Construction and Content: BMC Bioinformatics

BMC Bioinformatics 2008, 9:260 http://www.biomedcentral.
com/1471-2105/9/260
maize seeds, maize oil, tomato seeds, ketchup, soybean Construction and content
seeds, soybean oil, rapeseed seeds, and cotton seeds [4]. System architecture
The whole system is developed with PHP5 (using frame-
To make sure the successful enforcement of the GMO work for development, including Zend Framework 1.0
labelling, protein and nucleic acid-based detection tech- and Smarty 2.6), MySQL5 for primer information storage.
niques have been developed, or are in the process of Besides, NCBI BLAST2, and BioPerl package [20] are also
development, such as ELISA, lateral flow strip, PCR, and introduced to GMDD to achieve a BLAST function for all
micro-array etc [5-13]. Among these techniques, PCR is the exogenous inserted sequences. WWW Primer 3 [21] is
the most popular technique for GMOs analysis because of also integrated into GMDD, which will help users with
its versatility (from screening to identification), specifi- primers' design.
city, high throughput, and efficiency, therefore the PCR
detection methods have been developed for many GMOs. Data collection
The introduced DNA fragments are usually integrated into In this GMO detection method database (GMDD), we
the genome of GMOs by random transformation events: provide the information on two aspects of each approved
based on the different amplification fragments of the GMO event, one is the general information on each trans-
inserted DNA sequences, PCR detection methods of formation event for detection purposes, and the other is
GMOs are grouped into four types, such as the screen-, its detailed detection method information. The general
gene-, construct-, and event-specific PCR methods [6,7]. information of GMO events includes the event name,
Moreover, to overcome the difficulties in obtaining the OECD UI (Organization for Economic Co-operation and
certified reference materials (CRMs) of GMOs, standard Development OECD Unique Identifier), trade name, spe-
reference molecules are developed and used in PCR detec- cies, newly introduced traits, exogenous inserts, transfor-
tion [14-16]. This is a new research hotspot in the field of mation methods, transformation vectors and developing
GMO detection, and this will greatly facilitate the utiliza- or licensed company.
tion of PCR detection methods.
In particular, the inserted sequences of GMOs in GMDD
Up to now, hundreds of GMOs detection methods have have been collected from published research articles, Gen-
been developed, and their number is increasing more and bank [22], patents, and producer's petitions to govern-
more rapidly. However, with so many detection methods ments, some sequences are assembled by Vector NTI
to choose, an analyst may feel confused. To select the Advance™ 10.3 Contig Express software [23]. In addition
most informative analyses beforehand, it is necessary to to the sequence information, for other information on the
establish one public database for GMOs analysis meth- transformation event, references have been cited from the
ods, providing update analysis information to the ana- original US petitions, Japanese petitions, Agbios [17],
lysts. Even though there are some GMO databases related GMO-Compass [18], Biodiv LMO Database [19], and
to GMO safety assessment, including Agbios [17], GMO- GMO watch report [24], etc.
Compass [18], and Biodiv LMO Database [19], etc (all the
databases are available till now, 17th April, 2008), these The GMOs detection method information is grouped into
databases are mainly engaged in collecting the informa- nucleic acid-based method and protein-based method.
tion of GMOs' risk assessment, and relatively little infor- The nucleic acid-based method information includes
mation on GMO detection is included. primers, probes, amplicon length, figures showing primer
pair positions, endogenous reference genes, certified refer-
Here, we report the development of a new database for ence materials, standard reference molecules, information
GMO detection methods. In this database, we have col- on validation status, and reference articles. Currently,
lected almost all the previous developed GMOs detection most protein-based methods are based on commercial-
methods, thus providing a user-friendly search service for ized kits, and that is the reason why GMDD covers both
GMOs by event name, gene, and protein information, etc. commercial kits as well as non-kits methods. The GMO
In particular, we supply sequence information of exoge- detection information in GMDD has been mainly col-
nous inserts, if available, as well as endogenous reference lected from published research papers, Community Refer-
genes, and standard reference materials for GMOs analysis ence Laboratory for Genetically Modified Food and Feed
in our database. Furthermore, registered users can submit (CRL-GMFF) validation reports, national standards and
new GMO detection methods or sequences to this data- international standards, for instance, China and interna-
base, which makes this database open. tional standardization organization (ISO) standards, etc.
Data quantity
By mid April 2008, we have collected a total number of
136 GMO events, more than 400 pairs of PCR detection
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