Chemical XML formatting

PubChem provides examples of both sorts of Web service. To search PubChem for a particular chemical name, then, you can use the Entrez Programming Utilities (http //www.ncbi.nlm.nih.gov/books/bv.fcgi rid=coursework.chapter.eutils). Requests to these go via the URL and can be typed into a browser by hand. For more sophisticated requests, PubChem provides the Power User Gateway (http // pubchem.ncbi.nlm.nih.gov/pug/pughelp.html). This uses a complicated XML format for requests, much of which is there for job control for large batches. 

A number of formafs are available for data export. These formats include SDF, image, small image, SMILES, InChl, XML, and either text or binary ASN.l. The PubChem native archive data format is ASN.l all other formats are converted from the original ASN.l. The XML formatted data is exactly equivalent to the ASN.l in content. SDF format is the industry standard for conveyance of chemical sfructure information and is readily imported into a large number of chemistry programs. Unfortunately, the SDF format is unable to handle all aspects of the ASN.l data and may not contain all archived information. The PubChem ASN.l specification, XML schema, and a description of PubChem SDF sfrucfure dafa (SD) fags are all found on fhe PubChem FTP sife in the "specifications" directory. 

CML is an Extensible Markup Language (XML) format for chemical information [58]. CML reads multiple information elements from the stmcture file molecule, atom, bond, name, formula, and the attribute hydrogenCount, formalCharge, isotope, isotopeNumber, spiuMultiplicity, radical (from Marvin), atomRefs4 (for at-omParity), atomID ( id), elementType, atomRefs, atomic bond (). The CML file ends with (Fig. 1.21). 

The text/plain example above demonstrates that HTTP networks can support distributed information systems when given appropriate languages, that is, languages that describe abstractions appropriate to that information system. Many other standard MIME types are useful. Most are very specific, for example, image/gif is a specific format for bitmapped images, application/PDF is a page description format and application/tar is a 4.3 BSD archive. Some describe more general abstractions, for example, application/xml . Private (unauthorized) MIME types are also available, for example, chemical/x-pdb and chemical/x-smiles . 

One of the most widely used chemical structure-encoding schemas in the pharmaceutical industry is the MDL Connection Table (CT) File Format. Both Molfile and SD File are based on MDL CT File Format to represent chemical structures. A Molfile represents a single chemical structure. An SD File contains one to many records, each of which has a chemical structure and other data that are associated with the structure. MDL Connection Table File Format also supports RG File to describe a single Rgroup query, rxnfile, which contains structural information of a single reaction, RD File, which has one to many records, each of which has a reaction and data associated with the reaction, and lastly, MDL s newly developed XML representation of the above—XD File. The CT File Format definition can be downloaded from the MDL website http //www.mdl.com/downloads/public/ctfile/ctfile.jsp. 

CML (Murray-Rust and Rzepa 1999,2003) is an XML-based format with basic characteristics very similar to those of CTFiles when it comes to description of chemical structures. There are two main published versions of CML CML 1 and CML 2. As the former one is already considered obsolete, we will describe only the properties of CML 2. 

The decision of CML s authors to base a new chemical format on XML was very providential, even though at the time of CML s creation XML did not have today s general acceptance. In the meantime XML has become widely supported, and many other formats were based on its foundations. 

Formats for the capture of molecular structures and reactions are obviously of paramount importance in chemical data mining. Fortunately, a lot of experience had been amassed before the invention of XML, so it was not necessary to start from the beginning. Computational chemists are used to using connectivity tables, and XML provides a very convenient syntax for their formal specification. 

CML. The Chemical Markup Language. Based on XML and HTML, it provides a standard self-documenting molecule file and information interchange format. Information is described by tags and values. A CML document... 

This service takes as input a chemical structure and (if sfandardization is possible) oufputs a chemical sfrucfure. Allowed sfructural inpuf and output formats include SMILES, InChl, or SDF file however, fhe input and output formats need not be the same. As with structure search, the standardization service is queued on PubChem servers, meaning a request may not start right away or may not complete immediately. One may also import and export standardization requests to a local XML file to serve as an example for consfrucfing queries for the PUG interface (described in detail later). 

There have been numerous attempts to develop standard connection table formats for data exchange, almost all of which have sunk rapidly and without trace. An XML-based connection table format, Chemical Markup Language (CML) was proposed in the late 1990s and has now reached version 2.4 which incorporates a number of extensions for representation of features such as spectra, reactions and polymers. Though there is now an extensive CML literature, its adoption by commercial software vendors has thus far been very limited. Greater penetration has been achieved by the lUPAC Chemical Identifier, which is essentially a highly-compacted connection table, discussed in the next section. 

An interesting encoding format called CML (chemical markup language) which aims at structuring chemical information in a form far beyond what is possible within HTML, has been proposed." CML is based on XML and consequently has some similarity to HTML. The automatic indexing of chemical information from the original document without human intervention becomes much more feasible with this type of approach. Please refer to Internet-based Computational Chemistry Tools for a more detailed discussion. 

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