BioNumbers
BioNumbers is a free-access database of quantitative data in biology designed to provide the scientific community with access to the large amount of data now generated in the biological literature. The database aims to make quantitative values more easily available, to aid fields such as systems biology.
The BioNumbers project performs literature-based curation of various sources.[1] It is a regularly updated online resource that contains >13,000 entries from ~1,000 distinct references.[2] Examples of data include transcription and translation rates, organism and organelle sizes, metabolites concentrations and growth rates. Entries are provided with full reference and details such as measurement method and comments.
BioNumbers also publishes a monthly review of a problem in quantitative biology.
History
BioNumbers was created as a Wikipedia-format community collaborative initiative in 2007 by Ron Milo, Paul Jorgensen and Mike Springer at the Systems Biology Department at Harvard Medical School.[3][1] It is currently managed and curated at the Milo Lab from the Weizmann Institute of Science.
The database is funded by the Systems Biology Department at Harvard Medical School, and Weizmann Institute of Science.[2][4]
References
- ^ a b Phillips, Rob; Milo, Ron (2009-12-22). "A feeling for the numbers in biology". Proceedings of the National Academy of Sciences of the United States of America. 106 (51): 21465–21471. Bibcode:2009PNAS..10621465P. doi:10.1073/pnas.0907732106. ISSN 0027-8424. PMC 2799844. PMID 20018695.
- ^ a b Milo, Ron; Jorgensen, Paul; Moran, Uri; Weber, Griffin; Springer, Michael (2010). "BioNumbers—the database of key numbers in molecular and cell biology". Nucleic Acids Research. 38 (Database issue): D750–D753. doi:10.1093/nar/gkp889. ISSN 0305-1048. PMC 2808940. PMID 19854939.
- ^ Community, Physics (2022-02-24). "Interactions: Ron Milo and the BioNumbers database". Physics Community. Retrieved 2023-11-11.
- ^ "About Us". BioNumbers. Retrieved 2023-11-11.
External links
- BioNumbers
- BioNumbers on OpenWetWare
- Barry Schwartz BioNumbers – Specialty Biology Answer Search Engine March 24, 2009
- Milo Lab
- Ron Milo; Rob B. Phillips, Cell biology by the numbers, Wikidata Q106357478
- v
- t
- e
- Sequence databases: GenBank, European Nucleotide Archive, DNA Data Bank of Japan and China National GeneBank
- Secondary databases: UniProt, database of protein sequences grouping together Swiss-Prot, TrEMBL and Protein Information Resource
- Other databases: BioNumbers, Protein Data Bank, Ensembl, InterPro, KEGG, and Gene Ontology
- Specialised genomic databases: BOLD, Saccharomyces Genome Database, FlyBase, VectorBase, WormBase, Rat Genome Database, PHI-base, Arabidopsis Information Resource, GISAID and Zebrafish Information Network
- Server: ExPASy
- Rosalind (education platform)
- Broad Institute
- Computational Biology Department (CBD)
- Microsoft Research - University of Trento Centre for Computational and Systems Biology (COSBI)
- Database Center for Life Science (DBCLS)
- DNA Data Bank of Japan (DDBJ)
- European Bioinformatics Institute (EMBL-EBI)
- European Molecular Biology Laboratory (EMBL)
- Flatiron Institute
- J. Craig Venter Institute (JCVI)
- Max Planck Institute of Molecular Cell Biology and Genetics (MPI-CBG)
- US National Center for Biotechnology Information (NCBI)
- Japanese Institute of Genetics
- Netherlands Bioinformatics Centre (NBIC)
- Philippine Genome Center (PGC)
- Scripps Research
- Swiss Institute of Bioinformatics (SIB)
- Wellcome Sanger Institute
- Whitehead Institute
- African Society for Bioinformatics and Computational Biology (ASBCB)
- Australia Bioinformatics Resource (EMBL-AR)
- European Molecular Biology network (EMBnet)
- International Nucleotide Sequence Database Collaboration (INSDC)
- International Society for Biocuration (ISB)
- International Society for Computational Biology (ISCB)
- Student Council (ISCB-SC)
- Institute of Genomics and Integrative Biology (CSIR-IGIB)
- Japanese Society for Bioinformatics (JSBi)
- Basel Computational Biology Conference ([BC2])
- European Conference on Computational Biology (ECCB)
- Intelligent Systems for Molecular Biology (ISMB)
- International Conference on Bioinformatics (InCoB)
- International Conference on Computational Intelligence Methods for Bioinformatics and Biostatistics (CIBB)
- ISCB Africa ASBCB Conference on Bioinformatics
- Pacific Symposium on Biocomputing (PSB)
- Research in Computational Molecular Biology (RECOMB)
- CRAM format
- FASTA format
- FASTQ format
- NeXML format
- Nexus format
- Pileup format
- SAM format
- Stockholm format
- VCF format
- GFF format
- GTF format
- Category
- Commons