MetaNetX Ontology
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MetaNetX Ontology

Release: 2017-11-13

Modified on: 2024-05-14
This version:
http://purl.org/net/mnx/1.0
Authors:
Marco Pagni, https://www.sib.swiss✉
Sébastien Moretti, https://www.sib.swiss✉
Download serialization:
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License:
https://creativecommons.org/licenses/by/4.0/
Visualization:
Visualize with WebVowl
Cite as:
MetaNetX/MNXref: unified namespace for metabolites and biochemical reactions in the context of metabolic models Sébastien Moretti, Van Du T Tran, Florence Mehl, Mark Ibberson, Marco Pagni Nucleic Acids Research (2021), 49(D1):D570-D574
Provenance of this page
Ontology Specification Draft

Abstract

MetaNetX/MNXref is a reconciliation of metabolites and biochemical reactions, providing cross-links between major public biochemistry and Genome-Scale Metabolic Network (GSMN) databases.

Introduction back to ToC

GSMN reconstruction is one of the foundations of Systems Biology. The development of such reconstruction involves the integration of knowledge about reactions and metabolites from the scientific literature, public databases and previously published GSMNs. Historically, many GSMNs were formulated using metabolites represented as "symbols", i.e. without explicit reference to a molecular structure. The initial motivation for creating this resource ten years ago was to add molecular structures to existing GSMNs. More generally, the goal was to establish cross-links between symbols in GSMNs published by different groups and the molecules found in the major biochemical databases. This problem is trivial as long as one-to-one mappings can be established between the different resources, but this is not always the case. Merging metabolites in a metabolic network may lead to the merging of reactions, possibly altering the model properties, and hence the predictions that could be made using it.
drawing

MetaNetX Ontology: Overview back to ToC

This ontology has the following classes and properties.

Classes

Object Properties

Data Properties

Named Individuals

MetaNetX Ontology: Description back to ToC

MetaNetX/MNXref: unified namespace for metabolites and biochemical reactions in the context of metabolic models

Cross-reference for MetaNetX Ontology classes, object properties and data properties back to ToC

This section provides details for each class and property defined by MetaNetX Ontology.

Classes

C A T Ac back to ToC or Class ToC

IRI: https://rdf.metanetx.org/schema/CATA

The type of a helper class to describe one or several protein complexes
is in domain of
cplx op, pept op
is in range of
cata op

G P Rc back to ToC or Class ToC

IRI: https://rdf.metanetx.org/schema/GPR

The type for Gene-Protein-Reaction, i.e. this is a helper class to associate a reaction (mnx:REAC) with zero, one or more catalyzers (mnx:CATA)
is in domain of
cata op, reac op
is in range of
gpr op

MetaNetX compartment, i.e. a set of sub-cellular compartmentsc back to ToC or Class ToC

IRI: https://rdf.metanetx.org/schema/COMP

The type of all sub-cellular compartments, including specific and generic compartments
is in domain of
comp In M N Xref dp, comp Refer op, comp Replaced By op, comp Source op, comp Xref op, is Generic Comp dp
is in range of
comp Replaced By op
has members
mnx:BOUNDARY ni

MetaNetX metabolite classc back to ToC or Class ToC

IRI: https://rdf.metanetx.org/schema/CHEM

A MetaNetX metabolite is defined as a collection of chemical entity identifiers gathered from external resources and mapped together because they refer to the same underlying compound.
is in domain of
charge dp, chem In M N Xref dp, chem Refer op, chem Replaced By op, chem Source op, contains chem member op, formula dp, has stereo child op, inchi dp, inchikey dp, mass dp, smiles dp
is in range of
chem Replaced By op, has stereo child op
has members
mnx:BIOMASS ni, mnx:HYDROXYDE ni, mnx:PMF ni, mnx:PROTON ni, mnx:WATER ni

MetaNetX reaction, i.e. a set of chemical reactionc back to ToC or Class ToC

IRI: https://rdf.metanetx.org/schema/REAC

The type of all reactions, as defined in MNXref (with generic compartments) and in MetaNetX models (with specific compartments)
is in domain of
classification dp, has reference chem op, is Balanced dp, is Transport dp, left op, mnxr op, reac In M N Xref dp, reac Isom op, reac Replaced By op, reac Source op, reac Xref op, right op, side op
is in range of
mnxr op, reac op, reac Isom op, reac Replaced By op

mnx:EMPTY c back to ToC or Class ToC

IRI: https://rdf.metanetx.org/schema/EMPTY

A symbol for reaction which both sides are empty, and that should not appear in a model. Typically, acid-base reactions become empty as the reconciliation merges different protonation states of a given metabolite.

mnx:MNXR01c back to ToC or Class ToC

IRI: https://rdf.metanetx.org/schema/MNXR01

An artificial reaction that exchange proton for PMF (a very trumpian deal)

P A R Tc back to ToC or Class ToC

IRI: https://rdf.metanetx.org/schema/PART

The type for a helper class, consisting of a compartmentalized chemical species (mnx:CHEM and mnx:COMP) associated with a particular stoichiometric coefficient
is in range of
left op, right op, side op

P E P Tc back to ToC or Class ToC

IRI: https://rdf.metanetx.org/schema/PEPT

The type for a gene or a protein that appears in MetaNetX models
is in domain of
gene Name op, pept Xref op
is in range of
pept op, subu op
has members
mnx:SPONTANEOUS ni

Object Properties

cataop back to ToC or Object Property ToC

IRI: https://rdf.metanetx.org/schema/cata

contains the following catalyzers (enzymatic complex(s) and flux constraints)
has domain
G P R c
has range
C A T A c

chem Referop back to ToC or Object Property ToC

IRI: https://rdf.metanetx.org/schema/chemRefer

A predicate to design the public IRI that best represents a MNXref metabolite
has domain
MetaNetX metabolite class c
has range
Resource c

chem Replaced Byop back to ToC or Object Property ToC

IRI: https://rdf.metanetx.org/schema/chemReplacedBy

indicate how to replace a deprecated entity
has domain
MetaNetX metabolite class c
has range
MetaNetX metabolite class c

chem Sourceop back to ToC or Object Property ToC

IRI: https://rdf.metanetx.org/schema/chemSource

A predicate to design the public IRI that best represents a MNXref metabolite
has domain
MetaNetX metabolite class c
has range
Resource c

comp Referop back to ToC or Object Property ToC

IRI: https://rdf.metanetx.org/schema/compRefer

A predicate to design the public IRI that best represents a MNXref compartment
has domain
MetaNetX compartment, i.e. a set of sub-cellular compartments c
has range
Resource c

comp Replaced Byop back to ToC or Object Property ToC

IRI: https://rdf.metanetx.org/schema/compReplacedBy

indicate how to replace a deprecated entity
has domain
MetaNetX compartment, i.e. a set of sub-cellular compartments c
has range
MetaNetX compartment, i.e. a set of sub-cellular compartments c

comp Sourceop back to ToC or Object Property ToC

IRI: https://rdf.metanetx.org/schema/compSource

A predicate to design the public IRI that best represents a MNXref compartment
has domain
MetaNetX compartment, i.e. a set of sub-cellular compartments c
has range
Resource c

comp Xrefop back to ToC or Object Property ToC

IRI: https://rdf.metanetx.org/schema/compXref

A predicate to list all public IRIs that are included in a MNXref compartment
has domain
MetaNetX compartment, i.e. a set of sub-cellular compartments c
has range
Resource c

contains chem memberop back to ToC or Object Property ToC

IRI: https://rdf.metanetx.org/schema/chemXref

A predicate to list all public IRIs that are included in a MNXref metabolite
has domain
MetaNetX metabolite class c
has range
Resource c

cplxop back to ToC or Object Property ToC

IRI: https://rdf.metanetx.org/schema/cplx

requires the full list of genes or proteins to be functional
has domain
C A T A c
has range
C P L X c

gene Nameop back to ToC or Object Property ToC

IRI: https://rdf.metanetx.org/schema/geneName

A predicate to list all gene name that correspond to a gene or a protein
has domain
P E P T c
has range
Resource c

gprop back to ToC or Object Property ToC

IRI: https://rdf.metanetx.org/schema/gpr

A predicate to list GPRs that make the core of any model
has domain
M N E T c
has range
G P R c

has reference chemop back to ToC or Object Property ToC

IRI: https://rdf.metanetx.org/schema/reacRefer

A predicate to design the public IRI that best represents a MNXref reaction
has domain
MetaNetX reaction, i.e. a set of chemical reaction c
has range
Resource c

has stereo childop back to ToC or Object Property ToC

IRI: https://rdf.metanetx.org/schema/chemIsom

has domain
MetaNetX metabolite class c
has range
MetaNetX metabolite class c
is same as
has Isomeric Child ni
is also defined as
named individual

leftop back to ToC or Object Property ToC

IRI: https://rdf.metanetx.org/schema/left

A predicate to specify the parts (mnx:PART) on the left side of a chemical equation (mnx:REAC)
has domain
MetaNetX reaction, i.e. a set of chemical reaction c
has range
P A R T c

mnxrop back to ToC or Object Property ToC

IRI: https://rdf.metanetx.org/schema/mnxr

belongs to the MNXref reaction
has domain
MetaNetX reaction, i.e. a set of chemical reaction c
has range
MetaNetX reaction, i.e. a set of chemical reaction c

peptop back to ToC or Object Property ToC

IRI: https://rdf.metanetx.org/schema/pept

implies the list of genes or proteins (no logical constraint specified here)
has domain
C A T A c
has range
P E P T c

pept Xrefop back to ToC or Object Property ToC

IRI: https://rdf.metanetx.org/schema/peptXref

A predicate to list all public IRIs that correspond to a gene or a protein
has domain
P E P T c
has range
Resource c

reacop back to ToC or Object Property ToC

IRI: https://rdf.metanetx.org/schema/reac

contains the following catalyzers (mnx:CATA)
has domain
G P R c
has range
MetaNetX reaction, i.e. a set of chemical reaction c

reac Isomop back to ToC or Object Property ToC

IRI: https://rdf.metanetx.org/schema/reacIsom

has domain
MetaNetX reaction, i.e. a set of chemical reaction c
has range
MetaNetX reaction, i.e. a set of chemical reaction c
is also defined as
annotation property

reac Replaced Byop back to ToC or Object Property ToC

IRI: https://rdf.metanetx.org/schema/reacReplacedBy

indicate how to replace a deprecated entity
has domain
MetaNetX reaction, i.e. a set of chemical reaction c
has range
MetaNetX reaction, i.e. a set of chemical reaction c

reac Sourceop back to ToC or Object Property ToC

IRI: https://rdf.metanetx.org/schema/reacSource

A predicate to design the public IRI that best represents a MNXref reaction
has domain
MetaNetX reaction, i.e. a set of chemical reaction c
has range
Resource c

reac Xrefop back to ToC or Object Property ToC

IRI: https://rdf.metanetx.org/schema/reacXref

A predicate to list all public IRIs that are included in a MNXref reaction
has domain
MetaNetX reaction, i.e. a set of chemical reaction c
has range
Resource c

rightop back to ToC or Object Property ToC

IRI: https://rdf.metanetx.org/schema/right

A predicate to specify the parts (mnx:PART) on the right side of a chemical equation (mnx:REAC)
has domain
MetaNetX reaction, i.e. a set of chemical reaction c
has range
P A R T c

sideop back to ToC or Object Property ToC

IRI: https://rdf.metanetx.org/schema/side

A predicate to specify the parts (mnx:PART) on the both sides of a chemical equation (mnx:REAC)
has domain
MetaNetX reaction, i.e. a set of chemical reaction c
has range
P A R T c

subuop back to ToC or Object Property ToC

IRI: https://rdf.metanetx.org/schema/subu

A predicate to enumerate sub-units (mnx:PEPT) that make of an enzyme or transporter (mnx:CPLX)
has domain
C P L X c
has range
P E P T c

Data Properties

can Growdp back to ToC or Data Property ToC

IRI: https://rdf.metanetx.org/schema/canGrow

is the model able to simulate growth
has domain
M N E T c
has range
string

chargedp back to ToC or Data Property ToC

IRI: https://rdf.metanetx.org/schema/charge

has domain
MetaNetX metabolite class c
has range
integer

chem Countdp back to ToC or Data Property ToC

IRI: https://rdf.metanetx.org/schema/chemCount

Number of chemicals
has domain
M N E T c
has range
integer

chem In M N Xrefdp back to ToC or Data Property ToC

IRI: https://rdf.metanetx.org/schema/chemInMNXref

identifies metabolites in MNXref
has domain
MetaNetX metabolite class c
has range
boolean

classificationdp back to ToC or Data Property ToC

IRI: https://rdf.metanetx.org/schema/classification

has domain
MetaNetX reaction, i.e. a set of chemical reaction c
has range
string

comp Countdp back to ToC or Data Property ToC

IRI: https://rdf.metanetx.org/schema/compCount

Number of compartments
has domain
M N E T c
has range
integer

comp In M N Xrefdp back to ToC or Data Property ToC

IRI: https://rdf.metanetx.org/schema/compInMNXref

identifies (generic) compartments in MNXref
has domain
MetaNetX compartment, i.e. a set of sub-cellular compartments c
has range
boolean

formuladp back to ToC or Data Property ToC

IRI: https://rdf.metanetx.org/schema/formula

has domain
MetaNetX metabolite class c
has range
string

inchidp back to ToC or Data Property ToC

IRI: https://rdf.metanetx.org/schema/inchi

has domain
MetaNetX metabolite class c
has range
string

inchikeydp back to ToC or Data Property ToC

IRI: https://rdf.metanetx.org/schema/inchikey

has domain
MetaNetX metabolite class c
has range
string

is Balanceddp back to ToC or Data Property ToC

IRI: https://rdf.metanetx.org/schema/isBalanced

Is the reaction balanced?
has domain
MetaNetX reaction, i.e. a set of chemical reaction c
has range
boolean

is Generic Compdp back to ToC or Data Property ToC

IRI: https://rdf.metanetx.org/schema/isGenericComp

tags generic/placeholder compartment
has domain
MetaNetX compartment, i.e. a set of sub-cellular compartments c
has range
boolean

is Transportdp back to ToC or Data Property ToC

IRI: https://rdf.metanetx.org/schema/isTransport

has domain
MetaNetX reaction, i.e. a set of chemical reaction c
has range
boolean

lineagedp back to ToC or Data Property ToC

IRI: https://rdf.metanetx.org/schema/lineage

Organism lineage
has domain
M N E T c
has range
string

massdp back to ToC or Data Property ToC

IRI: https://rdf.metanetx.org/schema/mass

has domain
MetaNetX metabolite class c
has range
decimal

organismdp back to ToC or Data Property ToC

IRI: https://rdf.metanetx.org/schema/organism

Organism name
has domain
M N E T c
has range
string

pept Countdp back to ToC or Data Property ToC

IRI: https://rdf.metanetx.org/schema/peptCount

Number of genes/peptides
has domain
M N E T c
has range
integer

pmiddp back to ToC or Data Property ToC

IRI: https://rdf.metanetx.org/schema/pmid

Cites a PubMed identifier
has range
M N E T c

reac Countdp back to ToC or Data Property ToC

IRI: https://rdf.metanetx.org/schema/reacCount

Number of reactions
has domain
M N E T c
has range
integer

reac In M N Xrefdp back to ToC or Data Property ToC

IRI: https://rdf.metanetx.org/schema/reacInMNXref

identifies reactions in MNXref
has domain
MetaNetX reaction, i.e. a set of chemical reaction c
has range
boolean

smilesdp back to ToC or Data Property ToC

IRI: https://rdf.metanetx.org/schema/smiles

has domain
MetaNetX metabolite class c
has range
string

spec Countdp back to ToC or Data Property ToC

IRI: https://rdf.metanetx.org/schema/specCount

Number of compartmentalized chemical species
has domain
M N E T c
has range
integer

taxiddp back to ToC or Data Property ToC

IRI: https://rdf.metanetx.org/schema/taxid

indicates an NCBI Taxid
has range
M N E T c

Named Individuals

has stereo childni back to ToC or Named Individual ToC

IRI: https://rdf.metanetx.org/schema/chemIsom

is same as
has Isomeric Child ni
has facts
same As ep has Isomeric Child ni
is also defined as
object property

Marco Pagnini back to ToC or Named Individual ToC

IRI: https://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
name ap "Marco Pagni"

mnx:BIOMASSni back to ToC or Named Individual ToC

IRI: https://rdf.metanetx.org/schema/BIOMASS

A symbol to represent biomass
belongs to
MetaNetX metabolite class c

mnx:BOUNDARYni back to ToC or Named Individual ToC

IRI: https://rdf.metanetx.org/schema/BOUNDARY

A symbol to represent a model boundary and that appears in so-called external reactions
belongs to
MetaNetX compartment, i.e. a set of sub-cellular compartments c

mnx:HYDROXYDEni back to ToC or Named Individual ToC

IRI: https://rdf.metanetx.org/schema/HYDROXYDE

A symbol to represent hydroxide (OH-). In principle, it can be substituted for mnx:PROTON or mnx:PMF on the other side of a chemical equation, hence it should not appear in MetaNetX models
belongs to
MetaNetX metabolite class c

mnx:PMFni back to ToC or Named Individual ToC

IRI: https://rdf.metanetx.org/schema/PMF

A symbol to represent the proton motive force (PMF). PMF is often confounded with (balance) proton. MetaNetX attempts to distinguish them systematically
belongs to
MetaNetX metabolite class c

mnx:PROTONni back to ToC or Named Individual ToC

IRI: https://rdf.metanetx.org/schema/PROTON

A symbol to represent the proton (H+) that is used to balance chemical equations
belongs to
MetaNetX metabolite class c

mnx:SPONTANEOUSni back to ToC or Named Individual ToC

IRI: https://rdf.metanetx.org/schema/SPONTANEOUS

A symbol to tag reactions that occur spontaneously
belongs to
P E P T c

mnx:WATERni back to ToC or Named Individual ToC

IRI: https://rdf.metanetx.org/schema/WATER

A symbol to represent water
belongs to
MetaNetX metabolite class c

Sébastien Morettini back to ToC or Named Individual ToC

IRI: https://orcid.org/0000-0003-3947-488X

belongs to
Person c
Person c
has facts
affiliation ap https://www.sib.swiss ep
email ap mailto:Sebastien.Moretti@sib.swiss ep
name ap "Sébastien Moretti"

Legend back to ToC

c: Classes
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.