Bioinformatic Harvester

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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[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 bioinformatic resources.

Harvester crosslinks several types of information[edit]

Text based information[edit]

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[edit]

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[edit]

• 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[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]

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

Literature[edit]

• 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. Methods in Enzymology. 404: 19–26. doi:10.1016/S0076-6879(05)04003-6. ISBN 9780121828097. PMID 16413254.

Notes and references[edit]

External links[edit]

• Official website ^{[permanent dead link]} Bioinformatic Harvester V at KIT Karlsruhe Institute of Technology
• "Harvester42 at KIT - integrating 50 general search engines". Archived from the original on 2013-01-06. Retrieved 2013-01-06.