Usage and applications of Semantic Web techniques and technologies to support chemistry research

Abstract

BackgroundThe drug discovery process is now highly dependent on the management, curation and integration of large amounts of potentially useful data. Semantics are necessary in order to interpret the information and derive knowledge. Advances in recent years have mitigated concerns that the lack of robust, usable tools has inhibited the adoption of methodologies based on semantics.ResultsThis paper presents three examples of how Semantic Web techniques and technologies can be used in order to support chemistry research: a controlled vocabulary for quantities, units and symbols in physical chemistry; a controlled vocabulary for the classification and labelling of chemical substances and mixtures; and, a database of chemical identifiers. This paper also presents a Web-based service that uses the datasets in order to assist with the completion of risk assessment forms, along with a discussion of the legal implications and value-proposition for the use of such a service.ConclusionsWe have introduced the Semantic Web concepts, technologies, and methodologies that can be used to support chemistry research, and have demonstrated the application of those techniques in three areas very relevant to modern chemistry research, generating three new datasets that we offer as exemplars of an extensible portfolio of advanced data integration facilities. We have thereby established the importance of Semantic Web techniques and technologies for meeting Wild’s fourth “grand challenge”.

A new wave of innovation in Semantic web tools for drug discovery

“…Borkum and Frey in 2014 [40] expressed the value of linked datasets and ontologies to aid chemical research, giving examples of general vocabularies such as SKOS [41] and Dublin Core [42], in addition to describing their own work to create some controlled vocabularies for specific chemical terminology. This line of thinking has gained traction in recent years as many more linked repositories, datasets and ontologies are being curated and created in the area of drug discovery, and in general the uptake of semantic web technologies to aid managing and leveraging higher value from drug discovery data has increased significantly.…”

“…All three reviews of semantic web technologies within the scientific domain had a strong focus on the linking of data through the use of RDF and Ontologies [18,40,44]. Machado et al illustrated that out of the 11 semantic drug discovery applications that they surveyed, seven of these used controlled vocabularies in their systems; demonstrating that this was a common method of using these technologies.…”

The XML and Semantic Web: A Systematic Review on Technologies

“…The differences between SW technologies and XML schema data models require usage of different semantics and query languages that render data retrieval difficult. However, it is prudent to develop tools and algorithms that can bridge the gap between SW technologies and XML schemas, and notably, it is not plausible and practical to convert all the pertinent XML schema data and legacy data in general to SW data (Borkum & Frey, 2014;Chen, Chirkova, Sadri, & Salo, 2013;Ishaq et al, 2013). Such is the limitation encountered in bridging the gap, and it is essential to consider making SW and XML schema interoperable and integrable to ensure smoother data query services over the internet.…”

Many InChIs and quite some feat

“…RSC has extracted chemical names from over 30,000 articles, and has integrated the primary compounds of interest into the ChemSpider [14, 62, 71-73, 95,114,115] database. Readers of the article HTML on the RSC's publishing platform can highlight compounds, and click on the compounds to link directly through to the compound record on ChemSpider to discover additional data and compound information sources.…”