title: From XML to RDF: how semantic web technologies will change the design of 'omic' standards.
abstract: With the ongoing rapid increase in both volume and diversity of 'omic' data (genomics, transcriptomics, proteomics, and others), the development and adoption of data standards is of paramount importance to realize the promise of systems biology. A recent trend in data standard development has been to use extensible markup language (XML) as the preferred mechanism to define data representations. But as illustrated here with a few examples from proteomics data, the syntactic and document-centric XML cannot achieve the level of interoperability required by the highly dynamic and integrated bioinformatics applications. In the present article, we discuss why semantic web technologies, as recommended by the World Wide Web consortium (W3C), expand current data standard technology for biological data representation and management.
authors.affiliation: Department of Biostatistics, Bioinformatics and Epidemiology, Medical University of South Carolina, 135 Cannon St. Suite 303, Charleston, South Carolina 29403-5720, USA.
authors.forename: Xiaoshu
authors.initials: X
authors.lastname: Wang
authors.forename: Robert
authors.initials: R
authors.lastname: Gorlitsky
authors.forename: Jonas S
authors.initials: JS
authors.lastname: Almeida
mesh_terms: D000465:Algorithms; D001709:Biotechnology / Q000379:methods / Q000639:trends*; D019992:Databases as Topic; D015180:Electrophoresis, Gel, Two-Dimensional; D023281:Genomics; D016247:Information Storage and Retrieval; D020407:Internet; D011381:Programming Languages; D040901:Proteomics; D012333:RNA, Messenger / Q000378:metabolism; D012660:Semantics; D012984:Software; D013223:Statistics as Topic; D049490:Systems Biology; D018511:Systems Integration; D013672:Technology
chemical_list: D012333:RNA, Messenger