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Converting KGML-encoded KEGG pathways to the SIF file format

Copyright 2019 Arnaud Poret

This work is licensed under the Apache License Version 2.0 (the "License"). You may not use this work except in compliance with the License. You may obtain a copy of the License at https://www.apache.org/licenses/LICENSE-2.0.

kgml2sif

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

For information about the KGML file format see at the end of this readme file.

For information about the SIF file format see at the end of this readme file.

Requirements

  • Python 3
  • a unix-based operating system

Usage

Ensure that kgml2sif is executable:

chmod ugo+x kgml2sif

Usage: kgml2sif [-h] [-s <file>] [-c <file>] <kgmlfile> [<kgmlfile> ...]

Positional arguments:

  • <kgmlfile>: a KGML-encoded KEGG pathway

Optional arguments:

  • -h/--help: show help and exit
  • -s/--symbol <file>: a conversion table for translating KEGG gene IDs to gene symbols (see the file kegg2symbol.csv provided with kgml2sif in the conv folder)
  • -c/--compound <file>: a conversion table for translating compound IDs to compound names (see the file compound2name.csv provided with kgml2sif in the conv folder)

Currently:

  • kgml2sif is more suitable for processing KEGG signaling pathways
  • however, extending it to better handle other types of KEGG pathways (such as metabolic ones) is envisioned
  • the following node types are considered:
    • gene
    • compound
    • group (in KGML, groups are complexes)
  • the following relation types are considered (in KGML, relations are edges):
    • PPrel (protein-protein)
    • GErel (gene expression)
    • PCrel (protein-compound)
    • ECrel (enzyme-compound)

In the output SIF file:

  • relation names (i.e. edge names) are suffixed with their corresponding type, ex:
    • phosphorylation_PPrel
    • repression_GErel
  • if necessary, edges having multiple types are split in order to obtain one type per edge (warning: it can create multi-edges)
  • multi-edges, if any, are left inside the output SIF file and kgml2sif warns about the presence of such edges
  • the non-KGML membership_CPXrel relation is added to indicate when a node is component of a complex (CPXrel stands for relations involving complexes, an added non-KGML relation type)
  • 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_CPXrel cp1::cp2::cp3
    • cp2 membership_CPXrel cp1::cp2::cp3
    • cp3 membership_CPXrel cp1::cp2::cp3

If -s/--symbol or -c/--compound are used:

  • the conversion tables must be 2-columns CSV files with semicolon as field separator (see the conv folder)
  • unmatched IDs are left unchanged in the output SIF file

Cautions

  • currently, the file kegg2symbol.csv provided with kgml2sif in the conv folder only works with KEGG human gene IDs.

Examples

These examples come from downloaded human KEGG pathways.

ErbB signaling pathway:

./kgml2sif -s conv/kegg2symbol.csv -c conv/compound2name.csv examples/ErbB_signaling_pathway/ErbB_signaling_pathway.xml

Insulin signaling pathway:

./kgml2sif -s conv/kegg2symbol.csv -c conv/compound2name.csv examples/Insulin_signaling_pathway/Insulin_signaling_pathway.xml

Note that kgml2sif raises warnings when processing Insulin_signaling_pathway.xml (see Insulin_signaling_pathway-warnings.txt):

PCrel: 67 --> 23: missing name, skipping

This warning indicates that a PCrel edge linking the node 67 to the node 23 (identified by their IDs inside the KGML file) has no name (i.e. no information about the modeled biological interaction) and is therefore skipped by kgml2sif.

p53 signaling pathway:

./kgml2sif -s conv/kegg2symbol.csv -c conv/compound2name.csv examples/p53_signaling_pathway/p53_signaling_pathway.xml

Note that kgml2sif indicates that there are multi-edges in p53_signaling_pathway.xml (see p53_signaling_pathway-multi.sif):

TP53    activation_PPrel    MDM2
TP53    expression_GErel    MDM2

When processing p53_signaling_pathway.xml, kgml2sif identifies two edges linking TP53 to MDM2. Theses two edges are therefore multi-edges. However, they are not considered invalid by kgml2sif since it can not determine if one of them is wrong, or which is the most relevant, or if they are both meaningful (kgml2sif is not a human expert able to perform such judgments).

Consequently, because these edges are not considered invalid by kgml2sif, they are left inside the output SIF file and the user is warned about the presence of such edges.

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 KEGG Pathway itself or using the KEGG API.

For full explanations about 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