Constant Field Values

Contents

• org.molgenis.*

org.molgenis.*

org.molgenis.data.annotation.LocusAnnotator

Modifier and Type	Constant Field	Value
public static final String	CHROMOSOME	"#CHROM"
public static final String	POSITION	"POS"

org.molgenis.data.annotation.VariantAnnotator

Modifier and Type	Constant Field	Value
public static final String	ALTERNATIVE	"ALT"
public static final String	REFERENCE	"REF"

org.molgenis.data.annotation.VcfUtils

Modifier and Type	Constant Field	Value
public static final String	TAB	"\t"

org.molgenis.data.annotation.impl.CaddServiceAnnotator

Modifier and Type	Constant Field	Value
public static final String	CADD_ABS	"CADDABS"
public static final String	CADD_FILE_LOCATION_PROPERTY	"cadd_location"
public static final String	CADD_SCALED	"CADDSCALED"

org.molgenis.data.annotation.impl.ClinicalGenomicsDatabaseServiceAnnotator

Modifier and Type	Constant Field	Value
public static final String	ALLELIC_CONDITIONS	"ALLELIC CONDITIONS"
public static final String	CGD_AGE_GROUP	"CGDAGE"
public static final String	CGD_CONDITION	"CGDCOND"
public static final String	CGD_FILE_LOCATION	"cgd_location"
public static final String	CGD_GENERALIZED_INHERITANCE	"CGDGIN"
public static final String	CGD_INHERITANCE	"CGDINH"
public static final String	COMMENTS	"COMMENTS"
public static final String	ENTREZ_GENE_ID	"ENTREZ GENE ID"
public static final String	GENE	"GENE"
public static final String	HGNC_ID	"HGNC ID"
public static final String	INTERVENTION_CATEGORIES	"INTERVENTION CATEGORIES"
public static final String	INTERVENTION_RATIONALE	"INTERVENTION/RATIONALE"
public static final String	MANIFESTATION_CATEGORIES	"MANIFESTATION CATEGORIES"
public static final String	REFERENCES	"REFERENCES"

org.molgenis.data.annotation.impl.ClinVarServiceAnnotator

Modifier and Type	Constant Field	Value
public static final String	ALLELEID	"AlleleID"
public static final String	ASSEMBLY	"Assembly"
public static final String	CLINICALSIGNIFICANCE	"ClinicalSignificance"
public static final String	CLINVAR_CHROMOSOME	"Chromosome"
public static final String	CLINVAR_FILE_LOCATION_PROPERTY	"clinvar_location"
public static final String	CYTOGENETIC	"Cytogenetic"
public static final String	GENE_NAME	"Name"
public static final String	GENEID	"GeneID"
public static final String	GENESYMBOL	"GeneSymbol"
public static final String	GUIDELINES	"Guidelines"
public static final String	HGVS_C	"HGVS(c.)"
public static final String	HGVS_P	"HGVS(p.)"
public static final String	LASTEVALUATED	"LastEvaluated"
public static final String	NSV_DBVAR	"nsv (dbVar)"
public static final String	NUMBERSUBMITTERS	"NumberSubmitters"
public static final String	ORIGIN	"Origin"
public static final String	OTHERIDS	"OtherIDs"
public static final String	PHENOTYPEIDS	"PhenotypeIDs"
public static final String	RCVACCESSION	"RCVaccession"
public static final String	REVIEWSTATUS	"ReviewStatus"
public static final String	RS_DBSNP	"RS (dbSNP)"
public static final String	START	"Start"
public static final String	STOP	"Stop"
public static final String	TESTEDINGTR	"TestedInGTR"
public static final String	TYPE	"Type"
public static final String	VARIANTIDS	"VariantID"

org.molgenis.data.annotation.impl.CosmicServiceAnnotator

Modifier and Type	Constant Field	Value
public static final String	ALT_ALLELES	"alt_alleles"
public static final String	CONSEQUENCE_TYPE	"consequence_type"
public static final String	END	"end"
public static final String	ENSEMBLE_ID	"ensemblId"
public static final String	FEATURE_TYPE	"feature_type"
public static final String	ID	"ID"
public static final String	NAME	"Cosmic"
public static final String	SEQ_REGION_NAME	"seq_region_name"
public static final String	START	"start"
public static final String	STRAND	"strand"

org.molgenis.data.annotation.impl.DbnsfpGeneServiceAnnotator

Modifier and Type	Constant Field	Value
public static final String	GENE_FILE_LOCATION_PROPERTY	"dbnsfp_gene_location"

org.molgenis.data.annotation.impl.DbnsfpVariantServiceAnnotator

Modifier and Type	Constant Field	Value
public static final String	CHROMOSOME_FILE_LOCATION_PROPERTY	"dbsnfp_variant_location"

org.molgenis.data.annotation.impl.EbiServiceAnnotator

Modifier and Type	Constant Field	Value
public static final String	NAME	"EBI-CHeMBL"
public static final String	UNIPROT_ID	"uniprot_id"

org.molgenis.data.annotation.impl.ExACServiceAnnotator

Modifier and Type	Constant Field	Value
public static final String	EXAC_MAF	"EXAC_MAF"
public static final String	EXAC_VCFGZ_LOCATION	"exac_location"

org.molgenis.data.annotation.impl.GoNLServiceAnnotator

Modifier and Type	Constant Field	Value
public static final String	GONL_DIRECTORY_LOCATION_PROPERTY	"gonl_location"
public static final String	GONL_GTC	"GONL_GTC"
public static final String	GONL_MAF	"GONL_MAF"

org.molgenis.data.annotation.impl.KeggServiceAnnotator

Modifier and Type	Constant Field	Value
public static final String	KEGG_GENE_ID	"KEGG_gene_id"
public static final String	KEGG_PATHWAYS_IDS	"KEGG_pathway_ids"
public static final String	KEGG_PATHWAYS_NAMES	"KEGG_pathway_names"

org.molgenis.data.annotation.impl.OmimHpoAnnotator

Modifier and Type	Constant Field	Value
public static final String	HPO_DESCRIPTIONS	"HPO_Descriptions"
public static final String	HPO_DISEASE_DATABASE	"HPO_Disease_Database"
public static final String	HPO_DISEASE_DATABASE_ENTRY	"HPO_Disease_Database_Entry"
public static final String	HPO_ENTREZ_ID	"HPO_Entrez_ID"
public static final String	HPO_GENE_NAME	"HPO_Gene_Name"
public static final String	HPO_IDENTIFIERS	"HPO_IDs"
public static final String	OMIM_CAUSAL_IDENTIFIER	"OMIM_Causal_ID"
public static final String	OMIM_CYTOGENIC_LOCATION	"OMIM_Cytogenic_Location"
public static final String	OMIM_DISORDERS	"OMIM_Disorders"
public static final String	OMIM_ENTRY	"OMIM_Entry"
public static final String	OMIM_HGNC_IDENTIFIERS	"OMIM_HGNC_IDs"
public static final String	OMIM_IDENTIFIERS	"OMIM_IDs"
public static final String	OMIM_TYPE	"OMIM_Type"

org.molgenis.data.annotation.impl.SnpEffServiceAnnotator

Modifier and Type	Constant Field	Value
public static final String	ANNOTATION	"Annotation"
public static final String	C_DNA_POSITION	"cDNA_position"
public static final String	CDS_POSITION	"CDS_position"
public static final String	DISTANCE_TO_FEATURE	"Distance_to_feature"
public static final String	ERRORS	"Errors"
public static final String	FEATURE_ID	"Feature_ID"
public static final String	FEATURE_TYPE	"Feature_type"
public static final String	GENE_ID	"Gene_ID"
public static final String	GENE_NAME	"Gene_Name"
public static final String	HGVS_C	"HGVS_c"
public static final String	HGVS_P	"HGVS_p"
public static final String	LOF	"LOF"
public static final String	NMD	"NMD"
public static final String	PROTEIN_POSITION	"Protein_position"
public static final String	PUTATIVE_IMPACT	"Putative_impact"
public static final String	RANK_TOTAL	"Rank_total"
public static final String	SNPEFF_JAR_LOCATION_PROPERTY	"snpeff_jar_location"
public static final String	TRANSCRIPT_BIOTYPE	"Transcript_biotype"

org.molgenis.data.annotation.impl.ThousandGenomesServiceAnnotator

Modifier and Type	Constant Field	Value
public static final String	THGEN_DIRECTORY_LOCATION_PROPERTY	"1000G_location"
public static final String	THGEN_MAF	"1000G_MAF"

org.molgenis.data.annotation.provider.CgdDataProvider

Modifier and Type	Constant Field	Value
public static final String	CGD_FILE_LOCATION_PROPERTY	"cgd_location"

org.molgenis.data.annotation.provider.ClinvarDataProvider

Modifier and Type	Constant Field	Value
public static final String	CLINVAR_FILE_LOCATION_PROPERTY	"clinvar_location"

org.molgenis.data.annotation.provider.HgncLocationsProvider

Modifier and Type	Constant Field	Value
public static final String	DEFAULT_HGNC_LOCATIONS_VALUE	"https://molgenis26.target.rug.nl/downloads/5gpm/GRCh37p13_HGNC_GeneLocations_noPatches.tsv"
public static final String	KEY_HGNC_LOCATIONS_VALUE	"plugin.annotators.hgcn.locations.url"

org.molgenis.data.annotation.provider.HpoMappingProvider

Modifier and Type	Constant Field	Value
public static final String	DEFAULT_HPO_MAPPING_VALUE	"https://molgenis26.target.rug.nl/downloads/5gpm/ALL_SOURCES_ALL_FREQUENCIES_diseases_to_genes_to_phenotypes.txt"
public static final String	KEY_HPO_MAPPING	"plugin.annotators.hpo.mapping.url"