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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 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 by the 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"
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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]
External links
- http://harvester.fzk.de Bioinformatic Harvester III at KIT Karlsruhe Institute of Technology
- Liebel-Lab at KIT
