de.hu.berlin.wbi.objects

Class Gene

java.lang.Object

de.hu.berlin.wbi.objects.Gene

public class Gene
extends Object

Represents a gene mention found by any Named Enttiy Recognition and Normalization tool. In this work we always used GNAT and gene2pubmed

Author:

Philippe Thomas

Constructor Summary

Constructors

Constructor and Description
Gene() Empty constructor
Gene(int pmid, int geneID, int species)

Method Summary

Modifier and Type	Method and Description
boolean	equals(Object obj) (non-Javadoc)
int	getConfidence() Gets the confidence for this gene.
String	getEntity() Gets the string in the text.
int	getGeneID() Gets the gene-ID (Entrez in our case).
EntityOffset	getLocation() Gets the found at which position.
int	getPmid() Gets the article ID.
int	getSpecies() Gets the species.
int	hashCode() (non-Javadoc)
static void	init(DatabaseConnection connection, String geneTable, String gene2Pubmed) Initializes the prepared statements for retrieving gene information for one PubMed article
static Set<Gene>	queryGenesForArticle(int pmid) Search for all genes contained in an Article using PubMed ID.
String	toString() (non-Javadoc)

Methods inherited from class java.lang.Object

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

Constructor Detail

Gene

public Gene()

Empty constructor

Gene

public Gene(int pmid,
            int geneID,
            int species)

Parameters:

pmid - PubMed-ID

geneID - Entrez Gene ID

confidence - NER/NEN confidence

species - Associated species

location - Position in text

entity - Entity mention

Method Detail

getPmid

public int getPmid()

Gets the article ID.

Returns:

the article ID

getGeneID

public int getGeneID()

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

Returns:

the gene-ID (Entrez in our case)

getConfidence

public int getConfidence()

Gets the confidence for this gene.

Returns:

the confidence for this gene

getSpecies

public int getSpecies()

Gets the species.

Returns:

the species

getLocation

public EntityOffset getLocation()

Gets the found at which position.

Returns:

the found at which position

getEntity

public String getEntity()

Gets the string in the text.

Returns:

the string in the text

toString

public String toString()

(non-Javadoc)

Overrides:

toString in class Object

See Also:

Object.toString()

hashCode

public int hashCode()

(non-Javadoc)

Overrides:

hashCode in class Object

See Also:

Object.hashCode()

equals

public boolean equals(Object obj)

(non-Javadoc)

Overrides:

equals in class Object

See Also:

Object.equals(java.lang.Object)

init

public static void init(DatabaseConnection connection,
                        String geneTable,
                        String gene2Pubmed)
                 throws SQLException

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

Parameters:

connection - Database connection

geneTable - Table name for GNAT results

gene2Pubmed - Table name for gene2PubMed results

Throws:

SQLException

queryGenesForArticle

public static Set<Gene> queryGenesForArticle(int pmid)

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

Parameters:

pmid - PubMed-ID

Returns:

all genes contained in a specific article