org.molgenis.data.annotation.impl

Class DbnsfpGeneServiceAnnotator

java.lang.Object

org.molgenis.data.annotation.AbstractRepositoryAnnotator

org.molgenis.data.annotation.LocusAnnotator

org.molgenis.data.annotation.impl.DbnsfpGeneServiceAnnotator

All Implemented Interfaces:

EventListener, RepositoryAnnotator, org.springframework.context.ApplicationListener<org.springframework.context.event.ContextRefreshedEvent>

@Component(value="dbnsfpGeneService")
public class DbnsfpGeneServiceAnnotator
extends LocusAnnotator

This class uses a location to retrieve a gene from the ... class. This gene can then be used to approach the dbNSFP gene file. It extracts relevant gene annotations from this file. This can be run seperately from the dbNSFP variant service.

dbNSFP gene returns: Gene_name Ensembl_gene chr Gene_old_names Gene_other_names Uniprot_acc Uniprot_id Entrez_gene_id CCDS_id Refseq_id ucsc_id MIM_id Gene_full_name Pathway(Uniprot) Pathway(ConsensusPathDB) Function_description Disease_description MIM_phenotype_id MIM_disease Trait_association(GWAS) GO_Slim_biological_process GO_Slim_cellular_component GO_Slim_molecular_function Expression(egenetics) Expression(GNF/Atlas) Interactions(IntAct) Interactions(BioGRID) Interactions(ConsensusPathDB) P(HI) P(rec) Known_rec_info Essential_gene

Version:

dbNSFP version 2.3 downloaded January 26, 2014

Author:

mdehaan

Field Summary

Fields

Modifier and Type	Field and Description
static String	GENE_FILE_LOCATION_PROPERTY

Fields inherited from class org.molgenis.data.annotation.LocusAnnotator

CHROMOSOME, POSITION

Fields inherited from interface org.molgenis.data.annotation.RepositoryAnnotator

ANNOTATOR_PREFIX

Constructor Summary

Constructors

Constructor and Description
DbnsfpGeneServiceAnnotator(MolgenisSettings molgenisSettings, AnnotationService annotatorService, HgncLocationsProvider hgncLocationsProvider)

Method Summary

Modifier and Type	Method and Description
List<Entity>	annotateEntity(Entity entity)
boolean	annotationDataExists() Checks if folder and files that were set with a runtime property actually exist, or if a webservice can be reached
EntityMetaData	getOutputMetaData()
String	getSimpleName()
void	onApplicationEvent(org.springframework.context.event.ContextRefreshedEvent event)

Methods inherited from class org.molgenis.data.annotation.LocusAnnotator

getInputMetaData

Methods inherited from class org.molgenis.data.annotation.AbstractRepositoryAnnotator

annotate, canAnnotate, getFullName

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Methods inherited from interface org.molgenis.data.annotation.RepositoryAnnotator

annotate, canAnnotate, getDescription, getFullName

Field Detail

GENE_FILE_LOCATION_PROPERTY

public static final String GENE_FILE_LOCATION_PROPERTY

See Also:

Constant Field Values

Constructor Detail

DbnsfpGeneServiceAnnotator

@Autowired
public DbnsfpGeneServiceAnnotator(MolgenisSettings molgenisSettings,
                                             AnnotationService annotatorService,
                                             HgncLocationsProvider hgncLocationsProvider)
                                      throws IOException

Throws:

IOException

Method Detail

onApplicationEvent

public void onApplicationEvent(org.springframework.context.event.ContextRefreshedEvent event)

Specified by:

onApplicationEvent in interface org.springframework.context.ApplicationListener<org.springframework.context.event.ContextRefreshedEvent>

Overrides:

onApplicationEvent in class AbstractRepositoryAnnotator

getSimpleName

public String getSimpleName()

annotationDataExists

public boolean annotationDataExists()

Description copied from class: AbstractRepositoryAnnotator

Checks if folder and files that were set with a runtime property actually exist, or if a webservice can be reached

Specified by:

annotationDataExists in class AbstractRepositoryAnnotator

Returns:

boolean

annotateEntity

public List<Entity> annotateEntity(Entity entity)
                            throws IOException

Specified by:

annotateEntity in class AbstractRepositoryAnnotator

Throws:

IOException

getOutputMetaData

public EntityMetaData getOutputMetaData()