Tutorial

PADMet format

Padmet is an object representing the metabolic network of a species (organism) based on a reference database.

This format contains Node, Policy and Relation:

a Node is an Object that contains information about an element of the network (can be a pathway, reaction…).
a Policy defines the way Node and Relation are associated.
a Relation defines how two nodes are connected. In a relation there is a node “in” and a node “out”. (reactionX (node in) consumes metaboliteX (node out))

A Padmet object contains 3 attributes:

dicOfNode: a dictionary of node: key=Node’s unique id / value = <Node>
dicOfRelationIn: a dictionary of relation with: key= nodeIN id / value = list of <relation>
dicOfRelationOut: a dictionary of relation with: key= nodeOut id / value = list of <relation>

Node

A Node represent an element in a metabolic network.

A Node has a type (‘reaction’,’pathway’), an ID and a dictionary of miscellaneous data. Node can be find in the dicOfNode, this dicitonary contains Node IDs as key and Node object as values.

As an example we use the padmet_1.padmet from test data:

>>> from padmet.classes import PadmetSpec

# Creation of a padmet object from the padmet file.
>>> padmet_object = PadmetSpec('test_data/padmet/padmet_1.padmet')

# Selection of the Node corresponding to the reaction 'ENOYL-COA-HYDRAT-RXN'
>>> enoyl_coa_node = padmet_object.dicOfNode['ENOYL-COA-HYDRAT-RXN']

>>> enoyl_coa_node.id
'ENOYL-COA-HYDRAT-RXN'

>>> enoyl_coa_node.type
'reaction'

>>> enoyl_coa_node.misc
{'EC-NUMBER': ['EC-4.2.1.17'], 'DIRECTION': ['LEFT-TO-RIGHT']}

Relation

A Relation represent a link between two elements (node) in a metabolic network.

A Relation contains 4 attributes:

type: The type of the relation (e.g: ‘consumes’ or ‘produces’)
id_in: the identifier of the node corresponding to the subject of the relation (e.g: ‘RXN-1’)
id_out: the identifier of the node corresponding to the object of the relation (e.g: ‘CPD-1’)
misc: A dictionary of miscellaneous data, k = tag of the data, v = list of values (e.g: {‘STOICHIOMETRY’:[1.0]})

We will use the same example as the Node section:

>>> from padmet.classes import PadmetSpec

# Creation of a padmet object from the padmet file.
>>> padmet_object = PadmetSpec('test_data/padmet/padmet_1.padmet')

# Selection of the Node corresponding to the reaction 'ENOYL-COA-HYDRAT-RXN'
>>> enoyl_coa_relation = padmet_object.dicOfRelationIn['ENOYL-COA-HYDRAT-RXN']

>>> len(enoyl_coa_relation)
6
# Node 'ENOYL-COA-HYDRAT-RXN' is an ID in for 6 Relations

# What is the type of the first relation when this Node is In
>>> padmet_object.dicOfRelationIn['ENOYL-COA-HYDRAT-RXN'][0].type
'is_in_pathway'

>>> padmet_object.dicOfRelationIn['ENOYL-COA-HYDRAT-RXN'][0].id_in
'ENOYL-COA-HYDRAT-RXN'

>>> padmet_object.dicOfRelationIn['ENOYL-COA-HYDRAT-RXN'][0].id_out
'FAO-PWY'

>>> padmet_object.dicOfRelationIn['ENOYL-COA-HYDRAT-RXN'][0].toString()
'ENOYL-COA-HYDRAT-RXN\tis_in_pathway\tFAO-PWY'

Create padmet

Padmet files can be created using the padmet padmet pgdb_to_padmet command. This command takes as input the result of Pathway Tools software. You can get these files by using the mpwt package.

usage:
    padmet pgdb_to_padmet --pgdb=DIR --output=FILE [--version=V] [--db=ID] [--padmetRef=FILE] [--source=STR] [-v] [--enhance]
    padmet pgdb_to_padmet --pgdb=DIR --output=FILE --extract-gene [--no-orphan] [--keep-self-rxn] [--version=V] [--db=ID] [--padmetRef=FILE] [--source=STR] [-v] [--enhance]

options:
    -h --help     Show help.
    --version=V    Xcyc version [default: N.A].
    --db=ID    Biocyc database corresponding to the pgdb (metacyc, ecocyc, ...) [default: N.A].
    --output=FILE    padmet file corresponding to the DB.
    --pgdb=DIR    directory containg all the .dat files of metacyc (data).
    --padmetRef=FILE    padmet of reference.
    --source=STR    Tag associated to the source of the reactions, used to ensure traceability [default: GENOME].
    --enhance    use the metabolic-reactions.xml file to enhance the database.
    --extract-gene    extract genes from genes_file (use if its a specie's pgdb, if metacyc, do not use).
    --no-orhpan    remove reactions without gene associaiton (use if its a specie's pgdb, if metacyc, do not use).
    --keep-self-rxn    remove reactions with no reactants (use if its a specie's pgdb, if metacyc, do not use).
    -v   print info.

The input folder (–pgdb) should be like:

input_folder
├── classes.dat
├── compound-links.dat
├── compounds.dat
├── dnabindsites.dat
├── enzrxns.dat
├── gene-links.dat
├── genes.dat
├── pathway-links.dat
├── pathways.dat
├── promoters.dat
├── protein-features.dat
├── protein-links.dat
├── proteins.dat
├── protligandcplxes.dat
├── pubs.dat
├── reaction-links.dat
├── reactions.dat
├── regulation.dat
├── regulons.dat
├── rnas.dat
├── species.dat
├── terminators.dat
└── transunits.dat

This command will create a padmet file.

Explore padmet

List of reactions, compounds, pathways and genes of a metabolic network can be extracted using getter on the padmet:

>>> from padmet.classes import PadmetSpec

# Creation of a padmet object from the padmet file.
>>> padmet_object = PadmetSpec('test_data/padmet/padmet_1.padmet')

# Get the list of reaction IDs in the padmet.
>>> list_reaction_ids = padmet_object.getReactions()

# Get the list of compounds in the padmet.
>>> list_compound_ids = padmet_object.getCompounds()

# Get the list of genes in the padmet.
>>> list_gene_ids = padmet_object.getGenes()

# Get the list of pathways in the padmet.
>>> list_pathway_ids = padmet_object.getPathways()

It is also possible to get a list of nodes:

# Get the list of reaction IDs in the padmet.
>>> list_reaction_nodes = padmet_object.getReactions(get_id=False)