| http://www.biopax.org/relea... | rdfs:comment | This is version 1.0 of the BioPAX Level 2 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). | lld:biogrid |
| http://www.biopax.org/relea... | rdfs:comment | This is version 1.0 of the BioPAX Level 2 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). | lld:cellmap |
| http://www.biopax.org/relea... | rdfs:comment | This is version 1.0 of the BioPAX Level 2 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). | lld:imid |
| http://www.biopax.org/relea... | rdfs:comment | 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. The XREF property may contain a publicationXref referencing a publication describing the data source (e.g. a database publication). A unificationXref may be used e.g. when pointing to an entry in a database of databases describing this database.
Examples: A database or person name. | lld:biogrid |
| http://www.biopax.org/relea... | rdfs:comment | 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. The XREF property may contain a publicationXref referencing a publication describing the data source (e.g. a database publication). A unificationXref may be used e.g. when pointing to an entry in a database of databases describing this database.
Examples: A database or person name. | lld:cellmap |
| http://www.biopax.org/relea... | rdfs:comment | 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. The XREF property may contain a publicationXref referencing a publication describing the data source (e.g. a database publication). A unificationXref may be used e.g. when pointing to an entry in a database of databases describing this database.
Examples: A database or person name. | lld:imid |
| http://www.biopax.org/relea... | rdfs:comment | Definition: Used to import terms from external controlled vocabularies (CVs) into the ontology. To support consistency and compatibility, open, freely available CVs should be used whenever possible, such as the Gene Ontology (GO) or other open biological CVs listed on the OBO website (http://obo.sourceforge.net/).
Comment: The ID property in unification xrefs to GO and other OBO ontologies should include the ontology name in the ID property (e.g. ID="GO:0005634" instead of ID="0005634"). | lld:biogrid |
| http://www.biopax.org/relea... | rdfs:comment | Definition: Used to import terms from external controlled vocabularies (CVs) into the ontology. To support consistency and compatibility, open, freely available CVs should be used whenever possible, such as the Gene Ontology (GO) or other open biological CVs listed on the OBO website (http://obo.sourceforge.net/).
Comment: The ID property in unification xrefs to GO and other OBO ontologies should include the ontology name in the ID property (e.g. ID="GO:0005634" instead of ID="0005634"). | lld:cellmap |
| http://www.biopax.org/relea... | rdfs:comment | Definition: Used to import terms from external controlled vocabularies (CVs) into the ontology. To support consistency and compatibility, open, freely available CVs should be used whenever possible, such as the Gene Ontology (GO) or other open biological CVs listed on the OBO website (http://obo.sourceforge.net/).
Comment: The ID property in unification xrefs to GO and other OBO ontologies should include the ontology name in the ID property (e.g. ID="GO:0005634" instead of ID="0005634"). | lld:imid |
| http://www.biopax.org/relea... | rdfs:comment | Definition: A DNA, RNA or protein participant in an interaction.
Comment: See physicalEntityParticipant for more documentation. | lld:biogrid |
| http://www.biopax.org/relea... | rdfs:comment | Definition: A DNA, RNA or protein participant in an interaction.
Comment: See physicalEntityParticipant for more documentation. | lld:cellmap |
| http://www.biopax.org/relea... | rdfs:comment | Definition: A DNA, RNA or protein participant in an interaction.
Comment: See physicalEntityParticipant for more documentation. | lld:imid |
| http://www.biopax.org/relea... | rdfs:comment | 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. | lld:biogrid |
| http://www.biopax.org/relea... | rdfs:comment | 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. | lld:cellmap |
| http://www.biopax.org/relea... | rdfs:comment | 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. | lld:imid |
| http://www.biopax.org/relea... | rdfs:comment | Definition: A conversion interaction in which a set of physical entities, at least one being a macromolecule (e.g. protein, RNA, DNA), aggregate via non-covalent interactions. One of the participants of a complexAssembly must be an instance of the class complex (via a physicalEntityParticipant instance).
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). | lld:biogrid |
| http://www.biopax.org/relea... | rdfs:comment | Definition: A conversion interaction in which a set of physical entities, at least one being a macromolecule (e.g. protein, RNA, DNA), aggregate via non-covalent interactions. One of the participants of a complexAssembly must be an instance of the class complex (via a physicalEntityParticipant instance).
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). | lld:cellmap |
| http://www.biopax.org/relea... | rdfs:comment | Definition: A conversion interaction in which a set of physical entities, at least one being a macromolecule (e.g. protein, RNA, DNA), aggregate via non-covalent interactions. One of the participants of a complexAssembly must be an instance of the class complex (via a physicalEntityParticipant instance).
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). | lld:imid |
| http://www.biopax.org/relea... | rdfs:comment | Definition: An entity with a physical structure. A pool of entities, not a specific molecular instance of an entity in a cell.
Comment: This class serves as the super-class for all physical entities, although its current set of subclasses is limited to molecules. As a highly abstract class in the ontology, instances of the physicalEntity class should never be created. Instead, more specific classes should be used.
Synonyms: part, interactor, object
Naming rationale: It's difficult to find a name that encompasses all of the subclasses of this class without being too general. E.g. PSI-MI uses 'interactor', BIND uses 'object', BioCyc uses 'chemicals'. physicalEntity seems to be a good name for this specialization of entity.
Examples: protein, small molecule, RNA | lld:biogrid |
| http://www.biopax.org/relea... | rdfs:comment | Definition: An entity with a physical structure. A pool of entities, not a specific molecular instance of an entity in a cell.
Comment: This class serves as the super-class for all physical entities, although its current set of subclasses is limited to molecules. As a highly abstract class in the ontology, instances of the physicalEntity class should never be created. Instead, more specific classes should be used.
Synonyms: part, interactor, object
Naming rationale: It's difficult to find a name that encompasses all of the subclasses of this class without being too general. E.g. PSI-MI uses 'interactor', BIND uses 'object', BioCyc uses 'chemicals'. physicalEntity seems to be a good name for this specialization of entity.
Examples: protein, small molecule, RNA | lld:cellmap |
| http://www.biopax.org/relea... | rdfs:comment | Definition: An entity with a physical structure. A pool of entities, not a specific molecular instance of an entity in a cell.
Comment: This class serves as the super-class for all physical entities, although its current set of subclasses is limited to molecules. As a highly abstract class in the ontology, instances of the physicalEntity class should never be created. Instead, more specific classes should be used.
Synonyms: part, interactor, object
Naming rationale: It's difficult to find a name that encompasses all of the subclasses of this class without being too general. E.g. PSI-MI uses 'interactor', BIND uses 'object', BioCyc uses 'chemicals'. physicalEntity seems to be a good name for this specialization of entity.
Examples: protein, small molecule, RNA | lld:imid |
| http://www.biopax.org/relea... | rdfs:comment | Definition: A unification xref defines a reference to an entity in an external resource that has the same biological identity as the referring entity. 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.. | lld:biogrid |
| http://www.biopax.org/relea... | rdfs:comment | Definition: A unification xref defines a reference to an entity in an external resource that has the same biological identity as the referring entity. 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.. | lld:cellmap |
| http://www.biopax.org/relea... | rdfs:comment | Definition: A unification xref defines a reference to an entity in an external resource that has the same biological identity as the referring entity. 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.. | lld:imid |
| http://www.biopax.org/relea... | rdfs:comment | Definition: An xref that defines a reference to an entity in an external resource that does not have the same biological identity as the referring entity.
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. | lld:biogrid |
| http://www.biopax.org/relea... | rdfs:comment | Definition: An xref that defines a reference to an entity in an external resource that does not have the same biological identity as the referring entity.
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. | lld:cellmap |
| http://www.biopax.org/relea... | rdfs:comment | Definition: An xref that defines a reference to an entity in an external resource that does not have the same biological identity as the referring entity.
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. | lld:imid |
| http://www.biopax.org/relea... | rdfs:comment | 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 comments on the PARTICPANTS property in the interaction class description). If sufficient information on the nature of a molecular interaction is available, a more specific BioPAX interaction class should be used.
Example: Two proteins observed to interact in a yeast-two-hybrid experiment where there is not enough experimental evidence to suggest that the proteins are forming a complex by themselves without any indirect involvement of other proteins. This is the case for most large-scale yeast two-hybrid screens. | lld:biogrid |
| http://www.biopax.org/relea... | rdfs:comment | 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 comments on the PARTICPANTS property in the interaction class description). If sufficient information on the nature of a molecular interaction is available, a more specific BioPAX interaction class should be used.
Example: Two proteins observed to interact in a yeast-two-hybrid experiment where there is not enough experimental evidence to suggest that the proteins are forming a complex by themselves without any indirect involvement of other proteins. This is the case for most large-scale yeast two-hybrid screens. | lld:cellmap |
| http://www.biopax.org/relea... | rdfs:comment | 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 comments on the PARTICPANTS property in the interaction class description). If sufficient information on the nature of a molecular interaction is available, a more specific BioPAX interaction class should be used.
Example: Two proteins observed to interact in a yeast-two-hybrid experiment where there is not enough experimental evidence to suggest that the proteins are forming a complex by themselves without any indirect involvement of other proteins. This is the case for most large-scale yeast two-hybrid screens. | lld:imid |
| http://www.biopax.org/relea... | rdfs:comment | 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 | lld:biogrid |
| http://www.biopax.org/relea... | rdfs:comment | 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 | lld:cellmap |
| http://www.biopax.org/relea... | rdfs:comment | 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 | lld:imid |
| http://www.biopax.org/relea... | rdfs:comment | Definition: A location on a nucleotide or amino acid sequence.
Comment: For organizational purposes only; direct instances of this class should not be created. | lld:biogrid |
| http://www.biopax.org/relea... | rdfs:comment | Definition: A location on a nucleotide or amino acid sequence.
Comment: For organizational purposes only; direct instances of this class should not be created. | lld:cellmap |
| http://www.biopax.org/relea... | rdfs:comment | Definition: A location on a nucleotide or amino acid sequence.
Comment: For organizational purposes only; direct instances of this class should not be created. | lld:imid |
| http://www.biopax.org/relea... | rdfs:comment | 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. | lld:biogrid |
| http://www.biopax.org/relea... | rdfs:comment | 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. | lld:cellmap |
| http://www.biopax.org/relea... | rdfs:comment | 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. | lld:imid |
| http://www.biopax.org/relea... | rdfs:comment | 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. | lld:biogrid |
| http://www.biopax.org/relea... | rdfs:comment | 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. | lld:cellmap |
| http://www.biopax.org/relea... | rdfs:comment | 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. | lld:imid |
| http://www.biopax.org/relea... | rdfs:comment | Definition: Describes a site on a sequence, i.e. the position of a single nucleotide or amino acid. | lld:biogrid |
| http://www.biopax.org/relea... | rdfs:comment | Definition: Describes a site on a sequence, i.e. the position of a single nucleotide or amino acid. | lld:cellmap |
| http://www.biopax.org/relea... | rdfs:comment | Definition: Describes a site on a sequence, i.e. the position of a single nucleotide or amino acid. | lld:imid |
| http://www.biopax.org/relea... | rdfs:comment | Definition: A conversion interaction in which one or more entities (substrates) undergo covalent changes to become one or more other entities (products). The substrates of biochemical reactions are defined in terms of sums of species. This is convention in biochemistry, and, in principle, all of the EC reactions should be biochemical reactions.
Examples: ATP + H2O = ADP + Pi
Comment: In the example reaction above, ATP is considered to be an equilibrium mixture of several species, namely ATP4-, HATP3-, H2ATP2-, MgATP2-, MgHATP-, and Mg2ATP. Additional species may also need to be considered if other ions (e.g. Ca2+) that bind ATP are present. Similar considerations apply to ADP and to inorganic phosphate (Pi). When writing biochemical reactions, it is not necessary to attach charges to the biochemical reactants or to include ions such as H+ and Mg2+ in the equation. The reaction is written in the direction specified by the EC nomenclature system, if applicable, regardless of the physiological direction(s) in which the reaction proceeds. Polymerization reactions involving large polymers whose structure is not explicitly captured should generally be represented as unbalanced reactions in which the monomer is consumed but the polymer remains unchanged, e.g. glycogen + glucose = glycogen. | lld:biogrid |
| http://www.biopax.org/relea... | rdfs:comment | Definition: A conversion interaction in which one or more entities (substrates) undergo covalent changes to become one or more other entities (products). The substrates of biochemical reactions are defined in terms of sums of species. This is convention in biochemistry, and, in principle, all of the EC reactions should be biochemical reactions.
Examples: ATP + H2O = ADP + Pi
Comment: In the example reaction above, ATP is considered to be an equilibrium mixture of several species, namely ATP4-, HATP3-, H2ATP2-, MgATP2-, MgHATP-, and Mg2ATP. Additional species may also need to be considered if other ions (e.g. Ca2+) that bind ATP are present. Similar considerations apply to ADP and to inorganic phosphate (Pi). When writing biochemical reactions, it is not necessary to attach charges to the biochemical reactants or to include ions such as H+ and Mg2+ in the equation. The reaction is written in the direction specified by the EC nomenclature system, if applicable, regardless of the physiological direction(s) in which the reaction proceeds. Polymerization reactions involving large polymers whose structure is not explicitly captured should generally be represented as unbalanced reactions in which the monomer is consumed but the polymer remains unchanged, e.g. glycogen + glucose = glycogen. | lld:cellmap |
| http://www.biopax.org/relea... | rdfs:comment | Definition: A conversion interaction in which one or more entities (substrates) undergo covalent changes to become one or more other entities (products). The substrates of biochemical reactions are defined in terms of sums of species. This is convention in biochemistry, and, in principle, all of the EC reactions should be biochemical reactions.
Examples: ATP + H2O = ADP + Pi
Comment: In the example reaction above, ATP is considered to be an equilibrium mixture of several species, namely ATP4-, HATP3-, H2ATP2-, MgATP2-, MgHATP-, and Mg2ATP. Additional species may also need to be considered if other ions (e.g. Ca2+) that bind ATP are present. Similar considerations apply to ADP and to inorganic phosphate (Pi). When writing biochemical reactions, it is not necessary to attach charges to the biochemical reactants or to include ions such as H+ and Mg2+ in the equation. The reaction is written in the direction specified by the EC nomenclature system, if applicable, regardless of the physiological direction(s) in which the reaction proceeds. Polymerization reactions involving large polymers whose structure is not explicitly captured should generally be represented as unbalanced reactions in which the monomer is consumed but the polymer remains unchanged, e.g. glycogen + glucose = glycogen. | lld:imid |
| http://www.biopax.org/relea... | rdfs:comment | Definition: A physical entity whose structure is comprised of other physical entities bound to each other non-covalently, at least one of which is a macromolecule (e.g. protein, DNA, or RNA). Complexes must be stable enough to function as a biological unit; in general, the temporary association of an enzyme with its substrate(s) should not be considered or represented as a complex. A complex is the physical product of an interaction (complexAssembly) and is not itself considered an interaction.
Comment: In general, complexes should not be defined recursively so that smaller complexes exist within larger complexes, i.e. a complex should not be a COMPONENT of another complex (see comments on the COMPONENT property). The boundaries on the size of complexes described by this class are not defined here, although elements of the cell as large and dynamic as, e.g., a mitochondrion would typically not be described using this class (later versions of this ontology may include a cellularComponent class to represent these). The strength of binding and the topology of the components cannot be described currently, but may be included in future versions of the ontology, depending on community need.
Examples: Ribosome, RNA polymerase II. Other examples of this class include complexes of multiple protein monomers and complexes of proteins and small molecules. | lld:biogrid |
| http://www.biopax.org/relea... | rdfs:comment | Definition: A physical entity whose structure is comprised of other physical entities bound to each other non-covalently, at least one of which is a macromolecule (e.g. protein, DNA, or RNA). Complexes must be stable enough to function as a biological unit; in general, the temporary association of an enzyme with its substrate(s) should not be considered or represented as a complex. A complex is the physical product of an interaction (complexAssembly) and is not itself considered an interaction.
Comment: In general, complexes should not be defined recursively so that smaller complexes exist within larger complexes, i.e. a complex should not be a COMPONENT of another complex (see comments on the COMPONENT property). The boundaries on the size of complexes described by this class are not defined here, although elements of the cell as large and dynamic as, e.g., a mitochondrion would typically not be described using this class (later versions of this ontology may include a cellularComponent class to represent these). The strength of binding and the topology of the components cannot be described currently, but may be included in future versions of the ontology, depending on community need.
Examples: Ribosome, RNA polymerase II. Other examples of this class include complexes of multiple protein monomers and complexes of proteins and small molecules. | lld:cellmap |
| http://www.biopax.org/relea... | rdfs:comment | Definition: A physical entity whose structure is comprised of other physical entities bound to each other non-covalently, at least one of which is a macromolecule (e.g. protein, DNA, or RNA). Complexes must be stable enough to function as a biological unit; in general, the temporary association of an enzyme with its substrate(s) should not be considered or represented as a complex. A complex is the physical product of an interaction (complexAssembly) and is not itself considered an interaction.
Comment: In general, complexes should not be defined recursively so that smaller complexes exist within larger complexes, i.e. a complex should not be a COMPONENT of another complex (see comments on the COMPONENT property). The boundaries on the size of complexes described by this class are not defined here, although elements of the cell as large and dynamic as, e.g., a mitochondrion would typically not be described using this class (later versions of this ontology may include a cellularComponent class to represent these). The strength of binding and the topology of the components cannot be described currently, but may be included in future versions of the ontology, depending on community need.
Examples: Ribosome, RNA polymerase II. Other examples of this class include complexes of multiple protein monomers and complexes of proteins and small molecules. | lld:imid |
| http://www.biopax.org/relea... | rdfs:comment | 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 | lld:biogrid |
| http://www.biopax.org/relea... | rdfs:comment | 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 | lld:cellmap |
| http://www.biopax.org/relea... | rdfs:comment | 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 | lld:imid |
| http://www.biopax.org/relea... | rdfs:comment | 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. | lld:biogrid |
| http://www.biopax.org/relea... | rdfs:comment | 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. | lld:cellmap |
| http://www.biopax.org/relea... | rdfs:comment | 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. | lld:imid |
| http://www.biopax.org/relea... | rdfs:comment | 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 never be created. Instead, more specific classes should be used.
Synonyms: thing, object, bioentity. | lld:biogrid |
| http://www.biopax.org/relea... | rdfs:comment | 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 never be created. Instead, more specific classes should be used.
Synonyms: thing, object, bioentity. | lld:cellmap |
| http://www.biopax.org/relea... | rdfs:comment | 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 never be created. Instead, more specific classes should be used.
Synonyms: thing, object, bioentity. | lld:imid |
| http://www.biopax.org/relea... | rdfs:comment | Definition: Confidence that the containing instance actually occurs or exists in vivo, usually a statistical measure. The xref must contain at least on publication that describes the method used to determine the confidence. There is currently no standard way of describing confidence values, so any string is valid for the confidence value. In the future, a controlled vocabulary of accepted confidence values could become available, in which case it will likely be adopted for use here to describe the value.
Examples: The statistical significance of a result, e.g. "p<0.05". | lld:biogrid |
| http://www.biopax.org/relea... | rdfs:comment | Definition: Confidence that the containing instance actually occurs or exists in vivo, usually a statistical measure. The xref must contain at least on publication that describes the method used to determine the confidence. There is currently no standard way of describing confidence values, so any string is valid for the confidence value. In the future, a controlled vocabulary of accepted confidence values could become available, in which case it will likely be adopted for use here to describe the value.
Examples: The statistical significance of a result, e.g. "p<0.05". | lld:cellmap |
| http://www.biopax.org/relea... | rdfs:comment | Definition: Confidence that the containing instance actually occurs or exists in vivo, usually a statistical measure. The xref must contain at least on publication that describes the method used to determine the confidence. There is currently no standard way of describing confidence values, so any string is valid for the confidence value. In the future, a controlled vocabulary of accepted confidence values could become available, in which case it will likely be adopted for use here to describe the value.
Examples: The statistical significance of a result, e.g. "p<0.05". | lld:imid |
| http://www.biopax.org/relea... | rdfs:comment | 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. | lld:biogrid |
| http://www.biopax.org/relea... | rdfs:comment | 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. | lld:cellmap |
| http://www.biopax.org/relea... | rdfs:comment | 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. | lld:imid |
| http://www.biopax.org/relea... | rdfs:comment | Definition: Utility classes are created when simple slots are insufficient to describe an aspect of an entity or to increase compatibility of this ontology with other standards. The utilityClass class is actually a metaclass and is only present to organize the other helper classes under one class hierarchy; instances of utilityClass should never be created. | lld:biogrid |
| http://www.biopax.org/relea... | rdfs:comment | Definition: Utility classes are created when simple slots are insufficient to describe an aspect of an entity or to increase compatibility of this ontology with other standards. The utilityClass class is actually a metaclass and is only present to organize the other helper classes under one class hierarchy; instances of utilityClass should never be created. | lld:cellmap |
| http://www.biopax.org/relea... | rdfs:comment | Definition: Utility classes are created when simple slots are insufficient to describe an aspect of an entity or to increase compatibility of this ontology with other standards. The utilityClass class is actually a metaclass and is only present to organize the other helper classes under one class hierarchy; instances of utilityClass should never be created. | lld:imid |
| http://www.biopax.org/relea... | rdfs:comment | Definition: A set or series of interactions, often forming a network, which biologists have found useful to group together for organizational, historic, biophysical or other reasons.
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 | lld:biogrid |
| http://www.biopax.org/relea... | rdfs:comment | Definition: A set or series of interactions, often forming a network, which biologists have found useful to group together for organizational, historic, biophysical or other reasons.
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 | lld:cellmap |
| http://www.biopax.org/relea... | rdfs:comment | Definition: A set or series of interactions, often forming a network, which biologists have found useful to group together for organizational, historic, biophysical or other reasons.
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 | lld:imid |
| http://www.biopax.org/relea... | rdfs:comment | 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. | lld:biogrid |
| http://www.biopax.org/relea... | rdfs:comment | 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. | lld:cellmap |
| http://www.biopax.org/relea... | rdfs:comment | 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. | lld:imid |
| http://www.biopax.org/relea... | rdfs:comment | 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. | lld:biogrid |
| http://www.biopax.org/relea... | rdfs:comment | 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. | lld:cellmap |
| http://www.biopax.org/relea... | rdfs:comment | 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. | lld:imid |
| http://www.biopax.org/relea... | rdfs:comment | 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. | lld:biogrid |
| http://www.biopax.org/relea... | rdfs:comment | 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. | lld:cellmap |
| http://www.biopax.org/relea... | rdfs:comment | 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. | lld:imid |
| http://www.biopax.org/relea... | rdfs:comment | Definition: A physical entity consisting of a sequence of amino acids; a protein monomer; a single polypeptide chain.
Examples: The epidermal growth factor receptor (EGFR) protein. | lld:biogrid |
| http://www.biopax.org/relea... | rdfs:comment | Definition: A physical entity consisting of a sequence of amino acids; a protein monomer; a single polypeptide chain.
Examples: The epidermal growth factor receptor (EGFR) protein. | lld:cellmap |
| http://www.biopax.org/relea... | rdfs:comment | Definition: A physical entity consisting of a sequence of amino acids; a protein monomer; a single polypeptide chain.
Examples: The epidermal growth factor receptor (EGFR) protein. | lld:imid |
| biopax3:Protein | rdfs:comment | Definition: A physical entity consisting of a sequence of amino acids; a protein monomer; a single polypeptide chain.
Examples: The epidermal growth factor receptor (EGFR) protein. | lld:biopax3 |
| biopax3:Protein | rdfs:comment | Definition: A physical entity consisting of a sequence of amino acids; a protein monomer; a single polypeptide chain.
Examples: The epidermal growth factor receptor (EGFR) protein. | lld:intact |
| biopax3:Protein | rdfs:comment | Definition: A physical entity consisting of a sequence of amino acids; a protein monomer; a single polypeptide chain.
Examples: The epidermal growth factor receptor (EGFR) protein. | lld:mint |
| http://www.biopax.org/relea... | rdfs:comment | Definition: A reference from an instance of a class in this ontology to an object in an external resource.
Comment: Instances of the xref class should never be created and more specific classes should be used instead. | lld:biogrid |
| http://www.biopax.org/relea... | rdfs:comment | Definition: A reference from an instance of a class in this ontology to an object in an external resource.
Comment: Instances of the xref class should never be created and more specific classes should be used instead. | lld:cellmap |
| http://www.biopax.org/relea... | rdfs:comment | Definition: A reference from an instance of a class in this ontology to an object in an external resource.
Comment: Instances of the xref class should never be created and more specific classes should be used instead. | lld:imid |
| http://www.biopax.org/relea... | rdfs:comment | Definition: The form of a physical entity in a particular experiment, as it may be modified for purposes of experimental design.
Examples: A His-tagged protein in a binding assay. A protein can be tagged by multiple tags, so can have more than 1 experimental form type terms | lld:biogrid |
| http://www.biopax.org/relea... | rdfs:comment | Definition: The form of a physical entity in a particular experiment, as it may be modified for purposes of experimental design.
Examples: A His-tagged protein in a binding assay. A protein can be tagged by multiple tags, so can have more than 1 experimental form type terms | lld:cellmap |
| http://www.biopax.org/relea... | rdfs:comment | Definition: The form of a physical entity in a particular experiment, as it may be modified for purposes of experimental design.
Examples: A His-tagged protein in a binding assay. A protein can be tagged by multiple tags, so can have more than 1 experimental form type terms | lld:imid |
| biopax3:ExperimentalForm | rdfs:comment | Definition: The form of a physical entity in a particular experiment, as it may be modified for purposes of experimental design.
Examples: A His-tagged protein in a binding assay. A protein can be tagged by multiple tags, so can have more than 1 experimental form type terms | lld:biopax3 |
| biopax3:ExperimentalForm | rdfs:comment | Definition: The form of a physical entity in a particular experiment, as it may be modified for purposes of experimental design.
Examples: A His-tagged protein in a binding assay. A protein can be tagged by multiple tags, so can have more than 1 experimental form type terms | lld:intact |
| biopax3:ExperimentalForm | rdfs:comment | Definition: The form of a physical entity in a particular experiment, as it may be modified for purposes of experimental design.
Examples: A His-tagged protein in a binding assay. A protein can be tagged by multiple tags, so can have more than 1 experimental form type terms | lld:mint |
| http://www.biopax.org/relea... | rdfs:comment | 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. | lld:biogrid |
| http://www.biopax.org/relea... | rdfs:comment | 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. | lld:cellmap |
| http://www.biopax.org/relea... | rdfs:comment | 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. | lld:imid |
| http://www.biopax.org/relea... | rdfs:comment | Definition: An interaction in which one entity regulates, modifies, or otherwise influences another. Two types of control interactions are defined: activation and inhibition.
Comment: In general, the targets of control processes (i.e. occupants of the CONTROLLED property) should be interactions. Conceptually, physical entities are involved in interactions (or events) and the events should be controlled or modified, not the physical entities themselves. For example, a kinase activating a protein is a frequent event in signaling pathways and is usually represented as an 'activation' arrow from the kinase to the substrate in signaling diagrams. This is an abstraction that can be ambiguous out of context. In BioPAX, this information should be captured as the kinase catalyzing (via an instance of the catalysis class) a reaction in which the substrate is phosphorylated, instead of as a control interaction in which the kinase activates the substrate. Since this class is a superclass for specific types of control, instances of the control class should only be created when none of its subclasses are applicable.
Synonyms: regulation, mediation
Examples: A small molecule that inhibits a pathway by an unknown mechanism controls the pathway. | lld:biogrid |
