Extensible markup language

Documents should be provided, where possible, as individual Portable Document Format (PDF) files, while Extensible Markup Language (XML) must be used to provide a user interface that enables navigation and viewing via a standard web browser. This offers the potential for an applicant to make a compete submission on... 

As stated on the OMG (Object Management) website (http //www.omg. org/), a lack of data standards results in data conversions, loss of information, lack of interoperability, etc. Current standards du jour are XML (Extensible Markup Language) [17], LSID (Life Sciences Identifiers), and now the RDF (Resource Description Framework) from the W3C (World Wide Web Consortium), which is extensible though hard to implement. Substantial work on OO (Object Oriented) modeling of life science data types takes place at the OMG s LSR (Life Sciences Research) group—this is discussed below. 

Extensible Markup Language (XML), in its various forms, is rapidly emerging as the dominant data format across all computer... 

In the bioinformatics realm, SRS (Sequence Retrieval System) [2] is a popular system, which uses a centralized collection of data resources primarily in flat text file form and, more recently, handles XML (Extensible Markup Language) files as well. Data resources are treated in a federated manner since each is maintained in its original form. However, SRS contains a large number of cross-references between corresponding fields in various data sources, so that keyword searches can be done across them. SRS thus performs more structured searches across the information than what a simple text search provides (such as web indexes perform, for example). Even though the data model implicit in the cross-reference tables is not very deep, SRS provides a useful way for users to browse and do simple queries across a large number of data sources as well as to integrate results from some computational methods. 

The technological foundations of this vision currently consist of extensible Markup Language (XML) [76], XML Schema [77], the Resource Description Framework (RDF) [61], RDF Schema [62], and the Web Ontology Language [63]. These technologies are interdependent and can thus be arranged in the form of a semantic layer cake (Fig. 9). 

Before reaching the point of complete data integration as given above, there are intermediary levels of data integration that are beneficial to better analysis of data from process analyzers. The best case would be to have all the data in a human readable form that is independent of the application data format. Over the years several attempts have been made to have a universal format for spectroscopic data, including JCAMP-DX and extensible markup language (XML). Because many instrument vendors use proprietary databases, and there is not a universal standard, the problem of multiple data formats persists. This has led to an entire business of data integration by third parties who aid in the transfer of data from one source to another, such as between instruments and the plant s distributed control system (DCS). 

D.C. McArthur, An Extensible XML Schema Definition for Automated Exchange of Protein Data PROXIML (PROtein extensible Markup Language). University of California, Santa Cruz, CA, 2001, available from http //xml.coverpages.org/ proximl.xml. 

The syntactic rules are specified in the World Wide Web Consortium (W3C) standard, Extensible Markup Language (XML). The first edition was issued in 1998 (Bray et al. 1998) the currently valid forth edition was published in 2006 (Bray et al. 2006b). If a document conforms to all rules given in this specification, it is said to be well formed. ... 

Xu, B., etal. (2005). Two-dimensional electrophoretic profiling of normal human kidney glomerulus proteome and construction of an extensible markup language (XML)-based database. Proteomics 5, 1083-1096. 

XML stands for Extensible Markup Language, the universal format for structured documents and data on the World Wide Web. 

As defined in Subsect. 2.1.2, a document is an aggregation of data and acts as a carrier of product data in a certain work context. One possibility to represent models of document contents is the use of the extensible Markup Language (XML) [1060] and its Document Type Definitions (DTDs), as suggested by Bayer and Marquardt [19]. Within a DTD, the structure of a specific document type can be described. Figure 2.9 shows the (incomplete) DTD of a specification sheet for vessels. Here, the different data items like temperature or construction material are indicated to specify the piece of equipment. However, the expressiveness of such document type definitions is rather restricted. A DTD specifies only the syntax of the document content but not its semantics. One possibility to enrich the DTD with meaning is to relate the single DTD elements to the classes and attributes of a product data model. This is exemplarily shown Fig. 2.9, where relations between some DTD elements and the corresponding classes of the product data model CLiP (cf. Subsect. 2.2.3) are indicated. 

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