KEGG Metabolic Relation Network (Directed)
Donated on 11/27/2011
KEGG Metabolic pathways modeled as directed relation network. Variety of graphical features presented.
Dataset Characteristics
Multivariate, Univariate, Text
Subject Area
Biology
Associated Tasks
Classification, Regression, Clustering
Feature Type
Integer, Real
# Instances
53414
# Features
-
Dataset Information
Additional Information
KEGG Metabolic pathways can be realized into network. Two kinds of network / graph can be formed. These include Reaction Network and Relation Network. In Reaction network, Substrate or Product compound are considered as Node and genes are treated as edge. Whereas in the relation network, Substrate and Product componds are considered as Edges while enzyme and genes are placed as nodes. We tool large number of metabolic pathways from KEGG XML. They were modeled into the graph as described above. With the help of Cytoscape tool, variety of network features were compunted.
Has Missing Values?
No
Variables Table
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0 to 10 of 24
Additional Variable Information
a) Pathway text b) Nodes integer (min:2, max:116) c) Edges integer (min:1, max:606) d) Connected Components integer (min:1, max:13) e) Network Diameter integer (min:1, max:30) f) Network Radius integer (min:1, max:2) g) Shortest Path integer (min:1, max:3277) h) Characteristic Path Length real (min:1, max:13.543) i) Avg.num.Neighbours real (min:1, max:14.163) j) Isolated Nodes integer (min:0, max:1) k) Number of Self Loops integer (min:0, max:0) l) Multi-edge Node Pair integer (min:0, max:57) m) NeighborhoodConnectivity real (min:1, max:17.41) n) Outdegree real (min:0.5, max:7.1639) o) Stress real (min:0, max:13870.674) p) SelfLoops integer (min:0, max:0) q) PartnerOfMultiEdgedNodePairs real (min:0, max:4.89) r) EdgeCount real (min:1, max:14.328) s) BetweennessCentrality real (min:0, max:0.33) t) Indegree real (min:0.5, max:7.1639) u) Eccentricity real (min:0.083, max:25.069) v) ClosenessCentrality real (min:0.083, max:1) w) AverageShortestPathLength real (min:0.083, max:11.754) x) ClusteringCoefficient real (min:0, max:0.746)
Dataset Files
| File | Size |
|---|---|
| Relation Network (Directed).data | 7 MB |
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pip install ucimlrepo
from ucimlrepo import fetch_ucirepo # fetch dataset kegg_metabolic_relation_network_directed = fetch_ucirepo(id=220) # data (as pandas dataframes) X = kegg_metabolic_relation_network_directed.data.features y = kegg_metabolic_relation_network_directed.data.targets # metadata print(kegg_metabolic_relation_network_directed.metadata) # variable information print(kegg_metabolic_relation_network_directed.variables)
Naeem, M. & Asghar, S. (2011). KEGG Metabolic Relation Network (Directed) [Dataset]. UCI Machine Learning Repository. https://doi.org/10.24432/C5CK52.
Creators
Muhammad Naeem
Sohail Asghar
DOI
License
This dataset is licensed under a Creative Commons Attribution 4.0 International (CC BY 4.0) license.
This allows for the sharing and adaptation of the datasets for any purpose, provided that the appropriate credit is given.