Version+1.0

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 * Version 1.0**

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)toc

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//: [] //Referred databases//: PubChem, ChEBI //Popular Identifiers//: CID, ChEBI, CAS //Subclasses//: Drug //Data Properties//:  ......name ......formula ..... <span class="wiki_link_ext">synonyms

<span style="font-family: 'Times New Roman','serif'; font-size: 12pt; line-height: 115%; margin: 0in 0in 0pt; text-indent: 0.5in;">..... <span style="font-family: 'Arial','sans-serif'; font-size: 9.5pt; line-height: 115%; margin: 0in 0in 0pt; text-indent: 0.5in;">fingerprint: use MACCS 166 public fingerprint

//<span style="font-family: 'Times New Roman','serif'; font-size: 12pt; line-height: 115%; margin: 0in 0in 0pt;">Object Properties: // <span style="font-family: 'Times New Roman','serif'; font-size: 12pt; line-height: 115%; margin: 0in 0in 0pt; text-indent: 0.5in;">......Compound hasNeighbor Compound <span style="font-family: 'Times New Roman','serif'; font-size: 12pt; line-height: 115%; margin: 0in 0in 0pt; text-indent: 0.5in;">......Compound hasInteraction ChemicalGeneInteraction <span style="font-family: 'Times New Roman','serif'; font-size: 12pt; line-height: 115%; margin: 0in 0in 0pt; text-indent: 0.5in;">......Compound hasReference Literature __<span style="font-family: 'Times New Roman','serif'; font-size: 12pt; line-height: 115%; margin: 0in 0in 0pt; text-indent: 0.5in;">......Compound hasBioAssay BioAssay __ <span style="font-family: 'Times New Roman','serif'; font-size: 12pt; line-height: 115%; margin: 0in 0in 0pt; text-indent: 0.5in;">......Compound causeDisease Disease

<span style="font-family: 'Times New Roman',serif; font-size: 16px; line-height: 18px;">......Compound hasPhysicalProperty PhysicalProperty <span style="font-family: 'Times New Roman',serif; font-size: 16px; line-height: 18px;">......Compound hasStructure ChemicalStructure

<span style="font-family: 'Times New Roman','serif'; font-size: 12pt; line-height: 115%; margin: 0in 0in 0pt;">Drug:
<span style="font-family: 'Times New Roman','serif'; font-size: 12pt; line-height: 115%;">//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) <span style="font-family: 'Times New Roman','serif'; font-size: 12pt; line-height: 115%; margin: 0in 0in 0pt;">//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 <span style="font-family: 'Times New Roman','serif'; font-size: 12pt; line-height: 115%; margin: 0in 0in 0pt;">Synonyms: <span style="font-family: 'Times New Roman','serif'; font-size: 12pt; line-height: 115%;">//Instance examples//: <span style="color: #666666; font-family: 'Arial','sans-serif'; font-size: 7.5pt; line-height: 115%;"> http://chem2bio2rdf.org/drugbank/resource/drugbank_drug/DB00039 <span style="font-family: 'Times New Roman','serif'; font-size: 12pt; line-height: 115%; margin: 0in 0in 0pt;">//Referred Database//: DrugBank, TTD, PharmGKB <span style="font-family: 'Times New Roman','serif'; font-size: 12pt; line-height: 115%; margin: 0in 0in 0pt;">//Popular Identifiers//: DBID <span style="font-family: 'Times New Roman','serif'; font-size: 12pt; line-height: 115%; margin: 0in 0in 0pt;">//Data Properties//: <span style="font-family: 'Times New Roman','serif'; font-size: 12pt; line-height: 115%; margin: 0in 0in 0pt; text-indent: 0.5in;">......Inherited from SmallMolecule <span style="font-family: 'Times New Roman','serif'; font-size: 12pt; line-height: 115%; margin: 0in 0in 0pt; text-indent: 0.5in;">...... <span style="font-family: 'Times New Roman','serif'; font-size: 12pt; line-height: 115%; margin: 0in 0in 0pt;">drugType: (approved, small molecule, experimental…) <span style="font-family: 'Times New Roman','serif'; font-size: 12pt; line-height: 115%; margin: 0in 0in 0pt; text-indent: 0.5in;">...... <span style="font-family: 'Times New Roman','serif'; font-size: 12pt; line-height: 115%; margin: 0in 0in 0pt;">description: usage in drugbank <span style="font-family: 'Times New Roman','serif'; font-size: 12pt; line-height: 115%; margin: 0in 0in 0pt;">......brandNames <span style="font-family: 'Times New Roman','serif'; font-size: 12pt; line-height: 115%; margin: 0in 0in 0pt;"> ......indication <span style="font-family: 'Times New Roman','serif'; font-size: 12pt; line-height: 115%; margin: 0in 0in 0pt;"> ......pharmacology <span style="font-family: 'Times New Roman','serif'; font-size: 12pt; line-height: 115%; margin: 0in 0in 0pt;"> ......mechanismOfAction //<span style="font-family: 'Times New Roman','serif'; font-size: 12pt; line-height: 115%; margin: 0in 0in 0pt;">Object Properties: // <span style="font-family: 'Times New Roman','serif'; font-size: 12pt; line-height: 115%; margin: 0in 0in 0pt; text-indent: 0.5in;">......Drug hasDrugDrugInteraction Drug <span style="font-family: 'Times New Roman','serif'; font-size: 12pt; line-height: 115%; margin: 0in 0in 0pt; text-indent: 0.5in;">......Drug causeSideEffect SideEffect <span style="font-family: 'Times New Roman','serif'; font-size: 12pt; line-height: 115%; margin: 0in 0in 0pt; text-indent: 0.5in;">......Drug treatDisease Disease <span style="font-family: 'Times New Roman','serif'; font-size: 12pt; line-height: 115%; margin: 0in 0in 0pt; text-indent: 0.5in;">......Drug hasReference Reference

<span style="font-family: 'Times New Roman','serif'; font-size: 12pt; line-height: 115%; margin: 0in 0in 0pt;">MacroMolecule:
<span style="font-family: 'Times New Roman','serif'; font-size: 12pt; line-height: 115%; margin: 0in 0in 0pt;">//Definition//: gene and its gene expression product <span style="font-family: 'Times New Roman','serif'; font-size: 12pt; line-height: 115%; margin: 0in 0in 0pt;">//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. <span style="font-family: 'Times New Roman','serif'; font-size: 12pt; line-height: 115%; margin: 0in 0in 0pt;">//Synonyms//: Gene, Protein, Target, Enzyme, BiologicalMacromolecules <span style="font-family: 'Times New Roman','serif'; font-size: 12pt; line-height: 115%;">//Instance examples//: <span style="color: #666666; font-family: 'Arial','sans-serif'; font-size: 7.5pt; line-height: 115%;">http://chem2bio2rdf.org/uniprot/resource/gene/AHI1 <span style="font-family: 'Times New Roman','serif'; font-size: 12pt; line-height: 115%; margin: 0in 0in 0pt;">//Related Databases//: UNIPROT, HGNC, PDB <span style="font-family: 'Times New Roman','serif'; font-size: 12pt; line-height: 115%; margin: 0in 0in 0pt;">//Popular Identifiers//: GI, UNIPROT ID, GENE Symbol, EC Number, PDB ID //<span style="font-family: 'Times New Roman','serif'; font-size: 12pt; line-height: 115%; margin: 0in 0in 0pt;">Data Properties: // <span style="font-family: 'Times New Roman','serif'; font-size: 12pt; line-height: 115%; margin: 0in 0in 0pt; text-indent: 0.5in;">...... <span style="font-family: 'Times New Roman','serif'; font-size: 12pt; line-height: 115%; margin: 0in 0in 0pt;">name: <span style="font-family: 'Times New Roman','serif'; font-size: 12pt; line-height: 115%; margin: 0in 0in 0pt; text-indent: 0.5in;">...... <span style="font-family: 'Times New Roman','serif'; font-size: 12pt; line-height: 115%; margin: 0in 0in 0pt;">type (gene, protein, mRNA, peptide) <span style="font-family: 'Times New Roman','serif'; font-size: 12pt; line-height: 115%; margin: 0in 0in 0pt; text-indent: 0.5in;">...... <span style="font-family: 'Times New Roman','serif'; font-size: 12pt; line-height: 115%; margin: 0in 0in 0pt;">sequence: <span style="font-family: 'Times New Roman','serif'; font-size: 12pt; line-height: 115%; margin: 0in 0in 0pt; text-indent: 0.5in;"><span class="wiki_link_ext">...... <span style="font-family: 'Arial','sans-serif'; font-size: 9.5pt; line-height: 115%; margin: 0in 0in 0pt;"><span class="wiki_link_ext">organism <span style="font-family: 'Times New Roman','serif'; font-size: 12pt; line-height: 115%; margin: 0in 0in 0pt; text-indent: 0.5in;"><span class="wiki_link_ext">...... <span style="font-family: 'Arial','sans-serif'; font-size: 9.5pt; line-height: 115%; margin: 0in 0in 0pt;"><span class="wiki_link_ext">synonyms <span style="font-family: 'Times New Roman','serif'; font-size: 12pt; line-height: 115%; margin: 0in 0in 0pt; text-indent: 0.5in;">...... <span style="font-family: 'Arial','sans-serif'; font-size: 9.5pt; line-height: 115%; margin: 0in 0in 0pt;">identifier <span style="font-family: 'Times New Roman','serif'; font-size: 12pt; line-height: 115%; margin: 0in 0in 0pt; text-indent: 0.5in;">...... <span style="font-family: 'Times New Roman','serif'; font-size: 12pt; line-height: 115%; margin: 0in 0in 0pt;">description <span style="font-family: 'Times New Roman',serif; font-size: 16px; line-height: 18px;">...... tissue <span style="font-family: 'Times New Roman',serif; font-size: 16px; line-height: 18px;">...... gene family

//<span style="font-family: 'Times New Roman','serif'; font-size: 12pt; line-height: 115%; margin: 0in 0in 0pt;">Object Properties: // <span style="font-family: 'Times New Roman','serif'; font-size: 12pt; line-height: 115%; margin: 0in 0in 0pt; text-indent: 0.5in;">......Gene hasInteraction ChemicalGeneInteraction <span style="font-family: 'Times New Roman','serif'; font-size: 12pt; line-height: 115%; margin: 0in 0in 0pt; text-indent: 0.5in;">......Gene hasNeighbor Gene(or hasInteraction) <span style="font-family: 'Times New Roman','serif'; font-size: 12pt; line-height: 115%; margin: 0in 0in 0pt; text-indent: 0.5in;">......Gene hasPathway Pathway __<span style="font-family: 'Times New Roman','serif'; font-size: 12pt; line-height: 115%; margin: 0in 0in 0pt; text-indent: 0.5in;">......Gene hasBioAssay BioAssay __ <span style="font-family: 'Times New Roman','serif'; font-size: 12pt; line-height: 115%; margin: 0in 0in 0pt; text-indent: 0.5in;">......Gene causeDisease Disease <span style="font-family: 'Times New Roman',serif; font-size: 16px; line-height: 18px;">......__Gene isPartOf GO__ <span style="font-family: 'Times New Roman','serif'; font-size: 12pt; line-height: 115%; margin: 0in 0in 0pt; text-indent: 0.5in;">...... <span style="font-family: 'Times New Roman','serif'; font-size: 12pt; line-height: 115%; margin: 0in 0in 0pt;">Gene hasReference Literature

//Subclasses//:

<span style="font-family: 'Times New Roman','serif'; font-size: 12pt; line-height: 115%; margin: 0in 0in 0pt;">Disease:
<span style="font-family: 'Times New Roman','serif'; font-size: 12pt; line-height: 115%; margin: 0in 0in 0pt;">//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) <span style="font-family: 'Times New Roman','serif'; font-size: 12pt; line-height: 115%; margin: 0in 0in 0pt;">//Comments//: refer to OMIM <span style="font-family: 'Times New Roman','serif'; font-size: 12pt; line-height: 115%; margin: 0in 0in 0pt;">//Synonyms//: Disorder <span style="font-family: 'Times New Roman','serif'; font-size: 12pt; line-height: 115%;">//Instance examples//: <span style="color: #666666; font-family: 'Arial','sans-serif'; font-size: 7.5pt; line-height: 115%;">http://chem2bio2rdf.org/omim/resource/omim_disease <span style="font-family: 'Times New Roman','serif'; font-size: 12pt; line-height: 115%; margin: 0in 0in 0pt;">//Related Databases//: OMIM, CTD Disease, PharmGKB disease <span style="font-family: 'Times New Roman','serif'; font-size: 12pt; line-height: 115%; margin: 0in 0in 0pt;">//Popular Identifiers//: OMIM, MESH term //<span style="font-family: 'Times New Roman','serif'; font-size: 12pt; line-height: 115%; margin: 0in 0in 0pt;">Data Properties: // <span style="font-family: 'Times New Roman','serif'; font-size: 12pt; line-height: 115%; margin: 0in 0in 0pt; text-indent: 0.5in;">...... <span style="font-family: 'Times New Roman','serif'; font-size: 12pt; line-height: 115%; margin: 0in 0in 0pt;">name <span style="font-family: 'Times New Roman','serif'; font-size: 12pt; line-height: 115%; margin: 0in 0in 0pt; text-indent: 0.5in;">...... <span style="font-family: 'Times New Roman','serif'; font-size: 12pt; line-height: 115%; margin: 0in 0in 0pt;">disorderClass //<span style="font-family: 'Times New Roman','serif'; font-size: 12pt; line-height: 115%; margin: 0in 0in 0pt;">Object Properties: // <span style="font-family: 'Times New Roman','serif'; font-size: 12pt; line-height: 115%; margin: 0in 0in 0pt; text-indent: 0.5in;">...... <span style="font-family: 'Times New Roman','serif'; font-size: 12pt; line-height: 115%; margin: 0in 0in 0pt;">Disease treatedBy Drug <span style="font-family: 'Times New Roman','serif'; font-size: 12pt; line-height: 115%; margin: 0in 0in 0pt; text-indent: 0.5in;">...... <span style="font-family: 'Times New Roman','serif'; font-size: 12pt; line-height: 115%; margin: 0in 0in 0pt;">Disease causedByChemical Disease (environmental toxicity) <span style="font-family: 'Times New Roman','serif'; font-size: 12pt; line-height: 115%; margin: 0in 0in 0pt; text-indent: 0.5in;">...... <span style="font-family: 'Times New Roman','serif'; font-size: 12pt; line-height: 115%; margin: 0in 0in 0pt;">Disease causedByGene Gene <span style="font-family: 'Times New Roman','serif'; font-size: 12pt; line-height: 115%; margin: 0in 0in 0pt; text-indent: 0.5in;">...... <span style="font-family: 'Times New Roman','serif'; font-size: 12pt; line-height: 115%; margin: 0in 0in 0pt;">Disease hasReference Reference

<span style="font-family: 'Times New Roman','serif'; font-size: 12pt; line-height: 115%; margin: 0in 0in 0pt;">SideEffect:
<span style="font-family: 'Times New Roman','serif'; font-size: 12pt; line-height: 115%; margin: 0in 0in 0pt;">//Definition//: undesired effect from a medicine <span style="font-family: 'Times New Roman','serif'; font-size: 12pt; line-height: 115%; margin: 0in 0in 0pt;">//Comments//: refer to SIDER, it does not need to be harmful. <span style="font-family: 'Times New Roman','serif'; font-size: 12pt; line-height: 115%; margin: 0in 0in 0pt;">//Synonyms//: AdverseEffect, DrugAdverseReaction <span style="font-family: 'Times New Roman','serif'; font-size: 12pt; line-height: 115%;">//Instance examples//: <span style="color: #666666; font-family: 'Arial','sans-serif'; font-size: 7.5pt; line-height: 115%;">http://chem2bio2rdf.org/sider/resource/sider/C0000768 <span style="font-family: 'Times New Roman','serif'; font-size: 12pt; line-height: 115%; margin: 0in 0in 0pt;">//Related Databases//: SIDER <span style="font-family: 'Times New Roman','serif'; font-size: 12pt; line-height: 115%;">//Popular Identifiers//: <span style="font-family: 'Arial','sans-serif'; font-size: 9.5pt; line-height: 115%;"><span class="wiki_link_ext">umls_id //<span style="font-family: 'Times New Roman','serif'; font-size: 12pt; line-height: 115%; margin: 0in 0in 0pt;">Data Properties: // <span style="font-family: 'Times New Roman','serif'; font-size: 12pt; line-height: 115%; margin: 0in 0in 0pt; text-indent: 0.5in;">...... <span style="font-family: 'Times New Roman','serif'; font-size: 12pt; line-height: 115%; margin: 0in 0in 0pt;">name //<span style="font-family: 'Times New Roman','serif'; font-size: 12pt; line-height: 115%; margin: 0in 0in 0pt;">Object Properties: // <span style="font-family: 'Times New Roman','serif'; font-size: 12pt; line-height: 115%; margin: 0in 0in 0pt; text-indent: 0.5in;">...... <span style="font-family: 'Times New Roman','serif'; font-size: 12pt; line-height: 115%; margin: 0in 0in 0pt;">SideEffect causedBy Drug <span style="font-family: 'Times New Roman','serif'; font-size: 12pt; line-height: 115%; margin: 0in 0in 0pt; text-indent: 0.5in;">...... <span style="font-family: 'Times New Roman','serif'; font-size: 12pt; line-height: 115%; margin: 0in 0in 0pt;">SideEffect hasReference Reference

<span style="font-family: 'Times New Roman','serif'; font-size: 12pt; line-height: 115%; margin: 0in 0in 0pt;">Pathway:
<span style="font-family: 'Times New Roman','serif'; font-size: 12pt; line-height: 115%; margin: 0in 0in 0pt;">//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) <span style="font-family: 'Times New Roman','serif'; font-size: 12pt; line-height: 115%; margin: 0in 0in 0pt;">//Comments//: different organizations have different definitions of pathway. <span style="font-family: 'Times New Roman','serif'; font-size: 12pt; line-height: 115%; margin: 0in 0in 0pt;">//Synonyms//: Network <span style="font-family: 'Times New Roman','serif'; font-size: 12pt; line-height: 115%;">//Instance examples//: <span style="color: #666666; font-family: 'Arial','sans-serif'; font-size: 7.5pt; line-height: 115%;"> http://chem2bio2rdf.org/kegg/resource/kegg_pathway/hsa00052 <span style="font-family: 'Times New Roman','serif'; font-size: 12pt; line-height: 115%; margin: 0in 0in 0pt;">//Related Databases//: KEGG, Reactome <span style="font-family: 'Times New Roman','serif'; font-size: 12pt; line-height: 115%; margin: 0in 0in 0pt;">//Popular Identifiers//: KEGG ID, //<span style="font-family: 'Times New Roman','serif'; font-size: 12pt; line-height: 115%; margin: 0in 0in 0pt;">Data Properties: // <span style="font-family: 'Times New Roman','serif'; font-size: 12pt; line-height: 115%; margin: 0in 0in 0pt; text-indent: 0.5in;">...... <span style="font-family: 'Times New Roman','serif'; font-size: 12pt; line-height: 115%; margin: 0in 0in 0pt;">name <span style="font-family: 'Times New Roman','serif'; font-size: 12pt; line-height: 115%; margin: 0in 0in 0pt; text-indent: 0.5in;">...... <span style="font-family: 'Times New Roman','serif'; font-size: 12pt; line-height: 115%; margin: 0in 0in 0pt;">description //<span style="font-family: 'Times New Roman','serif'; font-size: 12pt; line-height: 115%; margin: 0in 0in 0pt;">Object Properties: // <span style="font-family: 'Times New Roman','serif'; font-size: 12pt; line-height: 115%; margin: 0in 0in 0pt; text-indent: 0.5in;">...... <span style="font-family: 'Times New Roman','serif'; font-size: 12pt; line-height: 115%; margin: 0in 0in 0pt;">Pathway pathwayOf Gene

<span style="font-family: 'Times New Roman','serif'; font-size: 12pt; line-height: 115%; margin: 0in 0in 0pt;">Literature:
<span style="font-family: 'Times New Roman','serif'; font-size: 12pt; line-height: 115%; margin: 0in 0in 0pt;">//Definition//: a scientific article <span style="font-family: 'Times New Roman','serif'; font-size: 12pt; line-height: 115%; margin: 0in 0in 0pt;">//Comments//: refer to PubMed <span style="font-family: 'Times New Roman','serif'; font-size: 12pt; line-height: 115%; margin: 0in 0in 0pt;">//Synonyms//: Paper //<span style="font-family: 'Times New Roman','serif'; font-size: 12pt; line-height: 115%;">Instance examples: //<span style="color: #666666; font-family: 'Arial','sans-serif'; font-size: 7.5pt; line-height: 115%;">http://chem2bio2rdf.org/medline/resource/medline/12309849 <span style="font-family: 'Times New Roman','serif'; font-size: 12pt; line-height: 115%; margin: 0in 0in 0pt;">//Related Databases//: Medline <span style="font-family: 'Times New Roman','serif'; font-size: 12pt; line-height: 115%; margin: 0in 0in 0pt;">//Popular Identifiers//: PMID //<span style="font-family: 'Times New Roman','serif'; font-size: 12pt; line-height: 115%; margin: 0in 0in 0pt;">Data Properties: // <span style="font-family: 'Times New Roman','serif'; font-size: 12pt; line-height: 115%; margin: 0in 0in 0pt; text-indent: 0.5in;">...... <span style="font-family: 'Times New Roman','serif'; font-size: 12pt; line-height: 115%; margin: 0in 0in 0pt;">title <span style="font-family: 'Times New Roman','serif'; font-size: 12pt; line-height: 115%; margin: 0in 0in 0pt; text-indent: 0.5in;">...... <span style="font-family: 'Times New Roman','serif'; font-size: 12pt; line-height: 115%; margin: 0in 0in 0pt;">abstract <span style="font-family: 'Times New Roman','serif'; font-size: 12pt; line-height: 115%; margin: 0in 0in 0pt; text-indent: 0.5in;">...... <span style="font-family: 'Times New Roman','serif'; font-size: 12pt; line-height: 115%; margin: 0in 0in 0pt;">author <span style="font-family: 'Times New Roman','serif'; font-size: 12pt; line-height: 115%; margin: 0in 0in 0pt; text-indent: 0.5in;">...... <span style="font-family: 'Times New Roman','serif'; font-size: 12pt; line-height: 115%; margin: 0in 0in 0pt;">issn <span style="font-family: 'Times New Roman','serif'; font-size: 12pt; line-height: 115%; margin: 0in 0in 0pt; text-indent: 0.5in;">...... <span style="font-family: 'Times New Roman','serif'; font-size: 12pt; line-height: 115%; margin: 0in 0in 0pt;">year <span style="font-family: 'Times New Roman','serif'; font-size: 12pt; line-height: 115%; margin: 0in 0in 0pt; text-indent: 0.5in;">...... <span style="font-family: 'Times New Roman','serif'; font-size: 12pt; line-height: 115%; margin: 0in 0in 0pt;">journalName //<span style="font-family: 'Times New Roman','serif'; font-size: 12pt; line-height: 115%; margin: 0in 0in 0pt;">Object Properties: // <span style="font-family: 'Times New Roman','serif'; font-size: 12pt; line-height: 115%; margin: 0in 0in 0pt; text-indent: 0.5in;">...... <span style="font-family: 'Times New Roman','serif'; font-size: 12pt; line-height: 115%; margin: 0in 0in 0pt;">Literature isReferenceFor Compound <span style="font-family: 'Times New Roman','serif'; font-size: 12pt; line-height: 115%; margin: 0in 0in 0pt; text-indent: 0.5in;">...... <span style="font-family: 'Times New Roman','serif'; font-size: 12pt; line-height: 115%; margin: 0in 0in 0pt;">Literature isReferenceFor Drug <span style="font-family: 'Times New Roman','serif'; font-size: 12pt; line-height: 115%; margin: 0in 0in 0pt; text-indent: 0.5in;">...... <span style="font-family: 'Times New Roman','serif'; font-size: 12pt; line-height: 115%; margin: 0in 0in 0pt;">Literature isReferenceFor Gene <span style="font-family: 'Times New Roman','serif'; font-size: 12pt; line-height: 115%; margin: 0in 0in 0pt; text-indent: 0.5in;">...... <span style="font-family: 'Times New Roman','serif'; font-size: 12pt; line-height: 115%; margin: 0in 0in 0pt;">Literature isReferenceFor Pathway <span style="font-family: 'Times New Roman','serif'; font-size: 12pt; line-height: 115%; margin: 0in 0in 0pt; text-indent: 0.5in;">...... <span style="font-family: 'Times New Roman','serif'; font-size: 12pt; line-height: 115%; margin: 0in 0in 0pt;">Literature isReferenceFor SideEffect <span style="font-family: 'Times New Roman','serif'; font-size: 12pt; line-height: 115%; margin: 0in 0in 0pt; text-indent: 0.5in;">...... <span style="font-family: 'Times New Roman','serif'; font-size: 12pt; line-height: 115%; margin: 0in 0in 0pt;">Literature isReferenceFor Disease <span style="font-family: 'Times New Roman','serif'; font-size: 12pt; line-height: 115%; margin: 0in 0in 0pt; text-indent: 0.5in;">...... <span style="font-family: 'Times New Roman','serif'; font-size: 12pt; line-height: 115%; margin: 0in 0in 0pt;">Literature isReferenceFor BioAssay <span style="font-family: 'Times New Roman','serif'; font-size: 12pt; line-height: 115%; margin: 0in 0in 0pt; text-indent: 0.5in;">...... <span style="font-family: 'Times New Roman','serif'; font-size: 12pt; line-height: 115%; margin: 0in 0in 0pt;">Literature isReferenceFor DrugDrugInteraction <span style="font-family: 'Times New Roman','serif'; font-size: 12pt; line-height: 115%; margin: 0in 0in 0pt; text-indent: 0.5in;">...... <span style="font-family: 'Times New Roman','serif'; font-size: 12pt; line-height: 115%; margin: 0in 0in 0pt;">Literature isReferenceFor ProteinProteinInteraction <span style="font-family: 'Times New Roman','serif'; font-size: 12pt; line-height: 115%; margin: 0in 0in 0pt; text-indent: 0.5in;">...... <span style="font-family: 'Times New Roman','serif'; font-size: 12pt; line-height: 115%; margin: 0in 0in 0pt;">Literature isReferenceFor ChemicalGeneInteraction

<span style="font-family: 'Times New Roman','serif'; font-size: 12pt; line-height: 115%; margin: 0in 0in 0pt;">BioAssay:
<span style="font-family: 'Times New Roman','serif'; font-size: 12pt; line-height: 115%; margin: 0in 0in 0pt;">//Definition//: A scientific experiment to measure the effects of some substance on target, cell, or a living organism (wiki) <span style="font-family: 'Times New Roman','serif'; font-size: 12pt; line-height: 115%; margin: 0in 0in 0pt;">//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. <span style="font-family: 'Times New Roman','serif'; font-size: 12pt; line-height: 115%; margin: 0in 0in 0pt;">//Synonyms//: <span style="font-family: 'Times New Roman','serif'; font-size: 12pt; line-height: 115%;">//Instance examples//: <span style="color: #666666; font-family: 'Arial','sans-serif'; font-size: 7.5pt; line-height: 115%;">[] <span style="color: #666666; font-family: 'Arial','sans-serif'; font-size: 7.5pt; line-height: 115%; margin: 0in 0in 0pt;">http://chem2bio2rdf.org/pubchem/resource/pubchem_bioassay_interaction/1002 <span style="font-family: 'Times New Roman','serif'; font-size: 12pt; line-height: 115%; margin: 0in 0in 0pt;">//Related Databases//: PubChem BioAssay, ChEMBL Bioassay <span style="font-family: 'Times New Roman','serif'; font-size: 12pt; line-height: 115%; margin: 0in 0in 0pt;">//Popular Identifiers:// BioAssay ID //<span style="font-family: 'Times New Roman','serif'; font-size: 12pt; line-height: 115%; margin: 0in 0in 0pt;">Data Properties: // <span style="font-family: 'Times New Roman','serif'; font-size: 12pt; line-height: 115%; margin: 0in 0in 0pt; text-indent: 0.5in;">...... <span style="font-family: 'Times New Roman','serif'; font-size: 12pt; line-height: 115%; margin: 0in 0in 0pt;">name <span style="font-family: 'Times New Roman','serif'; font-size: 12pt; line-height: 115%; margin: 0in 0in 0pt; text-indent: 0.5in;">...... <span style="font-family: 'Times New Roman','serif'; font-size: 12pt; line-height: 115%; margin: 0in 0in 0pt;">description <span style="font-family: 'Times New Roman','serif'; font-size: 12pt; line-height: 115%; margin: 0in 0in 0pt; text-indent: 0.5in;">...... <span style="font-family: 'Times New Roman','serif'; font-size: 12pt; line-height: 115%; margin: 0in 0in 0pt;">type (functional, ADMET, binding) <span style="font-family: 'Times New Roman',serif; font-size: 16px; line-height: 18px;">......organism

//<span style="font-family: 'Times New Roman','serif'; font-size: 12pt; line-height: 115%; margin: 0in 0in 0pt;">Object Properties: // <span style="font-family: 'Times New Roman','serif'; font-size: 12pt; line-height: 115%; margin: 0in 0in 0pt; text-indent: 0.5in;">...... <span style="font-family: 'Times New Roman','serif'; font-size: 12pt; line-height: 115%; margin: 0in 0in 0pt;">BioAssay hasCompound Compound <span style="font-family: 'Times New Roman','serif'; font-size: 12pt; line-height: 115%; margin: 0in 0in 0pt; text-indent: 0.5in;">...... <span style="font-family: 'Times New Roman','serif'; font-size: 12pt; line-height: 115%; margin: 0in 0in 0pt;">BioAssay hasGene Gene <span style="font-family: 'Times New Roman','serif'; font-size: 12pt; line-height: 115%; margin: 0in 0in 0pt; text-indent: 0.5in;">...... <span style="font-family: 'Times New Roman','serif'; font-size: 12pt; line-height: 115%; margin: 0in 0in 0pt;">BioAssay hasInteraction Chemogenomics (only positive interaction considered, ie. IC50<30um) <span style="font-family: 'Times New Roman','serif'; font-size: 12pt; line-height: 115%; margin: 0in 0in 0pt; text-indent: 0.5in;">...... <span style="font-family: 'Times New Roman','serif'; font-size: 12pt; line-height: 115%; margin: 0in 0in 0pt;">BioAssay hasReference Literature <span style="font-family: 'Times New Roman',serif; font-size: 12pt; line-height: 18px; margin-bottom: 0pt; margin-left: 0in; margin-right: 0in; margin-top: 0in; text-indent: 0.5in;">...... <span style="font-family: 'Times New Roman',serif; font-size: 12pt; line-height: 18px; margin-bottom: 0pt; margin-left: 0in; margin-right: 0in; margin-top: 0in;">BioAssay hasOutcome Outcome

<span style="font-family: 'Times New Roman','serif'; font-size: 12pt; line-height: 115%; margin: 0in 0in 0pt;">Interaction:
<span style="font-family: 'Times New Roman','serif'; font-size: 12pt; line-height: 115%; margin: 0in 0in 0pt;">//Definition//: A single biological relationship between two or more entities. An interaction cannot be defined without the entities it relates.(from biopax) <span style="font-family: 'Times New Roman','serif'; font-size: 12pt; line-height: 115%; margin: 0in 0in 0pt;">//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. <span style="font-family: 'Times New Roman','serif'; font-size: 12pt; line-height: 115%; margin: 0in 0in 0pt;">//Subclasses//: <span style="font-family: 'Times New Roman','serif'; font-size: 12pt; line-height: 115%; margin: 0in 0in 0pt;"> DrugDrugInteraction <span style="font-family: 'Times New Roman','serif'; font-size: 12pt; line-height: 115%; margin: 0in 0in 0pt;"> ProteinProteinInteraction <span style="font-family: 'Times New Roman','serif'; font-size: 12pt; line-height: 115%; margin: 0in 0in 0pt;">ChemicalGeneInteraction

DrugDrugInteraction:
<span style="font-family: 'Times New Roman','serif'; font-size: 12pt; line-height: 115%; margin: 0in 0in 0pt;">//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) <span style="font-family: 'Times New Roman','serif'; font-size: 12pt; line-height: 115%; margin: 0in 0in 0pt;">//Comments:// Also consider combinatorial drugs, which shows polypharmacology //<span style="font-family: 'Times New Roman','serif'; font-size: 12pt; line-height: 115%;">Instance examples: // http://chem2bio2rdf.org/dcdb/resource/dcdb_drug_interaction/DI00001 <span style="font-family: 'Times New Roman','serif'; font-size: 12pt; line-height: 115%; margin: 0in 0in 0pt;">//Related Databases//: DCDB, DrugBank <span style="font-family: 'Times New Roman','serif'; font-size: 12pt; line-height: 115%; margin: 0in 0in 0pt;">//Popular Identifiers//: //<span style="font-family: 'Times New Roman','serif'; font-size: 12pt; line-height: 115%; margin: 0in 0in 0pt;">Data Properties: // <span style="font-family: 'Times New Roman','serif'; font-size: 12pt; line-height: 115%; margin: 0in 0in 0pt; text-indent: 0.5in;">......actionType <span style="font-family: 'Times New Roman','serif'; font-size: 12pt; line-height: 115%; margin: 0in 0in 0pt; text-indent: 0.5in;">......pharmacalClassification <span style="font-family: 'Times New Roman','serif'; font-size: 12pt; line-height: 115%; margin: 0in 0in 0pt; text-indent: 0.5in;">...... description //<span style="font-family: 'Times New Roman','serif'; font-size: 12pt; line-height: 115%; margin: 0in 0in 0pt;">Object Properties: // <span style="font-family: 'Times New Roman','serif'; font-size: 12pt; line-height: 115%; margin: 0in 0in 0pt; text-indent: 0.5in;">...... DrugDrugInteraction hasPart Drug <span style="font-family: 'Times New Roman','serif'; font-size: 12pt; line-height: 115%; margin: 0in 0in 0pt; text-indent: 0.5in;">...... DrugDrugInteraction hasReference Reference

ProteinProteinInteraction:
<span style="font-family: 'Times New Roman','serif'; font-size: 12pt; line-height: 115%; margin: 0in 0in 0pt;">//Definition:// two or more proteins bind together, often to carry out their biological function <span style="font-family: 'Times New Roman','serif'; font-size: 12pt; line-height: 115%; margin: 0in 0in 0pt;">//Comments:// consider protein protein or protein DNA interaction. Cover yeast 2-hybrid data //<span style="font-family: 'Times New Roman','serif'; font-size: 12pt; line-height: 115%;">Instance examples: // <span style="font-family: 'Times New Roman','serif'; font-size: 12pt; line-height: 115%; margin: 0in 0in 0pt;">//Related Databases//: HPRD <span style="font-family: 'Times New Roman','serif'; font-size: 12pt; line-height: 115%; margin: 0in 0in 0pt;">//Popular Identifiers//: //<span style="font-family: 'Times New Roman','serif'; font-size: 12pt; line-height: 115%; margin: 0in 0in 0pt;">Data Properties: // <span style="font-family: 'Times New Roman','serif'; font-size: 12pt; line-height: 115%; margin: 0in 0in 0pt; text-indent: 0.5in;">...... <span style="font-family: 'Times New Roman','serif'; font-size: 12pt; line-height: 115%; margin: 0in 0in 0pt;">experimentType //(in vitro, in vivo, yeast 2-hybrid)// //<span style="font-family: 'Times New Roman','serif'; font-size: 12pt; line-height: 115%; margin: 0in 0in 0pt;">Object Properties: // <span style="font-family: 'Times New Roman','serif'; font-size: 12pt; line-height: 115%; margin: 0in 0in 0pt; text-indent: 0.5in;">...... ProteinProteinInteraction hasPart Gene <span style="font-family: 'Times New Roman','serif'; font-size: 12pt; line-height: 115%; margin: 0in 0in 0pt; text-indent: 0.5in;">...... ProteinProteinInteraction hasReference Reference

<span style="font-family: 'Times New Roman','serif'; font-size: 12pt; line-height: 115%; margin: 0in 0in 0pt;">__ChemicalGeneInteraction:__
<span style="font-family: 'Times New Roman','serif'; font-size: 12pt; line-height: 115%; margin: 0in 0in 0pt;">//Definition//: a biological relationship between compound and gene. <span style="font-family: 'Times New Roman','serif'; font-size: 12pt; line-height: 115%; margin: 0in 0in 0pt;">//Comments//: it covers all types of relationships between compound and gene. Roughly we divide into three classes, which are somewhat overlapped. Not well defined. <span style="font-family: 'Times New Roman','serif'; font-size: 12pt; line-height: 115%; margin: 0in 0in 0pt;">//Subclasses//: <span style="font-family: 'Times New Roman','serif'; font-size: 12pt; line-height: 115%; margin: 0in 0in 0pt;"> Chemogenomics <span style="font-family: 'Times New Roman','serif'; font-size: 12pt; line-height: 115%; margin: 0in 0in 0pt;"> Pharmagenomics <span style="font-family: 'Times New Roman','serif'; font-size: 12pt; line-height: 115%; margin: 0in 0in 0pt;"> Toxicogenomics

//<span style="font-family: 'Times New Roman',serif; font-size: 12pt; line-height: 18px; margin-bottom: 0pt; margin-left: 0in; margin-right: 0in; margin-top: 0in;">Data Properties: // <span style="font-family: 'Times New Roman',serif; font-size: 12pt; line-height: 18px; margin-bottom: 0pt; margin-left: 0in; margin-right: 0in; margin-top: 0in; text-indent: 0.5in;">...... <span style="font-family: 'Times New Roman',serif; font-size: 12pt; line-height: 18px; margin-bottom: 0pt; margin-left: 0in; margin-right: 0in; margin-top: 0in;">biologicalInterst: (whether it is of biological interest, in general, it refers to the compound is active against that target) <span style="font-family: 'Times New Roman',serif; font-size: 12pt; line-height: 18px; margin-bottom: 0pt; margin-left: 0in; margin-right: 0in; margin-top: 0in; padding-bottom: 0px; padding-left: 0px; padding-right: 0px; padding-top: 0px;">......primary target <span style="font-family: 'Times New Roman',serif; font-size: 12pt; line-height: 18px; margin-bottom: 0pt; margin-left: 0in; margin-right: 0in; margin-top: 0in; padding-bottom: 0px; padding-left: 0px; padding-right: 0px; padding-top: 0px;">......interaction type:

<span style="font-family: 'Times New Roman','serif'; font-size: 12pt; line-height: 115%; margin: 0in 0in 0pt;">Chemogenomics: <span style="font-family: 'Times New Roman','serif'; font-size: 12pt; line-height: 115%; margin: 0in 0in 0pt;">//Definition//: the genomic responses to chemical compounds (from wiki) <span style="font-family: 'Times New Roman','serif'; font-size: 12pt; line-height: 115%; margin: 0in 0in 0pt;">//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. <span style="font-family: 'Times New Roman','serif'; font-size: 12pt; line-height: 115%; margin: 0in 0in 0pt;">Synonyms: DrugTarget //<span style="font-family: 'Times New Roman','serif'; font-size: 12pt; line-height: 115%;">Instance examples: //<span style="color: #666666; font-family: 'Arial','sans-serif'; font-size: 7.5pt; line-height: 115%;">http://chem2bio2rdf.org/bindingdb/resource/bindingdb_interaction/12 <span style="font-family: 'Times New Roman','serif'; font-size: 12pt; line-height: 115%; margin: 0in 0in 0pt;">//Related Databases//: DrugBank, TTD, BindingMOAD, BindingDB, ChEMBL, PubChem BioAssay, Kidb, QSAR, MATADOR <span style="font-family: 'Times New Roman','serif'; font-size: 12pt; line-height: 115%; margin: 0in 0in 0pt;">//Popular Identifiers//: NA <span style="font-family: 'Times New Roman','serif'; font-size: 12pt; line-height: 115%; margin: 0in 0in 0pt; text-indent: 0.5in;">...... <span style="font-family: 'Times New Roman','serif'; font-size: 12pt; line-height: 115%; margin: 0in 0in 0pt;">sources: (see related databases) //<span style="font-family: 'Times New Roman','serif'; font-size: 12pt; line-height: 115%; margin: 0in 0in 0pt;">Object Properties: // <span style="font-family: 'Times New Roman','serif'; font-size: 12pt; line-height: 115%; margin: 0in 0in 0pt; text-indent: 0.5in;">...... <span style="font-family: 'Times New Roman','serif'; font-size: 12pt; line-height: 115%; margin: 0in 0in 0pt;">Chemogenomics hasCompound Compound <span style="font-family: 'Times New Roman','serif'; font-size: 12pt; line-height: 115%; margin: 0in 0in 0pt; text-indent: 0.5in;">...... <span style="font-family: 'Times New Roman','serif'; font-size: 12pt; line-height: 115%; margin: 0in 0in 0pt;">Chemogenomics hasGene GENE <span style="font-family: 'Times New Roman','serif'; font-size: 12pt; line-height: 115%; margin: 0in 0in 0pt; text-indent: 0.5in;">...... <span style="font-family: 'Times New Roman','serif'; font-size: 12pt; line-height: 115%; margin: 0in 0in 0pt;">Chemogenomics hasBioAssay BioAssay <span style="font-family: 'Times New Roman','serif'; font-size: 12pt; line-height: 115%; margin: 0in 0in 0pt; text-indent: 0.5in;">...... <span style="font-family: 'Times New Roman','serif'; font-size: 12pt; line-height: 115%; margin: 0in 0in 0pt;">Chemogenomics hasReference Reference

<span style="font-family: 'Times New Roman','serif'; font-size: 12pt; line-height: 115%; margin: 0in 0in 0pt;">Pharmagenomics: <span style="font-family: 'Times New Roman','serif'; font-size: 12pt; line-height: 115%; margin: 0in 0in 0pt;">//Definition//: influence of genetic variation on drug response in patients by correlating gene expression or single-nucleotide polymorphisms (from wiki) <span style="font-family: 'Times New Roman','serif'; font-size: 12pt; line-height: 115%; margin: 0in 0in 0pt;">//Comments//: it emphasizes on genetic variation upon drug response <span style="font-family: 'Times New Roman','serif'; font-size: 12pt; line-height: 115%; margin: 0in 0in 0pt;">//Synonyms//: <span style="font-family: 'Times New Roman','serif'; font-size: 12pt; line-height: 115%;">//Instance examples//: <span style="color: #666666; font-family: 'Arial','sans-serif'; font-size: 7.5pt; line-height: 115%;">http://chem2bio2rdf.org/pharmgkb/resource/pharmgkb_pharmagenomics/10631CYP3A54016 <span style="font-family: 'Times New Roman','serif'; font-size: 12pt; line-height: 115%; margin: 0in 0in 0pt;">//Related Databases:// PharmGKB <span style="font-family: 'Times New Roman','serif'; font-size: 12pt; line-height: 115%; margin: 0in 0in 0pt;">//Popular Identifiers:// NA //<span style="font-family: 'Times New Roman','serif'; font-size: 12pt; line-height: 115%; margin: 0in 0in 0pt;">Data Properties: // <span style="font-family: 'Times New Roman','serif'; font-size: 12pt; line-height: 115%; margin: 0in 0in 0pt; text-indent: 0.5in;">...... //<span style="font-family: 'Times New Roman','serif'; font-size: 12pt; line-height: 115%; margin: 0in 0in 0pt;">CategoriesOfEvidence // //<span style="font-family: 'Times New Roman','serif'; font-size: 12pt; line-height: 115%; margin: 0in 0in 0pt;">Object Properties: // <span style="font-family: 'Times New Roman','serif'; font-size: 12pt; line-height: 115%; margin: 0in 0in 0pt; text-indent: 0.5in;">...... <span style="font-family: 'Times New Roman','serif'; font-size: 12pt; line-height: 115%; margin: 0in 0in 0pt;">Pharmagenomics hasDrug Drug <span style="font-family: 'Times New Roman','serif'; font-size: 12pt; line-height: 115%; margin: 0in 0in 0pt; text-indent: 0.5in;">...... <span style="font-family: 'Times New Roman','serif'; font-size: 12pt; line-height: 115%; margin: 0in 0in 0pt;">Pharmagenomics hasGene GENE <span style="font-family: 'Times New Roman','serif'; font-size: 12pt; line-height: 115%; margin: 0in 0in 0pt; text-indent: 0.5in;">...... <span style="font-family: 'Times New Roman','serif'; font-size: 12pt; line-height: 115%; margin: 0in 0in 0pt;">Pharmagenomics hasReference Reference

<span style="font-family: 'Times New Roman','serif'; font-size: 12pt; line-height: 115%; margin: 0in 0in 0pt;">Toxicogenomics: <span style="font-family: 'Times New Roman','serif'; font-size: 12pt; line-height: 115%; margin: 0in 0in 0pt;">//Definition//: gene and protein activity within particular cell or tissue of an organism in response to toxic substances <span style="font-family: 'Times New Roman','serif'; font-size: 12pt; line-height: 115%; margin: 0in 0in 0pt;">//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 <span style="font-family: 'Times New Roman','serif'; font-size: 12pt; line-height: 115%; margin: 0in 0in 0pt;">//Synonyms//: //<span style="font-family: 'Times New Roman','serif'; font-size: 12pt; line-height: 115%; margin: 0in 0in 0pt;">Instance examples: // <span style="font-family: 'Times New Roman','serif'; font-size: 12pt; line-height: 115%; margin: 0in 0in 0pt;">//Related Databases//: CTD <span style="font-family: 'Times New Roman','serif'; font-size: 12pt; line-height: 115%; margin: 0in 0in 0pt;">//Popular Identifiers//: //<span style="font-family: 'Times New Roman','serif'; font-size: 12pt; line-height: 115%; margin: 0in 0in 0pt;">Data Properties: // <span style="font-family: 'Times New Roman','serif'; font-size: 12pt; line-height: 115%; margin: 0in 0in 0pt; text-indent: 0.5in;">...... <span style="font-family: 'Times New Roman','serif'; font-size: 12pt; line-height: 115%; margin: 0in 0in 0pt;">interaction (description) <span style="font-family: 'Times New Roman','serif'; font-size: 12pt; line-height: 115%; margin: 0in 0in 0pt; text-indent: 0.5in;">...... <span style="font-family: 'Times New Roman','serif'; font-size: 12pt; line-height: 115%; margin: 0in 0in 0pt;">interactiontypes (78 types in CTD) <span style="font-family: 'Times New Roman','serif'; font-size: 12pt; line-height: 115%; margin: 0in 0in 0pt; text-indent: 0.5in;">...... <span style="font-family: 'Times New Roman','serif'; font-size: 12pt; line-height: 115%; margin: 0in 0in 0pt;">organism //<span style="font-family: 'Times New Roman','serif'; font-size: 12pt; line-height: 115%; margin: 0in 0in 0pt;">Object Properties: // <span style="font-family: 'Times New Roman','serif'; font-size: 12pt; line-height: 115%; margin: 0in 0in 0pt; text-indent: 0.5in;">...... <span style="font-family: 'Times New Roman','serif'; font-size: 12pt; line-height: 115%; margin: 0in 0in 0pt;">Toxicogenomics hasCompound Compound <span style="font-family: 'Times New Roman','serif'; font-size: 12pt; line-height: 115%; margin: 0in 0in 0pt; text-indent: 0.5in;">...... <span style="font-family: 'Times New Roman','serif'; font-size: 12pt; line-height: 115%; margin: 0in 0in 0pt;">Toxicogenomics hasGene GENE <span style="font-family: 'Times New Roman','serif'; font-size: 12pt; line-height: 115%; margin: 0in 0in 0pt; text-indent: 0.5in;">...... <span style="font-family: 'Times New Roman','serif'; font-size: 12pt; line-height: 115%; margin: 0in 0in 0pt;">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; //<span style="font-family: 'Times New Roman',serif;">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. <span style="font-family: 'Times New Roman',serif; font-size: 16px; line-height: 18px;">//Subclasses:// ExternalSource ChemicalStructure PhysicalProperty Outcome

ExternalSource //<span style="font-family: 'Times New Roman',serif;">Definition: // External identifiers as well as their resources <span style="font-family: 'Times New Roman',serif; font-size: 16px; line-height: 18px;"> Comments: Often, refers to Chem2Bio2RDF datasets <span style="font-family: 'Times New Roman',serif; font-size: 12pt; line-height: 18px; margin-bottom: 0pt; margin-left: 0in; margin-right: 0in; margin-top: 0in;"> Data Properties: <span style="font-family: 'Times New Roman',serif; font-size: 16px; line-height: 18px;"> ......identifier <span style="font-family: 'Times New Roman',serif; font-size: 16px; line-height: 18px;">......identifierType

ChemicalStructure

<span style="font-family: 'Times New Roman',serif; font-size: 16px; line-height: 18px; margin: 0px; padding: 0px;">//Definition:// Describes a small molecule structure <span style="font-family: 'Times New Roman',serif; font-size: 16px; line-height: 18px;"> Comments: refer to BioPAX <span style="font-family: 'Times New Roman',serif; font-size: 12pt; line-height: 18px; margin-bottom: 0pt; margin-left: 0in; margin-right: 0in; margin-top: 0in; padding: 0px;"> Data Properties:

<span style="font-family: 'Times New Roman',serif; font-size: 16px; line-height: 18px;">......structureData: <span style="font-family: 'Times New Roman',serif; font-size: 16px; line-height: 18px;">......structureFormat: {"InChi", "openeyeCanonicalSMILES", "openeyeISOSMILES"}

PhysicalProperty

//<span style="font-family: 'Times New Roman',serif;">Definition: //Chemical physical property <span style="font-family: 'Times New Roman',serif; font-size: 16px; line-height: 18px; margin: 0px; padding: 0px;"> Comments: <span style="font-family: 'Times New Roman',serif; font-size: 12pt; line-height: 18px; margin-bottom: 0pt; margin-left: 0in; margin-right: 0in; margin-top: 0in; padding: 0px;"> Data Properties:

<span style="font-family: 'Times New Roman',serif; font-size: 12pt; line-height: 18px; margin-bottom: 0pt; margin-left: 0in; margin-right: 0in; margin-top: 0in; text-indent: 0.5in;">....... <span style="font-family: Arial,sans-serif; font-size: 9.5pt; line-height: 14px; margin-bottom: 0pt; margin-left: 0in; margin-right: 0in; margin-top: 0in;">molecularWeight <span style="font-family: 'Times New Roman',serif; font-size: 12pt; line-height: 18px; margin-bottom: 0pt; margin-left: 0in; margin-right: 0in; margin-top: 0in; text-indent: 0.5in;">....... <span style="font-family: Arial,sans-serif; font-size: 9.5pt; line-height: 14px; margin-bottom: 0pt; margin-left: 0in; margin-right: 0in; margin-top: 0in;">alogP <span style="font-family: 'Times New Roman',serif; font-size: 12pt; line-height: 18px; margin-bottom: 0pt; margin-left: 0in; margin-right: 0in; margin-top: 0in; text-indent: 0.5in;">....... <span style="font-family: Arial,sans-serif; font-size: 9.5pt; line-height: 14px; margin-bottom: 0pt; margin-left: 0in; margin-right: 0in; margin-top: 0in;">hBondDonor: H-Bond Donor <span style="font-family: Arial,sans-serif; font-size: 9.5pt; line-height: 14px; margin-bottom: 0pt; margin-left: 0in; margin-right: 0in; margin-top: 0in; padding: 0px;">.......hBondAcceptor: <span style="font-family: Arial,sans-serif; font-size: 9.5pt; line-height: 14px; margin-bottom: 0pt; margin-left: 0in; margin-right: 0in; margin-top: 0in; padding: 0px;">.......rotatableBondCount: <span style="font-family: Arial,sans-serif; font-size: 9.5pt; line-height: 14px; margin-bottom: 0pt; margin-left: 0in; margin-right: 0in; margin-top: 0in; padding: 0px;">.......topologicalPolarSurfaceArea

Outcome

//<span style="font-family: 'Times New Roman',serif;">Definition: //the results of one assay experiment <span style="font-family: 'Times New Roman',serif; font-size: 16px; line-height: 18px; margin: 0px; padding: 0px;"> Comments: <span style="font-family: 'Times New Roman',serif; font-size: 12pt; line-height: 18px; margin-bottom: 0pt; margin-left: 0in; margin-right: 0in; margin-top: 0in; padding: 0px;"> Data Properties:

<span style="font-family: 'Times New Roman',serif; font-size: 12pt; line-height: 18px; margin-bottom: 0pt; margin-left: 0in; margin-right: 0in; margin-top: 0in; text-indent: 0.5in;">....... <span style="font-family: 'Times New Roman',serif; font-size: 12pt; line-height: 18px; margin-bottom: 0pt; margin-left: 0in; margin-right: 0in; margin-top: 0in;">measurement:( Ki, Kd, IC50, EC50) <span style="font-family: 'Times New Roman',serif; font-size: 12pt; line-height: 18px; margin-bottom: 0pt; margin-left: 0in; margin-right: 0in; margin-top: 0in; text-indent: 0.5in;">....... <span style="font-family: 'Times New Roman',serif; font-size: 12pt; line-height: 18px; margin-bottom: 0pt; margin-left: 0in; margin-right: 0in; margin-top: 0in;">value <span style="font-family: 'Times New Roman',serif; font-size: 12pt; line-height: 18px; margin-bottom: 0pt; margin-left: 0in; margin-right: 0in; margin-top: 0in; text-indent: 0.5in;">....... <span style="font-family: 'Times New Roman',serif; font-size: 12pt; line-height: 18px; margin-bottom: 0pt; margin-left: 0in; margin-right: 0in; margin-top: 0in;">unit (nm, um) <span style="font-family: 'Times New Roman',serif; font-size: 12pt; line-height: 18px; margin-bottom: 0pt; margin-left: 0in; margin-right: 0in; margin-top: 0in; text-indent: 0.5in;">....... <span style="font-family: 'Times New Roman',serif; font-size: 12pt; line-height: 18px; margin-bottom: 0pt; margin-left: 0in; margin-right: 0in; margin-top: 0in;">operator (>,>=,<, <=, =)

<span style="font-family: 'Times New Roman',serif; font-size: 16px; line-height: 18px;">**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//: