This is version 0.94 of the BioPAX Level 3 ontology. The goal of the BioPAX group is to develop a common exchange format for biological pathway data. More information is available at http://www.biopax.org. This ontology is freely available under the LGPL (http://www.gnu.org/copyleft/lesser.html). Definition: A physical entity consisting of a sequence of ribonucleotide monophosphates; a ribonucleic acid. Examples: messengerRNA, microRNA, ribosomalRNA. A specific example is the let-7 microRNA. Definition: An xref that defines a reference to a publication such as a book, journal article, web page, or software manual. 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. Comment: 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 Definition: An interaction in which one or more entities is physically transformed into one or more other entities. Comment: This class is designed to represent a simple, single-step transformation. Multi-step transformations, such as the conversion of glucose to pyruvate in the glycolysis pathway, should be represented as pathways, if known. Since it is a highly abstract class in the ontology, instances of the conversion class should never be created. More specific classes should be used instead. Examples: A biochemical reaction converts substrates to products, the process of complex assembly converts single molecules to a complex, transport converts entities in one compartment to the same entities in another compartment. 1 ACTIVATION Definition: A control interaction in which a physical entity (a catalyst) increases the rate of a conversion interaction by lowering its activation energy. Instances of this class describe a pairing between a catalyzing entity and a catalyzed conversion. Comment: A separate catalysis instance should be created for each different conversion that a physicalEntity may catalyze and for each different physicalEntity that may catalyze a conversion. For example, a bifunctional enzyme that catalyzes two different biochemical reactions would be linked to each of those biochemical reactions by two separate instances of the catalysis class. Also, catalysis reactions from multiple different organisms could be linked to the same generic biochemical reaction (a biochemical reaction is generic if it only includes small molecules). Generally, the enzyme catalyzing a conversion is known and the use of this class is obvious. In the cases where a catalyzed reaction is known to occur but the enzyme is not known, a catalysis instance should be created without a controller specified (i.e. the CONTROLLER property should remain empty). Synonyms: facilitation, acceleration. Examples: The catalysis of a biochemical reaction by an enzyme, the enabling of a transport interaction by a membrane pore complex, and the facilitation of a complex assembly by a scaffold protein. Hexokinase -> (The "Glucose + ATP -> Glucose-6-phosphate +ADP" reaction). A plasma membrane Na+/K+ ATPase is an active transporter (antiport pump) using the energy of ATP to pump Na+ out of the cell and K+ in. Na+ from cytoplasm to extracellular space would be described in a transport instance. K+ from extracellular space to cytoplasm would be described in a transport instance. The ATPase pump would be stored in a catalysis instance controlling each of the above transport instances. A biochemical reaction that does not occur by itself under physiological conditions, but has been observed to occur in the presence of cell extract, likely via one or more unknown enzymes present in the extract, would be stored in the CONTROLLED property, with the CONTROLLER property empty. Definition: A physical entity whose structure is comprised of other physical entities bound to each other non-covalently, at least one of which is a macromolecule (e.g. protein, DNA, or RNA). 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. Comment: In general, complexes should not be defined recursively so that smaller complexes exist within larger complexes, i.e. a complex should not be a COMPONENT of another complex (see comments on the COMPONENT property). The boundaries on the size of complexes described by this class are not defined here, although elements of the cell as large and dynamic as, e.g., a mitochondrion 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 and the topology of the components 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. A RNA reference is a grouping of several RNA entities that are either encoded by the same gene or replicates of the same genome. Members can differ in celular location, sequence features and bound partners. Currently conformational states (such as hairpin) are not covered. A small molecule reference is a grouping of several small molecule entities that have the same chemical structure. Members can differ in celular location and bound partners. Covalent modifications of small molecules are not considered as state changes but treated as different molecules. 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 Imposes ordering on a step in a biochemical pathway. A biochemical reaction can be reversible by itself, but can be physiologically directed in the context of a pathway, for instance due to flux of reactants and products. Only one conversion interaction can be ordered at a time, but multiple catalysis or modulation instances can be part of one step. Definition: An interaction in which at least one participant is a physical entity, e.g. a binding event. Comment: This class should be used by default for representing molecular interactions, such as those defined by PSI-MI level 2.5. The participants in a molecular interaction should be listed in the PARTICIPANTS slot. Note that this is one of the few cases in which the PARTICPANT slot should be directly populated with instances (see comments on the PARTICPANTS property in the interaction class description). If sufficient information on the nature of a molecular interaction is available, a more specific BioPAX interaction class should be used. Example: Two proteins observed to interact in a yeast-two-hybrid experiment where there is not enough experimental evidence to suggest that the proteins are forming a complex by themselves without any indirect involvement of other proteins. This is the case for most large-scale yeast two-hybrid screens. 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 Definition: Represents the results of a cleavage or degradation event. There are multiple cases: 1. A protein with a single cleavage site that converts the protein into two fragments (e.g. pro-insulin converted to insulin and C-peptide). TODO: CV term for sequence fragment? PSI-MI CV term for cleavage site? 2. A protein with two cleavage sites that removes an internal sequence e.g. an intein i.e. ABC -> AC 3. Cleavage of a circular sequence e.g. a plasmid. Definition: The biological source of an entity (e.g. protein, RNA or DNA). Some entities are considered source-neutral (e.g. small molecules), and the biological source of others can be deduced from their constituentss (e.g. complex, pathway). Examples: HeLa cells, human, and mouse liver tissue. 1 Definition: A conversion interaction in which a set of physical entities, at least one being a macromolecule (e.g. protein, RNA, DNA), aggregate via non-covalent interactions. One of the participants of a complexAssembly must be an instance of the class complex. Comment: This class is also used to represent complex disassembly. The assembly or disassembly of a complex is often a spontaneous process, in which case the direction of the complexAssembly (toward either assembly or disassembly) should be specified via the SPONTANEOUS property. Synonyms: aggregation, complex formation Examples: Assembly of the TFB2 and TFB3 proteins into the TFIIH complex, and assembly of the ribosome through aggregation of its subunits. Note: The following are not examples of complex assembly: Covalent phosphorylation of a protein (this is a biochemicalReaction); the TFIIH complex itself (this is an instance of the complex class, not the complexAssembly class). 1 2 Genetic interactions between genes occur when two genetic perturbations (e.g. mutations) have a combined phenotypic effect not caused by either perturbation alone. This is not a physical interaction, but rather logical. For example, a synthetic lethal interaction occurs when cell growth is possible without either gene A OR B, but not without both gene A AND B. If you knock out A and B together, the cell will die. A gene participant in a genetic interaction represents the gene that is perturbed. 1 The process of degrading a physical entity. The right side of the conversion is not specified, indicating degraded components. The conversion is not spontaneous. LEFT-TO-RIGHT Definition: Utility classes are created when simple slots are insufficient to describe an aspect of an entity or to increase compatibility of this ontology with other standards. The utilityClass class is actually a metaclass and is only present to organize the other helper classes under one class hierarchy; instances of utilityClass should never be created. 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. A region of DNA. Definition: The direct source of a pathway data or score. 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. The XREF property may contain a publicationXref referencing a publication describing the data source (e.g. a database publication). A unificationXref may be used e.g. when pointing to an entry in a database of databases describing this database. Examples: A database, scoring method or person name. 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 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 1 Definition: A control interaction in which a physical entity modulates a catalysis interaction. Biologically, most modulation interactions describe an interaction in which a small molecule alters the ability of an enzyme to catalyze a specific reaction. Instances of this class describe a pairing between a modulating entity and a catalysis interaction. Comment: A separate modulation instance should be created for each different catalysis instance that a physical entity may modulate and for each different physical entity that may modulate a catalysis instance. A typical modulation instance has a small molecule as the controller entity and a catalysis instance as the controlled entity. Examples: Allosteric activation and competitive inhibition of an enzyme's ability to catalyze a specific reaction. Definition: The support for a particular assertion, such as the existence of an interaction or pathway. At least one of CONFIDENCE, EVIDENCE-CODE, or EXPERIMENTAL-FORM 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. 1 1 1 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 Specifies the binding domains of two entities in a complex that are non-covalently bound to each other. Note that this is a n-ary specifier class on the boundTo property. The difference between this class and modificationFeature is that this is non-covalent and modificationFeature is covalent. 1 Definition: 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'⁰. delta-G'⁰ = -RT lnK' and delta-G'⁰ = delta-H'⁰ - T delta-S'⁰ delta-G'⁰ 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'⁰ T I pH pMg). This property may have multiple values, representing different measurements for delta-G'⁰ obtained under the different experimental conditions listed in the 5-tuple. (This definition from EcoCyc) Definition: A location on a nucleotide or amino acid sequence. Comment: For organizational purposes only; direct instances of this class should not be created. 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. Definition: A conversion interaction in which an entity (or set of entities) changes location within or with respect to the cell. A transport interaction does not include the transporter entity, even if one is required in order for the transport to occur. Instead, transporters are linked to transport interactions via the catalysis class. Comment: Transport interactions do not involve chemical changes of the participant(s). These cases are handled by the transportWithBiochemicalReaction class. Synonyms: translocation. Examples: The movement of Na+ into the cell through an open voltage-gated channel. Stoichiometric coefficient of a physical entity in the context of a conversion or complex. For each participating element there must be 0 or 1 stoichiometry element. A non-existing stoichiometric element is treated as unknown. This is an n-ary bridge for left, right and component properties. 1 1 1 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. 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". Definition: Describes a site on a sequence, i.e. the position of a single nucleotide or amino acid. 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/ 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. Currently this class only has subclasses that define physical interactions; later levels of BioPAX may define other types of interactions, such as genetic (e.g. synthetic lethal). 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 1 1 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)'. 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. 1 1 Definition: A unification xref defines a reference to an entity in an external resource that has the same biological identity as the referring entity. 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. Comment: Unification xrefs in physical entities are essential for data integration, but are less important in interactions. This is because unification xrefs on the physical entities in an interaction can be used to compute the equivalence of two interactions of the same type. 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.. Definition: An interaction in which one entity regulates, modifies, or otherwise influences another. Two types of control interactions are defined: activation and inhibition. Comment: In general, the targets of control processes (i.e. occupants of the CONTROLLED property) should be interactions. Conceptually, physical entities are involved in interactions (or events) and the events should be controlled or modified, not the physical entities themselves. For example, a kinase activating a protein is a frequent event in signaling pathways and is usually represented as an 'activation' arrow from the kinase to the substrate in signaling diagrams. This is an abstraction that can be ambiguous out of context. In BioPAX, this information should be captured as the kinase catalyzing (via an instance of the catalysis class) a reaction in which the substrate is phosphorylated, instead of as a control interaction in which the kinase activates the substrate. Since this class is a superclass for specific types of control, instances of the control class should only be created when none of its subclasses are applicable. Synonyms: regulation, mediation Examples: A small molecule that inhibits a pathway by an unknown mechanism controls the pathway. 1 Definition: The apparent equilibrium constant, K', and associated values. 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][P_i]/[ATP], The concentration of ATP refers to the total concentration of all of the following species: [ATP] = [ATP^4-] + [HATP^3-] + [H₂ATP^2-] + [MgATP^2-] + [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⁺]). Therefore, these quantities must be specified to be precise, and values for KEQ for biochemical reactions may be represented as 5-tuples of the form (K' T I pH pMg). This property may have multiple values, representing different measurements for K' obtained under the different experimental conditions listed in the 5-tuple. (This definition adapted from EcoCyc) See http://www.chem.qmul.ac.uk/iubmb/thermod/ for a thermodynamics tutorial. Definition: A conversion interaction in which one or more entities (substrates) undergo covalent changes to become one or more other entities (products). The substrates of biochemical reactions are defined in terms of sums of species. This is convention in biochemistry, and, in principle, all of the EC reactions should be biochemical reactions. Examples: ATP + H2O = ADP + Pi Comment: In the example reaction above, ATP is considered to be an equilibrium mixture of several species, namely ATP4-, HATP3-, H2ATP2-, MgATP2-, MgHATP-, and Mg2ATP. Additional species may also need to be considered if other ions (e.g. Ca2+) that bind ATP are present. Similar considerations apply to ADP and to inorganic phosphate (Pi). When writing biochemical reactions, it is not necessary to attach charges to the biochemical reactants or to include ions such as H+ and Mg2+ in the equation. The reaction is written in the direction specified by the EC nomenclature system, if applicable, regardless of the physiological direction(s) in which the reaction proceeds. Polymerization reactions involving large polymers whose structure is not explicitly captured should generally be represented as unbalanced reactions in which the monomer is consumed but the polymer remains unchanged, e.g. glycogen + glucose = glycogen. Definition: A physical entity consisting of a sequence of deoxyribonucleotide monophosphates; a deoxyribonucleic acid. Comment: This is not a 'gene', since gene is a genetic concept, not a physical entity. The concept of a gene may be added later in BioPAX. Examples: a chromosome, a plasmid. A specific example is chromosome 7 of Homo sapiens. Covalent bond within or between physical entities. A region of RNA Definition: A step in a pathway. Comment: Multiple interactions may occur in a pathway step, each should be listed in the STEP-INTERACTION property. Order relationships between pathway steps may be established with the NEXT-STEP slot. This order may not be temporally meaningful for specific steps, such as for a pathway loop or a reversible reaction, but represents a directed graph of step relationships that can be useful for describing the overall flow of a pathway, as may be useful in a pathway diagram. Example: A metabolic pathway may contain a pathway step composed of one biochemical reaction (BR1) and one catalysis (CAT1) instance, where CAT1 describes the catalysis of BR1. The M phase of the cell cycle, defined as a pathway, precedes the G1 phase, also defined as a pathway. Definition: An entity reference is a grouping of several physical entities across different contexts and molecular states, that share common physical properties and often named and treated as a single entity with multiple states by biologists. Entity references store the information common to a set of molecules in various states described in the BioPAX document, including database cross-references. For instance, the P53 protein can be phosphorylated in multiple different ways. Each separate P53 protein (pool) in a phosphorylation state would be represented as a different protein (child of physicalEntity) and all things common to all P53 proteins, including all possible phosphorylation sites, the sequence common to all of them and common references to protein databases containing more information about P53 would be stored in a Entity Reference. Comment: Many protein, small molecule and gene databases share this point of view, and such a grouping is an important prerequisite for interoperability with those databases. Biologists would often group different pools of molecules in different contexts under the same name. For example cytoplasmic and extracellular calcium have different effects on the cell's behavior, but they are still called calcium. This grouping has three semantic implications: 1. Members of different pools share many physical and biochemical properties. This includes their chemical structure, sequence, organism and set of molecules they react with. They will also share a lot of secondary information such as their names, functional groupings, annotation terms and database identifiers. 2. A small number of transitions seperates these pools. In other words it is relatively easy and frequent for a molecule to transform from one physical entity to another that belong to the same reference entity. For example an extracellular calcium can become cytoplasmic, and p53 can become phosphorylated. However no calcium virtually becomes sodium, or no p53 becomes mdm2. In the former it is the sheer energy barrier of a nuclear reaction, in the latter sheer statistical improbability of synthesizing the same sequence without a template. If one thinks about the biochemical network as molecules transforming into each other, and remove edges that respond to transcription, translation, degradation and covalent modification of small molecules, each remaining component is a reference entity. 3. Some of the pools in the same group can overlap. p53-p@ser15 can overlap with p53-p@thr18. Most of the experiments in molecular biology will only check for one state variable, rarely multiple, and never for the all possible combinations. So almost all statements that refer to the state of the molecule talk about a pool that can overlap with other pools. However no overlaps is possible between molecules of different groups. Definiton: This class represents a polymerization of a macromolecule from a template. E.g. DNA to RNA is transcription, RNA to protein is translation and DNA to protein is protein expression from DNA. Other examples are possible. To store a promoter region, create a regulatory element and add a promoter feature on it, using the sequence region vocabulary. Definition: An entity with a physical structure. A pool of entities, not a specific molecular instance of an entity in a cell. Comment: This class serves as the super-class for all physical entities, although its current set of subclasses is limited to molecules. As a highly abstract class in the ontology, instances of the physicalEntity class should never be created. Instead, more specific classes should be used. Synonyms: part, interactor, object Naming rationale: It's difficult to find a name that encompasses all of the subclasses of this class without being too general. E.g. PSI-MI uses 'interactor', BIND uses 'object', BioCyc uses 'chemicals'. physicalEntity seems to be a good name for this specialization of entity. Examples: protein, small molecule, RNA Definition: Used to import terms from external controlled vocabularies (CVs) into the ontology. To support consistency and compatibility, open, freely available CVs should be used whenever possible, such as the Gene Ontology (GO) or other open biological CVs listed on the OBO website (http://obo.sourceforge.net/). Comment: The ID property in unification xrefs to GO and other OBO ontologies should include the ontology name in the ID property (e.g. ID="GO:0005634" instead of ID="0005634"). 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. Comment: It is 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'. Synonyms: network Examples: glycolysis, valine biosynthesis Definition: The form of a physical entity in a particular experiment, as it may be modified for purposes of experimental design. Examples: A His-tagged protein in a binding assay. A protein can be tagged by multiple tags, so can have more than 1 experimental form type terms 1 Definition: A discrete biological unit used when describing pathways. This is an interacting entity, not just any entity. Comment: This is the root class for all interacting components in the ontology, which include pathways, interactions and physical entities. As the most abstract class in the ontology, instances of the entity class should never be created. Instead, more specific classes should be used. Synonyms: thing, object, bioentity. Definition: A conversion interaction that is both a biochemicalReaction and a transport. In transportWithBiochemicalReaction interactions, one or more of the substrates change both their location and their physical structure. Active transport reactions that use ATP as an energy source fall under this category, even if the only covalent change is the hydrolysis of ATP to ADP. Comment: This class was added to support a large number of transport events in pathway databases that have a biochemical reaction during the transport process. It is not expected that other double inheritance subclasses will be added to the ontology at the same level as this class. Examples: In the PEP-dependent phosphotransferase system, transportation of sugar into an E. coli cell is accompanied by the sugar's phosphorylation as it crosses the plasma membrane. A feature or aspect of a physical entity that can be changed while the entity still retains its biological identity. A reference to a term from a reference entity group ontology. There is no "best-practice" vocabulary for this one. 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. 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. Comment: 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. 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 Definition: A covalently modified feature on a sequence relevant to an interaction, such as a post-translational modification. The difference between this class and bindingFeature is that this is covalent and bindingFeature is non-covalent. Examples: A phosphorylation on a protein. ACTIVATION INHIBITION Definition: Regulation of the expression reaction by the controlling element such as a transcription factor or microRNA. E.g. To represent the binding of the transcription factor to a regulatory element in the TemplateReaction, create a complex of the transcription factor and the regulatory element and set that as the controller. A DNA reference is a grouping of several DNA entities that are common in sequence and genomic position. Members can differ in celular location, sequence features, SNPs, mutations and bound partners. Comments : Note that this is not a reference gene. A gene can possibly span multiple DNA molecules, sometimes even across chromosomes due to regulatory regions. Similarly a gene is not necessarily made up of deoxyribonucleic acid and can be present in multiple copies ( which are different DNA molecules). A protein reference is a grouping of several protein entities that are encoded by the same gene. Members can differ in celular location, sequence features and bound partners. Currently conformational states (such as open and closed) are not covered. 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 Definition: Describes an interval on a sequence. All of the sequence from the begin site to the end site (inclusive) is described, not any subset. Definition: A reference from an instance of a class in this ontology to an object in an external resource. Comment: Instances of the xref class should never be created and more specific classes should be used instead. 1 A continuant that encodes information that can be inherited through replication. This is a generalization of the prokaryotic and eukaryotic notion of a gene. This is used only for genetic interactions. Gene expression regulation makes use of DNA and RNA physical entities. Values of this property define external cross-references from this entity to entities in external databases. The stoichiometry of components in a complex Sequence features where the owner physical entity has a feature. If not specified, other potential features are not known. Location of the feature on the sequence of the interactor. One feature may have more than one location, used e.g. for features which involve sequence positions close in the folded, three-dimensional state of a protein, but non-continuous along the sequence. 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. An interaction or a pathway that are a part of this pathway step. The set of interactions and/or pathwaySteps in this pathway/network. Each instance of the pathwayStep class defines: 1) a set of interactions that together define a particular step in the pathway, for example a catalysis instance and the conversion that it catalyzes; 2) an order relationship to one or more other pathway steps (via the NEXT-STEP property). Note: This ordering is not necessarily temporal - the order described may simply represent connectivity between adjacent steps. Temporal ordering information should only be inferred from the direction of each interaction. 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'. The participants on the left side of the conversion interaction. Since conversion interactions may proceed in either the left-to-right or right-to-left direction, occupants of the LEFT property may be either reactants or products. LEFT is a sub-property of PARTICIPANTS. The ordering of components (interactions and pathways) in the context of this pathway. This is useful to specific circular or branched pathways or orderings when component biochemical reactions are normally reversible, but are directed in the context of this pathway. The product of a template reaction. This quantity is dimensionless and is usually a single number. The measured equilibrium constant for a biochemical reaction, encoded by the slot KEQ, is actually 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][P_i]/[ATP], The concentration of ATP refers to the total concentration of all of the following species: [ATP] = [ATP^4-] + [HATP^3-] + [H₂ATP^2-] + [MgATP^2-] + [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⁺]). Therefore, these quantities must be specified to be precise, and values for KEQ for biochemical reactions may be represented as 5-tuples of the form (K' T I pH pMg). This property may have multiple values, representing different measurements for K' obtained under the different experimental conditions listed in the 5-tuple. (This definition adapted from EcoCyc) Sequence features of the owner physical entity. The participants on the right side of the conversion interaction. Since conversion interactions may proceed in either the left-to-right or right-to-left direction, occupants of the RIGHT property may be either reactants or products. RIGHT is a sub-property of PARTICIPANTS. The experimental forms associated with an evidence instance. 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 Since Delta-G can change based on multiple factors including ionic strength and temperature a reaction can have multiple DeltaG values. The score of an interaction e.g. a genetic interaction score. Confidence in the containing instance. Usually a statistical measure. The gene or physical entity that this experimental form describes. A feature of the experimental form of the participant of the interaction, such as a protein tag. It is not expected to occur in vivo or be necessary for the interaction. The next step(s) of the pathway. Contains zero or more pathwayStep instances. If there is no next step, this property is empty. Multiple pathwayStep instances indicate pathway branching. A controlled vocabulary term describing the type of the sequence location such as C-Terminal or SH2 Domain. This property lists the entities that participate in this interaction. For example, in a biochemical reaction, the participants are the union of the reactants and the products of the reaction. This property has a number of sub-properties, such as LEFT and RIGHT used in the biochemicalInteraction class. Any participant listed in a sub-property will automatically be assumed to also be in PARTICIPANTS by a number of software systems, including Protege, so this property should not contain any instances if there are instances contained in a sub-property. The controlling entity, e.g., in a biochemical reaction, an enzyme is the controlling entity of the reaction. CONTROLLER is a sub-property of PARTICIPANTS. Stoichiometry of the left and right participants. Scientific evidence supporting the existence of the entity as described. Descriptor of this experimental form from a controlled vocabulary. Any cofactor(s) or coenzyme(s) required for catalysis of the conversion by the enzyme. COFACTOR is a sub-property of PARTICIPANTS. External controlled vocabulary annotating the interaction type, for example "phosphorylation". This is annotation useful for e.g. display on a web page or database searching, but may not be suitable for other computing tasks, like reasoning. The URL at which the publication can be found, if it is available through the Web. 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) 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. Describes the availability of this data (e.g. a copyright statement). The external controlled vocabulary term. 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. 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) The authors of this publication, one per property value. 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. The source in which the reference was published, such as: a book title, or a journal title and volume and pages. An entity feature that belongs to this homology grouping. Example: a homologous phosphorylation site across a protein family. This property stores the members of a generic physical entity. For representing homology generics a better way is to use generic entity references and generic features. However not all generic logic can be captured by this, such as complex generics or rare cases where feature cardinality is variable. Usages of this property should be limited to such cases. The sub region of a region. The sub region must be wholly part of the region, not outside of it. An entity reference that qualifies for the definition of this group. For example a member of a PFAM protein family. REVERSIBLE LEFT-TO-RIGHT RIGHT-TO-LEFT 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. The value of the score. The phenotype data from PATO, formatted as PhenoXML (defined at http://www.fruitfly.org/~cjm/obd/formats.html) CML InChI SMILES This property specifies which format is used to define chemical structure data. The primary identifier in the external database of the object to which this xref refers. 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. The template molecule that is used in this template reaction. 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. LEFT-TO-RIGHT RIGHT-TO-LEFT 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. 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. LEFT-TO-RIGHT RIGHT-TO-LEFT REVERSIBLE 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. An external controlled vocabulary of tissue types. A controlled vocabulary term that is used to describe the type of grouping such as homology or functional group. The begin position of a sequence interval. The phenotype quality used to define this genetic interaction e.g. viability. A cellular location, e.g. 'cytoplasm'. This should reference a term in the Gene Ontology Cellular Component ontology. The location referred to by this property should be as specific as is known. If an interaction is known to occur in multiple locations, separate interactions (and physicalEntities) must be created for each different location. If the location of a participant in a complex is unspecified, it may be assumed to be the same location as that of the complex. A molecule in two different cellular locations are considered two different physical entities. A measure of the concentration of magnesium (Mg) in solution. (pMg = -log₁₀[Mg²⁺]) 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) FORWARD REVERSE The direction of the template reaction on the template. The preferred full name for this entity. Temperature in Celsius INHIBITION ACTIVATION INHIBITION-COMPETITIVE INHIBITION-IRREVERSIBLE INHIBITION-OTHER INHIBITION-UNCOMPETITIVE ACTIVATION-NONALLOSTERIC ACTIVATION-ALLOSTERIC INHIBITION-NONCOMPETITIVE INHIBITION-ALLOSTERIC 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 the active site. INHIBITION-IRREVERSIBLE Irreversible inhibitors are compounds that irreversibly inhibit the specified enzyme activity by binding to the enzyme and dissociating so slowly that it is considered irreversible. For example, alkylating agents, such as iodoacetamide, irreversibly inhibit the catalytic activity of some enzymes by modifying cysteine side chains. INHIBITION-NONCOMPETITIVE Noncompetitive inhibitors are compounds that noncompetitively inhibit the specified enzyme by binding reversibly to both the free enzyme and to the enzyme-substrate complex. The inhibitor and substrate may be bound to the enzyme simultaneously and do not exclude each other. However, only the enzyme-substrate complex (not the enzyme-substrate-inhibitor complex) is catalytically active. INHIBITION-OTHER Compounds that inhibit the specified enzyme activity by a mechanism that has been characterized, but that cannot be clearly classified as irreversible, competitive, noncompetitive, uncompetitive, or allosteric. INHIBITION-UNCOMPETITIVE Uncompetitive inhibitors are compounds that uncompetitively inhibit the specified enzyme activity by binding reversibly to the enzyme-substrate complex but not to the enzyme alone. ACTIVATION-NONALLOSTERIC Nonallosteric activators increase the specified enzyme activity by means other than allosteric. ACTIVATION-ALLOSTERIC Allosteric activators increase the specified enzyme activity by binding reversibly to the enzyme and inducing a conformational change that increases the affinity of the enzyme to its substrates without affecting its VMAX. Absolute location as defined by the referenced sequence database record. E.g. an operon has a absolute region on the DNA molecule referenced by the UnificationXref. This flag represents whether the binding feature is within the same molecule or not. Defines the molecular weight of the molecule, in daltons. 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. 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) Defines the chemical structure and other information about this molecule, using an instance of class chemicalStructure. GREATER-THAN LESS-THAN EQUAL 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. The physical entity to be annotated with stoichiometry. 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. 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][P_i]/[ATP], The concentration of ATP refers to the total concentration of all of the following species: [ATP] = [ATP^4-] + [HATP^3-] + [H₂ATP^2-] + [MgATP^2-] + [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) 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. The entity that is controlled, e.g., in a biochemical reaction, the reaction is controlled by an enzyme. CONTROLLED is a sub-property of PARTICIPANTS. The year in which this publication was published. An organism, e.g. 'Homo sapiens'. This is the organism that the entity is found in. Pathways may not have an organism associated with them, for instance, reference pathways from KEGG. Sequence-based entities (DNA, protein, RNA) may contain an xref to a sequence database that contains organism information, in which case the information should be consistent with the value for ORGANISM. A cell type, e.g. 'HeLa'. This should reference a term in a controlled vocabulary of cell types. Best practice is to refer to OBO Cell Ontology. http://www.obofoundry.org/cgi-bin/detail.cgi?id=cell 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. 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'. Specifies whether a conversion occurs spontaneously or not. If the spontaneity is not known, the SPONTANEOUS property should be left empty. An xref to an organism taxonomy database, preferably NCBI taxon. This should be an instance of unificationXref, unless the organism is not in an existing database. The title of the publication. The name of the external database to which this xref refers. Description and classification of the feature. 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) The central process that take place at this step of the biochemical pathway. Reference entity for this physical entity. The end position of a sequence interval. A binding feature represents a "half" of the bond between two entities. This property points to another binding feature which represents the other half. The bond can be covalent or non-covalent. Variable features that are observed for this entity - such as known PTM or methylation sites and non-covalent bonds.