XML markup languages

CML. cml Chemical Markup Language extension of XML with specialization in chemistry nmjw.xml-crrd.org 57-59... 

Predictive Model Markup Language (PMML) is far more than just another format of a data container flat file [7]. As is clear from the name, it is an XML-based markup language delivering all the power of XML. Readers are recommended to consult Section 2.4.5 and the website www.xml.org for more details on XML and its applications in chemistry. 

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. 

Murray-Rust P, Rzepa HS. Chemical Markup Language and XML Part I. Basic Principles. / Chem Inform Comput Sci 1999 39 928-42. 

This method of data collection uses Portable Document Format (PDF) Forms. This approach is flexible and inexpensive. A number of commercial software packages such as Adobe Acrobat, LaText, and Microsoft Word and free software such as Python and R are used to create the PDF forms. Paper copies of the PDF forms may be used as an intermediate data collection. Electronic versions are completed at each site with Adobe Reader software. Completed forms are submitted on a CD or faxed as Extended Markup Language (XML)... 

There are two things that you may notice when looking at the lab normal data represented as XML. First, the file seems verbose. Whereas previously the lab normal file could be represented with three lines of pipe-delimited text, XML represents the same data with 30 lines of text. Second, you can read and somewhat understand the XML file just by looking at it if you know a markup language such as HTML or SGML. Let s look at how we can import these XML data into SAS. 

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

ISO 2008. ISO/lEC 29500-1 2008 Information technology — Document description and processing languages — Office Open XML File Formats — Part 1 Fundamentals and Markup Language Reference... 

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). 

One way to impart structure to otherwise unstructured documents is to utilize a suitable markup language. The function of markup languages is to combine the text of a document with further information about the text (markup languages typically add metadata - data about data) and while metadata is normally hidden from the view of a human reader, it is available to processing software. XML allows an author to add arbitrary metadata to documents through the use of tags, which are user-defined and annotate data sources. 

Adams N, Murray-Rust P, Winter J et al. (2008) Chemical markup, XML and the world wide web. 8. Polymer Markup Language. J Chem Inf Model 48 2118-2128... 

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 second example (Scheme 8-2) is an elaboration of the first fragment, but formalized below as CML (chemical markup language) (3). We emphasize that this chapter is not meant to be an instructional manual for any given markup language, with CML here serving only to illustrate the general principles involved. Many other scientific applications of XML have been developed (3, 4), and syntactically, either of these examples could be replaced by other such modularized markup languages. 

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