Abstract
BackgroundThe diversity and the largely independent nature of chemical research efforts over the past half century are, most likely, the major contributors to the current poor state of chemical computational resource and database interoperability. While open software for chemical format interconversion and database entry cross-linking have partially addressed database interoperability, computational resource integration is hindered by the great diversity of software interfaces, languages, access methods, and platforms, among others. This has, in turn, translated into limited reproducibility of computational experiments and the need for application-specific computational workflow construction and semi-automated enactment by human experts, especially where emerging interdisciplinary fields, such as systems chemistry, are pursued. Fortunately, the advent of the Semantic Web, and the very recent introduction of RESTful Semantic Web Services (SWS) may present an opportunity to integrate all of the existing computational and database resources in chemistry into a machine-understandable, unified system that draws on the entirety of the Semantic Web.ResultsWe have created a prototype framework of Semantic Automated Discovery and Integration (SADI) framework SWS that exposes the QSAR descriptor functionality of the Chemistry Development Kit. Since each of these services has formal ontology-defined input and output classes, and each service consumes and produces RDF graphs, clients can automatically reason about the services and available reference information necessary to complete a given overall computational task specified through a simple SPARQL query. We demonstrate this capability by carrying out QSAR analysis backed by a simple formal ontology to determine whether a given molecule is drug-like. Further, we discuss parameter-based control over the execution of SADI SWS. Finally, we demonstrate the value of computational resource envelopment as SADI services through service reuse and ease of integration of computational functionality into formal ontologies.ConclusionsThe work we present here may trigger a major paradigm shift in the distribution of computational resources in chemistry. We conclude that envelopment of chemical computational resources as SADI SWS facilitates interdisciplinary research by enabling the definition of computational problems in terms of ontologies and formal logical statements instead of cumbersome and application-specific tasks and workflows.
Highlights
The diversity and the largely independent nature of chemical research efforts over the past half century are, most likely, the major contributors to the current poor state of chemical computational resource and database interoperability
One limitation that arises as a consequence of the annotative nature of Semantic Automated Discovery and Integration (SADI) services is the requirement to support transformative functionalities by differentiating the input and output, even if both are of the same class in the software package
A method that removes hydrogen atoms from a given input molecule specified by a SMILES string and returns a SMILES string, would have to be converted into a SADI service that operates upon an input class that consists of molecules that have a SMILES string specified and produces output typed to a class that consists of molecules that are annotated with a SMILES string as well as a hydrogen-free SMILES string
Summary
The diversity and the largely independent nature of chemical research efforts over the past half century are, most likely, the major contributors to the current poor state of chemical computational resource and database interoperability. While open software for chemical format interconversion and database entry cross-linking have partially addressed database interoperability, computational resource integration is hindered by the great diversity of software interfaces, languages, access methods, and platforms, among others. This has, in turn, translated into limited reproducibility of computational experiments and the need for application-specific computational workflow construction and semi-automated enactment by human experts, especially where emerging interdisciplinary fields, such as systems chemistry, are pursued. The explosion of the diversity of the various software packages addressing every package integration to make any progress in their daily investigations This problem has been especially acute for interdisciplinary studies, perhaps rising in relevance and importance with the relatively recent rise of Systems Science to prominence. Tools to interconvert the output and input files for many of these software components have been developed [1,2], and a number of chemical packages offer access to their functionalities through programming interfaces (e.g.[3,4,5]), one is left wishing that researchers in chemistry-related fields could still do more science rather than pipelining
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