PDBML: the representation of archival macromolecular structure data in XML | Bioinformatics

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<div class="article-issue-info"> <div class="volume-issue__wrap"> <div class="volume trailing-comma">Volume 21</div> <div class="issue">Issue 7</div> </div> <div class="ii-pub-date"> April 2005 </div> </div> </a> </div> </div> <div class="content-nav"> <div class="widget widget-ArticleJumpLinks widget-instance-OUP_ArticleJumpLinks_Widget"> <h3 class="contents-title" >Article Contents</h3> <ul class="jumplink-list js-jumplink-list"> <li class="section-jump-link head-1" link-destination="394064293"> <div class="section-jump-link__link-wrap"> <a class="js-jumplink scrollTo" href="#394064293">Abstract</a> </div> </li> <li class="section-jump-link head-1" link-destination="394064298"> <div class="section-jump-link__link-wrap"> <a class="js-jumplink scrollTo" href="#394064298">XML SCHEMA FOR PDB DATA, PDBML</a> </div> </li> <li class="section-jump-link head-1" link-destination="394064304"> <div class="section-jump-link__link-wrap"> <a class="js-jumplink scrollTo" href="#394064304">PDBML DATA 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</div> <div class="wi-authors at-ArticleAuthors"> <div class="al-authors-list"> <span class="al-author-name-more js-flyout-wrap"> <button type="button" class="linked-name js-linked-name-trigger btn-as-link">John Westbrook</button><span class='delimiter'>, </span> <span class="al-author-info-wrap arrow-up"> <div class="info-card-author authorInfo_OUP_ArticleTop_Info_Widget"> <div class="name-role-wrap"> <div class="info-card-name"> John Westbrook <span class="info-card-footnote"><span class="xrefLink" id="jumplink-COR1"></span><a href="javascript:;" reveal-id="COR1" data-open="COR1" class="link link-ref link-reveal xref-default"></a></span> </div> </div> <div class="info-author-correspondence"> <div content-id="COR1"><sup>*</sup>To whom correspondence should be addressed.</div> </div> <div class="info-card-search-label"> Search for other works by this author on: </div> <div class="info-card-search info-card-search-internal"> <a 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Berman</button><span class='delimiter'></span> <span class="al-author-info-wrap arrow-up"> <div class="info-card-author authorInfo_OUP_ArticleTop_Info_Widget"> <div class="name-role-wrap"> <div class="info-card-name"> Helen M. 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</div> </div> </div> <div id="ContentTab" class="content active"> <div class="widget widget-ArticleFulltext widget-instance-OUP_Article_FullText_Widget"> <div class="module-widget"> <div class="widget-items" data-widgetname="ArticleFulltext"> <h2 scrollto-destination=394064293 id="394064293" class="abstract-title js-splitscreen-abstract-title" >Abstract</h2> <section class="abstract"><p class="chapter-para"><strong>Summary:</strong> The Protein Data Bank (PDB) has recently released versions of the PDB Exchange dictionary and the PDB archival data files in XML format collectively named PDBML. The automated generation of these XML files is driven by the data dictionary infrastructure in use at the PDB. The correspondences between the PDB dictionary and the XML schema metadata are described as well as the XML representations of PDB dictionaries and data files.</p><p class="chapter-para"><strong>Availability:</strong> The current software translated XML schema file is located at <a class="link link-uri openInAnotherWindow" href="http://deposit.pdb.org/pdbML/pdbx-v1.000.xsd" target="_blank">http://deposit.pdb.org/pdbML/pdbx-v1.000.xsd</a>, and on the PDB mmCIF resource page at <a class="link link-uri openInAnotherWindow" href="http://deposit.pdb.org/mmcif/" target="_blank">http://deposit.pdb.org/mmcif/</a>. PDBML files are stored on the PDB beta ftp site at <a class="link link-uri openInAnotherWindow" href="ftp://beta.rcsb.org/pub/pdb/uniformity/data/XML" target="_blank">ftp://beta.rcsb.org/pub/pdb/uniformity/data/XML</a></p><p class="chapter-para"><strong>Contact:</strong> <a href="mailto:jwest@rcsb.rutgers.edu">jwest@rcsb.rutgers.edu</a></p></section> <div class="article-metadata-panel clearfix at-ArticleMetadata"></div> <p class="chapter-para">The Protein Data Bank (PDB) (<span class="xrefLink" id="jumplink-B3"></span><a href="javascript:;" reveal-id="B3" data-open="B3" class="link link-ref link-reveal xref-default">Bernstein <em>et al</em>., 1977</a>; <span class="xrefLink" id="jumplink-B1"></span><a href="javascript:;" reveal-id="B1" data-open="B1" class="link link-ref link-reveal xref-default">Berman <em>et al</em>., 2000</a>) is the single worldwide repository for macromolecular structure data. For more than 30 years (<span class="xrefLink" id="jumplink-B3"></span><a href="javascript:;" reveal-id="B3" data-open="B3" class="link link-ref link-reveal xref-default">Bernstein <em>et al</em>., 1977</a>), the PDB has used a column-oriented data format to store archival entries. This format resembles many other data formats constrained by the limitations of paper punch card technology. Examples of the data format are shown in <span class="xrefLink" id="jumplink-FIG1"></span><a href="javascript:;" reveal-id="FIG1" data-open="FIG1" class="link link-ref link-reveal xref-default">Figure 1</a>.</p><p class="chapter-para">The representation of coordinate, sequence, secondary structure and citation data in the PDB has remained remarkably stable since the original format definition in 1972. The data records in the PDB format are prefixed with a record tag (e.g. CRYST1, ATOM) followed by individual items of data (<span class="xrefLink" id="jumplink-FIG1"></span><a href="javascript:;" reveal-id="FIG1" data-open="FIG1" class="link link-ref link-reveal xref-default">Figure 1a</a>). The specifications for the records in this data format are described informally in the PDB Content Guide: Atomic Coordinate Entry Format Description (<span class="xrefLink" id="jumplink-B5"></span><a href="javascript:;" reveal-id="B5" data-open="B5" class="link link-ref link-reveal xref-default">Callaway <em>et al</em>., 1996</a>). The description of the experimental details of structure determination has been encoded largely in the form of remark records. Although these records have some internal structure, the organization of these records has changed over time. For example, in <span class="xrefLink" id="jumplink-FIG1"></span><a href="javascript:;" reveal-id="FIG1" data-open="FIG1" class="link link-ref link-reveal xref-default">Figure 1b</a> the details of refinement are presented as unstructured text, and in <span class="xrefLink" id="jumplink-FIG1"></span><a href="javascript:;" reveal-id="FIG1" data-open="FIG1" class="link link-ref link-reveal xref-default">Figure 1c</a> these details are presented as semi-structured remark records.</p><p class="chapter-para">The growing interest in database development and electronic publication in the late 1980s created a need for a more structured representation of PDB data. In 1990, the International Union of Crystallography (IUCr) commissioned a working group (see <a class="link link-uri openInAnotherWindow" href="http://ndbserver.rutgers.edu/mmcif/background/index.html" target="_blank">http://ndbserver.rutgers.edu/mmcif/background/index.html</a>; <span class="xrefLink" id="jumplink-B6"></span><a href="javascript:;" reveal-id="B6" data-open="B6" class="link link-ref link-reveal xref-default">Fitzgerald <em>et al</em>., 2004</a>) to develop macromolecular extensions to the data representation used to describe small molecule structures and crystallographic structure determination, called the Crystallographic Information File (CIF) (<span class="xrefLink" id="jumplink-B7"></span><a href="javascript:;" reveal-id="B7" data-open="B7" class="link link-ref link-reveal xref-default">Hall <em>et al</em>., 1991</a>). The CIF representation had been designed and deployed by the IUCr to support electronic publication of small molecule crystal structures. The efforts of the working group and many community experts lead to the development of the macromolecular Crystallographic Information Framework (mmCIF) dictionary. The first version of this data dictionary released in 1996 contained 1700 data definitions (<span class="xrefLink" id="jumplink-B4"></span><a href="javascript:;" reveal-id="B4" data-open="B4" class="link link-ref link-reveal xref-default">Bourne <em>et al</em>., 1997</a>). The content of the mmCIF dictionary, a superset of PDB crystallographic content, included detailed definitions describing macromolecular structure and the current state of the macromolecular crystallographic experiment.</p><p class="chapter-para">In 1998, the Research Collaboratory for Structure Bioinformatics (RCSB) assumed the management of the PDB. RCSB adopted the mmCIF data dictionary as the foundation of their data processing and data management infrastructure. The members of the worldwide PDB (wwPDB) (<span class="xrefLink" id="jumplink-B2"></span><a href="javascript:;" reveal-id="B2" data-open="B2" class="link link-ref link-reveal xref-default">Berman <em>et al</em>., 2003</a>), that includes the RCSB, the Macromolecular Structure Database (MSD) at the European Bioinformatics Institute (EBI) and the PDBj at Osaka University, have collaborated to extend the mmCIF dictionary to include all of the data managed and distributed by the PDB. These extensions include data definitions describing internal bookkeeping, non-crystallographic structure determination methods (e.g. NMR and cryo-electron microscopy), greater detail in experimental crystallography and the details of protein production. These extensions are collected into the PDB Exchange data dictionary (<span class="xrefLink" id="jumplink-B10"></span><a href="javascript:;" reveal-id="B10" data-open="B10" class="link link-ref link-reveal xref-default">Westbrook <em>et al</em>., 2004a</a>). This data dictionary provides the foundation for the generation of XML schema (World Wide Web Consortium, 2001a,b,c) and XML data files described in the remainder of this article.</p> <h2 scrollto-destination=394064298 id="394064298" class="section-title js-splitscreen-section-title" >XML SCHEMA FOR PDB DATA, PDBML</h2> <p class="chapter-para">The representation of PDB data in XML builds from the content of the PDB Exchange dictionary, both for assignment of data item names and for defining data organization. Although presented in very different syntaxes, the PDB Exchange and XML representations use the same logical data organization. A side effect of maintaining a logical correspondence with the PDB Exchange representation is that the PDBML files lack the hierarchical structure characteristic of many XML data applications. However, preserving the logical data model of the PDB Exchange dictionary has three important advantages. First, the semantics of PDB data are completely preserved across the two formats. Second, the translation of the PDB Exchange dictionary and PDB Exchange data files to XML is greatly simplified. Third, the straightforward mapping of PDB data to relational database systems is retained.</p><p class="chapter-para">The correspondences between the metadata attributes used in the PDB Exchange dictionary (<span class="xrefLink" id="jumplink-B9"></span><a href="javascript:;" reveal-id="B9" data-open="B9" class="link link-ref link-reveal xref-default">Westbrook and Bourne, 2000</a>; <span class="xrefLink" id="jumplink-B11"></span><a href="javascript:;" reveal-id="B11" data-open="B11" class="link link-ref link-reveal xref-default">Westbrook <em>et al</em>., 2004b</a>) and those of XML schema are summarized in <span class="xrefLink" id="jumplink-TBL1"></span><a href="javascript:;" reveal-id="TBL1" data-open="TBL1" class="link link-ref link-reveal xref-default">Table 1</a>. The top level of scope in the PDB Exchange dictionary or data file is the data block. The data block encloses complete data dictionaries or data entries. The dictionary data block is mapped to the standard top-level XML <em>schema</em> element, and the data file data block is mapped to a <em>datablock</em> element. The <em>schema</em> and <em>datablock</em> elements provide namespace definitions, linkages to the supporting XML schema definition documents and linkages to the location of the current supporting schema.</p><p class="chapter-para">Category or table definitions in the Exchange dictionary are described as XML <em>complexTypes</em>. The category definition and examples are mapped to XML <em>annotation</em> and <em>documentation</em> elements. The data items within the category are defined as an unordered sequence of XML elements named according to the attribute portion of their dictionary equivalents. The special data items that form the primary key for the category are defined as XML attributes.</p><p class="chapter-para">Individual data items have a definition and an optional set of examples. The item-level definition and examples are mapped to XML <em>annotation</em> and <em>documentation</em> elements. Parent–child relationships between data items in the Exchange dictionary are represented as XML <em>key</em> and <em>keyref</em> elements. All parent data items are identified as named XML <em>keys</em>, and their associated children are identified as named XML <em>keyrefs</em>. Primitive data types in the Exchange dictionary are described as XML <em>simpleTypes</em>. Allowed ranges are represented as <em>restriction</em> elements within <em>simpleTypes</em>. Complicated boundary conditions are represented as unions of <em>simpleTypes</em> containing <em>restriction</em> elements. Controlled vocabularies and allowed values are represented as <em>simpleTypes</em> with <em>restrictions</em> including <em>enumeration</em> elements. Where physical units of measurement are included in a definition in the absence of any other range restrictions, this information is mapped to a XML <em>simpleContent</em> element containing a <em>fixed attribute</em> element representing the measurement units. There are currently no mappings for the item-level dictionary attributes describing item-level interdependency, exclusivity or subcategory membership.</p><p class="chapter-para">The correspondences between the PDB dictionary and XML schema metadata described in this section make the automatic translation of the PDB dictionary to XML schema possible. The current software translated XML schema file is located at <a class="link link-uri openInAnotherWindow" href="http://deposit.pdb.org/pdbML/pdbx-v1.000.xsd" target="_blank">http://deposit.pdb.org/pdbML/pdbx-v1.000.xsd</a>, and on the PDB mmCIF resource page at <a class="link link-uri openInAnotherWindow" href="http://deposit.pdb.org/mmcif/" target="_blank">http://deposit.pdb.org/mmcif/</a>.</p> <h2 scrollto-destination=394064304 id="394064304" class="section-title js-splitscreen-section-title" >PDBML DATA FILES</h2> <p class="chapter-para">The PDBML data files follow the same logical organization as their PDB Exchange data file counterparts. <span class="xrefLink" id="jumplink-FIG2"></span><a href="javascript:;" reveal-id="FIG2" data-open="FIG2" class="link link-ref link-reveal xref-default">Figure 2</a> provides an abbreviated example comparing the presentation of a category describing polymer features in the two syntaxes. In <span class="xrefLink" id="jumplink-FIG2"></span><a href="javascript:;" reveal-id="FIG2" data-open="FIG2" class="link link-ref link-reveal xref-default">Figure 2a</a>, a single row of the <em>entity_poly</em> data category is illustrated within a data block named <em>EXAMPLE</em>. The corresponding XML representation of this information is shown in <span class="xrefLink" id="jumplink-FIG2"></span><a href="javascript:;" reveal-id="FIG2" data-open="FIG2" class="link link-ref link-reveal xref-default">Figure 2b</a>. Here the root-level enclosing XML <em>datablock</em> element identifies the namespace and the associated schema files. The <em>entity_poly</em> data category is enclosed by an XML <em>entity_polyCategory</em> element. Each row of the category is defined within an XML <em>entity_poly</em> element where the category key, <em>entity_id</em>, is included as an XML attribute. The remaining data items in the row are represented as XML elements.</p><p class="chapter-para">The XML organization illustrated in <span class="xrefLink" id="jumplink-FIG2"></span><a href="javascript:;" reveal-id="FIG2" data-open="FIG2" class="link link-ref link-reveal xref-default">Figure 2b</a> is repeated for each data category in the data file. Because of its size the <em>atom_site</em> category is also represented in an alternative form. Examples of the fully marked-up atom record and the simplified alternative are shown in <span class="xrefLink" id="jumplink-FIG3"></span><a href="javascript:;" reveal-id="FIG3" data-open="FIG3" class="link link-ref link-reveal xref-default">Figure 3</a>. The alternative representation of the <em>atom_site</em> category in <span class="xrefLink" id="jumplink-FIG3"></span><a href="javascript:;" reveal-id="FIG3" data-open="FIG3" class="link link-ref link-reveal xref-default">Figure 3b</a> simplifies the fully marked-up style in <span class="xrefLink" id="jumplink-FIG3"></span><a href="javascript:;" reveal-id="FIG3" data-open="FIG3" class="link link-ref link-reveal xref-default">Figure 3a</a> by presenting the data items within the <em>atom_site</em> category in a white-space delimited string. The current schema fragment describing the alternative <em>atom_site</em> representation is located at <a class="link link-uri openInAnotherWindow" href="http://deposit.pdb.org/pdbML/pdbx-v1.000-alt.xsd" target="_blank">http://deposit.pdb.org/pdbML/pdbx-v1.000-alt.xsd</a>.</p><p class="chapter-para">PDBML files are stored on the PDB beta ftp site at <a class="link link-uri openInAnotherWindow" href="ftp://beta.rcsb.org/pub/pdb/uniformity/data/XML" target="_blank">ftp://beta.rcsb.org/pub/pdb/uniformity/data/XML</a>. The files are updated during each weekly PDB update. These files are currently under beta test. Comments and data issues related to these files may be reported at <a class="link link-uri openInAnotherWindow" href="http://pdb-forum.rutgers.edu/" target="_blank">http://pdb-forum.rutgers.edu/</a>. Three XML data files are produced from each PDB Exchange data file. One XML file contains the fully marked-up translation of the PDB Exchange data file. A second XML file contains the full PDB Exchange data file content omitting coordinate data. A third XML file contains only the simplified representation of the coordinate data in which each atom record is marked up as a single XML string.</p> <h2 scrollto-destination=394064308 id="394064308" class="section-title js-splitscreen-section-title" >SUPPORTING SOFTWARE TOOLS</h2> <p class="chapter-para">The XML schema and data files described in this article are produced by software translation of the PDB Exchange dictionary and data files, respectively. The software tools that RCSB has developed to automate the production of XML schema and dictionaries can be downloaded from the website <a class="link link-uri openInAnotherWindow" href="http://deposit.pdb.org/mmcif/MMCIF-XML-UTIL/" target="_blank">http://deposit.pdb.org/mmcif/MMCIF-XML-UTIL/</a>. The molecular graphics viewer, PDBjViewer (Kinoshita and Nakamura, in press) that PDBj has developed can parse the current PDBML files to display macromolecular structures <a class="link link-uri openInAnotherWindow" href="http://www.pdbj.org/PDBjViewer/" target="_blank">http://www.pdbj.org/PDBjViewer/</a>. These tools are available in full source under an Open Source software license. The XML-based Protein Structure Search Service (xPSSS) is a browser with the XPath-SOAP service, based on the PDBML files using a native XML-DB at PDBj <a class="link link-uri openInAnotherWindow" href="http://www.pdbj.org/xpsss/" target="_blank">http://www.pdbj.org/xpsss/</a>.</p><p class="chapter-para"></p> <a id="394064312" scrollto-destination="394064312"></a> <div data-id="fig1" data-content-id="fig1" class="fig fig-section js-fig-section" swap-content-for-modal="true"><div class="graphic-wrap"><img class="content-image" src="https://oup.silverchair-cdn.com/oup/backfile/Content_public/Journal/bioinformatics/21/7/10.1093_bioinformatics_bti082/1/m_bioinformatics_21_7_988_f1.jpeg?Expires=1734479211&Signature=NMxr6ShwQBxKYwcvw8444CB28zNHYzHlTfIXjOAZRHJg2o2oudQ3ZE1jVgYXlRUqKKSx5rnZjUiAqTAH3AiT-X4Pb~2q8w4SrFIK6L1EE8egsbI3jl-tOZWXKEKIj5oDIn49TlmVhZ65PQDvTboV2o0O9ArYcwU7XkqbvFmMCdsP~zkf~2ottFqu-Rqda94bGwvs8bEkQdjNqka2brA9K0ktKfsLvzY386z0kAaNEZm6ggS4ijV1zlmkzr9d21s4rsR4iTfVHR1liDV~AHiqLXiZtP3D49u63fp3IN7zk8LQS7ASQTbZsmE~q-CxFOPi6coseXiHjh6yhxk1TEyTug__&Key-Pair-Id=APKAIE5G5CRDK6RD3PGA" alt="Excerpts of records from a PDB data files. (a) Structured PDB records describing crystallographic cell constants (CRYST1), transformation matrices between orthogonal and fractional coordinates (ORIGX and SCALE) and the atomic coordinates (ATOM). (b) Unstructured PDB records describing the details of crystallographic refinement used in PDB data files before 1996. (c) Semi-structured PDB records describing crystallographic refinement used in PDB data files after 1996." data-path-from-xml="BIOINFORMATICS_21_7_988_f1.jpeg" /><div class="graphic-bottom"><div class="label fig-label" id="label-394064312"><strong>Fig. 1</strong></div><div class="caption fig-caption"><p class="chapter-para">Excerpts of records from a PDB data files. (<strong>a</strong>) Structured PDB records describing crystallographic cell constants (CRYST1), transformation matrices between orthogonal and fractional coordinates (ORIGX and SCALE) and the atomic coordinates (ATOM). (<strong>b</strong>) Unstructured PDB records describing the details of crystallographic refinement used in PDB data files before 1996. (<strong>c</strong>) Semi-structured PDB records describing crystallographic refinement used in PDB data files after 1996.</p></div><div class="ajax-articleAbstract-exclude-regex fig-orig original-slide figure-button-wrap"><a class="fig-view-orig js-view-large at-figureViewLarge openInAnotherWindow" role="button" aria-describedby="label-394064312" href="/view-large/figure/394064312/BIOINFORMATICS_21_7_988_f1.jpeg" data-path-from-xml="BIOINFORMATICS_21_7_988_f1.jpeg" target="_blank">Open in new tab</a><a class="download-slide" role="button" aria-describedby="label-394064312" data-section="394064312" href="/DownloadFile/DownloadImage.aspx?image=https://oup.silverchair-cdn.com/oup/backfile/Content_public/Journal/bioinformatics/21/7/10.1093_bioinformatics_bti082/1/bioinformatics_21_7_988_f1.jpeg?Expires=1734479211&Signature=BwkPJ93FVsPImaZ82cGFa38YDJr38VUx7IOslvlm3uTlJC4pqoP14klHafMW13YLUXtX7JzQTP-NKspyG~YURRjhQ~kwvQ~aHDnUhjP4TnkHudSwk369jm~egSBcGZB4xB00eaFbyAYWurjghtcqZQg56Y3d~QfWbBVNMsFPsk5JEVTDHa4NKnUp0yOoFuyM0F-Wu1bzLMZ-aunpAwbsCZbxvK7ZaUcVjwiL8za7pFS35u6-Z6ScWv7oKtXi0YrM0xYpq1kzqJsElRZFOHlD9ekPA7RNVEmv8f-iKXXN1FgF5ew~RE0nykEwUk~GAIzvIKsayO~6QGWOuI8-j9Fi6Q__&Key-Pair-Id=APKAIE5G5CRDK6RD3PGA&sec=394064312&ar=268819&xsltPath=~/UI/app/XSLT&imagename=&siteId=5139" data-path-from-xml="BIOINFORMATICS_21_7_988_f1.jpeg">Download slide</a></div></div></div></div><p class="chapter-para"></p> <a id="394064314" scrollto-destination="394064314"></a> <div content-id="TBL1" class="table-modal table-full-width-wrap"><div class="table-wrap table-wide standard-table"><div class="table-wrap-title" id="TBL1" data-id="TBL1"><span class="label title-label" id="label-21208"><strong>Table 1</strong></span><div class="
 graphic-wrap table-open-button-wrap
 "><a class="fig-view-orig at-tableViewLarge openInAnotherWindow btn js-view-large" role="button" target="_blank" href="
 /view-large/394064314" aria-describedby="label-21208"> Open in new tab </a></div><div class="caption caption-id-" id="caption-21208"><p class="chapter-para">Summary of the correspondences between PDB Exchange data dictionary and XML schema metadata</p></div> </div><div class="table-overflow"><table role="table" aria-labelledby="
 label-21208" aria-describedby="
 caption-21208"><thead><tr><th>PDB Exchange data dictionary attributes<span aria-hidden="true" style="display: none;"> . </span></th><th>XML schema mapping<span aria-hidden="true" style="display: none;"> . </span></th></tr></thead><tbody><tr><td>Data block</td><td>Root level <em>schema element</em></td></tr><tr><td colspan="2">Category groups</td></tr><tr><td>Categories</td><td><em>complexTypes</em></td></tr><tr><td> Definition</td><td><em>annotation</em> and <em>documentation</em> elements</td></tr><tr><td> Examples</td><td><em>annotation</em> and <em>documentation</em> elements</td></tr><tr><td> Primary keys</td><td><em>attributes</em> of the data category</td></tr><tr><td>Items</td><td><em>elements</em> of the data category</td></tr><tr><td> Definition</td><td><em>annotation</em> and <em>documentation</em> elements</td></tr><tr><td> Examples</td><td>annotation and documentation elements</td></tr><tr><td> Data types</td><td><em>simpleTypes</em></td></tr><tr><td> Range restrictions and allowed values</td><td><em>restrictions</em> within <em>simpleTypes</em> or <em>unions</em> of <em>simpleTypes</em></td></tr><tr><td> Mandatory data code</td><td>Element attributes <em>minOccurs</em> and <em>nillable</em></td></tr><tr><td> Parent-child relationships</td><td><em>key/keyref</em> elements</td></tr><tr><td> Interdependency/exclusivity</td><td></td></tr><tr><td> Units of measurement</td><td>Additional <em>fixed attributes</em></td></tr><tr><td> Subcategory membership</td><td></td></tr></tbody></table></div><div class="table-modal"><table><thead><tr><th>PDB Exchange data dictionary attributes<span aria-hidden="true" style="display: none;"> . </span></th><th>XML schema mapping<span aria-hidden="true" style="display: none;"> . </span></th></tr></thead><tbody><tr><td>Data block</td><td>Root level <em>schema element</em></td></tr><tr><td colspan="2">Category groups</td></tr><tr><td>Categories</td><td><em>complexTypes</em></td></tr><tr><td> Definition</td><td><em>annotation</em> and <em>documentation</em> elements</td></tr><tr><td> Examples</td><td><em>annotation</em> and <em>documentation</em> elements</td></tr><tr><td> Primary keys</td><td><em>attributes</em> of the data category</td></tr><tr><td>Items</td><td><em>elements</em> of the data category</td></tr><tr><td> Definition</td><td><em>annotation</em> and <em>documentation</em> elements</td></tr><tr><td> Examples</td><td>annotation and documentation elements</td></tr><tr><td> Data types</td><td><em>simpleTypes</em></td></tr><tr><td> Range restrictions and allowed values</td><td><em>restrictions</em> within <em>simpleTypes</em> or <em>unions</em> of <em>simpleTypes</em></td></tr><tr><td> Mandatory data code</td><td>Element attributes <em>minOccurs</em> and <em>nillable</em></td></tr><tr><td> Parent-child relationships</td><td><em>key/keyref</em> elements</td></tr><tr><td> Interdependency/exclusivity</td><td></td></tr><tr><td> Units of measurement</td><td>Additional <em>fixed attributes</em></td></tr><tr><td> Subcategory membership</td><td></td></tr></tbody></table></div></div></div><div class="table-full-width-wrap"><div class="table-wrap table-wide standard-table"><div class="table-wrap-title" id="TBL1" data-id="TBL1"><span class="label title-label" id="label-21208"><strong>Table 1</strong></span><div class="
 graphic-wrap table-open-button-wrap
 "><a class="fig-view-orig at-tableViewLarge openInAnotherWindow btn js-view-large" role="button" target="_blank" href="
 /view-large/394064314" aria-describedby="label-21208"> Open in new tab </a></div><div class="caption caption-id-" id="caption-21208"><p class="chapter-para">Summary of the correspondences between PDB Exchange data dictionary and XML schema metadata</p></div> </div><div class="table-overflow"><table role="table" aria-labelledby="
 label-21208" aria-describedby="
 caption-21208"><thead><tr><th>PDB Exchange data dictionary attributes<span aria-hidden="true" style="display: none;"> . </span></th><th>XML schema mapping<span aria-hidden="true" style="display: none;"> . </span></th></tr></thead><tbody><tr><td>Data block</td><td>Root level <em>schema element</em></td></tr><tr><td colspan="2">Category groups</td></tr><tr><td>Categories</td><td><em>complexTypes</em></td></tr><tr><td> Definition</td><td><em>annotation</em> and <em>documentation</em> elements</td></tr><tr><td> Examples</td><td><em>annotation</em> and <em>documentation</em> elements</td></tr><tr><td> Primary keys</td><td><em>attributes</em> of the data category</td></tr><tr><td>Items</td><td><em>elements</em> of the data category</td></tr><tr><td> Definition</td><td><em>annotation</em> and <em>documentation</em> elements</td></tr><tr><td> Examples</td><td>annotation and documentation elements</td></tr><tr><td> Data types</td><td><em>simpleTypes</em></td></tr><tr><td> Range restrictions and allowed values</td><td><em>restrictions</em> within <em>simpleTypes</em> or <em>unions</em> of <em>simpleTypes</em></td></tr><tr><td> Mandatory data code</td><td>Element attributes <em>minOccurs</em> and <em>nillable</em></td></tr><tr><td> Parent-child relationships</td><td><em>key/keyref</em> elements</td></tr><tr><td> Interdependency/exclusivity</td><td></td></tr><tr><td> Units of measurement</td><td>Additional <em>fixed attributes</em></td></tr><tr><td> Subcategory membership</td><td></td></tr></tbody></table></div><div class="table-modal"><table><thead><tr><th>PDB Exchange data dictionary attributes<span aria-hidden="true" style="display: none;"> . </span></th><th>XML schema mapping<span aria-hidden="true" style="display: none;"> . </span></th></tr></thead><tbody><tr><td>Data block</td><td>Root level <em>schema element</em></td></tr><tr><td colspan="2">Category groups</td></tr><tr><td>Categories</td><td><em>complexTypes</em></td></tr><tr><td> Definition</td><td><em>annotation</em> and <em>documentation</em> elements</td></tr><tr><td> Examples</td><td><em>annotation</em> and <em>documentation</em> elements</td></tr><tr><td> Primary keys</td><td><em>attributes</em> of the data category</td></tr><tr><td>Items</td><td><em>elements</em> of the data category</td></tr><tr><td> Definition</td><td><em>annotation</em> and <em>documentation</em> elements</td></tr><tr><td> Examples</td><td>annotation and documentation elements</td></tr><tr><td> Data types</td><td><em>simpleTypes</em></td></tr><tr><td> Range restrictions and allowed values</td><td><em>restrictions</em> within <em>simpleTypes</em> or <em>unions</em> of <em>simpleTypes</em></td></tr><tr><td> Mandatory data code</td><td>Element attributes <em>minOccurs</em> and <em>nillable</em></td></tr><tr><td> Parent-child relationships</td><td><em>key/keyref</em> elements</td></tr><tr><td> Interdependency/exclusivity</td><td></td></tr><tr><td> Units of measurement</td><td>Additional <em>fixed attributes</em></td></tr><tr><td> Subcategory membership</td><td></td></tr></tbody></table></div></div></div><p class="chapter-para"></p> <a id="394064316" scrollto-destination="394064316"></a> <div data-id="fig2" data-content-id="fig2" class="fig fig-section js-fig-section" swap-content-for-modal="true"><div class="graphic-wrap"><img class="content-image" src="https://oup.silverchair-cdn.com/oup/backfile/Content_public/Journal/bioinformatics/21/7/10.1093_bioinformatics_bti082/1/m_bioinformatics_21_7_988_f2.jpeg?Expires=1734479211&Signature=n-0rLi47c-4JgJP~aM0uxfRVwkV2cz79CDumyV64niNZc4QlCCySXFZPhHZSPI~dg4Z4PK3h~5Y2y1jXcAKq75p-jfnbAxR1h4ds9oImIDBmY4HNX7YDvgvZ4NsrikgoZnCifQXs6XVGBgTR3cb1RDOTBSU5x735IaTJAbH8kL9U7GWOlZ9u01D-Pp5pr-D3RqgKteI3zQArZoaPYIrXMsdoFd7OgAQ8peqfcUHufL9MdHBNMIV1~m6XG6GrR2p1nAhbXoRUlno7scLTr3stf0sfo2~mdQBGiw6k1jRKPJNv-gCA3pFe9r3zyGKT7DzrEsNJD9-JdEM~0N9fejm7yg__&Key-Pair-Id=APKAIE5G5CRDK6RD3PGA" alt="Examples of PDB Exchange data and PDBML data representations. (a) PDB Exchange data file example with a single category describing some of the features of polymer molecule, (b) the corresponding example of polymer description in a PDBML data file." data-path-from-xml="BIOINFORMATICS_21_7_988_f2.jpeg" /><div class="graphic-bottom"><div class="label fig-label" id="label-394064316"><strong>Fig. 2</strong></div><div class="caption fig-caption"><p class="chapter-para">Examples of PDB Exchange data and PDBML data representations. (<strong>a</strong>) PDB Exchange data file example with a single category describing some of the features of polymer molecule, (<strong>b</strong>) the corresponding example of polymer description in a PDBML data file.</p></div><div class="ajax-articleAbstract-exclude-regex fig-orig original-slide figure-button-wrap"><a class="fig-view-orig js-view-large at-figureViewLarge openInAnotherWindow" role="button" aria-describedby="label-394064316" href="/view-large/figure/394064316/BIOINFORMATICS_21_7_988_f2.jpeg" data-path-from-xml="BIOINFORMATICS_21_7_988_f2.jpeg" target="_blank">Open in new tab</a><a class="download-slide" role="button" aria-describedby="label-394064316" data-section="394064316" href="/DownloadFile/DownloadImage.aspx?image=https://oup.silverchair-cdn.com/oup/backfile/Content_public/Journal/bioinformatics/21/7/10.1093_bioinformatics_bti082/1/bioinformatics_21_7_988_f2.jpeg?Expires=1734479211&Signature=U6iVaTa1mXiANY86O2wIo6q~sRYly0tMY~xHpsOic~U-PKSB6yt9zXD1gpKVs5lwcRiwA4t3liVYAmBBD6Dikji9SB39F3~f-rZnEThLp31guMhDQBX9OeErElCH3Th5nZTSYqVnIBGBEFHm3lMTWLWUqU~TFoJaulWdUMtoFIUXQDaMkCh-cVAl4Clx4vbpU3WbnXg2QRFW7~tU~C~MsjSxFdg0XKrLWwUs3DvGZuwFuugqvRfC~c4T07Qt-SXnnBfzgiAS0KFhqsAWXU2jXg~2CYBQqGrDSzXFiMsKAtFWyyOO4kUumDJSkCL8MXUOfAqHz7qMVKK-zUpaYfYrhA__&Key-Pair-Id=APKAIE5G5CRDK6RD3PGA&sec=394064316&ar=268819&xsltPath=~/UI/app/XSLT&imagename=&siteId=5139" data-path-from-xml="BIOINFORMATICS_21_7_988_f2.jpeg">Download slide</a></div></div></div></div><p class="chapter-para"></p> <a id="394064318" scrollto-destination="394064318"></a> <div data-id="fig3" data-content-id="fig3" class="fig fig-section js-fig-section" swap-content-for-modal="true"><div class="graphic-wrap"><img class="content-image" src="https://oup.silverchair-cdn.com/oup/backfile/Content_public/Journal/bioinformatics/21/7/10.1093_bioinformatics_bti082/1/m_bioinformatics_21_7_988_f3.jpeg?Expires=1734479211&Signature=RrrzILF8n7Ljwy3JsXdRZwQTSrAGCEshp5~eHpIKFNGBch5DbtX5I-jT~OduovN-Ld52cY~bG644~ZomSC-57J5u7EbRU4kGVwVsqCRa3DxtRrV4Pwb9oMrRjojxiCXfUnv6iRkx0cNnlR8ID48BInuZf1CScASMdFclCUawldXBkvZeHgUZCU8rylO3BZgJ0BL9Xtfp-XL8favuTbBWKcdPhfzZZaafnI0ORd5OWBNUZHvilmBiKYVpovyPa58W4sW1GSC6gYjSM0Q23i-vNEP6lSmdy4P4-gRN1C67tgNboRBOJXYSS37ntdKqenyAV3ct~uH~s~dOblYjnfqv5g__&Key-Pair-Id=APKAIE5G5CRDK6RD3PGA" alt="Examples of PDBML atom records. (a) Example of a fully marked-up PDBML atom record. The content of this record is equivalent to the content of the PDB Exchange data file. Empty data records are not translated to the XML data file. (b) Example of a simplified PDBML atom record. The information in this record is also the equivalent to the PDB Exchange data file; however, it is formatted as a white-space delimited string." data-path-from-xml="BIOINFORMATICS_21_7_988_f3.jpeg" /><div class="graphic-bottom"><div class="label fig-label" id="label-394064318"><strong>Fig. 3</strong></div><div class="caption fig-caption"><p class="chapter-para">Examples of PDBML atom records. (<strong>a</strong>) Example of a fully marked-up PDBML atom record. The content of this record is equivalent to the content of the PDB Exchange data file. Empty data records are not translated to the XML data file. (<strong>b</strong>) Example of a simplified PDBML atom record. The information in this record is also the equivalent to the PDB Exchange data file; however, it is formatted as a white-space delimited string.</p></div><div class="ajax-articleAbstract-exclude-regex fig-orig original-slide figure-button-wrap"><a class="fig-view-orig js-view-large at-figureViewLarge openInAnotherWindow" role="button" aria-describedby="label-394064318" href="/view-large/figure/394064318/BIOINFORMATICS_21_7_988_f3.jpeg" data-path-from-xml="BIOINFORMATICS_21_7_988_f3.jpeg" target="_blank">Open in new tab</a><a class="download-slide" role="button" aria-describedby="label-394064318" data-section="394064318" href="/DownloadFile/DownloadImage.aspx?image=https://oup.silverchair-cdn.com/oup/backfile/Content_public/Journal/bioinformatics/21/7/10.1093_bioinformatics_bti082/1/bioinformatics_21_7_988_f3.jpeg?Expires=1734479211&Signature=zsXXj7hskNfpBRt2fxM0TyfK9yRGH3UeIfqlKnQufrW9UA0ucvcQoasN9ynzuoRQqKIk3DggerXXLbLsHEv8Il-KzmVoY1cpYVmi~uSJFY0WAcXRrWSDH1oeZlniAyx3TlCWuN7mZpGmF9X12Nzev9jIOYjZHDfx5KkWAiyi8QsYwU1M1h1iDtSLVmGCVNdnRNV2DXmK7BCyE9j57PIQDlb~xY7wyo-aUcBkL82mDiHCqVmVKnCexiHsghjjtxhrPgrsq~Mnz154tT7ELFXUPfyZmvWw0u8wK4TY09r5YM8IHu3DR4T4W-y52ubKBNCWhP8UBUOWwB14OvzF0vxkmw__&Key-Pair-Id=APKAIE5G5CRDK6RD3PGA&sec=394064318&ar=268819&xsltPath=~/UI/app/XSLT&imagename=&siteId=5139" data-path-from-xml="BIOINFORMATICS_21_7_988_f3.jpeg">Download slide</a></div></div></div></div><p class="chapter-para">The authors thank Ms Kaori Kobayashi, Mr Hisashi Sakamoto, Ms Reiko Yamashita, Dr Daron Standley and Dr Arno Paehler at PDBj for their help to develop the schema and validation system for the PDBML. The RCSB PDB is operated by Rutgers, The State University of New Jersey; The San Diego Supercomputer Center at the University of California, San Diego; and the Center for Advanced Research in Biotechnology of the National Institute of Standards and Technology—three members of the Research Collaboratory for Structural Bioinformatics (RCSB). The work reported in this paper has been supported by grants from the NSF, NIGMS, DOE, NLM, NCI, NCRR, NIBIB and NINDS. The MSD-EBI is supported by funds from the Wellcome Trust, the European Union (TEMBLOR, NMRQUAL, SPINE, AUTOSTRUCT, and IIMS awards), CCP4, the Biotechnology and Biological Sciences Research Council (UK), the Medical Research Council (UK), and the European Molecular Biology Laboratory. The PDBj is supported by grant-in-aid from the Institute for Bioinformatics Research and Development of the Japan Science and Technology Agency (BIRD-JST), and the Ministry of Education, Culture, Sports, Science and Technology (MEXT).</p> <h2 scrollto-destination=394064321 id="394064321" class="backreferences-title js-splitscreen-backreferences-title" data-legacy-id=ref1>REFERENCES</h2> <div class="ref-list js-splitview-ref-list"><div content-id="B1" class="js-splitview-ref-item" data-legacy-id="B1"><div class="refLink-parent"><span class="refLink"><a name="jumplink-B1" href="javascript:;" aria-label="jumplink-B1" data-id=""></a></span></div><div class="ref false"><div id="ref-auto-B1" class="ref-content " data-id="B1"><div class="mixed-citation citation"><p class="mixed-citation-compatibility">Berman, H.M., Westbrook, J., Feng, Z., Gilliland, G., Bhat, T.N., Weissig, H., Shindyalov, I.N., Bourne, P.E. <div class="year">2000</div>The Protein Data Bank. <div class="source ">Nucleic Acids Res.</div><div class="volume">28</div><div class="fpage">235</div>–242</p></div></div></div></div><div content-id="B2" class="js-splitview-ref-item" data-legacy-id="B2"><div class="refLink-parent"><span class="refLink"><a name="jumplink-B2" href="javascript:;" aria-label="jumplink-B2" data-id=""></a></span></div><div class="ref false"><div id="ref-auto-B2" class="ref-content " data-id="B2"><div class="mixed-citation citation"><p class="mixed-citation-compatibility">Berman, H.M., Henrick, K., Nakamura, H. <div class="year">2003</div>Announcing the worldwide Protein Data Bank. <div class="source ">Nat. Struct. Biol.</div><div class="volume">10</div><div class="fpage">980</div></p></div></div></div></div><div content-id="B3" class="js-splitview-ref-item" data-legacy-id="B3"><div class="refLink-parent"><span class="refLink"><a name="jumplink-B3" href="javascript:;" aria-label="jumplink-B3" data-id=""></a></span></div><div class="ref false"><div id="ref-auto-B3" class="ref-content " data-id="B3"><div class="mixed-citation citation"><p class="mixed-citation-compatibility">Bernstein, F.C., Koetzle, T.F., Williams, G.J.B., Meyer, E.F., Jr., Brice, M.D., Rodgers, J.R., Kennard, O., Shimanouchi, T., Tasumi, M. <div class="year">1977</div>Protein Data Bank: a computer-based archival file for macromolecular structures. <div class="source ">J. Mol. Biol.</div><div class="volume">112</div><div class="fpage">535</div>–542</p></div></div></div></div><div content-id="B4" class="js-splitview-ref-item" data-legacy-id="B4"><div class="refLink-parent"><span class="refLink"><a name="jumplink-B4" href="javascript:;" aria-label="jumplink-B4" data-id=""></a></span></div><div class="ref false"><div id="ref-auto-B4" class="ref-content " data-id="B4"><div class="mixed-citation citation"><p class="mixed-citation-compatibility">Bourne, P.E., Berman, H.M., Watenpaugh, K., Westbrook, J.D., Fitzgerald, P.M.D. <div class="year">1997</div>The macromolecular Crystallographic Information File (mmCIF). <div class="source ">Meth. Enzymol.</div><div class="volume">277</div><div class="fpage">571</div>–590</p></div></div></div></div><div content-id="B5" class="js-splitview-ref-item" data-legacy-id="B5"><div class="refLink-parent"><span class="refLink"><a name="jumplink-B5" href="javascript:;" aria-label="jumplink-B5" data-id=""></a></span></div><div class="ref false"><div id="ref-auto-B5" class="ref-content " data-id="B5"><div class="mixed-citation citation"><p class="mixed-citation-compatibility">Callaway, J., Cummings, M., Deroski, B., Esposito, P., Forman, A., Langdon, P., Libeson, M., McCarthy, J., Sikora, J., Xue, D., et al. <div class="source ">Protein Data Bank Contents Guide: Atomic Coordinate Entry Format Description</div><div class="year">1996</div> Brookhaven National Laboratory</p></div></div></div></div><div content-id="B6" class="js-splitview-ref-item" data-legacy-id="B6"><div class="refLink-parent"><span class="refLink"><a name="jumplink-B6" href="javascript:;" aria-label="jumplink-B6" data-id=""></a></span></div><div class="ref false"><div id="ref-auto-B6" class="ref-content " data-id="B6"><div class="mixed-citation citation"><p class="mixed-citation-compatibility">Fitzgerald, P.M.D., Westbrook, J.D., Bourne, P.E., McMahon, B., Watenpaugh, K.D., Berman, H.M. <div class="year">2004</div>Classification and use of macromolecular data. In Hall, S.R. and McMahon, B. (Eds.). <div class="source ">International Tables for Crystallography vol G</div> , Dordrecht (in press) Kluwer Academic Publishers</p></div></div></div></div><div content-id="B7" class="js-splitview-ref-item" data-legacy-id="B7"><div class="refLink-parent"><span class="refLink"><a name="jumplink-B7" href="javascript:;" aria-label="jumplink-B7" data-id=""></a></span></div><div class="ref false"><div id="ref-auto-B7" class="ref-content " data-id="B7"><div class="mixed-citation citation"><p class="mixed-citation-compatibility">Hall, S.R., Allen, A.H., Brown, I.D. <div class="year">1991</div>The Crystallographic Information File (CIF): a new standard archive file for crystallography. <div class="source ">Acta Crystallogr A</div><div class="volume">47</div>, pp. <div class="fpage">655</div>–685</p></div></div></div></div><div content-id="B8" class="js-splitview-ref-item" data-legacy-id="B8"><div class="refLink-parent"><span class="refLink"><a name="jumplink-B8" href="javascript:;" aria-label="jumplink-B8" data-id=""></a></span></div><div class="ref false"><div id="ref-auto-B8" class="ref-content " data-id="B8"><div class="mixed-citation citation"><p class="mixed-citation-compatibility">Kinoshita, K. and Nakamura, H. <div class="year">2004</div>eF-site and PDBjViewer: database and viewer for protein functional sites. <div class="source ">Bioinformatics</div><div class="volume">20</div><div class="fpage">1329</div>–1330</p></div></div></div></div><div content-id="B9" class="js-splitview-ref-item" data-legacy-id="B9"><div class="refLink-parent"><span class="refLink"><a name="jumplink-B9" href="javascript:;" aria-label="jumplink-B9" data-id=""></a></span></div><div class="ref false"><div id="ref-auto-B9" class="ref-content " data-id="B9"><div class="mixed-citation citation"><p class="mixed-citation-compatibility">Westbrook, J. and Bourne, P.E. <div class="year">2000</div>STAR/mmCIF: an extensive ontology for macromolecular structure and beyond. <div class="source ">Bioinformatics</div><div class="volume">16</div><div class="fpage">159</div>–168</p></div></div></div></div><div content-id="B10" class="js-splitview-ref-item" data-legacy-id="B10"><div class="refLink-parent"><span class="refLink"><a name="jumplink-B10" href="javascript:;" aria-label="jumplink-B10" data-id=""></a></span></div><div class="ref false"><div id="ref-auto-B10" class="ref-content " data-id="B10"><div class="mixed-citation citation"><p class="mixed-citation-compatibility">Westbrook, J., Henrick, K., Ulrich, E.L., Berman, H.M. <div class="year">2004</div>The Protein Data Bank exchange dictionary. In Hall, S.R. and McMahon, B. (Eds.). <div class="source ">International Tables for Crystallography</div> , Dordrecht (in press) Kluwer Academic Publishers</p></div></div></div></div><div content-id="B11" class="js-splitview-ref-item" data-legacy-id="B11"><div class="refLink-parent"><span class="refLink"><a name="jumplink-B11" href="javascript:;" aria-label="jumplink-B11" data-id=""></a></span></div><div class="ref false"><div id="ref-auto-B11" class="ref-content " data-id="B11"><div class="mixed-citation citation"><p class="mixed-citation-compatibility">Westbrook, J.D., Berman, H.M., Hall, S.R. <div class="year">2004</div>Specification of a relational Dictionary Definition Language (DDL2). In Hall, S.R. and McMahon, B. (Eds.). <div class="source ">International Tables for Crystallography</div> , Dordrecht (in press) Kluwer Academic Publishers</p></div></div></div></div><div content-id="B12" class="js-splitview-ref-item" data-legacy-id="B12"><div class="refLink-parent"><span class="refLink"><a name="jumplink-B12" href="javascript:;" aria-label="jumplink-B12" data-id=""></a></span></div><div class="ref false"><div id="ref-auto-B12" class="ref-content " data-id="B12"><div class="mixed-citation citation"><p class="mixed-citation-compatibility">World Wide Web Consortium. (Ed.). <div class="source ">XML Schema Part 0: Primer, W3C Recommendation</div><div class="year">2001</div><a class="link link-uri openInAnotherWindow" href="http://www.w3.org/TR/2001/REC-xmlschema-2000-20010502/" target="_blank">http://www.w3.org/TR/2001/REC-xmlschema-2000-20010502/</a></p></div></div></div></div><div content-id="B13" class="js-splitview-ref-item" data-legacy-id="B13"><div class="refLink-parent"><span class="refLink"><a name="jumplink-B13" href="javascript:;" aria-label="jumplink-B13" data-id=""></a></span></div><div class="ref false"><div id="ref-auto-B13" class="ref-content " data-id="B13"><div class="mixed-citation citation"><p class="mixed-citation-compatibility">World Wide Web Consortium. (Eds.). <div class="source ">XML Schema Part 1: Structures W3C Recommendation</div><div class="year">2001</div> W3C. <a class="link link-uri openInAnotherWindow" href="http://www.w3.org/TR/2001/REC-xmlschema-2001-20010502/" target="_blank">http://www.w3.org/TR/2001/REC-xmlschema-2001-20010502/</a></p></div></div></div></div><div content-id="B14" class="js-splitview-ref-item" data-legacy-id="B14"><div class="refLink-parent"><span class="refLink"><a name="jumplink-B14" href="javascript:;" aria-label="jumplink-B14" data-id=""></a></span></div><div class="ref false"><div id="ref-auto-B14" class="ref-content " data-id="B14"><div class="mixed-citation citation"><p class="mixed-citation-compatibility">World Wide Web Consortium. (Eds.). <div class="source ">XML Schema Part 2: Datatypes W3C Recommendation</div><div class="year">2001</div> W3C pp. <a class="link link-uri openInAnotherWindow" href="http://www.w3.org/TR/xmlschema-2/" target="_blank">http://www.w3.org/TR/xmlschema-2/</a></p></div></div></div></div></div>  <div class="widget widget-ArticlePubStateInfo widget-instance-OUP_ArticlePubStateInfo"> </div> <div class="article-metadata-standalone-panel clearfix"></div> <div class="copyright copyright-statement">© The Author 2004. Published by Oxford University Press. All rights reserved. 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PDBML: the representation of archival macromolecular structure data in XML | Bioinformatics | Oxford Academic