KEGG - Kyoto Encyclopedia of Genes and Genomes (`kegg`)¶

KEGG - Kyoto Encyclopedia of Genes and Genomes¶

kegg is a python module for accessing KEGG (Kyoto Encyclopedia of Genes and Genomes) using its web services.

Note

This module requires slumber and requests packages.

>>> from orangecontrib.bio.kegg import *
>>> # Create a KEGG Genes database interface
>>> genome = KEGGGenome()
>>> # List all available entry ids
>>> keys = genome.keys()
>>> print(keys[0])
T01001
>>> # Retrieve the entry for the key.
>>> entry = genome[keys[0]]
>>> print(entry.entry_key)
T01001
>>> print(entry.definition)
Homo sapiens (human)
>>> print(str(entry)) 
ENTRY       T01001            Complete  Genome
NAME        hsa, HUMAN, 9606
DEFINITION  Homo sapiens (human)
...

The Organism class can be a convenient starting point for organism specific databases.

>>> organism = Organism("Homo sapiens")  # searches for the organism by name
>>> print(organism.org_code)  # prints the KEGG organism code
hsa
>>> genes = organism.genes  # get the genes database for the organism
>>> gene_ids = genes.keys() # KEGG gene identifiers
>>> entry = genes["hsa:672"]
>>> print(entry.definition)
breast cancer 1, early onset
>>> # print the entry in DBGET database format.
>>> print(entry) 
ENTRY       672               CDS       T01001
NAME        BRCA1, BRCAI, BRCC1, BROVCA1, FANCS, IRIS, PNCA4, PPP1R53, PSCP, RNF53
DEFINITION  breast cancer 1, early onset
...

class orangecontrib.bio.kegg.Organism(org, genematcher=None)¶

A convenience class for retrieving information regarding an organism in the KEGG Genes database.

Parameters:	org (str) – KEGG organism code (e.g. “hsa”, “sce”). Can also be a descriptive name (e.g. ‘yeast’, “homo sapiens”) in which case the organism code will be searched for by using KEGG find api.

DBEntry (`entry`)¶

The entry.DBEntry represents a DBGET databas entry. The individual KEGG Database interfaces below provide their own specialization for this base class.

class orangecontrib.bio.kegg.entry.DBEntry(text=None)¶

Bases: object

A DBGET entry object.

entry_key¶: Primary entry key used for identifying the entry.

parse(text)¶: Parse text string containing a formated DBGET entry.

format(section_indent=12)¶: Return a DBGET formated string representation.

KEGG Databases interface (`databases`)¶

class orangecontrib.bio.kegg.databases.DBDataBase(**kwargs)¶

Bases: object

Base class for a DBGET database interface.

ENTRY_TYPE¶

ENTRY_TYPE constructor (a DBEntry subclass). This should be redefined in subclasses.

alias of DBEntry

DB = None¶: A database name/abbreviation (e.g. ‘pathway’). Needs to be set in a subclass or object instance’s constructor before calling the base. __init__

keys()¶: Return a list of database keys. These are unique KEGG identifiers that can be used to query the database.

iterkeys()¶: Return an iterator over the keys.

items()¶: Return a list of all (key, DBDataBase.ENTRY_TYPE instance) tuples.

iteritems()¶: Return an iterator over the items.

values()¶: Return a list of all DBDataBase.ENTRY_TYPE instances.

itervalues()¶: Return an iterator over all DBDataBase.ENTRY_TYPE instances.

get(key, default=None)¶: Return an DBDataBase.ENTRY_TYPE instance for the key. Raises KeyError if not found.

get_text(key)¶: Return the database entry for key as plain text.

get_entry(key)¶: Return the database entry for key as an instance of ENTRY_TYPE.

find(name)¶: Find name using kegg find api.

pre_cache(keys=None, batch_size=10, progress_callback=None)¶: Retrieve all the entries for keys and cache them locally for faster subsequent retrieval. If keys is None then all entries will be retrieved.

batch_get(keys)¶: Batch retrieve all entries for keys. This can be significantly faster then getting each entry separately especially if entries are not yet cached.

class orangecontrib.bio.kegg.databases.GenomeEntry(text)¶

Bases: orangecontrib.bio.kegg.entry.DBEntry

Entry for a KEGG Genome database.

organism_code¶: A three or four letter KEGG organism code (e.g. ‘hsa’, ‘sce’, ...)

taxid¶: Organism NCBI taxonomy id.

annotation¶: ANNOTATION

chromosome¶: CHROMOSOME

comment¶: COMMENT

data_source¶: DATA_SOURCE

definition¶: DEFINITION

disease¶: DISEASE

entry¶: ENTRY

keywords¶: KEYWORDS

name¶: NAME

original_db¶: ORIGINAL_DB

plasmid¶: PLASMID

reference¶: REFERENCE

statistics¶: STATISTICS

taxonomy¶: TAXONOMY

class orangecontrib.bio.kegg.databases.Genome¶

Bases: orangecontrib.bio.kegg.databases.DBDataBase

An interface to the A KEGG GENOME database.

ENTRY_TYPE¶: alias of GenomeEntry

org_code_to_entry_key(code)¶: Map an organism code (‘hsa’, ‘sce’, ...) to the corresponding kegg identifier (T + 5 digit number).

search(string, relevance=False)¶: Search the genome database for string using bfind.

class orangecontrib.bio.kegg.databases.GeneEntry(text=None)¶

Bases: orangecontrib.bio.kegg.entry.DBEntry

aaseq¶: AASEQ

class_¶: CLASS

dblinks¶: DBLINKS

definition¶: DEFINITION

disease¶: DISEASE

drug_target¶: DRUG_TARGET

entry¶: ENTRY

module¶: MODULE

motif¶: MOTIF

name¶: NAME

ntseq¶: NTSEQ

organism¶: ORGANISM

orthology¶: ORTHOLOGY

pathway¶: PATHWAY

position¶: POSITION

structure¶: STRUCTURE

class orangecontrib.bio.kegg.databases.Genes(org_code)¶

Bases: orangecontrib.bio.kegg.databases.DBDataBase

Interface to the KEGG Genes database.

Parameters:	org_code (str) – KEGG organism code (e.g. ‘hsa’).

class orangecontrib.bio.kegg.databases.CompoundEntry(text=None)¶

Bases: orangecontrib.bio.kegg.entry.DBEntry

atom¶: ATOM

bond¶: BOND

brite¶: BRITE

comment¶: COMMENT

dblinks¶: DBLINKS

entry¶: ENTRY

enzyme¶: ENZYME

exact_mass¶: EXACT_MASS

formula¶: FORMULA

mol_weight¶: MOL_WEIGHT

name¶: NAME

pathway¶: PATHWAY

reaction¶: REACTION

reference¶: REFERENCE

remark¶: REMARK

class orangecontrib.bio.kegg.databases.Compound¶: Bases: orangecontrib.bio.kegg.databases.DBDataBase

class orangecontrib.bio.kegg.databases.ReactionEntry(text=None)¶

Bases: orangecontrib.bio.kegg.entry.DBEntry

definition¶: DEFINITION

entry¶: ENTRY

enzyme¶: ENZYME

equation¶: EQUATION

name¶: NAME

class orangecontrib.bio.kegg.databases.Reaction¶: Bases: orangecontrib.bio.kegg.databases.DBDataBase

class orangecontrib.bio.kegg.databases.EnzymeEntry(text=None)¶

Bases: orangecontrib.bio.kegg.entry.DBEntry

all_reac¶: ALL_REAC

class_¶: CLASS

comment¶: COMMENT

dblinks¶: DBLINKS

entry¶: ENTRY

genes¶: GENES

name¶: NAME

orthology¶: ORTHOLOGY

pathway¶: PATHWAY

product¶: PRODUCT

reaction¶: REACTION

reference¶: REFERENCE

substrate¶: SUBSTRATE

sysname¶: SYSNAME

class orangecontrib.bio.kegg.databases.Enzyme¶: Bases: orangecontrib.bio.kegg.databases.DBDataBase

class orangecontrib.bio.kegg.databases.PathwayEntry(text=None)¶

Bases: orangecontrib.bio.kegg.entry.DBEntry

class_¶: CLASS

compound¶: COMPOUND

dblinks¶: DBLINKS

description¶: DESCRIPTION

disease¶: DISEASE

drug¶: DRUG

entry¶: ENTRY

enzyme¶: ENZYME

ko_pathway¶: KO_PATHWAY

module¶: MODULE

name¶: NAME

organism¶: ORGANISM

pathway_map¶: PATHWAY_MAP

reference¶: REFERENCE

rel_pathway¶: REL_PATHWAY

class orangecontrib.bio.kegg.databases.Pathway(prefix='map')¶

Bases: orangecontrib.bio.kegg.databases.DBDataBase

KEGG Pathway database

Parameters:	prefix (str) – KEGG Organism code (‘hsa’, ...) or ‘map’, ‘ko’, ‘ec’ or ‘rn’

KEGG Pathway (`pathway`)¶

class orangecontrib.bio.kegg.pathway.Pathway(pathway_id, local_cache=None, connection=None)¶

Bases: object

Class representing a KEGG Pathway (parsed from a “kgml” file)

Parameters:	pathway_id (str) – A KEGG pathway id (e.g. ‘path:hsa05130’)

name¶: Pathway name/id (e.g. “path:hsa05130”)

org¶: Pathway organism code (e.g. ‘hsa’)

number¶: Pathway number as a string (e.g. ‘05130’)

title¶: Pathway title string.

image¶: URL of the pathway image.

link¶: URL to a pathway on the KEGG web site.

get_image()¶: Return an local filesystem path to an image of the pathway. The image will be downloaded if not already cached.

classmethod list(organism)¶: List all pathways for KEGG organism code organism.

Utilities¶

class orangecontrib.bio.kegg.entry.parser.DBGETEntryParser¶

A DBGET entry parser (inspired by xml.dom.pulldom).

>>> stream = StringIO("ENTRY foo\n"
...                   "NAME  foo's name\n"
...                   "  BAR A subsection of 'NAME'\n")
...
>>> parser = DBGETEntryParser()
>>> for event, title, contents_part in parser.parse(stream):
...    print(parser.EVENTS[event], title, repr(contents_part))
...
ENTRY_START None None
SECTION_START ENTRY 'foo\n'
SECTION_END ENTRY None
SECTION_START NAME "foo's name\n"
SUBSECTION_START BAR "A subsection of 'NAME'\n"
SUBSECTION_END BAR None
SECTION_END NAME None
ENTRY_END None None

ENTRY_END = 1¶: Entry end event

ENTRY_START = 0¶: Entry start events

SECTION_END = 3¶: Section end event

SECTION_START = 2¶: Section start event

SUBSECTION_END = 5¶: Subsection end event

SUBSECTION_START = 4¶: Subsection start event

TEXT = 6¶: Text element event

KEGG - Kyoto Encyclopedia of Genes and Genomes (`kegg`)¶