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Biology Articles » Botany » MetaCrop: a detailed database of crop plant metabolism » Database description

Database description
- MetaCrop: a detailed database of crop plant metabolism

Content
MetaCrop contains hand-curated information of about 40 majormetabolic pathways in various crop plants with special emphasison the metabolism of agronomically important organs such asseed and tuber. Species of both monocotyledons and dicotyledonsare represented. Reactions incorporate information about involvedenzymes (e.g. EC and CAS number), metabolites (e.g. CAS number,molecular weight and chemical formula), stoichiometry and detailedlocation (species, organ, tissue, compartment and developmentalstage). Furthermore, for central metabolism (sucrose breakdown,glycolysis, TCA cycle) kinetic data is available for the reactions.References and relevant PubMed IDs are given. In order to havea controlled vocabulary allowing the comparison of data fromdifferent sources ontology terms were used (8,9).

Currently the database focuses on the monocotyledon speciesHordeum vulgare (barley), Triticum aestivum (wheat), Oryza sativa(rice), Zea mays (maize) and the dicotyledon species Solanumtuberosum (potato) and Brassica napus (canola). Additional dataof other crop and non-crop plants is currently being added tothe database. In total, about 400 enzymatic reactions, 60 transportprocesses, 5 compartments and 740 references are representedin MetaCrop (see Table 1, content as of July 2007). In orderto enable the export of detailed metabolic networks for systemsbiology approaches, most of the data contained in the databasecorresponds to biochemical data (e.g. taxon-specific enzymaticinformation). In the case of missing biochemical information,proteomic information and genetic information, respectively,is represented for a given enzymatic reaction or transport process.

Web interface
The web interface of the database is accessible at http://metacrop.ipk-gatersleben.de.It allows detailed browsing and searching of data, user feedbackand data export. Figure 1 shows some screenshots of the MetaCropweb interface starting with a complete pathway (sucrose breakdownin dicotyledon species including compartmentalization, transportersand isoenzymes) to detailed information about reaction kinetics.Additionally to searchable data tables, the user is guided byclickable image maps of the pathways. Entire pathways containingall available information on the respective reactions and metabolitescan be downloaded in the standardized systems biology exchangeformat systems biology markup language (SBML) (10), which canbe imported into modelling tools such as COPASI (11,12).

The functionality of the web interface is documented in a tutorialavailable on the website. It is also possible to edit entries,extend the content of MetaCrop and create user-specific models.To ensure data quality, such changes cannot be done anonymously.Users interested in these functionalities are invited to obtainan editing account for MetaCrop. Changes performed by all accountsare logged and checked by curators to guarantee consistencyand quality of the inserted data. The web interface is basedon the Oracle Application Express technology.

Database implementation
MetaCrop uses the information system Meta-All (13) and is basedon the database management system Oracle. The database schemacomprises 51 relational tables and can be divided into severalparts. The main parts are conversions, substances, pathways,locations, references and versioning. Conversions and substancesare the central parts of the schema. A conversion is a reactionor a translocation, which is either active or passive. Substancescomprise transporters, enzymes, metabolites and macromolecules.They take place in conversions and play certain roles, suchas reactant or product, modulator, catalyst, etc. All necessaryinformation, e.g. name, formula or kinetic data, can be storedtogether with conversions and substances. In order to distinguishdata originating from different publications, each record canbe enriched by reference information. The term location describesa combination of taxonomy, developmental stage and cytologyof plants in order to distinguish where and when conversionstake place. Therefore, controlled vocabulary is used. Additionally,the database schema supports parallel versioning of data records,e.g. in case of different opinions of experimentalists. Finally,pathways are combinations of conversions taking place at a certainlocation.

The complete information represented in MetaCrop is also availableas a dump of the database, i.e. the data is available for bulkdownload. The dump can easily be imported into a user's instanceof the open source information system Meta-All (13), thereforeenabling users to run their local version of the database.

 

 

 


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