Bioinformatic Harvester

The Bioinformatic-Harvester is a bioinformatic meta search engine at 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 >28 popular bioinformatic resources and allows cross searches. A ranking system similar to Google pagerank sorts the search results and displays the more relevant information. Harvester serves 10.000s of pages every day to scientists and physicians.

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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:

• ~68.000 human, ~53.000 mouse, ~42.000 rat, ~51.000 zebrafish, ~35.000 arabidopsis and ~33.000 drosophila protein pages, which are curated and updated on a regular basis.

Harvester collects several types of information

Text based information

...from the following databases:

• UniProt, world largest protein database
• 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

...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.

• NCBI-BLAST, an algorithm for comparing biological sequences NCBI.
• Ensembl, automatic gene annotation. 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 EMBL.
• Zebrafish_Information_Network.
• LOCATE subcellular localization database (mouse).

"linkouts"

• 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. (2004) 'Harvester': a fast meta search engine of human protein resources. Bioinformatics. 2004 Aug 12;20(12):1962-3. Epub 2004 Feb 26.[1]

• Liebel,U., & Kindler,B.,Pepperkok,R. (2004) Bioinformatic "Harvester": a search engine for genome-wide human, mouse, and rat protein resources. Methods Enzymol. 2005;404:19-26[2]