Saturday, March 5, 2016

Axeleratio: Advancing nanoscience by encoding and communicating molecular architectures and their properties
Axeleratio is a web portal for cheminformatics and chemical data mining. It is home of the CurlySMILES Project. Axeleratio engages in the design of  applications and chemical pipelining tools to advance domain-relevant capturing and sharing of nanostructure-anchored information.

Breakthroughs in chemical research, materials design and life sciences are brought on by genuine ideas and out-of-the-box tinkering—and sometimes by applying a fresh approach to a proven concept. In any case, inspiring and reliable resources of data and knowledge are critical. “Big and bigger data” are becoming available by rapidly growing research activities and eager publication of their results in diversifying formats. For researchers, engineers and reviewers, the need to access information within a desired context is obvious, but often convoluted by ambiguity in terminology, lack of context-embedding and diversity in description regarding scope, scale and granularity.

Axeleratio enhances and integrates the chemical language CurlySMILES to meet challenges in identifying, communicating and modeling information of a multitude of chemical structures and arrangements at various levels of detail, including small molecules, coordination compounds, polymers and nanomaterials. We apply CurlySMILES to data mining and chemical property estimation. Further, we set up pipelining scripts for task-specific extraction, filtering, and analysis of data, including properties of solvents such as ionic liquids, electrolyte and polymer solutions. Below, we provide selected links to publications, snapshots and open-access tools of our current software and concepts.

CurlySMILES: a language to navigate and conquer chemical space

CurlySMILES provides a grammar to capture and share information on chemical species and their combinations in complex architectures, phases and materials. The CurlySMILES Project curated by Axeleratio furnishes encoding examples and establishes a forum to discuss and advance CurlySMILES toward emerging needs and novel ideas in cheminformatics. The extension and application of CurlySMILES to the encoding of polymer system was introduced the ACS 250th National Meeting in Boston.

Chemical data mining and filtering

Axeleratio implements data mining software by combining CurlySMILES and XML technologies. Currently, we are developing Python- and PowerShell-based scripts to inspect and mine the ThermoML Archive.     

Chemical calculation: data interpolation and estimation

Axeleratio provides online calculators; for example for the density of liquid water as a function of temperature. Calculators to quickly access concentration- and temperature-dependent solution and mixture properties are currently tested and implemented.

Molecular similarity and molecular difference

Computer-assisted evaluation of the similarity between molecular compounds with automatic recognition of the structural difference between them, is a powerful strategy for both chemical property prediction and design of new compounds with desired properties. This approach is especially attractive when large structure-property matrices are available as search databases and training sets. The molecular difference approach has been demonstrated for organic compounds and silicon/germanium-organic compounds. Axeleratio is looking forward to integrate this approach into the design of applications combining data mining and chemical property estimation algorithms.

MicroData: chemical identifiers on the Web

Axeleratio encourages microdata annotation of web pages to support web crawlers and search engines to identify domain-specific items on web pages and extract them in context of chemical queries and applications. We put forward ChemId, a Vocabulary for Chemical Species Identification, and BibScope for microdata wrapping of document references and bibliographic items.

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