Function Repository Resource:

KEGGModule

Source Notebook

Get information about a KEGG module

Contributed by: Lina Marcela Ruiz Galvis and Keiko Hirayama

ResourceFunction["KEGGModule"]["Modules"]

gives a Dataset with basic information for all the KEGG modules.

ResourceFunction["KEGGModule"][keggcode,prop]

gives a property prop for a specific keggcode.

ResourceFunction["KEGGModule"][keyword,"Query"]

gives a dataset for a specific keyword referring to a module.

Details

KEGG MODULE database consists of KEGG modules identified by M-numeric identifiers and KEGG reaction modules identified by RM-numeric identifiers. These are manually defined functional units of gene sets and reaction sets, respectively.
Supported values for keggcode are those referring to KEGG Modules including string IDs or lists of at most ten IDs.
prop supports the following values:
"Module"information for keggcode referring to KEGG module (i.e., M00001)
"Entry"ExternalIdentifier of the module KEGG code
"EntryType"the module type
"Name"the module name
"FullName"the module full name
"ReactionInName"the reaction specified in the module name
"Definition"definition of module where the comma indicates alternatives, plus represents a complex, and minus denotes a non-essential component in the complex
"DiagramLink"thumbnail of the corresponding MODULE diagram link
"DiagramImage"thumbnail of the corresponding MODULE diagram image
"Orthology"the list of KEGG ORTHOLOGY identifiers
"Taxonomy"link to the taxonomy information
"OrthologTable"link to the ortholog table
"Class"classification of modules
"PathwayExternalID"ExternalIdentifier corresonding to the KEGG pathway map
"PathwayHyperlink"Hyperlink corresonding to the KEGG pathway map
"Reaction"the list of reactions (R numbers) in the metabolic pathway module
"Compound"the list of compounds (C numbers) in the metabolic pathway module
"RModule"corresponding pathway modules (Reaction module only)
"Comment"free text comment
"Reference"reference information
The "Query" property performs a search operation to retrieve the module entry identifier associated with a given keyword.
Accepted keyword values correspond to module names as found in the "Name" property of entries in ResourceFunction["KEGGModule"]["Modules"]. They refers to the names of functional units of gene sets or reaction sets that consitutes a biological activity or function. Examples include "Glycolysis", "Penicillin biosynthesis", or "Nodulation", among others.

Examples

Basic Examples (3) 

Get the list of all the modules in the KEGG module database:

In[1]:=
ResourceFunction["KEGGModule"]["Modules"]
Out[1]=

Get the information from KEGG about a specific module:

In[2]:=
ResourceFunction["KEGGModule"]["M00118"]
Out[2]=

Get the information from KEGG about a list of modules:

In[3]:=
ResourceFunction["KEGGModule"][{"M00620", "M00982"}]
Out[3]=

Scope (2) 

Get the KEGG module codes for a specific query:

In[4]:=
ResourceFunction["KEGGModule"]["Citrate", "Query"]
Out[4]=

Keywords may have more than one word:

In[5]:=
ResourceFunction["KEGGModule"]["Prodigiosin biosynthesis", "Query"]
Out[5]=

Options (2) 

Get the dataset properties independently for each module:

In[6]:=
ResourceFunction["KEGGModule"]["M00422", "Definition"]
Out[6]=

Get the dataset properties independently for a list of modules:

In[7]:=
ResourceFunction[
 "KEGGModule"][{"M00422", "M00528", "M00798"}, "Definition"]
Out[7]=

Properties and Relations (2) 

Get information for a specific identifier:

In[8]:=
ResourceFunction["KEGGModule"]["M00744"]
Out[8]=

This is equivalent to explicitly requesting the "Module" information:

In[9]:=
ResourceFunction["KEGGModule"]["M00744", "Module"]
Out[9]=

Possible Issues (1) 

Only keywords known by KEGG are supported:

In[10]:=
ResourceFunction["KEGGModule"]["oxigenu", "Query"]
Out[10]=

Neat Examples (6) 

Get the pathway associated to the glycolysis module:

In[11]:=
pathway = ResourceFunction["KEGGModule"]["M00008", "PathwayExternalID"]
Out[11]=

Get reactions associated to the glycolysis module:

In[12]:=
reactions = ResourceFunction["KEGGModule"]["M00008", "Reaction"]
Out[12]=

Get the compounds associated to the glycolysis module:

In[13]:=
compounds = ResourceFunction["KEGGModule"]["M00008", "Compound"]
Out[13]=

Get the vertices and edges list associated to the pentose phosphate pathway associated with the glycolysis module:

In[14]:=
vNamesRules = Normal[ResourceFunction[
ResourceObject[<|"Name" -> "KEGGPathway", "ShortName" -> "KEGGPathway", "UUID" -> "c26fb78f-9391-4e5b-8348-1b3a9bcb8293", "ResourceType" -> "Function", "Version" -> "1.2.1", "Description" -> "Get the graph and additional information of a KEGG pathway", "RepositoryLocation" -> URL[
         "https://www.wolframcloud.com/obj/resourcesystem/api/1.0"], "SymbolName" -> "FunctionRepository`$cf8afda6cda14c308cd1e656f8629ece`KEGGPathway", "FunctionLocation" -> CloudObject[
         "https://www.wolframcloud.com/obj/81066f03-423e-4566-800b-da9d03968a36"]|>, {ResourceSystemBase -> "https://www.wolframcloud.com/obj/resourcesystem/api/1.0"}]]["hsa", "00030", "Entries"][
    All, #EntryID -> #EntryGraphName &]];
graph = ResourceFunction[
ResourceObject[<|"Name" -> "KEGGPathway", "ShortName" -> "KEGGPathway", "UUID" -> "c26fb78f-9391-4e5b-8348-1b3a9bcb8293", "ResourceType" -> "Function", "Version" -> "1.2.1", "Description" -> "Get the graph and additional information of a KEGG pathway", "RepositoryLocation" -> URL[
       "https://www.wolframcloud.com/obj/resourcesystem/api/1.0"], "SymbolName" -> "FunctionRepository`$cf8afda6cda14c308cd1e656f8629ece`KEGGPathway", "FunctionLocation" -> CloudObject[
       "https://www.wolframcloud.com/obj/81066f03-423e-4566-800b-da9d03968a36"]|>, {ResourceSystemBase -> "https://www.wolframcloud.com/obj/resourcesystem/api/1.0"}]]["hsa", "00030", "Graph"];
In[15]:=
vNames = VertexList[graph] /. vNamesRules
Out[15]=
In[16]:=
edNames = EdgeList[graph] /. vNamesRules
Out[16]=

Using the information about reactions and compounds from the glycolysis module, we get the next list of vertices and edges to highlight in the pentose phosphate pathway:

In[17]:=
vertx = Thread[Intersection[vNames, compounds[[All, 2]]] -> Red]
Out[17]=
In[18]:=
edges = {DirectedEdge["C01172", "C01236"] -> Red, DirectedEdge["C01236", "C00345"] -> Red}
Out[18]=

Highlight in red (i.e.,vertices and edges) the M00008 module in the pentose phosphate pathway:

In[19]:=
ResourceFunction[
ResourceObject[<|"Name" -> "KEGGPathway", "ShortName" -> "KEGGPathway", "UUID" -> "c26fb78f-9391-4e5b-8348-1b3a9bcb8293", "ResourceType" -> "Function", "Version" -> "1.2.1", "Description" -> "Get the graph and additional information of a KEGG pathway", "RepositoryLocation" -> URL[
     "https://www.wolframcloud.com/obj/resourcesystem/api/1.0"], "SymbolName" -> "FunctionRepository`$cf8afda6cda14c308cd1e656f8629ece`KEGGPathway", "FunctionLocation" -> CloudObject[
     "https://www.wolframcloud.com/obj/81066f03-423e-4566-800b-da9d03968a36"]|>, {ResourceSystemBase -> "https://www.wolframcloud.com/obj/resourcesystem/api/1.0"}]]["hsa", "00030", "Graph",
 VertexSize -> Medium,
 VertexStyle -> vertx,
 EdgeStyle -> edges]
Out[19]=

Publisher

Lina Marcela

Requirements

Wolfram Language 13.0 (December 2021) or above

Version History

  • 1.0.0 – 10 April 2025

Source Metadata

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License Information