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ReconX RDF vocabulary
- This version:
- https://reconx.vital-it.ch/kg/ontology_version/1.0.2
- Revision:
- 1.0.2
- Authors:
- Marco Pagni, https://www.sib.swiss✉
- Download serialization:
- License:
- Visualization:
- Cite as:
- Marco Pagni. ReconX RDF vocabulary. Revision: 1.0.2. Retrieved from: https://reconx.vital-it.ch/kg/ontology_version/1.0.2
Ontology Specification Draft
Abstract
This vocabulary is meant to faciliate the comparison of metabolic neworks from different origins. It replaces and improves a part of the MetaNetX schema.Introduction back to ToC
## Recon4IMD As a contibution to Recon4IMD, a knowledge graph named ReconXKG was created to iteratively annotate the VMH metabolic reconstruction with information about metabolites, reactions, Gene/Protein-complex/Reaction relationships (GPRs) from a range of different resources, including the Virtual Metabolic Human (VMH) database (NUIG-Thiele), human metabolic network reconstructions sourced from MetaNetX (SIB-Pagni), as well as the UniProt and RHEA knowledge bases (SIB-Bridge). The integration of these complementary sources of information is challenged by the different formats, different vocabularies and different conventions used in the different resources. The Resource Description Framework (RDF), a standard for data representation and exchange developed by the World Wide Web Consortium (W3C), and its associated SPARQL query language, was chosen as a technological platform to address this challenge. ## Data flow The figure below summarizes the data flow to build the ReconXKG knowledge graph. The data flow to build the ReconXKG knowledge graph. Some resources are already distributed as RDF (e.g. SwissProt) albeit expressed with their own vocabularies, while others are not (e.g. VMH). The SPARQL update language is used to manipulate the data within the triple store (database).  ## ReconX vocabulary A specific vocabulary named ReconX was designed to define an integration layer built on top of the data from different origins. The figure below presents its core architecture.  The core of ReconX RDF schema is meant to capture metabolic networks, including metabolic models. The upper branch in the diagram represents enzymatic complexes. The lower branch is for biochemical reactions. The boxed arrows contain class names, and the rounded rectangles represent their instances. The blue arrows are the most important properties with their relation cardinalities. The rounded rectangles filled with plain green contain stable and public identifiers. The rounded rectangles filled with gridded green contain hashed identifiers resulting from internal canonicalization steps.ReconX RDF vocabulary: Overview back to ToC
This ontology has the following classes and properties.Classes
- An gene or peptide
- Biochemical reaction
- Chem Xref
- Chemical
- Comp Xref
- Compartimentalized chemical species
- Compartment
- Enzymatic complex
- Enzyme or catalyzer
- Metabolic network
- Part of a biochemical equation (spec+coef)
- Pept Xref
- Reaction equation
Object Properties
- catalyzes
- has biochemical equation part (spec+coef)
- has biochemical reaction
- has biochemical reaction source
- has chemical
- has compartimentalized chemical species
- has compartment
- has enzymatic complex
- has enzymatic complex from source
- has enzymatic complex mapped to UniProt
- has enzymatic complex mapped to VMH
- has enzyme
- has geneid (from VMH)
- has reaction equation
- has reaction equation from source
- has reaction equation mapped to MetaNetx
- has reaction equation mapped to RHEA and decompartimentalized
- has reaction equation mapped to VMH
- has reaction equation mapped to VMH and decompartimentalized
- has subunit
- has VMH prefered indetifier for chem
- has VMH prefered indetifier for comp
- has VMH prefered indetifier for reac
Data Properties
- direction
- has lower flux bound (MNet)
- has lower flux bound (Reac)
- has short name
- has stoichiometry coefficient
- has upper flux bound (MNet)
- has upper flux bound (Reac)
- has version
- is equation flipped
- is from organism
- is MNX equation flipped
- is MNX_dc equation flipped
- is source equation flipped
- is VMH equation flipped
- is VMH_dc equation flipped
Named Individuals
ReconX RDF vocabulary: Description back to ToC
The RDF vocabulary describing concepts defined in ReconX knowledge graphCross-reference for ReconX RDF vocabulary classes, object properties and data properties back to ToC
This section provides details for each class and property defined by ReconX RDF vocabulary.Classes
- An gene or peptide
- Biochemical reaction
- Chem Xref
- Chemical
- Comp Xref
- Compartimentalized chemical species
- Compartment
- Enzymatic complex
- Enzyme or catalyzer
- Metabolic network
- Part of a biochemical equation (spec+coef)
- Pept Xref
- Reaction equation
An gene or peptidec back to ToC or Class ToC
IRI: https://reconx.vital-it.ch/kg/Pept
An instance of this class can be shared by different MNet
- is in domain of
- has short name dp
- is in range of
- has subunit op
Biochemical reactionc back to ToC or Class ToC
IRI: https://reconx.vital-it.ch/kg/Reac
An instances of this class is unique to a MNet
- is in domain of
- has biochemical reaction source op, has lower flux bound (Reac) dp, has reaction equation op, has short name dp, has upper flux bound (Reac) dp, is MNX equation flipped dp, is MNX_dc equation flipped dp, is VMH equation flipped dp, is VMH_dc equation flipped dp, is equation flipped dp, is source equation flipped dp
- is in range of
- catalyzes op, has biochemical reaction op
Chem Xrefc back to ToC or Class ToC
IRI: https://rdf.metanetx.org/schema/ChemXref
- is equivalent to
- Chemical c
Chemicalc back to ToC or Class ToC
IRI: https://reconx.vital-it.ch/kg/Chem
Identifier of a chemical compound in an external resource . A variety of identifiers are expected here. Instances of this class can be shared among different MNet
- is in domain of
- has short name dp
- is in range of
- has chemical op
Comp Xrefc back to ToC or Class ToC
IRI: https://rdf.metanetx.org/schema/CompXref
- is equivalent to
- Compartment c
Compartimentalized chemical speciesc back to ToC or Class ToC
IRI: https://reconx.vital-it.ch/kg/Spec
A compartimentalized chemical species. A row of the stoichiometric matrix. Instances of this class can be shared among different MNet
- is in domain of
- has chemical op, has compartment op, has short name dp
- is in range of
- has compartimentalized chemical species op
Compartmentc back to ToC or Class ToC
IRI: https://reconx.vital-it.ch/kg/Comp
Identifier of a sub-cellular compartment in an external resource . A variety of identifiers are expected here. Instances of this class can be shared among different MNet
- is in domain of
- has short name dp
- is in range of
- has compartment op
Enzymatic complexc back to ToC or Class ToC
IRI: https://reconx.vital-it.ch/kg/Cplx
An instance of this class can be shared by different MNet
- is in domain of
- has short name dp, has subunit op
- is in range of
- has enzymatic complex op
Enzyme or catalyzerc back to ToC or Class ToC
IRI: https://reconx.vital-it.ch/kg/Enzy
An instances of this class is unique to a MNet
- is in domain of
- catalyzes op, direction dp, has enzymatic complex op, has short name dp
- is in range of
- has enzyme op
Metabolic networkc back to ToC or Class ToC
IRI: https://reconx.vital-it.ch/kg/MNet
An identifier for a metabolic network (MNet). The purpose of the reconx vocabulary is to represent the content multiple MNet. An instance of this class is unique to a MNet.
- is in domain of
- has biochemical reaction op, has enzyme op, has lower flux bound (MNet) dp, has short name dp, has upper flux bound (MNet) dp, has version dp, is from organism dp
Part of a biochemical equation (spec+coef)c back to ToC or Class ToC
IRI: https://reconx.vital-it.ch/kg/Part
An instances of this class can be by different MNet
- is in domain of
- has compartimentalized chemical species op, has stoichiometry coefficient dp
- is in range of
- has biochemical equation part (spec+coef) op
Pept Xrefc back to ToC or Class ToC
IRI: https://rdf.metanetx.org/schema/PeptXref
- is equivalent to
- An gene or peptide c
Reaction equationc back to ToC or Class ToC
IRI: https://reconx.vital-it.ch/kg/Equa
An instances of this class can be shared by different MNet
- is in domain of
- has biochemical equation part (spec+coef) op, has short name dp
- is in range of
- has reaction equation op
Object Properties
- catalyzes
- has biochemical equation part (spec+coef)
- has biochemical reaction
- has biochemical reaction source
- has chemical
- has compartimentalized chemical species
- has compartment
- has enzymatic complex
- has enzymatic complex from source
- has enzymatic complex mapped to UniProt
- has enzymatic complex mapped to VMH
- has enzyme
- has geneid (from VMH)
- has reaction equation
- has reaction equation from source
- has reaction equation mapped to MetaNetx
- has reaction equation mapped to RHEA and decompartimentalized
- has reaction equation mapped to VMH
- has reaction equation mapped to VMH and decompartimentalized
- has subunit
- has VMH prefered indetifier for chem
- has VMH prefered indetifier for comp
- has VMH prefered indetifier for reac
catalyzesop back to ToC or Object Property ToC
IRI: https://reconx.vital-it.ch/kg/cata
Not all reactions have a known catalyzer
- has domain
- Enzyme or catalyzer c
- has range
- Biochemical reaction c
has biochemical equation part (spec+coef)op back to ToC or Object Property ToC
IRI: https://reconx.vital-it.ch/kg/part
- has domain
- Reaction equation c
- has range
- Part of a biochemical equation (spec+coef) c
has biochemical reactionop back to ToC or Object Property ToC
IRI: https://reconx.vital-it.ch/kg/reac
Transport reactions are included
- has domain
- Metabolic network c
- has range
- Biochemical reaction c
has biochemical reaction sourceop back to ToC or Object Property ToC
IRI: https://reconx.vital-it.ch/kg/reacSource
Point to the original reaction identifier(s)
- has domain
- Biochemical reaction c
- has range
- Reac Xref c
has chemicalop back to ToC or Object Property ToC
IRI: https://reconx.vital-it.ch/kg/chem
- has domain
- Compartimentalized chemical species c
- has range
- Chemical c
has compartimentalized chemical speciesop back to ToC or Object Property ToC
IRI: https://reconx.vital-it.ch/kg/spec
- has domain
- Part of a biochemical equation (spec+coef) c
- has range
- Compartimentalized chemical species c
has compartmentop back to ToC or Object Property ToC
IRI: https://reconx.vital-it.ch/kg/comp
Compartimentalization is enforced in ReconXKG
- has domain
- Compartimentalized chemical species c
- has range
- Compartment c
has enzymatic complexop back to ToC or Object Property ToC
IRI: https://reconx.vital-it.ch/kg/cplx
See detailed comments in sub-properties
- has sub-properties
- has enzymatic complex from source op, has enzymatic complex mapped to UniProt op, has enzymatic complex mapped to VMH op
- has domain
- Enzyme or catalyzer c
- has range
- Enzymatic complex c
has enzymatic complex from sourceop back to ToC or Object Property ToC
IRI: https://reconx.vital-it.ch/kg/cplxSource
Has ezymatic complex description with identifiers as given originally. This is the least transformed version of complex description.
- has super-properties
- has enzymatic complex op
has enzymatic complex mapped to UniProtop back to ToC or Object Property ToC
IRI: https://reconx.vital-it.ch/kg/cplxUP
Has enzymatic complex description made of UniProt protein identifiers, whenether possible. Mapping between UniProt entries and NCBI geneid is often but not always one-to-one.
- has super-properties
- has enzymatic complex op
has enzymatic complex mapped to VMHop back to ToC or Object Property ToC
IRI: https://reconx.vital-it.ch/kg/cplxVMH
Has enzymatic complex description made of NCBI geneid identifiers, whenether possible. Mapping between UniProt protein identifiers and NCBI geneid is often but not always one-to-one.
- has super-properties
- has enzymatic complex op
has enzymeop back to ToC or Object Property ToC
IRI: https://reconx.vital-it.ch/kg/enzy
- has domain
- Metabolic network c
- has range
- Enzyme or catalyzer c
has geneid (from VMH)op back to ToC or Object Property ToC
IRI: https://reconx.vital-it.ch/kg/geneid
has reaction equationop back to ToC or Object Property ToC
IRI: https://reconx.vital-it.ch/kg/equa
See detailed comments in sub-properties
- has sub-properties
- has reaction equation from source op, has reaction equation mapped to MetaNetx op, has reaction equation mapped to RHEA and decompartimentalized op, has reaction equation mapped to VMH op, has reaction equation mapped to VMH and decompartimentalized op
- has domain
- Biochemical reaction c
- has range
- Reaction equation c
has reaction equation from sourceop back to ToC or Object Property ToC
IRI: https://reconx.vital-it.ch/kg/equaSource
Has reaction equation with identifiers as given originally. This is the least transformed version of equations.
- has super-properties
- has reaction equation op
has reaction equation mapped to MetaNetxop back to ToC or Object Property ToC
IRI: https://reconx.vital-it.ch/kg/equaMNX
Has reaction equation terms mapped to MetaNetx reference identifiers for chemicals and compartments. For chemicals these identifiers are often the ChEBI identifiers used by RHEA. For compartments these identifiers are often GO terms. Transported protons are converted into mnx:PMF. Balance protons are removed.
- has super-properties
- has reaction equation op
has reaction equation mapped to RHEA and decompartimentalizedop back to ToC or Object Property ToC
IRI: https://reconx.vital-it.ch/kg/equaMNX_dc
For chemicals the mapping is the same as for reconx:equaMNX. But, the compartment identifiers are canonicalized using mnx:MNXD1 and mnx:MNXD2. This permits the comparison of MNets ignoring the original compartments. The original directions of transport reactions are lost. The resulting metabolic networks cannot be simulated anymore.
- has super-properties
- has reaction equation op
has reaction equation mapped to VMHop back to ToC or Object Property ToC
IRI: https://reconx.vital-it.ch/kg/equaVMH
Has reaction equation mapped to VMH identifiers for chem and BiGG identifiers for comp, if available. Otherwise MetaNetX reference identifiers are used. Transported protons are converted into mnx:PMF. Balance protons are removed.
- has super-properties
- has reaction equation op
has reaction equation mapped to VMH and decompartimentalizedop back to ToC or Object Property ToC
IRI: https://reconx.vital-it.ch/kg/equaVMH_dc
For chemicals the mapping is the same as for reconx:equaVMH. But, the compartment identifiers are canonicalized using mnx:MNXD1 and mnx:MNXD2. This permits the comparison of MNets ignoring the original compartments. The original directions of transport reactions are lost. The resulting metabolic networks cannot be simulated anymore.
- has super-properties
- has reaction equation op
has subunitop back to ToC or Object Property ToC
IRI: https://reconx.vital-it.ch/kg/subu
Enzymatic complexes are made of one or several subunits. The number of occurences of each sub-unit per complex is not encoded here.
- has domain
- Enzymatic complex c
- has range
- An gene or peptide c
has VMH prefered indetifier for chemop back to ToC or Object Property ToC
IRI: https://reconx.vital-it.ch/kg/chemReferVMH
Similar to mnx:chemRefer but for the VMH namespace
has VMH prefered indetifier for compop back to ToC or Object Property ToC
IRI: https://reconx.vital-it.ch/kg/compReferVMH
Similar to mnx:compRefer but for the VMH namespace
has VMH prefered indetifier for reacop back to ToC or Object Property ToC
IRI: https://reconx.vital-it.ch/kg/reacReferVMH
Similar to mnx:reacRefer but for the VMH namespace
Data Properties
- direction
- has lower flux bound (MNet)
- has lower flux bound (Reac)
- has short name
- has stoichiometry coefficient
- has upper flux bound (MNet)
- has upper flux bound (Reac)
- has version
- is equation flipped
- is from organism
- is MNX equation flipped
- is MNX_dc equation flipped
- is source equation flipped
- is VMH equation flipped
- is VMH_dc equation flipped
directiondp back to ToC or Data Property ToC
IRI: https://reconx.vital-it.ch/kg/dir
Property inherited from MetaNetX
- has domain
- Enzyme or catalyzer c
- has range
- string
has lower flux bound (MNet)dp back to ToC or Data Property ToC
IRI: https://reconx.vital-it.ch/kg/LB
Default global lower bound of this MNet
- has domain
- Metabolic network c
- has range
- decimal
has lower flux bound (Reac)dp back to ToC or Data Property ToC
IRI: https://reconx.vital-it.ch/kg/lb
Overwrite reconx:LB value
- has domain
- Biochemical reaction c
- has range
- decimal
has short namedp back to ToC or Data Property ToC
IRI: https://reconx.vital-it.ch/kg/label
- has domain
- Chemical c or Compartment c or Enzymatic complex c or Enzyme or catalyzer c or Reaction equation c or Metabolic network c or An gene or peptide c or Biochemical reaction c or Compartimentalized chemical species c
- has range
- string
- is also defined as
- annotation property
has stoichiometry coefficientdp back to ToC or Data Property ToC
IRI: https://reconx.vital-it.ch/kg/coef
- has domain
- Part of a biochemical equation (spec+coef) c
- has range
- decimal
has upper flux bound (MNet)dp back to ToC or Data Property ToC
IRI: https://reconx.vital-it.ch/kg/UB
Default global higher bound of this MNet
- has domain
- Metabolic network c
- has range
- decimal
has upper flux bound (Reac)dp back to ToC or Data Property ToC
IRI: https://reconx.vital-it.ch/kg/ub
Overwrite reconx:UB value
- has domain
- Biochemical reaction c
- has range
- decimal
has versiondp back to ToC or Data Property ToC
IRI: https://reconx.vital-it.ch/kg/modelVersion
Would be nice to have
- has domain
- Metabolic network c
- has range
- string
is equation flippeddp back to ToC or Data Property ToC
IRI: https://reconx.vital-it.ch/kg/flip
To achieve a canonical representation of biochemical equations, one must chose which term is put on the left and which term to put on the right sides, independantly from the original direction. In about half of the cases the sides must be flipped. The primary purpose of this flip boolean values is to permit to retrieve the original sides, which explain why this property is attached the reaction and not to the equation. This is especially relevant to produce the stoichiometric matrix of a MNet.
- has sub-properties
- is MNX equation flipped dp, is MNX_dc equation flipped dp, is VMH equation flipped dp, is VMH_dc equation flipped dp, is source equation flipped dp
- has domain
- Biochemical reaction c
- has range
- boolean
is from organismdp back to ToC or Data Property ToC
IRI: https://reconx.vital-it.ch/kg/organism
Would be nice to have
- has domain
- Metabolic network c
- has range
- string
is MNX equation flippeddp back to ToC or Data Property ToC
IRI: https://reconx.vital-it.ch/kg/flipMNX
See super-property comment
- has super-properties
- is equation flipped dp
- has domain
- Biochemical reaction c
- has range
- boolean
is MNX_dc equation flippeddp back to ToC or Data Property ToC
IRI: https://reconx.vital-it.ch/kg/flipMNX_dc
See super-property comment
- has super-properties
- is equation flipped dp
- has domain
- Biochemical reaction c
- has range
- boolean
is source equation flippeddp back to ToC or Data Property ToC
IRI: https://reconx.vital-it.ch/kg/flipSource
See super-property comment
- has super-properties
- is equation flipped dp
- has domain
- Biochemical reaction c
- has range
- boolean
is VMH equation flippeddp back to ToC or Data Property ToC
IRI: https://reconx.vital-it.ch/kg/flipVMH
See super-property comment
- has super-properties
- is equation flipped dp
- has domain
- Biochemical reaction c
- has range
- boolean
is VMH_dc equation flippeddp back to ToC or Data Property ToC
IRI: https://reconx.vital-it.ch/kg/flipVMH_dc
See super-property comment
- has super-properties
- is equation flipped dp
- has domain
- Biochemical reaction c
- has range
- boolean
Named Individuals
Marco Pagnini back to ToC or Named Individual ToC
IRI: http://orcid.org/0000-0001-9292-9463
- belongs to
- / Person c
- Person c
- has facts
- affiliation ap https://www.sib.swiss ep
- email ap mailto:marco.pagni@sib.swiss ep
- identifier ap Marco Pagni ni
- name ap "Marco Pagni"
Legend back to ToC
c: Classes
op: Object Properties
dp: Data Properties
ni: Named Individuals
ep: External Properties
op: Object Properties
dp: Data Properties
ni: Named Individuals
ep: External Properties
References back to ToC
Add your references here. It is recommended to have them as a list.Acknowledgments back to ToC
The authors would like to thank Silvio Peroni for developing LODE, a Live OWL Documentation Environment, which is used for representing the Cross Referencing Section of this document and Daniel Garijo for developing Widoco, the program used to create the template used in this documentation.