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PhenomicDB is a free phenotype oriented database. It contains data for some of the main model organisms such as Homo |
'''PhenomicDB''' is a free [[phenotype]] oriented [[database]]. It contains data for some of the main model organisms such as ''Homo sapiens, Mus musculus, Drosophila melanogaster'', and others. PhenomicDB merges and structures phenotypic data from various public sources: [[WormBase]], [[FlyBase]], [[Entrez|NCBI Gene]], [[Mouse_Genome_Informatics|MGI]], and [[ZFIN]] using clustering algorithms. |
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PhenomicDB suggests an interesting new approach for organizing and representing the phenotypic data using clustering algorithms. The phenotipic clusters may provide an alternative way for obtaining new knowledge. |
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== Further reading == |
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* {{cite journal |author=Groth P, Kalev I, Kirov I, Traikov B, Leser U, Weiss B |title=Phenoclustering: online mining of cross-species phenotypes |journal=[[Bioinformatics (journal)|Bioinformatics]] |volume=26 |issue=15 |pages=1924–5 |year=2010 |month=August |pmid=20562418 |pmc=2905556 |doi=10.1093/bioinformatics/btq311 |url=http://bioinformatics.oxfordjournals.org/cgi/pmidlookup?view=long&pmid=20562418 |accessdate=2011-03-17}} |
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* {{cite journal |author=Groth P, Pavlova N, Kalev I, Tonov S, Georgiev G, Pohlenz HD, Weiss B |title=PhenomicDB: a new cross-species genotype/phenotype resource |journal=[[Nucleic Acids Research]] |volume=35 |issue=Database issue |pages=D696–9 |year=2007 |month=January |pmid=16982638 |pmc=1781118 |doi=10.1093/nar/gkl662 |url=http://nar.oxfordjournals.org/cgi/pmidlookup?view=long&pmid=16982638 |accessdate=2011-03-17}} |
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==Publications== |
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* {{cite journal |author=Kahraman A, Avramov A, Nashev LG, Popov D, Ternes R, Pohlenz HD, Weiss B |title=PhenomicDB: a multi-species genotype/phenotype database for comparative phenomics |journal=Bioinformatics |volume=21 |issue=3 |pages=418–20 |year=2005 |month=February |pmid=15374875 |doi=10.1093/bioinformatics/bti010 |url=http://bioinformatics.oxfordjournals.org/cgi/pmidlookup?view=long&pmid=15374875 |accessdate=2011-03-17}} |
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1. Groth P, Kalev I, Kirov I, Traikov B, Leser U, Weiss B. Phenoclustering: online mining of cross-species phenotypes. (Bioinformatics 2010 26(15):1924-1925), PMID: [http://www.ncbi.nlm.nih.gov/pubmed?term=20562418 20562418]<br /> |
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* {{cite doi|10.2174/157489306777828008}} |
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* {{cite doi|10.1186/1471-2105-9-136}} |
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2. Groth P, Pavlova N, Kalev I, Tonov S, Georgiev G, Pohlenz HD, Weiss B. PhenomicDB: a new cross-species genotype/phenotype resource. Nucleic Acids Res. 2006 Sep 28, PMID: [http://www.ncbi.nlm.nih.gov/pubmed?term=16982638 16982638] <br /> |
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3. Abdullah Kahraman, Andrey Avramov, Lyubomir Nashev, Dimitar Popov, Rainer Ternes, Hans-Dieter Pohlenz, and Bertram Weiss. PhenomicDB: a multi-species genotype/phenotype database for comparative phenomics (Bioinformatics 2005 21: 418-420), PMID: [http://www.ncbi.nlm.nih.gov/pubmed?term=15374875 15374875]<br /> |
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4. Groth, P. & Weiss, B. Phenotype Data: A Neglected Resource in Biomedical Research? [http://www.ingentaconnect.com/content/ben/cbio/2006/00000001/00000003/art00008?crawler=true#search=%22groth%20weiss%20phenotype%20data%20neglected%20resource%22 Current Bioinformatics, Volume 1, Number 3, August 2006, pp. 347-358(12)]<br /> |
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5. Groth P, Weiss B, Pohlenz HD, Leser U Mining phenotypes for gene function prediction [http://www.biomedcentral.com/1471-2105/9/136 BMC Bioinformatics 2008, 9:136 doi:10.1186/1471-2105-9-136]<br /> |
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==External links== |
==External links== |
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* {{Official|http://www.phenomicdb.de}} |
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Revision as of 10:34, 17 March 2011
PhenomicDB is a free phenotype oriented database. It contains data for some of the main model organisms such as Homo sapiens, Mus musculus, Drosophila melanogaster, and others. PhenomicDB merges and structures phenotypic data from various public sources: WormBase, FlyBase, NCBI Gene, MGI, and ZFIN using clustering algorithms.
Further reading
- Groth P, Kalev I, Kirov I, Traikov B, Leser U, Weiss B (2010). "Phenoclustering: online mining of cross-species phenotypes". Bioinformatics. 26 (15): 1924–5. doi:10.1093/bioinformatics/btq311. PMC 2905556. PMID 20562418. Retrieved 2011-03-17.
{{cite journal}}: Unknown parameter|month=ignored (help)CS1 maint: multiple names: authors list (link) - Groth P, Pavlova N, Kalev I, Tonov S, Georgiev G, Pohlenz HD, Weiss B (2007). "PhenomicDB: a new cross-species genotype/phenotype resource". Nucleic Acids Research. 35 (Database issue): D696–9. doi:10.1093/nar/gkl662. PMC 1781118. PMID 16982638. Retrieved 2011-03-17.
{{cite journal}}: Unknown parameter|month=ignored (help)CS1 maint: multiple names: authors list (link) - Kahraman A, Avramov A, Nashev LG, Popov D, Ternes R, Pohlenz HD, Weiss B (2005). "PhenomicDB: a multi-species genotype/phenotype database for comparative phenomics". Bioinformatics. 21 (3): 418–20. doi:10.1093/bioinformatics/bti010. PMID 15374875. Retrieved 2011-03-17.
{{cite journal}}: Unknown parameter|month=ignored (help)CS1 maint: multiple names: authors list (link) - Attention: This template ({{cite doi}}) is deprecated. To cite the publication identified by doi:10.2174/157489306777828008, please use {{cite journal}} (if it was published in a bona fide academic journal, otherwise {{cite report}} with
|doi=10.2174/157489306777828008instead. - Attention: This template ({{cite doi}}) is deprecated. To cite the publication identified by doi:10.1186/1471-2105-9-136, please use {{cite journal}} (if it was published in a bona fide academic journal, otherwise {{cite report}} with
|doi=10.1186/1471-2105-9-136instead.