3 xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"
4 xmlns:protege="http://protege.stanford.edu/plugins/owl/protege#"
5 xmlns:xsp="http://www.owl-ontologies.com/2005/08/07/xsp.owl#"
6 xmlns="http://www.biopax.org/release/biopax-level3.owl#"
7 xmlns:owl="http://www.w3.org/2002/07/owl#"
8 xmlns:xsd="http://www.w3.org/2001/XMLSchema#"
9 xmlns:swrl="http://www.w3.org/2003/11/swrl#"
10 xmlns:swrlb="http://www.w3.org/2003/11/swrlb#"
11 xmlns:rdfs="http://www.w3.org/2000/01/rdf-schema#"
12 xml:base="http://www.biopax.org/release/biopax-level3.owl">
13 <owl:Ontology rdf:about="">
14 <rdfs:comment rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
15 >This is version 0.93 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).</rdfs:comment>
17 <owl:Class rdf:ID="Stoichiometry">
19 <owl:Class rdf:ID="UtilityClass"/>
23 <owl:cardinality rdf:datatype="http://www.w3.org/2001/XMLSchema#int"
26 <owl:FunctionalProperty rdf:ID="stoichiometricCoefficient"/>
33 <owl:FunctionalProperty rdf:ID="physicalEntity"/>
35 <owl:cardinality rdf:datatype="http://www.w3.org/2001/XMLSchema#int"
39 <rdfs:comment rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
40 >Definition: Stoichiometric coefficient of a physical entity in the context of an interaction or complex. Note that this class is an n-ary specifier for LEFT and RIGHT properties.</rdfs:comment>
42 <owl:Class rdf:ID="FragmentFeature">
44 <owl:Class rdf:ID="EntityFeature"/>
46 <rdfs:comment rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
47 >Definition: An entity feature that represents the resulting physical entity subsequent to a cleavage or degradation event.
49 Usage: Fragment Feature can be used to cover multiple types of modfications to the sequence of the physical entity:
50 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?
51 2. A protein with two cleavage sites that removes an internal sequence e.g. an intein i.e. ABC -> A
52 3. Cleavage of a circular sequence e.g. a plasmid.
54 In the case of removal ( e.g. intron) the fragment that is *removed* is specified in the feature location property. In the case of a "cut" (e.g. restriction enzyme cut site) the location of the cut is specified instead.</rdfs:comment>
56 <owl:Class rdf:ID="Interaction">
58 <owl:Class rdf:ID="Entity"/>
60 <rdfs:comment rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
61 >Definition: A single biological relationship between two or more entities. An interaction cannot be defined without the entities it relates.
62 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).
63 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.
64 Examples: protein-protein interaction, biochemical reaction, enzyme catalysis</rdfs:comment>
66 <owl:Class rdf:ID="Gene"/>
69 <owl:Class rdf:ID="PhysicalEntity"/>
72 <owl:Class rdf:ID="Pathway"/>
75 <owl:Class rdf:about="#Gene">
78 <owl:maxCardinality rdf:datatype="http://www.w3.org/2001/XMLSchema#int"
79 >1</owl:maxCardinality>
81 <owl:FunctionalProperty rdf:ID="organism"/>
86 <owl:Class rdf:about="#Entity"/>
89 <owl:Class rdf:about="#PhysicalEntity"/>
92 <owl:Class rdf:about="#Pathway"/>
94 <owl:disjointWith rdf:resource="#Interaction"/>
95 <rdfs:comment rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
96 >A continuant that encodes information that can be inherited through replication.
98 Gene is often confused with DNA and RNA fragments that are physical encoding of the gene. Gene is and abstract continuant that can be best described as a "schema". Gene in BioPAX is a generelization over eukaryotic and prokaryotic genes and used only for genetic interactions. Gene expression regulation makes use of DNA and RNA physical entities.</rdfs:comment>
100 <owl:Class rdf:ID="Control">
101 <rdfs:comment rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
102 >Definition: An interaction in which one entity regulates, modifies, or otherwise influences another. Two types of control interactions are defined: activation and inhibition.
103 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.
104 Synonyms: regulation, mediation
105 Examples: A small molecule that inhibits a pathway by an unknown mechanism controls the pathway.</rdfs:comment>
106 <rdfs:subClassOf rdf:resource="#Interaction"/>
108 <owl:Class rdf:ID="GeneticInteraction"/>
111 <owl:Class rdf:ID="SequenceLocation">
112 <rdfs:comment rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
113 >Definition: A location on a nucleotide or amino acid sequence.
114 Comment: For organizational purposes only; direct instances of this class should not be created.</rdfs:comment>
116 <owl:Class rdf:about="#UtilityClass"/>
119 <owl:Class rdf:ID="Score">
120 <rdfs:comment rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
121 >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.
122 Examples: The statistical significance of a result, e.g. "p<0.05".</rdfs:comment>
126 <owl:FunctionalProperty rdf:ID="value"/>
128 <owl:cardinality rdf:datatype="http://www.w3.org/2001/XMLSchema#int"
133 <owl:Class rdf:about="#UtilityClass"/>
136 <owl:Class rdf:ID="TransportWithBiochemicalReaction">
137 <rdfs:comment rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
138 >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.
139 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.
140 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.</rdfs:comment>
142 <owl:Class rdf:ID="BiochemicalReaction"/>
145 <owl:Class rdf:ID="Transport"/>
148 <owl:Class rdf:ID="InteractionVocabulary">
150 <owl:Class rdf:ID="ControlledVocabulary"/>
152 <rdfs:comment rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
153 >Definition: A term that describes the type of interaction selected from the PSI Molecular Interaction ontology (MI) interaction type. Usage: The top level of the PSI-MI hierarchy partially mirrors the BioPAX interaction classes. This interaction vocabulary should be used in parallel to BioPAX classes to more specifically annotate the type of interaction. For example a BioPAX conversion can be explicated as a phosphorylation. As a best practice, most specific applicable term must be chosen for annotation.
155 http://www.psidev.info/.
156 http://www.ebi.ac.uk/ontology-lookup/browse.do?ontName=MI&amp;termId=MI%3A0190&amp;termName=interaction%20type</rdfs:comment>
158 <owl:Class rdf:ID="Dna">
159 <rdfs:comment rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
160 >Definition: A physical entity consisting of a sequence of deoxyribonucleotide monophosphates; a deoxyribonucleic acid.
161 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.
162 Examples: a chromosome, a plasmid. A specific example is chromosome 7 of Homo sapiens.</rdfs:comment>
164 <owl:Class rdf:about="#PhysicalEntity"/>
169 <owl:TransitiveProperty rdf:ID="memberPhysicalEntity"/>
171 <owl:allValuesFrom rdf:resource="#Dna"/>
177 <owl:FunctionalProperty rdf:ID="entityReference"/>
180 <owl:Class rdf:ID="DnaReference"/>
185 <owl:Class rdf:ID="Protein"/>
188 <owl:Class rdf:ID="Rna"/>
191 <owl:Class rdf:ID="SequenceSite">
192 <rdfs:comment rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
193 >Definition: Describes a site on a sequence, i.e. the position of a single nucleotide or amino acid.</rdfs:comment>
194 <rdfs:subClassOf rdf:resource="#SequenceLocation"/>
196 <owl:Class rdf:ID="PathwayStep">
197 <rdfs:comment rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
198 >Definition: A step in a pathway.
199 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.
200 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.</rdfs:comment>
202 <owl:Class rdf:about="#UtilityClass"/>
205 <owl:Class rdf:about="#DnaReference">
206 <rdfs:comment rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
207 >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.
209 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).</rdfs:comment>
212 <owl:allValuesFrom rdf:resource="#DnaReference"/>
214 <owl:TransitiveProperty rdf:ID="memberEntityReference"/>
219 <owl:Class rdf:ID="EntityReference"/>
222 <owl:Class rdf:ID="KPrime">
225 <owl:cardinality rdf:datatype="http://www.w3.org/2001/XMLSchema#int"
228 <owl:FunctionalProperty rdf:ID="kPrime"/>
233 <owl:Class rdf:about="#UtilityClass"/>
235 <rdfs:comment rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
236 >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:
238 K' = [ADP][P<sub>i</sub>]/[ATP],
240 The concentration of ATP refers to the total concentration of all of the following species:
242 [ATP] = [ATP<sup>4-</sup>] + [HATP<sup>3-</sup>] + [H<sub>2</sub>ATP<sup>2-</sup>] + [MgATP<sup>2-</sup>] + [MgHATP<sup>-</sup>] + [Mg<sub>2</sub>ATP].
244 The apparent equilibrium constant is formally dimensionless, and can be kept so by inclusion of as many of the terms (1 mol/dm<sup>3</sup>) in the numerator or denominator as necessary. It is a function of temperature (T), ionic strength (I), pH, and pMg (pMg = -log<sub>10</sub>[Mg<sup>2+</sup>]). 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)
246 See http://www.chem.qmul.ac.uk/iubmb/thermod/ for a thermodynamics tutorial.</rdfs:comment>
248 <owl:Class rdf:ID="Catalysis">
251 <owl:maxCardinality rdf:datatype="http://www.w3.org/2001/XMLSchema#int"
252 >1</owl:maxCardinality>
254 <owl:ObjectProperty rdf:ID="controller"/>
260 <owl:hasValue rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
261 >ACTIVATION</owl:hasValue>
263 <owl:FunctionalProperty rdf:ID="controlType"/>
267 <rdfs:subClassOf rdf:resource="#Control"/>
271 <owl:FunctionalProperty rdf:ID="controlled"/>
274 <owl:Class rdf:ID="Conversion"/>
278 <rdfs:comment rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
279 >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.
280 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).
281 Synonyms: facilitation, acceleration.
282 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.</rdfs:comment>
284 <owl:Class rdf:ID="RnaReference">
285 <rdfs:comment rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
286 >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.</rdfs:comment>
288 <owl:Class rdf:about="#EntityReference"/>
293 <owl:TransitiveProperty rdf:about="#memberEntityReference"/>
295 <owl:allValuesFrom rdf:resource="#RnaReference"/>
299 <owl:Class rdf:ID="PhenotypeVocabulary">
301 <owl:Class rdf:about="#ControlledVocabulary"/>
303 <rdfs:comment rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
304 >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.</rdfs:comment>
306 <owl:Class rdf:about="#GeneticInteraction">
308 <owl:Class rdf:ID="MolecularInteraction"/>
311 <owl:Class rdf:ID="TemplateReaction"/>
315 <owl:cardinality rdf:datatype="http://www.w3.org/2001/XMLSchema#int"
318 <owl:FunctionalProperty rdf:ID="phenotype"/>
324 <owl:minCardinality rdf:datatype="http://www.w3.org/2001/XMLSchema#int"
325 >2</owl:minCardinality>
327 <owl:ObjectProperty rdf:ID="participant"/>
331 <owl:disjointWith rdf:resource="#Control"/>
333 <owl:Class rdf:about="#Conversion"/>
335 <rdfs:comment rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
336 >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.</rdfs:comment>
337 <rdfs:subClassOf rdf:resource="#Interaction"/>
340 <owl:maxCardinality rdf:datatype="http://www.w3.org/2001/XMLSchema#int"
341 >1</owl:maxCardinality>
343 <owl:ObjectProperty rdf:ID="interactionType"/>
349 <owl:allValuesFrom rdf:resource="#Gene"/>
351 <owl:ObjectProperty rdf:about="#participant"/>
356 <owl:Class rdf:about="#MolecularInteraction">
357 <owl:disjointWith rdf:resource="#GeneticInteraction"/>
358 <rdfs:comment rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
359 >Definition: An interaction in which at least one participant is a physical entity, e.g. a binding event.
360 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.
361 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.</rdfs:comment>
362 <rdfs:subClassOf rdf:resource="#Interaction"/>
366 <owl:Class rdf:about="#PhysicalEntity"/>
369 <owl:ObjectProperty rdf:about="#participant"/>
374 <owl:Class rdf:ID="CellularLocationVocabulary">
375 <rdfs:comment rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
376 >Definition: Name of the subcellular location selected from Gene Ontology Cellular Component (GO CC) ontology.
379 http://www.geneontology.org
380 http://www.ebi.ac.uk/ontology-lookup/browse.do?ontName=GO</rdfs:comment>
382 <owl:Class rdf:about="#ControlledVocabulary"/>
385 <owl:Class rdf:about="#TemplateReaction">
386 <rdfs:subClassOf rdf:resource="#Interaction"/>
390 <owl:ObjectProperty rdf:about="#participant"/>
393 <owl:Class rdf:about="#PhysicalEntity"/>
397 <owl:disjointWith rdf:resource="#GeneticInteraction"/>
398 <rdfs:comment rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
399 >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.</rdfs:comment>
401 <owl:Class rdf:about="#UtilityClass">
402 <rdfs:comment rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
403 >Definition: This is a placeholder for classes, used for annotating the "Entity" and its subclasses but are not an "Entity" themselves. Examples include references to external databases, controlled vocabularies, evidence and provenance.
405 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.
407 Instances: 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.</rdfs:comment>
409 <owl:Class rdf:ID="Complex">
411 <owl:Class rdf:about="#PhysicalEntity"/>
416 <owl:TransitiveProperty rdf:about="#memberPhysicalEntity"/>
418 <owl:allValuesFrom rdf:resource="#Complex"/>
421 <rdfs:comment rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
422 >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.
423 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.
424 Examples: Ribosome, RNA polymerase II. Other examples of this class include complexes of multiple protein monomers and complexes of proteins and small molecules.</rdfs:comment>
426 <owl:Class rdf:ID="TissueVocabulary">
428 <owl:Class rdf:about="#ControlledVocabulary"/>
430 <rdfs:comment rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
431 >Definition: A term defining the type of tissue that this pathway, protein reference, dna reference, rna reference or gene was observed. This is a reference to the BRENDA source tissue ontology(BTO).
433 Instances: ganglioglioma cell, scutellum, gymnothecium
436 http://www.brenda-enzymes.info/.
437 http://www.ebi.ac.uk/ontology-lookup/browse.do?ontName=BTO</rdfs:comment>
439 <owl:Class rdf:ID="RelationshipXref">
441 <owl:Class rdf:ID="Xref"/>
443 <rdfs:comment rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
444 >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.
445 Comment: There is currently no controlled vocabulary of relationship types for BioPAX, although one will be created in the future if a need develops.
446 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.</rdfs:comment>
448 <owl:Class rdf:ID="ProteinReference">
449 <rdfs:comment rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
450 >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.</rdfs:comment>
454 <owl:TransitiveProperty rdf:about="#memberEntityReference"/>
456 <owl:allValuesFrom rdf:resource="#ProteinReference"/>
460 <owl:Class rdf:about="#EntityReference"/>
463 <owl:Class rdf:ID="Degradation">
465 <owl:Class rdf:about="#Conversion"/>
469 <owl:hasValue rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
470 >LEFT-TO-RIGHT</owl:hasValue>
472 <owl:FunctionalProperty rdf:ID="conversionDirection"/>
476 <rdfs:comment rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
477 >The process of degrading a physical entity. The right side of the conversion is not specified, indicating degraded components. The conversion is not spontaneous.</rdfs:comment>
479 <owl:Class rdf:about="#Protein">
480 <rdfs:comment rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
481 >Definition: A physical entity consisting of a sequence of amino acids; a protein monomer; a single polypeptide chain.
482 Examples: The epidermal growth factor receptor (EGFR) protein.</rdfs:comment>
484 <owl:Class rdf:about="#Rna"/>
486 <owl:disjointWith rdf:resource="#Dna"/>
488 <owl:Class rdf:about="#PhysicalEntity"/>
493 <owl:TransitiveProperty rdf:about="#memberPhysicalEntity"/>
495 <owl:allValuesFrom rdf:resource="#Protein"/>
501 <owl:FunctionalProperty rdf:about="#entityReference"/>
503 <owl:allValuesFrom rdf:resource="#ProteinReference"/>
507 <owl:Class rdf:about="#ControlledVocabulary">
508 <rdfs:subClassOf rdf:resource="#UtilityClass"/>
512 <owl:ObjectProperty rdf:ID="xref"/>
515 <owl:Class rdf:ID="UnificationXref"/>
519 <rdfs:comment rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
520 >Definition: standard referenceble terms agreed by communities for enabling consistent and compatible annotation. This class acts as a reference to externally maintained CVs.
522 Rationale: BioPAX conciously avoids pysically including CVs and instead references to standard controlled vocabularies for modularity and compatibility. Small lists are occasionaly required when a standard vocabulary does not exist, such as controlType and conversionDirection.These are included as term restricted properties.
524 Usage: As a best practice, CVs should be used whenever possible. Some CVs, agreed on by the BioPAX community as standard, are listed within subclasses of this class. When an agreed on standard does not exist open, freely available CVs should be preferred. See also usage for the UnificationXref class in relation to controlled vocabularies.</rdfs:comment>
526 <owl:Class rdf:ID="BioSource">
527 <rdfs:comment rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
528 >Definition: The biological source (organism, tissue or cell type) of an "Entity".
530 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).
532 Instances: HeLa cells, Homo sapiens, and mouse liver tissue.</rdfs:comment>
536 <owl:Class rdf:about="#UnificationXref"/>
539 <owl:ObjectProperty rdf:about="#xref"/>
546 <owl:ObjectProperty rdf:about="#xref"/>
548 <owl:cardinality rdf:datatype="http://www.w3.org/2001/XMLSchema#int"
552 <rdfs:subClassOf rdf:resource="#UtilityClass"/>
554 <owl:Class rdf:ID="SequenceModificationVocabulary">
555 <rdfs:comment rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
556 >Definition: A term that describes the covalent modifications to an amino
557 acid or nucleic acid chain. For proteins this is reference to the PSI
558 Molecular Interaction ontology (MI) of covalent sequence modifications.
559 For nucleic acids, there is currently no recommended standard CV. Usage:
560 Whenever possible the most specific term in the ontology should be used.
561 For example PSI-MI term o-phospho-serine should be used instead of the
562 parent &quot;phosphorylated residue&quot; when annotating a phosphorylation at a
563 known serine amino acid. See: http://www.psidev.info/.
564 http://www.ebi.ac.uk/ontology-lookup/browse.do?ontName=MI&amp;termId=MI%3A0252&amp;termName=biological%20feature.
565 Candidate RNA modification CV:
566 http://library.med.utah.edu/cgi-bin/rnafind.cgi.</rdfs:comment>
567 <rdfs:subClassOf rdf:resource="#ControlledVocabulary"/>
569 <owl:Class rdf:ID="Evidence">
570 <rdfs:subClassOf rdf:resource="#UtilityClass"/>
573 <owl:unionOf rdf:parseType="Collection">
575 <owl:minCardinality rdf:datatype="http://www.w3.org/2001/XMLSchema#int"
576 >1</owl:minCardinality>
578 <owl:ObjectProperty rdf:ID="confidence"/>
583 <owl:ObjectProperty rdf:ID="evidenceCode"/>
585 <owl:minCardinality rdf:datatype="http://www.w3.org/2001/XMLSchema#int"
586 >1</owl:minCardinality>
590 <owl:ObjectProperty rdf:ID="experimentalForm"/>
592 <owl:minCardinality rdf:datatype="http://www.w3.org/2001/XMLSchema#int"
593 >1</owl:minCardinality>
598 <rdfs:comment rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
599 >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.
600 Examples: A description of a molecular binding assay that was used to detect a protein-protein interaction.</rdfs:comment>
602 <owl:Class rdf:ID="SmallMoleculeReference">
603 <rdfs:comment rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
604 >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.</rdfs:comment>
606 <owl:Class rdf:about="#EntityReference"/>
611 <owl:TransitiveProperty rdf:about="#memberEntityReference"/>
613 <owl:allValuesFrom rdf:resource="#SmallMoleculeReference"/>
617 <owl:Class rdf:ID="ExperimentalForm">
618 <rdfs:subClassOf rdf:resource="#UtilityClass"/>
622 <owl:ObjectProperty rdf:ID="experimentalFormDescription"/>
624 <owl:minCardinality rdf:datatype="http://www.w3.org/2001/XMLSchema#int"
625 >1</owl:minCardinality>
628 <rdfs:comment rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
629 >Definition: The form of a physical entity in a particular experiment, as it may be modified for purposes of experimental design.
630 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</rdfs:comment>
632 <owl:Class rdf:ID="CovalentBindingFeature">
634 <owl:Class rdf:ID="BindingFeature"/>
637 <owl:Class rdf:ID="ModificationFeature"/>
639 <rdfs:comment rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
640 >Definition : An entity feature that represent the covalently bound state of a physical entity.
642 Rationale: Most frequent covalent modifications to proteins and DNA, such as phosphorylation and metylation are covered by the ModificationFeature class. In these cases, the added groups are simple and stateless therefore they can be captured by a controlled vocabulary. In other cases, such as ThiS-Thil acyl-disulfide(http://biocyc.org/ECOLI/NEW-IMAGE?type=REACTION&object=RXN-9788), the covalently linked molecules are best represented as a molecular complex. CovalentBindingFeature should be used to model such covalently linked complexes.
644 Using this construct, it is possible to represent small molecules as a covalent complex of two other small molecules. The demarcation of small
645 molecules is a general problem and is delegated to small molecule databases.The best practice is not to model using covalent complexes
646 unless at least one of the participants is a protein, DNA or RNA.
650 UhpC + glc-6P -> Uhpc-glc-6p
651 acetyl-ACP -> decenoyl-ACP
652 charged tRNA</rdfs:comment>
654 <owl:Class rdf:about="#Pathway">
655 <owl:disjointWith rdf:resource="#Gene"/>
657 <owl:Class rdf:about="#PhysicalEntity"/>
659 <owl:disjointWith rdf:resource="#Interaction"/>
660 <rdfs:comment rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
661 >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.
662 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'.
664 Examples: glycolysis, valine biosynthesis</rdfs:comment>
666 <owl:Class rdf:about="#Entity"/>
669 <owl:Class rdf:about="#BiochemicalReaction">
671 <owl:Class rdf:about="#Conversion"/>
673 <rdfs:comment rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
674 >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.
675 Examples: ATP + H2O = ADP + Pi
676 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.</rdfs:comment>
678 <owl:Class rdf:ID="RnaRegionReference">
682 <owl:ObjectProperty rdf:ID="subRegion"/>
684 <owl:allValuesFrom rdf:resource="#RnaRegionReference"/>
688 <owl:Class rdf:about="#EntityReference"/>
691 <owl:Class rdf:ID="Provenance">
692 <rdfs:subClassOf rdf:resource="#UtilityClass"/>
697 <owl:unionOf rdf:parseType="Collection">
698 <owl:Class rdf:ID="PublicationXref"/>
699 <owl:Class rdf:about="#UnificationXref"/>
704 <owl:ObjectProperty rdf:about="#xref"/>
708 <rdfs:comment rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
709 >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.
710 Examples: A database, scoring method or person name.</rdfs:comment>
712 <owl:Class rdf:about="#BindingFeature">
714 <owl:Class rdf:about="#EntityFeature"/>
716 <rdfs:comment rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
717 >Definition : An entity feature that represent the bound state of a physical entity. A pair of binding features represents a bond.
719 Rationale: A physical entity in a molecular complex is considered as a new state of an entity as it is structurally and functionally different. Binding features provide facilities for describing these states. Similar to other features, a molecule can have bound and not-bound states.
721 Usage: Typically, binding features are present in pairs, each describing the binding characteristic for one of the interacting physical entities. One exception is using a binding feature with no paired feature to describe any potential binding. For example, an unbound receptor can be described by using a "not-feature" property with an unpaired binding feature as its value. BindingSiteType and featureLocation allows annotating the binding location.
723 IntraMolecular property should be set to "true" if the bond links two parts of the same molecule. A pair of binding features are still used where they are owned by the same physical entity.
725 If the binding is due to the covalent interactions, for example in the case of lipoproteins, CovalentBindingFeature subclass should be used instead of this class.</rdfs:comment>
727 <owl:Class rdf:ID="EntityReferenceTypeVocabulary">
728 <rdfs:comment rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
729 >Definition: A reference to a term from a reference entity group ontology. Reference entities can be grouped by homology, functional or structural similarity, phenotype or some other relationship.
730 Usage: There is no agreed on standard for this CV.</rdfs:comment>
731 <rdfs:subClassOf rdf:resource="#ControlledVocabulary"/>
733 <owl:Class rdf:about="#Xref">
734 <rdfs:subClassOf rdf:resource="#UtilityClass"/>
735 <rdfs:comment rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
736 >Definition: A reference from an instance of a class in this ontology to an object in an external resource.
737 Comment: Instances of the xref class should never be created and more specific classes should be used instead.</rdfs:comment>
739 <owl:Class rdf:ID="BiochemicalPathwayStep">
740 <rdfs:subClassOf rdf:resource="#PathwayStep"/>
744 <owl:ObjectProperty rdf:ID="stepProcess"/>
748 <owl:unionOf rdf:parseType="Collection">
749 <owl:Class rdf:about="#Control"/>
750 <owl:Class rdf:about="#Conversion"/>
756 <rdfs:comment rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
757 >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.</rdfs:comment>
759 <owl:Class rdf:about="#Transport">
761 <owl:Class rdf:about="#Conversion"/>
763 <rdfs:comment rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
764 >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.
765 Comment: Transport interactions do not involve chemical changes of the participant(s). These cases are handled by the transportWithBiochemicalReaction class.
766 Synonyms: translocation.
767 Examples: The movement of Na+ into the cell through an open voltage-gated channel.</rdfs:comment>
769 <owl:Class rdf:about="#Rna">
770 <rdfs:comment rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
771 >Definition: A physical entity consisting of a sequence of ribonucleotide monophosphates; a ribonucleic acid.
772 Examples: messengerRNA, microRNA, ribosomalRNA. A specific example is the let-7 microRNA.</rdfs:comment>
773 <owl:disjointWith rdf:resource="#Protein"/>
774 <owl:disjointWith rdf:resource="#Dna"/>
776 <owl:Class rdf:about="#PhysicalEntity"/>
781 <owl:TransitiveProperty rdf:about="#memberPhysicalEntity"/>
783 <owl:allValuesFrom rdf:resource="#Rna"/>
789 <owl:FunctionalProperty rdf:about="#entityReference"/>
791 <owl:allValuesFrom rdf:resource="#RnaReference"/>
795 <owl:Class rdf:ID="TemplateReactionRegulation">
796 <rdfs:comment rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
797 >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.</rdfs:comment>
800 <owl:allValuesFrom rdf:resource="#TemplateReaction"/>
802 <owl:FunctionalProperty rdf:about="#controlled"/>
809 <owl:FunctionalProperty rdf:about="#controlType"/>
813 <owl:oneOf rdf:parseType="Resource">
814 <rdf:rest rdf:parseType="Resource">
815 <rdf:rest rdf:resource="http://www.w3.org/1999/02/22-rdf-syntax-ns#nil"/>
816 <rdf:first rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
817 >INHIBITION</rdf:first>
819 <rdf:first rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
820 >ACTIVATION</rdf:first>
829 <owl:Class rdf:about="#PhysicalEntity"/>
832 <owl:ObjectProperty rdf:about="#controller"/>
836 <rdfs:subClassOf rdf:resource="#Control"/>
838 <owl:Class rdf:about="#UnificationXref">
841 <owl:cardinality rdf:datatype="http://www.w3.org/2001/XMLSchema#int"
844 <owl:FunctionalProperty rdf:ID="id"/>
848 <rdfs:subClassOf rdf:resource="#Xref"/>
852 <owl:FunctionalProperty rdf:ID="db"/>
854 <owl:cardinality rdf:datatype="http://www.w3.org/2001/XMLSchema#int"
859 <owl:Class rdf:about="#PublicationXref">
860 <rdfs:subClassOf rdf:resource="#Xref"/>
863 <owl:cardinality rdf:datatype="http://www.w3.org/2001/XMLSchema#int"
866 <owl:FunctionalProperty rdf:ID="year"/>
872 <owl:cardinality rdf:datatype="http://www.w3.org/2001/XMLSchema#int"
875 <owl:FunctionalProperty rdf:ID="title"/>
879 <rdfs:comment rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
880 >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.
881 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".
882 Examples: PubMed:10234245</rdfs:comment>
884 <owl:Class rdf:ID="Modulation">
887 <owl:allValuesFrom rdf:resource="#Catalysis"/>
889 <owl:FunctionalProperty rdf:about="#controlled"/>
893 <rdfs:subClassOf rdf:resource="#Control"/>
897 <owl:ObjectProperty rdf:about="#controller"/>
899 <owl:maxCardinality rdf:datatype="http://www.w3.org/2001/XMLSchema#int"
900 >1</owl:maxCardinality>
903 <rdfs:comment rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
904 >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.
905 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.
906 Examples: Allosteric activation and competitive inhibition of an enzyme's ability to catalyze a specific reaction.</rdfs:comment>
908 <owl:Class rdf:ID="RnaRegion">
912 <owl:FunctionalProperty rdf:about="#entityReference"/>
914 <owl:allValuesFrom rdf:resource="#RnaRegionReference"/>
918 <owl:Class rdf:about="#PhysicalEntity"/>
920 <rdfs:comment rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
921 >A region of RNA</rdfs:comment>
923 <owl:Class rdf:about="#Entity">
924 <rdfs:comment rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
925 >Definition: A discrete biological unit used when describing pathways. This is an interacting entity, not just any entity.
926 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.
927 Synonyms: thing, object, bioentity.</rdfs:comment>
929 <owl:Class rdf:ID="DeltaG">
930 <rdfs:comment rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
931 >Definition: Standard transformed Gibbs energy change for a reaction written in terms of biochemical reactants. Delta-G is represented as a 5-tuple of delta-G'<sup>0</sup>, temperature, ionic strength , pH, and pMg . A conversion in BioPAX may have multiple Delta-G values, representing different measurements for delta-G'<sup>0</sup> obtained under the different experimental conditions.</rdfs:comment>
935 <owl:FunctionalProperty rdf:ID="deltaGPrime0"/>
937 <owl:cardinality rdf:datatype="http://www.w3.org/2001/XMLSchema#int"
941 <rdfs:subClassOf rdf:resource="#UtilityClass"/>
943 <owl:Class rdf:ID="SequenceRegionVocabulary">
944 <rdfs:subClassOf rdf:resource="#ControlledVocabulary"/>
945 <rdfs:comment rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
947 <TODO: Sequence ontology only partially covers polypeptide
948 domains and interpro is protein specific. What should be the standard way
949 to refer sequence regions?> A term that describes the type of the sequence
950 region based on sequence, topology and/or function.
952 Instances: SH2 domain, promoter, 5' UTR, C-terminal region.
955 http://www.sequenceontology.org/. http://www.ebi.ac.uk/ontology-lookup/browse.do?ontName=SO</rdfs:comment>
957 <owl:Class rdf:ID="DnaRegion">
958 <rdfs:comment rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
959 >A region of DNA.</rdfs:comment>
963 <owl:Class rdf:ID="DnaRegionReference"/>
966 <owl:FunctionalProperty rdf:about="#entityReference"/>
971 <owl:Class rdf:about="#PhysicalEntity"/>
974 <owl:Class rdf:ID="ChemicalStructure">
977 <owl:cardinality rdf:datatype="http://www.w3.org/2001/XMLSchema#int"
980 <owl:FunctionalProperty rdf:ID="structureData"/>
986 <owl:cardinality rdf:datatype="http://www.w3.org/2001/XMLSchema#int"
989 <owl:FunctionalProperty rdf:ID="structureFormat"/>
993 <rdfs:subClassOf rdf:resource="#UtilityClass"/>
994 <rdfs:comment rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
995 >Definition: The chemical structure of a small molecule.
997 Usage Notes: 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.
999 Instances: The following SMILES string describes the structure of glucose-6-phosphate:
1000 'C(OP(=O)(O)O)[CH]1([CH](O)[CH](O)[CH](O)[CH](O)O1)'.</rdfs:comment>
1002 <owl:Class rdf:about="#EntityReference">
1003 <rdfs:comment rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
1004 >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. An entity reference is not a physical entity, it is an abstraction based on
1007 For DNA, RNA and Proteins the grouping is defined based on a wildtype sequence, for small molecules it is defined by the chemical structure.
1010 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.
1012 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:
1014 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.
1016 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.
1018 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.</rdfs:comment>
1019 <rdfs:subClassOf rdf:resource="#UtilityClass"/>
1021 <owl:Class rdf:about="#DnaRegionReference">
1025 <owl:ObjectProperty rdf:about="#subRegion"/>
1027 <owl:allValuesFrom rdf:resource="#DnaRegionReference"/>
1030 <rdfs:subClassOf rdf:resource="#EntityReference"/>
1032 <owl:Class rdf:ID="EvidenceCodeVocabulary">
1033 <rdfs:subClassOf rdf:resource="#ControlledVocabulary"/>
1034 <rdfs:comment rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
1035 >Definition: Name of the experimental method used for detecting this interaction selected from PSI Molecular Interaction ontology (MI) experimental method types, including "interaction detection method", "participant identification method", "feature detection method".
1036 Terms from the Pathway Tools Evidence Ontology may also be used.
1039 http://www.psidev.info/
1040 http://www.ebi.ac.uk/ontology-lookup/browse.do?ontName=MI
1041 http://brg.ai.sri.com/evidence-ontology/</rdfs:comment>
1043 <owl:Class rdf:about="#PhysicalEntity">
1044 <rdfs:comment rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
1045 >Definition: A pool of molecules, not a specific molecular instance of an entity in a cell.
1046 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.
1047 Synonyms: part, interactor, object
1048 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.
1049 Examples: protein, small molecule, RNA</rdfs:comment>
1050 <owl:disjointWith rdf:resource="#Gene"/>
1051 <owl:disjointWith rdf:resource="#Pathway"/>
1052 <owl:disjointWith rdf:resource="#Interaction"/>
1053 <rdfs:subClassOf rdf:resource="#Entity"/>
1055 <owl:Class rdf:about="#Conversion">
1056 <rdfs:subClassOf rdf:resource="#Interaction"/>
1060 <owl:ObjectProperty rdf:about="#participant"/>
1062 <owl:allValuesFrom rdf:resource="#PhysicalEntity"/>
1065 <rdfs:comment rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
1066 >Definition: An interaction in which one or more physical entities in the is physically transformed into one or more other entities.
1069 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.
1070 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.</rdfs:comment>
1071 <owl:disjointWith rdf:resource="#GeneticInteraction"/>
1073 <owl:Class rdf:ID="SequenceInterval">
1074 <rdfs:comment rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
1075 >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.</rdfs:comment>
1076 <rdfs:subClassOf rdf:resource="#SequenceLocation"/>
1078 <owl:Class rdf:about="#ModificationFeature">
1079 <rdfs:comment rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
1080 >Definition: An entity feature that represents the covalently modified state of a dna, rna or a protein.
1082 Rationale: In Biology, identity of DNA, RNA and Protein entities are defined around a wildtype sequence. Covalent modifications to this basal sequence are represented using modificaton features. Since small molecules are identified based on their chemical structure, not sequence, a covalent modification to a small molecule would result in a different molecule.
1084 Usage: The added groups should be simple and stateless, such as phosphate or methyl groups and are captured by the modificationType controlled vocabulary. In other cases, such as covalently linked proteins, use CovalentBindingFeature instead.
1086 Instances: A phosphorylation on a protein, a methylation on a DNA.</rdfs:comment>
1088 <owl:Class rdf:about="#EntityFeature"/>
1091 <owl:Class rdf:ID="RelationshipTypeVocabulary">
1092 <rdfs:subClassOf rdf:resource="#ControlledVocabulary"/>
1093 <rdfs:comment rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
1094 ><TODO: Substantial amount of these relationships are now covered in BioPAX level 3 and using some of the terms are bad-practice like primary identification number. Data providers also use their own terms - do we want to keep using this? >Definition: A term that defines the type of relationship stated in a relationshipXref. This is a reference to the "cross-reference type" subtree of the PSI Molecular Interaction ontology (MI). Homepage at http://www.psidev.info/.
1096 Example: The term "gene-product" can be used for linking proteins and genes.
1099 See : http://www.ebi.ac.uk/ontology-lookup/browse.do?ontName=MI&termId=MI%3A0353&termName=cross-reference%20type</rdfs:comment>
1101 <owl:Class rdf:ID="ComplexAssembly">
1102 <rdfs:comment rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
1103 >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.
1104 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.
1105 Synonyms: aggregation, complex formation
1106 Examples: Assembly of the TFB2 and TFB3 proteins into the TFIIH complex, and assembly of the ribosome through aggregation of its subunits.
1107 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).</rdfs:comment>
1108 <rdfs:subClassOf rdf:resource="#Conversion"/>
1110 <owl:Class rdf:ID="CellVocabulary">
1111 <rdfs:subClassOf rdf:resource="#ControlledVocabulary"/>
1112 <rdfs:comment rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
1113 >Definition: Name of the cell type selected from Cell Type Ontology (CL).
1115 http://obofoundry.org/cgi-bin/detail.cgi?cell
1116 http://www.ebi.ac.uk/ontology-lookup/browse.do?ontName=CL</rdfs:comment>
1118 <owl:Class rdf:ID="SmallMolecule">
1119 <rdfs:comment rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
1120 >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.
1121 Comment: Recently, a number of small molecule databases have become available to cross-reference from this class.
1122 Examples: glucose, penicillin, phosphatidylinositol
1123 Note: Complex carbohydrates are not currently modeled in BioPAX or most pathway databases, due to the lack of a publicly available complex carbohydrate database.</rdfs:comment>
1124 <rdfs:subClassOf rdf:resource="#PhysicalEntity"/>
1127 <owl:allValuesFrom rdf:resource="#BindingFeature"/>
1129 <owl:ObjectProperty rdf:ID="notFeature"/>
1136 <owl:ObjectProperty rdf:ID="feature"/>
1138 <owl:allValuesFrom rdf:resource="#BindingFeature"/>
1144 <owl:TransitiveProperty rdf:about="#memberPhysicalEntity"/>
1146 <owl:allValuesFrom rdf:resource="#SmallMolecule"/>
1152 <owl:FunctionalProperty rdf:about="#entityReference"/>
1154 <owl:allValuesFrom rdf:resource="#SmallMoleculeReference"/>
1158 <owl:Class rdf:about="#EntityFeature">
1159 <rdfs:comment rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
1160 >Description: A characteristic of a physical entity that can change while the entity still retains its biological identity.
1162 Rationale: Two phosphorylated forms of a protein are strictly speaking different chemical molecules. It is, however, standard in biology to treat them as different states of the same entity, where the entity is loosely defined based on sequence. Entity Feature class and its subclassses captures these variable characteristics. A Physical Entity in BioPAX represents a pool of molecules rather than an individual molecule. This is a notion imported from chemistry( See PhysicalEntity). Pools are defined by a set of Entity Features in the sense that a single molecule must have all of the features in the set in order to be considered a member of the pool. Since it is impossible to list and experimentally test all potential features for an entity, features that are not listed in the selection criteria is neglected Pools can also be defined by the converse by specifying features that are known to NOT exist in a specific context. As DNA, RNA and Proteins can be hierarchicaly organized into families based on sequence homology so can entity features. The memberFeature property allows capturing such hierarchical classifications among entity features.
1164 &lt;todo describe evidence??&gt;
1166 Usage: Subclasses of entity feature describe most common biological instances and sholud be preferred whenever possible. One common usecase for instatiating entity feature is, for describing active/inactive states of proteins where more specific feature information is not available.
1168 Instances: Open/close conformational state of channel proteins, "active"/"inactive" states, excited states of photoreactive groups.</rdfs:comment>
1169 <rdfs:subClassOf rdf:resource="#UtilityClass"/>
1171 <owl:Class rdf:ID="ExperimentalFormVocabulary">
1172 <rdfs:subClassOf rdf:resource="#ControlledVocabulary"/>
1173 <rdfs:comment rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
1174 >Definiition: A term that describes the form of the physical entity in the context of the experiment. This is a reference to the PSI Molecular Interaction ontology (MI) participant identification method (e.g. mass spectrometry), experimental role (e.g. bait, prey) or experimental preparation (e.g. expression level) type.
1176 Rationale: <ratify with Gary>
1178 http://www.psidev.info/.
1179 http://www.ebi.ac.uk/ontology-lookup/browse.do?ontName=MI&termId=MI%3A0002&termName=participant%20identification%20method
1180 http://www.ebi.ac.uk/ontology-lookup/browse.do?ontName=MI&termId=MI%3A0495&termName=experimental%20role
1181 http://www.ebi.ac.uk/ontology-lookup/browse.do?ontName=MI&termId=MI%3A0346&termName=experimental%20preparation</rdfs:comment>
1183 <owl:ObjectProperty rdf:ID="experimentalFeature">
1184 <rdfs:domain rdf:resource="#ExperimentalForm"/>
1185 <rdfs:range rdf:resource="#EntityFeature"/>
1186 <rdfs:comment rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
1187 >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.</rdfs:comment>
1188 </owl:ObjectProperty>
1189 <owl:ObjectProperty rdf:ID="product">
1190 <rdfs:subPropertyOf>
1191 <owl:ObjectProperty rdf:about="#participant"/>
1192 </rdfs:subPropertyOf>
1195 <owl:unionOf rdf:parseType="Collection">
1196 <owl:Class rdf:about="#Dna"/>
1197 <owl:Class rdf:about="#Protein"/>
1198 <owl:Class rdf:about="#Rna"/>
1202 <rdfs:domain rdf:resource="#TemplateReaction"/>
1203 <rdfs:comment rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
1204 >The product of a template reaction.</rdfs:comment>
1205 </owl:ObjectProperty>
1206 <owl:ObjectProperty rdf:about="#controller">
1209 <owl:unionOf rdf:parseType="Collection">
1210 <owl:Class rdf:about="#PhysicalEntity"/>
1211 <owl:Class rdf:about="#Pathway"/>
1215 <rdfs:subPropertyOf>
1216 <owl:ObjectProperty rdf:about="#participant"/>
1217 </rdfs:subPropertyOf>
1218 <rdfs:comment xml:lang="en">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.</rdfs:comment>
1219 <rdfs:domain rdf:resource="#Control"/>
1220 </owl:ObjectProperty>
1221 <owl:ObjectProperty rdf:about="#interactionType">
1222 <rdfs:range rdf:resource="#InteractionVocabulary"/>
1223 <rdfs:domain rdf:resource="#Interaction"/>
1224 <rdfs:comment rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
1225 >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.</rdfs:comment>
1226 </owl:ObjectProperty>
1227 <owl:ObjectProperty rdf:ID="componentStoichiometry">
1228 <rdfs:domain rdf:resource="#Complex"/>
1229 <rdfs:range rdf:resource="#Stoichiometry"/>
1230 <rdfs:comment rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
1231 >The stoichiometry of components in a complex</rdfs:comment>
1232 </owl:ObjectProperty>
1233 <owl:ObjectProperty rdf:about="#evidenceCode">
1234 <rdfs:domain rdf:resource="#Evidence"/>
1235 <rdfs:range rdf:resource="#EvidenceCodeVocabulary"/>
1236 <rdfs:comment rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
1237 >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'.</rdfs:comment>
1238 </owl:ObjectProperty>
1239 <owl:ObjectProperty rdf:ID="dataSource">
1240 <rdfs:range rdf:resource="#Provenance"/>
1241 <rdfs:comment rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
1242 >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.</rdfs:comment>
1243 <rdfs:domain rdf:resource="#Entity"/>
1244 </owl:ObjectProperty>
1245 <owl:ObjectProperty rdf:about="#experimentalForm">
1246 <rdfs:range rdf:resource="#ExperimentalForm"/>
1247 <rdfs:domain rdf:resource="#Evidence"/>
1248 <rdfs:comment rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
1249 >The experimental forms associated with an evidence instance.</rdfs:comment>
1250 </owl:ObjectProperty>
1251 <owl:ObjectProperty rdf:about="#feature">
1252 <rdfs:domain rdf:resource="#PhysicalEntity"/>
1253 <rdfs:range rdf:resource="#EntityFeature"/>
1254 <rdfs:comment rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
1255 >Sequence features of the owner physical entity.</rdfs:comment>
1256 </owl:ObjectProperty>
1257 <owl:ObjectProperty rdf:ID="right">
1258 <rdfs:subPropertyOf>
1259 <owl:ObjectProperty rdf:about="#participant"/>
1260 </rdfs:subPropertyOf>
1261 <rdfs:domain rdf:resource="#Conversion"/>
1262 <rdfs:range rdf:resource="#PhysicalEntity"/>
1263 <rdfs:comment rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
1264 >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.</rdfs:comment>
1265 </owl:ObjectProperty>
1266 <owl:ObjectProperty rdf:about="#stepProcess">
1267 <rdfs:domain rdf:resource="#PathwayStep"/>
1270 <owl:unionOf rdf:parseType="Collection">
1271 <owl:Class rdf:about="#Pathway"/>
1272 <owl:Class rdf:about="#Interaction"/>
1276 <rdfs:comment rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
1277 >An interaction or a pathway that are a part of this pathway step.</rdfs:comment>
1278 </owl:ObjectProperty>
1279 <owl:ObjectProperty rdf:ID="evidence">
1280 <rdfs:range rdf:resource="#Evidence"/>
1283 <owl:unionOf rdf:parseType="Collection">
1284 <owl:Class rdf:about="#PathwayStep"/>
1285 <owl:Class rdf:about="#EntityFeature"/>
1286 <owl:Class rdf:about="#EntityReference"/>
1287 <owl:Class rdf:about="#Entity"/>
1291 <rdfs:comment rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
1292 >Scientific evidence supporting the existence of the entity as described.</rdfs:comment>
1293 </owl:ObjectProperty>
1294 <owl:ObjectProperty rdf:ID="pathwayComponent">
1297 <owl:unionOf rdf:parseType="Collection">
1298 <owl:Class rdf:about="#Interaction"/>
1299 <owl:Class rdf:about="#Pathway"/>
1303 <rdfs:comment rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
1304 >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.</rdfs:comment>
1305 <rdfs:domain rdf:resource="#Pathway"/>
1306 </owl:ObjectProperty>
1307 <owl:ObjectProperty rdf:about="#notFeature">
1308 <rdfs:range rdf:resource="#EntityFeature"/>
1309 <rdfs:domain rdf:resource="#PhysicalEntity"/>
1310 <rdfs:comment rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
1311 >Sequence features where the owner physical entity has a feature. If not specified, other potential features are not known.</rdfs:comment>
1312 </owl:ObjectProperty>
1313 <owl:ObjectProperty rdf:about="#experimentalFormDescription">
1314 <rdfs:comment rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
1315 >Descriptor of this experimental form from a controlled vocabulary.</rdfs:comment>
1316 <rdfs:domain rdf:resource="#ExperimentalForm"/>
1317 <rdfs:range rdf:resource="#ExperimentalFormVocabulary"/>
1318 </owl:ObjectProperty>
1319 <owl:ObjectProperty rdf:ID="participantStoichiometry">
1320 <rdfs:domain rdf:resource="#Conversion"/>
1321 <rdfs:comment rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
1322 >Stoichiometry of the left and right participants.</rdfs:comment>
1323 <rdfs:range rdf:resource="#Stoichiometry"/>
1324 </owl:ObjectProperty>
1325 <owl:ObjectProperty rdf:ID="cofactor">
1326 <rdfs:range rdf:resource="#PhysicalEntity"/>
1327 <rdfs:domain rdf:resource="#Catalysis"/>
1328 <rdfs:comment xml:lang="en">Any cofactor(s) or coenzyme(s) required for catalysis of the conversion by the enzyme. COFACTOR is a sub-property of PARTICIPANTS.</rdfs:comment>
1329 <rdfs:subPropertyOf>
1330 <owl:ObjectProperty rdf:about="#participant"/>
1331 </rdfs:subPropertyOf>
1332 </owl:ObjectProperty>
1333 <owl:ObjectProperty rdf:ID="deltaG">
1334 <rdfs:comment rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
1335 >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'<sup>o</sup>.
1337 delta-G'<sup>o</sup> = -RT lnK'
1339 delta-G'<sup>o</sup> = delta-H'<sup>o</sup> - T delta-S'<sup>o</sup>
1341 delta-G'<sup>o</sup> has units of kJ/mol. Like K', it is a function of temperature (T), ionic strength (I), pH, and pMg (pMg = -log<sub>10</sub>[Mg<sup>2+</sup>]). Therefore, these quantities must be specified, and values for DELTA-G for biochemical reactions are represented as 5-tuples of the form (delta-G'<sup>o</sup> T I pH pMg). This property may have multiple values, representing different measurements for delta-G'<sup>o</sup> obtained under the different experimental conditions listed in the 5-tuple.
1343 (This definition from EcoCyc)</rdfs:comment>
1344 <rdfs:domain rdf:resource="#BiochemicalReaction"/>
1345 <rdfs:range rdf:resource="#DeltaG"/>
1346 </owl:ObjectProperty>
1347 <owl:ObjectProperty rdf:ID="interactionScore">
1348 <rdfs:domain rdf:resource="#GeneticInteraction"/>
1349 <rdfs:comment rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
1350 >The score of an interaction e.g. a genetic interaction score.</rdfs:comment>
1351 <rdfs:range rdf:resource="#Score"/>
1352 </owl:ObjectProperty>
1353 <owl:ObjectProperty rdf:ID="left">
1354 <rdfs:comment rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
1355 >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.</rdfs:comment>
1356 <rdfs:range rdf:resource="#PhysicalEntity"/>
1357 <rdfs:subPropertyOf>
1358 <owl:ObjectProperty rdf:about="#participant"/>
1359 </rdfs:subPropertyOf>
1360 <rdfs:domain rdf:resource="#Conversion"/>
1361 </owl:ObjectProperty>
1362 <owl:ObjectProperty rdf:ID="regionType">
1365 <owl:unionOf rdf:parseType="Collection">
1366 <owl:Class rdf:about="#DnaRegionReference"/>
1367 <owl:Class rdf:about="#RnaRegionReference"/>
1371 <rdfs:range rdf:resource="#SequenceRegionVocabulary"/>
1372 </owl:ObjectProperty>
1373 <owl:ObjectProperty rdf:ID="relationshipType">
1374 <rdfs:domain rdf:resource="#RelationshipXref"/>
1375 <rdfs:range rdf:resource="#RelationshipTypeVocabulary"/>
1376 </owl:ObjectProperty>
1377 <owl:ObjectProperty rdf:about="#participant">
1378 <rdfs:range rdf:resource="#Entity"/>
1379 <rdfs:comment rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
1380 >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.</rdfs:comment>
1381 <rdfs:domain rdf:resource="#Interaction"/>
1382 </owl:ObjectProperty>
1383 <owl:ObjectProperty rdf:about="#confidence">
1384 <rdfs:domain rdf:resource="#Evidence"/>
1385 <rdfs:comment rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
1386 >Confidence in the containing instance. Usually a statistical measure.</rdfs:comment>
1387 <rdfs:range rdf:resource="#Score"/>
1388 </owl:ObjectProperty>
1389 <owl:ObjectProperty rdf:ID="kEQ">
1390 <rdfs:range rdf:resource="#KPrime"/>
1391 <rdfs:domain rdf:resource="#BiochemicalReaction"/>
1392 <rdfs:comment rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
1393 >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:
1395 K' = [ADP][P<sub>i</sub>]/[ATP],
1397 The concentration of ATP refers to the total concentration of all of the following species:
1399 [ATP] = [ATP<sup>4-</sup>] + [HATP<sup>3-</sup>] + [H<sub>2</sub>ATP<sup>2-</sup>] + [MgATP<sup>2-</sup>] + [MgHATP<sup>-</sup>] + [Mg<sub>2</sub>ATP].
1401 The apparent equilibrium constant is formally dimensionless, and can be kept so by inclusion of as many of the terms (1 mol/dm<sup>3</sup>) in the numerator or denominator as necessary. It is a function of temperature (T), ionic strength (I), pH, and pMg (pMg = -log<sub>10</sub>[Mg<sup>2+</sup>]). 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)</rdfs:comment>
1402 </owl:ObjectProperty>
1403 <owl:ObjectProperty rdf:ID="nextStep">
1404 <rdfs:domain rdf:resource="#PathwayStep"/>
1405 <rdfs:comment rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
1406 >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.</rdfs:comment>
1407 <rdfs:range rdf:resource="#PathwayStep"/>
1408 </owl:ObjectProperty>
1410 <owl:ObjectProperty rdf:about="#subRegion">
1413 <owl:unionOf rdf:parseType="Collection">
1414 <owl:Class rdf:about="#RnaRegionReference"/>
1415 <owl:Class rdf:about="#DnaRegionReference"/>
1419 <rdfs:comment rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
1420 >The sub region of a region. The sub region must be wholly part of the region, not outside of it.</rdfs:comment>
1423 <owl:unionOf rdf:parseType="Collection">
1424 <owl:Class rdf:about="#DnaRegionReference"/>
1425 <owl:Class rdf:about="#RnaRegionReference"/>
1429 </owl:ObjectProperty>
1430 <owl:ObjectProperty rdf:ID="containerEntityReference">
1433 <owl:unionOf rdf:parseType="Collection">
1434 <owl:Class rdf:about="#DnaReference"/>
1435 <owl:Class rdf:about="#RnaReference"/>
1439 <rdf:type rdf:resource="http://www.w3.org/2002/07/owl#FunctionalProperty"/>
1442 <owl:unionOf rdf:parseType="Collection">
1443 <owl:Class rdf:about="#RnaRegionReference"/>
1444 <owl:Class rdf:about="#DnaRegionReference"/>
1448 </owl:ObjectProperty>
1449 <owl:ObjectProperty rdf:about="#xref">
1452 <owl:unionOf rdf:parseType="Collection">
1453 <owl:Class rdf:about="#ControlledVocabulary"/>
1454 <owl:Class rdf:about="#Entity"/>
1455 <owl:Class rdf:about="#Provenance"/>
1456 <owl:Class rdf:about="#Evidence"/>
1457 <owl:Class rdf:about="#EntityReference"/>
1458 <owl:Class rdf:about="#BioSource"/>
1462 <rdfs:comment xml:lang="en">Values of this property define external cross-references from this entity to entities in external databases.</rdfs:comment>
1463 <rdfs:range rdf:resource="#Xref"/>
1464 </owl:ObjectProperty>
1465 <owl:ObjectProperty rdf:ID="experimentalFormEntity">
1466 <rdfs:comment rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
1467 >The gene or physical entity that this experimental form describes.</rdfs:comment>
1468 <rdfs:domain rdf:resource="#ExperimentalForm"/>
1471 <owl:unionOf rdf:parseType="Collection">
1472 <owl:Class rdf:about="#PhysicalEntity"/>
1473 <owl:Class rdf:about="#Gene"/>
1477 </owl:ObjectProperty>
1478 <owl:DatatypeProperty rdf:ID="term">
1479 <rdfs:domain rdf:resource="#ControlledVocabulary"/>
1480 <rdfs:range rdf:resource="http://www.w3.org/2001/XMLSchema#string"/>
1481 <rdfs:comment rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
1482 >The external controlled vocabulary term.</rdfs:comment>
1483 </owl:DatatypeProperty>
1484 <owl:DatatypeProperty rdf:ID="availability">
1485 <rdfs:domain rdf:resource="#Entity"/>
1486 <rdfs:comment xml:lang="en">Describes the availability of this data (e.g. a copyright statement).</rdfs:comment>
1487 <rdfs:range rdf:resource="http://www.w3.org/2001/XMLSchema#string"/>
1488 </owl:DatatypeProperty>
1489 <owl:DatatypeProperty rdf:ID="author">
1490 <rdfs:domain rdf:resource="#PublicationXref"/>
1491 <rdfs:range rdf:resource="http://www.w3.org/2001/XMLSchema#string"/>
1492 <rdfs:comment xml:lang="en">The authors of this publication, one per property value.</rdfs:comment>
1493 </owl:DatatypeProperty>
1494 <owl:DatatypeProperty rdf:ID="name">
1495 <rdfs:range rdf:resource="http://www.w3.org/2001/XMLSchema#string"/>
1498 <owl:unionOf rdf:parseType="Collection">
1499 <owl:Class rdf:about="#EntityReference"/>
1500 <owl:Class rdf:about="#BioSource"/>
1501 <owl:Class rdf:about="#Entity"/>
1502 <owl:Class rdf:about="#Provenance"/>
1506 <rdfs:comment xml:lang="en">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.</rdfs:comment>
1507 </owl:DatatypeProperty>
1508 <owl:DatatypeProperty rdf:ID="source">
1509 <rdfs:domain rdf:resource="#PublicationXref"/>
1510 <rdfs:comment rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
1511 >The source in which the reference was published, such as: a book title, or a journal title and volume and pages.</rdfs:comment>
1512 <rdfs:range rdf:resource="http://www.w3.org/2001/XMLSchema#string"/>
1513 </owl:DatatypeProperty>
1514 <owl:DatatypeProperty rdf:ID="eCNumber">
1515 <rdfs:domain rdf:resource="#BiochemicalReaction"/>
1516 <rdfs:range rdf:resource="http://www.w3.org/2001/XMLSchema#string"/>
1517 <rdfs:comment rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
1518 >The unique number assigned to a reaction by the Enzyme Commission of the International Union of Biochemistry and Molecular Biology.
1520 Note that not all biochemical reactions currently have EC numbers assigned to them.</rdfs:comment>
1521 </owl:DatatypeProperty>
1522 <owl:DatatypeProperty rdf:ID="deltaS">
1523 <rdfs:comment rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
1524 >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'<sup>o</sup>.
1526 delta-G'<sup>o</sup> = delta-H'<sup>o</sup> - T delta-S'<sup>o</sup>
1528 (This definition from EcoCyc)</rdfs:comment>
1529 <rdfs:range rdf:resource="http://www.w3.org/2001/XMLSchema#float"/>
1530 <rdfs:domain rdf:resource="#BiochemicalReaction"/>
1531 </owl:DatatypeProperty>
1532 <owl:DatatypeProperty rdf:ID="deltaH">
1533 <rdfs:comment rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
1534 >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'<sup>o</sup>.
1536 delta-G'<sup>o</sup> = delta-H'<sup>o</sup> - T delta-S'<sup>o</sup>
1540 (This definition from EcoCyc)</rdfs:comment>
1541 <rdfs:range rdf:resource="http://www.w3.org/2001/XMLSchema#float"/>
1542 <rdfs:domain rdf:resource="#BiochemicalReaction"/>
1543 </owl:DatatypeProperty>
1544 <owl:DatatypeProperty rdf:ID="url">
1545 <rdfs:domain rdf:resource="#PublicationXref"/>
1546 <rdfs:comment xml:lang="en">The URL at which the publication can be found, if it is available through the Web.</rdfs:comment>
1547 <rdfs:range rdf:resource="http://www.w3.org/2001/XMLSchema#string"/>
1548 </owl:DatatypeProperty>
1549 <owl:DatatypeProperty rdf:ID="comment">
1550 <rdfs:comment rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
1551 >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.</rdfs:comment>
1552 <rdfs:range rdf:resource="http://www.w3.org/2001/XMLSchema#string"/>
1555 <owl:unionOf rdf:parseType="Collection">
1556 <owl:Class rdf:about="#UtilityClass"/>
1557 <owl:Class rdf:about="#Entity"/>
1561 </owl:DatatypeProperty>
1562 <owl:TransitiveProperty rdf:ID="memberFeature">
1563 <rdf:type rdf:resource="http://www.w3.org/2002/07/owl#ObjectProperty"/>
1564 <rdfs:domain rdf:resource="#EntityFeature"/>
1565 <rdfs:comment rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
1566 >An entity feature that belongs to this homology grouping. Example: a homologous phosphorylation site across a protein family.</rdfs:comment>
1567 <rdfs:range rdf:resource="#EntityFeature"/>
1568 </owl:TransitiveProperty>
1569 <owl:TransitiveProperty rdf:about="#memberEntityReference">
1570 <rdf:type rdf:resource="http://www.w3.org/2002/07/owl#ObjectProperty"/>
1571 <rdfs:domain rdf:resource="#EntityReference"/>
1572 <rdfs:comment rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
1573 >An entity reference that qualifies for the definition of this group. For example a member of a PFAM protein family.</rdfs:comment>
1574 <rdfs:range rdf:resource="#EntityReference"/>
1575 </owl:TransitiveProperty>
1576 <owl:TransitiveProperty rdf:about="#memberPhysicalEntity">
1577 <rdf:type rdf:resource="http://www.w3.org/2002/07/owl#ObjectProperty"/>
1578 <rdfs:domain rdf:resource="#PhysicalEntity"/>
1579 <rdfs:comment rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
1580 >This property stores the members of a generic physical entity.
1582 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.</rdfs:comment>
1583 <rdfs:range rdf:resource="#PhysicalEntity"/>
1584 </owl:TransitiveProperty>
1585 <owl:SymmetricProperty rdf:ID="bindsTo">
1586 <rdfs:domain rdf:resource="#BindingFeature"/>
1587 <rdfs:comment rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
1588 >An entity that is non-covalently bound to this entity within the context of the respective protein. All bound physical entity must be in the same complex.</rdfs:comment>
1589 <rdfs:range rdf:resource="#BindingFeature"/>
1590 <rdf:type rdf:resource="http://www.w3.org/2002/07/owl#FunctionalProperty"/>
1591 <rdf:type rdf:resource="http://www.w3.org/2002/07/owl#ObjectProperty"/>
1592 <owl:inverseOf rdf:resource="#bindsTo"/>
1593 </owl:SymmetricProperty>
1594 <owl:FunctionalProperty rdf:ID="absoluteRegion">
1595 <rdfs:comment rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
1596 >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.</rdfs:comment>
1597 <rdf:type rdf:resource="http://www.w3.org/2002/07/owl#ObjectProperty"/>
1598 <rdfs:range rdf:resource="#SequenceInterval"/>
1601 <owl:unionOf rdf:parseType="Collection">
1602 <owl:Class rdf:about="#DnaRegionReference"/>
1603 <owl:Class rdf:about="#RnaRegionReference"/>
1607 </owl:FunctionalProperty>
1608 <owl:FunctionalProperty rdf:ID="stepConversion">
1609 <rdfs:range rdf:resource="#Conversion"/>
1610 <rdf:type rdf:resource="http://www.w3.org/2002/07/owl#ObjectProperty"/>
1611 <rdfs:subPropertyOf rdf:resource="#stepProcess"/>
1612 <rdfs:domain rdf:resource="#BiochemicalPathwayStep"/>
1613 <rdfs:comment rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
1614 >The central process that take place at this step of the biochemical pathway.</rdfs:comment>
1615 </owl:FunctionalProperty>
1616 <owl:FunctionalProperty rdf:ID="sequencePosition">
1617 <rdfs:domain rdf:resource="#SequenceSite"/>
1618 <rdfs:range rdf:resource="http://www.w3.org/2001/XMLSchema#int"/>
1619 <rdfs:comment rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
1620 >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'.</rdfs:comment>
1621 <rdf:type rdf:resource="http://www.w3.org/2002/07/owl#DatatypeProperty"/>
1622 </owl:FunctionalProperty>
1623 <owl:FunctionalProperty rdf:ID="chemicalFormula">
1624 <rdfs:range rdf:resource="http://www.w3.org/2001/XMLSchema#string"/>
1625 <rdfs:comment rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
1626 >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.</rdfs:comment>
1627 <rdfs:domain rdf:resource="#SmallMoleculeReference"/>
1628 <rdf:type rdf:resource="http://www.w3.org/2002/07/owl#DatatypeProperty"/>
1629 </owl:FunctionalProperty>
1630 <owl:FunctionalProperty rdf:about="#controlType">
1631 <rdfs:domain rdf:resource="#Control"/>
1634 <owl:oneOf rdf:parseType="Resource">
1635 <rdf:first rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
1636 >INHIBITION</rdf:first>
1637 <rdf:rest rdf:parseType="Resource">
1638 <rdf:first rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
1639 >ACTIVATION</rdf:first>
1640 <rdf:rest rdf:parseType="Resource">
1641 <rdf:first rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
1642 >INHIBITION-ALLOSTERIC</rdf:first>
1643 <rdf:rest rdf:parseType="Resource">
1644 <rdf:rest rdf:parseType="Resource">
1645 <rdf:rest rdf:parseType="Resource">
1646 <rdf:rest rdf:parseType="Resource">
1647 <rdf:first rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
1648 >INHIBITION-OTHER</rdf:first>
1649 <rdf:rest rdf:parseType="Resource">
1650 <rdf:first rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
1651 >INHIBITION-UNCOMPETITIVE</rdf:first>
1652 <rdf:rest rdf:parseType="Resource">
1653 <rdf:first rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
1654 >ACTIVATION-NONALLOSTERIC</rdf:first>
1655 <rdf:rest rdf:parseType="Resource">
1656 <rdf:rest rdf:resource="http://www.w3.org/1999/02/22-rdf-syntax-ns#nil"/>
1657 <rdf:first rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
1658 >ACTIVATION-ALLOSTERIC</rdf:first>
1663 <rdf:first rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
1664 >INHIBITION-NONCOMPETITIVE</rdf:first>
1666 <rdf:first rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
1667 >INHIBITION-IRREVERSIBLE</rdf:first>
1669 <rdf:first rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
1670 >INHIBITION-COMPETITIVE</rdf:first>
1677 <rdfs:comment rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
1678 >Defines the nature of the control relationship between the CONTROLLER and the CONTROLLED entities.
1680 The following terms are possible values:
1682 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.
1684 The following term can not be used in the catalysis class:
1685 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.
1687 The following terms can only be used in the modulation class (these definitions from EcoCyc):
1688 INHIBITION-ALLOSTERIC
1689 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.
1691 INHIBITION-COMPETITIVE
1692 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.
1694 INHIBITION-IRREVERSIBLE
1695 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.
1697 INHIBITION-NONCOMPETITIVE
1698 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.
1701 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.
1703 INHIBITION-UNCOMPETITIVE
1704 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.
1706 ACTIVATION-NONALLOSTERIC
1707 Nonallosteric activators increase the specified enzyme activity by means other than allosteric.
1709 ACTIVATION-ALLOSTERIC
1710 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.</rdfs:comment>
1711 <rdf:type rdf:resource="http://www.w3.org/2002/07/owl#DatatypeProperty"/>
1712 </owl:FunctionalProperty>
1713 <owl:FunctionalProperty rdf:ID="patoData">
1714 <rdfs:range rdf:resource="http://www.w3.org/2001/XMLSchema#string"/>
1715 <rdfs:domain rdf:resource="#PhenotypeVocabulary"/>
1716 <rdfs:comment rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
1717 >The phenotype data from PATO, formatted as PhenoXML (defined at http://www.fruitfly.org/~cjm/obd/formats.html)</rdfs:comment>
1718 <rdf:type rdf:resource="http://www.w3.org/2002/07/owl#DatatypeProperty"/>
1719 </owl:FunctionalProperty>
1720 <owl:FunctionalProperty rdf:ID="structure">
1721 <rdfs:domain rdf:resource="#SmallMoleculeReference"/>
1722 <rdf:type rdf:resource="http://www.w3.org/2002/07/owl#ObjectProperty"/>
1723 <rdfs:range rdf:resource="#ChemicalStructure"/>
1724 <rdfs:comment xml:lang="en">Defines the chemical structure and other information about this molecule, using an instance of class chemicalStructure.</rdfs:comment>
1725 </owl:FunctionalProperty>
1726 <owl:FunctionalProperty rdf:ID="featureLocation">
1727 <rdfs:range rdf:resource="#SequenceLocation"/>
1728 <rdfs:comment rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
1729 >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.</rdfs:comment>
1730 <rdfs:domain rdf:resource="#EntityFeature"/>
1731 <rdf:type rdf:resource="http://www.w3.org/2002/07/owl#ObjectProperty"/>
1732 </owl:FunctionalProperty>
1733 <owl:FunctionalProperty rdf:ID="cellularLocation">
1734 <rdfs:range rdf:resource="#CellularLocationVocabulary"/>
1735 <rdfs:domain rdf:resource="#PhysicalEntity"/>
1736 <rdf:type rdf:resource="http://www.w3.org/2002/07/owl#ObjectProperty"/>
1737 <rdfs:comment rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
1738 >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 physicalEntityParticipants) must be created for each different location. Note: If a location is unknown then the GO term for 'cellular component unknown' (GO:0008372) should be used in the LOCATION property. 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. In case of conflicting information, the location of the most outer layer of any nesting should be considered correct. Note: Cellular location describes a specific location of a physical entity as it would be used in e.g. a transport reaction. It does not describe all of the possible locations that the physical entity could be in the cell.</rdfs:comment>
1739 </owl:FunctionalProperty>
1740 <owl:FunctionalProperty rdf:ID="tissue">
1741 <rdf:type rdf:resource="http://www.w3.org/2002/07/owl#ObjectProperty"/>
1742 <rdfs:range rdf:resource="#TissueVocabulary"/>
1743 <rdfs:comment xml:lang="en">An external controlled vocabulary of tissue types.</rdfs:comment>
1744 <rdfs:domain rdf:resource="#BioSource"/>
1745 </owl:FunctionalProperty>
1746 <owl:FunctionalProperty rdf:ID="scoreSource">
1747 <rdf:type rdf:resource="http://www.w3.org/2002/07/owl#ObjectProperty"/>
1748 <rdfs:range rdf:resource="#Provenance"/>
1749 <rdfs:domain rdf:resource="#Score"/>
1750 </owl:FunctionalProperty>
1751 <owl:FunctionalProperty rdf:ID="standardName">
1752 <rdf:type rdf:resource="http://www.w3.org/2002/07/owl#DatatypeProperty"/>
1753 <rdfs:comment xml:lang="en">The preferred full name for this entity.</rdfs:comment>
1754 <rdfs:range rdf:resource="http://www.w3.org/2001/XMLSchema#string"/>
1755 <rdfs:subPropertyOf rdf:resource="#name"/>
1756 </owl:FunctionalProperty>
1757 <owl:FunctionalProperty rdf:about="#controlled">
1758 <rdfs:subPropertyOf rdf:resource="#participant"/>
1759 <rdfs:domain rdf:resource="#Control"/>
1760 <rdf:type rdf:resource="http://www.w3.org/2002/07/owl#ObjectProperty"/>
1761 <rdfs:comment xml:lang="en">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.</rdfs:comment>
1764 <owl:unionOf rdf:parseType="Collection">
1765 <owl:Class rdf:about="#Interaction"/>
1766 <owl:Class rdf:about="#Pathway"/>
1770 </owl:FunctionalProperty>
1771 <owl:FunctionalProperty rdf:ID="displayName">
1772 <rdfs:comment rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
1773 >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.</rdfs:comment>
1774 <rdfs:subPropertyOf rdf:resource="#name"/>
1775 <rdfs:range rdf:resource="http://www.w3.org/2001/XMLSchema#string"/>
1776 <rdf:type rdf:resource="http://www.w3.org/2002/07/owl#DatatypeProperty"/>
1777 </owl:FunctionalProperty>
1778 <owl:FunctionalProperty rdf:ID="spontaneous">
1779 <rdfs:domain rdf:resource="#Conversion"/>
1780 <rdfs:comment rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
1781 >Specifies whether a conversion occurs spontaneously or not. If the spontaneity is not known, the SPONTANEOUS property should be left empty.</rdfs:comment>
1782 <rdf:type rdf:resource="http://www.w3.org/2002/07/owl#DatatypeProperty"/>
1783 <rdfs:range rdf:resource="http://www.w3.org/2001/XMLSchema#boolean"/>
1784 </owl:FunctionalProperty>
1785 <owl:FunctionalProperty rdf:about="#entityReference">
1786 <rdfs:range rdf:resource="#EntityReference"/>
1789 <owl:unionOf rdf:parseType="Collection">
1790 <owl:Class rdf:about="#Protein"/>
1791 <owl:Class rdf:about="#Rna"/>
1792 <owl:Class rdf:about="#Dna"/>
1793 <owl:Class rdf:about="#SmallMolecule"/>
1794 <owl:Class rdf:about="#DnaRegion"/>
1795 <owl:Class rdf:about="#RnaRegion"/>
1799 <rdfs:comment rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
1800 >Reference entity for this physical entity.</rdfs:comment>
1801 <rdf:type rdf:resource="http://www.w3.org/2002/07/owl#ObjectProperty"/>
1802 </owl:FunctionalProperty>
1803 <owl:FunctionalProperty rdf:ID="pMg">
1804 <rdf:type rdf:resource="http://www.w3.org/2002/07/owl#DatatypeProperty"/>
1807 <owl:unionOf rdf:parseType="Collection">
1808 <owl:Class rdf:about="#KPrime"/>
1809 <owl:Class rdf:about="#DeltaG"/>
1813 <rdfs:comment rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
1814 >A measure of the concentration of magnesium (Mg) in solution. (pMg = -log<sub>10</sub>[Mg<sup>2+</sup>])</rdfs:comment>
1815 <rdfs:range rdf:resource="http://www.w3.org/2001/XMLSchema#float"/>
1816 </owl:FunctionalProperty>
1817 <owl:FunctionalProperty rdf:ID="intraMolecular">
1818 <rdfs:range rdf:resource="http://www.w3.org/2001/XMLSchema#boolean"/>
1819 <rdfs:comment rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
1820 >This flag represents whether the binding feature is within the same molecule or not.</rdfs:comment>
1821 <rdfs:domain rdf:resource="#BindingFeature"/>
1822 <rdf:type rdf:resource="http://www.w3.org/2002/07/owl#DatatypeProperty"/>
1823 </owl:FunctionalProperty>
1824 <owl:FunctionalProperty rdf:about="#physicalEntity">
1825 <rdf:type rdf:resource="http://www.w3.org/2002/07/owl#ObjectProperty"/>
1826 <rdfs:comment xml:lang="en">The physical entity annotated with stoichiometry and cellular location attributes from the physicalEntityParticipant instance.</rdfs:comment>
1827 <rdfs:range rdf:resource="#PhysicalEntity"/>
1828 <rdfs:domain rdf:resource="#Stoichiometry"/>
1829 </owl:FunctionalProperty>
1830 <owl:FunctionalProperty rdf:about="#structureData">
1831 <rdf:type rdf:resource="http://www.w3.org/2002/07/owl#DatatypeProperty"/>
1832 <rdfs:range rdf:resource="http://www.w3.org/2001/XMLSchema#string"/>
1833 <rdfs:domain rdf:resource="#ChemicalStructure"/>
1834 <rdfs:comment rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
1835 >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.</rdfs:comment>
1836 </owl:FunctionalProperty>
1837 <owl:FunctionalProperty rdf:ID="ph">
1838 <rdfs:comment rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
1839 >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)</rdfs:comment>
1842 <owl:unionOf rdf:parseType="Collection">
1843 <owl:Class rdf:about="#KPrime"/>
1844 <owl:Class rdf:about="#DeltaG"/>
1848 <rdfs:range rdf:resource="http://www.w3.org/2001/XMLSchema#float"/>
1849 <rdf:type rdf:resource="http://www.w3.org/2002/07/owl#DatatypeProperty"/>
1850 </owl:FunctionalProperty>
1851 <owl:FunctionalProperty rdf:about="#kPrime">
1852 <rdf:type rdf:resource="http://www.w3.org/2002/07/owl#DatatypeProperty"/>
1853 <rdfs:range rdf:resource="http://www.w3.org/2001/XMLSchema#float"/>
1854 <rdfs:comment rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
1855 >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:
1857 K' = [ADP][P<sub>i</sub>]/[ATP],
1859 The concentration of ATP refers to the total concentration of all of the following species:
1861 [ATP] = [ATP<sup>4-</sup>] + [HATP<sup>3-</sup>] + [H<sub>2</sub>ATP<sup>2-</sup>] + [MgATP<sup>2-</sup>] + [MgHATP<sup>-</sup>] + [Mg<sub>2</sub>ATP].
1863 The apparent equilibrium constant is formally dimensionless, and can be kept so by inclusion of as many of the terms (1 mol/dm<sup>3</sup>) in the numerator or denominator as necessary. It is a function of temperature (T), ionic strength (I), pH, and pMg (pMg = -log<sub>10</sub>[Mg<sup>2+</sup>]).
1864 (Definition from EcoCyc)</rdfs:comment>
1865 <rdfs:domain rdf:resource="#KPrime"/>
1866 </owl:FunctionalProperty>
1867 <owl:FunctionalProperty rdf:ID="molecularWeight">
1868 <rdfs:range rdf:resource="http://www.w3.org/2001/XMLSchema#float"/>
1869 <rdfs:comment xml:lang="en">Defines the molecular weight of the molecule, in daltons.</rdfs:comment>
1870 <rdf:type rdf:resource="http://www.w3.org/2002/07/owl#DatatypeProperty"/>
1871 <rdfs:domain rdf:resource="#SmallMoleculeReference"/>
1872 </owl:FunctionalProperty>
1873 <owl:FunctionalProperty rdf:ID="template">
1874 <rdfs:subPropertyOf rdf:resource="#participant"/>
1875 <rdfs:comment rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
1876 >The template molecule that is used in this template reaction.</rdfs:comment>
1877 <rdf:type rdf:resource="http://www.w3.org/2002/07/owl#ObjectProperty"/>
1878 <rdfs:domain rdf:resource="#TemplateReaction"/>
1881 <owl:unionOf rdf:parseType="Collection">
1882 <owl:Class rdf:about="#DnaRegion"/>
1883 <owl:Class rdf:about="#RnaRegion"/>
1887 </owl:FunctionalProperty>
1888 <owl:FunctionalProperty rdf:about="#phenotype">
1889 <rdfs:domain rdf:resource="#GeneticInteraction"/>
1890 <rdf:type rdf:resource="http://www.w3.org/2002/07/owl#ObjectProperty"/>
1891 <rdfs:range rdf:resource="#PhenotypeVocabulary"/>
1892 <rdfs:comment rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
1893 >The phenotype quality used to define this genetic interaction e.g. viability.</rdfs:comment>
1894 </owl:FunctionalProperty>
1895 <owl:FunctionalProperty rdf:ID="idVersion">
1896 <rdf:type rdf:resource="http://www.w3.org/2002/07/owl#DatatypeProperty"/>
1897 <rdfs:domain rdf:resource="#Xref"/>
1898 <rdfs:comment rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
1899 >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.</rdfs:comment>
1900 <rdfs:range rdf:resource="http://www.w3.org/2001/XMLSchema#string"/>
1901 </owl:FunctionalProperty>
1902 <owl:FunctionalProperty rdf:about="#stoichiometricCoefficient">
1903 <rdfs:range rdf:resource="http://www.w3.org/2001/XMLSchema#float"/>
1904 <rdfs:domain rdf:resource="#Stoichiometry"/>
1905 <rdfs:comment rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
1906 >Each value of this property represents the stoichiometric coefficient for one of the entities in an interaction or complex. For a given interaction, the stoichiometry should always be used where possible instead of representing the number of participants with separate instances of each participant. If there are three ATP molecules, one ATP molecule should be represented as a participant and the stoichiometry should be set to 3.</rdfs:comment>
1907 <rdf:type rdf:resource="http://www.w3.org/2002/07/owl#DatatypeProperty"/>
1908 </owl:FunctionalProperty>
1909 <owl:FunctionalProperty rdf:about="#structureFormat">
1910 <rdf:type rdf:resource="http://www.w3.org/2002/07/owl#DatatypeProperty"/>
1911 <rdfs:domain rdf:resource="#ChemicalStructure"/>
1914 <owl:oneOf rdf:parseType="Resource">
1915 <rdf:rest rdf:parseType="Resource">
1916 <rdf:rest rdf:parseType="Resource">
1917 <rdf:rest rdf:resource="http://www.w3.org/1999/02/22-rdf-syntax-ns#nil"/>
1918 <rdf:first rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
1921 <rdf:first rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
1924 <rdf:first rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
1929 <rdfs:comment xml:lang="en">This property specifies which format is used to define chemical structure data.</rdfs:comment>
1930 </owl:FunctionalProperty>
1931 <owl:FunctionalProperty rdf:ID="sequence">
1932 <rdf:type rdf:resource="http://www.w3.org/2002/07/owl#DatatypeProperty"/>
1935 <owl:unionOf rdf:parseType="Collection">
1936 <owl:Class rdf:about="#DnaReference"/>
1937 <owl:Class rdf:about="#RnaReference"/>
1938 <owl:Class rdf:about="#ProteinReference"/>
1939 <owl:Class rdf:about="#DnaRegionReference"/>
1940 <owl:Class rdf:about="#RnaRegionReference"/>
1944 <rdfs:comment xml:lang="en">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.</rdfs:comment>
1945 <rdfs:range rdf:resource="http://www.w3.org/2001/XMLSchema#string"/>
1946 </owl:FunctionalProperty>
1947 <owl:FunctionalProperty rdf:about="#organism">
1948 <rdf:type rdf:resource="http://www.w3.org/2002/07/owl#ObjectProperty"/>
1949 <rdfs:comment xml:lang="en">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.</rdfs:comment>
1952 <owl:unionOf rdf:parseType="Collection">
1953 <owl:Class rdf:about="#Pathway"/>
1954 <owl:Class rdf:about="#DnaReference"/>
1955 <owl:Class rdf:about="#RnaReference"/>
1956 <owl:Class rdf:about="#ProteinReference"/>
1957 <owl:Class rdf:about="#Gene"/>
1961 <rdfs:range rdf:resource="#BioSource"/>
1962 </owl:FunctionalProperty>
1963 <owl:FunctionalProperty rdf:about="#title">
1964 <rdfs:comment xml:lang="en">The title of the publication.</rdfs:comment>
1965 <rdfs:domain rdf:resource="#PublicationXref"/>
1966 <rdf:type rdf:resource="http://www.w3.org/2002/07/owl#DatatypeProperty"/>
1967 <rdfs:range rdf:resource="http://www.w3.org/2001/XMLSchema#string"/>
1968 </owl:FunctionalProperty>
1969 <owl:FunctionalProperty rdf:ID="sequenceIntervalBegin">
1970 <rdfs:comment rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
1971 >The begin position of a sequence interval.</rdfs:comment>
1972 <rdfs:range rdf:resource="#SequenceSite"/>
1973 <rdfs:domain rdf:resource="#SequenceInterval"/>
1974 <rdf:type rdf:resource="http://www.w3.org/2002/07/owl#ObjectProperty"/>
1975 </owl:FunctionalProperty>
1976 <owl:FunctionalProperty rdf:about="#db">
1977 <rdfs:range rdf:resource="http://www.w3.org/2001/XMLSchema#string"/>
1978 <rdf:type rdf:resource="http://www.w3.org/2002/07/owl#DatatypeProperty"/>
1979 <rdfs:comment xml:lang="en">The name of the external database to which this xref refers.</rdfs:comment>
1980 <rdfs:domain rdf:resource="#Xref"/>
1981 </owl:FunctionalProperty>
1982 <owl:FunctionalProperty rdf:ID="dbVersion">
1983 <rdfs:domain rdf:resource="#Xref"/>
1984 <rdf:type rdf:resource="http://www.w3.org/2002/07/owl#DatatypeProperty"/>
1985 <rdfs:comment xml:lang="en">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.</rdfs:comment>
1986 <rdfs:range rdf:resource="http://www.w3.org/2001/XMLSchema#string"/>
1987 </owl:FunctionalProperty>
1988 <owl:FunctionalProperty rdf:about="#value">
1989 <rdf:type rdf:resource="http://www.w3.org/2002/07/owl#DatatypeProperty"/>
1990 <rdfs:domain rdf:resource="#Score"/>
1991 <rdfs:range rdf:resource="http://www.w3.org/2001/XMLSchema#string"/>
1992 <rdfs:comment rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
1993 >The value of the score.</rdfs:comment>
1994 </owl:FunctionalProperty>
1995 <owl:FunctionalProperty rdf:ID="sequenceIntervalEnd">
1996 <rdfs:domain rdf:resource="#SequenceInterval"/>
1997 <rdfs:range rdf:resource="#SequenceSite"/>
1998 <rdfs:comment rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
1999 >The end position of a sequence interval.</rdfs:comment>
2000 <rdf:type rdf:resource="http://www.w3.org/2002/07/owl#ObjectProperty"/>
2001 </owl:FunctionalProperty>
2002 <owl:FunctionalProperty rdf:ID="ionicStrength">
2003 <rdfs:comment rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
2004 >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
2005 (Definition from http://www.lsbu.ac.uk/biology/enztech/ph.html)</rdfs:comment>
2006 <rdfs:range rdf:resource="http://www.w3.org/2001/XMLSchema#float"/>
2009 <owl:unionOf rdf:parseType="Collection">
2010 <owl:Class rdf:about="#KPrime"/>
2011 <owl:Class rdf:about="#DeltaG"/>
2015 <rdf:type rdf:resource="http://www.w3.org/2002/07/owl#DatatypeProperty"/>
2016 </owl:FunctionalProperty>
2017 <owl:FunctionalProperty rdf:ID="modificationType">
2018 <rdfs:comment rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
2019 >Description and classification of the feature.</rdfs:comment>
2020 <rdfs:domain rdf:resource="#ModificationFeature"/>
2021 <rdfs:range rdf:resource="#SequenceModificationVocabulary"/>
2022 <rdf:type rdf:resource="http://www.w3.org/2002/07/owl#ObjectProperty"/>
2023 </owl:FunctionalProperty>
2024 <owl:FunctionalProperty rdf:about="#id">
2025 <rdfs:range rdf:resource="http://www.w3.org/2001/XMLSchema#string"/>
2026 <rdf:type rdf:resource="http://www.w3.org/2002/07/owl#DatatypeProperty"/>
2027 <rdfs:comment xml:lang="en">The primary identifier in the external database of the object to which this xref refers.</rdfs:comment>
2028 <rdfs:domain rdf:resource="#Xref"/>
2029 </owl:FunctionalProperty>
2030 <owl:FunctionalProperty rdf:ID="temperature">
2031 <rdfs:comment rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
2032 >Temperature in Celsius</rdfs:comment>
2033 <rdfs:range rdf:resource="http://www.w3.org/2001/XMLSchema#float"/>
2034 <rdf:type rdf:resource="http://www.w3.org/2002/07/owl#DatatypeProperty"/>
2037 <owl:unionOf rdf:parseType="Collection">
2038 <owl:Class rdf:about="#KPrime"/>
2039 <owl:Class rdf:about="#DeltaG"/>
2043 </owl:FunctionalProperty>
2044 <owl:FunctionalProperty rdf:about="#year">
2045 <rdf:type rdf:resource="http://www.w3.org/2002/07/owl#DatatypeProperty"/>
2046 <rdfs:domain rdf:resource="#PublicationXref"/>
2047 <rdfs:range rdf:resource="http://www.w3.org/2001/XMLSchema#int"/>
2048 <rdfs:comment xml:lang="en">The year in which this publication was published.</rdfs:comment>
2049 </owl:FunctionalProperty>
2050 <owl:FunctionalProperty rdf:ID="stepDirection">
2051 <rdf:type rdf:resource="http://www.w3.org/2002/07/owl#DatatypeProperty"/>
2052 <rdfs:domain rdf:resource="#BiochemicalPathwayStep"/>
2055 <owl:oneOf rdf:parseType="Resource">
2056 <rdf:first rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
2057 >REVERSIBLE</rdf:first>
2058 <rdf:rest rdf:parseType="Resource">
2059 <rdf:first rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
2060 >RIGHT-TO-LEFT</rdf:first>
2061 <rdf:rest rdf:parseType="Resource">
2062 <rdf:rest rdf:resource="http://www.w3.org/1999/02/22-rdf-syntax-ns#nil"/>
2063 <rdf:first rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
2064 >LEFT-TO-RIGHT</rdf:first>
2070 <rdfs:comment rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
2071 >Direction of the conversion in this particular pathway context.</rdfs:comment>
2072 </owl:FunctionalProperty>
2073 <owl:FunctionalProperty rdf:ID="cellType">
2074 <rdf:type rdf:resource="http://www.w3.org/2002/07/owl#ObjectProperty"/>
2075 <rdfs:comment xml:lang="en">A cell type, e.g. 'HeLa'. This should reference a term in a controlled vocabulary of cell types.</rdfs:comment>
2076 <rdfs:range rdf:resource="#CellVocabulary"/>
2077 <rdfs:domain rdf:resource="#BioSource"/>
2078 </owl:FunctionalProperty>
2079 <owl:FunctionalProperty rdf:ID="entityReferenceType">
2080 <rdf:type rdf:resource="http://www.w3.org/2002/07/owl#ObjectProperty"/>
2081 <rdfs:range rdf:resource="#EntityReferenceTypeVocabulary"/>
2082 <rdfs:comment rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
2083 >A controlled vocabulary term that is used to describe the type of grouping such as homology or functional group.</rdfs:comment>
2084 <rdfs:domain rdf:resource="#EntityReference"/>
2085 </owl:FunctionalProperty>
2086 <owl:FunctionalProperty rdf:ID="positionStatus">
2087 <rdf:type rdf:resource="http://www.w3.org/2002/07/owl#DatatypeProperty"/>
2088 <rdfs:comment rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
2089 >The confidence status of the sequence position. This could be:
2090 EQUAL: The SEQUENCE-POSITION is known to be at the SEQUENCE-POSITION.
2091 GREATER-THAN: The site is greater than the SEQUENCE-POSITION.
2092 LESS-THAN: The site is less than the SEQUENCE-POSITION.</rdfs:comment>
2093 <rdfs:domain rdf:resource="#SequenceSite"/>
2096 <owl:oneOf rdf:parseType="Resource">
2097 <rdf:first rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
2099 <rdf:rest rdf:parseType="Resource">
2100 <rdf:first rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
2101 >LESS-THAN</rdf:first>
2102 <rdf:rest rdf:parseType="Resource">
2103 <rdf:rest rdf:resource="http://www.w3.org/1999/02/22-rdf-syntax-ns#nil"/>
2104 <rdf:first rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
2105 >GREATER-THAN</rdf:first>
2111 </owl:FunctionalProperty>
2112 <owl:FunctionalProperty rdf:about="#conversionDirection">
2113 <rdf:type rdf:resource="http://www.w3.org/2002/07/owl#DatatypeProperty"/>
2116 <owl:oneOf rdf:parseType="Resource">
2117 <rdf:rest rdf:parseType="Resource">
2118 <rdf:first rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
2119 >RIGHT-TO-LEFT</rdf:first>
2120 <rdf:rest rdf:parseType="Resource">
2121 <rdf:rest rdf:resource="http://www.w3.org/1999/02/22-rdf-syntax-ns#nil"/>
2122 <rdf:first rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
2123 >LEFT-TO-RIGHT</rdf:first>
2126 <rdf:first rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
2127 >REVERSIBLE</rdf:first>
2131 <rdfs:domain rdf:resource="#Conversion"/>
2132 </owl:FunctionalProperty>
2133 <owl:FunctionalProperty rdf:about="#deltaGPrime0">
2134 <rdf:type rdf:resource="http://www.w3.org/2002/07/owl#DatatypeProperty"/>
2135 <rdfs:comment rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
2136 >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'<sup>o</sup>.
2138 delta-G'<sup>o</sup> = -RT lnK'
2140 delta-G'<sup>o</sup> = delta-H'<sup>o</sup> - T delta-S'<sup>o</sup>
2142 delta-G'<sup>o</sup> has units of kJ/mol. Like K', it is a function of temperature (T), ionic strength (I), pH, and pMg (pMg = -log<sub>10</sub>[Mg<sup>2+</sup>]). Therefore, these quantities must be specified, and values for DELTA-G for biochemical reactions are represented as 5-tuples of the form (delta-G'<sup>o</sup> T I pH pMg).
2144 (This definition from EcoCyc)</rdfs:comment>
2145 <rdfs:range rdf:resource="http://www.w3.org/2001/XMLSchema#float"/>
2146 <rdfs:domain rdf:resource="#DeltaG"/>
2147 </owl:FunctionalProperty>
2148 <owl:InverseFunctionalProperty rdf:ID="entityFeature">
2149 <rdf:type rdf:resource="http://www.w3.org/2002/07/owl#ObjectProperty"/>
2150 <rdfs:domain rdf:resource="#EntityReference"/>
2151 <rdfs:range rdf:resource="#EntityFeature"/>
2152 <rdfs:comment rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
2153 >Variable features that are observed for this entity - such as known PTM or methylation sites and non-covalent bonds.</rdfs:comment>
2154 </owl:InverseFunctionalProperty>
2155 <owl:InverseFunctionalProperty rdf:ID="component">
2156 <rdfs:domain rdf:resource="#Complex"/>
2157 <rdf:type rdf:resource="http://www.w3.org/2002/07/owl#ObjectProperty"/>
2158 <rdfs:comment xml:lang="en">Defines the PhysicalEntity subunits of this complex. This property should not contain other complexes, i.e. it should always be a flat representation of the complex. For example, if two protein complexes join to form a single larger complex via a complex assembly interaction, the component of the new complex should be the individual proteins of the smaller complexes, not the two smaller complexes themselves. Exceptions are black-box complexes (i.e. complexes in which the component property is empty), which may be used as component of other complexes because their constituent parts are unknown / unspecified. The reason for keeping complexes flat is to signify that there is no information stored in the way complexes are nested, such as assembly order. Otherwise, the complex assembly order may be implicitly encoded and interpreted by some users, while others created hierarchical complexes randomly, which could lead to data loss. Additionally, the physicalEntityParticipants used in the component property are in the context of the complex, thus should not be reused between complexes. For instance, a protein may participate in two different complexes, but have different conformation in each.</rdfs:comment>
2159 <rdfs:range rdf:resource="#PhysicalEntity"/>
2160 </owl:InverseFunctionalProperty>
2161 <owl:InverseFunctionalProperty rdf:ID="pathwayOrder">
2162 <rdf:type rdf:resource="http://www.w3.org/2002/07/owl#ObjectProperty"/>
2163 <rdfs:comment rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
2164 >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.</rdfs:comment>
2165 <rdfs:range rdf:resource="#PathwayStep"/>
2166 <rdfs:domain rdf:resource="#Pathway"/>
2167 </owl:InverseFunctionalProperty>
2170 <!-- Created with Protege (with OWL Plugin 3.4, Build 505) http://protege.stanford.edu -->