Skip to main content

Table 2 COPD specific knowledge base

From: Knowledge management for systems biology a general and visually driven framework applied to translational medicine

Source database

Information type

Current statistics

Level of curation

Updates/Version

BIND

Protein interaction

Molecular complexes

Pathways

6256 Interactions

High throughput data submission and manually curated from literature

last public version 20.3.07

BioGrid

Protein interaction

19 707 interactions

Manually curated from literature

Different evidence codes

updated monthly

BRENDA

Enzyme kinetics

4 729

Manually curated from literature

updated monthly

ChEBI

Compound information

15 367

Curated from different data sources

updated weekly

Comparative

Toxicogenomics

Database

(CTD)

Compound-gene, Compound-disease and Gene-disease relationships

259 898 relations

Manually curated from literature

updated monthly

EntrezGene

Gene functional information

80 793 human, mouse and rat genes

Curated information integrated from different databases, based on RefSeq genomes

updated weekly

Enzyme

Enzyme related functional information

4 833

Manually curated from literature

updated weekly

GEO

Functional genomics

data (expression, ChIP-chip etc.)

>400 000 individual experiments

User submission

updated weekly

IntAct

Protein interaction

21 584 binary interactions

Literature curation

User submission

updated weekly

KEGG

Pathways

418 pathways

Manually curated from literature

updated monthly

LIGAND

Compound information

15 185

Manually curated from the published literature

updated monthly

MIPS

Mammalian

Protein Interaction

410 interactions

Manually curated from literature

current release 31.10.07

OMIM

Gene - disease relations

20 823

Curated from literature

updated weekly

Pfam

Protein family information

10 340 families

Manually curated from sequence alignments

23.0

ProLinks

Interaction

>1.4 million

Automatic inference

last release 18.10.04

PubChem

Compound information

>26 million

Automatic collection

updated weekly

PubMed

Literature abstracts

>19 million

Automatic collection with manual curation

updated weekly

Reactome

Interactions and pathways

>600 pathways, >24 000

Inteactions

Manual curation

updated monthly

RefSeq

DNA and protein sequences

>11 million

Automatic processing and manual curation

updated weekly

Unigene

Transcript sequences

>2 million

User submission followed by automatic clustering

updated monthly

UniProt

Protein sequences

>10 million

Automatic processing, Swissprot subsection manual curation

updated bi-weekly

  1. Public data integrated into BioXM in the current version of the BioBridge COPD knowledge base.