Bioinformatic Harvester

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.

Bioinformatic Harvester
Developer(s)	Urban Liebel, Björn Kindler
Stable release	4 / May 24, 2011; 8 months ago (2011-05-24)
Operating system	Web based
Type	Bioinformatics tool
License	Public Domain
Website	http://harvester.kit.edu

1 How Harvester works
2 Harvester crosslinks several types of information
3 What one can find
4 See also
5 Literature
6 External links

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.

Harvester crosslinks 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 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).

"linkouts"

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. 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.

External links

http://harvester.kit.edu Bioinformatic Harvester V at KIT Karlsruhe Institute of Technology
Harvester42 at KIT - integrating 50 general search engines