A central benefit of Pathway Studio is the ability for our customers to create, update, mine, and use for experimental data analysis databases beyond Ariadne's core products for human (ResNet Mammalian) or plant (ResNet Plant) research. The two Ariadne’s commercial databases and the MedScan technology are extensible. Through collaboration with Ariadne, innovative research groups can create a pathway analysis system that is highly tailored to their unique requirements for work with particular species.

Ariadne’s technology can and has been successfully applied to other species and research topics beyond pathway analysis in human/mouse/rat and Arabidopsis. Successful projects, such as creation of species-specific databases, were based on close collaboration between Ariadne and innovative research groups or consortiums with domain expertise in the subject. These projects typically fall into one of two types:

Type 1: Using Orthologs to Extend Databases to Other Species

Customization of either ResNet Mammalian or ResNet Plant database to extend their application to other suitable species is relatively simple. The species under investigation must meet the requirement of a minimum level of information to qualify. This usually means that there are stable and systematic protein names along with known or predicted sequences available. Orthologous proteins may be defined between the new species and human or Arabidopsis and thus extension to protein-protein relations may be made.

Ariadne customers use this strategy to expand ResNet Mammalian database to bovine, chicken, and dog research. In plants, Rice and eight other plants have already been integrated into the primarily Arabidopsis-centric ResNet Plant 2.0 database.

There are additional costs associated with this project type.

Type 2: Customized Information Extraction for Other Species

This type of project requires customizations of both a ResNet database and the MedScan information extraction tool. You would typically need some experience or additional in-house resources, such as text mining and programming personnel, to customize MedScan dictionaries and to curate the database. In most cases Ariadne is contracted to create custom information extraction patterns if you need to extract new types of relations. Once you have a customized MedScan module (dictionary and information extraction patterns), you can use it to regularly update the database with information from appropriate text sources.

Customized projects of this kind were completed for the following species: Saccharomyces cerevisiae, Caenorhabditis elegans, and Drosophila melanogaster, and for biomarker and siRNA/microRNA as extensions to Ariadne’s Mammalian research tools.

There are additional costs associated with this project type.

Getting Started

Both Type 1 and Type 2 projects require additional investment on behalf of the customer, both in their time and in contracting for professional services and training with Ariadne. If you think your organization is suited to take on and support a Type 1 or Type 2 project, please contact Ariadne to arrange a private consultation.

For more information, please contact Ariadne Sales at sales@ariadnegenomics.com.