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. 2015 Jul 14:7:34.
doi: 10.1186/s13321-015-0084-4. eCollection 2015.

PubChemRDF: towards the semantic annotation of PubChem compound and substance databases

Gang Fu  1 , Colin Batchelor  2 , Michel Dumontier  3 , Janna Hastings  4 , Egon Willighagen  5 , Evan Bolton  1
Affiliations

PubChemRDF: towards the semantic annotation of PubChem compound and substance databases

Gang Fu et al. J Cheminform. .

Abstract

Background: PubChem is an open repository for chemical structures, biological activities and biomedical annotations. Semantic Web technologies are emerging as an increasingly important approach to distribute and integrate scientific data. Exposing PubChem data to Semantic Web services may help enable automated data integration and management, as well as facilitate interoperable web applications.

Description: This work, one of a series covering the PubChemRDF project, describes an approach to translate PubChem Substance and Compound information into Resource Description Framework (RDF) format. Basic examples are provided to demonstrate its use. The aim of this effort is to provide two new primary benefits to researchers in a cost-effective manner. Firstly, we aim to remove the inherent limitations of using the web-based resource PubChem by allowing a researcher to use readily available semantic technologies (namely, RDF triple stores and their corresponding SPARQL query engines) to query and analyze PubChem data on local computing resources. Secondly, this work intends to help improve data sharing, analysis, and integration of PubChem data to resources external to NCBI and across scientific domains, by means of the association of PubChem data to existing ontological frameworks, including CHEMical INFormation ontology, Semanticscience Integrated Ontology, and others.

Conclusions: With the goal of semantically describing information available in the PubChem archive, pre-existing ontological frameworks were used, rather than creating new ones. Semantic relationships between compounds and substances, chemical descriptors associated with compounds and substances, interrelationships between chemicals, as well as provenance and attribute metadata of substances are described. Graphical abstract:Schematic representation of the semantic links for PubChem compounds and substances.

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Figures

Graphical abstract:
Graphical abstract:
Schematic representation of the semantic links for PubChem compounds and substances.
Figure 1
Figure 1
RDF diagram representing the attributes for substances SID103554720, SID43118161, SID26697365, SID822166, and compound CID60823, as well as the annotations for synonym and InChIKey instances.
Figure 2
Figure 2
RDF diagram representing PubChem data provenance model.
Figure 3
Figure 3
RDF diagram representing the calculated attributes of CID60823, and its interconnections with other compounds.
Figure 4
Figure 4
RDF diagram representing PubChem 2-/3-D similarity neighboring and score.
See this image and copyright information in PMC

References

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