Easier Searching With GenomeCUBE®
Blog Nov 20, 2014
Since its development at RZPD, GenomeCUBE® has become a valuable search engine for genetic clones. An updated version of GenomeCUBE® has recently been launched by Source BioScience, incorporating a range of new features.
We spoke to Melanie Busse, Product Manager, Clones, Source BioScience, to find out about some of the improvements and new additions, and how this will benefit users.
AM: Can you tell me a little about Source BioScience?
MB: Source BioScience is a trusted provider of state of the art products and services to the healthcare and clinical, life and applied scientific and biopharma industries.
We are an international business with centres in 4 countries and customers in over 90 countries. The Group offers a portfolio of products and services including clinical diagnostics, genomics, proteomics, drug discovery and development research as well as controlled environment storage and testing services for a diverse range of markets. These products and services are provided to a large and diverse customer base including the top 50 pharmaceutical companies, leading universities and research institutes worldwide, the UK NHS and other healthcare providers.
The commercial activities of the Group are organised into three divisions - Healthcare, LifeSciences and Stability and Bio Storage.
The Healthcare division comprises our Diagnostics services, including diagnostic testing for cancer and other diseases and Cytology and Serology products, including cervical cancer screening and blood banking serology reagents.
The LifeSciences division provides ultra-fast DNA sequencing services and related products, delivered by Source BioScience's international network of laboratories and distributors to academic research groups, biotechnology and pharmaceutical companies.
The Stability and Bio Storage division provides support for drug discovery, from biomarker discovery and clinical trial services through to stability storage and sample archiving under environmentally controlled conditions.
AM: Can you tell me about your search engine, GenomeCUBE®?
MB: GenomeCUBE® was originally developed at RZPD, a central service unit within the German Human Genome Project (DHGP), it became the largest database for genetic clones worldwide and was associated with many of the major national and international gene and genome research projects.
In September we launched the updated version of GenomeCUBE®, an intelligent and intuitive-to-use search and buying tool which gives researchers easy access to millions of clones, hundreds of thousands of antibodies and the ability to purchase various reagents from one source. The powerful search function enables the retrieval of gene-based research material as well as a free text based screening of all Source BioScience resources in one step.
The gene-based search relies on the new comprehensive “BioInfo core database” merging gene and protein related information from different public databases (e.g. NCBI, Ensembl, UniProt). As a result, various Identifiers can be applied as search terms. Furthermore the massive scale of the BioInfo database allows for easy mapping of various resources, which was highly important for the inclusion of our antibody portfolio.
With regards to the mapping of clones GenomeCUBE® provides a unique feature: the mapping is based on Unigene Clusters connecting the Clone Accessions to gene related information, a method which depends on sequence homologies. The new GenomeCUBE ensures that you will get very specific search results although we have highly extended the access to our comprehensive clone resources.
GenomeCUBE® search results are presented in a well-structured manner, the clones are categorised according to potential applications, allowing the customer to easily select the most suitable product based on requirements.
The BioInfo data will be monthly updated so that GenomeCUBE® provides reference content on each of the products, including ‘real-time’ annotated information from multiple public databases.
AM: GenomeCUBE® eliminates the need for searching on the internet, what is feedback like from researchers?
MB: Feedback from researchers has been very good. The most popular update is the ability to apply various search terms within GenomeCUBE® which provides easy access to our various resources, wherever you come from. There is no need to identify the official gene symbol anymore, you can simply search with gene or protein names (even with synonyms), or you can use the different Identifiers as listed in the most common public databases.
Additionally, lots of our clones can be retrieved by clone names as applied in public databases. This is of high relevance for example for our genomic clones whose annotation is represented clearly in different Genome Browers (Ensembl, UCSC, MapViewer). Having located the appropriate clone you can type the Name or Accession directly into GenomeCUBE® and the corresponding clone will be displayed highlighted as an exact match.
During the implementation of GenomeCUBE® we took into account the representation of the listed products within public databases as well as on the websites of the originators in order to include all of the available information in the most appropriate way. Furthermore, our BioInfo database is linked back to these public databases to enable researchers to easily check all the gene/protein related information. This means there are various links to public databases and international consortia (e.g. NCBI, wormbase, ZFIN, ORFeome Collaboration), as well as back to GenomeCUBE® building up a network which facilitates navigation, this has been praised by researchers.
In most cases we can offer several clones in the same category for a particular gene, to allow researchers to make an informed choice we provide a comprehensive Data Sheet for each product, presenting all the relevant biological data.
The search function in GenomeCUBE® browses our complete product portfolio (clones, antibodies, reagents and kits) in one step, populating three different tabs showing the results for each product type. The tool automatically provides a separate list of Data Sheets for the related products that the user may need. This means that users can purchase all products that they require directly through GenomeCUBE®, eliminating the need to search the internet for various providers, again this has been well used and praised by researchers.
AM: An updated version of GenomeCUBE® has recently been launched. What improvements and extra features does this offer? How will these benefit users?
MB: One important additional feature present within the new GenomeCUBE® is the highly extended search function. In the past the search function was limited to official gene symbols and GenBank Accessions, however, within the updated version you can also search using alias names for genes and proteins, making searching much easier.
We have also broadened the access to our various resources by merging different gene and protein related Identifiers from the most common public databases in our comprehensive BioInfo database. Apart from different Identifiers derived from NCBI databases (e.g. Entrez Gene Id, GenBank Accessions like Ref.Seqs and Clone Accessions, Unigene Ids) in the new version the most important Identifiers from Ensembl (Ensembl Gene Id, Ensembl Transcript Id ) can be used as well.
To meet the requirements of our customers who are working in a protein based area we also implemented UniProt Ids. As our C.elegans collections are quite popular we set up links between GenePair Ids and UnigeneClusters / gene symbols wherever possible. Furthermore, we built up a core database for miRNA data. We are currently working on the implementation of the according resources which will be released soon.
The huge extension of the BioInfo database was a precondition to include the primary antibodies and recombinant proteins in the gene based search procedure. Using the updated version of GenomeCUBE® customers are able to identify all gene related products like clones, antibodies and proteins in one place, again saving time for researchers.
A further improvement which has been made is the set-up of links to specific related products on each Product Data Sheet which enables customers to easily order any kits or reagents that you would expect the user to need, again saving valuable time.
Additional to the “online” search function using GenomeCUBE® we offer batch data dump outs and batch searches on demand. The dump out function allows us to provide our customers with up-to-date clone lists compiling all relevant biological data needed for any specific application. The batch searches form the basis for the set-up of complex project flows combining our various resources and services due to the customers´ requirements.
For more information, please visit www.lifesciences.sourcebioscience.com
Melanie Busse was speaking to Anna-Marie MacDonald, Editor for Technology Networks.