Converting KGML encoded KEGG human pathways to the SIF file format

Copyright (C) 2019-2020 Arnaud Poret

This work is licensed under the GNU General Public License.

To view a copy of this license, visit https://www.gnu.org/licenses/gpl.html.

kgml2sif

Requirements

• Python 3
• a unix based operating system (ex: Linux, macOS)

Usage

Ensure that kgml2sif is executable:

chmod ugo+rx kgml2sif

Usage: kgml2sif [-h] [-g <tsvFile>] <kgmlFile> [<kgmlFile> ...]

Positional arguments:

• <kgmlFile>: a KGML encoded KEGG human pathway

Optional arguments:

• -g <tsvFile>, --geneSymbol <tsvFile>: a conversion table for translating KEGG human gene IDs to gene symbols (see the file gene2symbol.tsv provided with kgml2sif in the conv folder)
• -h, --help: show help

Help

Convert KGML encoded KEGG human pathways to the SIF file format.

Currently:

• the following node types are considered:
  • gene (in KGML, genes also stand for the corresponding proteins/gene products)
  • compound
  • group (in KGML, groups stand for complexes)
• the following relation types are considered (in KGML, relations stand for edges):
  • PPrel: protein-protein relations
  • GErel: protein-gene relations (i.e. gene expression regulations)
  • PCrel: protein-compound relations
  • ECrel: enzyme-enzyme relations sharing a common compound (as product for the first enzyme and as substrate for the second one)

In the output SIF file:

• edges for which the name is missing are automatically named unknown
• multiedges, if any, are merged if possible, otherwise they are left inside the output SIF file and kgml2sif warns about them
• the non KGML membership edges are added in order to indicate when nodes are component of complexes
• complexes are named as follows:
  • cp1&cp2&cp3
  • where cp1, cp2 and cp3 are the complex components
• by the way, in this example of a 3 components complex, the following edges would be added as explain above:
  • cp1 membership cp1&cp2&cp3
  • cp2 membership cp1&cp2&cp3
  • cp3 membership cp1&cp2&cp3

If -g/--geneSymbol is used:

• kgml2sif attempts to name gene nodes according to a provided conversion table
• the conversion table must be a 2 columns TSV file (see the file gene2symbol.tsv provided with kgml2sif in the conv folder)
• unmatched KEGG IDs are left unchanged in the output SIF file and kgml2sif warns about them

Node name prefixes in KGML:

• specify the node type
• the name of nodes representing human genes is prefixed with hsa:
• the name of nodes representing compounds is prefixed with cpd:
• the name of nodes representing glycans (a subtype of compounds) is prefixed with gl:
• the name of nodes representing drugs (a subtype of compounds) is prefixed with dr:

Full explanation of the KGML file format at https://www.kegg.jp/kegg/xml/docs/.

For explanations about the SIF file format, see at the end of this file.

Examples

These examples come from downloaded human KEGG pathways.

The SIF files produced by kgml2sif from these examples are also in the SVG file format for visualization purpose.

Apoptosis

./kgml2sif -g conv/gene2symbol.tsv examples/Apoptosis/Apoptosis.xml

ErbB signaling pathway

./kgml2sif -g conv/gene2symbol.tsv examples/ErbB_signaling_pathway/ErbB_signaling_pathway.xml

Insulin signaling pathway

./kgml2sif -g conv/gene2symbol.tsv examples/Insulin_signaling_pathway/Insulin_signaling_pathway.xml

p53 signaling pathway

./kgml2sif -g conv/gene2symbol.tsv examples/p53_signaling_pathway/p53_signaling_pathway.xml

TNF signaling pathway

./kgml2sif -g conv/gene2symbol.tsv examples/TNF_signaling_pathway/TNF_signaling_pathway.xml

The KGML file format

KGML stands for KEGG Markup Language. It is an XML representation of KEGG pathways and is a file format in which KEGG pathways can be downloaded, either from the KEGG web site or using the KEGG API.

For a complete explanation of the KGML file format, see https://www.kegg.jp/kegg/xml/docs/.

The SIF file format

In a SIF file encoding a network, each line encodes an edge as follows:

source \t interaction \t target

Note that the field separator is the tabulation: the SIF file format is the tab separated values format (TSV) with exactly 3 columns.

For example, the edge representing the activation of RAF1 by HRAS is a line of a SIF file encoded as follows:

HRAS \t activation \t RAF1