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SEM-DISNET

Release 2022-03-30

Contributors:
Andrea Álvarez Pérez (MEDAL)
Ana Iglesias Molina (OEG)
Lucía Prieto Santamaría (MEDAL)
Alejandro Rodríguez González (MEDAL)
Publisher:
Medical Data Analytics Laboratory (MEDAL): https://medal.ctb.upm.es/
Ontology Engineering Group (OEG): https://oeg.fi.upm.es/
Download serialization:
JSON-LD RDF/XML N-Triples TTL
License:
http://purl.org/NET/rdflicense/cc-by-nc-sa4.0
Provenance of this page
Ontology Specification Draft

Introduction back to ToC

SEM-DISNET ontology provides a integrated ontology used to describe the defined entities which appear in the DISNET database. It is an ontology aimed at facilitating the analysis of biomedical data, allowing the discovery of new patterns and associations between genes, drugs and their targets to be applied in cases of drug repositioning. This project has been carried out within the DISNET project of MEDAL Laboratory (Medical Data Analytics) at the CTB-UPM, together with DRUGS4COVID, developed by the OEG-UPM (Ontology Engineering Group).

Namespace declarations

Table 1: Namespaces used in the document
base<http://w3id.org/eboca/sem-disnet>
metadata<http://data.bioontology.org/metadata>
rdfs<http://www.w3.org/2000/01/rdf-schema>
rdf<http://www.w3.org/1999/02/22-rdf-syntax-ns>
skos<http://www.w3.org/2004/02/skos/core>
xsd<http://www.w3.org/2001/XMLSchema>
dc<http://purl.org/dc/elements/1.1>
dcterms<http://purl.org/dc/terms>
ncit<http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl>
sct<http://purl.bioontology.org/ontology/SNOMEDCT>
wp<http://vocabularies.wikipathways.org/wp>
sio<http://semanticscience.org/resource>
ordo<http://www.orpha.net/ORDO>
obo<http://purl.obolibrary.org/obo>
owl<http://www.w3.org/2002/07/owl>
cco<http://rdf.ebi.ac.uk/terms/chembl>
ctd<http://bio2rdf.org/ctd_vocabulary:>
oboInOwl<http://www.geneontology.org/formats/oboInOwl>
up_core<http://www.purl.uniprot.org/core/>
xml<http://www.w3.org/XML/1998/namespace>
bio2rdf<http://bio2rdf.org/bio2rdf_vocabulary:>
vann<http://purl.org/vocab/vann>
foaf<http://xmlns.com/foaf/0.1>
void<http://rdfs.org/ns/void>
EVS<http://ncicb.nci.nih.gov/xml/owl/EVS>
efo<http://www.ebi.ac.uk/efo>

SEM-DISNET: Overview back to ToC

This ontology has the following classes and properties.

Classes

Object Properties

Data Properties

SEM-DISNET: Description back to ToC

Figure 1 provides a general overview of SEM-DISNET Ontology. For the sake of clarity and understanding, the diagram was designed including in each of the boxes, the DISNET label (disnet:disnetLabel associated with each class, along with the class identifier (dcterms:identifier of the original ontology, including its namespace. For this reason, the following text will refer to the classes using these attributes, although all classes are by defect described by their original label (rdfs:label). This diagram follows the Chowlk notation.

General overview of the SEM-DISNET Ontology.
Figure 1 - SEM-DISNET schema for the representation of DISNET data.

SEM-DISNET Ontology is built mostly from the reuse of existing ontology concepts. Mainly, it is based on the ontology developed by DisGeNET (DisGeNET-RDF), one of the main sources used by DISNET. Other important reused concepts or Classes were taken from National Cancer Institute thesaurus (NCIT), Semanticscience Integrated Ontology (SIO), CHEMBL, SNOMED, Comparative Toxicogenomics Database (CTD), Orphanet Rare Disease Ontology (ORDO) and WikiPathways. It also reuses Object Propeties from NCIT and SIO ontologies.

The ontology schema is organized around the central classes Disease and Drug.

  • Disease class

    This class was taken from NCIT and represents a condition that is relevant to human neoplasms and non-neoplasms disorders. It is specified the Semantic Type (disgenet:UMLS Semantic Type), the Disease class it belongs (obo:Disease class) and the marker it can be associated with (ncit: Disease Marker), including the type of sample (disnet:sample) and the marker concentration (disnet: concentration). Disease references (sio:'is referred to by') to classes which represent relationships between concepts:

    • Association between a Disease and a ncRNA: although the association class was designed de novo by DISNET (disnet:Disease ncRNA Association), ncRNA class was taken from NCIT (ncit:ncRNA). Also, attributes as the ncRNA category, which refers to the classification according to HMDD (Human microRNA Disease Database) and LncRNADisease database (disnet:category), the ncRNA effect in the organism (disnet:type) and the causality (disnet:causality) are given.
    • Association between a Disease and rare diseases: this module was entirely reused from Orphanet database. In this case, Disease is directly related to rare disease class (ordo:Orpha), and the association class (ordo:Prevalence) associates the rare disease with its annual incidence (ordo:Prevalence class) specifying the geographical location (disnet:geo).
    • Association between a Disease and a Variant: the association (disnet:Variant Disease Association) has an associated score (sio:'has measurement value') defined by the ncit:Score class. Variants (obo:Variant) are resources defined by attributes such as chromosome number (ncit:Chromosome), position (ncit:Chromosome position) and other parameters (disgenet:Disease specificity and disgenet: Disease pleiotropy)
    • Association between a Disease and a Gene: the same way as with variants, the association is defined by a score (ncit:Score). Gene class (ncit:Gene) attributes embraces the corresponding symbol (ncit:Gene Symbol), the metabolic pathway(s) to which it belongs (wp:Pathway), class reused from WikiPathways, and other parameters (disgenet:Disease specificity and disgenet: Disease pleiotropy). Other properties attributed to Gene entity include the sequence (disnet:geneSequence), the strand (disnet:strand), sequence start (disnet:seqStart) and end (disnet:seqEnd) positions, and the chromosome version (disnet:chrVersion). Gene class encodes (sio:'encondes') certain Protein (ncit:Protein) whose sequence is present as an attribute (cco:proteinSequence) reused from ChEMBL ontology. Each protein also belongs to a class (obo:Protein class) and participates (sio:'is participant in') in protein-protein interactions (ncit:PPI). Furthermore, both Protein and Gene classes are present in Organisms (ncit:Organism), and either Organism and Protein are can act as a target (sio:'is target in', being related to Target class (cco:Target).
    • Association between a Disease and a Phenotype: this association and the related class Phenotype (disnet:Phenotype) have been modelled de novo, since no existing classes were found in other ontologies with the meaning corresponding to the one in DISNET database. The phenotype refers to the observable and detectable signs in a patient due to the effects caused by a Disease or a Drug causing changes in their original appearence. Therefore, this class is also connected to Drug class in more than one way (explained below). Phenotypes are also associated with a specific Semantic Type (disgenet:UMLS Semantic Type)

    • The association between both central classes, Disease and Drug was reused from the CTD, the main source from which the information stored in the DISNET database is obtained. However, this class has (owl:sameAs) an associated class in SIO (sio:'chemical-disease association'). In addition, this association has been modelled de novo with two subclasses emerging from it. Drug-disease pairs are classified into these subclasses depending on the effect the drug has on the disease. A chemical that correlates with a disease or may play a role in the etiology of a disease, acting as a marker of those diseases (disnet:Drug Disease Marker) or it can be used to treat the disease, having a known or potential therapeutic effect on it (disnet:Drug Disease Therapeutic). Additionally, the association is identified by an inferred score established by CTD-curated chemical-gene interactions (sio:'has value').

  • Drug class

    This class (cco:Drug) was reused from ChEMBL database and represents, according to the Chemical Entities of Biological Interest (ChEBI), any substance which when absorbed into a living organism may modify one or more of its functions. The information housed in DISNET was integrated from different sources, as DrugBank, RXCUI and DisGeNET. Other de novo properties associated with Drug concept include the chemical structure (disnet:chemicalStructure), the inchi Key (disnet:inchiKey) and synonymous names for the drugs (disnet:synonymous). The ATC classification (cco:atcClassification) and the substance (or molecular) type (cco:substanceType) attributes were taken from ChEML ontolgy. Moreover, it references (sio:'is referred to by') to classes which represent relationships between drugs and other entities:

    • Association between a Drug and a Target: this relationship (cco:Drug Target Association) is also known as the mechanism of action of the drug when it addresses to the Target (cco:Target), a molecule in the body, usually a protein, that is intrinsically associated with a particular disease to which is directed the drug. Target class has correspondence (owl:sameAs) with Drug Target Ontology (DTO) dto:drug target too, and its type is defined by ChEMBL attribute cco:targetType. Mechanism class data was taken from ChEMBL and DrugBank databases (skos:exactMatch) , corresponds with DTO dto:drug target role class (owl:sameAs) and is defined by the attribute cco:mechanismActionType which belongs to ChEMBL ontology.
    • Association between a Drug and a Phenotype: the relationship between a drug and a phenotype can be defined according to several criteria. For this reason, both classes (cco:Drug and disnet:Phenotype) are connected by three association classes, each of them refering to a possible causality of the interaction between a drug and a phenotype:

      • Drug Phenotype Indication: indication is the term for the approved uses of a medication. In other words, indicates the relationship of the desirable measurable effects that cause changes in a patient's phenotype and the response to treatment with a drug which is indicated to treat them. This relationship (cco:Drug Phenotype Indication) can be classified due to the highest development phase at which that indication has been investigated (cco:highestDevelopmentPhase).
      • Drug Phenotype Side Effect: describes the association between symptoms considered as adverse effects that cause patient phenotype changes in response to the treatment with a drug. This class was resued from SNOMED CT database (sct:Drug Phenotype Side Effect) although the data stored in DISNET database is integrated from SIDER, and also includes the highest development phase ChEMBL attribute (cco:highestDevelopmentPhase). In this case, the Object Properties which relate this association class with Drug and Phenotype were created de novo and classified as subproperties of the original ones taken from ChEMBL and the main SIO properties (sio:'refers to' and sio:'is referred to by') that are used all over the ontology. This approach is specified in the boxes above the diagram, so highlighted Object Properties are subproperties of SIO and another reused ontology.
      • Drug Drug Interaction: is an interaction in which two drugs interact in such a way to produce a non-additive biological response (sio:DDI). The ain source (skos:exactMatch) is DrugBank. However, TWOSIDES provides the information about the potential adverse side effects that the DDI causes in a phenotype, and it is related to Phenotype class by two de novo Object Properties (disnet:isSideEffect and disnet:hasSideEffect). Furthermore, drug participate (sio:'is participant in') drug-drug interactions.

    • The classes corresponding to the associations between concepts (Figure 2A) were incorporated into a class hierarchy, represented as a tree independently of the main diagram for the sake of clarity, since hierarchical relationships facilitates data integration. All Association classes represented in the diagram are subclasses of the central SIO class sio:Association.

    Example: Gene Disease Association is directly reuses from SIO as a subclass of Association, but the association between a drug and a target suits better with ChEMBL's ChEMBL Mechanism Class. The strategy consisted in creating a new DISNET class Drug Target Association, classified as a subclass of ChEMBL and SIO.

    In the case of the Object Properties (Figure 2B), the objective was to make the relationships between the entities as homogeneous as possible, so, as far as possible, an attempt was made to reuse the Object Properties of SIO or, in default, NCIT. However, in cases where an Object Property was not found in these ontologies with the meaning given by DISNET, an Object Property was created de novo under DISNET's namespace and classified as a subclass of the relation of the other ontology with which its meaning corresponded and as a subclass of one of the two main Object Properties of SIO, sio:'refers to' or sio:'is referred to by'.

    Example: the core class Drug uses ChEMBL's Object Property cco:hasMechanism to relate to the Drug Target Association (range) class, but uses SNOMED's Object Property sct:causative_agent_of in the relationship with Drug Phenotype Side Effect class (range). In order for the relationships to be homogeneous, the intermediate classes disnet:drugForMechanism and disnet:drugForSideEffect were created de novo and classified as subclasses of those of ChEMBL and SNOMED and of sio:'is referred to by'.

    General overview of the SEM-DISNET Ontology Class and object properties hierarchy
    Figure 2 - SEM-DISNET hierarchies for Association Classes (A) and Object Properties (B).

    Cross-reference for SEM-DISNET classes, object properties and data properties back to ToC

    This section provides details for each class and property defined by SEM-DISNET.

    Classes

    A CTD association between a chemical and a disease c back to ToC or Class ToC

    IRI: http://bio2rdf.org/ctd_vocabulary:Chemical-Disease-Association

    has sub-classes
    Drug-Disease Association c
    Is defined by
    http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C43817
    has super-classes
    concept c

    Adverse reaction to drugc back to ToC or Class ToC

    IRI: http://purl.bioontology.org/ontology/SNOMEDCT/62014003

    has sub-classes
    Drug-Phenotype Side Effect c

    annual incidencec back to ToC or Class ToC

    IRI: http://www.orpha.net/ORDO/Orphanet_409967

    ChEMBL Drug Indication Classc back to ToC or Class ToC

    IRI: http://rdf.ebi.ac.uk/terms/chembl#DrugIndication

    has sub-classes
    Drug-Phenotype Indication c

    ChEMBL Mechanism Classc back to ToC or Class ToC

    IRI: http://rdf.ebi.ac.uk/terms/chembl#Mechanism

    has sub-classes
    Drug-Target Association c

    ChEMBL Target Classc back to ToC or Class ToC

    IRI: http://rdf.ebi.ac.uk/terms/chembl#Target

    is in domain of
    ChEMBL Target Entity Type ChEMBL Target Entity Type dp, Target For Drug-Target Association op, is target in op
    is in range of
    Drug-Target Has Target op, has target op
    is disjoint with
    ChEMBL Substance Class ChEMBL Substance Class c

    chromosomec back to ToC or Class ToC

    IRI: http://semanticscience.org/resource/SIO_000899

    A chromosome is a molecular complex of circular or linear DNA and bound proteins.
    Is defined by
    http://semanticscience.org/ontology/sio.owl

    conceptc back to ToC or Class ToC

    IRI: http://semanticscience.org/resource/SIO_000326

    Is defined by
    http://semanticscience.org/ontology/sio.owl

    Disease Markerc back to ToC or Class ToC

    IRI: http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C18329

    is in domain of
    Concentration dp, Sample dp

    Disease, Disorder or Findingc back to ToC or Class ToC

    IRI: http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C7057

    is disjoint with
    Gene c, Score c, Untranslated RNA c, sequence_variant c, ChEMBL Substance Class ChEMBL Substance Class c

    Disease-ncRNA Associationc back to ToC or Class ToC

    IRI: https://w3id.org/eboca/sem-disnet#DiseaseNcrna

    A disease-ncRNA association is an association between a disease and an untranslated RNA (ncRNA).
    has super-classes
    association c
    is in domain of
    Category dp, Causality dp, Disease-ncRNA Association type dp
    is disjoint with
    association c, gene-disease association c, Drug-Disease Association c

    Disease-Phenotype Associationc back to ToC or Class ToC

    IRI: https://w3id.org/eboca/sem-disnet#DiseasePhenotype

    A disease-phenotype association is an association between disease and a phenotype, which corresponds to a subjective evidence of disease perceived by the patient.
    has super-classes
    association c

    Disease-Variant Associationc back to ToC or Class ToC

    IRI: https://w3id.org/eboca/sem-disnet#DiseaseVariant

    Association between a disease and a genetic variant.
    has super-classes
    association c

    DisGeNET disease specificityc back to ToC or Class ToC

    IRI: http://semanticscience.org/resource/SIO_001351

    Is defined by
    http://semanticscience.org/ontology/sio.owl

    DisGeNET Pleiotropy Indexc back to ToC or Class ToC

    IRI: http://semanticscience.org/resource/SIO_001352

    Is defined by
    http://semanticscience.org/ontology/sio.owl

    Drug Disease Inferredc back to ToC or Class ToC

    IRI: https://w3id.org/eboca/sem-disnet#DrugDiseaseInferred

    Drug Disease Associations not classifed as Therapeutic or Marker which are given an associated inferred score.
    has super-classes
    Drug-Disease Association c

    Drug Disease Markerc back to ToC or Class ToC

    IRI: https://w3id.org/eboca/sem-disnet#DrugDiseaseMarker

    Drug that acts like a marker when associated with a disease. A chemical that correlates with a disease or may play a role in the etiology of a disease.
    has super-classes
    Drug-Disease Association c

    Drug Disease Therapeuticc back to ToC or Class ToC

    IRI: https://w3id.org/eboca/sem-disnet#DrugDiseaseTherapeutic

    Drug that has a therapeutic effect when associated with a disease. The drug is used to treat the disease in order to reduce or eliminate its symptoms.
    has super-classes
    Drug-Disease Association c

    drug drug interactionc back to ToC or Class ToC

    IRI: http://semanticscience.org/resource/SIO_001006

    Is defined by
    http://semanticscience.org/ontology/sio.owl
    has super-classes
    association c
    is in domain of
    DDI Has Side Effect op
    is in range of
    Phenotype Side Effect Due To DDI op
    is disjoint with
    Drug-Disease Association c, Drug-Phenotype Indication c, Drug-Phenotype Side Effect c, Drug-Target Association c

    Drug-Phenotype Indicationc back to ToC or Class ToC

    IRI: https://w3id.org/eboca/sem-disnet#DrugPhenotypeIndication

    Relationship between the desirable measurable effects that cause changes in a patient's phenotype and the response to treatment with a drug which is indicated to treat them.
    has super-classes
    ChEMBL Drug Indication Class ChEMBL Drug Indication Class c, association c
    is in domain of
    Indication Has Drug op
    is in range of
    Drug For Drug-Phenotype Indication op
    is disjoint with
    drug drug interaction c, Drug-Disease Association c, Drug-Phenotype Side Effect c, Drug-Target Association c

    Drug-Phenotype Side Effectc back to ToC or Class ToC

    IRI: https://w3id.org/eboca/sem-disnet#DrugPhenotypeSideEffect

    Secondary and undesirable measurable effects that cause patient phenotype changes in response to the treatment with a drug.
    has super-classes
    Adverse reaction to drug c, association c
    is in domain of
    Drug-Phenotype Side Effect Has Phenotype op, Side Effect Has Drug op
    is in range of
    Drug For Drug-Phenotype Side Effect op, Phenotype For Drug-Phenotype Side Effect op
    is disjoint with
    drug drug interaction c, Drug-Disease Association c, Drug-Phenotype Indication c, Drug-Target Association c

    Drug-Target Associationc back to ToC or Class ToC

    IRI: https://w3id.org/eboca/sem-disnet#DrugTarget

    Association between a drug and a target in order to achieve disease treatment by different action types or mechanism of action.
    has super-classes
    ChEMBL Mechanism Class ChEMBL Mechanism Class c, association c
    is in domain of
    ChEMBL Mechanism Action Type ChEMBL Mechanism Action Type dp, Drug-Target Association Has Drug op, Drug-Target Has Target op
    is in range of
    Drug For Drug-Target Association op, Target For Drug-Target Association op
    is disjoint with
    drug drug interaction c, Drug-Disease Association c, Drug-Phenotype Indication c, Drug-Phenotype Side Effect c

    Genec back to ToC or Class ToC

    IRI: http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C16612

    is in domain of
    Chromosome No Version dp, Gene Sequence dp, Gene_Found_In_Organism op, Gene_Mutant_Encodes_Gene_Product_Sequence_Variation op, Sequence end position dp, Sequence start position dp, Strand dp, encodes op, is represented by op
    is in range of
    is associated with op, is encoded by op, represents op
    is disjoint with
    Score c, Disease, Disorder or Finding c

    Gene Symbolc back to ToC or Class ToC

    IRI: http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C43568

    is in domain of
    represents op
    is in range of
    is represented by op

    gene-disease associationc back to ToC or Class ToC

    IRI: http://semanticscience.org/resource/SIO_000983

    Is defined by
    http://semanticscience.org/ontology/sio.owl
    has super-classes
    association c
    is disjoint with
    association c, Disease-ncRNA Association c, Drug-Disease Association c

    geographyc back to ToC or Class ToC

    IRI: http://www.orpha.net/ORDO/Orphanet_C009

    has sub-classes
    Prevalence c

    group of disordersc back to ToC or Class ToC

    IRI: http://www.orpha.net/ORDO/Orphanet_557492

    Organismc back to ToC or Class ToC

    IRI: http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C14250

    is in range of
    Gene_Found_In_Organism op, Gene_Product_Has_Organism_Source op

    Pathwayc back to ToC or Class ToC

    IRI: http://vocabularies.wikipathways.org/wp#Pathway

    A biological process representing a set of interactions and relationships among genes, proteins, metabolites, and other factors in the context of cellular compartments, tissues and organisms.

    Phenotypec back to ToC or Class ToC

    IRI: https://w3id.org/eboca/sem-disnet#Phenotype

    Observable and detectable signs in a patient due to the effects caused by a disease or a drug causing changes in their original appearence.
    is in domain of
    Phenotype For Drug-Phenotype Side Effect op, Phenotype Side Effect Due To DDI op
    is in range of
    DDI Has Side Effect op, Drug-Phenotype Side Effect Has Phenotype op
    is disjoint with
    ChEMBL Substance Class ChEMBL Substance Class c

    Phenotypic abnormalityc back to ToC or Class ToC

    IRI: http://purl.obolibrary.org/obo/HP_0000118

    A phenotypic abnormality.
    This is the root of the phenotypic abnormality subontology of the HPO.
    is disjoint with
    Protein c

    Prevalencec back to ToC or Class ToC

    IRI: https://w3id.org/eboca/sem-disnet#Prevalence

    Association between an oprhan disease and the incidence according to the geographical location.
    has super-classes
    association c, geography c
    is in domain of
    Geography dp

    Proteinc back to ToC or Class ToC

    IRI: http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C17021

    is in domain of
    Gene_Product_Has_Organism_Source op, Protein sequence for given ChEMBL entity Protein sequence for given ChEMBL entity dp, is encoded by op
    is in range of
    encodes op
    is disjoint with
    Phenotypic abnormality c

    Protein-Protein Interactionc back to ToC or Class ToC

    IRI: http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C18469

    has sub-classes
    PPI c

    PPIc back to ToC or Class ToC

    IRI: https://w3id.org/eboca/sem-disnet#Ppi

    Association between two proteins by physical contacts of high specificity that occur in a specific molecular context with a certain confidence value.
    has super-classes
    Protein-Protein Interaction c, association c
    is in domain of
    Confidence Value dp

    ProteinClassc back to ToC or Class ToC

    IRI: http://purl.obolibrary.org/obo/PR_000000001

    Scorec back to ToC or Class ToC

    IRI: http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C25338

    is disjoint with
    Gene c, Disease, Disorder or Finding c, sequence_variant c

    sequence start positionc back to ToC or Class ToC

    IRI: http://semanticscience.org/resource/SIO_000791

    Is defined by
    http://semanticscience.org/ontology/sio.owl

    sequence_variantc back to ToC or Class ToC

    IRI: http://purl.obolibrary.org/obo/SO_0001060

    A sequence_variant is a non exact copy of a sequence_feature or genome exhibiting one or more sequence_alteration.
    is in domain of
    Consequence dp, is associated with op, is located in op
    is in range of
    Gene_Mutant_Encodes_Gene_Product_Sequence_Variation op, is location of op
    is disjoint with
    Score c, Disease, Disorder or Finding c

    Untranslated RNAc back to ToC or Class ToC

    IRI: http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C26549

    is in domain of
    ncRNA Category dp
    is disjoint with
    Disease, Disorder or Finding c

    Object Properties

    Association between ChEMBL Target and Mechanism op back to ToC or Object Property ToC

    IRI: http://rdf.ebi.ac.uk/terms/chembl#isTargetForMechanism

    has sub-properties
    Target For Drug-Target Association op
    is inverse of
    ChEMBL Target Association ChEMBL Target Association op

    Causative agent ofop back to ToC or Object Property ToC

    IRI: http://purl.bioontology.org/ontology/SNOMEDCT/causative_agent_of

    has sub-properties
    Drug For Drug-Phenotype Side Effect op
    is inverse of
    Has causative agent op

    Cause ofop back to ToC or Object Property ToC

    IRI: http://purl.bioontology.org/ontology/SNOMEDCT/cause_of

    has sub-properties
    Phenotype For Drug-Phenotype Side Effect op
    is inverse of
    Due to op

    ChEMBL Drug Indication Associationop back to ToC or Object Property ToC

    IRI: http://rdf.ebi.ac.uk/terms/chembl#hasDrugIndication

    Association between the entity and a ChEMBL Drug Indication
    has sub-properties
    Drug For Drug-Phenotype Indication op

    ChEMBL Mechanism Associationop back to ToC or Object Property ToC

    IRI: http://rdf.ebi.ac.uk/terms/chembl#hasMechanism

    Association between the entity and a ChEMBL Mechanism of Action
    has sub-properties
    Drug For Drug-Target Association op
    is inverse of
    ChEMBL Molecule Association ChEMBL Molecule Association op

    ChEMBL Molecule Associationop back to ToC or Object Property ToC

    IRI: http://rdf.ebi.ac.uk/terms/chembl#hasMolecule

    Association between the entity and a ChEMBL Molecule
    has sub-properties
    Drug-Target Association Has Drug op, Indication Has Drug op
    is inverse of
    ChEMBL Mechanism Association ChEMBL Mechanism Association op

    ChEMBL Target Associationop back to ToC or Object Property ToC

    IRI: http://rdf.ebi.ac.uk/terms/chembl#hasTarget

    Association between the entity and a ChEMBL Target
    has sub-properties
    Drug-Target Has Target op
    is inverse of
    Association between ChEMBL Target and Mechanism Association between ChEMBL Target and Mechanism op

    DDI Has Side Effectop back to ToC or Object Property ToC

    IRI: https://w3id.org/eboca/sem-disnet#hasSideEffect

    has domain
    drug drug interaction c
    has range
    Phenotype c
    is inverse of
    Phenotype Side Effect Due To DDI op

    Drug For Drug-Phenotype Indicationop back to ToC or Object Property ToC

    IRI: https://w3id.org/eboca/sem-disnet#drugForDrugIndication

    has super-properties
    ChEMBL Drug Indication Association ChEMBL Drug Indication Association op, is referred to by op
    has domain
    ChEMBL Substance Class ChEMBL Substance Class c
    has range
    Drug-Phenotype Indication c
    is inverse of
    Indication Has Drug op

    Drug For Drug-Phenotype Side Effectop back to ToC or Object Property ToC

    IRI: https://w3id.org/eboca/sem-disnet#drugForSideEffect

    has super-properties
    Causative agent of op, is referred to by op
    has domain
    ChEMBL Substance Class ChEMBL Substance Class c
    has range
    Drug-Phenotype Side Effect c
    is inverse of
    Side Effect Has Drug op

    Drug For Drug-Target Associationop back to ToC or Object Property ToC

    IRI: https://w3id.org/eboca/sem-disnet#drugForMechanism

    has super-properties
    ChEMBL Mechanism Association ChEMBL Mechanism Association op, is referred to by op
    has domain
    ChEMBL Substance Class ChEMBL Substance Class c
    has range
    Drug-Target Association c
    is inverse of
    Drug-Target Association Has Drug op

    Drug-Phenotype Side Effect Has Phenotypeop back to ToC or Object Property ToC

    IRI: https://w3id.org/eboca/sem-disnet#hasPhenotype

    has super-properties
    Due to op, refers to op
    has domain
    Drug-Phenotype Side Effect c
    has range
    Phenotype c
    is inverse of
    Phenotype For Drug-Phenotype Side Effect op

    Drug-Target Association Has Drugop back to ToC or Object Property ToC

    IRI: https://w3id.org/eboca/sem-disnet#mechanismHasMolecule

    has super-properties
    ChEMBL Molecule Association ChEMBL Molecule Association op, refers to op
    has domain
    Drug-Target Association c
    has range
    ChEMBL Substance Class ChEMBL Substance Class c
    is inverse of
    Drug For Drug-Target Association op

    Drug-Target Has Targetop back to ToC or Object Property ToC

    IRI: https://w3id.org/eboca/sem-disnet#hasTarget

    has super-properties
    ChEMBL Target Association ChEMBL Target Association op, refers to op
    has domain
    Drug-Target Association c
    has range
    ChEMBL Target Class ChEMBL Target Class c
    is inverse of
    Target For Drug-Target Association op

    Due toop back to ToC or Object Property ToC

    IRI: http://purl.bioontology.org/ontology/SNOMEDCT/due_to

    has sub-properties
    Drug-Phenotype Side Effect Has Phenotype op
    is inverse of
    Cause of op

    encodesop back to ToC or Object Property ToC

    IRI: http://semanticscience.org/resource/SIO_010078

    Is defined by
    http://semanticscience.org/ontology/sio.owl
    Example
    an open reading frame encodes a protein (it contains information that specifies the amino acid composition and topology)
    has domain
    Gene c
    has range
    Protein c
    is inverse of
    is encoded by op

    Gene_Found_In_Organismop back to ToC or Object Property ToC

    IRI: http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#R41

    has domain
    Gene c
    has range
    Organism c

    Gene_Mutant_Encodes_Gene_Product_Sequence_Variationop back to ToC or Object Property ToC

    IRI: http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#R178

    has domain
    Gene c
    has range
    sequence_variant c
    is inverse of
    is associated with op

    Gene_Product_Has_Organism_Sourceop back to ToC or Object Property ToC

    IRI: http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#R45

    has domain
    Protein c
    has range
    Organism c

    has attributeop back to ToC or Object Property ToC

    IRI: http://semanticscience.org/resource/SIO_000008

    Is defined by
    http://semanticscience.org/ontology/sio.owl
    has sub-properties
    has measurement value op, has member op
    has domain
    Disease, Disorder or Finding c or Phenotype c
    has range
    Disease Marker c or concept c
    is inverse of
    is attribute of op

    Has causative agentop back to ToC or Object Property ToC

    IRI: http://purl.bioontology.org/ontology/SNOMEDCT/has_causative_agent

    has sub-properties
    Side Effect Has Drug op
    is inverse of
    Causative agent of op

    has measurement valueop back to ToC or Object Property ToC

    IRI: http://semanticscience.org/resource/SIO_000216

    Is defined by
    http://semanticscience.org/ontology/sio.owl
    has super-properties
    has attribute op
    has domain
    Disease, Disorder or Finding c or sequence_variant c or association c or gene-disease association c
    has range
    Score c or DisGeNET disease specificity c or DisGeNET Pleiotropy Index c
    is inverse of
    is measurement value of op

    has memberop back to ToC or Object Property ToC

    IRI: http://semanticscience.org/resource/SIO_000059

    Is defined by
    http://semanticscience.org/ontology/sio.owl
    Example
    a collection of cars has as a car as a member

    has characteristics: irreflexive

    has super-properties
    has attribute op
    has domain
    Phenotypic abnormality c or ProteinClass c
    has range
    Protein c or Disease, Disorder or Finding c
    is inverse of
    is member of op

    has partop back to ToC or Object Property ToC

    IRI: http://semanticscience.org/resource/SIO_000028

    Is defined by
    http://semanticscience.org/ontology/sio.owl
    Example
    a collection of cars has as a car as a part;a car has an engine as a part; a car has a piston as a part;
    has super-properties
    is location of op
    has domain
    Pathway c or group of disorders c
    has range
    Gene c or Disease, Disorder or Finding c
    is inverse of
    is part of op

    has participantop back to ToC or Object Property ToC

    IRI: http://semanticscience.org/resource/SIO_000132

    Is defined by
    http://semanticscience.org/ontology/sio.owl
    has domain
    Protein-Protein Interaction c or drug drug interaction c
    has range
    Protein c or ChEMBL Substance Class ChEMBL Substance Class c
    is inverse of
    is participant in op

    has targetop back to ToC or Object Property ToC

    IRI: http://semanticscience.org/resource/SIO_000291

    Is defined by
    http://semanticscience.org/ontology/sio.owl
    has domain
    Organism c or Protein c
    has range
    ChEMBL Target Class ChEMBL Target Class c
    is inverse of
    is target in op

    Indication Has Drugop back to ToC or Object Property ToC

    IRI: https://w3id.org/eboca/sem-disnet#indicationHasMolecule

    has super-properties
    ChEMBL Molecule Association ChEMBL Molecule Association op, refers to op
    has domain
    Drug-Phenotype Indication c
    has range
    ChEMBL Substance Class ChEMBL Substance Class c
    is inverse of
    Drug For Drug-Phenotype Indication op

    is associated withop back to ToC or Object Property ToC

    IRI: http://semanticscience.org/resource/SIO_001403

    x is associated with y when x and y are logically or statistically related to one another.
    Is defined by
    http://semanticscience.org/ontology/sio.owl
    has domain
    sequence_variant c
    has range
    Gene c
    is inverse of
    Gene_Mutant_Encodes_Gene_Product_Sequence_Variation op

    is attribute ofop back to ToC or Object Property ToC

    IRI: http://semanticscience.org/resource/SIO_000011

    Is defined by
    http://semanticscience.org/ontology/sio.owl
    has sub-properties
    is measurement value of op, is member of op
    has domain
    Disease Marker c or concept c
    has range
    Disease, Disorder or Finding c or Phenotype c
    is inverse of
    has attribute op

    is encoded byop back to ToC or Object Property ToC

    IRI: http://semanticscience.org/resource/SIO_010079

    Is defined by
    http://semanticscience.org/ontology/sio.owl
    has domain
    Protein c
    has range
    Gene c
    is inverse of
    encodes op

    is located inop back to ToC or Object Property ToC

    IRI: http://semanticscience.org/resource/SIO_000061

    Is defined by
    http://semanticscience.org/ontology/sio.owl
    Example
    A parasite in the interior of a person's intestine is located in their intestinal lumen.
    has sub-properties
    is part of op
    has domain
    sequence_variant c
    has range
    sequence start position c or chromosome c
    is inverse of
    is location of op

    is location ofop back to ToC or Object Property ToC

    IRI: http://semanticscience.org/resource/SIO_000145

    Is defined by
    http://semanticscience.org/ontology/sio.owl
    has sub-properties
    has part op
    has domain
    sequence start position c or chromosome c
    has range
    sequence_variant c
    is inverse of
    is located in op

    is measurement value ofop back to ToC or Object Property ToC

    IRI: http://semanticscience.org/resource/SIO_000215

    Is defined by
    http://semanticscience.org/ontology/sio.owl
    has super-properties
    is attribute of op
    has domain
    Score c or DisGeNET disease specificity c or DisGeNET Pleiotropy Index c
    has range
    Disease, Disorder or Finding c or sequence_variant c or association c or gene-disease association c
    is inverse of
    has measurement value op

    is member ofop back to ToC or Object Property ToC

    IRI: http://semanticscience.org/resource/SIO_000095

    Is defined by
    http://semanticscience.org/ontology/sio.owl
    has super-properties
    is attribute of op
    has domain
    Protein c or Disease, Disorder or Finding c
    has range
    Phenotypic abnormality c or ProteinClass c
    is inverse of
    has member op

    is part ofop back to ToC or Object Property ToC

    IRI: http://semanticscience.org/resource/SIO_000068

    Is defined by
    http://semanticscience.org/ontology/sio.owl
    has super-properties
    is located in op
    has domain
    Gene c or Disease, Disorder or Finding c
    has range
    Pathway c or group of disorders c
    is inverse of
    has part op

    is participant inop back to ToC or Object Property ToC

    IRI: http://semanticscience.org/resource/SIO_000062

    Is defined by
    http://semanticscience.org/ontology/sio.owl
    Example
    a car is a participant in a car race; glucose is a participant in glycolysis
    has domain
    Protein c or ChEMBL Substance Class ChEMBL Substance Class c
    has range
    Protein-Protein Interaction c or drug drug interaction c
    is inverse of
    has participant op

    is represented byop back to ToC or Object Property ToC

    IRI: http://semanticscience.org/resource/SIO_000205

    Is defined by
    http://semanticscience.org/ontology/sio.owl
    has super-properties
    is referred to by op
    has domain
    Gene c
    has range
    Gene Symbol c
    is inverse of
    represents op

    is target inop back to ToC or Object Property ToC

    IRI: http://semanticscience.org/resource/SIO_000292

    Is defined by
    http://semanticscience.org/ontology/sio.owl
    Example
    glucose is a target in the hexokinase-mediated conversion of glucose to glucose-6-phosphate.
    has domain
    ChEMBL Target Class ChEMBL Target Class c
    has range
    Organism c or Protein c
    is inverse of
    has target op

    Phenotype For Drug-Phenotype Side Effectop back to ToC or Object Property ToC

    IRI: https://w3id.org/eboca/sem-disnet#phenotypeForSideEffect

    has super-properties
    Cause of op, is referred to by op
    has domain
    Phenotype c
    has range
    Drug-Phenotype Side Effect c
    is inverse of
    Drug-Phenotype Side Effect Has Phenotype op

    Phenotype Side Effect Due To DDIop back to ToC or Object Property ToC

    IRI: https://w3id.org/eboca/sem-disnet#isSideEffect

    has domain
    Phenotype c
    has range
    drug drug interaction c
    is inverse of
    DDI Has Side Effect op

    representsop back to ToC or Object Property ToC

    IRI: http://semanticscience.org/resource/SIO_000210

    Is defined by
    http://semanticscience.org/ontology/sio.owl
    has super-properties
    refers to op
    has domain
    Gene Symbol c
    has range
    Gene c
    is inverse of
    is represented by op

    Side Effect Has Drugop back to ToC or Object Property ToC

    IRI: https://w3id.org/eboca/sem-disnet#sideEffectHasMolecule

    has super-properties
    Has causative agent op, refers to op
    has domain
    Drug-Phenotype Side Effect c
    has range
    ChEMBL Substance Class ChEMBL Substance Class c
    is inverse of
    Drug For Drug-Phenotype Side Effect op

    Target For Drug-Target Associationop back to ToC or Object Property ToC

    IRI: https://w3id.org/eboca/sem-disnet#targetForMechanism

    has super-properties
    Association between ChEMBL Target and Mechanism Association between ChEMBL Target and Mechanism op, is referred to by op
    has domain
    ChEMBL Target Class ChEMBL Target Class c
    has range
    Drug-Target Association c
    is inverse of
    Drug-Target Has Target op

    Data Properties

    ATC Codedp back to ToC or Data Property ToC

    IRI: http://rdf.ebi.ac.uk/terms/chembl#atcClassification

    ATC Classification Code
    has domain
    ChEMBL Substance Class ChEMBL Substance Class c
    has range
    string

    Categorydp back to ToC or Data Property ToC

    IRI: https://w3id.org/eboca/sem-disnet#category

    has domain
    Disease-ncRNA Association c
    has range
    string

    Causalitydp back to ToC or Data Property ToC

    IRI: https://w3id.org/eboca/sem-disnet#causality

    has domain
    Disease-ncRNA Association c
    has range
    string

    ChEMBL Mechanism Action Typedp back to ToC or Data Property ToC

    IRI: http://rdf.ebi.ac.uk/terms/chembl#mechanismActionType

    Type of action of the drug on the target e.g., agonist/antagonist etc (foreign key to action_type table)
    has domain
    Drug-Target Association c
    has range
    string

    ChEMBL Molecule Development Phasedp back to ToC or Data Property ToC

    IRI: http://rdf.ebi.ac.uk/terms/chembl#highestDevelopmentPhase

    The highest phase the molecule has reached in drug approval process (4 = approved)
    has domain
    Drug-Phenotype Indication c or Drug-Phenotype Side Effect c
    has range
    integer

    ChEMBL Substance Entity Typedp back to ToC or Data Property ToC

    IRI: http://rdf.ebi.ac.uk/terms/chembl#substanceType

    ChEMBL Substance Entity Type
    has domain
    ChEMBL Substance Class ChEMBL Substance Class c
    has range
    string

    ChEMBL Target Entity Typedp back to ToC or Data Property ToC

    IRI: http://rdf.ebi.ac.uk/terms/chembl#targetType

    Describes whether target is a protein, an organism, a tissue etc.
    has domain
    ChEMBL Target Class ChEMBL Target Class c
    has range
    string

    Chemical Structuredp back to ToC or Data Property ToC

    IRI: https://w3id.org/eboca/sem-disnet#chemicalStructure

    has domain
    ChEMBL Substance Class ChEMBL Substance Class c
    has range
    string

    Chromosome No Versiondp back to ToC or Data Property ToC

    IRI: https://w3id.org/eboca/sem-disnet#chrVersion

    has domain
    Gene c
    has range
    string

    Concentrationdp back to ToC or Data Property ToC

    IRI: https://w3id.org/eboca/sem-disnet#concentration

    has domain
    Disease Marker c
    has range
    string

    Confidence Valuedp back to ToC or Data Property ToC

    IRI: https://w3id.org/eboca/sem-disnet#confidenceValue

    has domain
    PPI c
    has range
    string

    Consequencedp back to ToC or Data Property ToC

    IRI: https://w3id.org/eboca/sem-disnet#consequence

    has domain
    sequence_variant c
    has range
    string

    Disease-ncRNA Association typedp back to ToC or Data Property ToC

    IRI: https://w3id.org/eboca/sem-disnet#type

    has domain
    Disease-ncRNA Association c
    has range
    string

    Gene Sequencedp back to ToC or Data Property ToC

    IRI: https://w3id.org/eboca/sem-disnet#geneSequence

    has domain
    Gene c
    has range
    string

    Geographydp back to ToC or Data Property ToC

    IRI: https://w3id.org/eboca/sem-disnet#geo

    has domain
    Prevalence c
    has range
    string

    has valuedp back to ToC or Data Property ToC

    IRI: http://semanticscience.org/resource/SIO_000300

    Is defined by
    http://semanticscience.org/ontology/sio.owl

    has characteristics: functional

    has domain
    Score c or Gene Symbol c or sequence start position c or chromosome c or DisGeNET disease specificity c or DisGeNET Pleiotropy Index c or annual incidence c or Drug-Disease Association c
    has range
    double or integer or string

    Inchi Keydp back to ToC or Data Property ToC

    IRI: https://w3id.org/eboca/sem-disnet#inchiKey

    has domain
    ChEMBL Substance Class ChEMBL Substance Class c
    has range
    string

    ncRNA Categorydp back to ToC or Data Property ToC

    IRI: https://w3id.org/eboca/sem-disnet#rnaCategory

    has domain
    Untranslated RNA c
    has range
    string

    Protein sequence for given ChEMBL entitydp back to ToC or Data Property ToC

    IRI: http://rdf.ebi.ac.uk/terms/chembl#proteinSequence

    Protein sequence for given ChEMBL entity
    has domain
    Protein c
    has range
    string

    Sampledp back to ToC or Data Property ToC

    IRI: https://w3id.org/eboca/sem-disnet#sample

    has domain
    Disease Marker c
    has range
    string

    Sequence end positiondp back to ToC or Data Property ToC

    IRI: https://w3id.org/eboca/sem-disnet#seqEnd

    has domain
    Gene c
    has range
    integer

    Sequence start positiondp back to ToC or Data Property ToC

    IRI: https://w3id.org/eboca/sem-disnet#seqStart

    has domain
    Gene c
    has range
    integer

    Stranddp back to ToC or Data Property ToC

    IRI: https://w3id.org/eboca/sem-disnet#strand

    has domain
    Gene c
    has range
    integer

    Synonymousdp back to ToC or Data Property ToC

    IRI: https://w3id.org/eboca/sem-disnet#synonymous

    has domain
    ChEMBL Substance Class ChEMBL Substance Class c
    has range
    string

    The ChEMBL ID for a given entitydp back to ToC or Data Property ToC

    IRI: http://rdf.ebi.ac.uk/terms/chembl#chemblId

    has domain
    Drug-Phenotype Indication c or Drug-Phenotype Side Effect c
    has range
    string

    Legend back to ToC

    c: Classes
    op: Object Properties
    dp: Data Properties

    References back to ToC

    Add your references here. It is recommended to have them as a list.

    Acknowledgments back to ToC

    The authors would like to thank Silvio Peroni for developing LODE, a Live OWL Documentation Environment, which is used for representing the Cross Referencing Section of this document and Daniel Garijo for developing Widoco, the program used to create the template used in this documentation.