Exploring the HCLS Cloud

The HCLS cloud contains resources from multiple datasets. Navigating this endpoint requires an over all knowledge of what types of things are present and how they are connected. To help simplify the process we have generated a graph summary based on the types of resources present and how they are connected. Each node, ball, represents a distinct entity in the linked data cloud. Arrows between clouds represent a connection that exists between the resource of a particular type and and another resource's type.

Another way to explore the linked data cloud is the through the use: Pivot Brovser, SparQLed editor.

Canvas 1Layer 1DrugChemicalSide_EffectChemical_Disease_AssociationInference_ScoreGeneGeneInference_GeneDirect_EvidenceDiseasePhenotypeChemical_Gene_InteractionChemical_Gene_Interaction_ActionGeneOrganismOrganismReferenceChemical_Pathway_RelationPValueTarget_Total_QtyTotal_Match_QtyCorrected_P_ValueBackground_Match_QtyBiochemical_PathwayDisease_Pathway_AssociationGene_Pathway_AssociationAnnotation_Entry\NTarget_Match_QtyBackground_Total_QtyAssayNucleic_AcidProteinOrganismSubcellularTissueCell_LineAdmetActivityArticleConfidence_scoreStandard_TypeStandard_UnitsCompoundCanonical_SmilesAcd_most_bpkaHydrogen_Bond_AcceptorsStandard_Inchi_KeyHydrogen_Bond_DonorsAcd_most_apkaStandard_InchiPolar_Surface_AreaRotatable_BondsAlogPFull_Molecular_WeightRo2_PassAcd_LogdRule_Of_5_ViolationsAcd_LogpDrug_Information_LabelFrequencyCytogenetic_LocationMouse_CorrelateGene_StatusMethodAnnotation_EntryTASISSIDAIGINASNDRCAIMPICIEAIBAIEPIPIProteinReferenceJournalLower_BoundUpper_BoundequivalentClassside_effectinference_scoreinference_geneinference_geneinference_genedirect_evidencediseasediseasechemicalgeneorganismorganismreferencechemicalpValuetarget_total_qtytarget_match_qtycorrected_P_Valuebackground_match_qtychemicalpathwayinference_geneinference_geneinference_genediseasediseasepathwaygenepathwaygo_annotationtarget_total_qtytarget_match_qtycorrected_p_valuepvaluebackground_match_qtychemicalBackground_Total_Qtytargettargettargettargettargettargettargetactivityassay_tax_idassay_tax_idcites_as_data_sourceconfidence_scorestandard_typestandard_unitscompoundsmilesacd_most_bpkahydrogen_bond_acceptorsstandard_inchi_keyhydrogen_bond_donorsacd_most_apkastandard_inchiactive_compoundpolar_surface_arearotatable_bondsalogpfull_molecular_weightcites_as_referencero2_passacd_logdrule_of_5_violationsparent_compoundacd_logpequivalentClassequivalentClassequivalentClassidentifies_side_effectfrequencyinvolves_druggenecytogenetic_locationrelated_tomouse_correlategene_statusmethodequivalentClassequivalentClassorganismevidence_codeevidence_codeevidence_codeevidence_codeevidence_codeevidence_codeevidence_codeevidence_codeevidence_codeevidence_codeevidence_codeevidence_codeevidence_codeis_aboutreferencejournalgenegenegenegenegenelower_boundupper_bound

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Datasets

The following datasets have been integrated into the HCLS datacloud:

ChEMBL Database

The ChEMBL database contains information on medicinal chemicals and related bio assay information. Information covers a wide range of bioassay types including ADMET and binding assays and multiple organisms and targets.

ChEMBL Database Statistics

MetricValueQuery
How many Compounds in ChEMBL----+ show
PREFIX chembl: <http://hcls.sindice.com/chembl_vocabulary:>
SELECT COUNT DISTINCT ?compound
WHERE{
	?compound a chembl:Compound .
}
How many Assays in ChEMBL----+ show
PREFIX chembl: <http://hcls.sindice.com/chembl_vocabulary:>
SELECT COUNT DISTINCT ?assay
WHERE{
	?assay a chembl:Assay .
}
How many Targets in ChEMBL----+ show
PREFIX chembl: <http://hcls.sindice.com/chembl_vocabulary:>
SELECT COUNT DISTINCT ?target
WHERE{
	?target a chembl:Target .
}
How many Organisms in ChEMBL----+ show
PREFIX chembl: <http://hcls.sindice.com/chembl_vocabulary:>
SELECT COUNT(DISTINCT(?o))
WHERE{
	?o a chembl:Organism .
}
Types of Assays in ChEMBLhttp://hcls.sindice.com/chembl:ADMET
http://hcls.sindice.com/chembl:Binding
http://hcls.sindice.com/chembl:Functional
http://hcls.sindice.com/chembl:Property
http://hcls.sindice.com/chembl:Unassigned
+ show
PREFIX chembl: <http://hcls.sindice.com/chembl_vocabulary:>
SELECT DISTINCT(?o)
WHERE{
?assay a chembl:Assay ;
	chembl:assay_type ?o .
}

Gene Ontology Annotation Database

The Gene Ontology Annotation Database (GOA) is a database that revolves around proteins and associated Gene Ontology annotations. The Gene Ontology represents a resource for organizing vocabulary associated with a proteins molecular function, cellular location, and biological process. Annotation of proteins using the Gene Ontology vocabulary enables analysis of shared relationships between sets of genes/proteins based on their defined relations in the ontology.

Gene Ontology Annotation Database Statistics

MetricValueQuery
Number of Annotations in GOA----+ show
PREFIX goa: <http://hcls.sindice.com/goa_vocabulary:>
SELECT COUNT DISTINCT ?ae
WHERE{
	?ae a goa:Annotation_Entry .
}
Number of Genes in GOA----+ show
PREFIX goa: <http://hcls.sindice.com/goa_vocabulary:>
SELECT COUNT DISTINCT ?gene
WHERE{
	?gene a goa:Gene .
}
Number of Proteins in GOA----+ show
PREFIX goa: <http://hcls.sindice.com/goa_vocabulary:>
SELECT COUNT DISTINCT ?protein
WHERE{
	?protein a goa:Protein .
}
Number of Organisms in GOA----+ show
PREFIX goa: <http://hcls.sindice.com/goa_vocabulary:>
SELECT COUNT DISTINCT ?organism
WHERE{
	?organism a goa:Organism .
}

Online Mendelian Inheritance in Man (OMIM)

The OMIM database provides information linking genes, diseases, and phenotypes. This information has proved useful in uncovering novel linkages in the disease process.

Online Mendelian Inheritance in Man Database Statistics

MetricValueQuery
Number of Genes in OMIM----+ show
PREFIX omim: <http://hcls.sindice.com/omim_vocabulary:>
SELECT COUNT(DISTINCT(?o))
WHERE{
	?o a omim:Gene .
}
Number of Phenotypes in OMIM----+ show
PREFIX omim: <http://hcls.sindice.com/omim_vocabulary:>
SELECT COUNT(DISTINCT(?o))
WHERE{
	?o a omim:Phenotype .
}

Comparative Toxicogenomics Database (CTD)

The CTD is a database providing linkages between chemical, gene, disease, and pathway information and targets. Each annotation is manually curated by a documented curation process. The goal to aid the investigation into the etiology of disease by understanding the interactions between environmental factors and genes responsible for modulating physiological process.

Comparative Toxicogenomics Database Statistics

MetricValueQuery
Unique Chemicals in CTD----+ show
PREFIX ctd: <http://hcls.sindice.com/ctd_vocabulary:>
SELECT COUNT(DISTINCT(?chemical)) 
WHERE{
	?chemical a ctd:Chemical .
}
Unique genes in CTD----+ show
PREFIX ctd: <http://hcls.sindice.com/ctd_vocabulary:>
SELECT COUNT(DISTINCT(?gene)) 
WHERE{
	?gene a ctd:Gene .
}
Unique diseases in CTD----+ show
PREFIX ctd: <http://hcls.sindice.com/ctd_vocabulary:>
SELECT COUNT(DISTINCT(?disease)) 
WHERE{
	?disease a ctd:Disease .
}
Unique pathways in CTD----+ show
PREFIX ctd: <http://hcls.sindice.com/ctd_vocabulary:>
SELECT COUNT(DISTINCT(?pathway)) 
WHERE{
	?pathway a ctd:Biochemical_Pathway .
}
Unique chemical-disease relationships in CTD----+ show
PREFIX ctd: <http://hcls.sindice.com/ctd_vocabulary:>
SELECT COUNT(DISTINCT(?chem_disease)) 
WHERE{
	?chem_disease a ctd:Chemical_Disease_Association .
}
Unique Chemical Gene Interactions in CTD----+ show
PREFIX ctd: <http://hcls.sindice.com/ctd_vocabulary:>
SELECT COUNT(DISTINCT(?chem_gene_inxs)) 
WHERE{
	?chem_gene_inxs a ctd:Chemical_Gene_Interaction .
}
Unique Organisms in CTD----+ show
PREFIX ctd: <http://hcls.sindice.com/ctd_vocabulary:>
SELECT COUNT(DISTINCT(?taxon)) 
WHERE{
	?taxon a ctd:Organism .
}

Side Effects Resource Database (SIDER)

SIDER contains information related to marketed medicines and the frequencies of side effects experienced.

SIDER Database Statistics

MetricValueQuery
Unique drugs (chemicals) in SIDER----+ show
PREFIX sider: <http://hcls.sindice.com/sider_vocabulary:>
SELECT COUNT DISTINCT ?chemical
WHERE{
	?chemical a sider:Drug .
}
Unique side effects in SIDER----+ show
PREFIX sider: <http://hcls.sindice.com/sider_vocabulary:>
SELECT COUNT DISTINCT ?side_effect
WHERE{
	?side_effect a sider:Side_Effect .
}

Cross dataset statistics

MetricValueQuery
Overlap of chemicals between CTD and ChEMBL (based on chembl2mesh mapping file)----+ show
PREFIX ctd: <http://hcls.sindice.com/ctd_vocabulary:>
PREFIX chembl: <http://hcls.sindice.com/chembl_vocabulary:>
SELECT COUNT DISTINCT ?ctd
WHERE{
	?ctd a ctd:Chemical ;
		owl:equivalentClass ?chembl . 
	?chembl a chembl:Compound .
}
Overlap of chemicals between SIDER and CTD (based on sider2mesh mapping file)----+ show
PREFIX ctd: <http://hcls.sindice.com/ctd_vocabulary:>
PREFIX chembl: <http://hcls.sindice.com/chembl_vocabulary:>
PREFIX sider: <http://hcls.sindice.com/sider_vocabulary:>
SELECT COUNT DISTINCT ?sider
WHERE{
	?sider a sider:Drug;
		owl:equivalentClass ?mesh .
	?mesh a ctd:Chemical .
}