Bioinformatic Harvester
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The Bioinformatic Harvester is a bioinformatic meta search engine at KIT Karlsruhe Institute of Technology for genes and protein-associated information. Harvester currently works for human, mouse, rat, zebrafish, drosophila and arabidopsis thaliana based information. Harvester cross-links >50 popular bioinformatic resources and allows cross searches. Harvester serves 10.000s of pages every day to scientists and physicians.
| Developer(s) | Urban Liebel, Björn Kindler |
|---|---|
| Stable release | 4 / May 24, 2011 |
| Operating system | Web based |
| Type | Bioinformatics tool |
| License | Public Domain |
| Website | http://harvester.kit.edu |
Contents |
[edit] How Harvester works
Harvester collects information from protein and gene databases along with information from so called "prediction servers." Prediction server e.g. provide online sequence analysis for a single protein. Harvesters search index is based on the IPI and UniProt protein information collection. The collections consists of:
- ~72.000 human, ~57.000 mouse, ~41.000 rat, ~51.000 zebrafish, ~35.000 arabidopsis protein pages, which cross-link ~50 major bioinfiormatic resources.
[edit] Harvester crosslinks several types of information
[edit] Text based information
...from the following databases:
- UniProt, world largest protein database
- SOURCE, convenient gene information overview
- Simple Modular Architecture Research Tool (SMART),
- SOSUI, predicts transmembrane domains
- PSORT, predicts protein localisation
- HomoloGene, compares proteins from different species
- gfp-cdna, protein localisation with fluorescence microscopy
- International Protein Index (IPI).
[edit] Databases rich in graphical elements
...are not collected, but crosslinked via iframes. Iframes are transparent windows within a HTML pages. The iframe windows allows up-to-date viewing of the "iframed," linked databases. Several such iframes are combined on a Harvester protein page. This method allows convenient comparison of information from several databases.
- NCBI-BLAST, an algorithm for comparing biological sequences from the NCBI.
- Ensembl, automatic gene annotation by the EMBL-EBI and Sanger Institute
- FlyBase is a database of model organism Drosophila melanogaster.
- GoPubMed is a knowledge-based search engine for biomedical texts.
- iHOP, information hyperlinked over proteins via gene/protein synonyms
- Mendelian Inheritance in Man project catalogues all the known diseases.
- RZPD, German resources Center for genome research in Berlin/Heidelberg.
- STRING, Search Tool for the Retrieval of Interacting Genes/Proteins, developed by EMBL, SIB and UZH.
- Zebrafish Information Network.
- LOCATE subcellular localization database (mouse).
[edit] "linkouts"
- Genome browser, working draft assemblies for genomes UCSC
- Google Scholar
- Mitocheck
- PolyMeta, meta search engine for Google, Yahoo, MSN, Ask, Exalead, AllTheWeb, GigaBlast
[edit] What one can find
Harvester allows a combination of different search terms and single words.
Search Examples:
- Gene-name: "golga3"
- Gene-alias: "ADAP-S ADAS ADHAPS ADPS" (one gene name is sufficient)
- Gene-Ontologies: "Enzyme linked receptor protein signaling pathway"
- Unigene-Cluster: "Hs.449360"
- Go-annotation: "intra-Golgi transport"
- Molecular function: "protein kinase binding"
- Protein: "Q9NPD3"
- Protein domain: "SH2 sar"
- Protein Localisation: "endoplasmic reticulum"
- Chromosome: "2q31"
- Disease relevant: use the word "diseaselink"
- Combinations: "golgi diseaselink" (finds all golgi proteins associated with a disease)
- mRNA: "AL136897"
- Word: "Cancer"
- Comment: "highly expressed in heart"
- Author: "Merkel, Schmidt"
- Publication or project: "cDNA sequencing project"
[edit] See also
- Biological databases
- Entrez
- European Bioinformatics Institute
- Human Protein Reference Database
- Metadata
- Sequence profiling tool
[edit] Literature
- Liebel U, Kindler B, Pepperkok R (August 2004). "'Harvester': a fast meta search engine of human protein resources". Bioinformatics 20 (12): 1962–3. doi:10.1093/bioinformatics/bth146. PMID 14988114. http://bioinformatics.oxfordjournals.org/cgi/pmidlookup?view=long&pmid=14988114.
- Liebel U, Kindler B, Pepperkok R (2005). "Bioinformatic "Harvester": a search engine for genome-wide human, mouse, and rat protein resources". Meth. Enzymol. 404: 19–26. doi:10.1016/S0076-6879(05)04003-6. PMID 16413254. http://linkinghub.elsevier.com/retrieve/pii/S0076-6879(05)04003-6.
[edit] External links
- http://harvester.kit.edu Bioinformatic Harvester V at KIT Karlsruhe Institute of Technology
- Harvester42 at KIT - integrating 50 general search engines
