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  • Members: 9
  • Category: Biology
  • Founded: Mar 2, 2005
  • Language: English
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[Fwd: Re: proposal C refinement documentation]   Message List  
Reply Message #9 of 11 |
[Fwd: Re: proposal C refinement documentation]

Hi Emek,

So does the proposal wiki that you set up (e-mail to the discuss
list yesterday) supersede this states subgroup?

cheers
Geeta

--- In biopax-states@yahoogroups.com, Emek Demir <emek@c...> wrote:
>
> Hi All,
>
> Previously we have suggested several proposals for modeling states
in
> BioPAX. Recently we refined one of them, proposal C
>
<http://f6.grp.yahoofs.com/v1/MCmvQqNwlb9ryEeXJTCEUYohBjA1f7fewAHtGRa
W3IpKYZ_PGfNszRYlBftrojEM5IXnPjmJzHvtxB1RQN5NTg/2005%20BioPAX%
20State%20Proposal%20C.ppt>.
> This document summarizes those refinements and clarifications.
Attached
> is also an owl document that gives a formal definition of what we
are
> proposing.
>
> I would much appreciate if you could go over the proposal and let
us
> know your concerns. This is still a proposal but we believe that
it can
> act as a foundation for our discussions in ISMB.
>
> Best,
> Emek
>
>
>
>
> <?xml version="1.0"?>
> <rdf:RDF
> xmlns="http://www.biopax.org/release/biopax-level3.owl#"
> xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"
> xmlns:rdfs="http://www.w3.org/2000/01/rdf-schema#"
> xmlns:owl="http://www.w3.org/2002/07/owl#"
> xml:base="http://www.biopax.org/release/biopax-level3.owl">
> <owl:Ontology rdf:about="">
> <rdfs:comment
rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
> >This is version 0.1 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>
> </owl:Ontology>
> <owl:Class rdf:ID="dataSource">
> <owl:disjointWith>
> <owl:Class rdf:ID="openControlledVocabulary"/>
> </owl:disjointWith>
> <rdfs:comment
rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
> >Definition: The direct source of this data. 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.
> Examples: A database or person name.</rdfs:comment>
> <owl:disjointWith>
> <owl:Class rdf:ID="xref"/>
> </owl:disjointWith>
> <owl:disjointWith>
> <owl:Class rdf:ID="bioSource"/>
> </owl:disjointWith>
> <rdfs:subClassOf>
> <owl:Class rdf:ID="externalReferenceUtilityClass"/>
> </rdfs:subClassOf>
> </owl:Class>
> <owl:Class rdf:about="#openControlledVocabulary">
> <owl:disjointWith>
> <owl:Class rdf:about="#xref"/>
> </owl:disjointWith>
> <rdfs:comment
rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
> >Definition: Used to import terms from external controlled
vocabularies (CVs) into the ontology. To support consistency and
compatibility, open, freely available CVs should be used whenever
possible, such as the Gene Ontology (GO)15 or other open biological
CVs listed on the OBO website
(http://obo.sourceforge.net/).</rdfs:comment>
> <owl:disjointWith rdf:resource="#dataSource"/>
> <owl:disjointWith>
> <owl:Class rdf:about="#bioSource"/>
> </owl:disjointWith>
> <rdfs:subClassOf>
> <owl:Class rdf:about="#externalReferenceUtilityClass"/>
> </rdfs:subClassOf>
> </owl:Class>
> <owl:Class rdf:ID="sequenceParticipant">
> <rdfs:comment
rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
> >Definition: A biological sequence participant in an
interaction. Describes any additional special characteristics of a
protein, such as post-translational modifications, that are relevant
to its participation in an interaction.</rdfs:comment>
> <rdfs:subClassOf>
> <owl:Class rdf:ID="physicalEntityParticipant"/>
> </rdfs:subClassOf>
> <rdfs:subClassOf>
> <owl:Restriction>
> <owl:allValuesFrom>
> <owl:Class>
> <owl:unionOf rdf:parseType="Collection">
> <owl:Class rdf:ID="protein"/>
> <owl:Class rdf:ID="rna"/>
> <owl:Class rdf:ID="dna"/>
> </owl:unionOf>
> </owl:Class>
> </owl:allValuesFrom>
> <owl:onProperty>
> <owl:ObjectProperty rdf:ID="PHYSICAL-ENTITY"/>
> </owl:onProperty>
> </owl:Restriction>
> </rdfs:subClassOf>
> </owl:Class>
> <owl:Class rdf:ID="transportWithBiochemicalReaction">
> <rdfs:subClassOf>
> <owl:Class rdf:ID="biochemicalReaction"/>
> </rdfs:subClassOf>
> <rdfs:subClassOf>
> <owl:Class rdf:ID="transport"/>
> </rdfs:subClassOf>
> <rdfs:comment
rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
> >Definition: A conversion interaction that is both a
biochemicalReaction and a transport. In
transportWithBiochemicalReaction interactions, one or more of the
substrates change both their location and their physical structure.
Active transport reactions that use ATP as an energy source fall
under this category, even if the only covalent change is the
hydrolysis of ATP to ADP.
> Comment: This class was added to support a large number of
transport events in pathway databases that have a biochemical
reaction during the transport process. It is not expected that other
double inheritance subclasses will be added to the ontology at the
same level as this class.
> Examples: In the PEP-dependent phosphotransferase system,
transportation of sugar into an E. coli cell is accompanied by the
sugar’s phosphorylation as it crosses the plasma
membrane.</rdfs:comment>
> </owl:Class>
> <owl:Class rdf:ID="complexAssembly">
> <rdfs:subClassOf>
> <owl:Class rdf:ID="conversion"/>
> </rdfs:subClassOf>
> <rdfs:comment
rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
> >Definition: A conversion interaction in which a set of
physical entities, at least one being a macromolecule (protein, RNA,
or DNA), aggregate via non-covalent interactions. One of the
participants of a complexAssembly must be an instance of the class
complex.
> Comment: This class is also used to represent complex disassembly.
The assembly or disassembly of a complex is often a spontaneous
process, in which case the direction of the complexAssembly (toward
either assembly or disassembly) should be specified via the
SPONTANEOUS property.
> Synonyms: aggregation, complex formation
> Examples: Assembly of the TFB2 and TFB3 proteins into the TFIIH
complex, and assembly of the ribosome through aggregation of its
subunits.
> Note: The following are not examples of complex assembly: Covalent
phosphorylation of a protein (this is a biochemicalReaction); the
TFIIH complex itself (this is an instance of the complex class, not
the complexAssembly class).</rdfs:comment>
> <owl:disjointWith>
> <owl:Class rdf:about="#biochemicalReaction"/>
> </owl:disjointWith>
> <owl:disjointWith>
> <owl:Class rdf:about="#transport"/>
> </owl:disjointWith>
> </owl:Class>
> <owl:Class rdf:ID="physicalEntity">
> <owl:disjointWith>
> <owl:Class rdf:ID="interaction"/>
> </owl:disjointWith>
> <rdfs:subClassOf>
> <owl:Class rdf:ID="entity"/>
> </rdfs:subClassOf>
> <rdfs:comment
rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
> >Definition: An entity with a physical structure.
> Comment: This class serves as the super-class for all physical
entities, although its current set of subclasses is limited to
molecules. This list may be expanded to include photon, environment,
cell and cellular component in later levels of BioPAX, depending on
community need. As a highly abstract class in the ontology,
instances of the physicalEntity class should be created rarely, if
ever.
> Synonyms: part, interactor, object
> Naming rationale: It’s difficult to find a name that encompasses
all of the subclasses of this class without being too general. E.g.
PSI-MI uses ‘interactor’, BIND uses ‘object’, BioCyc uses
‘chemicals’. physicalEntity seems to be a good name for this
specialization of entity.
> Examples: protein, small molecule, RNA</rdfs:comment>
> <owl:disjointWith>
> <owl:Class rdf:ID="pathway"/>
> </owl:disjointWith>
> </owl:Class>
> <owl:Class rdf:ID="unificationXref">
> <rdfs:subClassOf>
> <owl:Restriction>
> <owl:cardinality
rdf:datatype="http://www.w3.org/2001/XMLSchema#int"
> >1</owl:cardinality>
> <owl:onProperty>
> <owl:DatatypeProperty rdf:ID="ID"/>
> </owl:onProperty>
> </owl:Restriction>
> </rdfs:subClassOf>
> <rdfs:subClassOf>
> <owl:Class rdf:about="#xref"/>
> </rdfs:subClassOf>
> <owl:disjointWith>
> <owl:Class rdf:ID="relationshipXref"/>
> </owl:disjointWith>
> <rdfs:subClassOf>
> <owl:Restriction>
> <owl:onProperty>
> <owl:DatatypeProperty rdf:ID="DB"/>
> </owl:onProperty>
> <owl:cardinality
rdf:datatype="http://www.w3.org/2001/XMLSchema#int"
> >1</owl:cardinality>
> </owl:Restriction>
> </rdfs:subClassOf>
> <owl:disjointWith>
> <owl:Class rdf:ID="publicationXref"/>
> </owl:disjointWith>
> <rdfs:comment
rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
> >Definition: A unification xref defines a reference to an
entity in an external resource that has the same biological identity
as the referring entity. For example, if one wished to link from a
database record, C, describing a chemical compound in a BioPAX data
collection to a record, C’, describing the same chemical compound
in an external database, one would use a unification xref since
records C and C' describe the same biological identity. Generally,
unification xrefs should be used whenever possible, although there
are cases where they might not be useful, such as application to
application data exchange.
> Comment: Unification xrefs in physical entities are essential for
data integration, but are less important in interactions. This is
because unification xrefs on the physical entities in an interaction
can be used to compute the equivalence of two interactions of the
same type. An xref in a protein pointing to a gene, e.g. in the
LocusLink database17, would not be a unification xref since the two
entities do not have the same biological identity (one is a protein,
the other is a gene). Instead, this link should be a captured as a
relationship xref. References to an external controlled vocabulary
term within the OpenControlledVocabulary class should use a
unification xref where possible (e.g. GO:0005737)
> Examples: An xref in a protein instance pointing to an entry in
the Swiss-Prot database, and an xref in an RNA instance pointing to
the corresponding RNA sequence in the RefSeq
database..</rdfs:comment>
> </owl:Class>
> <owl:Class rdf:about="#relationshipXref">
> <rdfs:comment
rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
> >Definition: An xref that defines a reference to an entity in
an external resource that does not have the same biological identity
as the referring entity.
> Comment: There is currently no controlled vocabulary of
relationship types for BioPAX, although one will be created in the
future if a need develops.
> Examples: A link between a gene G in a BioPAX data collection, and
the protein product P of that gene in an external database. This is
not a unification xref because G and P are different biological
entities (one is a gene and one is a protein). Another example is a
relationship xref for a protein that refers to the Gene Ontology
biological process, e.g. ‘immune response,’ that the protein is
involved in.</rdfs:comment>
> <rdfs:subClassOf>
> <owl:Restriction>
> <owl:onProperty>
> <owl:DatatypeProperty rdf:about="#DB"/>
> </owl:onProperty>
> <owl:cardinality
rdf:datatype="http://www.w3.org/2001/XMLSchema#int"
> >1</owl:cardinality>
> </owl:Restriction>
> </rdfs:subClassOf>
> <rdfs:subClassOf>
> <owl:Restriction>
> <owl:onProperty>
> <owl:DatatypeProperty rdf:about="#ID"/>
> </owl:onProperty>
> <owl:cardinality
rdf:datatype="http://www.w3.org/2001/XMLSchema#int"
> >1</owl:cardinality>
> </owl:Restriction>
> </rdfs:subClassOf>
> <owl:disjointWith rdf:resource="#unificationXref"/>
> <rdfs:subClassOf>
> <owl:Restriction>
> <owl:onProperty>
> <owl:DatatypeProperty rdf:ID="RELATIONSHIP-TYPE"/>
> </owl:onProperty>
> <owl:maxCardinality
rdf:datatype="http://www.w3.org/2001/XMLSchema#int"
> >1</owl:maxCardinality>
> </owl:Restriction>
> </rdfs:subClassOf>
> <rdfs:subClassOf>
> <owl:Class rdf:about="#xref"/>
> </rdfs:subClassOf>
> <owl:disjointWith>
> <owl:Class rdf:about="#publicationXref"/>
> </owl:disjointWith>
> </owl:Class>
> <owl:Class rdf:ID="physicalInteraction">
> <rdfs:comment
rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
> >Definition: An interaction in which at least one participant
is a physical entity, e.g. a binding event.
> Comment: This class should be used by default for representing
molecular interactions, such as those defined by PSI-MI level 2. 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
above comments on the PARTICPANTS in the interaction class
description). If sufficient information on the nature of a molecular
interaction is available, a more specific BioPAX interaction class
may be used. It is expected that a geneticInteraction class will be
added as a sibling to physicalInteraction in a future level, hence
the specialization of the interaction class to physicalInteraction.
> Example: Two proteins observed to interact in a yeast-two-hybrid
experiment.</rdfs:comment>
> <rdfs:subClassOf>
> <owl:Restriction>
> <owl:someValuesFrom>
> <owl:Class rdf:about="#physicalEntityParticipant"/>
> </owl:someValuesFrom>
> <owl:onProperty>
> <owl:ObjectProperty rdf:ID="PARTICIPANTS"/>
> </owl:onProperty>
> </owl:Restriction>
> </rdfs:subClassOf>
> <rdfs:subClassOf>
> <owl:Class rdf:about="#interaction"/>
> </rdfs:subClassOf>
> </owl:Class>
> <owl:Class rdf:ID="smallMolecule">
> <owl:disjointWith>
> <owl:Class rdf:about="#protein"/>
> </owl:disjointWith>
> <rdfs:subClassOf>
> <owl:Restriction>
> <owl:maxCardinality
rdf:datatype="http://www.w3.org/2001/XMLSchema#int"
> >1</owl:maxCardinality>
> <owl:onProperty>
> <owl:DatatypeProperty rdf:ID="CHEMICAL-FORMULA"/>
> </owl:onProperty>
> </owl:Restriction>
> </rdfs:subClassOf>
> <rdfs:subClassOf>
> <owl:Restriction>
> <owl:maxCardinality
rdf:datatype="http://www.w3.org/2001/XMLSchema#int"
> >1</owl:maxCardinality>
> <owl:onProperty>
> <owl:DatatypeProperty rdf:ID="MOLECULAR-WEIGHT"/>
> </owl:onProperty>
> </owl:Restriction>
> </rdfs:subClassOf>
> <rdfs:subClassOf rdf:resource="#physicalEntity"/>
> <rdfs:comment
rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
> >Definition: Any bioactive molecule that is not a peptide,
DNA, or RNA. Generally these are non-polymeric, but complex
carbohydrates are not explicitly modeled as classes in this version
of the ontology, thus are forced into this class.
> Comment: Recently, a number of small molecule databases have
become available to cross-reference from this class.
> Examples: glucose, penicillin, phosphatidylinositol</rdfs:comment>
> <owl:disjointWith>
> <owl:Class rdf:about="#rna"/>
> </owl:disjointWith>
> <owl:disjointWith>
> <owl:Class rdf:about="#dna"/>
> </owl:disjointWith>
> <owl:disjointWith>
> <owl:Class rdf:ID="complex"/>
> </owl:disjointWith>
> </owl:Class>
> <owl:Class rdf:ID="sequenceLocation">
> <owl:disjointWith>
> <owl:Class rdf:ID="confidence"/>
> </owl:disjointWith>
> <rdfs:comment
rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
> >Definition: A location on a nucleotide or amino acid sequence.
> Comment: For organizational purposes only; direct instances of
this class should not be created.</rdfs:comment>
> <owl:disjointWith>
> <owl:Class rdf:ID="evidence"/>
> </owl:disjointWith>
> <owl:disjointWith>
> <owl:Class rdf:ID="chemicalStructure"/>
> </owl:disjointWith>
> <rdfs:subClassOf>
> <owl:Class rdf:ID="utilityClass"/>
> </rdfs:subClassOf>
> <owl:disjointWith>
> <owl:Class rdf:ID="pathwayStep"/>
> </owl:disjointWith>
> <owl:disjointWith>
> <owl:Class rdf:about="#externalReferenceUtilityClass"/>
> </owl:disjointWith>
> <owl:disjointWith>
> <owl:Class rdf:about="#physicalEntityParticipant"/>
> </owl:disjointWith>
> </owl:Class>
> <owl:Class rdf:ID="sequenceState">
> <rdfs:subClassOf>
> <owl:Class rdf:ID="state"/>
> </rdfs:subClassOf>
> <rdfs:comment
rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
> >A proposed state of a sequence (DNA, RNA or Protein)
> This specialization of state has been created because the only
state variable we are proposing in BioPAX Level 3 pertains only to
biological sequences, not to small molecules or complexes. Later,
we may want to specialize state further and add different types of
state variables.</rdfs:comment>
> </owl:Class>
> <owl:Class rdf:about="#state">
> <rdfs:comment
rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
> >A proposed state class for BioPAX Level 3
>
> The state class is used when you don't want to duplicate
information stored in the physical entity participant. In this
case, define the information you don't want to duplicate in the
state, and reuse it via the physical entity participant in your
interactions.</rdfs:comment>
> <rdfs:subClassOf>
> <owl:Restriction>
> <owl:cardinality
rdf:datatype="http://www.w3.org/2001/XMLSchema#int"
> >1</owl:cardinality>
> <owl:onProperty>
> <owl:ObjectProperty rdf:about="#PHYSICAL-ENTITY"/>
> </owl:onProperty>
> </owl:Restriction>
> </rdfs:subClassOf>
> <rdfs:subClassOf>
> <owl:Restriction>
> <owl:maxCardinality
rdf:datatype="http://www.w3.org/2001/XMLSchema#int"
> >1</owl:maxCardinality>
> <owl:onProperty>
> <owl:ObjectProperty rdf:ID="CELLULAR-LOCATION"/>
> </owl:onProperty>
> </owl:Restriction>
> </rdfs:subClassOf>
> <rdfs:subClassOf>
> <owl:Class rdf:about="#utilityClass"/>
> </rdfs:subClassOf>
> </owl:Class>
> <owl:Class rdf:ID="sequenceInterval">
> <rdfs:subClassOf rdf:resource="#sequenceLocation"/>
> <owl:disjointWith>
> <owl:Class rdf:ID="sequenceSite"/>
> </owl:disjointWith>
> <rdfs:subClassOf>
> <owl:Restriction>
> <owl:maxCardinality
rdf:datatype="http://www.w3.org/2001/XMLSchema#int"
> >1</owl:maxCardinality>
> <owl:onProperty>
> <owl:ObjectProperty rdf:ID="SEQUENCE-INTERVAL-END"/>
> </owl:onProperty>
> </owl:Restriction>
> </rdfs:subClassOf>
> <rdfs:subClassOf>
> <owl:Restriction>
> <owl:maxCardinality
rdf:datatype="http://www.w3.org/2001/XMLSchema#int"
> >1</owl:maxCardinality>
> <owl:onProperty>
> <owl:ObjectProperty rdf:ID="SEQUENCE-INTERVAL-BEGIN"/>
> </owl:onProperty>
> </owl:Restriction>
> </rdfs:subClassOf>
> <owl:disjointWith>
> <owl:Class rdf:ID="sequenceFeature"/>
> </owl:disjointWith>
> <rdfs:comment
rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
> >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>
> </owl:Class>
> <owl:Class rdf:about="#transport">
> <owl:disjointWith rdf:resource="#complexAssembly"/>
> <rdfs:comment
rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
> >Definition: A conversion interaction in which an entity (or
set of entities) changes location within or with respect to the
cell. A transport interaction does not include the transporter
entity, even if one is required in order for the transport to occur.
Instead, transporters are linked to transport interactions via the
catalysis class.
> Comment: Transport interactions do not involve chemical changes of
the participant(s). These cases are handled by the
transportWithBiochemicalReaction class.
> Synonyms: translocation.
> Examples: The movement of Na+ into the cell through an open
voltage-gated channel.</rdfs:comment>
> <rdfs:subClassOf>
> <owl:Class rdf:about="#conversion"/>
> </rdfs:subClassOf>
> </owl:Class>
> <owl:Class rdf:about="#sequenceSite">
> <rdfs:comment
rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
> >Definition: Describes a site on a sequence, i.e. the position
of a single nucleotide or amino acid.</rdfs:comment>
> <rdfs:subClassOf>
> <owl:Restriction>
> <owl:onProperty>
> <owl:DatatypeProperty rdf:ID="SEQUENCE-POSITION"/>
> </owl:onProperty>
> <owl:maxCardinality
rdf:datatype="http://www.w3.org/2001/XMLSchema#int"
> >1</owl:maxCardinality>
> </owl:Restriction>
> </rdfs:subClassOf>
> <owl:disjointWith>
> <owl:Class rdf:about="#sequenceFeature"/>
> </owl:disjointWith>
> <rdfs:subClassOf>
> <owl:Restriction>
> <owl:onProperty>
> <owl:DatatypeProperty rdf:ID="POSITION-STATUS"/>
> </owl:onProperty>
> <owl:maxCardinality
rdf:datatype="http://www.w3.org/2001/XMLSchema#int"
> >1</owl:maxCardinality>
> </owl:Restriction>
> </rdfs:subClassOf>
> <rdfs:subClassOf rdf:resource="#sequenceLocation"/>
> <owl:disjointWith rdf:resource="#sequenceInterval"/>
> </owl:Class>
> <owl:Class rdf:about="#biochemicalReaction">
> <rdfs:comment
rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
> >Definition: A conversion interaction in which one or more
entities (substrates) undergo covalent changes to become one or more
other entities (products). The substrates of biochemical reactions
are defined in terms of sums of species. This is convention in
biochemistry, and, in principle, all of the EC reactions should be
biochemical reactions.
> Examples: ATP + H2O = ADP + Pi
> Comment: In the example reaction above, ATP is considered to be an
equilibrium mixture of several species, namely ATP4-, HATP3-, H2ATP2-
, MgATP2-, MgHATP-, and Mg2ATP. Additional species may also need to
be considered if other ions (e.g. Ca2+) that bind ATP are present.
Similar considerations apply to ADP and to inorganic phosphate (Pi).
When writing biochemical reactions, it is important not to attach
charges to the biochemical reactants and not 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>
> <owl:disjointWith rdf:resource="#complexAssembly"/>
> <rdfs:subClassOf>
> <owl:Class rdf:about="#conversion"/>
> </rdfs:subClassOf>
> </owl:Class>
> <owl:Class rdf:about="#complex">
> <owl:disjointWith>
> <owl:Class rdf:about="#rna"/>
> </owl:disjointWith>
> <owl:disjointWith>
> <owl:Class rdf:about="#protein"/>
> </owl:disjointWith>
> <rdfs:comment
rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
> >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 (protein, DNA, or RNA). Complexes
must be stable enough to function as a biological unit; in general,
the temporary association of an enzyme with its substrate(s) should
not be considered or represented as a complex. A complex is the
physical product of an interaction (complexAssembly) and is not
itself considered an interaction.
> Comment: In general, complexes should not be defined recursively
so that smaller complexes exist within larger complexes, i.e. a
complex should not be a COMPONENT of another complex (see comments
on the COMPONENT property). The boundaries on the size of complexes
described by this class are not defined here, although elements of
the cell as large and dynamic as, e.g., a mitochondrion would
typically not be described using this class (later versions of this
ontology may include a cellularComponent class to represent these).
The strength of binding and the topology of the components cannot be
described currently, but may be included in future versions of the
ontology, depending on community need.
> Examples: Ribosome, RNA polymerase II. Other examples of this
class include complexes of multiple protein monomers and complexes
of proteins and small molecules.</rdfs:comment>
> <owl:disjointWith rdf:resource="#smallMolecule"/>
> <rdfs:subClassOf rdf:resource="#physicalEntity"/>
> <owl:disjointWith>
> <owl:Class rdf:about="#dna"/>
> </owl:disjointWith>
> </owl:Class>
> <owl:Class rdf:about="#publicationXref">
> <rdfs:comment
rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
> >Definition: An xref that defines a reference to a publication
such as a book, journal article, web page, or software manual. The
reference may or may not be in a database, although references to
PubMed are preferred when possible. The publication should make a
direct reference to the instance it is attached to.
> Comment: Publication xrefs should make use of PubMed IDs wherever
possible. The DB property of an xref to an entry in PubMed should
use the string “PubMed” and not “MEDLINE”.
> Examples: PubMed:10234245</rdfs:comment>
> <rdfs:subClassOf>
> <owl:Class rdf:about="#xref"/>
> </rdfs:subClassOf>
> <owl:disjointWith rdf:resource="#relationshipXref"/>
> <rdfs:subClassOf>
> <owl:Restriction>
> <owl:maxCardinality
rdf:datatype="http://www.w3.org/2001/XMLSchema#int"
> >1</owl:maxCardinality>
> <owl:onProperty>
> <owl:DatatypeProperty rdf:ID="YEAR"/>
> </owl:onProperty>
> </owl:Restriction>
> </rdfs:subClassOf>
> <rdfs:subClassOf>
> <owl:Restriction>
> <owl:maxCardinality
rdf:datatype="http://www.w3.org/2001/XMLSchema#int"
> >1</owl:maxCardinality>
> <owl:onProperty>
> <owl:DatatypeProperty rdf:ID="TITLE"/>
> </owl:onProperty>
> </owl:Restriction>
> </rdfs:subClassOf>
> <owl:disjointWith rdf:resource="#unificationXref"/>
> </owl:Class>
> <owl:Class rdf:about="#sequenceFeature">
> <owl:disjointWith rdf:resource="#sequenceSite"/>
> <rdfs:subClassOf>
> <owl:Restriction>
> <owl:onProperty>
> <owl:DatatypeProperty rdf:ID="SHORT-NAME"/>
> </owl:onProperty>
> <owl:maxCardinality
rdf:datatype="http://www.w3.org/2001/XMLSchema#int"
> >1</owl:maxCardinality>
> </owl:Restriction>
> </rdfs:subClassOf>
> <rdfs:comment
rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
> >Definition: A feature on a sequence relevant to an
interaction, such as a binding site or post-translational
modification.
> Examples: A phosphorylation on a protein.</rdfs:comment>
> <rdfs:subClassOf>
> <owl:Class rdf:about="#utilityClass"/>
> </rdfs:subClassOf>
> <rdfs:subClassOf>
> <owl:Restriction>
> <owl:maxCardinality
rdf:datatype="http://www.w3.org/2001/XMLSchema#int"
> >1</owl:maxCardinality>
> <owl:onProperty>
> <owl:DatatypeProperty rdf:ID="NAME"/>
> </owl:onProperty>
> </owl:Restriction>
> </rdfs:subClassOf>
> <owl:disjointWith rdf:resource="#sequenceInterval"/>
> <rdfs:subClassOf>
> <owl:Restriction>
> <owl:maxCardinality
rdf:datatype="http://www.w3.org/2001/XMLSchema#int"
> >1</owl:maxCardinality>
> <owl:onProperty>
> <owl:ObjectProperty rdf:ID="FEATURE-TYPE"/>
> </owl:onProperty>
> </owl:Restriction>
> </rdfs:subClassOf>
> </owl:Class>
> <owl:Class rdf:about="#entity">
> <rdfs:subClassOf
rdf:resource="http://www.w3.org/2002/07/owl#Thing"/>
> <rdfs:subClassOf>
> <owl:Restriction>
> <owl:maxCardinality
rdf:datatype="http://www.w3.org/2001/XMLSchema#int"
> >1</owl:maxCardinality>
> <owl:onProperty>
> <owl:DatatypeProperty rdf:about="#NAME"/>
> </owl:onProperty>
> </owl:Restriction>
> </rdfs:subClassOf>
> <rdfs:comment
rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
> >Definition: A discrete biological unit used when describing
pathways.
> Comment: This is the root class for all biological concepts in the
ontology, which include pathways, interactions and physical
entities. As the most abstract class in the ontology, instances of
the entity class should be created rarely, if ever.
> Synonyms: thing, object, bioentity.</rdfs:comment>
> <owl:disjointWith>
> <owl:Class rdf:about="#utilityClass"/>
> </owl:disjointWith>
> <rdfs:subClassOf>
> <owl:Restriction>
> <owl:maxCardinality
rdf:datatype="http://www.w3.org/2001/XMLSchema#int"
> >1</owl:maxCardinality>
> <owl:onProperty>
> <owl:DatatypeProperty rdf:about="#SHORT-NAME"/>
> </owl:onProperty>
> </owl:Restriction>
> </rdfs:subClassOf>
> </owl:Class>
> <owl:Class rdf:about="#confidence">
> <owl:disjointWith>
> <owl:Class rdf:about="#externalReferenceUtilityClass"/>
> </owl:disjointWith>
> <rdfs:subClassOf>
> <owl:Class rdf:about="#utilityClass"/>
> </rdfs:subClassOf>
> <owl:disjointWith>
> <owl:Class rdf:about="#physicalEntityParticipant"/>
> </owl:disjointWith>
> <owl:disjointWith rdf:resource="#sequenceLocation"/>
> <owl:disjointWith>
> <owl:Class rdf:about="#chemicalStructure"/>
> </owl:disjointWith>
> <rdfs:comment
rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
> >Definition: Confidence that the containing instance actually
occurs or exists in vivo, usually a statistical measure.
> Examples: The statistical significance of a result, e.g.
“p&lt;0.05”.</rdfs:comment>
> <owl:disjointWith>
> <owl:Class rdf:about="#pathwayStep"/>
> </owl:disjointWith>
> <rdfs:subClassOf>
> <owl:Restriction>
> <owl:maxCardinality
rdf:datatype="http://www.w3.org/2001/XMLSchema#int"
> >1</owl:maxCardinality>
> <owl:onProperty>
> <owl:DatatypeProperty rdf:ID="CONFIDENCE-VALUE"/>
> </owl:onProperty>
> </owl:Restriction>
> </rdfs:subClassOf>
> <owl:disjointWith>
> <owl:Class rdf:about="#evidence"/>
> </owl:disjointWith>
> </owl:Class>
> <owl:Class rdf:about="#pathwayStep">
> <owl:disjointWith>
> <owl:Class rdf:about="#chemicalStructure"/>
> </owl:disjointWith>
> <owl:disjointWith>
> <owl:Class rdf:about="#evidence"/>
> </owl:disjointWith>
> <owl:disjointWith>
> <owl:Class rdf:about="#externalReferenceUtilityClass"/>
> </owl:disjointWith>
> <owl:disjointWith>
> <owl:Class rdf:about="#physicalEntityParticipant"/>
> </owl:disjointWith>
> <rdfs:subClassOf>
> <owl:Restriction>
> <owl:onProperty>
> <owl:ObjectProperty rdf:ID="STEP-INTERACTIONS"/>
> </owl:onProperty>
> <owl:minCardinality
rdf:datatype="http://www.w3.org/2001/XMLSchema#int"
> >1</owl:minCardinality>
> </owl:Restriction>
> </rdfs:subClassOf>
> <rdfs:comment
rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
> >Definition: A step in a pathway.
> Comment: Multiple interactions may occur in a pathway step, each
should be listed in the STEP-INTERACTIONS property. Order
relationships between pathway steps may be established with the NEXT-
STEP slot. This order may not be temporally meaningful for specific
steps, such as for a pathway loop or a reversible reaction, but
represents a directed graph of step relationships that can be useful
for describing the overall flow of a pathway, as may be useful in a
pathway diagram.
> Example: A metabolic pathway may contain a pathway step composed
of one biochemical reaction (BR1) and one catalysis (CAT1) instance,
where CAT1 describes the catalysis of BR1.</rdfs:comment>
> <owl:disjointWith rdf:resource="#sequenceLocation"/>
> <rdfs:subClassOf>
> <owl:Class rdf:about="#utilityClass"/>
> </rdfs:subClassOf>
> <owl:disjointWith rdf:resource="#confidence"/>
> </owl:Class>
> <owl:Class rdf:about="#utilityClass">
> <rdfs:comment
rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
> >Utility classes are created when simple slots are
insufficient to describe an aspect of an entity or to increase
compatibility of this ontology with other standards. The
utilityClass class is only present to organize the other helper
classes under one class hierarchy; instances of utilityClass should
never be created.</rdfs:comment>
> <owl:disjointWith rdf:resource="#entity"/>
> </owl:Class>
> <owl:Class rdf:about="#pathway">
> <owl:disjointWith>
> <owl:Class rdf:about="#interaction"/>
> </owl:disjointWith>
> <rdfs:subClassOf rdf:resource="#entity"/>
> <rdfs:comment
rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
> >Definition: A set or series of interactions, often forming a
network, which biologists have found useful to group together for
organizational, historic, biophysical or other reasons.
> Comment: It is possible to define a pathway without specifying the
interactions within the pathway. In this case, the pathway instance
could consist simply of a name and could be treated as a ‘black
box’.
> Synonyms: network
> Examples: glycolysis, valine biosynthesis</rdfs:comment>
> <owl:disjointWith rdf:resource="#physicalEntity"/>
> <rdfs:subClassOf>
> <owl:Restriction>
> <owl:onProperty>
> <owl:ObjectProperty rdf:ID="ORGANISM"/>
> </owl:onProperty>
> <owl:maxCardinality
rdf:datatype="http://www.w3.org/2001/XMLSchema#int"
> >1</owl:maxCardinality>
> </owl:Restriction>
> </rdfs:subClassOf>
> </owl:Class>
> <owl:Class rdf:about="#externalReferenceUtilityClass">
> <rdfs:subClassOf rdf:resource="#utilityClass"/>
> <rdfs:comment
rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
> >Definition: A pointer to an external object, such as an entry
in a database or a term in a controlled vocabulary.
> Comment: This class is for organizational purposes only; direct
instances of this class should not be created.</rdfs:comment>
> <owl:disjointWith rdf:resource="#pathwayStep"/>
> <owl:disjointWith>
> <owl:Class rdf:about="#evidence"/>
> </owl:disjointWith>
> <owl:disjointWith>
> <owl:Class rdf:about="#chemicalStructure"/>
> </owl:disjointWith>
> <owl:disjointWith rdf:resource="#sequenceLocation"/>
> <owl:disjointWith>
> <owl:Class rdf:about="#physicalEntityParticipant"/>
> </owl:disjointWith>
> <owl:disjointWith rdf:resource="#confidence"/>
> </owl:Class>
> <owl:Class rdf:about="#dna">
> <owl:disjointWith rdf:resource="#complex"/>
> <owl:disjointWith>
> <owl:Class rdf:about="#rna"/>
> </owl:disjointWith>
> <rdfs:comment
rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
> >Definition: A physical entity consisting of a sequence of
deoxyribonucleotide monophosphates; a deoxyribonucleic acid.
> Comment: This is not a ‘gene’, since gene is a genetic
concept, not a physical entity. The concept of a gene may be added
later in BioPAX.
> Examples: a chromosome, a plasmid. A specific example is
chromosome 7 of Homo sapiens.</rdfs:comment>
> <owl:disjointWith rdf:resource="#smallMolecule"/>
> <owl:disjointWith>
> <owl:Class rdf:about="#protein"/>
> </owl:disjointWith>
> <rdfs:subClassOf rdf:resource="#physicalEntity"/>
> </owl:Class>
> <owl:Class rdf:ID="modulation">
> <owl:disjointWith>
> <owl:Class rdf:ID="catalysis"/>
> </owl:disjointWith>
> <rdfs:comment
rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
> >Definition: A control interaction in which a physical entity
modulates a catalysis interaction. Biologically, most modulation
interactions describe an interaction in which a small molecule
alters the ability of an enzyme to catalyze a specific reaction.
Instances of this class describe a pairing between a modulating
entity and a catalysis interaction.
> Comment: A separate modulation instance should be created for each
different catalysis instance that a physical entity may modulate and
for each different physical entity that may modulate a catalysis
instance. A typical modulation instance has a small molecule as the
controller entity and a catalysis instance as the controlled entity.
> Examples: Allosteric activation and competitive inhibition of an
enzyme’s ability to catalyze a specific reaction.</rdfs:comment>
> <rdfs:subClassOf>
> <owl:Class rdf:ID="control"/>
> </rdfs:subClassOf>
> <rdfs:subClassOf>
> <owl:Restriction>
> <owl:onProperty>
> <owl:ObjectProperty rdf:ID="CONTROLLER"/>
> </owl:onProperty>
> <owl:maxCardinality
rdf:datatype="http://www.w3.org/2001/XMLSchema#int"
> >1</owl:maxCardinality>
> </owl:Restriction>
> </rdfs:subClassOf>
> <rdfs:subClassOf>
> <owl:Restriction>
> <owl:onProperty>
> <owl:ObjectProperty rdf:ID="CONTROLLED"/>
> </owl:onProperty>
> <owl:allValuesFrom>
> <owl:Class rdf:about="#catalysis"/>
> </owl:allValuesFrom>
> </owl:Restriction>
> </rdfs:subClassOf>
> </owl:Class>
> <owl:Class rdf:about="#xref">
> <rdfs:subClassOf>
> <owl:Restriction>
> <owl:maxCardinality
rdf:datatype="http://www.w3.org/2001/XMLSchema#int"
> >1</owl:maxCardinality>
> <owl:onProperty>
> <owl:DatatypeProperty rdf:ID="DB-VERSION"/>
> </owl:onProperty>
> </owl:Restriction>
> </rdfs:subClassOf>
> <rdfs:subClassOf>
> <owl:Restriction>
> <owl:maxCardinality
rdf:datatype="http://www.w3.org/2001/XMLSchema#int"
> >1</owl:maxCardinality>
> <owl:onProperty>
> <owl:DatatypeProperty rdf:about="#ID"/>
> </owl:onProperty>
> </owl:Restriction>
> </rdfs:subClassOf>
> <owl:disjointWith rdf:resource="#dataSource"/>
> <rdfs:subClassOf
rdf:resource="#externalReferenceUtilityClass"/>
> <owl:disjointWith>
> <owl:Class rdf:about="#bioSource"/>
> </owl:disjointWith>
> <owl:disjointWith rdf:resource="#openControlledVocabulary"/>
> <rdfs:subClassOf>
> <owl:Restriction>
> <owl:onProperty>
> <owl:DatatypeProperty rdf:ID="ID-VERSION"/>
> </owl:onProperty>
> <owl:maxCardinality
rdf:datatype="http://www.w3.org/2001/XMLSchema#int"
> >1</owl:maxCardinality>
> </owl:Restriction>
> </rdfs:subClassOf>
> <rdfs:subClassOf>
> <owl:Restriction>
> <owl:maxCardinality
rdf:datatype="http://www.w3.org/2001/XMLSchema#int"
> >1</owl:maxCardinality>
> <owl:onProperty>
> <owl:DatatypeProperty rdf:about="#DB"/>
> </owl:onProperty>
> </owl:Restriction>
> </rdfs:subClassOf>
> <rdfs:comment
rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
> >Definition: A reference from an instance of a class in this
ontology to an object in an external resource.
> Comment: As the most abstract xref class in the ontology,
instances of the xref class should be created rarely, if
ever.</rdfs:comment>
> </owl:Class>
> <owl:Class rdf:about="#protein">
> <rdfs:subClassOf rdf:resource="#physicalEntity"/>
> <rdfs:subClassOf>
> <owl:Restriction>
> <owl:onProperty>
> <owl:ObjectProperty rdf:about="#ORGANISM"/>
> </owl:onProperty>
> <owl:maxCardinality
rdf:datatype="http://www.w3.org/2001/XMLSchema#int"
> >1</owl:maxCardinality>
> </owl:Restriction>
> </rdfs:subClassOf>
> <owl:disjointWith rdf:resource="#complex"/>
> <rdfs:subClassOf>
> <owl:Restriction>
> <owl:onProperty>
> <owl:DatatypeProperty rdf:ID="SEQUENCE"/>
> </owl:onProperty>
> <owl:maxCardinality
rdf:datatype="http://www.w3.org/2001/XMLSchema#int"
> >1</owl:maxCardinality>
> </owl:Restriction>
> </rdfs:subClassOf>
> <owl:disjointWith rdf:resource="#dna"/>
> <rdfs:comment
rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
> >Definition: A physical entity consisting of a sequence of
amino acids; a protein monomer; a single polypeptide chain.
> Examples: The epidermal growth factor receptor (EGFR)
protein.</rdfs:comment>
> <owl:disjointWith>
> <owl:Class rdf:about="#rna"/>
> </owl:disjointWith>
> <owl:disjointWith rdf:resource="#smallMolecule"/>
> </owl:Class>
> <owl:Class rdf:ID="experimentalForm">
> <rdfs:subClassOf>
> <owl:Restriction>
> <owl:onProperty>
> <owl:ObjectProperty rdf:ID="EXPERIMENTAL-FORM-TYPE"/>
> </owl:onProperty>
> <owl:maxCardinality
rdf:datatype="http://www.w3.org/2001/XMLSchema#int"
> >1</owl:maxCardinality>
> </owl:Restriction>
> </rdfs:subClassOf>
> <rdfs:subClassOf>
> <owl:Restriction>
> <owl:onProperty>
> <owl:ObjectProperty rdf:ID="PARTICIPANT"/>
> </owl:onProperty>
> <owl:cardinality
rdf:datatype="http://www.w3.org/2001/XMLSchema#int"
> >1</owl:cardinality>
> </owl:Restriction>
> </rdfs:subClassOf>
> <rdfs:comment
rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
> >Definition: The form of a physical entity in a particular
experiment, as it may be modified for purposes of experimental
design.
> Examples: A His-tagged protein in a binding assay.</rdfs:comment>
> <rdfs:subClassOf rdf:resource="#utilityClass"/>
> </owl:Class>
> <owl:Class rdf:about="#rna">
> <rdfs:subClassOf rdf:resource="#physicalEntity"/>
> <rdfs:subClassOf>
> <owl:Restriction>
> <owl:onProperty>
> <owl:DatatypeProperty rdf:about="#SEQUENCE"/>
> </owl:onProperty>
> <owl:maxCardinality
rdf:datatype="http://www.w3.org/2001/XMLSchema#int"
> >1</owl:maxCardinality>
> </owl:Restriction>
> </rdfs:subClassOf>
> <owl:disjointWith rdf:resource="#dna"/>
> <owl:disjointWith rdf:resource="#smallMolecule"/>
> <rdfs:comment
rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
> >Definition: A physical entity consisting of a sequence of
ribonucleotide monophosphates; a ribonucleic acid.
> Examples: messengerRNA, microRNA, ribosomalRNA. A specific example
is the let-7 microRNA.</rdfs:comment>
> <rdfs:subClassOf>
> <owl:Restriction>
> <owl:onProperty>
> <owl:ObjectProperty rdf:about="#ORGANISM"/>
> </owl:onProperty>
> <owl:maxCardinality
rdf:datatype="http://www.w3.org/2001/XMLSchema#int"
> >1</owl:maxCardinality>
> </owl:Restriction>
> </rdfs:subClassOf>
> <owl:disjointWith rdf:resource="#complex"/>
> <owl:disjointWith rdf:resource="#protein"/>
> </owl:Class>
> <owl:Class rdf:about="#control">
> <rdfs:comment
rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
> >Definition: An interaction in which one entity regulates,
modifies, or otherwise influences another. Two types of control
interactions are defined: activation and inhibition.
> Comment: In general, the targets of control processes (i.e.
occupants of the CONTROLLED property) should be interactions.
Conceptually, entities are involved in interactions (or events) and
the events should be controlled or modified, not the entities
themselves. For example, a kinase activating a protein is a frequent
event in signaling pathways and is usually represented as an
‘activation’ arrow from the kinase to the substrate in signaling
diagrams. This is an abstraction that can be ambiguous out of
context. In BioPAX, this information should be captured as the
kinase catalyzing (via an instance of the catalysis class) a
reaction in which the substrate is phosphorylated, instead of as a
control interaction in which the kinase activates the substrate.
Since this class is a superclass for specific types of control,
instances of the control class should only be created when none of
its subclasses are applicable.
> Synonyms: regulation, mediation
> Examples: Enzyme catalysis controls a biochemical reaction,
transport catalysis controls transport, a small molecule that
inhibits a pathway by an unknown mechanism controls the
pathway.</rdfs:comment>
> <rdfs:subClassOf>
> <owl:Restriction>
> <owl:maxCardinality
rdf:datatype="http://www.w3.org/2001/XMLSchema#int"
> >1</owl:maxCardinality>
> <owl:onProperty>
> <owl:DatatypeProperty rdf:ID="CONTROL-TYPE"/>
> </owl:onProperty>
> </owl:Restriction>
> </rdfs:subClassOf>
> <owl:disjointWith>
> <owl:Class rdf:about="#conversion"/>
> </owl:disjointWith>
> <rdfs:subClassOf rdf:resource="#physicalInteraction"/>
> </owl:Class>
> <owl:Class rdf:about="#physicalEntityParticipant">
> <rdfs:subClassOf>
> <owl:Restriction>
> <owl:onProperty>
> <owl:DatatypeProperty rdf:ID="STOICHIOMETRIC-
COEFFICIENT"/>
> </owl:onProperty>
> <owl:maxCardinality
rdf:datatype="http://www.w3.org/2001/XMLSchema#int"
> >1</owl:maxCardinality>
> </owl:Restriction>
> </rdfs:subClassOf>
> <owl:disjointWith>
> <owl:Class rdf:about="#chemicalStructure"/>
> </owl:disjointWith>
> <rdfs:comment
rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
> >Definition: Any additional special characteristics of a
physical entity in the context of an interaction. These currently
include stoichiometric coefficient and cellular location, but this
list may be expanded in later levels.
> Comment: PhysicalEntityParticipants should not be used in multiple
interaction or complex instances. Instead, each interaction and
complex should reference its own unique set of
physicalEntityParticipants. The reason for this is that a user may
add new information about a physicalEntityParticipant for one
interaction or complex, such as the presence of a previously unknown
post-translational modification, and unwittingly invalidate the
physicalEntityParticipant for the other interactions or complexes
that make use of it.
> Example: In the interaction describing the transport of L-arginine
into the cytoplasm in E. coli, the LEFT property in the interaction
would be filled with an instance of physicalEntityParticipant that
specified the location of L-arginine as periplasm and the
stoichiometric coefficient as one.</rdfs:comment>
> <owl:disjointWith rdf:resource="#pathwayStep"/>
> <owl:disjointWith rdf:resource="#confidence"/>
> <owl:disjointWith>
> <owl:Class rdf:about="#evidence"/>
> </owl:disjointWith>
> <owl:disjointWith rdf:resource="#sequenceLocation"/>
> <rdfs:subClassOf>
> <owl:Restriction>
> <owl:onProperty>
> <owl:ObjectProperty rdf:about="#CELLULAR-LOCATION"/>
> </owl:onProperty>
> <owl:maxCardinality
rdf:datatype="http://www.w3.org/2001/XMLSchema#int"
> >1</owl:maxCardinality>
> </owl:Restriction>
> </rdfs:subClassOf>
> <rdfs:subClassOf rdf:resource="#utilityClass"/>
> <owl:disjointWith
rdf:resource="#externalReferenceUtilityClass"/>
> <rdfs:subClassOf>
> <owl:Restriction>
> <owl:cardinality
rdf:datatype="http://www.w3.org/2001/XMLSchema#int"
> >1</owl:cardinality>
> <owl:onProperty>
> <owl:ObjectProperty rdf:about="#PHYSICAL-ENTITY"/>
> </owl:onProperty>
> </owl:Restriction>
> </rdfs:subClassOf>
> </owl:Class>
> <owl:Class rdf:about="#interaction">
> <rdfs:subClassOf>
> <owl:Restriction>
> <owl:someValuesFrom>
> <owl:Class>
> <owl:unionOf rdf:parseType="Collection">
> <owl:Class rdf:about="#entity"/>
> <owl:Class rdf:about="#physicalEntityParticipant"/>
> </owl:unionOf>
> </owl:Class>
> </owl:someValuesFrom>
> <owl:onProperty>
> <owl:ObjectProperty rdf:about="#PARTICIPANTS"/>
> </owl:onProperty>
> </owl:Restriction>
> </rdfs:subClassOf>
> <owl:disjointWith rdf:resource="#physicalEntity"/>
> <owl:disjointWith rdf:resource="#pathway"/>
> <rdfs:subClassOf rdf:resource="#entity"/>
> <rdfs:comment
rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
> >Definition: A single biological relationship between two or
more entities. An interaction cannot be defined without the entities
it relates.
> Comment: Since it is a highly abstract class in the ontology,
instances of the interaction class should be created rarely.
Currently this class only has subclasses that define physical
interactions; later levels of BioPAX may define other types of
interactions, such as genetic (e.g. synthetic lethal).
> Naming rationale: A number of names were considered for this
concept, including “process”, “synthesis” and
“relationship”; Interaction was chosen as it is understood by
biologists in a biological context and is compatible with PSI-MI.
> Examples: protein-protein interaction, biochemical reaction,
enzyme catalysis</rdfs:comment>
> </owl:Class>
> <owl:Class rdf:about="#catalysis">
> <rdfs:subClassOf>
> <owl:Restriction>
> <owl:onProperty>
> <owl:DatatypeProperty rdf:ID="DIRECTION"/>
> </owl:onProperty>
> <owl:maxCardinality
rdf:datatype="http://www.w3.org/2001/XMLSchema#int"
> >1</owl:maxCardinality>
> </owl:Restriction>
> </rdfs:subClassOf>
> <rdfs:subClassOf>
> <owl:Restriction>
> <owl:onProperty>
> <owl:ObjectProperty rdf:about="#CONTROLLER"/>
> </owl:onProperty>
> <owl:maxCardinality
rdf:datatype="http://www.w3.org/2001/XMLSchema#int"
> >1</owl:maxCardinality>
> </owl:Restriction>
> </rdfs:subClassOf>
> <rdfs:subClassOf>
> <owl:Restriction>
> <owl:allValuesFrom>
> <owl:Class rdf:about="#conversion"/>
> </owl:allValuesFrom>
> <owl:onProperty>
> <owl:ObjectProperty rdf:about="#CONTROLLED"/>
> </owl:onProperty>
> </owl:Restriction>
> </rdfs:subClassOf>
> <rdfs:comment
rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
> >Definition: A control interaction in which a physical entity
(a catalyst) increases the rate of a conversion interaction by
lowering its activation energy. Instances of this class describe a
pairing between a catalyzing entity and a catalyzed conversion.
> Comment: A separate catalysis instance should be created for each
different conversion that a physicalEntity may catalyze and for each
different physicalEntity that may catalyze a conversion. For
example, a bifunctional enzyme that catalyzes two different
biochemical reactions would be linked to each of those biochemical
reactions by two separate instances of the catalysis class. Also,
catalysis reactions from multiple different organisms could be
linked to the same generic biochemical reaction (a biochemical
reaction is generic if it only includes small molecules). Generally,
the enzyme catalyzing a conversion is known and the use of this
class is obvious. In the cases where a reaction is known to occur
but the enzyme is not known, a catalysis instance should be created
without a controller specified (i.e. the CONTROLLER property should
remain empty).
> Synonyms: facilitation, acceleration.
> Examples: The catalysis of a biochemical reaction by an enzyme,
the enabling of a transport interaction by a membrane pore complex,
and the facilitation of a complex assembly by a scaffold protein.
Hexokinase -> (The “Glucose + ATP -> Glucose-6-phosphate +ADP”
reaction). A plasma membrane Na+/K+ ATPase is an active transporter
(antiport pump) using the energy of ATP to pump Na+ out of the cell
and K+ in. Na+ from cytoplasm to extracellular space would be
described in a transport instance. K+ from extracellular space to
cytoplasm would be described in a transport instance. The ATPase
pump would be stored in a catalysis instance controlling each of the
above transport instances.</rdfs:comment>
> <rdfs:subClassOf>
> <owl:Restriction>
> <owl:onProperty>
> <owl:DatatypeProperty rdf:about="#CONTROL-TYPE"/>
> </owl:onProperty>
> <owl:hasValue
rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
> >ACTIVATION</owl:hasValue>
> </owl:Restriction>
> </rdfs:subClassOf>
> <rdfs:subClassOf rdf:resource="#control"/>
> <owl:disjointWith rdf:resource="#modulation"/>
> </owl:Class>
> <owl:Class rdf:about="#conversion">
> <rdfs:subClassOf rdf:resource="#physicalInteraction"/>
> <rdfs:comment
rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
> >Definition: An interaction in which one or more entities is
physically transformed into one or more other entities.
> Comment: This class is designed to represent a simple, single-step
transformation. Multi-step transformations, such as the conversion
of glucose to pyruvate in the glycolysis pathway, should be
represented as pathways, if known. Since it is a highly abstract
class in the ontology, instances of the conversion class should be
created rarely, if ever.
> 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>
> <owl:disjointWith rdf:resource="#control"/>
> <rdfs:subClassOf>
> <owl:Restriction>
> <owl:onProperty>
> <owl:DatatypeProperty rdf:ID="SPONTANEOUS"/>
> </owl:onProperty>
> <owl:maxCardinality
rdf:datatype="http://www.w3.org/2001/XMLSchema#int"
> >1</owl:maxCardinality>
> </owl:Restriction>
> </rdfs:subClassOf>
> <rdfs:subClassOf>
> <owl:Restriction>
> <owl:allValuesFrom
rdf:resource="#physicalEntityParticipant"/>
> <owl:onProperty>
> <owl:ObjectProperty rdf:about="#PARTICIPANTS"/>
> </owl:onProperty>
> </owl:Restriction>
> </rdfs:subClassOf>
> </owl:Class>
> <owl:Class rdf:about="#evidence">
> <owl:disjointWith>
> <owl:Class rdf:about="#chemicalStructure"/>
> </owl:disjointWith>
> <rdfs:comment
rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
> >Definition: The support for a particular assertion, such as
the existence of an interaction or pathway.
> Examples: A description of a molecular binding assay that was used
to detect a protein-protein interaction.</rdfs:comment>
> <owl:disjointWith rdf:resource="#sequenceLocation"/>
> <owl:disjointWith
rdf:resource="#externalReferenceUtilityClass"/>
> <owl:disjointWith rdf:resource="#confidence"/>
> <owl:disjointWith rdf:resource="#pathwayStep"/>
> <owl:disjointWith rdf:resource="#physicalEntityParticipant"/>
> <rdfs:subClassOf rdf:resource="#utilityClass"/>
> </owl:Class>
> <owl:Class rdf:about="#bioSource">
> <owl:disjointWith rdf:resource="#xref"/>
> <rdfs:comment
rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
> >Definition: The biological source of an entity (e.g. protein,
RNA or DNA). Some entities are considered source-neutral (e.g. small
molecules), and the biological source of others can be deduced from
their constituentss (e.g. complex, pathway).
> Examples: HeLa cells, human, and mouse liver tissue.</rdfs:comment>
> <rdfs:subClassOf>
> <owl:Restriction>
> <owl:onProperty>
> <owl:ObjectProperty rdf:ID="CELLTYPE"/>
> </owl:onProperty>
> <owl:maxCardinality
rdf:datatype="http://www.w3.org/2001/XMLSchema#int"
> >1</owl:maxCardinality>
> </owl:Restriction>
> </rdfs:subClassOf>
> <rdfs:subClassOf>
> <owl:Restriction>
> <owl:cardinality
rdf:datatype="http://www.w3.org/2001/XMLSchema#int"
> >1</owl:cardinality>
> <owl:onProperty>
> <owl:ObjectProperty rdf:ID="TAXON-XREF"/>
> </owl:onProperty>
> </owl:Restriction>
> </rdfs:subClassOf>
> <rdfs:subClassOf>
> <owl:Restriction>
> <owl:maxCardinality
rdf:datatype="http://www.w3.org/2001/XMLSchema#int"
> >1</owl:maxCardinality>
> <owl:onProperty>
> <owl:DatatypeProperty rdf:about="#NAME"/>
> </owl:onProperty>
> </owl:Restriction>
> </rdfs:subClassOf>
> <rdfs:subClassOf
rdf:resource="#externalReferenceUtilityClass"/>
> <rdfs:subClassOf>
> <owl:Restriction>
> <owl:maxCardinality
rdf:datatype="http://www.w3.org/2001/XMLSchema#int"
> >1</owl:maxCardinality>
> <owl:onProperty>
> <owl:ObjectProperty rdf:ID="TISSUE"/>
> </owl:onProperty>
> </owl:Restriction>
> </rdfs:subClassOf>
> <owl:disjointWith rdf:resource="#openControlledVocabulary"/>
> <owl:disjointWith rdf:resource="#dataSource"/>
> </owl:Class>
> <owl:Class rdf:about="#chemicalStructure">
> <owl:disjointWith rdf:resource="#confidence"/>
> <owl:disjointWith rdf:resource="#pathwayStep"/>
> <rdfs:subClassOf>
> <owl:Restriction>
> <owl:onProperty>
> <owl:DatatypeProperty rdf:ID="STRUCTURE-FORMAT"/>
> </owl:onProperty>
> <owl:cardinality
rdf:datatype="http://www.w3.org/2001/XMLSchema#int"
> >1</owl:cardinality>
> </owl:Restriction>
> </rdfs:subClassOf>
> <rdfs:subClassOf rdf:resource="#utilityClass"/>
> <owl:disjointWith rdf:resource="#evidence"/>
> <rdfs:subClassOf>
> <owl:Restriction>
> <owl:cardinality
rdf:datatype="http://www.w3.org/2001/XMLSchema#int"
> >1</owl:cardinality>
> <owl:onProperty>
> <owl:DatatypeProperty rdf:ID="STRUCTURE-DATA"/>
> </owl:onProperty>
> </owl:Restriction>
> </rdfs:subClassOf>
> <owl:disjointWith rdf:resource="#sequenceLocation"/>
> <owl:disjointWith rdf:resource="#physicalEntityParticipant"/>
> <owl:disjointWith
rdf:resource="#externalReferenceUtilityClass"/>
> <rdfs:comment
rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
>
> >Definition: Describes a small molecule structure. Structure
information is stored in the property STRUCTURE-DATA, in one of
three formats: the CML format (see URL www.xml-cml.org), the SMILES
format (see URL www.daylight.com/dayhtml/smiles/) or the InChI
format (http://www.iupac.org/inchi/). The STRUCTURE-FORMAT property
specifies which format is used.
> Comment: By virtue of the expressivity of CML, an instance of this
class can also provide additional information about a small
molecule, such as its chemical formula, names, and synonyms, if CML
is used as the structure format.
> Examples: The following SMILES string, which describes the
structure of glucose-6-phosphate:
> ‘C(OP(=O)(O)O)[CH]1([CH](O)[CH](O)[CH](O)[CH](O)O1)
’.</rdfs:comment>
> </owl:Class>
> <owl:ObjectProperty rdf:about="#CONTROLLER">
> <rdfs:subPropertyOf>
> <owl:ObjectProperty rdf:about="#PARTICIPANTS"/>
> </rdfs:subPropertyOf>
> <rdfs:range rdf:resource="#physicalEntityParticipant"/>
> <rdfs:domain rdf:resource="#control"/>
> <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>
> </owl:ObjectProperty>
> <owl:ObjectProperty rdf:about="#PARTICIPANTS">
> <rdfs:range>
> <owl:Class>
> <owl:unionOf rdf:parseType="Collection">
> <owl:Class rdf:about="#entity"/>
> <owl:Class rdf:about="#physicalEntityParticipant"/>
> </owl:unionOf>
> </owl:Class>
> </rdfs:range>
> <rdfs:domain rdf:resource="#interaction"/>
> <rdfs:comment
rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
> >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 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 Protégé,
so this property should not contain any instances if there are
instances contained in a sub-property.</rdfs:comment>
> </owl:ObjectProperty>
> <owl:ObjectProperty rdf:ID="XREF">
> <rdfs:domain>
> <owl:Class>
> <owl:unionOf rdf:parseType="Collection">
> <owl:Class rdf:about="#openControlledVocabulary"/>
> <owl:Class rdf:about="#entity"/>
> <owl:Class rdf:about="#sequenceFeature"/>
> <owl:Class rdf:about="#dataSource"/>
> <owl:Class rdf:about="#evidence"/>
> <owl:Class rdf:about="#confidence"/>
> </owl:unionOf>
> </owl:Class>
> </rdfs:domain>
> <rdfs:range rdf:resource="#xref"/>
> <rdfs:comment xml:lang="en">Values of this property define
external cross-references from this entity to entities in external
databases.</rdfs:comment>
> </owl:ObjectProperty>
> <owl:ObjectProperty rdf:about="#FEATURE-TYPE">
> <rdfs:comment
rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
> >Description and classification of the feature.</rdfs:comment>
> <rdfs:range rdf:resource="#openControlledVocabulary"/>
> <rdfs:domain rdf:resource="#sequenceFeature"/>
> </owl:ObjectProperty>
> <owl:ObjectProperty rdf:ID="PATHWAY-COMPONENTS">
> <rdfs:domain rdf:resource="#pathway"/>
> <rdfs:comment
rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
> >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>
> <rdfs:range>
> <owl:Class>
> <owl:unionOf rdf:parseType="Collection">
> <owl:Class rdf:about="#interaction"/>
> <owl:Class rdf:about="#pathwayStep"/>
> <owl:Class rdf:about="#pathway"/>
> </owl:unionOf>
> </owl:Class>
> </rdfs:range>
> </owl:ObjectProperty>
> <owl:ObjectProperty rdf:about="#PARTICIPANT">
> <rdfs:domain rdf:resource="#experimentalForm"/>
> <rdfs:comment
rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
> >The participant that has the experimental form being
described.</rdfs:comment>
> <rdfs:range rdf:resource="#physicalEntityParticipant"/>
> </owl:ObjectProperty>
> <owl:ObjectProperty rdf:about="#PHYSICAL-ENTITY">
> <rdfs:range>
> <owl:Class>
> <owl:unionOf rdf:parseType="Collection">
> <owl:Class rdf:about="#physicalEntity"/>
> <owl:Class rdf:about="#state"/>
> </owl:unionOf>
> </owl:Class>
> </rdfs:range>
> <rdfs:domain>
> <owl:Class>
> <owl:unionOf rdf:parseType="Collection">
> <owl:Class rdf:about="#physicalEntityParticipant"/>
> <owl:Class rdf:about="#state"/>
> </owl:unionOf>
> </owl:Class>
> </rdfs:domain>
> <rdfs:comment xml:lang="en">The physical entity annotated with
stoichiometry and cellular location attributes from the
physicalEntityParticipant instance.</rdfs:comment>
> </owl:ObjectProperty>
> <owl:ObjectProperty rdf:ID="EVIDENCE">
> <rdfs:domain>
> <owl:Class>
> <owl:unionOf rdf:parseType="Collection">
> <owl:Class rdf:about="#interaction"/>
> <owl:Class rdf:about="#pathway"/>
> </owl:unionOf>
> </owl:Class>
> </rdfs:domain>
> <rdfs:comment
rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
> >Scientific evidence supporting the existence of the entity as
described.</rdfs:comment>
> <rdfs:range rdf:resource="#evidence"/>
> </owl:ObjectProperty>
> <owl:ObjectProperty rdf:ID="RIGHT">
> <rdfs:subPropertyOf rdf:resource="#PARTICIPANTS"/>
> <rdfs:range rdf:resource="#physicalEntityParticipant"/>
> <rdfs:comment
rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
> >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>
> <rdfs:domain rdf:resource="#conversion"/>
> </owl:ObjectProperty>
> <owl:ObjectProperty rdf:about="#SEQUENCE-INTERVAL-BEGIN">
> <rdfs:range rdf:resource="#sequenceSite"/>
> <rdfs:domain rdf:resource="#sequenceInterval"/>
> <rdfs:comment
rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
> >The begin position of a sequence interval.</rdfs:comment>
> </owl:ObjectProperty>
> <owl:ObjectProperty rdf:about="#STEP-INTERACTIONS">
> <rdfs:comment
rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
> >The interactions that take place at this step of the
pathway.</rdfs:comment>
> <rdfs:domain rdf:resource="#pathwayStep"/>
> <rdfs:range>
> <owl:Class>
> <owl:unionOf rdf:parseType="Collection">
> <owl:Class rdf:about="#interaction"/>
> <owl:Class rdf:about="#pathway"/>
> </owl:unionOf>
> </owl:Class>
> </rdfs:range>
> </owl:ObjectProperty>
> <owl:ObjectProperty rdf:ID="INTERACTION-TYPE">
> <rdfs:comment
rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
> >External controlled vocabulary characterizing the interaction
type, for example "phosphorylation".</rdfs:comment>
> <rdfs:domain rdf:resource="#physicalInteraction"/>
> <rdfs:range rdf:resource="#openControlledVocabulary"/>
> </owl:ObjectProperty>
> <owl:ObjectProperty rdf:ID="CONFIDENCE">
> <rdfs:range rdf:resource="#confidence"/>
> <rdfs:comment
rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
> >Confidence in the containing instance. Usually a statistical
measure.</rdfs:comment>
> <rdfs:domain rdf:resource="#evidence"/>
> </owl:ObjectProperty>
> <owl:ObjectProperty rdf:ID="EVIDENCE-CODE">
> <rdfs:domain rdf:resource="#evidence"/>
> <rdfs:range rdf:resource="#openControlledVocabulary"/>
> <rdfs:comment
rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
> >A pointer to a term in an external controlled vocabulary,
such as the GO or BioCyc evidence codes, that describes the nature
of the support.</rdfs:comment>
> </owl:ObjectProperty>
> <owl:ObjectProperty rdf:about="#ORGANISM">
> <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>
> <rdfs:domain>
> <owl:Class>
> <owl:unionOf rdf:parseType="Collection">
> <owl:Class rdf:about="#rna"/>
> <owl:Class rdf:about="#protein"/>
> <owl:Class rdf:about="#pathway"/>
> <owl:Class rdf:about="#complex"/>
> <owl:Class rdf:about="#dna"/>
> </owl:unionOf>
> </owl:Class>
> </rdfs:domain>
> <rdfs:range rdf:resource="#bioSource"/>
> </owl:ObjectProperty>
> <owl:ObjectProperty rdf:ID="STRUCTURE">
> <rdfs:range rdf:resource="#chemicalStructure"/>
> <rdfs:domain rdf:resource="#smallMolecule"/>
> <rdfs:comment xml:lang="en">Defines the chemical structure and
other information about this molecule, using an instance of class
chemicalStructure.</rdfs:comment>
> </owl:ObjectProperty>
> <owl:ObjectProperty rdf:ID="SEQUENCE-FEATURE-LIST">
> <rdfs:domain rdf:resource="#sequenceParticipant"/>
> <rdfs:comment
rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
> >Sequence features relevant for the interaction, for example
binding domains or modification sites.</rdfs:comment>
> <rdfs:range rdf:resource="#sequenceFeature"/>
> </owl:ObjectProperty>
> <owl:ObjectProperty rdf:about="#TAXON-XREF">
> <rdfs:range rdf:resource="#xref"/>
> <rdfs:comment
rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
> >An xref to an organism taxonomy database, preferably NCBI
taxon. This should be an instance of unificationXref, unless the
organism is not in an existing database.</rdfs:comment>
> <rdfs:domain rdf:resource="#bioSource"/>
> </owl:ObjectProperty>
> <owl:ObjectProperty rdf:ID="LEFT">
> <rdfs:domain rdf:resource="#conversion"/>
> <rdfs:comment
rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
> >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>
> <rdfs:subPropertyOf rdf:resource="#PARTICIPANTS"/>
> <rdfs:range rdf:resource="#physicalEntityParticipant"/>
> </owl:ObjectProperty>
> <owl:ObjectProperty rdf:about="#CONTROLLED">
> <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>
> <rdfs:subPropertyOf rdf:resource="#PARTICIPANTS"/>
> <rdfs:range>
> <owl:Class>
> <owl:unionOf rdf:parseType="Collection">
> <owl:Class rdf:about="#entity"/>
> <owl:Class rdf:about="#physicalEntityParticipant"/>
> </owl:unionOf>
> </owl:Class>
> </rdfs:range>
> <rdfs:domain rdf:resource="#control"/>
> </owl:ObjectProperty>
> <owl:ObjectProperty rdf:about="#TISSUE">
> <rdfs:domain rdf:resource="#bioSource"/>
> <rdfs:comment xml:lang="en">An external controlled vocabulary
of tissue types.</rdfs:comment>
> <rdfs:range rdf:resource="#openControlledVocabulary"/>
> </owl:ObjectProperty>
> <owl:ObjectProperty rdf:ID="COMPONENTS">
> <rdfs:domain rdf:resource="#complex"/>
> <rdf:type
rdf:resource="http://www.w3.org/2002/07/owl#TransitiveProperty"/>
> <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 COMPONENTS 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 COMPONENTS property
is empty), which may be used as COMPONENTS 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.</rdfs:comment>
> <rdfs:range rdf:resource="#physicalEntityParticipant"/>
> </owl:ObjectProperty>
> <owl:ObjectProperty rdf:ID="COFACTOR">
> <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>
> <rdfs:subPropertyOf rdf:resource="#PARTICIPANTS"/>
> <rdfs:domain rdf:resource="#catalysis"/>
> <rdfs:range rdf:resource="#physicalEntityParticipant"/>
> </owl:ObjectProperty>
> <owl:ObjectProperty rdf:about="#CELLULAR-LOCATION">
> <rdfs:range rdf:resource="#openControlledVocabulary"/>
> <rdfs:domain>
> <owl:Class>
> <owl:unionOf rdf:parseType="Collection">
> <owl:Class rdf:about="#physicalEntityParticipant"/>
> <owl:Class rdf:about="#state"/>
> </owl:unionOf>
> </owl:Class>
> </rdfs:domain>
> <rdfs:comment
rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
> >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>
> </owl:ObjectProperty>
> <owl:ObjectProperty rdf:ID="NEXT-STEP">
> <rdfs:domain rdf:resource="#pathwayStep"/>
> <rdfs:comment
rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
> >The next step(s) of the pathway. Contains zero or more
pathwayStep instances. If there is no next step, this property is
empty.</rdfs:comment>
> <rdfs:range rdf:resource="#pathwayStep"/>
> </owl:ObjectProperty>
> <owl:ObjectProperty rdf:ID="FEATURE-LOCATION">
> <rdfs:domain rdf:resource="#sequenceFeature"/>
> <rdfs:range rdf:resource="#sequenceLocation"/>
> <rdfs:comment
rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
> >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>
> </owl:ObjectProperty>
> <owl:ObjectProperty rdf:ID="EXPERIMENTAL-FORM">
> <rdfs:comment
rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
> >The experimental forms associated with an evidence
instance.</rdfs:comment>
> <rdfs:range rdf:resource="#experimentalForm"/>
> <rdfs:domain rdf:resource="#evidence"/>
> </owl:ObjectProperty>
> <owl:ObjectProperty rdf:about="#SEQUENCE-INTERVAL-END">
> <rdfs:domain rdf:resource="#sequenceInterval"/>
> <rdfs:comment
rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
> >The end position of a sequence interval.</rdfs:comment>
> <rdfs:range rdf:resource="#sequenceSite"/>
> </owl:ObjectProperty>
> <owl:ObjectProperty rdf:about="#EXPERIMENTAL-FORM-TYPE">
> <rdfs:range rdf:resource="#openControlledVocabulary"/>
> <rdfs:domain rdf:resource="#experimentalForm"/>
> <rdfs:comment
rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
> >Descriptor of this experimental form from a controlled
vocabulary.</rdfs:comment>
> </owl:ObjectProperty>
> <owl:ObjectProperty rdf:ID="DATA-SOURCE">
> <rdfs:range rdf:resource="#dataSource"/>
> <rdfs:comment
rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
> >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>
> <rdfs:domain rdf:resource="#entity"/>
> </owl:ObjectProperty>
> <owl:ObjectProperty rdf:about="#CELLTYPE">
> <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>
> <rdfs:range rdf:resource="#openControlledVocabulary"/>
> <rdfs:domain rdf:resource="#bioSource"/>
> </owl:ObjectProperty>
> <owl:DatatypeProperty rdf:ID="AUTHORS">
> <rdfs:domain rdf:resource="#publicationXref"/>
> <rdfs:comment xml:lang="en">The authors of this publication,
one per property value.</rdfs:comment>
> <rdfs:range
rdf:resource="http://www.w3.org/2001/XMLSchema#string"/>
> </owl:DatatypeProperty>
> <owl:DatatypeProperty rdf:about="#MOLECULAR-WEIGHT">
> <rdfs:range
rdf:resource="http://www.w3.org/2001/XMLSchema#double"/>
> <rdfs:domain rdf:resource="#smallMolecule"/>
> <rdfs:comment xml:lang="en">Defines the molecular weight of
the molecule, in daltons.</rdfs:comment>
> </owl:DatatypeProperty>
> <owl:DatatypeProperty rdf:about="#CHEMICAL-FORMULA">
> <rdfs:domain rdf:resource="#smallMolecule"/>
> <rdfs:comment
rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
> >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>
> <rdfs:range
rdf:resource="http://www.w3.org/2001/XMLSchema#string"/>
> </owl:DatatypeProperty>
> <owl:DatatypeProperty rdf:about="#NAME">
> <rdfs:domain>
> <owl:Class>
> <owl:unionOf rdf:parseType="Collection">
> <owl:Class rdf:about="#bioSource"/>
> <owl:Class rdf:about="#entity"/>
> <owl:Class rdf:about="#dataSource"/>
> <owl:Class rdf:about="#sequenceFeature"/>
> </owl:unionOf>
> </owl:Class>
> </rdfs:domain>
> <rdfs:comment xml:lang="en">The preferred full name for this
entity.</rdfs:comment>
> <rdfs:range
rdf:resource="http://www.w3.org/2001/XMLSchema#string"/>
> </owl:DatatypeProperty>
> <owl:DatatypeProperty rdf:about="#STRUCTURE-FORMAT">
> <rdfs:comment xml:lang="en">This property specifies which
format is used to define chemical structure data.</rdfs:comment>
> <rdfs:range>
> <owl:DataRange>
> <owl:oneOf rdf:parseType="Resource">
> <rdf:rest rdf:parseType="Resource">
> <rdf:rest rdf:parseType="Resource">
> <rdf:first
rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
> >InChI</rdf:first>
> <rdf:rest rdf:resource="http://www.w3.org/1999/02/22-
rdf-syntax-ns#nil"/>
> </rdf:rest>
> <rdf:first
rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
> >SMILES</rdf:first>
> </rdf:rest>
> <rdf:first
rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
> >CML</rdf:first>
> </owl:oneOf>
> </owl:DataRange>
> </rdfs:range>
> <rdfs:domain rdf:resource="#chemicalStructure"/>
> </owl:DatatypeProperty>
> <owl:DatatypeProperty rdf:about="#SPONTANEOUS">
> <rdfs:domain rdf:resource="#conversion"/>
> <rdfs:comment
rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
> >Specifies whether a conversion occurs spontaneously (i.e.
uncatalyzed, under biological conditions) left-to-right, right-to-
left, or not at all. If a conversion is not spontaneous, or if the
spontaneity is not known, the SPONTANEOUS property should be left
empty.</rdfs:comment>
> <rdfs:range>
> <owl:DataRange>
> <owl:oneOf rdf:parseType="Resource">
> <rdf:first
rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
> >L-R</rdf:first>
> <rdf:rest rdf:parseType="Resource">
> <rdf:first
rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
> >R-L</rdf:first>
> <rdf:rest rdf:resource="http://www.w3.org/1999/02/22-
rdf-syntax-ns#nil"/>
> </rdf:rest>
> </owl:oneOf>
> </owl:DataRange>
> </rdfs:range>
> </owl:DatatypeProperty>
> <owl:DatatypeProperty rdf:about="#DB">
> <rdfs:comment xml:lang="en">The name of the external database
to which this xref refers.</rdfs:comment>
> <rdfs:domain rdf:resource="#xref"/>
> <rdfs:range
rdf:resource="http://www.w3.org/2001/XMLSchema#string"/>
> </owl:DatatypeProperty>
> <owl:DatatypeProperty rdf:about="#SEQUENCE-POSITION">
> <rdfs:comment
rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
> >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>
> <rdfs:domain rdf:resource="#sequenceSite"/>
> <rdfs:range
rdf:resource="http://www.w3.org/2001/XMLSchema#unsignedLong"/>
> </owl:DatatypeProperty>
> <owl:DatatypeProperty rdf:about="#SHORT-NAME">
> <rdfs:domain>
> <owl:Class>
> <owl:unionOf rdf:parseType="Collection">
> <owl:Class rdf:about="#sequenceFeature"/>
> <owl:Class rdf:about="#entity"/>
> </owl:unionOf>
> </owl:Class>
> </rdfs:domain>
> <rdfs:range
rdf:resource="http://www.w3.org/2001/XMLSchema#string"/>
> <rdfs:comment
rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
> >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>
> </owl:DatatypeProperty>
> <owl:DatatypeProperty rdf:ID="AVAILABILITY">
> <rdfs:comment xml:lang="en">Describes the availability of this
data (e.g. a copyright statement).</rdfs:comment>
> <rdfs:domain rdf:resource="#entity"/>
> <rdfs:range
rdf:resource="http://www.w3.org/2001/XMLSchema#string"/>
> </owl:DatatypeProperty>
> <owl:DatatypeProperty rdf:about="#STRUCTURE-DATA">
> <rdfs:domain rdf:resource="#chemicalStructure"/>
> <rdfs:comment
rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
> >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>
> <rdfs:range
rdf:resource="http://www.w3.org/2001/XMLSchema#string"/>
> </owl:DatatypeProperty>
> <owl:DatatypeProperty rdf:ID="SYNONYMS">
> <rdfs:domain>
> <owl:Class>
> <owl:unionOf rdf:parseType="Collection">
> <owl:Class rdf:about="#sequenceFeature"/>
> <owl:Class rdf:about="#entity"/>
> </owl:unionOf>
> </owl:Class>
> </rdfs:domain>
> <rdfs:comment xml:lang="en">One or more synonyms for the name
of this entity. This should include the values of the NAME and SHORT-
NAME property so that it is easy to find all known names in one
place.</rdfs:comment>
> <rdfs:range
rdf:resource="http://www.w3.org/2001/XMLSchema#string"/>
> </owl:DatatypeProperty>
> <owl:DatatypeProperty rdf:about="#SEQUENCE">
> <rdfs:range
rdf:resource="http://www.w3.org/2001/XMLSchema#string"/>
> <rdfs:domain>
> <owl:Class>
> <owl:unionOf rdf:parseType="Collection">
> <owl:Class rdf:about="#rna"/>
> <owl:Class rdf:about="#protein"/>
> <owl:Class rdf:about="#dna"/>
> </owl:unionOf>
> </owl:Class>
> </rdfs:domain>
> <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>
> </owl:DatatypeProperty>
> <owl:DatatypeProperty rdf:ID="DELTA-S">
> <rdfs:range
rdf:resource="http://www.w3.org/2001/XMLSchema#double"/>
> <rdfs:domain rdf:resource="#biochemicalReaction"/>
> <rdfs:comment
rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
> >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'&lt;sup>o&lt;/sup>.
>
> delta-G'&lt;sup>o&lt;/sup> = delta-H'&lt;sup>o&lt;/sup> - T
delta-S'&lt;sup>o&lt;/sup>
>
> (This definition from EcoCyc)</rdfs:comment>
> </owl:DatatypeProperty>
> <owl:DatatypeProperty rdf:ID="SOURCE">
> <rdfs:domain rdf:resource="#publicationXref"/>
> <rdfs:range
rdf:resource="http://www.w3.org/2001/XMLSchema#string"/>
> <rdfs:comment
rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
> >The source in which the reference was published, such as: a
book title, or a journal title and volume and pages.</rdfs:comment>
> </owl:DatatypeProperty>
> <owl:DatatypeProperty rdf:ID="DELTA-H">
> <rdfs:domain rdf:resource="#biochemicalReaction"/>
> <rdfs:range
rdf:resource="http://www.w3.org/2001/XMLSchema#double"/>
> <rdfs:comment
rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
> >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'&lt;sup>o&lt;/sup>.
>
> delta-G'&lt;sup>o&lt;/sup> = delta-H'&lt;sup>o&lt;/sup> - T
delta-S'&lt;sup>o&lt;/sup>
>
> (This definition from EcoCyc)</rdfs:comment>
> </owl:DatatypeProperty>
> <owl:DatatypeProperty rdf:ID="COMMENT">
> <rdfs:range
rdf:resource="http://www.w3.org/2001/XMLSchema#string"/>
> <rdfs:domain>
> <owl:Class>
> <owl:unionOf rdf:parseType="Collection">
> <owl:Class rdf:about="#utilityClass"/>
> <owl:Class rdf:about="#entity"/>
> </owl:unionOf>
> </owl:Class>
> </rdfs:domain>
> <rdfs:comment
rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
> >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>
> </owl:DatatypeProperty>
> <owl:DatatypeProperty rdf:about="#DB-VERSION">
> <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>
> <rdfs:range
rdf:resource="http://www.w3.org/2001/XMLSchema#string"/>
> <rdfs:domain rdf:resource="#xref"/>
> </owl:DatatypeProperty>
> <owl:DatatypeProperty rdf:ID="URL">
> <rdfs:comment xml:lang="en">The URL at which the publication
can be found, if it is available through the Web.</rdfs:comment>
> <rdfs:range
rdf:resource="http://www.w3.org/2001/XMLSchema#string"/>
> <rdfs:domain rdf:resource="#publicationXref"/>
> </owl:DatatypeProperty>
> <owl:DatatypeProperty rdf:about="#CONFIDENCE-VALUE">
> <rdfs:comment
rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
> >The value of the confidence measure.</rdfs:comment>
> <rdfs:range
rdf:resource="http://www.w3.org/2001/XMLSchema#string"/>
> <rdfs:domain rdf:resource="#confidence"/>
> </owl:DatatypeProperty>
> <owl:DatatypeProperty rdf:ID="TERM">
> <rdfs:domain rdf:resource="#openControlledVocabulary"/>
> <rdfs:range
rdf:resource="http://www.w3.org/2001/XMLSchema#string"/>
> <rdfs:comment
rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
> >The external controlled vocabulary term.</rdfs:comment>
> </owl:DatatypeProperty>
> <owl:DatatypeProperty rdf:about="#TITLE">
> <rdfs:range
rdf:resource="http://www.w3.org/2001/XMLSchema#string"/>
> <rdfs:comment xml:lang="en">The title of the
publication.</rdfs:comment>
> <rdfs:domain rdf:resource="#publicationXref"/>
> </owl:DatatypeProperty>
> <owl:DatatypeProperty rdf:ID="DELTA-G">
> <rdfs:comment
rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
> >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'&lt;sup>o&lt;/sup>.
>
> delta-G'&lt;sup>o&lt;/sup> = -RT lnK'
> and
> delta-G'&lt;sup>o&lt;/sup> = delta-H'&lt;sup>o&lt;/sup> - T
delta-S'&lt;sup>o&lt;/sup>
>
> delta-G'&lt;sup>o&lt;/sup> has units of kJ/mol. Like K', it is a
function of temperature (T), ionic strength (I), pH, and pMg (pMg = -
log&lt;sub>10&lt;/sub>[Mg&lt;sup>2+&lt;/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'&lt;sup>o&lt;/sup> T I pH pMg). This property may have multiple
values, representing different measurements for delta-
G'&lt;sup>o&lt;/sup> obtained under the different experimental
conditions listed in the 5-tuple.
>
> (This definition from EcoCyc)</rdfs:comment>
> <rdfs:domain rdf:resource="#biochemicalReaction"/>
> <rdfs:range
rdf:resource="http://www.w3.org/2001/XMLSchema#double"/>
> </owl:DatatypeProperty>
> <owl:DatatypeProperty rdf:about="#RELATIONSHIP-TYPE">
> <rdfs:range
rdf:resource="http://www.w3.org/2001/XMLSchema#string"/>
> <rdfs:comment
rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
> >This property names the type of relationship between the
BioPAX object linked from, and the external object linked to, such
as 'gene of this protein', or 'protein with similar
sequence'.</rdfs:comment>
> <rdfs:domain rdf:resource="#relationshipXref"/>
> </owl:DatatypeProperty>
> <owl:DatatypeProperty rdf:about="#POSITION-STATUS">
> <rdfs:domain rdf:resource="#sequenceSite"/>
> <rdfs:comment
rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
> >The confidence status of the sequence position. This could be:
> UNCERTAIN: The site is not certain. This could be used to describe
a post-translational modification that is known to occur on a
protein, but the location is not known.
> GREATER-THAN: The site is greater than the SEQUENCE-POSITION.
> LESS-THAN: The site is less than the SEQUENCE-POSITION.
> CERTAIN: The SEQUENCE-POSITION is known with
certainty.</rdfs:comment>
> <rdfs:range>
> <owl:DataRange>
> <owl:oneOf rdf:parseType="Resource">
> <rdf:first
rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
> >CERTAIN</rdf:first>
> <rdf:rest rdf:parseType="Resource">
> <rdf:rest rdf:parseType="Resource">
> <rdf:first
rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
> >LESS-THAN</rdf:first>
> <rdf:rest rdf:parseType="Resource">
> <rdf:first
rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
> >GREATER-THAN</rdf:first>
> <rdf:rest
rdf:resource="http://www.w3.org/1999/02/22-rdf-syntax-ns#nil"/>
> </rdf:rest>
> </rdf:rest>
> <rdf:first
rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
> >UNCERTAIN</rdf:first>
> </rdf:rest>
> </owl:oneOf>
> </owl:DataRange>
> </rdfs:range>
> </owl:DatatypeProperty>
> <owl:DatatypeProperty rdf:about="#ID">
> <rdfs:domain rdf:resource="#xref"/>
> <rdfs:comment xml:lang="en">The primary identifier in the
external database of the object to which this xref
refers.</rdfs:comment>
> <rdfs:range
rdf:resource="http://www.w3.org/2001/XMLSchema#string"/>
> </owl:DatatypeProperty>
> <owl:DatatypeProperty rdf:about="#ID-VERSION">
> <rdfs:range
rdf:resource="http://www.w3.org/2001/XMLSchema#string"/>
> <rdfs:domain rdf:resource="#xref"/>
> <rdfs:comment
rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
> >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>
> </owl:DatatypeProperty>
> <owl:DatatypeProperty rdf:ID="EC-NUMBER">
> <rdfs:comment
rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
> >The unique number assigned to a reaction by the Enzyme
Commission of the International Union of Biochemistry and Molecular
Biology.
>
> Note that not all biochemical reactions currently have EC numbers
assigned to them.</rdfs:comment>
> <rdfs:domain rdf:resource="#biochemicalReaction"/>
> <rdfs:range
rdf:resource="http://www.w3.org/2001/XMLSchema#string"/>
> </owl:DatatypeProperty>
> <owl:DatatypeProperty rdf:about="#YEAR">
> <rdfs:domain rdf:resource="#publicationXref"/>
> <rdfs:range
rdf:resource="http://www.w3.org/2001/XMLSchema#positiveInteger"/>
> <rdfs:comment xml:lang="en">The year in which this publication
was published.</rdfs:comment>
> </owl:DatatypeProperty>
> <owl:DatatypeProperty rdf:about="#DIRECTION">
> <rdfs:range>
> <owl:DataRange>
> <owl:oneOf rdf:parseType="Resource">
> <rdf:first
rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
> >REVERSIBLE</rdf:first>
> <rdf:rest rdf:parseType="Resource">
> <rdf:first
rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
> >PHYSIOL-LEFT-TO-RIGHT</rdf:first>
> <rdf:rest rdf:parseType="Resource">
> <rdf:first
rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
> >PHYSIOL-RIGHT-TO-LEFT</rdf:first>
> <rdf:rest rdf:parseType="Resource">
> <rdf:first
rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
> >IRREVERSIBLE-LEFT-TO-RIGHT</rdf:first>
> <rdf:rest rdf:parseType="Resource">
> <rdf:rest
rdf:resource="http://www.w3.org/1999/02/22-rdf-syntax-ns#nil"/>
> <rdf:first
rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
> >IRREVERSIBLE-RIGHT-TO-LEFT</rdf:first>
> </rdf:rest>
> </rdf:rest>
> </rdf:rest>
> </rdf:rest>
> </owl:oneOf>
> </owl:DataRange>
> </rdfs:range>
> <rdfs:domain rdf:resource="#catalysis"/>
> <rdfs:comment
rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
> >Specifies the reaction direction of the interaction catalyzed
by this instance of the catalysis class.
>
> Possible values of this slot are:
>
> REVERSIBLE: Interaction occurs in both directions in physiological
settings.
>
> PHYSIOL-LEFT-TO-RIGHT
> PHYSIOL-RIGHT-TO-LEFT
> The interaction occurs in the specified direction in physiological
settings, because of several possible factors including the
energetics of the reaction, local concentrations
> of reactants and products, and the regulation of the enzyme or its
expression.
>
> IRREVERSIBLE-LEFT-TO-RIGHT
> IRREVERSIBLE-RIGHT-TO-LEFT
> For all practical purposes, the interactions occurs only in the
specified direction in physiological settings, because of chemical
properties of the reaction.
>
> (This definition from EcoCyc)</rdfs:comment>
> </owl:DatatypeProperty>
> <owl:DatatypeProperty rdf:ID="KEQ">
> <rdfs:range
rdf:resource="http://www.w3.org/2001/XMLSchema#double"/>
> <rdfs:comment
rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
> >This quantity is dimensionless and is usually a single
number. The measured equilibrium constant for a biochemical
reaction, encoded by the slot KEQ, is actually the apparent
equilibrium constant, K'. Concentrations in the equilibrium
constant equation refer to the total concentrations of all forms of
particular biochemical reactants. For example, in the equilibrium
constant equation for the biochemical reaction in which ATP is
hydrolyzed to ADP and inorganic phosphate:
>
> K' = [ADP][P&lt;sub>i&lt;/sub>]/[ATP],
>
> The concentration of ATP refers to the total concentration of all
of the following species:
>
> [ATP] = [ATP&lt;sup>4-&lt;/sup>] + [HATP&lt;sup>3-&lt;/sup>] +
[H&lt;sub>2&lt;/sub>ATP&lt;sup>2-&lt;/sup>] + [MgATP&lt;sup>2-
&lt;/sup>] + [MgHATP&lt;sup>-&lt;/sup>] + [Mg&lt;sub>2&lt;/sub>ATP].
>
> The apparent equilibrium constant is formally dimensionless, and
can be kept so by inclusion of as many of the terms (1
mol/dm&lt;sup>3&lt;/sup>) in the numerator or denominator as
necessary. It is a function of temperature (T), ionic strength (I),
pH, and pMg (pMg = -log&lt;sub>10&lt;/sub>[Mg&lt;sup>2+&lt;/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>
> <rdfs:domain rdf:resource="#biochemicalReaction"/>
> </owl:DatatypeProperty>
> <owl:DatatypeProperty rdf:about="#CONTROL-TYPE">
> <rdfs:range>
> <owl:DataRange>
> <owl:oneOf rdf:parseType="Resource">
> <rdf:rest rdf:parseType="Resource">
> <rdf:rest rdf:parseType="Resource">
> <rdf:first
rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
> >INHIBITION-ALLOSTERIC</rdf:first>
> <rdf:rest rdf:parseType="Resource">
> <rdf:first
rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
> >INHIBITION-COMPETITIVE</rdf:first>
> <rdf:rest rdf:parseType="Resource">
> <rdf:rest rdf:parseType="Resource">
> <rdf:rest rdf:parseType="Resource">
> <rdf:first
rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
> >INHIBITION-OTHER</rdf:first>
> <rdf:rest rdf:parseType="Resource">
> <rdf:rest rdf:parseType="Resource">
> <rdf:first
rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
> >INHIBITION-UNKMECH</rdf:first>
> <rdf:rest rdf:parseType="Resource">
> <rdf:first
rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
> >ACTIVATION-UNKMECH</rdf:first>
> <rdf:rest rdf:parseType="Resource">
> <rdf:first
rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
> >ACTIVATION-NONALLOSTERIC</rdf:first>
> <rdf:rest rdf:parseType="Resource">
> <rdf:first
rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
> >ACTIVATION-ALLOSTERIC</rdf:first>
> <rdf:rest
rdf:resource="http://www.w3.org/1999/02/22-rdf-syntax-ns#nil"/>
> </rdf:rest>
> </rdf:rest>
> </rdf:rest>
> </rdf:rest>
> <rdf:first
rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
> >INHIBITION-UNCOMPETITIVE</rdf:first>
> </rdf:rest>
> </rdf:rest>
> <rdf:first
rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
> >INHIBITION-NONCOMPETITIVE</rdf:first>
> </rdf:rest>
> <rdf:first
rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
> >INHIBITION-IRREVERSIBLE</rdf:first>
> </rdf:rest>
> </rdf:rest>
> </rdf:rest>
> <rdf:first
rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
> >ACTIVATION</rdf:first>
> </rdf:rest>
> <rdf:first
rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
> >INHIBITION</rdf:first>
> </owl:oneOf>
> </owl:DataRange>
> </rdfs:range>
> <rdfs:domain rdf:resource="#control"/>
> <rdfs:comment
rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
> >Defines the nature of the control relationship between the
CONTROLLER and the CONTROLLED entities.
>
> The following terms are possible values:
>
> ACTIVATION: General activation
>
> The following term can not be used in the catalysis class:
> INHIBITION: General inhibition
>
> The following terms can only be used in the modulation class
(these definitions from EcoCyc):
> INHIBITION-ALLOSTERIC
> Allosteric inhibitors decrease the specified enzyme activity by
binding reversibly to the enzyme and inducing a conformational
change that decreases the affinity of the enzyme to its substrates
without affecting its VMAX. Allosteric inhibitors can be competitive
or noncompetitive inhibitors, therefore, those inhibition categories
can be used in conjunction with this category.
>
> INHIBITION-COMPETITIVE
> Competitive inhibitors are compounds that competitively inhibit
the specified enzyme activity by binding reversibly to the enzyme
and preventing the substrate from binding. Binding of the inhibitor
and substrate are mutually exclusive because it is assumed that the
inhibitor and substrate can both bind only to the free enzyme. A
competitive inhibitor can either bind to the active site of the
enzyme, directly excluding the substrate from binding there, or it
can bind to another site on the enzyme, altering the conformation of
the enzyme such that the substrate can not bind to the active site.
>
> INHIBITION-IRREVERSIBLE
> Irreversible inhibitors are compounds that irreversibly inhibit
the specified enzyme activity by binding to the enzyme and
dissociating so slowly that it is considered irreversible. For
example, alkylating agents, such as iodoacetamide, irreversibly
inhibit the catalytic activity of some enzymes by modifying cysteine
side chains.
>
> INHIBITION-NONCOMPETITIVE
> Noncompetitive inhibitors are compounds that noncompetitively
inhibit the specified enzyme by binding reversibly to both the free
enzyme and to the enzyme-substrate complex. The inhibitor and
substrate may be bound to the enzyme simultaneously and do not
exclude each other. However, only the enzyme-substrate complex (not
the enzyme-substrate-inhibitor complex) is catalytically active.
>
> INHIBITION-OTHER
> Compounds that inhibit the specified enzyme activity by a
mechanism that has been characterized, but that cannot be clearly
classified as irreversible, competitive, noncompetitive,
uncompetitive, or allosteric.
>
> INHIBITION-UNCOMPETITIVE
> Uncompetitive inhibitors are compounds that uncompetitively
inhibit the specified enzyme activity by binding reversibly to the
enzyme-substrate complex but not to the enzyme alone.
>
> INHIBITION-UNKMECH
> 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.
>
> ACTIVATION-UNKMECH
> 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.
>
> ACTIVATION-NONALLOSTERIC
> Nonallosteric activators increase the specified enzyme activity by
means other than allosteric.
>
> ACTIVATION-ALLOSTERIC
> Allosteric activators increase the specified enzyme activity by
binding reversibly to the enzyme and inducing a conformational
change that increases the affinity of the enzyme to its substrates
without affecting its VMAX.</rdfs:comment>
> </owl:DatatypeProperty>
> <owl:DatatypeProperty rdf:about="#STOICHIOMETRIC-COEFFICIENT">
> <rdfs:range
rdf:resource="http://www.w3.org/2001/XMLSchema#double"/>
> <rdfs:comment
rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
> >Each value of this property represents the stoichiometric
coefficient for one of the physical 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>
> <rdfs:domain rdf:resource="#physicalEntityParticipant"/>
> </owl:DatatypeProperty>
> </rdf:RDF>
>
> <!-- Created with Protege (with OWL Plugin 1.3, Build 225.4)
http://protege.stanford.edu -->
>
Wed Oct 26, 2005 4:22 pm

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joshitope
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Hi All, Previously we have suggested several proposals for modeling states in BioPAX. Recently we refined one of them, proposal C ... 		Emek Demir
emekdemir Offline Send Email 		Jun 15, 2005
8:57 am

Hi Emek, So does the proposal wiki that you set up (e-mail to the discuss list yesterday) supersede this states subgroup? cheers Geeta ... in ... ...
joshitope Offline Send Email Oct 26, 2005
4:23 pm

Hi Geeta, Not really, it is rather a rewrite of what was proposed and discussed and maybe some of Alan's comments. Also please note that it is by no means...
emek@...
emekdemir Offline Send Email 		Oct 26, 2005
9:16 pm
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