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johnmay edited this page Jan 21, 2013 · 7 revisions

There are several ways a reconstruction can be persisted with Metingear. Internally Metingear uses a binary format to provide fast load and save times but it is also possible to export as System Biology Markup Language (SBML). This page details aspects of each export.

# Internal Format - `.mr`

Metingear saves four files under a directory suffixed with .mr (metingear reconstruction).

  • *.mr/entities - binary storage of reconstruction structure and basic entity information (id/name/abbreviation)
  • *.mr/entity-annotations - binary storage of annotations on entities
  • *.mr/entity-observations - binary storage of observations (local homology results) on entities
  • *.mr/info.properties - information about the version which was used to write the files

Clicking Save will save a reconstruction to the user home directory using the reconstruction identifier as the filename. A reconstruction with id ibsu1103 would save to /Users/joeblogs/ibsu1103.mr or C:\Users\joeblogs\ibsu1103.mr.

file-save

It is also possible to specify the name with File > Save As and open a .mr file with File > Open. File > Open Recent will maintain a list of recently opened files.

file-open-recent

# SMBL - `.xml`

File > Export SBML

The active reconstruction can be exported to SBML level 2 version 4 using JSBML. Entity annotations are export as identifiers.org (cross-references) and InChI (chemical structure) RDF annotations.

file-export-sbml

A species entry in SBML exported from Metingear.

<species id="M12311_e" name="Glycolate" metaid="_000001869" compartment="e">
        <annotation>
          <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:bqmodel="http://biomodels.net/model-qualifiers/">
            <rdf:Description rdf:about="#_000001869">
              <bqbiol:is>
                <rdf:Bag>
                  <rdf:li rdf:resource="http://identifiers.org/kegg.compound/C00160/"/>
                  <rdf:li rdf:resource="http://identifiers.org/obo.chebi/CHEBI:7857/"/>
                  <rdf:li rdf:resource="http://identifiers.org/obo.chebi/CHEBI:29805/"/>
                  <rdf:li rdf:resource="http://rdf.openmolecules.net/?InChI=1S/C2H4O3/c3-1-2(4)5/h3H,1H2,(H,4,5)"/>
                </rdf:Bag>
              </bqbiol:is>
            </rdf:Description>
          </rdf:RDF>
        </annotation>
</species>

A reaction entry in SBML exported from Metingear.

<reaction id="R197147" name="galacturonate transport in via proton symport|D-galacturonate transport via proton symport, reversible" metaid="_000002198" reversible="true">
        <annotation>
          <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:bqmodel="http://biomodels.net/model-qualifiers/">
            <rdf:Description rdf:about="#_000002198">
              <bqbiol:is>
                <rdf:Bag>
                  <rdf:li rdf:resource="urn:miriam:tcdb:TC-2.A.1.14"/>
                </rdf:Bag>
              </bqbiol:is>
            </rdf:Description>
          </rdf:RDF>
        </annotation>
        <listOfReactants>
          <speciesReference id="M12199_e_R197147_0" species="M12199_e" stoichiometry="1"/>
          <speciesReference id="M12570_e_R197147_1" species="M12570_e" stoichiometry="1"/>
        </listOfReactants>
        <listOfProducts>
          <speciesReference id="M12199_c_R197147_2" species="M12199_c" stoichiometry="1"/>
          <speciesReference id="M12570_c_R197147_3" species="M12570_c" stoichiometry="1"/>
        </listOfProducts>
      </reaction>
# Structure Data File - `.sdf`

File > Export > Metabolites (.sdf) - requires a selection of metabolites

Metingear can export the chemical structures of metabolite to a Structure Data File (SDF). Simply select the metabolites you which to export the structures of. Click the menu item and choose the location to save the .sdf.

# Matrix

When a stoichiometric matrix has been built for a reconstruction (see. Tools) it can be exported for visualisation in Cyctoscape or manipulation as a tabular tsv.

#### Cyctoscape - `.sif`

The stoichiometric matrix can be exported as a network for visualisation in Cytoscape. Metingear writes .sif files which can be opened directly in Cyctoscape. Firstly create the matrix then select File > Export > Matrix.

file-export-matrix

This will open a dialog with several options. Select the option Sif (Cytoscape) as the format.

export-matrix-dialog

In Cytoscape select File > Import > Network (Multiple File Types).

cyto-import-network

Choose the location of the .sif file you created from Metingear.

cyto-import-path

Once imported you can apply a layout algorithm.

cyto-ct3

Connection Threshold - by default the export will split metabolites which have a degree (number of connections) greater then 3. This can be changed by adjusting the Connection Threshold property. This threshold is useful as metabolic networks have several currency metabolites which are highly connected. Exporting with a higher threshold leads to the classical hairball network. Below is an example of a network which include nodes up to degree 15.

cyto-ct15

#### Tabular - `.tsv`

The matrix can also be exported as tabular tsv file. As with Cytoscape export create the matrix and select File > Export > Matrix. Select Table (tsv) as the output format. By default this will write the matrix as integer values. You can change this so the stoichiometries are written as double values by selecting store values as double precision .

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