Bioinformatic Harvester

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Bioinformatic Harvester
Developer(s)Urban Liebel, Björn Kindler
Stable release
4 / May 24, 2011; 8 years ago (2011-05-24)
Operating systemWeb based
TypeBioinformatics tool
Websitehttp://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:

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.

Access from external application

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

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. 404: 19–26. doi:10.1016/S0076-6879(05)04003-6. PMID 16413254.

Notes and references

  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