS - Class in de.hu.berlin.wbi.objects

Represents a HGVS reference, like NR_027062.1:c.157+25766C>T.

HGVS(String) - Constructor for class de.hu.berlin.wbi.objects.HGVS

Construct a HGVS object based on a HGVS string (e.g.

I

init(DatabaseConnection, String, String) - Static method in class de.hu.berlin.wbi.objects.dbSNP

Initializes prepared statements for retrieving SNP information

init(DatabaseConnection, String, String) - Static method in class de.hu.berlin.wbi.objects.Gene

Initializes the prepared statements for retrieving gene information for one PubMed article

init(DatabaseConnection, String) - Static method in class de.hu.berlin.wbi.objects.Transcript

Initializes the prepared statements for retrieving sequence information for one Gene

init(DatabaseConnection, String) - Static method in class de.hu.berlin.wbi.objects.UniprotFeature

Initializes prepared statements to retrieve UniProt features, like signaling peptide information

isAlleleOrder() - Method in class de.hu.berlin.wbi.objects.dbSNPNormalized

Returns true if Alleles are in the same order in dbSNP as in the text mention

isAmbiguous() - Method in class de.hu.berlin.wbi.objects.MutationMention

isExactMatch() - Method in class de.hu.berlin.wbi.objects.TranscriptNormalized

isExactPosition() - Method in class de.hu.berlin.wbi.objects.dbSNPNormalized

isFeatureMatch() - Method in class de.hu.berlin.wbi.objects.dbSNPNormalized

isFeatureMatch() - Method in class de.hu.berlin.wbi.objects.TranscriptNormalized

isMatchesLongForm() - Method in class edu.uchsc.ccp.nlp.ei.mutation.PointMutation

Return if the originally matched wildtype or mutated allele matched a long form (e.g., Lysine -> true, L -> false)

isMethioneMatch() - Method in class de.hu.berlin.wbi.objects.dbSNPNormalized

isNsm() - Method in class de.hu.berlin.wbi.objects.MutationMention

isPsm() - Method in class de.hu.berlin.wbi.objects.dbSNPNormalized

isPsm() - Method in class de.hu.berlin.wbi.objects.MutationMention

isPsm() - Method in class de.hu.berlin.wbi.objects.TranscriptNormalized

isValid() - Method in class de.hu.berlin.wbi.stuff.xml.PSM

Checks if the PSM object is valid.

isValid() - Method in class edu.uchsc.ccp.nlp.ei.mutation.PointMutation

Only Nucleotide Sequence Mutations (NSM) are allowed to have a positional offset of < 0 This method checks if the position of a mutation is valid;

L

location - Variable in class de.hu.berlin.wbi.objects.MutationMention

Location in the text.

M

main(String[]) - Static method in class cnveth.CNVETH

main(String[]) - Static method in class cnveth.RegionRecognizer

main(String[]) - Static method in class de.hu.berlin.wbi.process.Evaluate

main(String[]) - Static method in class de.hu.berlin.wbi.process.EvaluateNoGeneNER

main(String[]) - Static method in class de.hu.berlin.wbi.process.MinimalExample

Minimal example for SNP normalization

main(String[]) - Static method in class de.hu.berlin.wbi.process.Normalize

main(String[]) - Static method in class de.hu.berlin.wbi.process.NormalizeDB

main(String[]) - Static method in class de.hu.berlin.wbi.process.osiris.CheckOsiris

main(String[]) - Static method in class de.hu.berlin.wbi.process.osiris.EvaluateOsiris

Evaluate our normalization procedure on the Osiris corpus.

main(String[]) - Static method in class de.hu.berlin.wbi.process.osiris.ModifyOsiris

main(String[]) - Static method in class de.hu.berlin.wbi.stuff.xml.ParseXMLToFile

main(String[]) - Static method in class edu.uchsc.ccp.nlp.ei.mutation.MutationFinder

The main method demonstrates the execution of MutationFinder.

main(String[]) - Static method in class seth.ner.wrapper.SETHNERApp

main(String[]) - Static method in class seth.ner.wrapper.SETHNERAppMut

main(String[]) - Static method in class seth.seth.eval.ApplyNER

main(String[]) - Static method in class seth.seth.eval.ApplyNerToVerspoor

main(String[]) - Static method in class seth.seth.eval.ApplyNERToWei

main(String[]) - Static method in class seth.seth.eval.EvaluateNER

main(String[]) - Static method in class seth.seth.eval.EvaluateVerspoor

main(String[]) - Static method in class seth.seth.eval.EvaluateWei

main(String[]) - Static method in class seth.SETH

Minimal example to perform named entity recognition and normalization using SETH

MatchOptions - Enum in de.hu.berlin.wbi.objects

Represents the different possibilities to match a MutationMention to a dbSNP entry or UniProt entry

MinimalExample - Class in de.hu.berlin.wbi.process

Class contains source code for a minimal example, required to normalize a SNP

MinimalExample() - Constructor for class de.hu.berlin.wbi.process.MinimalExample

ModifyOsiris - Class in de.hu.berlin.wbi.process.osiris

ModifyOsiris() - Constructor for class de.hu.berlin.wbi.process.osiris.ModifyOsiris

MUT_RES - Static variable in class edu.uchsc.ccp.nlp.ei.mutation.MutationFinder

Mutation - Class in edu.uchsc.ccp.nlp.ei.mutation

Mutation is a base class for different types of mutations.

Mutation(int) - Constructor for class edu.uchsc.ccp.nlp.ei.mutation.Mutation

Mutation(String) - Constructor for class edu.uchsc.ccp.nlp.ei.mutation.Mutation

MutationException - Exception in edu.uchsc.ccp.nlp.ei.mutation

Exception thrown by MutationFinder

MutationException(String) - Constructor for exception edu.uchsc.ccp.nlp.ei.mutation.MutationException

MutationExtractor - Class in edu.uchsc.ccp.nlp.ei.mutation

A base class for extracting Mutations from text

MutationExtractor() - Constructor for class edu.uchsc.ccp.nlp.ei.mutation.MutationExtractor

MutationFinder - Class in edu.uchsc.ccp.nlp.ei.mutation

This is the Java implementation of MutationFinder (original version in Python by J.

MutationFinder() - Constructor for class edu.uchsc.ccp.nlp.ei.mutation.MutationFinder

Initialization of MutationFinder requires a set of regular expressions that will be used to detect mutations.

MutationFinder(String) - Constructor for class edu.uchsc.ccp.nlp.ei.mutation.MutationFinder

Initialization of MutationFinder requires a set of regular expressions that will be used to detect mutations.

MutationFinder(File) - Constructor for class edu.uchsc.ccp.nlp.ei.mutation.MutationFinder

Initialization of MutationFinder requires a set of regular expressions that will be used to detect mutations.

MutationFinder(Set<String>) - Constructor for class edu.uchsc.ccp.nlp.ei.mutation.MutationFinder

Initialization of MutationFinder requires a set of regular expressions that will be used to detect mutations.

MutationMention - Class in de.hu.berlin.wbi.objects

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

MutationMention() - Constructor for class de.hu.berlin.wbi.objects.MutationMention

Empty constructor

MutationMention(String) - Constructor for class de.hu.berlin.wbi.objects.MutationMention

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

MutationMention(EntityOffset, String) - Constructor for class de.hu.berlin.wbi.objects.MutationMention

MutationMention(int, int, String, String, String, String, String, Type, MutationMention.Tool) - Constructor for class de.hu.berlin.wbi.objects.MutationMention

MutationMention.Tool - Enum in de.hu.berlin.wbi.objects

Enumeration of all named entity recognition components

MutationValidation - Class in de.hu.berlin.wbi.objects

This object represents a MutationMention from the validation corpus, where we already know which dbSNP entry is associated with this gene.

MutationValidation(int, EntityOffset, String, String, String, String, String) - Constructor for class de.hu.berlin.wbi.objects.MutationValidation

Constructor

mutResidue - Variable in class de.hu.berlin.wbi.objects.MutationMention

Mutated residue.

MyPattern - Class in edu.uchsc.ccp.nlp.ei.mutation

This class contains an apache Pattern object and a pattern Id Especially useful to enable later which regex found which entity

MyPattern(Pattern, String, int) - Constructor for class edu.uchsc.ccp.nlp.ei.mutation.MyPattern

N

Normalize - Class in de.hu.berlin.wbi.process

This is an example class for using snp-normalizer

Normalize() - Constructor for class de.hu.berlin.wbi.process.Normalize

normalized - Variable in class de.hu.berlin.wbi.objects.MutationMention

List with normalized SNPs

NormalizeDB - Class in de.hu.berlin.wbi.process

Class is used to normalize all mutation mentions stored in a database to SNPs

NormalizeDB() - Constructor for class de.hu.berlin.wbi.process.NormalizeDB

normalizeResidueIdentity(String) - Method in class edu.uchsc.ccp.nlp.ei.mutation.PointMutation

Normalize three-letter and full residue names to their one-letter abbreviations.

normalizeSequences(Set<Transcript>, List<UniprotFeature>, boolean) - Method in class de.hu.berlin.wbi.objects.MutationMention

This method evaluates if some of the Transcript provided in candidateTranscripts equals the text-mined MutationMention.

normalizeSNP(int) - Method in class de.hu.berlin.wbi.objects.MutationMention

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

normalizeSNP(List<dbSNP>, List<UniprotFeature>, boolean) - Method in class de.hu.berlin.wbi.objects.MutationMention

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

nsm - Variable in class de.hu.berlin.wbi.objects.MutationMention

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

O

OldNomenclature - Class in seth

This class can be used to find mutation mentions (deletions, IVS-substitions, insertions, and frameshifts) written in deprecated nomenclature

OldNomenclature() - Constructor for class seth.OldNomenclature

P

ParseXMLToFile - Class in de.hu.berlin.wbi.stuff.xml

Created with IntelliJ IDEA.

ParseXMLToFile() - Constructor for class de.hu.berlin.wbi.stuff.xml.ParseXMLToFile

patternId - Variable in class de.hu.berlin.wbi.objects.MutationMention

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

Performance - Class in seth.seth.eval

Created with IntelliJ IDEA.

Performance() - Constructor for class seth.seth.eval.Performance

PointMutation - Class in edu.uchsc.ccp.nlp.ei.mutation

A class for storing information about protein point mutations

PointMutation(String, String, String) - Constructor for class edu.uchsc.ccp.nlp.ei.mutation.PointMutation

populateAminoAcidNameToOneLookupMap - Static variable in class edu.uchsc.ccp.nlp.ei.mutation.MutationExtractor

This method simple fills the two mappings between amino acid name and the amino acid one-letter code

populateAminoAcidOneToOneLookupMap() - Method in class edu.uchsc.ccp.nlp.ei.mutation.PointMutation

populateAminoAcidThreeToOneLookupMap - Static variable in class edu.uchsc.ccp.nlp.ei.mutation.MutationExtractor

This method simple fills the two mappings between amino acid one letter code and the amino acid three letter code

POS - Static variable in class edu.uchsc.ccp.nlp.ei.mutation.MutationFinder

position - Variable in class de.hu.berlin.wbi.objects.MutationMention

Location of the mutation wrt residue or nucleotides

protein_sequence - Variable in class de.hu.berlin.wbi.objects.Transcript

Protein Sequence

psm - Variable in class de.hu.berlin.wbi.objects.MutationMention

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

PSM - Class in de.hu.berlin.wbi.stuff.xml

Class represents a protein sequence mutation

PSM(int, int, String, String) - Constructor for class de.hu.berlin.wbi.stuff.xml.PSM

Q

query(String) - Method in class de.hu.berlin.wbi.objects.DatabaseConnection

Wrapper for querying the database

queryGenesForArticle(int) - Static method in class de.hu.berlin.wbi.objects.Gene

Search for all genes contained in an Article using PubMed ID.

R

readGoldStandard(String) - Static method in class seth.seth.eval.EvaluateNER

Loads goldstandard annotations

readGoldStandard(String) - Static method in class seth.seth.eval.EvaluateVerspoor

Loads goldstandard annotations

readGoldStandard(String) - Static method in class seth.seth.eval.EvaluateWei

Loads goldstandard annotations

readMutations(String) - Static method in class de.hu.berlin.wbi.objects.MutationMention

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

readMutationsValidation(String) - Static method in class de.hu.berlin.wbi.objects.MutationValidation

Reads the mutation from the annotated corpus and returns these mutations.

readPredictions(String) - Static method in class seth.seth.eval.EvaluateNER

Loads SETH predictions

readRegions() - Method in class cnveth.RegionRecognizer

function to read chromosomal regions and associated genes into a hash

ref - Variable in class de.hu.berlin.wbi.objects.MutationMention

Used reference sequence (e.g.

region - Variable in class cnveth.RegionMention

region mention

RegionMention - Class in cnveth

RegionMention(String, int, int, ArrayList<String>) - Constructor for class cnveth.RegionMention

RegionRecognizer - Class in cnveth

RegionRecognizer() - Constructor for class cnveth.RegionRecognizer

RegionRecognizer(String) - Constructor for class cnveth.RegionRecognizer

removeTagsFromPythonRegex(String) - Static method in class edu.uchsc.ccp.nlp.ei.mutation.MutationFinder

residues - Variable in class de.hu.berlin.wbi.objects.dbSNP

known mutated amino acid residues for this SNP

rsID - Variable in class de.hu.berlin.wbi.objects.dbSNP

dbSNP internal id.

S

setAaLoc(int) - Method in class de.hu.berlin.wbi.stuff.xml.PSM

setAaPosition(int) - Method in class de.hu.berlin.wbi.objects.dbSNP

setAmbiguous(boolean) - Method in class de.hu.berlin.wbi.objects.MutationMention

setEntrez(int) - Method in class de.hu.berlin.wbi.stuff.xml.PSM

setGeneID(int) - Method in class de.hu.berlin.wbi.objects.dbSNP

Set the associated entrez gene identifier

seth - package seth

Package contains most logic of SETH

SETH - Class in seth

This class encapsulates modified MutationFinder, SETHNER, OldNomenclature, and dbSNPRecognizer.

SETH() - Constructor for class seth.SETH

Parameter free constructor for SETH.

SETH(String, boolean, boolean) - Constructor for class seth.SETH

Initializes MutationFinder and SETHNER.

seth.ner.wrapper - package seth.ner.wrapper

Java wrapper for accessing the scala part of SETH (aka SETH-NER) SETH-NER performs Named Entity Recognition of variation mentions in the latest HGVS nomenclature based on a Backus Naur grammar

seth.seth.eval - package seth.seth.eval

Code for applying and evaluating SETH on various corpora

setHgvs(Set<HGVS>) - Method in class de.hu.berlin.wbi.objects.dbSNP

SETHNER - Class in seth.ner.wrapper

Java wrapper for actual seth.ner.SETHNER code written in Scala

SETHNER(boolean) - Constructor for class seth.ner.wrapper.SETHNER

Constructor for SETH-NER

SETHNERApp - Class in seth.ner.wrapper

Minimal example to apply SETHNER (exluding MutationFinder) on free text

SETHNERApp() - Constructor for class seth.ner.wrapper.SETHNERApp

SETHNERAppMut - Class in seth.ner.wrapper

Minimal example to apply SETHNER (including MutationFinder) on free text

SETHNERAppMut() - Constructor for class seth.ner.wrapper.SETHNERAppMut

setId(int) - Method in class edu.uchsc.ccp.nlp.ei.mutation.Mutation

setMutResidue(String) - Method in class de.hu.berlin.wbi.objects.MutationMention

Sets the residues.

setNsm(boolean) - Method in class de.hu.berlin.wbi.objects.MutationMention

setPatternId(int) - Method in class de.hu.berlin.wbi.objects.MutationMention

Sets pattern ID

setPosition(String) - Method in class de.hu.berlin.wbi.objects.MutationMention

Sets the position.

setPsm(boolean) - Method in class de.hu.berlin.wbi.objects.MutationMention

setResidues(Set<String>) - Method in class de.hu.berlin.wbi.objects.dbSNP

setRsID(int) - Method in class de.hu.berlin.wbi.objects.dbSNP

Set the dbSNP identifier (e.g., rs334)

setWildtype(String) - Method in class de.hu.berlin.wbi.stuff.xml.PSM

setWtResidue(String) - Method in class de.hu.berlin.wbi.objects.MutationMention

Sets the residue.

SNP - Class in de.hu.berlin.wbi.stuff.xml

Represents a SNP consisting of dbSNP id several (at least one) protein sequence mutations several HGVS representations

SNP(int) - Constructor for class de.hu.berlin.wbi.stuff.xml.SNP

startElement(String, String, String, Attributes) - Method in class de.hu.berlin.wbi.stuff.xml.ParseXMLToFile

stmt - Variable in class de.hu.berlin.wbi.objects.DatabaseConnection

T

text - Variable in class de.hu.berlin.wbi.objects.MutationMention

Text mention in the text.

tn - Variable in class seth.seth.eval.Performance

toHGVS() - Method in class de.hu.berlin.wbi.objects.MutationMention

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

toNormalized() - Method in class de.hu.berlin.wbi.objects.MutationMention

tool - Variable in class de.hu.berlin.wbi.objects.MutationMention

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

toString() - Method in class cnveth.RegionMention

toString() - Method in class de.hu.berlin.wbi.objects.DatabaseConnection

Returns a string representation of the object

toString() - Method in class de.hu.berlin.wbi.objects.dbSNP

(non-Javadoc)

toString() - Method in class de.hu.berlin.wbi.objects.dbSNPNormalized

(non-Javadoc)

toString() - Method in class de.hu.berlin.wbi.objects.EntityOffset

(non-Javadoc)

toString() - Method in class de.hu.berlin.wbi.objects.Gene

(non-Javadoc)

toString() - Method in class de.hu.berlin.wbi.objects.HGVS

(non-Javadoc)

toString() - Method in class de.hu.berlin.wbi.objects.MutationMention

(non-Javadoc)

toString() - Method in class de.hu.berlin.wbi.objects.MutationValidation

(non-Javadoc)

toString() - Method in class de.hu.berlin.wbi.objects.Transcript

toString() - Method in class de.hu.berlin.wbi.objects.UniprotFeature

(non-Javadoc)

toString() - Method in class de.hu.berlin.wbi.stuff.xml.PSM

toString() - Method in class de.hu.berlin.wbi.stuff.xml.SNP

toString() - Method in class edu.uchsc.ccp.nlp.ei.mutation.Mutation

To be overridden by subclasses

toString() - Method in exception edu.uchsc.ccp.nlp.ei.mutation.MutationException

toString() - Method in class edu.uchsc.ccp.nlp.ei.mutation.PointMutation

Override toString(), returns mutation as a string in wNm format

toString() - Method in class seth.seth.eval.Entity

tp - Variable in class seth.seth.eval.Performance

Transcript - Class in de.hu.berlin.wbi.objects

Class to represents a transcript (Protein as well as coding sequence) Therefore one gene usually contains one or more Transcript

Transcript() - Constructor for class de.hu.berlin.wbi.objects.Transcript

Transcript(int, String, String, String, String, String, String) - Constructor for class de.hu.berlin.wbi.objects.Transcript

TranscriptNormalized - Class in de.hu.berlin.wbi.objects

Represents a MutationMention mention which has been successfully normalized to a Transcript .

transcripts - Variable in class de.hu.berlin.wbi.objects.MutationMention

Set of transcripts with which we successfully associated this Element

type - Variable in class de.hu.berlin.wbi.objects.MutationMention

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

Type - Enum in seth.ner.wrapper

Mutation types found by SETHNER, MutationFinder currently extracts only Substitutions

U

uniprot - Variable in class de.hu.berlin.wbi.objects.Transcript

UniProt-ID.

UniprotFeature - Class in de.hu.berlin.wbi.objects

Represents a UniProt entry; loaded from database.

UniprotFeature(int, String, int, int) - Constructor for class de.hu.berlin.wbi.objects.UniprotFeature

updateMapping(Map<String, String>, Map<String, String>) - Method in class edu.uchsc.ccp.nlp.ei.mutation.Mutation

V

valueOf(String) - Static method in enum de.hu.berlin.wbi.objects.MatchOptions

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum de.hu.berlin.wbi.objects.MutationMention.Tool

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum seth.ner.wrapper.Type

Returns the enum constant of this type with the specified name.

values() - Static method in enum de.hu.berlin.wbi.objects.MatchOptions

Returns an array containing the constants of this enum type, in the order they are declared.

values() - Static method in enum de.hu.berlin.wbi.objects.MutationMention.Tool

Returns an array containing the constants of this enum type, in the order they are declared.

values() - Static method in enum seth.ner.wrapper.Type

Returns an array containing the constants of this enum type, in the order they are declared.

W

warn(String) - Method in class edu.uchsc.ccp.nlp.ei.mutation.Mutation

warn(String) - Method in class edu.uchsc.ccp.nlp.ei.mutation.MutationExtractor

wildtype - Variable in class de.hu.berlin.wbi.objects.dbSNP

Mutation has one wildtype

WT_RES - Static variable in class edu.uchsc.ccp.nlp.ei.mutation.MutationFinder

wtResidue - Variable in class de.hu.berlin.wbi.objects.MutationMention

Wildtype residue.

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