Database Commons is a curated catalogue of biological databases, providing people with easy access to a
comprehensive collection of publicly available biological databases encompassing different data types and
spanning diverse organisms. It integrates relevant information for all collected databases (including
database name, URL, description, hosted institution, related publication(s), contact information, etc.) and
catalogues each database based on its data type, organism and locating, accordingly enabling people to
easily find a specific collection of databases of interest.
Database Commons allows any one to rate any database by considering data quality & quantity, content
organization & presentation, and system accessibility & reliability, facilitating efficient location of
appropriate databases of interest.
Together, Database Commons features cataloguing databases under different criteria and incorporating
community rating on database utility, thus serving as a valuable resource for effective exploitation of all
publicly available databases.
To date, databases in Database Commons are collected primarily from journals including Nucleic Acid
Research, Database, Bioinformatics, BMC Bioinformatics, etc.
A database may encompass multiple data objects. In Database Commons, there are a total of 6 data objects as
A database may encompass multiple data types. In Database Commons, there are a total of 3 data types as
- DNA: gene/chromosome/genome sequence, DNA mutation/modification, DNA structure, DNA
elements including probe, primer, motif, repeat sequence, etc.
- RNA: RNA sequence, coding & non-coding transcripts, alternative splicing, RNA
editing/modification, RNA probe and primer, RNA motif and structure, RNA expression
- Protein: protein sequence, protein motif and domain, protein structure, protein
modification, protein-protein interaction, protein expression
A database may encompass multiple database categories. In Database Commons, there are a total of 13 database categories as detailed below.
- Raw bio-data: raw data of nucleic acid/protein sequencing and microarray, and
image, digit, video, audio from biological and medical research
- Gene, genome and annotation: gene/genetic element annotation, gene
structure/family/motif/domain annotation, genome annotation, comparative genome (metagenome, pan-genome)
analysis and annotation
- Genotype, phenotype and variation: genotypes, phenotypes, multiple-scale variations
(including SNP, INDEL, CNV, chromosomal rearrangement and other structural variation),
- Phylogeny and homology: phylogeny reconstruction of genes/species, evolutionary
history/process/event among individuals/organisms, homology identification
- Expression: RNA/protein expression, expression abundance and pattern, RNA probe or
primer used for gene expression detection, differential expression analysis
- Modification: DNA modification, post-transcriptional modification of mRNA and
non-coding RNA, post-translational modification of protein, modification type/technology/function
- Structure: secondary, tertiary and quaternary structure of DNA/RNA/protein, chromatin
- Interaction: direct (physical) and indirect (functional) associations, including
protein-protein interaction, RNA-protein interaction, DNA-protein interaction, gene regulatory
interaction, biochemical reaction, antigen and antibody, and genetic interaction
- Pathway: biological pathways for metabolic, signaling, gene regulatory analysis
- Health and medicine: disease variation/genotype-phenotype association, immune reaction,
disease model, clinical biomarker, therapeutic target, drug & chemical compound, pharmacogenomics and
pharmacodynamics, electronic health record
- Standard, ontology and nomenclature: standard, ontology and nomenclature for biological
- Literature: literature information, literature/text mining, textual annotation based on
- Metadata: metadata information for biological entities, e.g.,
Database Commons features community rating on database utility by taking account of the following three
Data quality & quantity: consider data integrity, accuracy, standardization, consistency and
Content organization & presentation: consider whether content is organized in an appropriate
manner which makes content easily readable and understandable and is presented by user friendly web
System accessibility & reliability: consider whether system is always accessible and reliably
A database containing high-quality curated data is abortive if data is poorly organized or presented.
A database containing high-quality curated data is unavailing if this database cannot be accessible or
HTTP Status Codes
Here is a list of HTTP status codes with a brief explanation, which are represented by three digits and fall
into five classes.
1xx Informational: e.g., 101 Switching Protocols
2xx Success: e.g., 200 OK, that is standard response for successful HTTP requests.
3xx Redirection: e.g., 301 Moved Permanently
4xx Client Error: e.g., 403 Forbidden, 404 Not Found
5xx Server Error: e.g., 500 Internal Server Error, 503 Service Unavailable
More information about HTTP status code can be found at Wikipedia.
In addition, unexpected exceptions including timeout, errors occurred when sending requests, etc., are
indicated by "-1".
BIG Data Center, Beijing Institute of Genomics, Chinese Academy of Sciences
No.1 Beichen West Road
Chaoyang District, Beijing 100101
Email: Dr. Lina Ma (malina (AT) big.ac.cn), Dr. Zhang Zhang (zhangzhang (AT)
Tel: +86 (10) 84097845
Fax: +86 (10) 84097298