The Bioinformatic Harvester was a bioinformatic meta

search engine A search engine is a software system that provides hyperlinks to web pages, and other relevant information on World Wide Web, the Web in response to a user's web query, query. The user enters a query in a web browser or a mobile app, and the sea ...

created by the

European Molecular Biology Laboratory The European Molecular Biology Laboratory (EMBL) is an intergovernmental organization dedicated to molecular biology research and is supported by 29 member states, two prospect member states, and one associate member state. EMBL was created in ...

and subsequently hosted and further developed by KIT

Karlsruhe Institute of Technology The Karlsruhe Institute of Technology (KIT; ) is both a German public research university in Karlsruhe, Baden-Württemberg, and a research center of the Helmholtz Association. KIT was created in 2009 when the University of Karlsruhe (), founde ...

for

gene In biology, the word gene has two meanings. The Mendelian gene is a basic unit of heredity. The molecular gene is a sequence of nucleotides in DNA that is transcribed to produce a functional RNA. There are two types of molecular genes: protei ...

s and protein-associated information. Harvester currently works for

human Humans (''Homo sapiens'') or modern humans are the most common and widespread species of primate, and the last surviving species of the genus ''Homo''. They are Hominidae, great apes characterized by their Prehistory of nakedness and clothing ...

mouse A mouse (: mice) is a small rodent. Characteristically, mice are known to have a pointed snout, small rounded ears, a body-length scaly tail, and a high breeding rate. The best known mouse species is the common house mouse (''Mus musculus'' ...

rat Rats are various medium-sized, long-tailed rodents. Species of rats are found throughout the order Rodentia, but stereotypical rats are found in the genus ''Rattus''. Other rat genera include '' Neotoma'' (pack rats), '' Bandicota'' (bandicoo ...

zebrafish The zebrafish (''Danio rerio'') is a species of freshwater ray-finned fish belonging to the family Danionidae of the order Cypriniformes. Native to South Asia, it is a popular aquarium fish, frequently sold under the trade name zebra danio (an ...

drosophila ''Drosophila'' (), from Ancient Greek δρόσος (''drósos''), meaning "dew", and φίλος (''phílos''), meaning "loving", is a genus of fly, belonging to the family Drosophilidae, whose members are often called "small fruit flies" or p ...

and

arabidopsis thaliana ''Arabidopsis thaliana'', the thale cress, mouse-ear cress or arabidopsis, is a small plant from the mustard family (Brassicaceae), native to Eurasia and Africa. Commonly found along the shoulders of roads and in disturbed land, it is generally ...

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 Proteins are large biomolecules and macromolecules that comprise one or more long chains of amino acid residue (biochemistry), residues. Proteins perform a vast array of functions within organisms, including Enzyme catalysis, catalysing metab ...

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 UniProt is a freely accessible database of protein sequence and functional information, many entries being derived from genome sequencing projects. It contains a large amount of information about the biological function of proteins derived fro ...

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: *

, 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 Hypertext Markup Language (HTML) is the standard markup language for documents designed to be displayed in a web browser. It defines the content and structure of web content. It is often assisted by technologies such as Cascading Style Sheets ( ...

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 The National Center for Biotechnology Information (NCBI) is part of the National Library of Medicine (NLM), a branch of the National Institutes of Health (NIH). It is approved and funded by the government of the United States. The NCBI is loca ...

* Ensembl, automatic gene annotation by the EMBL- EBI and

Sanger Institute The Wellcome Sanger Institute, previously known as The Sanger Centre and Wellcome Trust Sanger Institute, is a non-profit organisation, non-profit British genomics and genetics research institute, primarily funded by the Wellcome Trust. It is l ...

* FlyBase is a database of model organism ''

Drosophila melanogaster ''Drosophila melanogaster'' is a species of fly (an insect of the Order (biology), order Diptera) in the family Drosophilidae. The species is often referred to as the fruit fly or lesser fruit fly, or less commonly the "vinegar fly", "pomace fly" ...

'' * 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 String or strings may refer to: *String (structure), a long flexible structure made from threads twisted together, which is used to tie, bind, or hang other objects Arts, entertainment, and media Films * ''Strings'' (1991 film), a Canadian anim ...

, 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

* Genome browser, working draft assemblies for genomes UCSC *

Google Scholar Google Scholar is a freely accessible web search engine that indexes the full text or metadata of Academic publishing, scholarly literature across an array of publishing formats and disciplines. Released in Beta release, beta in November 2004, th ...

* 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 In molecular biology, messenger ribonucleic acid (mRNA) is a single-stranded molecule of RNA that corresponds to the genetic sequence of a gene, and is read by a ribosome in the process of Protein biosynthesis, synthesizing a protein. mRNA is ...

: "AL136897" * Word: "Cancer" * Comment: "highly expressed in heart" * Author: "Merkel, Schmidt" * Publication or project: "

cDNA In genetics, complementary DNA (cDNA) is DNA that was reverse transcribed (via reverse transcriptase) from an RNA (e.g., messenger RNA or microRNA). cDNA exists in both single-stranded and double-stranded forms and in both natural and engin ...

sequencing project"

Literature

* *

Notes and references

External links

* Bioinformatic Harvester V at KIT

* {{Cite web , url=http://harvester42.fzk.de/ , title=Harvester42 at KIT - integrating 50 general search engines , access-date=2013-01-06 , archive-url=https://archive.today/20130106060017/http://harvester42.fzk.de/ , archive-date=2013-01-06 , url-status=dead Bioinformatics software Biological databases Biology websites Internet search engines Science and technology in Cambridgeshire South Cambridgeshire District