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Bioinformatic Harvester

The Bioinformatic Harvester was a bioinformatics search engine created by the European Molecular Biology Laboratory to search genes and proteins across multiple databases. It indexed information from over 50 databases and allowed users to simultaneously view and compare results. At its peak, Harvester served tens of thousands of queries per day but was shut down in 2014. It indexed data on human, mouse, rat, zebrafish, fruit fly, and plant genes and proteins.

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65 views3 pages

Bioinformatic Harvester

The Bioinformatic Harvester was a bioinformatics search engine created by the European Molecular Biology Laboratory to search genes and proteins across multiple databases. It indexed information from over 50 databases and allowed users to simultaneously view and compare results. At its peak, Harvester served tens of thousands of queries per day but was shut down in 2014. It indexed data on human, mouse, rat, zebrafish, fruit fly, and plant genes and proteins.

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william919
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© © All Rights Reserved
We take content rights seriously. If you suspect this is your content, claim it here.
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Bioinformatic Harvester

The Bioinformatic Harvester was a bioinformatic meta search


Bioinformatic Harvester
engine created by the European Molecular Biology Laboratory[1]
and subsequently hosted and further developed by KIT Karlsruhe Developer(s) Urban Liebel,
Institute of Technology for genes and protein-associated Björn Kindler
information. Harvester currently works for human, mouse, rat,
Stable release 4 / May 24,
zebrafish, drosophila and arabidopsis thaliana based information.
2011
Harvester cross-links >50 popular bioinformatic resources and
allows cross searches. Harvester serves tens of thousands of pages Operating system Web based
every day to scientists and physicians. Since 2014 the service is Type Bioinformatics
down. tool
Website harvester.kit
How Harvester works .edu (http://har
vester.kit.edu)
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 bioinformatic resources.

Harvester crosslinks several types of information

Text based information

From the following databases:

UniProt, one of the largest protein databases


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


These databases are not collected, but are crosslinked, being displayed via iframes. An iframe is a window
within an HTML page for an embedded view of and interactive access to the linked database. Several such
iframes are combined on a single Harvester protein page. This allows simultaneous 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 (https://web.archive.org/web/20171231015119/http://locate.imb.uq.edu.au/)
subcellular localization database (mouse)

Access from external application


Genome browser, working draft assemblies for genomes UCSC
Google Scholar
Mitocheck
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.

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"

See also
List of academic databases and search engines
Biological databases
Entrez
European Bioinformatics Institute
Human Protein Reference Database
Metadata
Sequence profiling tool

Literature
Liebel U, Kindler B, Pepperkok R (August 2004). " 'Harvester': a fast meta search engine of
human protein resources" (https://doi.org/10.1093%2Fbioinformatics%2Fbth146).
Bioinformatics. 20 (12): 1962–3. doi:10.1093/bioinformatics/bth146 (https://doi.org/10.1093%
2Fbioinformatics%2Fbth146). PMID 14988114 (https://pubmed.ncbi.nlm.nih.gov/14988114).
Liebel U, Kindler B, Pepperkok R (2005). "Bioinformatic "Harvester": a search engine for
genome-wide human, mouse, and rat protein resources". Meth. Enzymol. Methods in
Enzymology. 404: 19–26. doi:10.1016/S0076-6879(05)04003-6 (https://doi.org/10.1016%2F
S0076-6879%2805%2904003-6). ISBN 9780121828097. PMID 16413254 (https://pubmed.n
cbi.nlm.nih.gov/16413254).

Notes and references


1. Manoj, M; Elizabeth, Jacob (Oct 2008). "Information retrieval on Internet using meta-search
engines: A review" (http://nopr.niscair.res.in/bitstream/123456789/2243/1/JSIR%2067(10)%2
0739-746.pdf?trk=right_banner&id=1400972373&ref=88d4042477e42c447b6b62f13e16f07
a) (PDF). Journal of Scientific & Industrial Research. 67 (10): 739–746. ISSN 0022-4456 (htt
ps://www.worldcat.org/issn/0022-4456).

External links
Official website (http://harvester.kit.edu) Bioinformatic Harvester V at KIT Karlsruhe Institute
of Technology
"Harvester42 at KIT - integrating 50 general search engines" (https://archive.today/2013010
6060017/http://harvester42.fzk.de/). Archived from the original (http://harvester42.fzk.de/) on
2013-01-06. Retrieved 2013-01-06.

Retrieved from "https://en.wikipedia.org/w/index.php?title=Bioinformatic_Harvester&oldid=1098947598"

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