Bioinformatic Harvester

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 localization 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

• Biological databases
• Entrez
• European Bioinformatics Institute
• Human Protein Reference Database
• Metadata
• Sequence profiling tool

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

External links

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