Bioinformatic Harvester

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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.

Contents

[edit] 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.
A screenshot of the Harvester search engine
A screenshot of the Harvester search engine

[edit] Harvester collects several types of information

[edit] 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).

[edit] 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).

[edit] "linkouts"

[edit] 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"

[edit] See also

[edit] 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]

[edit] External links

Databases supported by Bioinformatic Harvester
NCBI-BLAST | CDD | Ensembl | Entrez | Flybase | Flymine | GFP-cDNA | Genome_browser | GeneCard | Google_Scholar | GoPubMed | HomoloGene | iHOP | IPI | OMIM | Mitocheck | PSORT | PolyMeta | UniProt | SOURCE | SOSUI | RZPD | Sciencenet | STRING | SMART | ZFIN |
Languages