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For the high level class, we originally grouped our data into 5 categories: chemical, biological, chemogenomics, systems, and phenotype. In order to make it more decent, we’d like to have the following class instead: (SmallMolecule, MacroMolecule, BioAssay, Pathway, Disease, SideEffect, Interaction, and Literature)




















Diagram:

chem2bio2owl1.JPG

Classes

SmallMolecule:

Definition: A small bioactive molecule. It includes the compounds of biological interest, the compounds tested in the BioAssay, drugs, metabolites and peptides
Comments: We use the definition in biopax, but include peptides. As we consider all the compounds in PubChem, which may have peptides.
Synonyms: Compound, Chemical
Instance examples: http://chem2bio2rdf.org/pubchem/resource/pubchem_compound/10555
Referred databases: PubChem, ChEBI
Popular Identifiers: CID, ChEBI, CAS
Subclasses: Drug
Data Properties:
......name
......formula
.....synonyms

.....fingerprint: use MACCS 166 public fingerprint

Object Properties:
......Compound hasNeighbor Compound
......Compound hasInteraction ChemicalGeneInteraction
......Compound hasReference Literature
......Compound hasBioAssay BioAssay
......Compound causeDisease Disease

......Compound hasPhysicalProperty PhysicalProperty
......Compound hasStructure ChemicalStructure

Drug:

Definition: A substance that modifies a biological process (from pharmagenomics ontology). A chemical substance used in the treatment, cure, prevention, or diagnosis of disease or used to otherwise enhance physical or mental well-being. (from wiki)
Comments: refer to DrugBank. It does not include the drugs that are combinatorial drugs consisting of multiple compounds.Many ontologies set the relation between compound and drug as Ingredient, however, here, drug is a part of compounds, and the properties inherit from compound
Synonyms:
Instance examples: http://chem2bio2rdf.org/drugbank/resource/drugbank_drug/DB00039
Referred Database: DrugBank, TTD, PharmGKB
Popular Identifiers: DBID
Data Properties:
......Inherited from SmallMolecule
......drugType: (approved, small molecule, experimental…)
......description: usage in drugbank
......brandNames
......indication
......pharmacology
......mechanismOfAction
Object Properties:
......Drug hasDrugDrugInteraction Drug
......Drug causeSideEffect SideEffect
......Drug treatDisease Disease
......Drug hasReference Reference

MacroMolecule:

Definition: gene and its gene expression product
Comments: we use a very broad definition of MacroMolecule due to the nature of the its instances. The definition of gene in biopax(A continuant that encodes information that can be inherited through replication. This is an eneralization of the prokaryotic and eukaryotic notion of a gene. This is used only for genetic interactions. Gene expression regulation makes use of DNA and RNA physical entities.) Here, we not only include gene but also its gene expression products (e.g., protein, mRNA). Since chemogenomics is often talking about the interactions between chemical and protein. In general, it’s assumed that the proteins expressed from the same gene have very similar binding activity, so we often use compound XXX interacts with XXX (gene symbol) in literature and other places. We cover pharmagenomics and toxigenomics as well, which have the data that describes compound interacting gene indirectly. Thus lots of biological information is ignored here. In addition, we also refer marcomolecule as possible drug targets, although there is a very complicated definition of drug target (refer to Drug target central by Lee Harland). Since target property and function might be different among species, and our databases (e.g., HGNC, Tissue expression) refer to human, we only consider macromolecule expressed in human.
Synonyms: Gene, Protein, Target, Enzyme, BiologicalMacromolecules
Instance examples: http://chem2bio2rdf.org/uniprot/resource/gene/AHI1
Related Databases: UNIPROT, HGNC, PDB
Popular Identifiers: GI, UNIPROT ID, GENE Symbol, EC Number, PDB ID
Data Properties:
......name:
......type (gene, protein, mRNA, peptide)
......sequence:
......organism
......synonyms
......identifier
......description
...... tissue
...... gene family

Object Properties:
......Gene hasInteraction ChemicalGeneInteraction
......Gene hasNeighbor Gene(or hasInteraction)
......Gene hasPathway Pathway
......Gene hasBioAssay BioAssay
......Gene causeDisease Disease
......Gene isPartOf GO
......Gene hasReference Literature

Subclasses:


Disease:

Definition: any condition that causes pain, dysfunction, distress, social problems, and/or death to the person afflicted, or similar problems for those in contact with the person(from wiki)
Comments: refer to OMIM
Synonyms: Disorder
Instance examples: http://chem2bio2rdf.org/omim/resource/omim_disease
Related Databases: OMIM, CTD Disease, PharmGKB disease
Popular Identifiers: OMIM, MESH term
Data Properties:
......name
......disorderClass
Object Properties:
......Disease treatedBy Drug
......Disease causedByChemical Disease (environmental toxicity)
......Disease causedByGene Gene
......Disease hasReference Reference

SideEffect:

Definition: undesired effect from a medicine
Comments: refer to SIDER, it does not need to be harmful.
Synonyms: AdverseEffect, DrugAdverseReaction
Instance examples: http://chem2bio2rdf.org/sider/resource/sider/C0000768
Related Databases: SIDER
Popular Identifiers: umls_id
Data Properties:
......name
Object Properties:
......SideEffect causedBy Drug
......SideEffect hasReference Reference

Pathway:

Definition: A set or series of interactions, often forming a network, which biologists have found useful to group together for organizational, historic, biophysical or other reasons.(from Biopax)
Comments: different organizations have different definitions of pathway.
Synonyms: Network
Instance examples: http://chem2bio2rdf.org/kegg/resource/kegg_pathway/hsa00052
Related Databases: KEGG, Reactome
Popular Identifiers: KEGG ID,
Data Properties:
......name
......description
Object Properties:
......Pathway pathwayOf Gene

Literature:

Definition: a scientific article
Comments: refer to PubMed
Synonyms: Paper
Instance examples: http://chem2bio2rdf.org/medline/resource/medline/12309849
Related Databases: Medline
Popular Identifiers: PMID
Data Properties:
......title
......abstract
......author
......issn
......year
......journalName
Object Properties:
......Literature isReferenceFor Compound
......Literature isReferenceFor Drug
......Literature isReferenceFor Gene
......Literature isReferenceFor Pathway
......Literature isReferenceFor SideEffect
......Literature isReferenceFor Disease
......Literature isReferenceFor BioAssay
......Literature isReferenceFor DrugDrugInteraction
......Literature isReferenceFor ProteinProteinInteraction
......Literature isReferenceFor ChemicalGeneInteraction

BioAssay:

Definition: A scientific experiment to measure the effects of some substance on target, cell, or a living organism (wiki)
Comments: refer to BioAssay Ontology project. Should be further carefully defined. Since we are focusing on the binding assay which has particular targets and provides outcomes (i.e, IC50, EC50). Need to think whether should set functional assay, ADMET, and binding Assay as data properties or subclasses.
Synonyms:
Instance examples: http://chem2bio2rdf.org/chembl/resource/chembl_assays/14
http://chem2bio2rdf.org/pubchem/resource/pubchem_bioassay_interaction/1002
Related Databases: PubChem BioAssay, ChEMBL Bioassay
Popular Identifiers: BioAssay ID
Data Properties:
......name
......description
......type (functional, ADMET, binding)
......organism


Object Properties:
......BioAssay hasCompound Compound
......BioAssay hasGene Gene
......BioAssay hasInteraction Chemogenomics (only positive interaction considered, ie. IC50<30um)
......BioAssay hasReference Literature
......BioAssay hasOutcome Outcome

Interaction:

Definition: A single biological relationship between two or more entities. An interaction cannot be defined without the entities it relates.(from biopax)
Comment: Since it is a highly abstract class in the ontology, instances of the interaction class should never be created. Instead, more specific classes should be used. Biological relationship does not limit to physical interaction. Drug drug interaction, for instance, should be one of the interactions.
Subclasses:
DrugDrugInteraction
ProteinProteinInteraction
ChemicalGeneInteraction

DrugDrugInteraction:

Definition: A drug interaction is a situation in which a substance affects the activity of a drug, i.e. the effects are increased or decreased, or they produce a new effect that neither produces on its own.(from wiki)
Comments: Also consider combinatorial drugs, which shows polypharmacology
Instance examples: http://chem2bio2rdf.org/dcdb/resource/dcdb_drug_interaction/DI00001
Related Databases: DCDB, DrugBank
Popular Identifiers:
Data Properties:
......actionType
......pharmacalClassification
......description
Object Properties:
...... DrugDrugInteraction hasPart Drug
...... DrugDrugInteraction hasReference Reference

ProteinProteinInteraction:

Definition: two or more proteins bind together, often to carry out their biological function
Comments: consider protein protein or protein DNA interaction. Cover yeast 2-hybrid data
Instance examples:
Related Databases: HPRD
Popular Identifiers:
Data Properties:
...... experimentType (in vitro, in vivo, yeast 2-hybrid)
Object Properties:
...... ProteinProteinInteraction hasPart Gene
...... ProteinProteinInteraction hasReference Reference

ChemicalGeneInteraction:

Definition: a biological relationship between compound and gene.
Comments: it covers all types of relationships between compound and gene. Roughly we divide into three classes, which are somewhat overlapped. Not well defined.
Subclasses:
Chemogenomics
Pharmagenomics
Toxicogenomics


Data Properties:
......biologicalInterst: (whether it is of biological interest, in general, it refers to the compound is active against that target)
......primary target
......interaction type:


Chemogenomics:
Definition: the genomic responses to chemical compounds (from wiki)
Comments: In general, it describe the physical interaction between compound and gene (or gene expression products), it always have binding affinity values. In addition, we consider drug target interaction as chemogenomics, although sometimes, the drug is not really interacting with the target.
Synonyms: DrugTarget
Instance examples: http://chem2bio2rdf.org/bindingdb/resource/bindingdb_interaction/12
Related Databases: DrugBank, TTD, BindingMOAD, BindingDB, ChEMBL, PubChem BioAssay, Kidb, QSAR, MATADOR
Popular Identifiers: NA
......sources: (see related databases)
Object Properties:
......Chemogenomics hasCompound Compound
......Chemogenomics hasGene GENE
......Chemogenomics hasBioAssay BioAssay
......Chemogenomics hasReference Reference

Pharmagenomics:
Definition: influence of genetic variation on drug response in patients by correlating gene expression or single-nucleotide polymorphisms (from wiki)
Comments: it emphasizes on genetic variation upon drug response
Synonyms:
Instance examples: http://chem2bio2rdf.org/pharmgkb/resource/pharmgkb_pharmagenomics/10631CYP3A54016
Related Databases: PharmGKB
Popular Identifiers: NA
Data Properties:
......CategoriesOfEvidence
Object Properties:
......Pharmagenomics hasDrug Drug
......Pharmagenomics hasGene GENE
......Pharmagenomics hasReference Reference

Toxicogenomics:
Definition: gene and protein activity within particular cell or tissue of an organism in response to toxic substances
Comments: it might overlap with chemogenomics, but it focuses on the long term environmental factors. It does not limit to the physical binding between chemical and protein/gene
Synonyms:
Instance examples:
Related Databases: CTD
Popular Identifiers:
Data Properties:
......interaction (description)
......interactiontypes (78 types in CTD)
......organism
Object Properties:
......Toxicogenomics hasCompound Compound
......Toxicogenomics hasGene GENE
......Toxicogenomics hasReference Reference

UtilityClass:

Definition: Utility classes are created when simple slots are insufficient to describe an aspect of an entity or to increase compatibility of this ontology with other standards. The utilityClass class is actually a metaclass and is only present to organize the other helper classes under one class hierarchy;
Comments: It refers to BioPAX, aiming to deal with the hierarchical class, for example: SmallMolecule has PhysicalProperties that include ALOGP, weight and so on. The instances of subclasses might have members but they often go along with other main classes.
Subclasses:
ExternalSource
ChemicalStructure
PhysicalProperty
Outcome

ExternalSource
Definition: External identifiers as well as their resources
Comments: Often, refers to Chem2Bio2RDF datasets
Data Properties:
......identifier
......identifierType

ChemicalStructure

Definition: Describes a small molecule structure
Comments: refer to BioPAX
Data Properties:

......structureData:
......structureFormat: {"InChi", "openeyeCanonicalSMILES", "openeyeISOSMILES"}

PhysicalProperty

Definition: Chemical physical property
Comments:
Data Properties:

.......molecularWeight
.......alogP
.......hBondDonor: H-Bond Donor
.......hBondAcceptor:
.......rotatableBondCount:
.......topologicalPolarSurfaceArea


Outcome

Definition: the results of one assay experiment
Comments:
Data Properties:

.......measurement:( Ki, Kd, IC50, EC50)
.......value
.......unit (nm, um)
.......operator (>,>=,<, <=, =)



Properties:

Objects:

hasNeighbor:
characteristic: transitive;symmetric
Description: Domains (SmallMolecule); Ranges (SmallMolecules)
comments: A neighbor of a chemical is another chemical with a certain structural similarity. Here, we defined Tanimoto coefficient >0.95 using MACCS as fingerprint

hasReference
characteristic:
Description: Domains(SmallMolecule, Disease, SideEffect, BioAssay, MacroMolecule, DrugDrugInteraction, ProteinProteinInteraction, ChemicalGeneInteraction) ; Ranges(Literature), inverse (isReferenceOf)
comments:

isReferenceOf
characteristic:
Description: Domains(Literature) ; Ranges(SmallMolecule, Disease,SideEffect, BioAssay, MacroMolecule, DrugDrugInteraction, ProteinProteinInteraction, ChemicalGeneInteraction), inverse (hasReference)
comments:

hasBioAssay
characteristic:
Description: Domain(SmallMolecule;MacroMolecule, ChemicalGeneInteraction) ; Ranges (BioAssay); inverse (hasCompound, hasTarget, hasInteraction)
comments:

hasCompound
characteristic:
Description: Domain (BioAssay, ChemicalGeneInteraction); Ranges (SmallMolecule); inverse (hasBioAssay,hasInteraction)
comments:

hasInteraction
characteristic:
Description: Domain (SmallMolecule); Ranges (ChemicalGeneInteraction); inverse (hasCompound)
comments:

causeSideEffect
characteristic:
Description: Domain (Drug); Ranges (SideEffect); inverse (causedByDrug)
comments:

causedByDrug
characteristic:
Description: Domain (SideEffect); Ranges (Drug); inverse (causeSideEffect)
comments:

treatDisease
characteristic:
Description: Domain (Drug); Ranges (Disease); inverse(treatedByDrug)
comments:

treatedByDrug
characteristic:
Description: Domain (Disease); Ranges (Drug); inverse (treatDisease)
comments:

causeDisease
characteristic:
Description: Domain (Drug, MacroMolecule); Ranges (Disease); inverse (causedByChemical, causedByGene)
comments:

causedByChemical
characteristic:
Description: Domain (Disease); Ranges (SmallMolecule); inverse (causeDisease)
comments:

causedByGene
characteristic:
Description: Domain (Disease); Ranges (MacroMolecule); inverse (causedDisease)
comments:

hasDrugDrugInteraction
characteristic:
Description: Domain (Drug); Ranges (DrugDrugInteraction); inverse (hasPart)
comments:

hasPart
characteristic:
Description: Domain (DrugDrugInteraction, ProteinProteinInteraction); Ranges (Drug, MacroMolecule); inverse (hasDrugDrugInteraction,hasNeighbor)
comments:

hasTarget
characteristic:
Description: Domain (BioAssay, ChemicalGeneInteraction); Ranges (MacroMolecule); inverse (hasBioAssay, hasChemicalGeneInteraction)
comments:

hasPathway
characteristic:
Description: Domain (MacroMolecule); Ranges (Pathway); inverse(isPathwayOf)
comments:

isPathwayOf
characteristic:
Description: Domain (Pathway); Ranges (hasPathway); inverse(hasPathway)
comments:

hasProteinProteinInteraction
characteristic:
Description: Domain (MacroMolecule); Ranges (hasProteinProteinInteraction); inverse (hasPart)
comments:

hasChemicalGeneInteraction
characteristic:
Description: Domain (MacroMolecule, BioAssay); Ranges (ChemicalGeneInteraction); inverse (hasTarget, hasBioAssay)
comments:


Data Properties:


Individuals: