Bioinformatic Harvester

Bioinformatic Harvester
Developer(s)	Urban Liebel, Björn Kindler
Stable release	4 / May 24, 2011; 12 years ago
Operating system	Web based
Type	Bioinformatics tool
Website	harvester.kit.edu [permanent dead link]

The Bioinformatic Harvester was a bioinformatic meta search engine created by the European Molecular Biology Laboratory^[1] and subsequently hosted and further developed by 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 tens of thousands of pages every day to scientists and physicians. Since 2014 the service is down.

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 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 subcellular localisation 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"

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.
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. ISBN 9780121828097. PMID 16413254.

Notes and references

^ Manoj, M; Elizabeth, Jacob (Oct 2008). "Information retrieval on Internet using meta-search engines: A review" (PDF). Journal of Scientific & Industrial Research. 67 (10): 739–746. ISSN 0022-4456.

External links

Official website ^{[permanent dead link]} Bioinformatic Harvester V at KIT Karlsruhe Institute of Technology
"Harvester42 at KIT - integrating 50 general search engines". Archived from the original on 2013-01-06. Retrieved 2013-01-06.

[1] Manoj, M; Elizabeth, Jacob (Oct 2008). "Information retrieval on Internet using meta-search engines: A review" (PDF). Journal of Scientific & Industrial Research. 67 (10): 739–746. ISSN 0022-4456.