Bioinformatic Harvester

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The Bioinformatic Harvester is 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.

Bioinformatic Harvester
Developer(s) Urban Liebel, Björn Kindler
Stable release 4 / May 24, 2011; 3 years ago (2011-05-24)
Operating system Web based
Type Bioinformatics tool
License Public Domain
Website http://harvester.kit.edu

How Harvester works[edit]

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[edit]

Text based information[edit]

from the following databases:

Databases rich in graphical elements[edit]

...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.

Access from external application[edit]

What one can find[edit]

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[edit]

Literature[edit]

Notes and references[edit]

  1. ^ Manoj, M, Elizabeth, Jacob (Oct 2008). "Information retrieval on Internet using meta-search engines: A review". JSIR (CSIR). 67 (10): 739–746. ISSN 0022-4456. 

External links[edit]