- Bioinformatic Harvester
The Bioinformatic-Harvester is a bioinformatic meta
search engineat KIT Karlsruhe Institute of Technologyfor genes and protein-associated information. Harvester currently works for human, mouse, rat, zebrafish, drosophilaand arabidopsis thalianabased information. Harvester cross-links >28 popular bioinformatic resources and allows cross searches. A ranking system similar to pageranksorts the search results and displays the more relevant information. Harvester serves 10.000s of pages every day to scientists and physicians.
How Harvester works
Harvester collects information from
proteinand 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 IPIand UniProtprotein information collection. The collections consists of:
* ~68.000 human, ~53.000 mouse, ~42.000 rat, ~51.000 zebrafish, ~35.000 arabidopsis and ~33.000 drosophila protein pages, which are curated and updated on a regular basis.
Harvester collects several types of information
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).
Databases rich in graphical elements
...are not collected, but crosslinked via
iframes. Iframes are transparent windows within a HTMLpages. 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.
BLAST, an algorithm for comparing biological sequences from the NCBI.
Ensembl, automatic gene annotation by the EMBL-EBI and Sanger-Institute
FlyBaseis a database of model organism " Drosophila melanogaster".
GoPubMedis a knowledge-based search engine for biomedical texts.
* iHOP, information hyperlinked over proteins via gene/protein synonyms
Mendelian Inheritance in Manproject 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 by the EMBL.
Zebrafish Information Network.
* [http://locate.imb.uq.edu.au/ LOCATE] subcellular localization database (mouse).
Genome browser, working draft assemblies for genomes UCSC
PolyMeta, meta search engine for Google, Yahoo, MSN, Ask, Exalead, AllTheWeb, GigaBlast
What one can find
Harvester allows a combination of different search terms and single words.
* Gene-name: "golga3"
* Gene-alias: "ADAP-S ADAS ADHAPS ADPS" (one gene name is sufficient)
* Gene-Ontologies: "Enzyme linked receptor protein signaling pathway"
* 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)
* Word: "Cancer"
* Comment: "highly expressed in heart"
* Author: "Merkel, Schmidt"
* Publication or project: "
European Bioinformatics Institute
* Human Protein Reference Database
Sequence profiling tool
* Liebel,U., & Kindler,B.,Pepperkok,R. (2004) "'Harvester': a fast meta search engine of human protein resources." Bioinformatics. 2004 Aug 12;20(12):1962-3. Epub 2004 Feb 26. [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=14988114&query_hl=5&itool=pubmed_docsum]
* Liebel,U., & Kindler,B.,Pepperkok,R. (2004) "Bioinformatic "Harvester": a search engine for genome-wide human, mouse, and rat protein resources." Methods Enzymol. 2005;404:19-26 [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=16413254&query_hl=3&itool=pubmed_docsum]
* http://harvester.fzk.de Bioinformatic Harvester III at KIT
Karlsruhe Institute of Technology
* [http://harvester42.fzk.de Harvester42] at KIT - integrating 10 general search engines
* [http://liebel-lab.fzk.de Liebel-Lab] at KIT
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