org.molgenis.data.annotation.impl

Class OmimHpoAnnotator

java.lang.Object

org.molgenis.data.annotation.AbstractRepositoryAnnotator

org.molgenis.data.annotation.LocusAnnotator

org.molgenis.data.annotation.impl.OmimHpoAnnotator

All Implemented Interfaces:

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

@Component(value="omimHpoService")
public class OmimHpoAnnotator
extends LocusAnnotator

Created by jvelde on 2/12/14. uses:

- http://compbio.charite.de/hudson/job/hpo.annotations.monthly/lastStableBuild/artifact/annotation/ ALL_SOURCES_ALL_FREQUENCIES_diseases_to_genes_to_phenotypes.txt - https://molgenis26.target.rug.nl/downloads/5gpm/GRCh37p13_HGNC_GeneLocations_noPatches.tsv - ftp://ftp.omim.org/omim/morbidmap

Field Summary

Fields

Modifier and Type	Field and Description
static String	HPO_DESCRIPTIONS
static String	HPO_DISEASE_DATABASE
static String	HPO_DISEASE_DATABASE_ENTRY
static String	HPO_ENTREZ_ID
static String	HPO_GENE_NAME
static String	HPO_IDENTIFIERS
static String	OMIM_CAUSAL_IDENTIFIER
static String	OMIM_CYTOGENIC_LOCATION
static String	OMIM_DISORDERS
static String	OMIM_ENTRY
static String	OMIM_HGNC_IDENTIFIERS
static String	OMIM_IDENTIFIERS
static String	OMIM_TYPE

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
OmimHpoAnnotator(AnnotationService annotatorService, OmimMorbidMapProvider omimMorbidMapProvider, HgncLocationsProvider hgncLocationsProvider, HpoMappingProvider hpoMappingProvider, MolgenisSettings molgenisSettings, UrlPinger urlPinger)

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

OMIM_CAUSAL_IDENTIFIER

public static final String OMIM_CAUSAL_IDENTIFIER

See Also:

Constant Field Values

OMIM_DISORDERS

public static final String OMIM_DISORDERS

See Also:

Constant Field Values

OMIM_IDENTIFIERS

public static final String OMIM_IDENTIFIERS

See Also:

Constant Field Values

OMIM_TYPE

public static final String OMIM_TYPE

See Also:

Constant Field Values

OMIM_HGNC_IDENTIFIERS

public static final String OMIM_HGNC_IDENTIFIERS

See Also:

Constant Field Values

OMIM_CYTOGENIC_LOCATION

public static final String OMIM_CYTOGENIC_LOCATION

See Also:

Constant Field Values

OMIM_ENTRY

public static final String OMIM_ENTRY

See Also:

Constant Field Values

HPO_IDENTIFIERS

public static final String HPO_IDENTIFIERS

See Also:

Constant Field Values

HPO_GENE_NAME

public static final String HPO_GENE_NAME

See Also:

Constant Field Values

HPO_DESCRIPTIONS

public static final String HPO_DESCRIPTIONS

See Also:

Constant Field Values

HPO_DISEASE_DATABASE

public static final String HPO_DISEASE_DATABASE

See Also:

Constant Field Values

HPO_DISEASE_DATABASE_ENTRY

public static final String HPO_DISEASE_DATABASE_ENTRY

See Also:

Constant Field Values

HPO_ENTREZ_ID

public static final String HPO_ENTREZ_ID

See Also:

Constant Field Values

Constructor Detail

OmimHpoAnnotator

@Autowired
public OmimHpoAnnotator(AnnotationService annotatorService,
                                   OmimMorbidMapProvider omimMorbidMapProvider,
                                   HgncLocationsProvider hgncLocationsProvider,
                                   HpoMappingProvider hpoMappingProvider,
                                   MolgenisSettings molgenisSettings,
                                   UrlPinger urlPinger)
                            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()