draeger-lab / keggtranslator

A Java-based software for visualizing and translating the KEGG PATHWAY database. Conversion of KGML files into BioPAX, SBML, GraphML, GML, and various other formats.

KEGGtranslator

A Java-based software for visualizing and translating the KEGG PATHWAY database. Conversion of KGML files into BioPAX, SBML, GraphML, GML, and various other formats.

Authors: Clemens Wrzodek, Finja Wrzodek, Andreas Zell, Manuel Ruff, Andreas Dräger

Download

Latest versions of KEGGtranslator are available under Releases.

Please cite

1. Clemens Wrzodek. Inference and integration of biochemical networks with multilayered omics data. PhD thesis, University of Tuebingen, Tübingen, Germany, June 2013. [ link ]
2. Clemens Wrzodek, Finja Büchel, Manuel Ruff, Andreas Dräger, and Andreas Zell. Precise generation of systems biology models from KEGG pathways. BMC Systems Biology, 7(1):15, January 2013. [ DOI | link | pdf ]
3. Clemens Wrzodek, Andreas Dräger, and Andreas Zell. KEGGtranslator: visualizing and converting the KEGG PATHWAY database to various formats. Bioinformatics, 27(16):2314-2315, June 2011. [ DOI | link | pdf ]

KEGGtranslator options

The stand-alone tool provides a Graphical User Interface (GUI) mode and a command-line mode. All options (see section options) to customize the output (file format, and conversion options) are available through both modes. This allows users to use KEGGtranslator in a batch mode or with user interaction. The GUI can be started by passing the --gui option to the program. All other options passed to the program are adopted by the GUI.

Usage

Start the graphical user interface with:

java -jar KEGGtranslator.jar

To use the command-line capabilities, please use the following syntax:

java -jar KEGGtranslator.jar --input [in_file.xml] --output [out_file] --format [out_format]

Batch processing

KEGGtranslator can be used to batch convert multiple KGML formatted XML-files. To use this feature, simply give a folder as input argument, together with the desired output format and optional additional options. For example,

java -jar KEGGtranslator.jar --input C:/ --format SBML

will convert all KEGG files, found on drive C (including subdirectories) to SBML files.

For developers: embedding KEGGtranslator

If you wan't to use KEGGtranslator inside your own application, you can simply put the JAR file on your class path and use the classes and methods of KEGGtranslator as described in the Javadoc (version 2.0, 1.1).

Possible command-line arguments

1. Basic KEGGtranslator IO Options

Define the default input/ output files and the default output format.

-i<File>, --input[ |=]<File>

Path and name of the source, KGML formatted, XML-file. Akzeptiert kGML-Dateien (*.xml).

-o<File>, --output[ |=]<File>

Path and name, where the translated file should be put.

-f<Format>, --format[ |=]<Format>

Target file format for the translation. All possible values for type are: SBML, SBML_L2V4, SBML_L3V1, SBML_QUAL, SBML_CORE_AND_QUAL, SBGN, BioPAX_level2, BioPAX_level3, SIF, GraphML, GML, JPG, GIF, TGF, and YGF. Default value: SBML

2. KEGGtranslator Command Line Only Options

--cache-size[ |=]<Integer>

Specify the number of API entries from KEGG to keep into cache (default: 10000). Arguments must be in rage {[100,1000000]}. Default: 10000

--create-jpg

Create a visualization (as JPG) of the selected format. Always creates a JPG, even for SBML and others. Default: false

KEGGtranslator Options

1. Generic translation options Define various options that are used in all translations.

-ro, --remove-orphans

If true, remove all nodes that have no edges before translating the pathway. Default: false

--gene-names[ |=]<NODE_NAMING>

For one KEGG object, multiple names are available. Choose how to assign one name to this object. All possible values of <NODE_NAMING> are: SHORTEST_NAME, FIRST_NAME_FROM_KGML, FIRST_NAME, ALL_FIRST_NAMES, INTELLIGENT_WITH_EC_NUMBERS, and INTELLIGENT. Default: INTELLIGENT

-formula, --show-formula-for-compounds

If true, shows the chemical formula for all compounds, instead of the name. Default: false

-nowhite, --remove-white-gene-nodes

If true, removes all white gene-nodes in the KEGG document (usually enzymes that have no real instance on the current organism). Default: false

-ar<Boolean>, --autocomplete-reactions[ |=]<Boolean>

If true, automatically looks for missing reactants and enzymes of reactions and adds them to the document.

-ar<Boolean>, --autocomplete-reactions[ |=]<Boolean>

Default: true

-nopr, --remove-pathway-references

If true, removes all entries (nodes, species, etc.) referring to other pathways. Default: false

2. Translation options for graphical outputs

Define various options that are used in yFiles based translations.

-merge, --merge-nodes-with-same-edges

If true, merges all nodes that have exactly the same relations (sources, targets and types). Default: false

-cel, --create-edge-labels

If true, creates describing labels for each edge in the graph. Default: false

-hc, --hide-labels-for-compounds

If true, hides labels for all compounds (=small molecules). Default: false

-dar, --draw-grey-arrows-for-reactions

If true, creates grey arrows for reactions and arrows with transparent circles as heads for reaction modifiers. This does only affect reactions defined by KEGG, not the relations. Default: false

3. Translation options for SBML outputs

Define various options that are used in SBML based translations.

-layout, --add-layout-extension

If true, adds layout information, using the SBML layout extension to the SBML document.As a side-effect, this will create an SBML Level 3 model. Default: false

-groups<Boolean>, --use-groups-extension[ |=]<Boolean>

If true, uses the SBML level 3 groups extension to encode groups in the SBML document.As a side-effect, this will create an SBML Level 3 model. Default: true

-cbal<Boolean>, --check-atom-balance[ |=]<Boolean>

Check the atom balance of metabolic reactions and write a summary to the reaction notes. Depends on autocomplete reactions. Default: true Generic options for the graphical user interface

--check-for-updates[ |=]<Boolean>

Check for KEGGtranslator updates upon application start. Default: true

--gui

A graphical user interface is shown if this option is given. Default: false

--log-level[ |=]<String>

Change the log-level of this application. All possible values of <String> are: ALL, CONFIG, FINE, FINER, FINEST, INFO, OFF, SEVERE, and WARNING. Default: INFO

keggtranslator's Issues

Error converting files to SIF and BIOpax_level2

I got a fatal error exception shown at the bottom of the software when converting the systemic lupus erythematosus (SLE) pathway map into SIF and BIOpax_level2

to BioPAX L3: same pathways have different and not standard URIs in different files

@draeger
This is related to PathwayCommons/cpath2#205.

When a KEGG pathway with ID, e.g., hsa00010 is defined in its main biopax file (hsa_00010.owl), it has absolute URI like "path:hsa00010"; but when the same pathway is referenced from other files, e.g., hsa_00562.owl, its simplified/dummy version has a different URI "#pathhsa00010" (i.e,, "http://www.ra.cs.uni-tuebingen.de/software/KEGGtranslator/pathhsa00010") and the property looks like

<bp:pathwayComponent rdf:resource="#pathhsa00010" />

URIs of the same pathways must be exactly the same in all files, and be like "http://identifiers.org/kegg.pathway/hsa00010" instead.

Character encoding problem

It was reported by Deepa Maheshvare that the characters used to do the quote in the notes that pose problem in models generated by KEGGtranslator.

where is KEGGtranslator.jar?

I think the title speaks for itself. There is no file called KEGGtranslator.jar so how am I supposed to run your code? Or am I supposed to compile this? If so, there are no installation/compilation guidelines.

Where can I download KEGGtranslator.jar? By the way, it is not here: https://uni-tuebingen.de/fakultaeten/mathematisch-naturwissenschaftliche-fakultaet/fachbereiche/informatik/lehrstuehle/kognitive-systeme/software/

Known security vulnerabilities detected in third-party library

The library axis:axis is in version below 1.4 and needs to be upgraded.

File unreadable

Hi, I used the software to translate the KGML into SBML, but when I import the translated file to Cell Designer, it reported a fatal error that the file was unreadable. How can I solve this problem? Thanks for any advice.

Information that might be useful
example file: hsa04062.xml link: https://www.genome.jp/dbget-bin/www_bget?hsa04062
Cell designer version: v4.4.2

Preserve type attribute of KGML relation elements in SBML

Currently, the KEGGtranslator converts relations in KGML documents into Transitions in SBML documents. However, the SBML Transitions do not preserve the type of the KEGG relation (GErel, PPrel, PCrel, ECrel, or mapping). Downstream software (reading the SBML) may only want to consider particular classes of transitions (e.g., those deriving from GErel, PPrel, and PCrel relations) and ignore others.

This is a feature request to add an annotation or note to Transition elements in the SBML to preserve the type of the relation from KGML.

Availability of KEGGtranslator.jar and problem converting to SBML_L3V1

Hi,

First of all, thank you for developing this tool!

I recently started using KEGGtranslator and hoped to run it on command line. However, the 'Downloads' section on the webpage (http://www.ra.cs.uni-tuebingen.de/software/KEGGtranslator/downloads/index.htm) appeared blank. So I am wondering if KEGGtranslator.jar is still available?

The second question is, I was using KEGG translator 2.5 to translate KEGG PATHWAY eco01100 to SBML_L3V1, but the progress got stuck at 0% (see the screenshot below). But if I use eco00281, the conversion finishes up fine. Do you know what could have caused the failure for eco01100?

Thank you!
Fengdan

Encoding maplink relations in SBML format

Hello, I am using KEGGtranslator to generate models specifically for stoichiometric analyses. The tool fulfils most of my needs (although I am using version 2.5 downloaded here because it is still not clear to me how this repository is intended for use, see #5), but would like to obtain an encoding of maplink relations so that information on neighbouring pathways is also in the SBML (or extended format).

For example, KEGGconverter (which appears to be broken) does this by encoding neighbouring pathways as additional species and maplink relations as reactions between them and corresponding (e.g., metabolic) species. To quote directly from the paper:

"A core idea in this stage, is the conversion of the KGML elements, which point to other pathways, into additional SBML reactions. In this way, the map link information of the KGML pathway files is retained during this process."

Is there some way to achieve something similar using KEGGtranslator? If not identical to KEGGconverter framework (e.g. neighbouring as species), I don't mind post-processing the SBML files to achieve the specific stoichiometric model structure I want (I would have to do this anyway with KEGGconverter) so if you can just point me towards the best way to add this information in the output of the translator that would be great. Otherwise, if no such method for encoding the maplink relations is available, perhaps you could suggest an efficient way to combine the SBML with original KGML files and add this information myself? I apologise in advance if I have overlooked a simple solution to the problem, I am quite new to using the converters!

Possible to recover subcellular location?

KEGG pathways include (in an albeit obscure way) information about where reactions and relations occur in the cell (e.g., intercellular reactions that occur entirely in the cell, or ligand-receptor interactions that occur outside the cell and on the membrane). Is there any way for the KEGGtranslator to extract that info and encode it in the SBML?