- met4j-io
cd met4j-io;
mvn clean install;Put this in the pom.xml file of your project:
<dependencies>
...
<dependency>
<groupId>fr.inrae.toulouse.metexplore</groupId>
<artifactId>met4j-io</artifactId>
<version>1.0.1</version>
</dependency>
...
</dependencies>Adapt the version number if needed.
Examples can be found in https://forgemia.inra.fr/metexplore/tutorialmet4j in the package fr.inrae.toulouse.metexplore.tutorialmet4j.met4j_io.
JsbmlReader reader = new JsbmlReader(pathOfYourSbmlFile);
BioNetwork network = reader.read();The read method of the JsbmlReader imports all the metabolic entities and data in a BioNetwork instance. It also optimises the reading of a SBML file by using all the known plugins used to create and describe the metabolic entities.
- FBC : FBCParser
- groups for pathways :GroupPathwayParser
- Miriam annotation : AnnotationParser
- Html notes : NotesParser
If you want to enable only some plugins, you have to specify them. For instance, here, only FBC and GroupPathway plugins will be used.
ArrayList<PackageParser> pkgs = new ArrayList<>(Arrays.asList(new FBCParser(), new GroupPathwayParser()));
BioNetwork network = reader.read(pkgs);Without any package, the read method imports:
- Id and name of the BioNetwork
- Unit definitions for parameters (e.g. flux parameters). Can be retrieved with the method getUnitDefinitions of the NetworkAttributes class.
- Compartments
- Metabolites
- Reactions and reactants
- SBO terms (can be retrieved with the method getSboTerm of the GenericAttributes class)
- Flux bounds in the kinetic law tag if the FBC plugin is not activated
Example:
<sbml xmlns="http://www.sbml.org/sbml/level2" level="2" version="1" xmlns:html="http://www.w3.org/1999/xhtml">
<model id="Ec_iAF1260" name="Ec_iAF1260">
<listOfUnitDefinitions>
<unitDefinition id="mmol_per_gDW_per_hr">
<listOfUnits>
<unit kind="mole" scale="-3"/>
<unit kind="gram" exponent="-1"/>
<unit kind="second" multiplier=".00027777" exponent="-1"/>
</listOfUnits>
</unitDefinition>
</listOfUnitDefinitions>
...
<reaction id="R_12DGR120tipp" name="R_1_2_diacylglycerol_transport_via_flipping__periplasm_to_cytoplasm__n_C120_" reversible="false">
...
<kineticLaw>
<math xmlns="http://www.w3.org/1998/Math/MathML">
<ci> FLUX_VALUE </ci>
</math>
<listOfParameters>
<parameter id="LOWER_BOUND" value="0.000000" units="mmol_per_gDW_per_hr"/>
<parameter id="UPPER_BOUND" value="999999.000000" units="mmol_per_gDW_per_hr"/>
</listOfParameters>
</kineticLaw>
...
</reaction>Warning Data in the listOfModifiers tag is not imported by the met4j-io sbml reader !
This plugin is used to read charge, chemical formula, flux bounds and FBA objectives. Please read the package documentation for the specifications. The corresponding class in met4j-io is FBCParser.
Example:
<species id="M_glc__D_e" fbc:charge="0" fbc:chemicalFormula="C6H12O6" ... >Example:
<fbc:listOfGeneProducts>
<fbc:geneProduct fbc:id="G_s0001" fbc:label="s0001" fbc:name="s0001" ...>
</fbc:geneProduct>
<fbc:geneProduct fbc:id="G_b0451" fbc:label="b0451" fbc:name="amtB" ...>
</fbc:geneProduct>
</fbc:listOfGeneProducts>
...
<listOfReactions>
<reaction ...>
...
<fbc:geneProductAssociation>
<fbc:or>
<fbc:geneProductRef fbc:geneProduct="G_s0001"/>
<fbc:geneProductRef fbc:geneProduct="G_b0451"/>
</fbc:or>
</fbc:geneProductAssociation>
...
</reaction>
</listOfReactions>For each gene-reaction association, the path BioReaction-BioEnzyme(s)-BioProtein(s) is automatically created. For instance, if in your SBML file, you have a reaction R1 with this gene association : (G1) or (G2 and G3), three BioGene and three BioProtein will be created : G1, G2 and G3; and two BioEnzyme will be created : G1 and G2_AND_G3, both associated to the BioReaction R1.
- Flux lower and upper bounds for flux modelling
Example:
<listOfParameters>
<parameter value="-1000" id="cobra_default_lb" sboTerm="SBO:0000626" constant="true" units="mmol_per_gDW_per_hr"/>
<parameter value="1000" id="cobra_default_ub" sboTerm="SBO:0000626" constant="true" units="mmol_per_gDW_per_hr"/>
</listOfParameters>
...
<listOfReactions>
<reaction id="R_O2t" fast="false" reversible="true" name="O2 transport diffusion" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_default_lb">
...
</reaction>
</listOfReactions>To get lower and upper bounds of a reaction in a network, use the methods getLowerBound and getUpperBound of the class ReactionAttributes.
Example:
<fbc:listOfObjectives fbc:activeObjective="obj">
<fbc:objective fbc:id="obj" fbc:type="maximize">
<fbc:listOfFluxObjectives>
<fbc:fluxObjective fbc:reaction="R_BIOMASS_Ecoli_core_w_GAM" fbc:coefficient="1"/>
</fbc:listOfFluxObjectives>
</fbc:objective>
</fbc:listOfObjectives>To get the list of the objectives set for a network, use the method getObjectives of the class NetworkAttributes.
This plugin gets information about the metabolic pathways and the reactions involved in them. Please read the package documentation for specifications.
The corresponding class in met4j-io is GroupPathwayParser.
Example:
...
<groups:listOfGroups>
<groups:group groups:id="g31" groups:kind="classification" groups:name="Glutamate Metabolism">
<groups:listOfMembers>
<groups:member groups:idRef="R_GLUN"/>
<groups:member groups:idRef="R_GLUNpp"/>
<groups:member groups:idRef="R_GLUDC"/>
<groups:member groups:idRef="R_GLUSy"/>
<groups:member groups:idRef="R_GLNS"/>
<groups:member groups:idRef="R_GLUDy"/>
</groups:listOfMembers>
</groups:group>
...
</groups:listOfGroups>Get the list of pathways of a network with the method getPathwaysView of the BioNetwork class.
The Minimum information requested in the annotation of biochemical models (MIRIAM) define rules for annotating biological models and especially cross references. The corresponding class in met4j-io is AnnotationParser.
By default, you must note that all the cross references must follow the pattern https://identifiers.org/*/*. You can change the pattern by specifying it when you create a new instance of the AnnotationParser class.
Example:
<reaction fbc:lowerFluxBound="LOWER_BOUND_1000_0" fbc:upperFluxBound="UPPER_BOUND_1000_0" id="R_AIRC3" metaid="_021f4445-f5d6-492c-8d4a-315a04229545" name="Phosphoribosylaminoimidazole carboxylase (mutase rxn)" reversible="true" sboTerm="SBO:0000176">
<annotation>
<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
<rdf:Description rdf:about="#_021f4445-f5d6-492c-8d4a-315a04229545">
<bqbiol:is>
<rdf:Bag>
<rdf:li rdf:resource="https://identifiers.org/ec-code/5.4.99.18"/>
<rdf:li rdf:resource="https://identifiers.org/biocyc/META:RXN0-743"/>
<rdf:li rdf:resource="https://identifiers.org/seed.reaction/rxn05115"/>
<rdf:li rdf:resource="https://identifiers.org/rhea/13196"/>
</rdf:Bag>
</bqbiol:is>
</rdf:Description>
</rdf:RDF>
</annotation>
...
</reaction>You can retrieve the annotations using the method getRefs of any BioEntity. Example:
Set<BioRef> refs = reaction.getRefs("SBML");The ec number of the reaction is automatically set if an annotation starting by https://identifiers.org/ec-code/ is found.
The inchi of a BioMetabolite is also set if an annotation follows this format (example):
<species metaid="_metaM_10fthf5glu_c" id="M_10fthf5glu_c" name="10-Formyltetrahydrofolate-[Glu](5)" compartment="c" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false">
<annotation>
<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
<rdf:Description rdf:about="#_metaM_10fthf5glu_c">
<in:inchi xmlns:in="http://biomodels.net/inchi">InChI=1/C40H51N11O19/c41-40-49-32-31(37(66)50-40)43-19(15-42-32)16-51(17-52)20-3-1-18(2-4-20)33(62)47-24(38(67)68)5-10-26(53)44-21(6-11-27(54)55)34(63)45-22(7-12-28(56)57)35(64)46-23(8-13-29(58)59)36(65)48-25(39(69)70)9-14-30(60)61/h1-4,17,19,21-25,43H,5-16H2,(H,44,53)(H,45,63)(H,46,64)(H,47,62)(H,48,65)(H,54,55)(H,56,57)(H,58,59)(H,60,61)(H,67,68)(H,69,70)(H4,41,42,49,50,66)/p-6</in:inchi>
</rdf:Description>
</rdf:RDF>
</annotation>
...
</species>This plugin aims to read all the HTML notes found in SBML elements. These notes are often found in old SBML and correspond to ad-hoc rules or COBRA rules. We have tried to consider all the cases we have encountered but it is certain that we could not be exhaustive.
The corresponding class in met4j-io is NotesParser.
All the recognized patterns can be changed by changing the corresponding fields in the NotesParser instance.
Example:
<species id="M1" ...>
<notes>
<body xmlns="http://www.w3.org/1999/xhtml">
<p>Formula: C5H403</p>
<p>CHARGE: 3.0</p>
<p>INCHI: InChI=1S/C7H11N3O2/c1-10-3-5(9-4-10)2-6(8)7(11)12/h3-4,6H,2,8H2,1H3,(H,11,12)/t6-/m0/s1</p>
<p>SMILES: [H]OC(=O)[C@@]([H])(N([H])[H])C([H])([H])C1=C([H])N(C([H])=N1)C([H])([H])[H]</p>
</body>
</notes>
</species>Formula and charge can be retrieved by the methods getChemicalFormula and getCharge of the BioMetabolite class.
Inchi and smiles can be retrieved by the dedicated methods of the MetaboliteAttributes class.
Example:
<reaction id="R1" ... />
<notes>
<body xmlns="http://www.w3.org/1999/xhtml">
<p>EC-NUMBER: 1.1.1.2</p>
<p>PMID: 29718355;20444866</p>
<p>SCORE: 3</p>
<p>STATUS: Curated</p>
<p>COMMENTS: Reaction for the example</p>
</body>
</notes>
</reaction>
EC number can be retrieved thanks to the method getEcNumber of the BioReaction class.
PMID, score, status, and comments can be retrieved thanks to the corresponding methods of the ReactionAttributes class.
Genes, proteins, enzymes and links between enzymes and reactions can be created from reaction html notes.
Example:
<reaction id="R1" ... />
<notes>
<body xmlns="http://www.w3.org/1999/xhtml">
<p>GENE_ASSOCIATION: G1 or (G2 and G3)</p>
</body>
</notes>
</reaction>
See the example in Genes and Gene-reaction associations by FBCParser plugin to see how the path between genes and reactions are created.
Warning If the FBCParser plugin is activated and that genes have been set, no gene (even if absent in the FBC tags) will be set from the HTML notes.
Example:
<reaction id="R1" ... />
<notes>
<body xmlns="http://www.w3.org/1999/xhtml">
<p>SUBSYSTEM: pathway1 || pathway2</p>
</body>
</notes>
</reaction>Here the pathways are separated by " || " but this separator can be changed if you change the pathwaySep field in NotesParser.
Two pathways will be created and both will contain the R1 reaction.
Warning If the GroupPathwayParser plugin is activated and that pathways have been set, no pathay (even if absent in the groups tags) will be set from the HTML notes.
All other notes can be retrieved by the method getAttributes of a BioEntity instance.
JsbmlWriter writer = new JsbmlWriter("myNetwork.sbml", network);
writer.write();The write method uses similar plugins than the read method. By default, all the plugins are activated.
- FBC : FBCWriter
- groups for pathways :GroupPathwayWriter
- Miriam annotation : AnnotationWriter
- Html notes : NotesWriter.
If you don't want all the plugin data to be written in the SBML file, you can specify the plugins to be activated.
JsbmlWriter writer = new JsbmlWriter("myNetwork.sbml", network);
HashSet<PackageWriter> pkgs = new HashSet<>();
pkgs.add(new AnnotationWriter());
pkgs.add(new FBCWriter());
writer.write();