Development of registration and retrieval systems for chemical and biological data

The goals of StructurePendium’s developments for registration and retrieval systems for chemical and biological data is to evolve user friendly systems that fully integrate into the existing landscape of the customer for a seamless introduction of the new system into the existing Environment.

Over the years a broad variety of registration and retrieval systems has been developed partly by implementing systems on the market partly by programming systems from scratch. Very early systems were based on MDL’s ISIS and its Hviews, later on isentris using Integrated Data Sources (IDS), Pipeline Pilot or Insight. Most of the registration systems for chemical structures and reactions contain calls to structure normalization software like for example Accelrys Cheshire. (see "Automated Structure Modifications and Normalizations"). Other routines were written for individual tools like Accelrys/Draw to build a direct link to centrally administered structure templates or to simplify peptide sequence drawing by key board input in the context of structure registration and retrieval.

On the biological side Accelrys Assay Explorer was used for the registration of biological data as well as self-developed registration tools based on MS Excel. Most of the retrieval systems for biological data are part of the structure retrieval systems using ISIS, isentris, Pipeline Pilot, or Insight.

Proprietary developments have been done based on Oracle PL/SQL using the Accelrys Direct Cartridge with clients on VB/C# or Excel (for biological data).

Currently we are gaining more experiences with the products delivered by ChemAxon and the latest versions of the Accelrys software.

StructurePendium provides the following services for data registration and retrieval:

  • Implementation and integration of software packages by Accelrys or ChemAxon
  • Development of retrieval or reporting workflows for example based on Accelrys Isentris, Insight or PipelinePilot, ChemAxon’s JChem, or Knime
  • Development of in-house solutions using software components like the cartridges of Accelrys, ChemAxon, Biochemfusion or RDKit
  • Programming of registration and retrieval tools
  • Testing, training and maintenance (see “Project handling” for more details)