Bioinformatic Harvester

Bioinformatic HarvesterDeveloper(s)| Urban Liebel, Björn Kindler

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Stable release|

4 / May 24, 2011; 14 years ago (2011-05-24)

Operating system| Web based
Type| Bioinformatics tool
Website| harvester.kit.edu [yes|permanent dead link|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.

## Contents

* 1 How Harvester works
* 2 Harvester crosslinks several types of information
* 2.1 Text based information
* 2.2 Databases rich in graphical elements
* 2.3 Access from external application
* 3 What one can find
* 4 See also
* 5 Literature
* 6 Notes and references
* 7 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 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"

## See also

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

## Literature

* "'Harvester': a fast meta search engine of human protein resources". Bioinformatics 20 (12): 1962–3. August 2004. doi:10.1093/bioinformatics/bth146. PMID 14988114.
* "Bioinformatic "Harvester": a search engine for genome-wide human, mouse, and rat protein resources". Meth. Enzymol.. Methods in Enzymology 404: 19–26. 2005. doi:10.1016/S0076-6879(05)04003-6. ISBN 9780121828097. PMID 16413254.

## Notes and references

1. ↑ Manoj, M; Elizabeth, Jacob (Oct 2008). "Information retrieval on Internet using meta-search engines: A review". Journal of Scientific & Industrial Research 67 (10): 739–746. ISSN 0022-4456. http://nopr.niscair.res.in/bitstream/123456789/2243/1/JSIR 67(10) 739-746.pdf?trk=right_banner&id=1400972373&ref=88d4042477e42c447b6b62f13e16f07a.

## External links

* Bioinformatic Harvester V at KIT Karlsruhe Institute of Technology
* "Harvester42 at KIT - integrating 50 general search engines". http://harvester42.fzk.de/.

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