Table 2 |
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|
COPD specific knowledge base |
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|
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 |
|
|
||||
|
Public data integrated into BioXM in the current version of the BioBridge COPD knowledge base. |
||||
|
Maier et al. BMC Systems Biology 2011 5:38 doi:10.1186/1752-0509-5-38 |
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