Resource description framework technologies in chemistry

Abstract

EditorialThe Resource Description Framework (RDF) is provid-ing the life sciences with new standards around dataand knowledge management. The uptake in the lifesciences is significantly higher than the uptake of theeXtensible Markup Language (XML) and even relationaldatabases, as was recently shown by Splendiani et al. [1]Chemistry is adopting these methods too. For example,Murray-Rust and co-workers used RDF already in 2004to distribute news items where chemical structures wereembedded using RDF Site Summary 1.0 [2]. Frey imple-mented a system which would now be referred to as anelectronic lab notebook (ELN) [3]. The use of theSPARQL query language goes back to 2007 where itwas used in a system to annotate crystal structures [4].The American Chemical Society (ACS) Division ofChemical Information (CINF) invited scientists fromaround the world to present their use of RDF technolo-gies in chemistry on 22nd-23rd August 2010 at the240th ACS National Meeting in Boston, USA. Duringthree half-day sessions, the speakers demonstrated a mixof smaller and larger initiatives where RDF and relatedtechnologies are used in cheminformatics and bioinfor-matics as Open Standards for data exchange, commonlanguages (ontologies), and problem solving. The fifteenpresentations were grouped in the themes computation,ontologies, and chemical applications. Figures 1, 2 and 3display the most important keywords reflecting theabstracts of the talks in each session as word clouds [5].The goal of the meeting was to make more chemistsaware of what the RDF Open Standard has to offer tochemistry. We are delighted to continue this effort withthis Thematic Series, for which the speakers (andothers) were invited to present their work in more detailto a wider chemistry community. The choice of anOpen Access journal follows this goal. At this place, wewould like to thank Pfizer, Inc., who had partiallyfunded the article processing charges for this ThematicSeries. Pfizer, Inc. has had no input into the content ofthe publication or the articles themselves. All articles inthe series were independently prepared by the authorsand were subjected to the journal’s standard peer reviewprocess.In the remainder of this editorial, we will briefly out-line the various RDF technologies and how they havebeen used in chemistry so far.1 ConceptsThe core RDF specification was introduced by theWorld Wide Web Consortium (W3C) in 1999 [6] anddefines the foundation of the RDF technologies. It hasevolved into a set of recommendations by the W3Cpublished in 2004 (See Table 1). RDF specifies a verysimple data structure linking a subject to an object or avalue (literal) using a predicate. Cheminformaticians willrecognize this data structure as an edge from graph the-ory. This structure allowsus to represent facts like“vanillin dissolves in methyl alcohol” [7]. RDF uses Uni-form Resource Identifiers (URIs) to identify things.Therefore, the RDF equivalent of the solution statementcould be like this so-called triple:http://dbpedia.org/resource/Vanillinhttp://example.com/dissolvesInhttp://dbpedia.org/resource/Methanol.Since URIs may be used to reference resources on anyserver worldwide, RDF triples allow to span a globalgraph data structure. This is not surprising, since RDFis the core technology behind the proposed SemanticWeb [8]. In fact, the Web nature is clear here, as onecan follow both the URIs for vanillin and methanol toobtain further information on those two chemicals.These molecules’ URIs are said to be dereferencable,allowing agents to spider the Web for information fol-lowing the hyperlinks, quite like how you follow hyper-links on websites. Hence, the term Semantic Web.Recent projects such as Bio2RDF [9], Chem2Bio2RDF[10], and OpenTox [11] have brought genomic, chemical