chem2bio2rdf.owl
type: Ontology
contributor: Bin Chen; Ying Ding; David Wild
date: April, 2011
comment: A web ontology for chemogenomics/systems chemical biology. Current version 1.0 is available at http://chem2bio2rdf.org/chem2bio2rdf.owl see details at http://chem2bio2owl.wikispaces.com
creator: Bin Chen

hasNeighbor
type: ObjectProperty
type: SymmetricProperty
comment: structural similar compounds
range: SmallMolecule
domain: SmallMolecule

SmallMolecule
type: Class
subclass of: PhysicalEntity
comment: Definition: A small bioactive molecule. Small is not precisely defined, but includes all metabolites and most drugs and does not include large polymers, including complex carbohydrates. Comment: Recently, a number of small molecule databases have become available to cross-reference from this class. Examples: glucose, penicillin, phosphatidylinositol Note: Complex carbohydrates are not currently modeled in BioPAX or most pathway databases, due to the lack of a publicly available complex carbohydrate database. Synonyms: Compound, Chemical, Drug related databases: PubChem, ChEBI, DrugBank

hasOutcome
type: ObjectProperty
comment: The experimental results
domain: BioAssay
range: Outcome

BioAssay
type: Class
subclass of: Evidence
disjoint with: Disease
disjoint with: SideEffect
disjoint with: Gene
disjoint with: Interaction
disjoint with: Pathway
disjoint with: PhysicalEntity
comment: Definition: A scientific experiment to measure the effects of some substance on target, cell, or a living organism Comments: refer to BioAssay Ontology project. Related Databases: PubChem BioAssay, ChEMBL Bioassay

Outcome
type: Class
subclass of: UtilityClass
disjoint with: PhysicalProperty
disjoint with: ChemicalStructure
disjoint with: ControlledVocabulary
disjoint with: Evidence
disjoint with: Provenance
disjoint with: Score
disjoint with: Xref
comment: Definition: the output of bioassay experiment

iSA
type: ObjectProperty

confidence
type: ObjectProperty
comment: Confidence in the containing instance. Usually a statistical measure.
domain: Evidence
range: Score

Evidence
type: Class
subclass of: UtilityClass
disjoint with: Provenance
disjoint with: Score
disjoint with: Xref
comment: Definition: The support for a particular assertion, such as the existence of an interaction or pathway. Usage: At least one of confidence, evidenceCode, or experimentalForm must be instantiated when creating an evidence instance. XREF may reference a publication describing the experimental evidence using a publicationXref or may store a description of the experiment in an experimental description database using a unificationXref (if the referenced experiment is the same) or relationshipXref (if it is not identical, but similar in some way e.g. similar in protocol). Evidence is meant to provide more information than just an xref to the source paper. Examples: A description of a molecular binding assay that was used to detect a protein-protein interaction.

Score
type: Class
subclass of: UtilityClass
subclass of: chembio resource:arc4227b67
disjoint with: Xref
comment: Definition: A score associated with a publication reference describing how the score was determined, the name of the method and a comment briefly describing the method. Usage: The xref must contain at least one publication that describes the method used to determine the score value. There is currently no standard way of describing values, so any string is valid. Examples: The statistical significance of a result, e.g. "p<0.05".

dataSource
type: ObjectProperty
comment: A free text description of the source of this data, e.g. a database or person name. This property should be used to describe the source of the data. This is meant to be used by databases that export their data to the BioPAX format or by systems that are integrating data from multiple sources. The granularity of use (specifying the data source in many or few instances) is up to the user. It is intended that this property report the last data source, not all data sources that the data has passed through from creation.
range: Provenance

Provenance
type: Class
subclass of: UtilityClass
subclass of: chembio resource:arc4227b63
disjoint with: Score
disjoint with: Xref
comment: Definition: The direct source of pathway data or score. Usage: This does not store the trail of sources from the generation of the data to this point, only the last known source, such as a database, tool or algorithm. The xref property may contain a publicationXref referencing a publication describing the data source (e.g. a database publication). A unificationXref may be used when pointing to an entry in a database of databases describing this database. Examples: A database, scoring method or person name.

evidence
type: ObjectProperty
comment: Scientific evidence supporting the existence of the entity as described.
range: Evidence

evidenceCode
type: ObjectProperty
comment: A pointer to a term in an external controlled vocabulary, such as the GO, PSI-MI or BioCyc evidence codes, that describes the nature of the support, such as 'traceable author statement' or 'yeast two-hybrid'.
domain: Evidence
range: EvidenceCodeVocabulary

EvidenceCodeVocabulary
type: Class
subclass of: ControlledVocabulary
disjoint with: ExperimentalFormVocabulary
disjoint with: InteractionVocabulary
disjoint with: PhenotypeVocabulary
disjoint with: RelationshipTypeVocabulary
disjoint with: SequenceModificationVocabulary
disjoint with: SequenceRegionVocabulary
disjoint with: TissueVocabulary
comment: Definition: A reference to the PSI Molecular Interaction ontology (MI) experimental method types, including "interaction detection method", "participant identification method", "feature detection method". Homepage at http://www.psidev.info/. Browse at http://www.ebi.ac.uk/ontology-lookup/browse.do?ontName=MI Terms from the Pathway Tools Evidence Ontology may also be used. Homepage http://brg.ai.sri.com/evidence-ontology/

structure
type: ObjectProperty
type: FunctionalProperty
comment: Defines the chemical structure and other information about this molecule, using an instance of class chemicalStructure.
range: ChemicalStructure
domain: SmallMolecule

ChemicalStructure
type: Class
subclass of: UtilityClass
subclass of: chembio resource:arc4227b60
subclass of: chembio resource:arc4227b61
disjoint with: ControlledVocabulary
disjoint with: Evidence
disjoint with: Provenance
disjoint with: Score
disjoint with: Xref
comment: Definition: Describes a small molecule structure. Structure information is stored in the property STRUCTURE-DATA, in one of three formats: the CML format (see URL www.xml-cml.org), the SMILES format (see URL www.daylight.com/dayhtml/smiles/) or the InChI format (http://www.iupac.org/inchi/). The STRUCTURE-FORMAT property specifies which format is used. Comment: By virtue of the expressivity of CML, an instance of this class can also provide additional information about a small molecule, such as its chemical formula, names, and synonyms, if CML is used as the structure format. Examples: The following SMILES string, which describes the structure of glucose-6-phosphate: 'C(OP(=O)(O)O)[CH]1([CH](O)[CH](O)[CH](O)[CH](O)O1)'.

xref
type: ObjectProperty
comment: Values of this property define external cross-references from this entity to entities in external databases.
range: Xref

Xref
type: Class
subclass of: UtilityClass
comment: Definition: A reference from an instance of a class in this ontology to an object in an external resource. Rationale: Xrefs in the future can be removed in the future in favor of explicit miram links. Usage: For most cases one of the subclasses of xref should be used.

adjacent_to
type: ObjectProperty
comment: Note that adjacent_to as thus defined is not a symmetric relation, in contrast to its instance-level counterpart. For it can be the case that Cs are in general such as to be adjacent to instances of C1 while no analogous statement holds for C1s in general in relation to instances of C. Examples are: nuclear membrane adjacent_to cytoplasm; seminal vesicle adjacent_to urinary bladder; ovary adjacent_to parietal pelvic peritoneum
has alternative id: OBO_REL:0000012
has OBO namespace: relationship

agent_in
type: ObjectProperty
has alternative id: OBO_REL:0000022
has OBO namespace: relationship
sub property of: participates_in

participates_in
type: ObjectProperty
has OBO namespace: relationship
has alternative id: OBO_REL:0000020

contained_in
type: ObjectProperty
comment: Containment obtains in each case between material and immaterial continuants, for instance: lung contained_in thoracic cavity; bladder contained_in pelvic cavity. Hence containment is not a transitive relation. If c part_of c1 at t then we have also, by our definition and by the axioms of mereology applied to spatial regions, c located_in c1 at t. Thus, many examples of instance-level location relations for continuants are in fact cases of instance-level parthood. For material continuants location and parthood coincide. Containment is location not involving parthood, and arises only where some immaterial continuant is involved. To understand this relation, we first define overlap for continuants as follows: c1 overlap c2 at t =def for some c, c part_of c1 at t and c part_of c2 at t. The containment relation on the instance level can then be defined (see definition):
has OBO namespace: relationship
has alternative id: OBO_REL:0000010
inverse of: contains

contains
type: ObjectProperty
has alternative id: OBO_REL:0000011
has OBO namespace: relationship

derived_into
type: ObjectProperty
type: TransitiveProperty
has OBO namespace: relationship
has alternative id: OBO_REL:0000016

derives_from
type: ObjectProperty
type: TransitiveProperty
comment: Derivation as a relation between instances. The temporal relation of derivation is more complex. Transformation, on the instance level, is just the relation of identity: each adult is identical to some child existing at some earlier time. Derivation on the instance-level is a relation holding between non-identicals. More precisely, it holds between distinct material continuants when one succeeds the other across a temporal divide in such a way that at least a biologically significant portion of the matter of the earlier continuant is inherited by the later. Thus we will have axioms to the effect that from c derives_from c1 we can infer that c and c1 are not identical and that there is some instant of time t such that c1 exists only prior to and c only subsequent to t. We will also be able to infer that the spatial region occupied by c as it begins to exist at t overlaps with the spatial region occupied by c1 as it ceases to exist in the same instant.
has OBO namespace: relationship
has alternative id: OBO_REL:0000015
inverse of: derived_into

has_agent
type: ObjectProperty
has OBO namespace: relationship
has alternative id: OBO_REL:0000021
inverse of: agent_in
sub property of: has_participant

has_participant
type: ObjectProperty
comment: Has_participant is a primitive instance-level relation between a process, a continuant, and a time at which the continuant participates in some way in the process. The relation obtains, for example, when this particular process of oxygen exchange across this particular alveolar membrane has_participant this particular sample of hemoglobin at this particular time.
has OBO namespace: relationship
has alternative id: OBO_REL:0000019
inverse of: participates_in

has_improper_part
type: ObjectProperty
type: TransitiveProperty
comment: See reasons for obsoletion of improper_part_of
has OBO namespace: relationship
has alternative id: OBO_REL:0000024
sub property of: ObsoleteProperty
sub property of: has_part
inverse of: improper_part_of

has_part
type: ObjectProperty
type: TransitiveProperty
has alternative id: OBO_REL:0000003
has OBO namespace: relationship

improper_part_of
type: ObjectProperty
type: TransitiveProperty
comment: OBSOLETE. The definition is "As for part_of, with the additional constraint that subject and object may be identical". However, part_of is already reflexive, therefore improper_part_of is identical to part_of. If read differently, as "improper_part_of is part_of but not proper_part_of",improper_part_of becomes identity. So, improper_part_of is either identical to part_of or to identity, and not an intuitive synonym for either of them. [Robert Hoehndorf]
has OBO namespace: relationship
has alternative id: OBO_REL:0000025
sub property of: ObsoleteProperty
sub property of: part_of

has_integral_part
type: ObjectProperty
type: TransitiveProperty
has OBO namespace: relationship
has alternative id: OBO_REL:0000005
sub property of: has_part

has_proper_part
type: ObjectProperty
type: TransitiveProperty
has alternative id: OBO_REL:0000007
has OBO namespace: relationship
sub property of: has_part

part_of
type: ObjectProperty
type: TransitiveProperty
comment: Parthood as a relation between instances: The primitive instance-level relation p part_of p1 is illustrated in assertions such as: this instance of rhodopsin mediated phototransduction part_of this instance of visual perception. This relation satisfies at least the following standard axioms of mereology: reflexivity (for all p, p part_of p); anti-symmetry (for all p, p1, if p part_of p1 and p1 part_of p then p and p1 are identical); and transitivity (for all p, p1, p2, if p part_of p1 and p1 part_of p2, then p part_of p2). Analogous axioms hold also for parthood as a relation between spatial regions. For parthood as a relation between continuants, these axioms need to be modified to take account of the incorporation of a temporal argument. Thus for example the axiom of transitivity for continuants will assert that if c part_of c1 at t and c1 part_of c2 at t, then also c part_of c2 at t. Parthood as a relation between classes: To define part_of as a relation between classes we again need to distinguish the two cases of continuants and processes, even though the explicit reference to instants of time now falls away. For continuants, we have C part_of C1 if and only if any instance of C at any time is an instance-level part of some instance of C1 at that time, as for example in: cell nucleus part_ of cell.
has OBO namespace: relationship
has alternative id: OBO_REL:0000002
inverse of: has_part

integral_part_of
type: ObjectProperty
type: TransitiveProperty
has alternative id: OBO_REL:0000004
has OBO namespace: relationship
inverse of: has_integral_part
sub property of: part_of

located_in
type: ObjectProperty
type: TransitiveProperty
comment: Location as a relation between instances: The primitive instance-level relation c located_in r at t reflects the fact that each continuant is at any given time associated with exactly one spatial region, namely its exact location. Following we can use this relation to define a further instance-level location relation - not between a continuant and the region which it exactly occupies, but rather between one continuant and another. c is located in c1, in this sense, whenever the spatial region occupied by c is part_of the spatial region occupied by c1. Note that this relation comprehends both the relation of exact location between one continuant and another which obtains when r and r1 are identical (for example, when a portion of fluid exactly fills a cavity), as well as those sorts of inexact location relations which obtain, for example, between brain and head or between ovum and uterus
has alternative id: OBO_REL:0000008
has OBO namespace: relationship
inverse of: location_of

location_of
type: ObjectProperty
type: TransitiveProperty
has alternative id: OBO_REL:0000009
has OBO namespace: relationship

preceded_by
type: ObjectProperty
type: TransitiveProperty
comment: An example is: translation preceded_by transcription; aging preceded_by development (not however death preceded_by aging). Where derives_from links classes of continuants, preceded_by links classes of processes. Clearly, however, these two relations are not independent of each other. Thus if cells of type C1 derive_from cells of type C, then any cell division involving an instance of C1 in a given lineage is preceded_by cellular processes involving an instance of C. The assertion P preceded_by P1 tells us something about Ps in general: that is, it tells us something about what happened earlier, given what we know about what happened later. Thus it does not provide information pointing in the opposite direction, concerning instances of P1 in general; that is, that each is such as to be succeeded by some instance of P. Note that an assertion to the effect that P preceded_by P1 is rather weak; it tells us little about the relations between the underlying instances in virtue of which the preceded_by relation obtains. Typically we will be interested in stronger relations, for example in the relation immediately_preceded_by, or in relations which combine preceded_by with a condition to the effect that the corresponding instances of P and P1 share participants, or that their participants are connected by relations of derivation, or (as a first step along the road to a treatment of causality) that the one process in some way affects (for example, initiates or regulates) the other.
has OBO namespace: relationship
has alternative id: OBO_REL:0000017
inverse of: precedes

precedes
type: ObjectProperty
type: TransitiveProperty
has OBO namespace: relationship
has alternative id: OBO_REL:0000018

proper_part_of
type: ObjectProperty
type: TransitiveProperty
has OBO namespace: relationship
has alternative id: OBO_REL:0000006
inverse of: has_proper_part
sub property of: part_of

relationship
type: ObjectProperty
comment: this relation was superfluous, so it has been obsoleted
has OBO namespace: relationship
sub property of: ObsoleteProperty

transformation_of
type: ObjectProperty
type: TransitiveProperty
comment: When an embryonic oenocyte (a type of insect cell) is transformed into a larval oenocyte, one and the same continuant entity preserves its identity while instantiating distinct classes at distinct times. The class-level relation transformation_of obtains between continuant classes C and C1 wherever each instance of the class C is such as to have existed at some earlier time as an instance of the distinct class C1 (see Figure 2 in paper). This relation is illustrated first of all at the molecular level of granularity by the relation between mature RNA and the pre-RNA from which it is processed, or between (UV-induced) thymine-dimer and thymine dinucleotide. At coarser levels of granularity it is illustrated by the transformations involved in the creation of red blood cells, for example, from reticulocyte to erythrocyte, and by processes of development, for example, from larva to pupa, or from (post-gastrular) embryo to fetus or from child to adult. It is also manifest in pathological transformations, for example, of normal colon into carcinomatous colon. In each such case, one and the same continuant entity instantiates distinct classes at different times in virtue of phenotypic changes.
has OBO namespace: relationship
has alternative id: OBO_REL:0000013

transformed_into
type: ObjectProperty
comment: Obsoleted
has alternative id: OBO_REL:0000014
has OBO namespace: relationship
sub property of: ObsoleteProperty

abstract
type: DatatypeProperty
has definition: The abstract of a paper
range: Literal

actionType
type: DatatypeProperty
comment: The action type of drug drug interaction. refer to DCDB drug action type. Example: same target; metabolism
domain: DrugDrugInteraction
range: string

DrugDrugInteraction
type: Class
subclass of: Interaction
subclass of: chembio resource:arc4227b54
disjoint with: DrugInducedSideEffect
disjoint with: DrugTreament
disjoint with: ProteinProteinInteraction
comment: Definition: A drug interaction is a situation in which a substance affects the activity of a drug, i.e. the effects are increased or decreased, or they produce a new effect that neither produces on its own.(from wiki) Comments: Also consider combinatorial drugs, which shows polypharmacology Instance examples: http://chem2bio2rdf.org/dcdb/resource/dcdb_drug_interaction/DI00001 Related Databases: DCDB, DrugBank

assayType
type: DatatypeProperty
type: FunctionalProperty
comment: bioassy type
domain: BioAssay
range: chembio resource:arc4227b1

chembio resource:arc4227b2
first: ADMET
rest: chembio resource:arc4227b3

chembio resource:arc4227b3
first: binding
rest: chembio resource:arc4227b4

chembio resource:arc4227b4
first: functional
rest: nil

biologicalInterest
type: DatatypeProperty
comment: Chemical proteion interaction has biological interest. e.g, compound has positive results in bioassay(i.e, IC50<30um), compound is the subtrate of a reaction, etc.
domain: ChemicalProteinInteraction
range: boolean

ChemicalProteinInteraction
type: Class
subclass of: Interaction
subclass of: chembio resource:arc4227b52
subclass of: chembio resource:arc4227b53
disjoint with: DrugDrugInteraction
disjoint with: DrugInducedSideEffect
disjoint with: DrugTreament
disjoint with: ProteinProteinInteraction
comment: Definition: a biological relationship between compound and protein (or associated entities (i.e., mRNA)). Comments: Related Databases: ChEMBL, BindingDB, DPSP Ki, TTD, BindingMOAD, DrugBank, CTD, MATADOR, ArrayExpress, KEGG

brandName
type: DatatypeProperty
comment: drug brand name
range: string

categoriesOfEvidence
type: DatatypeProperty

description
type: DatatypeProperty
range: string

disorderClass
type: DatatypeProperty
type: FunctionalProperty
comment: disorder classification, refer to OMIM example: metabolic, Bone, Cancer
domain: Disease
range: string

Disease
type: Class
subclass of: Entity
disjoint with: Gene
disjoint with: Interaction
disjoint with: Pathway
disjoint with: PhysicalEntity
comment: 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. Comments: refer to OMIM Synonyms: Disorder Related Databases: OMIM, CTD Disease, PharmGKB disease, Disease ontology

drugTarget
type: DatatypeProperty
comment: whether the protein/gene is drug target. refer to DrugBank, TTD
domain: ChemicalProteinInteraction
range: boolean

drugType
type: DatatypeProperty
comment: drug type. Refer to DrugBank
range: chembio resource:arc4227b5

chembio resource:arc4227b6
first: approved
rest: chembio resource:arc4227b7

chembio resource:arc4227b7
first: biotech
rest: chembio resource:arc4227b8

chembio resource:arc4227b8
first: illicit
rest: chembio resource:arc4227b9

chembio resource:arc4227b9
first: investigational
rest: chembio resource:arc4227b10

chembio resource:arc4227b10
first: nutraceutical
rest: chembio resource:arc4227b11

chembio resource:arc4227b11
first: small molecule
rest: chembio resource:arc4227b12

chembio resource:arc4227b12
first: withdrawn
rest: nil

experimentType
type: DatatypeProperty
comment: include in vitro, in vivo, two-hybrid, etc.
domain: ProteinProteinInteraction

ProteinProteinInteraction
type: Class
subclass of: Interaction
subclass of: chembio resource:arc4227b59
comment: Definition: two or more proteins bind together, often to carry out their biological function Comments: consider protein protein or protein DNA interaction. Cover yeast 2-hybrid data Instance examples: Related Databases: HPRD, DIP, BIOGRID

fingerprint
type: DatatypeProperty
type: FunctionalProperty
comment: 166 MDL public keys
domain: SmallMolecule
range: string

gOID
type: DatatypeProperty
comment: Gene Ontology ID

geneFamily
type: DatatypeProperty
type: FunctionalProperty
comment: refer to HGNC gene family
range: string

group
type: DatatypeProperty
comment: it include small molecule, biotech, etc.
range: string

iSSN
type: DatatypeProperty
range: string

identifier
type: DatatypeProperty
comment: source id, either primary id of the original source or url
range: string

identifierType
type: DatatypeProperty
comment: source name (e.g., DrugBank, PubChem, etc)

indication
type: DatatypeProperty
range: string

journalName
type: DatatypeProperty
range: string

logP
type: DatatypeProperty
type: FunctionalProperty
has db xref: http://semanticscience.org/resource/CHEMINF_000251
has definition: The logarithm of octanol-water partition coefficient, which is the ratio of the molecules dissolved in octanol to those dissolved in pure un-ionized water upon mixture equilibration. This can be measured or predicted. The value is dimensionless. May depend on molecular conformation when computed
domain: PhysicalProperty
range: float

PhysicalProperty
type: Class
subclass of: UtilityClass
disjoint with: ChemicalStructure
disjoint with: ControlledVocabulary
disjoint with: Evidence
disjoint with: Provenance
disjoint with: Score
disjoint with: Xref
comment: Definition: Physical property of small molecule

measurement
type: DatatypeProperty
type: FunctionalProperty
comment: The method to measure the outcome. Example: Ki, Kd, IC50, EC50
domain: Outcome

mechanismOfAction
type: DatatypeProperty
range: string

numAtoms
type: DatatypeProperty
type: FunctionalProperty
comment: number of atoms
domain: PhysicalProperty
range: int

numHBAcceptors
type: DatatypeProperty
type: FunctionalProperty
comment: number of hydrogen acceptors
domain: PhysicalProperty
range: int

numHBDonors
type: DatatypeProperty
type: FunctionalProperty
comment: number of hydrogen donors
domain: PhysicalProperty
range: int

numRotatableBonds
type: DatatypeProperty
type: FunctionalProperty
comment: number of rotatable bonds
domain: PhysicalProperty
range: int

organism
type: DatatypeProperty
range: string

pharmacalClassification
type: DatatypeProperty
comment: pharmacal classification for drug drug interaction, refer to DCDB. Example: pharmacodynamical, pharmacokinetical
domain: DrugDrugInteraction
range: string

pharmacology
type: DatatypeProperty
range: string

pmid
type: DatatypeProperty
comment: pubmed id
range: int

relation
type: DatatypeProperty
comment: includes: >,>=,<=,<,=,~
domain: Outcome

synonym
type: DatatypeProperty
range: string

tissue
type: DatatypeProperty
range: string

unit
type: DatatypeProperty
comment: outcome unit. example: um, nm
domain: Outcome

value
type: DatatypeProperty
domain: Outcome
range: double

author
type: DatatypeProperty
comment: The authors of this publication, one per property value.
domain: PublicationXref
range: string

PublicationXref
type: Class
subclass of: Xref
disjoint with: UnificationXref
comment: Definition: An xref that defines a reference to a publication such as a book, journal article, web page, or software manual. Usage: The reference may or may not be in a database, although references to PubMed are preferred when possible. The publication should make a direct reference to the instance it is attached to. Publication xrefs should make use of PubMed IDs wherever possible. The DB property of an xref to an entry in PubMed should use the string "PubMed" and not "MEDLINE". Examples: PubMed:10234245

availability
type: DatatypeProperty
comment: Describes the availability of this data (e.g. a copyright statement).
range: string

catalysisDirection
type: DatatypeProperty
type: FunctionalProperty
comment: This property represents the direction of this catalysis under all physiological conditions if there is one. Note that chemically a catalyst will increase the rate of the reaction in both directions. In biology, however, there are cases where the enzyme is expressed only when the controlled bidirectional conversion is on one side of the chemical equilibrium [todo : example]. If that is the case and the controller, under biological conditions, is always catalyzing the conversion in one direction then this fact can be captured using this property. If the enzyme is active for both directions, or the conversion is not bidirectional, this property should be left empty.
range: chembio resource:arc4227b13

chembio resource:arc4227b14
first: LEFT-TO-RIGHT
rest: chembio resource:arc4227b15

chembio resource:arc4227b15
first: RIGHT-TO-LEFT
rest: nil

chemicalFormula
type: DatatypeProperty
type: FunctionalProperty
comment: The chemical formula of the small molecule. Note: chemical formula can also be stored in the STRUCTURE property (in CML). In case of disagreement between the value of this property and that in the CML file, the CML value takes precedence.
domain: SmallMolecule
range: string

comment
type: DatatypeProperty
comment: Comment on the data in the container class. This property should be used instead of the OWL documentation elements (rdfs:comment) for instances because information in 'comment' is data to be exchanged, whereas the rdfs:comment field is used for metadata about the structure of the BioPAX ontology.
range: string

controlType
type: DatatypeProperty
type: FunctionalProperty
comment: Defines the nature of the control relationship between the CONTROLLER and the CONTROLLED entities. The following terms are possible values: ACTIVATION: General activation. Compounds that activate the specified enzyme activity by an unknown mechanism. The mechanism is defined as unknown, because either the mechanism has yet to be elucidated in the experimental literature, or the paper(s) curated thus far do not define the mechanism, and a full literature search has yet to be performed. The following term can not be used in the catalysis class: INHIBITION: General inhibition. Compounds that inhibit the specified enzyme activity by an unknown mechanism. The mechanism is defined as unknown, because either the mechanism has yet to be elucidated in the experimental literature, or the paper(s) curated thus far do not define the mechanism, and a full literature search has yet to be performed. The following terms can only be used in the modulation class (these definitions from EcoCyc): INHIBITION-ALLOSTERIC Allosteric inhibitors decrease the specified enzyme activity by binding reversibly to the enzyme and inducing a conformational change that decreases the affinity of the enzyme to its substrates without affecting its VMAX. Allosteric inhibitors can be competitive or noncompetitive inhibitors, therefore, those inhibition categories can be used in conjunction with this category. INHIBITION-COMPETITIVE Competitive inhibitors are compounds that competitively inhibit the specified enzyme activity by binding reversibly to the enzyme and preventing the substrate from binding. Binding of the inhibitor and substrate are mutually exclusive because it is assumed that the inhibitor and substrate can both bind only to the free enzyme. A competitive inhibitor can either bind to the active site of the enzyme, directly excluding the substrate from binding there, or it can bind to another site on the enzyme, altering the conformation of the enzyme such that the substrate can not bind to th…
range: chembio resource:arc4227b16

chembio resource:arc4227b17
first: ACTIVATION
rest: chembio resource:arc4227b18

chembio resource:arc4227b18
first: ACTIVATION-ALLOSTERIC
rest: chembio resource:arc4227b19

chembio resource:arc4227b19
first: ACTIVATION-NONALLOSTERIC
rest: chembio resource:arc4227b20

chembio resource:arc4227b20
first: INHIBITION
rest: chembio resource:arc4227b21

chembio resource:arc4227b21
first: INHIBITION-ALLOSTERIC
rest: chembio resource:arc4227b22

chembio resource:arc4227b22
first: INHIBITION-COMPETITIVE
rest: chembio resource:arc4227b23

chembio resource:arc4227b23
first: INHIBITION-IRREVERSIBLE
rest: chembio resource:arc4227b24

chembio resource:arc4227b24
first: INHIBITION-NONCOMPETITIVE
rest: chembio resource:arc4227b25

chembio resource:arc4227b25
first: INHIBITION-OTHER
rest: chembio resource:arc4227b26

chembio resource:arc4227b26
first: INHIBITION-UNCOMPETITIVE
rest: nil

conversionDirection
type: DatatypeProperty
type: FunctionalProperty
comment: This property represents the direction of the reaction. If a reaction is fundamentally irreversible, then it will run in a single direction under all contexts. Otherwise it is reversible.
range: chembio resource:arc4227b27

chembio resource:arc4227b28
first: LEFT-TO-RIGHT
rest: chembio resource:arc4227b29

chembio resource:arc4227b29
first: REVERSIBLE
rest: chembio resource:arc4227b30

chembio resource:arc4227b30
first: RIGHT-TO-LEFT
rest: nil

db
type: DatatypeProperty
type: FunctionalProperty
comment: The name of the external database to which this xref refers.
domain: Xref
range: string

dbVersion
type: DatatypeProperty
type: FunctionalProperty
comment: The version of the external database in which this xref was last known to be valid. Resources may have recommendations for referencing dataset versions. For instance, the Gene Ontology recommends listing the date the GO terms were downloaded.
domain: Xref
range: string

deltaGPrime0
type: DatatypeProperty
type: FunctionalProperty
comment: For biochemical reactions, this property refers to the standard transformed Gibbs energy change for a reaction written in terms of biochemical reactants (sums of species), delta-G'o. delta-G'o = -RT lnK' and delta-G'o = delta-H'o - T delta-S'o delta-G'o has units of kJ/mol. Like K', it is a function of temperature (T), ionic strength (I), pH, and pMg (pMg = -log10[Mg2+]). Therefore, these quantities must be specified, and values for DELTA-G for biochemical reactions are represented as 5-tuples of the form (delta-G'o T I pH pMg). (This definition from EcoCyc)
range: float

deltaH
type: DatatypeProperty
comment: For biochemical reactions, this property refers to the standard transformed enthalpy change for a reaction written in terms of biochemical reactants (sums of species), delta-H'o. delta-G'o = delta-H'o - T delta-S'o Units: kJ/mole (This definition from EcoCyc)
range: float

deltaS
type: DatatypeProperty
comment: For biochemical reactions, this property refers to the standard transformed entropy change for a reaction written in terms of biochemical reactants (sums of species), delta-S'o. delta-G'o = delta-H'o - T delta-S'o (This definition from EcoCyc)
range: float

displayName
type: DatatypeProperty
type: FunctionalProperty
comment: An abbreviated name for this entity, preferably a name that is short enough to be used in a visualization application to label a graphical element that represents this entity. If no short name is available, an xref may be used for this purpose by the visualization application.
sub property of: name
range: string

name
type: DatatypeProperty
comment: One or more synonyms for the name of this individual. This should include the values of the standardName and displayName property so that it is easy to find all known names in one place.
range: string

eCNumber
type: DatatypeProperty
comment: The unique number assigned to a reaction by the Enzyme Commission of the International Union of Biochemistry and Molecular Biology. Note that not all biochemical reactions currently have EC numbers assigned to them.
range: string

id
type: DatatypeProperty
type: FunctionalProperty
comment: The primary identifier in the external database of the object to which this xref refers.
domain: Xref
range: string

idVersion
type: DatatypeProperty
type: FunctionalProperty
comment: The version number of the identifier (ID). E.g. The RefSeq accession number NM_005228.3 should be split into NM_005228 as the ID and 3 as the ID-VERSION.
domain: Xref
range: string

intraMolecular
type: DatatypeProperty
type: FunctionalProperty
comment: This flag represents whether the binding feature is within the same molecule or not.
range: boolean

ionicStrength
type: DatatypeProperty
type: FunctionalProperty
comment: The ionic strength is defined as half of the total sum of the concentration (ci) of every ionic species (i) in the solution times the square of its charge (zi). For example, the ionic strength of a 0.1 M solution of CaCl2 is 0.5 x (0.1 x 22 + 0.2 x 12) = 0.3 M (Definition from http://www.lsbu.ac.uk/biology/enztech/ph.html)
range: float

kPrime
type: DatatypeProperty
type: FunctionalProperty
comment: The apparent equilibrium constant K'. Concentrations in the equilibrium constant equation refer to the total concentrations of all forms of particular biochemical reactants. For example, in the equilibrium constant equation for the biochemical reaction in which ATP is hydrolyzed to ADP and inorganic phosphate: K' = [ADP][Pi]/[ATP], The concentration of ATP refers to the total concentration of all of the following species: [ATP] = [ATP4-] + [HATP3-] + [H2ATP2-] + [MgATP2-] + [MgHATP-] + [Mg2ATP]. The apparent equilibrium constant is formally dimensionless, and can be kept so by inclusion of as many of the terms (1 mol/dm3) in the numerator or denominator as necessary. It is a function of temperature (T), ionic strength (I), pH, and pMg (pMg = -log10[Mg2+]). (Definition from EcoCyc)
range: float

molecularWeight
type: DatatypeProperty
type: FunctionalProperty
comment: Defines the molecular weight of the molecule, in daltons.
range: float

pMg
type: DatatypeProperty
type: FunctionalProperty
comment: A measure of the concentration of magnesium (Mg) in solution. (pMg = -log10[Mg2+])
range: float

patoData
type: DatatypeProperty
type: FunctionalProperty
comment: The phenotype data from PATO, formatted as PhenoXML (defined at http://www.fruitfly.org/~cjm/obd/formats.html)
domain: PhenotypeVocabulary
range: string

PhenotypeVocabulary
type: Class
subclass of: ControlledVocabulary
disjoint with: RelationshipTypeVocabulary
disjoint with: SequenceModificationVocabulary
disjoint with: SequenceRegionVocabulary
disjoint with: TissueVocabulary
comment: Definition: The phenotype measured in the experiment e.g. growth rate or viability of a cell. This is only the type, not the value e.g. for a synthetic lethal interaction, the phenotype is viability, specified by ID: PATO:0000169, "viability", not the value (specified by ID: PATO:0000718, "lethal (sensu genetics)". A single term in a phenotype controlled vocabulary can be referenced using the xref, or the PhenoXML describing the PATO EQ model phenotype description can be stored as a string in PATO-DATA.

ph
type: DatatypeProperty
type: FunctionalProperty
comment: A measure of acidity and alkalinity of a solution that is a number on a scale on which a value of 7 represents neutrality and lower numbers indicate increasing acidity and higher numbers increasing alkalinity and on which each unit of change represents a tenfold change in acidity or alkalinity and that is the negative logarithm of the effective hydrogen-ion concentration or hydrogen-ion activity in gram equivalents per liter of the solution. (Definition from Merriam-Webster Dictionary)
domain: BioAssay
range: float

positionStatus
type: DatatypeProperty
type: FunctionalProperty
comment: The confidence status of the sequence position. This could be: EQUAL: The SEQUENCE-POSITION is known to be at the SEQUENCE-POSITION. GREATER-THAN: The site is greater than the SEQUENCE-POSITION. LESS-THAN: The site is less than the SEQUENCE-POSITION.
range: chembio resource:arc4227b31

chembio resource:arc4227b32
first: EQUAL
rest: chembio resource:arc4227b33

chembio resource:arc4227b33
first: GREATER-THAN
rest: chembio resource:arc4227b34

chembio resource:arc4227b34
first: LESS-THAN
rest: nil

sequence
type: DatatypeProperty
type: FunctionalProperty
comment: Polymer sequence in uppercase letters. For DNA, usually A,C,G,T letters representing the nucleosides of adenine, cytosine, guanine and thymine, respectively; for RNA, usually A, C, U, G; for protein, usually the letters corresponding to the 20 letter IUPAC amino acid code.
range: string

sequencePosition
type: DatatypeProperty
type: FunctionalProperty
comment: The integer listed gives the position. The first base or amino acid is position 1. In combination with the numeric value, the property 'POSITION-STATUS' allows to express fuzzy positions, e.g. 'less than 4'.
range: int

source
type: DatatypeProperty
comment: The source in which the reference was published, such as: a book title, or a journal title and volume and pages.
domain: PublicationXref
range: string

spontaneous
type: DatatypeProperty
type: FunctionalProperty
comment: Specifies whether a conversion occurs spontaneously or not. If the spontaneity is not known, the SPONTANEOUS property should be left empty.
range: boolean

standardName
type: DatatypeProperty
type: FunctionalProperty
comment: The preferred full name for this entity.
sub property of: name
range: string

stepDirection
type: DatatypeProperty
type: FunctionalProperty
comment: Direction of the conversion in this particular pathway context. This property can be used for annotating direction of enzymatic activity. Even if an enzyme catalyzes a reaction reversibly, the flow of matter through the pathway will force the equilibrium in a given direction for that particular pathway.
range: chembio resource:arc4227b35

chembio resource:arc4227b36
first: LEFT-TO-RIGHT
rest: chembio resource:arc4227b37

chembio resource:arc4227b37
first: REVERSIBLE
rest: chembio resource:arc4227b38

chembio resource:arc4227b38
first: RIGHT-TO-LEFT
rest: nil

stoichiometricCoefficient
type: DatatypeProperty
type: FunctionalProperty
comment: Stoichiometric coefficient for one of the entities in an interaction or complex. This value can be any rational number. Generic values such as "n" or "n+1" should not be used - polymers are currently not covered.
range: float

structureData
type: DatatypeProperty
type: FunctionalProperty
comment: This property holds a string of data defining chemical structure or other information, in either the CML or SMILES format, as specified in property Structure-Format. If, for example, the CML format is used, then the value of this property is a string containing the XML encoding of the CML data.
domain: ChemicalStructure
range: string

structureFormat
type: DatatypeProperty
type: FunctionalProperty
comment: This property specifies which format is used to define chemical structure data.
domain: ChemicalStructure
range: chembio resource:arc4227b39
range: chembio resource:arc4227b43

chembio resource:arc4227b40
first: CML
rest: chembio resource:arc4227b41

chembio resource:arc4227b41
first: InChI
rest: chembio resource:arc4227b42

chembio resource:arc4227b42
first: SMILES
rest: nil

chembio resource:arc4227b44
first: InChi
rest: chembio resource:arc4227b45

chembio resource:arc4227b45
first: openeyeCanonicalSMILES
rest: chembio resource:arc4227b46

chembio resource:arc4227b46
first: openeyeISOSMILES
rest: chembio resource:arc4227b47

chembio resource:arc4227b47
first: openeye_can_smiles
rest: chembio resource:arc4227b48

chembio resource:arc4227b48
first: openeye_iso_smiles
rest: nil

temperature
type: DatatypeProperty
type: FunctionalProperty
comment: Temperature in Celsius
range: float

templateDirection
type: DatatypeProperty
type: FunctionalProperty
comment: The direction of the template reaction on the template.
range: chembio resource:arc4227b49

chembio resource:arc4227b50
first: FORWARD
rest: chembio resource:arc4227b51

chembio resource:arc4227b51
first: REVERSE
rest: nil

term
type: DatatypeProperty
comment: The external controlled vocabulary term.
domain: ControlledVocabulary
range: string

ControlledVocabulary
type: Class
subclass of: UtilityClass
subclass of: chembio resource:arc4227b62
disjoint with: Evidence
disjoint with: Provenance
disjoint with: Score
disjoint with: Xref
comment: Used to reference terms from external controlled vocabularies (CVs) from the ontology. To support consistency and compatibility, open, freely available CVs should be used whenever possible, such as the Gene Ontology (GO)15 or other open biological CVs listed on the OBO website (http://obo.sourceforge.net/). See the section on controlled vocabularies in Section 4 for more information.

title
type: DatatypeProperty
type: FunctionalProperty
comment: The title of the publication.
domain: PublicationXref
range: string

url
type: DatatypeProperty
comment: The URL at which the publication can be found, if it is available through the Web.
domain: PublicationXref
range: string

value
type: DatatypeProperty
type: FunctionalProperty
comment: The value of the score.
domain: Score
range: string

year
type: DatatypeProperty
type: FunctionalProperty
comment: The year in which this publication was published.
domain: PublicationXref
range: int

ADP-ribosylation
type: Class
subclass of: Ribosylation
comment: Definition: The addition of a ADP-ribosyl group.

Ribosylation
type: Class
subclass of: MacromoleculeMetabolicProcess
comment: Definition: The addition of a ribosyl group.

Abundance
type: Class
subclass of: ProteinRegulatesChemical
disjoint with: SmallMoleculeMetabolicProcess
disjoint with: Transport
comment: Definition: The abundance of a chemical (if chemical synthesis is not known). Example: CYP27B1 protein affects the abundance of Calcitriol

ProteinRegulatesChemical
type: Class
subclass of: ChemicalProteinInteraction
comment: Definition: protein regulates the function or property of small molecule.

SmallMoleculeMetabolicProcess
type: Class
subclass of: ProteinRegulatesChemical
disjoint with: Transport
comment: Definition: The chemical reactions involving small molecules, any monomeric molecule of small relative molecular mass Synonym: Reaction
has db xref: GO:0044281

Transport
type: Class
subclass of: ProteinRegulatesChemical
comment: Definition: The movement of a molecule into or out of a cell.

Acetylation
type: Class
subclass of: MacromoleculeMetabolicProcess
comment: Definition: The addition of an acetyl group. Example: resveratrol results in decreased acetylation of TRP53 protein

MacromoleculeMetabolicProcess
type: Class
subclass of: ChemicalRegulatesProtein
disjoint with: Mutagenesis
disjoint with: Splicing
disjoint with: Stability
has db xref: GO:0043170
has definition: The chemical reactions and pathways involving macromolecules, any molecule of high relative molecular mass, the structure of which essentially comprises the multiple repetition of units derived, actually or conceptually, from molecules of low relative molecular mass
comment: Definition: The biochemical alteration of a molecule's structure (does not include changes in expression, stability, folding, localization, splicing).

Activation
type: Class
subclass of: Binding
disjoint with: Inhibition
comment: Definition: Any process that activates or increases the rate or extent of binding, the selective interaction of a molecule with one or more specific sites on another molecule. Synonym: positive regulation of binding; activation of binding
has db xref: GO:0051099

Binding
type: Class
subclass of: DirectActivityRegulation
comment: Definition:The selective, often stoichiometric, interaction of a molecule with one or more specific sites on another molecule. Comments: In general, it describes the physical interaction between compound and gene (or gene expression products), it always has binding affinity values. Related Databases: BindingDB, ChEMBL, PubChem BioAssay, Kidb
has db xref: GO:0005488

Inhibition
type: Class
subclass of: Binding
has db xref: GO:0051100
comment: Definition: Any process that stops or reduces the rate or extent of binding, the selective interaction of a molecule with one or more specific sites on another molecule Synonym: negative regulation of binding; inhibition of binding

Activity
type: Class
subclass of: ChemicalRegulatesProtein
disjoint with: Expression
disjoint with: Folding
disjoint with: Localization
disjoint with: MacromoleculeMetabolicProcess
disjoint with: Mutagenesis
disjoint with: Splicing
disjoint with: Stability
comment: Definition: An elemental function of a molecule.

ChemicalRegulatesProtein
type: Class
subclass of: ChemicalProteinInteraction
comment: Definition: Small molecule regulates the function or property of protein (or associated entities (i.e., mRNA))

Expression
type: Class
subclass of: ChemicalRegulatesProtein
disjoint with: Folding
disjoint with: Localization
disjoint with: MacromoleculeMetabolicProcess
disjoint with: Mutagenesis
disjoint with: Splicing
disjoint with: Stability
comment: Definition: The process in which a gene's sequence is converted into a mature gene product or products (proteins or RNA).
has db xref: GO:0010468

Folding
type: Class
subclass of: ChemicalRegulatesProtein
disjoint with: Localization
disjoint with: MacromoleculeMetabolicProcess
disjoint with: Mutagenesis
disjoint with: Splicing
disjoint with: Stability
has db xref: GO:0006457
comment: Definition: The bending and positioning of a molecule to achieve conformational integrity. Example: 1-Butanol affects the folding of GH1 protein.
has definition: The process of assisting in the covalent and noncovalent assembly of single chain polypeptides or multisubunit complexes into the correct tertiary structure.

Localization
type: Class
subclass of: ChemicalRegulatesProtein
disjoint with: MacromoleculeMetabolicProcess
disjoint with: Mutagenesis
disjoint with: Splicing
disjoint with: Stability
has db xref: GO:0051179
comment: Definition: Part of the cell where a molecule resides. Example: Cyclophosphamide affects the localization of HCRT protein.
has definition: Any process in which a cell, a substance, or a cellular entity, such as a protein complex or organelle, is transported to, and/or maintained in a specific location.

Mutagenesis
type: Class
subclass of: ChemicalRegulatesProtein
disjoint with: Splicing
disjoint with: Stability
comment: Definition: The genetic alteration of a gene product. Example: Acrylamide results in increased mutagenesis of HPRT1 gene Comment: This term was made obsolete in GO because mutagenesis is not a valid biological process in which gene products would normally participate.
has db xref: GO:0006280

Splicing
type: Class
subclass of: ChemicalRegulatesProtein
disjoint with: Stability
has db xref: GO:0006371
comment: Definition: The removal of introns to generate mRNA. Example: Fluorouracil affects the splicing of GAPDH mRNA. Comment: This term was made obsoletein GO because it represents several different processes.

Stability
type: Class
subclass of: ChemicalRegulatesProtein
comment: Definition: Overall molecular integrity. Example: Pentobarbital results in decreased stability of GSTD2 mRNA.

Acylation
type: Class
subclass of: MacromoleculeMetabolicProcess
comment: Definition: The addition of an acyl group.

Alkylation
type: Class
subclass of: MacromoleculeMetabolicProcess
comment: Definition: The addition of an alkyl group.

Amination
type: Class
subclass of: SmallMoleculeMetabolicProcess
comment: Definition: The addition of an amine group.

DirectActivityRegulation
type: Class
subclass of: Activity
disjoint with: Definition: The process of regulation via indirect interaction
comment: Definition: The process of regulation via direct physical interaction

SideEffect
type: Class
subclass of: Entity
disjoint with: Gene
disjoint with: Interaction
disjoint with: Pathway
disjoint with: PhysicalEntity
comment: Definition: undesired effect from a medicine Comments: refer to SIDER, it does not need to be harmful. Synonyms: AdverseEffect, DrugAdverseReaction Related Databases: SIDER Popular Identifiers: umls_id

Gene
type: Class
subclass of: Entity
disjoint with: Interaction
disjoint with: Pathway
disjoint with: PhysicalEntity
comment: Definition: A continuant that encodes information that can be inherited through replication. Rationale: Gene is an abstract continuant that can be best described as a "schema", a common conception commonly used by biologists to demark a component within genome. In BioPAX, Gene is considered a generalization over eukaryotic and prokaryotic genes and is used only in genetic interactions. Gene is often confused with DNA and RNA fragments, however, these are considered the physical encoding of a gene. N.B. Gene expression regulation makes use of DNA and RNA physical entities and not this class. Usage: Gene should only be used for describing GeneticInteractions.

Interaction
type: Class
subclass of: Entity
disjoint with: Pathway
disjoint with: PhysicalEntity
comment: Definition: A single biological relationship between two or more entities. An interaction cannot be defined without the entities it relates. 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. Naming rationale: A number of names were considered for this concept, including "process", "synthesis" and "relationship"; Interaction was chosen as it is understood by biologists in a biological context and is compatible with PSI-MI. Examples: protein-protein interaction, biochemical reaction, enzyme catalysis

Pathway
type: Class
subclass of: Entity
disjoint with: PhysicalEntity
comment: 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. Usage: Pathways can be used for demarcating any subnetwork of a BioPAX model. It is also possible to define a pathway without specifying the interactions within the pathway. In this case, the pathway instance could consist simply of a name and could be treated as a 'black box'. Pathways can also soverlap, i.e. a single interaction might belong to multiple pathways. Pathways can also contain sub-pathways. Pathways are continuants. Synonyms: network, module, cascade, Examples: glycolysis, valine biosynthesis, EGFR signaling Instance examples: http://chem2bio2rdf.org/kegg/resource/kegg_pathway/hsa00052 Related Databases: KEGG, Reactome Popular Identifiers: KEGG ID

PhysicalEntity
type: Class
subclass of: Entity
comment: Definition: A pool of molecules or molecular complexes. Comments: Each PhysicalEntity is defined by a sequence or structure based on an EntityReference AND any set of Features that are given. For example, ser46 phosphorylated p53 is a physical entity in BioPAX defined by the p53 sequence and the phosphorylation feature on the serine at position 46 in the sequence. Features are any combination of cellular location, covalent and non-covalent bonds with other molecules and covalent modifications. For a specific molecule to be a member of the pool it has to satisfy all of the specified features. Unspecified features are treated as unknowns or unneccesary. Features that are known to not be on the molecules should be explicitly stated with the "not feature" property. A physical entity in BioPAX never represents a specific molecular instance. Physical Entity can be heterogenous and potentially overlap, i.e. a single molecule can be counted as a member of multiple pools. This makes BioPAX semantics different than regular chemical notation but is necessary for dealing with combinatorial complexity. Synonyms: part, interactor, object, species Examples: extracellular calcium, ser 64 phosphorylated p53

Carbamoylation
type: Class
subclass of: MacromoleculeMetabolicProcess
comment: Definition: The addition of a carbamoyl group.

Carboxylation
type: Class
subclass of: MacromoleculeMetabolicProcess
comment: Definition: The addition of a carboxyl group.

Protein
type: Class
subclass of: PhysicalEntity
disjoint with: Rna
disjoint with: RnaRegion
disjoint with: SmallMolecule
comment: Definition: A physical entity consisting of a sequence of amino acids; a protein monomer; a single polypeptide chain. Examples: The epidermal growth factor receptor (EGFR) protein.

DrugInducedSideEffect
type: Class
subclass of: Interaction
subclass of: chembio resource:arc4227b55
subclass of: chembio resource:arc4227b56
disjoint with: DrugTreament
disjoint with: ProteinProteinInteraction
comment: Definition: A drug interaction that results in side effect related databases: SIDER

DrugTreament
type: Class
subclass of: Interaction
subclass of: chembio resource:arc4227b57
subclass of: chembio resource:arc4227b58
disjoint with: ProteinProteinInteraction
comment: Definition: The use of drug to treat disease Related databases: Diseasome

ChemicalSynthesis
type: Class
subclass of: SmallMoleculeMetabolicProcess
comment: Definition: A biochemical event resulting in a new chemical product.

Cleavage
type: Class
subclass of: Degradation
comment: Definition: The processing or splitting of a molecule, not necessarily leading to the destruction of the molecule.

Degradation
type: Class
subclass of: MacromoleculeMetabolicProcess
comment: Definition: Catabolism or breakdown.

Definition: The process of regulation via indirect interaction
type: Class
subclass of: Activity

Entity
type: Class
comment: Definition: A discrete unit involved in systems chemical biology/chemogenomics Rationale:It includes both continuants (physical entities, genes, disease) and occurents (interactions, pathways, side effects and bioassays). The definition of continuants and occurents are decribed in Basic Formal Ontology (BFO).

Ethylation
type: Class
subclass of: MacromoleculeMetabolicProcess
comment: Definition: The addition of an ethyl group.

Export
type: Class
subclass of: Secretion
comment: Definition: The movement of a molecule out of a cell (by more specific means than secretion).

Secretion
type: Class
subclass of: Transport
disjoint with: Uptake
comment: Definition: The movement of a molecule out of a cell (by less specific means than export).

Farnesylation
type: Class
subclass of: Lipidation
comment: Definition: The addition of a farnesyl group

Lipidation
type: Class
subclass of: MacromoleculeMetabolicProcess
comment: Definition: The addition of a lipid group.

Geranoylation
type: Class
subclass of: Lipidation
comment: Definition: The addition of a geranoyl group.

Glucuronidation
type: Class
subclass of: Glycosylation
comment: Definition: The addition of a sugar group to form a glucuronide, typically part of an inactivating or detoxifying reaction.

Glycosylation
type: Class
subclass of: MacromoleculeMetabolicProcess
comment: Definition: The addition of a sugar group.

Glutathionylation
type: Class
subclass of: MacromoleculeMetabolicProcess
comment: Definition: The addition of a glutathione group.

Glycation
type: Class
subclass of: MacromoleculeMetabolicProcess
comment: Definition: The non-enzymatic addition of a sugar.

Hydrolysis
type: Class
subclass of: Cleavage
comment: Definition: The splitting of a molecule via the specific use of water.

Hydroxylation
type: Class
subclass of: MacromoleculeMetabolicProcess
comment: Definition: The addition of a hydroxy group.

Import
type: Class
subclass of: Uptake
comment: Definition: The movement of a molecule into a cell (by more specific means than uptake).

Uptake
type: Class
subclass of: Transport
comment: Definition: The movement of a molecule into a cell (by less specific means than import).

Methylation
type: Class
subclass of: MacromoleculeMetabolicProcess
comment: Definition: The addition of a methyl group.

Myristoylation
type: Class
subclass of: Lipidation
comment: Definition: The addition of a myristoyl group.

N-linkedGlycosylation
type: Class
subclass of: Glycosylation
comment: Definition: The addition of a sugar group to an amide nitrogen.

NegativeRegulationOfExpression
type: Class
subclass of: Expression
disjoint with: PositiveRegulationOfExpression
has db xref: GO:0010629
comment: Definition: The process that decreases the frequency, rate or extent of gene expression. Example: 2-nitropropane results in decreased expression of PGCP mRNA

PositiveRegulationOfExpression
type: Class
subclass of: Expression
has db xref: GO:0010628
comment: Definition: The process that increases the frequency, rate or extent of gene expression. Example: 2,2-bis(4-hydroxyphenyl)-1,1,1-trichloroethane results in increased expression of ESR2 mRNA.

Nitrosation
type: Class
subclass of: MacromoleculeMetabolicProcess
comment: Definition: The addition of a nitroso or nitrosyl group.

Nucleotidylation
type: Class
subclass of: MacromoleculeMetabolicProcess
comment: Definition: The addition of a nucleotidyl group.

O-linkedGlycosylation
type: Class
subclass of: Glycosylation
comment: Definition: The addition of a sugar group to a hydroxyl group.

UtilityClass
type: Class
comment: Definition: This is a placeholder for classes, used for annotating the "Entity" and its subclasses. Mostly, these are not an "Entity" themselves. Examples include references to external databases, controlled vocabularies, evidence and provenance. Rationale: 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. Usage: The utilityClass class is actually a metaclass and is only present to organize the other helper classes under one class hierarchy; instances of utilityClass should never be created.

Oxidation
type: Class
subclass of: MacromoleculeMetabolicProcess
comment: Definition: the loss of electrons

Palmitoylation
type: Class
subclass of: Lipidation
comment: Definition: The addition of a palmitoyl group.

Phosphorylation
type: Class
subclass of: MacromoleculeMetabolicProcess
comment: Definition: The addition of a phosphate group.

Prenylation
type: Class
subclass of: Lipidation
comment: Definition: The addition of a prenyl group.

ReceptorAgonistActivity
type: Class
subclass of: Activation
has db xref: GO:0048018
comment: Definition: Interacts with receptors such that the proportion of receptors in the active form is increased. Example: Calcitriol binds to and results in increased activity of VDR protein.

ReceptorAntagonistActivity
type: Class
subclass of: Inhibition
has db xref: GO:0048019
comment: Definition: Interacts with receptors to reduce the action of another ligand.

Reduction
type: Class
subclass of: MacromoleculeMetabolicProcess
comment: Definition: The gain of electrons.

Sulfation
type: Class
subclass of: MacromoleculeMetabolicProcess
comment: Definition: The addition of a sulfate group.

Sumoylation
type: Class
subclass of: MacromoleculeMetabolicProcess
comment: Definition: The addition of a SUMO group.

Ubiquitination
type: Class
subclass of: MacromoleculeMetabolicProcess
comment: Definition: The addition of an ubiquitin group.

CellVocabulary
type: Class
subclass of: ControlledVocabulary
disjoint with: CellularLocationVocabulary
disjoint with: EntityReferenceTypeVocabulary
disjoint with: EvidenceCodeVocabulary
disjoint with: ExperimentalFormVocabulary
disjoint with: InteractionVocabulary
disjoint with: PhenotypeVocabulary
disjoint with: RelationshipTypeVocabulary
disjoint with: SequenceModificationVocabulary
disjoint with: SequenceRegionVocabulary
disjoint with: TissueVocabulary
comment: Definition: A reference to the Cell Type Ontology (CL). Homepage at http://obofoundry.org/cgi-bin/detail.cgi?cell. Browse at http://www.ebi.ac.uk/ontology-lookup/browse.do?ontName=CL

CellularLocationVocabulary
type: Class
subclass of: ControlledVocabulary
disjoint with: EntityReferenceTypeVocabulary
disjoint with: EvidenceCodeVocabulary
disjoint with: ExperimentalFormVocabulary
disjoint with: InteractionVocabulary
disjoint with: PhenotypeVocabulary
disjoint with: RelationshipTypeVocabulary
disjoint with: SequenceModificationVocabulary
disjoint with: SequenceRegionVocabulary
disjoint with: TissueVocabulary
comment: Definition: A reference to the Gene Ontology Cellular Component (GO CC) ontology. Homepage at http://www.geneontology.org. Browse at http://www.ebi.ac.uk/ontology-lookup/browse.do?ontName=GO

EntityReferenceTypeVocabulary
type: Class
subclass of: ControlledVocabulary
disjoint with: EvidenceCodeVocabulary
disjoint with: ExperimentalFormVocabulary
disjoint with: InteractionVocabulary
disjoint with: PhenotypeVocabulary
disjoint with: RelationshipTypeVocabulary
disjoint with: SequenceModificationVocabulary
disjoint with: SequenceRegionVocabulary
disjoint with: TissueVocabulary
comment: Definiiton: A reference to a term from an entity reference group ontology. As of the writing of this documentation, there is no standard ontology of these terms, though a common type is ‘homology’.

ExperimentalFormVocabulary
type: Class
subclass of: ControlledVocabulary
disjoint with: InteractionVocabulary
disjoint with: PhenotypeVocabulary
disjoint with: RelationshipTypeVocabulary
disjoint with: SequenceModificationVocabulary
disjoint with: SequenceRegionVocabulary
disjoint with: TissueVocabulary
comment: Definition: A reference to the PSI Molecular Interaction ontology (MI) participant identification method (e.g. mass spectrometry), experimental role (e.g. bait, prey), experimental preparation (e.g. expression level) type. Homepage at http://www.psidev.info/. Browse http://www.ebi.ac.uk/ontology-lookup/browse.do?ontName=MI&termId=MI%3A0002&termName=participant%20identification%20method http://www.ebi.ac.uk/ontology-lookup/browse.do?ontName=MI&termId=MI%3A0495&termName=experimental%20role http://www.ebi.ac.uk/ontology-lookup/browse.do?ontName=MI&termId=MI%3A0346&termName=experimental%20preparation

InteractionVocabulary
type: Class
subclass of: ControlledVocabulary
disjoint with: PhenotypeVocabulary
disjoint with: RelationshipTypeVocabulary
disjoint with: SequenceModificationVocabulary
disjoint with: SequenceRegionVocabulary
disjoint with: TissueVocabulary
comment: Definition: A reference to the PSI Molecular Interaction ontology (MI) interaction type. Homepage at http://www.psidev.info/. Browse at http://www.ebi.ac.uk/ontology-lookup/browse.do?ontName=MI&termId=MI%3A0190&termName=interaction%20type

RelationshipTypeVocabulary
type: Class
subclass of: ControlledVocabulary
disjoint with: SequenceModificationVocabulary
disjoint with: SequenceRegionVocabulary
disjoint with: TissueVocabulary
comment: Definition: Vocabulary for defining relationship Xref types. A reference to the PSI Molecular Interaction ontology (MI) Cross Reference type. Homepage at http://www.psidev.info/. Browse at http://www.ebi.ac.uk/ontology-lookup/browse.do?ontName=MI&termId=MI%3A0353&termName=cross-reference%20type

SequenceModificationVocabulary
type: Class
subclass of: ControlledVocabulary
disjoint with: SequenceRegionVocabulary
disjoint with: TissueVocabulary
comment: Definiiton: A reference to the PSI Molecular Interaction ontology (MI) of covalent sequence modifications. Homepage at http://www.psidev.info/. Browse at http://www.ebi.ac.uk/ontology-lookup/browse.do?ontName=MI&termId=MI%3A0252&termName=biological%20feature. Only children that are covelent modifications at specific positions can be used.

SequenceRegionVocabulary
type: Class
subclass of: ControlledVocabulary
disjoint with: TissueVocabulary
comment: Definition: A reference to a controlled vocabulary of sequence regions, such as InterPro or Sequence Ontology (SO). Homepage at http://www.sequenceontology.org/. Browse at http://www.ebi.ac.uk/ontology-lookup/browse.do?ontName=SO

TissueVocabulary
type: Class
subclass of: ControlledVocabulary
comment: Definition: A reference to the BRENDA (BTO). Homepage at http://www.brenda-enzymes.info/. Browse at http://www.ebi.ac.uk/ontology-lookup/browse.do?ontName=BTO

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Complex
type: Class
subclass of: PhysicalEntity
disjoint with: Dna
disjoint with: DnaRegion
disjoint with: Protein
disjoint with: Rna
disjoint with: RnaRegion
disjoint with: SmallMolecule
comment: Definition: A physical entity whose structure is comprised of other physical entities bound to each other covalently or non-covalently, at least one of which is a macromolecule (e.g. protein, DNA, or RNA) and the Stoichiometry of the components are known. Comment: Complexes must be stable enough to function as a biological unit; in general, the temporary association of an enzyme with its substrate(s) should not be considered or represented as a complex. A complex is the physical product of an interaction (complexAssembly) and is not itself considered an interaction. The boundaries on the size of complexes described by this class are not defined here, although possible, elements of the cell such a mitochondria would typically not be described using this class (later versions of this ontology may include a cellularComponent class to represent these). The strength of binding cannot be described currently, but may be included in future versions of the ontology, depending on community need. Examples: Ribosome, RNA polymerase II. Other examples of this class include complexes of multiple protein monomers and complexes of proteins and small molecules.

Dna
type: Class
subclass of: PhysicalEntity
disjoint with: DnaRegion
disjoint with: Protein
disjoint with: Rna
disjoint with: RnaRegion
disjoint with: SmallMolecule
comment: Definition: A physical entity consisting of a sequence of deoxyribonucleotide monophosphates; a deoxyribonucleic acid. Usage: DNA should be used for pools of individual DNA molecules. For describing subregions on those molecules use DNARegion. Examples: a chromosome, a plasmid. A specific example is chromosome 7 of Homo sapiens.

DnaRegion
type: Class
subclass of: PhysicalEntity
disjoint with: Protein
disjoint with: Rna
disjoint with: RnaRegion
disjoint with: SmallMolecule
comment: Definition: A region on a DNA molecule. Usage: DNARegion is not a pool of independent molecules but a subregion on these molecules. As such, every DNARegion has a defining DNA molecule. Examples: Protein encoding region, promoter

Rna
type: Class
subclass of: PhysicalEntity
disjoint with: RnaRegion
disjoint with: SmallMolecule
comment: Definition: A physical entity consisting of a sequence of ribonucleotide monophosphates; a ribonucleic acid. Usage: RNA should be used for pools of individual RNA molecules. For describing subregions on those molecules use RNARegion. Examples: messengerRNA, microRNA, ribosomalRNA. A specific example is the let-7 microRNA.

RnaRegion
type: Class
subclass of: PhysicalEntity
disjoint with: SmallMolecule
comment: Definition: A region on a RNA molecule. Usage: RNARegion is not a pool of independent molecules but a subregion on these molecules. As such, every RNARegion has a defining RNA molecule. Examples: CDS, 3' UTR, Hairpin

UnificationXref
type: Class
subclass of: Xref
subclass of: chembio resource:arc4227b68
subclass of: chembio resource:arc4227b69
comment: Definition: A unification xref defines a reference to an entity in an external resource that has the same biological identity as the referring entity Rationale: Unification xrefs are critically important for data integration. In the future they may be replaced by direct miriam links and rdf:id based identity management. Usage: For example, if one wished to link from a database record, C, describing a chemical compound in a BioPAX data collection to a record, C', describing the same chemical compound in an external database, one would use a unification xref since records C and C' describe the same biological identity. Generally, unification xrefs should be used whenever possible, although there are cases where they might not be useful, such as application to application data exchange.Identity of interactions can be computed based on the identity of its participants. An xref in a protein pointing to a gene, e.g. in the LocusLink database17, would not be a unification xref since the two entities do not have the same biological identity (one is a protein, the other is a gene). Instead, this link should be a captured as a relationship xref. References to an external controlled vocabulary term within the OpenControlledVocabulary class should use a unification xref where possible (e.g. GO:0005737). Examples: An xref in a protein instance pointing to an entry in the Swiss-Prot database, and an xref in an RNA instance pointing to the corresponding RNA sequence in the RefSeq database..

RelationshipXref
type: Class
subclass of: Xref
comment: Definition: An xref that defines a reference to an entity in an external resource that does not have the same biological identity as the referring entity. Usage: There is currently no controlled vocabulary of relationship types for BioPAX, although one will be created in the future if a need develops. Examples: A link between a gene G in a BioPAX data collection, and the protein product P of that gene in an external database. This is not a unification xref because G and P are different biological entities (one is a gene and one is a protein). Another example is a relationship xref for a protein that refers to the Gene Ontology biological process, e.g. 'immune response,' that the protein is involved in.

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