Andrea Álvarez Pérez (MEDAL) Ana Iglesias Molina (OEG) Lucía Prieto Santamaría (MEDAL) Alejandro Rodríguez González (MEDAL) 2022-03-30 MEDAL: https://medal.ctb.upm.es/ OEG: https://oeg.fi.upm.es/ SEM-DISNET ontology provides a integrated ontology used to describe the define 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). DISNET website: https://disnet.ctb.upm.es/ OEG website: https://oeg.fi.upm.es/ SEM-DISNET disnet NHC0 Conceptual Entity code code A property representing a concept unique identifier within the NCI Enterprise Vocabulary Service's NCI Thesaurus. true code Code P106 Conceptual Entity Semantic Type Semantic_Type Semantic_Type A property that represents a description of the sort of thing or category to which a concept belongs in the context of the UMLS semantic network. In general, applying semantic types aids in allowing users (or computer programs) to draw conclusions about concepts by virtue of the categories to which they have been assigned. We use a set of semantic types developed for the UMLS Metathesaurus. There are currently 134 semantic types in the UMLS. Semantic_Type Semantic Type P107 Conceptual Entity Display Name Display_Name Display Name Display_Name A property representing an alternative Preferred Name for use in some NCI systems. Display_Name Display Name P108 Conceptual Entity Preferred Name Preferred_Name Preferred Name Preferred Term Preferred_Name A property representing the word or phrase that NCI uses by preference to refer to the concept. Preferred_Name Preferred Name P322 Conceptual Entity Contributing Source Contributing_Source Contributing_Source A property is used to indicate when a non-EVS entity has contributed to, and has a stake in, a concept. This is used where such entities, within or outside NCI, have indicated the need to be able to track their own concepts. A single concept can have multiple instances of this property if multiple entities have such a defined stake. Contributing_Source Contributing Source P325 Conceptual Entity [source] Definition ALT_DEFINITION ALT_DEFINITION A property representing the English language definition of a concept from a source other than NCI. ALT_DEFINITION Alternative Definition P384 Conceptual Entity term-source A property representing the organization that is the supplier or owner of each FULL_SYN term. true Term Source Term Source P90 Conceptual Entity Term & Source Data FULL_SYN FULL_SYN Synonym with Source Data A property representing a fully qualified synonym, contains the string, term type, source, and an optional source code if appropriate. Each subfield is deliniated to facilitate interpretation by software. FULL_SYN Full Synonym P97 Conceptual Entity Definition DEFINITION DEFINITION A property representing the English language definitions of what NCI means by the concept. They may also include information about the definition's source and attribution in a form that can easily be interpreted by software. DEFINITION Definition P98 Conceptual Entity DesignNote DesignNote DesignNote A property representing notations made by NCI vocabulary curators. They are intended to provide supplemental, unstructured information to the user or additional insight about the concept. DesignNote Design Note DesignNote NCI Default A property representing the name of the organization to which an NCI Thesaurus concept is being linked to by cross reference. xRef Source XRef Source definition OBO Definition Equivalent To A property representing a reference to an identical or very similar object in another database. database_cross_reference xRef Database Cross Reference has_exact_synonym Has Exact Synonym has_obo_namespace Has OBO Namespace has_related_synonym Has Related Synonym has_synonym_type Has Synonym Type OBO ID label A resource has no more than one value of skos:prefLabel per language tag, and no more than one value of skos:prefLabel without language tag. The range of skos:prefLabel is the class of RDF plain literals. skos:prefLabel, skos:altLabel and skos:hiddenLabel are pairwise disjoint properties. preferred label The preferred lexical label for a resource, in a given language. Disnet Label Disnet Label R178 Conceptual Entity Gene_Mutant_Encodes_Gene_Product_Sequence_Variation Gene_Mutant_Encodes_Gene_Product_Sequence_Variation A role used to indicate that a specific molecular variation or mutation in a gene encodes a gene product sequence variant. The domain and range for this role are 'Gene Mutant' and 'Gene Product Sequence Variation', respectively. Gene_Mutant_Encodes_Gene_Product_Sequence_Variation Gene Associated With Variant Gene_Mutant_Encodes_Gene_Product_Sequence_Variation NCI R41 Conceptual Entity Found In Organism Gene_Found_In_Organism Gene_Found_In_Organism A role used to specify the organism of origin for a gene. It may be used to differentiate genes with the same name and functions that originate from different organisms. The domain and range for this role are 'Gene' and 'Organism', respectively. Currently, we only model human genes, but this role has obvious utility in future, if other organisms are modeled as well. Gene_Found_In_Organism Gene In Organism Gene_Found_In_Organism NCI R45 Conceptual Entity Has Organism Source Gene_Product_Has_Organism_Source Gene_Product_Has_Organism_Source A role used to differentiate homologous proteins from different organisms. The domain and range for this role are 'Gene Product' and 'Organism', respectively. Gene_Product_Has_Organism_Source Protein In Organism Gene_Product_Has_Organism_Source NCI Causative agent of Causative agent of Cause of Cause Of Due to Due To Has causative agent Has causative agent Association between the entity and a ChEMBL Drug Indication ChEMBL Drug Indication Association ChEMBL Drug Indication Association ChEMBL Has Drug Indication Association between the entity and a ChEMBL Mechanism of Action ChEMBL Mechanism Association ChEMBL Mechanism Association ChEMBL Has Drug Target Association between the entity and a ChEMBL Molecule ChEMBL Molecule Association ChEMBL Molecule Association ChEMBL Has Drug Association between the entity and a ChEMBL Target ChEMBL Target Association ChEMBL Target Association ChEMBL Has Target Association between ChEMBL Target and Mechanism Association between ChEMBL Target and Mechanism Is Target SIO_000008 has attribute is a relation that associates a entity with an attribute where an attribute is an intrinsic characteristic such as a quality, capability, disposition, function, or is an externally derived attribute determined from some descriptor (e.g. a quantity, position, label/identifier) either directly or indirectly through generalization of entities of the same type. core has attribute Has Attribute SIO_000011 is attribute of is a relation that associates an attribute with an entity where an attribute is an intrinsic characteristic such as a quality, capability, disposition, function, or is an externally derived attribute determined from some descriptor (e.g. a quantity, position, label/identifier) either directly or indirectly through generalization of entities of the same type. is attribute of Is Attribute Of SIO_000028 has part is a transitive, reflexive and antisymmetric relation between a whole and itself or a whole and its part. has part 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 Part SIO_000059 has member is a mereological relation between a collection and an item. core has member a collection of cars has as a car as a member Has Member SIO_000061 A is located in B iff the spatialtemporial region occupied by A is part of the spatialtemporal region occupied by B. [T][R] OBO_REL:located_in core is located in A parasite in the interior of a person's intestine is located in their intestinal lumen. Is Located In SIO_000062 is participant in is a relation that describes the participation of the subject in the (processual) object. is participant in a car is a participant in a car race; glucose is a participant in glycolysis Is Participant In SIO_000068 is part of is a transitive, reflexive and anti-symmetric mereological relation between a whole and itself or a part and its whole. OBO_REL:part_of core is part of Is Part Of SIO_000095 is member of is a mereological relation between a item and a collection. is member of Is Member Of SIO_000132 has participant is a relation that describes the participation of the object in the (processual) subject. OBO_REL:has_participant core has participant Has Participant SIO_000145 A is location of B iff the spatialtemporal region occupied by A has the spatialtemporal region occupied by B as a part. [T][R] nlp+ is location of Is Location Of SIO_000205 is represented by: a relation between an entity and some symbol. is represented by Is Represented By SIO_000210 a represents b when a serves as a sign, symbol or model of b. core represents Represents SIO_000212 A is referred to by B iff B is an informational entity that makes reference to A. is referred to by Is Referred To By SIO_000215 is measurement value of is a relation between a value and the entity that it is a measurement of. is measurement value of Is Measurement Value Of SIO_000216 has measurement value is a relation between a quality/realizable and a measurement value. core has measurement value Has Measurement Value SIO_000291 has target is a relation between a process and an entity, where the entity is present at the beginning of the process and undergoes a change or transformation in the process. has target Has Target SIO_000292 is target in is a relation between an entity and a process, where the entity is present at the beginning of the process and undergoes a change or transformation in the process. is target in glucose is a target in the hexokinase-mediated conversion of glucose to glucose-6-phosphate. Is Target In SIO_000628 refers to is a relation between one entity and the entity that it makes reference to. core nlp+ refers to Refers To x is associated with y when x and y are logically or statistically related to one another. SIO_001403 is associated with Is Associated With SIO_010078 A relation between two objects, in which the first object contains information that is used to produce the second object. encodes an open reading frame encodes a protein (it contains information that specifies the amino acid composition and topology) Encodes SIO_010079 A relation between two objects, in which the first object is produced from the information contained in the second object. is encoded by Is Encoded By Drug For Drug-Phenotype Indication Drug For Drug Phenotype Indication Drug For Drug-Target Association Drug For Drug Target Association Drug For Drug-Phenotype Side Effect Drug For Drug-Phenotype Side Effect Drug-Phenotype Side Effect Has Phenotype Drug-Phenotype Side Effect Has Phenotype DDI Has Side Effect DDI Has Side Effect Drug-Target Has Target Drug-Target Has Target Indication Has Drug Indication Has Drug Phenotype Side Effect Due To DDI Phenotype Side Effect Due To DDI Drug-Target Association Has Drug Drug-Target Association Has Drug Phenotype For Drug-Phenotype Side Effect Phenotype For Drug-Phenotype Side Effect Side Effect Has Drug Side Effect Has Drug Target For Drug-Target Association Is Target For Drug Target Association ATC Classification Code ATC Code ATC Code ATC Code The ChEMBL ID for a given entity The ChEMBL ID for a given entity CHEMBL ID The highest phase the molecule has reached in drug approval process (4 = approved) ChEMBL Molecule Development Phase ChEMBL Molecule Development Phase Highest Development Phase Type of action of the drug on the target e.g., agonist/antagonist etc (foreign key to action_type table) ChEMBL Mechanism Action Type ChEMBL Mechanism Action Type Drug Target Action Type Protein sequence for given ChEMBL entity Protein sequence for given ChEMBL entity Protein sequence for given ChEMBL entity Protein Sequence ChEMBL Substance Entity Type ChEMBL Substance Entity Type ChEMBL Substance Entity Type Describes whether target is a protein, an organism, a tissue etc. ChEMBL Target Entity Type ChEMBL Target Entity Type SIO_000300 A relation between a informational entity and its actual value (numeric, date, text, etc). core nlp relations sadi has value Has Value Category Category Causality Causality Chemical Structure Chemical Structure Chromosome No Version Chromosome Version Concentration Marker Concentration Confidence Value PPI Confidence Value Consequence Variant Consequence Gene Sequence Gene Sequence Geography Geography Inchi Key Inchi Key ncRNA Category ncRNA Category Sample Marker Sample Sequence end position Sequence End Position Sequence start position Sequence Start Position Strand Strand Synonymous Disease-ncRNA Association type Chemical-Disease-Association ctd_vocabulary http://bio2rdf.org/ctd_vocabulary:Chemical-Disease-Association ctd_vocabulary:Chemical-Disease-Association A CTD association between a chemical and a disease A CTD association between a chemical and a disease [ctd_vocabulary:Chemical-Disease-Association] A CTD association between a chemical and a disease [ctd_vocabulary:Chemical-Disease-Association] Drug Disease Associaton umls:T019 Congenital Abnormality UMLS Semantic Type (STY) [umls:T019] annotated to at least one disease in DisGeNET. STYs are identified by the UMLS TUI. Congenital Abnormality [umls:T019] umls:T020 Acquired Abnormality UMLS Semantic Type (STY) [umls:T020] annotated to at least one disease in DisGeNET. STYs are identified by the UMLS TUI. Acquired Abnormality [umls:T020] umls:T026 Cell Component UMLS Semantic Type (STY) [umls:T026] annotated to at least one disease in DisGeNET. STYs are identified by the UMLS TUI. Cell Component [umls:T026] umls:T031 Body Substance UMLS Semantic Type (STY) [umls:T031] annotated to at least one disease in DisGeNET. STYs are identified by the UMLS TUI. Body Substance [umls:T031] umls:T032 Organism Attribute UMLS Semantic Type (STY) [umls:T032] annotated to at least one disease in DisGeNET. STYs are identified by the UMLS TUI. Organism Attribute [umls:T032] umls:T033 Finding UMLS Semantic Type (STY) [umls:T033] annotated to at least one disease in DisGeNET. STYs are identified by the UMLS TUI. Finding [umls:T033] umls:T034 Laboratory or Test Result UMLS Semantic Type (STY) [umls:T034] annotated to at least one disease in DisGeNET. STYs are identified by the UMLS TUI. Laboratory or Test Result [umls:T034] umls:T037 Injury or Poisoning UMLS Semantic Type (STY) [umls:T037] annotated to at least one disease in DisGeNET. STYs are identified by the UMLS TUI. Injury or Poisoning [umls:T037] umls:T039 Physiologic Function UMLS Semantic Type (STY) [umls:T039] annotated to at least one disease in DisGeNET. STYs are identified by the UMLS TUI. Physiologic Function [umls:T039] umls:T040 Organism Function UMLS Semantic Type (STY) [umls:T040] annotated to at least one disease in DisGeNET. STYs are identified by the UMLS TUI. Organism Function [umls:T040] umls:T041 Mental Process UMLS Semantic Type (STY) [umls:T041] annotated to at least one disease in DisGeNET. STYs are identified by the UMLS TUI. Mental Process [umls:T041] umls:T042 Organ or Tissue Function UMLS Semantic Type (STY) [umls:T042] annotated to at least one disease in DisGeNET. STYs are identified by the UMLS TUI. Organ or Tissue Function [umls:T042] umls:T043 Cell Function UMLS Semantic Type (STY) [umls:T043] annotated to at least one disease in DisGeNET. STYs are identified by the UMLS TUI. Cell Function [umls:T043] umls:T044 Molecular Function UMLS Semantic Type (STY) [umls:T044] annotated to at least one disease in DisGeNET. STYs are identified by the UMLS TUI. Molecular Function [umls:T044] umls:T046 Pathologic Function UMLS Semantic Type (STY) [umls:T046] annotated to at least one disease in DisGeNET. STYs are identified by the UMLS TUI. Pathologic Function [umls:T046] umls:T047 Disease or Syndrome UMLS Semantic Type (STY) [umls:T047] annotated to at least one disease in DisGeNET. STYs are identified by the UMLS TUI. Disease or Syndrome [umls:T047] umls:T048 Mental or Behavioral Dysfunction UMLS Semantic Type (STY) [umls:T048] annotated to at least one disease in DisGeNET. STYs are identified by the UMLS TUI. Mental or Behavioral Dysfunction [umls:T048] umls:T049 Cell or Molecular Dysfunction UMLS Semantic Type (STY) [umls:T049] annotated to at least one disease in DisGeNET. STYs are identified by the UMLS TUI. Cell or Molecular Dysfunction [umls:T049] umls:T050 Experimental Model of Disease UMLS Semantic Type (STY) [umls:T050] annotated to at least one disease in DisGeNET. STYs are identified by the UMLS TUI. Experimental Model of Disease [umls:T050] umls:T054 Social Behavior UMLS Semantic Type (STY) [umls:T054] annotated to at least one disease in DisGeNET. STYs are identified by the UMLS TUI. Social Behavior [umls:T054] umls:T055 Individual Behavior UMLS Semantic Type (STY) [umls:T055] annotated to at least one disease in DisGeNET. STYs are identified by the UMLS TUI. Individual Behavior [umls:T055] umls:T059 Laboratory Procedure UMLS Semantic Type (STY) [umls:T059] annotated to at least one disease in DisGeNET. STYs are identified by the UMLS TUI. Laboratory Procedure [umls:T059] umls:T060 Diagnostic Procedure UMLS Semantic Type (STY) [umls:T060] annotated to at least one disease in DisGeNET. STYs are identified by the UMLS TUI. Diagnostic Procedure [umls:T060] umls:T079 Temporal Concept UMLS Semantic Type (STY) [umls:T079] annotated to at least one disease in DisGeNET. STYs are identified by the UMLS TUI. Temporal Concept [umls:T079] umls:T116 Amino Acid, Peptide, or Protein UMLS Semantic Type (STY) [umls:T116] annotated to at least one disease in DisGeNET. STYs are identified by the UMLS TUI. Amino Acid, Peptide, or Protein [umls:T116] umls:T129 Immunologic Factor UMLS Semantic Type (STY) [umls:T129] annotated to at least one disease in DisGeNET. STYs are identified by the UMLS TUI. Immunologic Factor [umls:T129] umls:T184 Sign or Symptom UMLS Semantic Type (STY) [umls:T184] annotated to at least one disease in DisGeNET. STYs are identified by the UMLS TUI. Sign or Symptom [umls:T184] umls:T185 Classification UMLS Semantic Type (STY) [umls:T185] annotated to at least one disease in DisGeNET. STYs are identified by the UMLS TUI. Classification [umls:T185] umls:T190 Anatomical Abnormality UMLS Semantic Type (STY) [umls:T190] annotated to at least one disease in DisGeNET. STYs are identified by the UMLS TUI. Anatomical Abnormality [umls:T190] umls:T191 Neoplastic Process UMLS Semantic Type (STY) [umls:T191] annotated to at least one disease in DisGeNET. STYs are identified by the UMLS TUI. Neoplastic Process [umls:T191] umls:T201 Clinical Attribute UMLS Semantic Type (STY) [umls:T201] annotated to at least one disease in DisGeNET. STYs are identified by the UMLS TUI. Clinical Attribute [umls:T201] C14250 Organism Organism BRIDG NICHD A living thing, such as an animal, a plant, a bacterium, or a fungus. Any individual living (or previously living) being. EXAMPLE(S): animal, human being BiologicEntity Organism Organismal Organisms Taxon organism A living entity. Organism Organism C16612 Gene or Genome Gene BRIDG A functional unit of heredity that occupies a specific position (locus) on a particular chromosome, is capable of reproducing itself exactly at each cell division, and directs the formation of a protein or other product. Comment Requested: In interest of re-using existing standards, should the above definition of Gene be replaced by the following from the NLM - The basic physical and functional unit of heredity. It is made up of DNA and act as instructions to make molecules called proteins. [Source: http://ghr.nlm.nih.gov/handbook/basics/gene] EXAMPLE(S): BRCA1 gene OTHER NAME(S): NOTE(S): The functional and physical unit of heredity passed from parent to offspring. Genes are pieces of DNA, and most genes contain the information for making a specific protein. Gene Genes gene A functional unit of heredity which occupies a specific position on a particular chromosome and serves as the template for a product that contributes to a phenotype or a biological function. The gene as a functional unit consists of a discrete segment of a giant DNA molecule containing the purine (adenine and guanine) and pyrimidine (cytosine and thymine) bases in the ordered and correct sequence that encodes a specific functional product (i.e., a protein or RNA molecule). Gene Gene C17021 Amino Acid, Peptide, or Protein Protein BRIDG GDC A molecule made up of amino acids that are needed for the body to function properly. Proteins are the basis of body structures such as skin and hair and of substances such as enzymes, cytokines, and antibodies. A representation of an organic macromolecule in public resources (e.g., UniProt or NCBI RefSeq) composed of one or more chains (linear polymers) of alpha-L-amino acids linked by peptide bonds and ranging in size from a few thousand to over 1 million Daltons. Comment Requested: In interest of re-using existing standards, should the above definition of Protein be replaced by the following from the NLM -- : A molecule made up of amino acids that are needed for the body to function properly. Proteins are the basis of body structures such as skin and hair and of substances such as enzymes, cytokines, and antibodies. [Source: http://ghr.nlm.nih.gov/glossary=protein] EXAMPLE(S): A protein record from UniProt Knowledgebase: http://www.uniprot.org/uniprot/P38398 OTHER NAME(S): NOTE(S): Protein Protein (NOS) Proteins protein A group of complex organic macromolecules composed of one or more chains (linear polymers) of alpha-L-amino acids linked by peptide bonds and ranging in size from a few thousand to over 1 million Daltons. Proteins are fundamental genetically encoded components of living cells with specific structures and functions dictated by amino acid sequence. Protein Protein C18329 Indicator, Reagent, or Diagnostic Aid Disease Marker Disease Marker Marker, Disease Markers, Disease Specific molecular signature of disease, physiological measurement, genotype structural or functional characteristic, metabolic changes, or other determinant that may simplify the diagnostic process, make diagnoses more accurate, distinguish different causes of disease, or enable physicians to make diagnoses before symptoms appear and to track disease progression. Disease Marker Disease Marker C18469 Molecular Function Protein-Protein Interaction Protein-Protein Interaction Temporary, non-covalent binding between protein molecules. Protein-protein interactions occur as a result of intermolecular physical forces and spatial complementation between domains or motifs. This interaction can be either homotypic or heterotypic and effect protein structure, conformation, and function. Protein-Protein Interaction PPI C25338 Quantitative Concept Score CDISC A number or range of numeric values that assess and order a result or response for purposes of comparison. SCORE Score A number or range of numeric values measuring performance, function, quality, or ability. Score Score C26549 Nucleic Acid, Nucleoside, or Nucleotide Untranslated RNA Functional RNA Non-Coding RNA Noncoding RNA Untranslated RNA ncRNA The product of so-called RNA genes; a functional RNA represents the final product of a gene rather than a transient molecule that will be translated into protein. Untranslated RNA ncRNA C43568 Intellectual Product Gene Symbol BRIDG CTDC A conventional sign used for representing the gene, based on the identified source. EXAMPLE(S): As a string with an optional code, an example of Gene.symbol is as follows: the value "BRCA1" is both the string and the code and the code system name is "HGNC". OTHER NAME(S): NOTE(S): Gene Name Gene Symbol Gene.symbol Official Gene Name gene A unique gene name approved by an organism specific nomenclature committee. Gene Symbol Gene Symbol C7057 Conceptual Entity Disease, Disorder or Finding Disease, Disorder or Finding A condition that is relevant to human neoplasms and non-neoplastic disorders. This includes observations, test results, history and other concepts relevant to the characterization of human pathologic conditions. Disease, Disorder or Finding Disease Adverse reaction to drug All noxious and unintended responses to a medicinal product related to any dose should be considered adverse drug reactions (from US FDA 'Guideline for Industry, Clinical Safety Data Management: Definitions and Standards for Expedited Reporting'). All noxious and unintended responses to a medicinal product related to any dose should be considered adverse drug reactions (from US FDA Guideline for Industry, Clinical Safety Data Management: Definitions and Standards for Expedited Reporting). Adverse reaction to drug Drug reaction Adverse reaction caused by drug (disorder) ADR - Adverse drug reaction Adverse reaction to medication Adverse reaction caused by drug Adverse drug effect Adverse drug reaction Drug Phenotype Side Effect A phenotypic abnormality. UMLS:C4021819 Organ abnormality human_phenotype HP:0000118 This is the root of the phenotypic abnormality subontology of the HPO. Phenotypic abnormality HP:0000118 Disease class A phenotypic abnormality. HPO:probinson ProteinClass Protein class A sequence_variant is a non exact copy of a sequence_feature or genome exhibiting one or more sequence_alteration. Jannovar:sequence_variant VAAST:sequence_variant sequence variant sequence ANNOVAR:unknown SO:0001060 sequence_variant Variant A sequence_variant is a non exact copy of a sequence_feature or genome exhibiting one or more sequence_alteration. SO:ke Jannovar:sequence_variant http://doc-openbio.readthedocs.org/projects/jannovar/en/master/var_effects.html VAAST:sequence_variant ANNOVAR:unknown http://www.openbioinformatics.org/annovar/annovar_download.html ChEMBL Drug Indication Class ChEMBL Drug Indication Class Drug Phenotype Indication ChEMBL Mechanism Class ChEMBL Mechanism Class Drug Target Association ChEMBL Substance Class ChEMBL Substance Class Drug ChEMBL Target Class ChEMBL Target Class Target SIO_000326 A concept is term that refers to a generalization of a set of attributes or entities. concept Semantic Type SIO_000791 A sequence start position is the start position for a sequence of characters. sequence start position Chromosome position SIO_000897 An assocation is a relationship between two or more entities derived by some informational analysis. association Association SIO_000899 A chromosome is a molecular complex of circular or linear DNA and bound proteins. A chromosome is a molecular complex of circular or linear DNA and bound proteins. chromosome Chromosome SIO_000983 A gene-disease association is an association between a gene and a disease. gene-disease association Gene Disease Association SIO_001006 A drug-drug interaction is an interaction in which two drugs interact in such a way to produce a non-additive biological response. drug drug interaction DDI SIO_001351 DisGeNET Disease specificity is a measure of disease coverage. It is calculated from the negative base 2 log of the ratio of number of diseases associated to the total number of diseases. The measure is described here: http://www.disgenet.org/web/DisGeNET/menu/dbinfo#specificity DisGeNET disease specificity Disease Specificity SIO_001352 The DisGeNET pleiotropy index is a measure of specificity as it pertains to classes of disease. The disease pleotropy index is computed from the ratio of the number of disease classes associated with an entity over the total number of disease classes multplied by 100. The measure is defined here: http://www.disgenet.org/web/DisGeNET/menu/dbinfo#pleiotropy DisGeNET Pleiotropy Index Disease Pleiotropy 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. Pathway Pathway DTO protein class [dto:DTO_00102000] in which at least one gene in DisGeNET is classified to. Protein classes are identified by the DTO id. http://drugtargetontology.org/ DTO protein class [dto:DTO_01300327] in which at least one gene in DisGeNET is classified to. Protein classes are identified by the DTO id. http://drugtargetontology.org/ DTO protein class [dto:DTO_02300001] in which at least one gene in DisGeNET is classified to. Protein classes are identified by the DTO id. http://drugtargetontology.org/ DTO protein class [dto:DTO_03300101] in which at least one gene in DisGeNET is classified to. Protein classes are identified by the DTO id. http://drugtargetontology.org/ DTO protein class [dto:DTO_05007378] in which at least one gene in DisGeNET is classified to. Protein classes are identified by the DTO id. http://drugtargetontology.org/ DTO protein class [dto:DTO_05007405] in which at least one gene in DisGeNET is classified to. Protein classes are identified by the DTO id. http://drugtargetontology.org/ DTO protein class [dto:DTO_05007527] in which at least one gene in DisGeNET is classified to. Protein classes are identified by the DTO id. http://drugtargetontology.org/ DTO protein class [dto:DTO_05007530] in which at least one gene in DisGeNET is classified to. Protein classes are identified by the DTO id. http://drugtargetontology.org/ DTO protein class [dto:DTO_05007542] in which at least one gene in DisGeNET is classified to. Protein classes are identified by the DTO id. http://drugtargetontology.org/ DTO protein class [dto:DTO_05007557] in which at least one gene in DisGeNET is classified to. Protein classes are identified by the DTO id. http://drugtargetontology.org/ DTO protein class [dto:DTO_05007575] in which at least one gene in DisGeNET is classified to. Protein classes are identified by the DTO id. http://drugtargetontology.org/ DTO protein class [dto:DTO_05007584] in which at least one gene in DisGeNET is classified to. Protein classes are identified by the DTO id. http://drugtargetontology.org/ DTO protein class [dto:DTO_05007599] in which at least one gene in DisGeNET is classified to. Protein classes are identified by the DTO id. http://drugtargetontology.org/ DTO protein class [dto:DTO_05007608] in which at least one gene in DisGeNET is classified to. Protein classes are identified by the DTO id. http://drugtargetontology.org/ DTO protein class [dto:DTO_05007612] in which at least one gene in DisGeNET is classified to. Protein classes are identified by the DTO id. http://drugtargetontology.org/ DTO protein class [dto:DTO_05007613] in which at least one gene in DisGeNET is classified to. Protein classes are identified by the DTO id. http://drugtargetontology.org/ DTO protein class [dto:DTO_05007616] in which at least one gene in DisGeNET is classified to. Protein classes are identified by the DTO id. http://drugtargetontology.org/ DTO protein class [dto:DTO_05007620] in which at least one gene in DisGeNET is classified to. Protein classes are identified by the DTO id. http://drugtargetontology.org/ DTO protein class [dto:DTO_05007621] in which at least one gene in DisGeNET is classified to. Protein classes are identified by the DTO id. http://drugtargetontology.org/ DTO protein class [dto:DTO_05007624] in which at least one gene in DisGeNET is classified to. Protein classes are identified by the DTO id. http://drugtargetontology.org/ DTO protein class [dto:DTO_05007697] in which at least one gene in DisGeNET is classified to. Protein classes are identified by the DTO id. http://drugtargetontology.org/ Number of newly diagnosed cases in a population in 1 year. annual incidence Prevalence class A collection of clinical entities sharing a set of common features. group of disorders Orpha Refers to a country, a continent or the whole world. geography Prevalence A disease-ncRNA association is an association between a disease and an untranslated RNA (ncRNA). Disease-ncRNA Association Disease ncRNA Association A disease-phenotype association is an association between disease and a phenotype, which corresponds to a subjective evidence of disease perceived by the patient. Disease-Phenotype Association Disease Phenotype Association Association between a disease and a genetic variant. Disease-Variant Association Disease Variant Association Drug-disease associations refer to the effects that can be induced by the interaction between a drug and a disease. Drug-Disease Association Drug Disease Association Drug Disease Associations not classifed as Therapeutic or Marker which are given an associated inferred score. Drug Disease Inferred Drug Disease Inferred 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. Drug Disease Marker Drug Disease Marker 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. Drug Disease Therapeutic Drug Disease Therapeutic 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. Drug-Phenotype Indication Drug Phenotype Indication Secondary and undesirable measurable effects that cause patient phenotype changes in response to the treatment with a drug. Drug-Phenotype Side Effect Drug Phenotype Side Effect Association between a drug and a target in order to achieve disease treatment by different action types or mechanism of action. Drug-Target Association Drug Target Association Observable and detectable signs in a patient due to the effects caused by a disease or a drug causing changes in their original appearence. Phenotype Phenotype Association between two proteins by physical contacts of high specificity that occur in a specific molecular context with a certain confidence value. Protein-Protein Interaction PPI Association between an oprhan disease and the incidence according to the geographical location. Prevalence Prevalence