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Module DBXRef
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<h1 class="epydoc">Source Code for <a href="Bio.DBXRef-module.html">Module Bio.DBXRef</a></h1>
<pre class="py-src">
<a name="DBXRef"></a><div id="DBXRef-def"><a name="L1"></a><tt class="py-lineno"> 1</tt> <a class="py-toggle" href="#" id="DBXRef-toggle" onclick="return toggle('DBXRef');">-</a><tt class="py-line"><tt class="py-keyword">class</tt> <a class="py-def-name" href="Bio.DBXRef.DBXRef-class.html">DBXRef</a><tt class="py-op">:</tt> </tt>
</div><div id="DBXRef-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="DBXRef-expanded"><a name="DBXRef.__init__"></a><div id="DBXRef.__init__-def"><a name="L2"></a><tt class="py-lineno"> 2</tt> <a class="py-toggle" href="#" id="DBXRef.__init__-toggle" onclick="return toggle('DBXRef.__init__');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.DBXRef.DBXRef-class.html#__init__">__init__</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">dbname</tt><tt class="py-op">,</tt> <tt class="py-param">dbid</tt><tt class="py-op">,</tt> <tt class="py-param">reftype</tt> <tt class="py-op">=</tt> <tt class="py-name">None</tt><tt class="py-op">,</tt> <tt class="py-param">negate</tt> <tt class="py-op">=</tt> <tt class="py-number">0</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="DBXRef.__init__-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="DBXRef.__init__-expanded"><a name="L3"></a><tt class="py-lineno"> 3</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">dbname</tt> <tt class="py-op">=</tt> <tt class="py-name">dbname</tt> </tt>
<a name="L4"></a><tt class="py-lineno"> 4</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-0" class="py-name" targets="Function Bio.Std.dbid()=Bio.Std-module.html#dbid"><a title="Bio.Std.dbid" class="py-name" href="#" onclick="return doclink('link-0', 'dbid', 'link-0');">dbid</a></tt> <tt class="py-op">=</tt> <tt id="link-1" class="py-name"><a title="Bio.Std.dbid" class="py-name" href="#" onclick="return doclink('link-1', 'dbid', 'link-0');">dbid</a></tt> </tt>
<a name="L5"></a><tt class="py-lineno"> 5</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">reftype</tt> <tt class="py-op">=</tt> <tt class="py-name">reftype</tt> </tt>
<a name="L6"></a><tt class="py-lineno"> 6</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">negate</tt> <tt class="py-op">=</tt> <tt class="py-name">negate</tt> </tt>
</div><a name="L7"></a><tt class="py-lineno"> 7</tt> <tt class="py-line"> </tt>
<a name="DBXRef.__str__"></a><div id="DBXRef.__str__-def"><a name="L8"></a><tt class="py-lineno"> 8</tt> <a class="py-toggle" href="#" id="DBXRef.__str__-toggle" onclick="return toggle('DBXRef.__str__');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.DBXRef.DBXRef-class.html#__str__">__str__</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="DBXRef.__str__-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="DBXRef.__str__-expanded"><a name="L9"></a><tt class="py-lineno"> 9</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">reftype</tt> <tt class="py-keyword">is</tt> <tt class="py-name">None</tt><tt class="py-op">:</tt> </tt>
<a name="L10"></a><tt class="py-lineno"> 10</tt> <tt class="py-line"> <tt class="py-name">reftype</tt> <tt class="py-op">=</tt> <tt class="py-string">""</tt> </tt>
<a name="L11"></a><tt class="py-lineno"> 11</tt> <tt class="py-line"> <tt class="py-keyword">else</tt><tt class="py-op">:</tt> </tt>
<a name="L12"></a><tt class="py-lineno"> 12</tt> <tt class="py-line"> <tt class="py-name">reftype</tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">reftype</tt> <tt class="py-op">+</tt> <tt class="py-string">"="</tt> </tt>
<a name="L13"></a><tt class="py-lineno"> 13</tt> <tt class="py-line"> <tt id="link-2" class="py-name" targets="Variable Martel.test.test_swissprot38.s=Martel.test.test_swissprot38-module.html#s"><a title="Martel.test.test_swissprot38.s" class="py-name" href="#" onclick="return doclink('link-2', 's', 'link-2');">s</a></tt> <tt class="py-op">=</tt> <tt class="py-string">"%s/%s%s"</tt> <tt class="py-op">%</tt> <tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">dbname</tt><tt class="py-op">,</tt> <tt class="py-name">reftype</tt><tt class="py-op">,</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-3" class="py-name"><a title="Bio.Std.dbid" class="py-name" href="#" onclick="return doclink('link-3', 'dbid', 'link-0');">dbid</a></tt><tt class="py-op">)</tt> </tt>
<a name="L14"></a><tt class="py-lineno"> 14</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">negate</tt><tt class="py-op">:</tt> </tt>
<a name="L15"></a><tt class="py-lineno"> 15</tt> <tt class="py-line"> <tt id="link-4" class="py-name"><a title="Martel.test.test_swissprot38.s" class="py-name" href="#" onclick="return doclink('link-4', 's', 'link-2');">s</a></tt> <tt class="py-op">=</tt> <tt class="py-string">"not(%s)"</tt> <tt class="py-op">%</tt> <tt id="link-5" class="py-name"><a title="Martel.test.test_swissprot38.s" class="py-name" href="#" onclick="return doclink('link-5', 's', 'link-2');">s</a></tt> </tt>
<a name="L16"></a><tt class="py-lineno"> 16</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt id="link-6" class="py-name"><a title="Martel.test.test_swissprot38.s" class="py-name" href="#" onclick="return doclink('link-6', 's', 'link-2');">s</a></tt> </tt>
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</div><a name="L18"></a><tt class="py-lineno"> 18</tt> <tt class="py-line"> </tt>
<a name="BioformatDBName"></a><div id="BioformatDBName-def"><a name="L19"></a><tt class="py-lineno"> 19</tt> <a class="py-toggle" href="#" id="BioformatDBName-toggle" onclick="return toggle('BioformatDBName');">-</a><tt class="py-line"><tt class="py-keyword">class</tt> <a class="py-def-name" href="Bio.DBXRef.BioformatDBName-class.html">BioformatDBName</a><tt class="py-op">:</tt> </tt>
</div><div id="BioformatDBName-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="BioformatDBName-expanded"><a name="BioformatDBName.__getitem__"></a><div id="BioformatDBName.__getitem__-def"><a name="L20"></a><tt class="py-lineno"> 20</tt> <a class="py-toggle" href="#" id="BioformatDBName.__getitem__-toggle" onclick="return toggle('BioformatDBName.__getitem__');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.DBXRef.BioformatDBName-class.html#__getitem__">__getitem__</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">name</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="BioformatDBName.__getitem__-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="BioformatDBName.__getitem__-expanded"><a name="L21"></a><tt class="py-lineno"> 21</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt id="link-9" class="py-name" targets="Variable Bio.Encodings.IUPACEncoding.name=Bio.Encodings.IUPACEncoding-module.html#name"><a title="Bio.Encodings.IUPACEncoding.name" class="py-name" href="#" onclick="return doclink('link-9', 'name', 'link-9');">name</a></tt> </tt>
</div></div><a name="UnknownDBName"></a><div id="UnknownDBName-def"><a name="L22"></a><tt class="py-lineno"> 22</tt> <a class="py-toggle" href="#" id="UnknownDBName-toggle" onclick="return toggle('UnknownDBName');">-</a><tt class="py-line"><tt class="py-keyword">class</tt> <a class="py-def-name" href="Bio.DBXRef.UnknownDBName-class.html">UnknownDBName</a><tt class="py-op">:</tt> </tt>
</div><div id="UnknownDBName-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="UnknownDBName-expanded"><a name="UnknownDBName.__getitem__"></a><div id="UnknownDBName.__getitem__-def"><a name="L23"></a><tt class="py-lineno"> 23</tt> <a class="py-toggle" href="#" id="UnknownDBName.__getitem__-toggle" onclick="return toggle('UnknownDBName.__getitem__');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.DBXRef.UnknownDBName-class.html#__getitem__">__getitem__</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">name</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="UnknownDBName.__getitem__-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="UnknownDBName.__getitem__-expanded"><a name="L24"></a><tt class="py-lineno"> 24</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-string">"x-unknown-"</tt> <tt class="py-op">+</tt> <tt id="link-10" class="py-name"><a title="Bio.Encodings.IUPACEncoding.name" class="py-name" href="#" onclick="return doclink('link-10', 'name', 'link-9');">name</a></tt><tt class="py-op">.</tt><tt class="py-name">lower</tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
</div></div><a name="L25"></a><tt class="py-lineno"> 25</tt> <tt class="py-line"> </tt>
<a name="L26"></a><tt class="py-lineno"> 26</tt> <tt class="py-line"><tt id="link-11" class="py-name" targets="Variable Bio.DBXRef.dbname_conversions=Bio.DBXRef-module.html#dbname_conversions"><a title="Bio.DBXRef.dbname_conversions" class="py-name" href="#" onclick="return doclink('link-11', 'dbname_conversions', 'link-11');">dbname_conversions</a></tt> <tt class="py-op">=</tt> <tt class="py-op">{</tt> </tt>
<a name="L27"></a><tt class="py-lineno"> 27</tt> <tt class="py-line"> <tt class="py-string">"bioformat"</tt><tt class="py-op">:</tt> <tt id="link-12" class="py-name" targets="Class Bio.DBXRef.BioformatDBName=Bio.DBXRef.BioformatDBName-class.html"><a title="Bio.DBXRef.BioformatDBName" class="py-name" href="#" onclick="return doclink('link-12', 'BioformatDBName', 'link-12');">BioformatDBName</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">,</tt> </tt>
<a name="L28"></a><tt class="py-lineno"> 28</tt> <tt class="py-line"> <tt class="py-string">"unknown"</tt><tt class="py-op">:</tt> <tt id="link-13" class="py-name" targets="Class Bio.DBXRef.UnknownDBName=Bio.DBXRef.UnknownDBName-class.html"><a title="Bio.DBXRef.UnknownDBName" class="py-name" href="#" onclick="return doclink('link-13', 'UnknownDBName', 'link-13');">UnknownDBName</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">,</tt> </tt>
<a name="L29"></a><tt class="py-lineno"> 29</tt> <tt class="py-line"> <tt class="py-string">"sp"</tt><tt class="py-op">:</tt> <tt class="py-op">{</tt><tt class="py-string">"AARHUS/GHENT-2DPAGE"</tt><tt class="py-op">:</tt> <tt class="py-string">"x-aarhus-ghent-2dpage"</tt><tt class="py-op">,</tt> </tt>
<a name="L30"></a><tt class="py-lineno"> 30</tt> <tt class="py-line"> <tt class="py-string">"CARBBANK"</tt><tt class="py-op">:</tt> <tt class="py-string">"x-carbbank"</tt><tt class="py-op">,</tt> </tt>
<a name="L31"></a><tt class="py-lineno"> 31</tt> <tt class="py-line"> <tt class="py-string">"DICTYDB"</tt><tt class="py-op">:</tt> <tt class="py-string">"x-dictydb"</tt><tt class="py-op">,</tt> </tt>
<a name="L32"></a><tt class="py-lineno"> 32</tt> <tt class="py-line"> <tt class="py-string">"ECO2DBASE"</tt><tt class="py-op">:</tt> <tt class="py-string">"x-eco2dbase"</tt><tt class="py-op">,</tt> </tt>
<a name="L33"></a><tt class="py-lineno"> 33</tt> <tt class="py-line"> <tt class="py-string">"ECOGENE"</tt><tt class="py-op">:</tt> <tt class="py-string">"x-ecogene"</tt><tt class="py-op">,</tt> </tt>
<a name="L34"></a><tt class="py-lineno"> 34</tt> <tt class="py-line"> <tt class="py-string">"EMBL"</tt><tt class="py-op">:</tt> <tt class="py-string">"embl"</tt><tt class="py-op">,</tt> <tt class="py-comment"># EMBL (in GO)</tt> </tt>
<a name="L35"></a><tt class="py-lineno"> 35</tt> <tt class="py-line"> <tt class="py-string">"FLYBASE"</tt><tt class="py-op">:</tt> <tt class="py-string">"fb"</tt><tt class="py-op">,</tt> <tt class="py-comment"># Flybase (in GO)</tt> </tt>
<a name="L36"></a><tt class="py-lineno"> 36</tt> <tt class="py-line"> <tt class="py-string">"GCRDB"</tt><tt class="py-op">:</tt> <tt class="py-string">"x-gcrdb"</tt><tt class="py-op">,</tt> </tt>
<a name="L37"></a><tt class="py-lineno"> 37</tt> <tt class="py-line"> <tt class="py-string">"HIV"</tt><tt class="py-op">:</tt> <tt class="py-string">"x-hiv"</tt><tt class="py-op">,</tt> </tt>
<a name="L38"></a><tt class="py-lineno"> 38</tt> <tt class="py-line"> <tt class="py-string">"HSC-2DPAGE"</tt><tt class="py-op">:</tt> <tt class="py-string">"x-hsc"</tt><tt class="py-op">,</tt> </tt>
<a name="L39"></a><tt class="py-lineno"> 39</tt> <tt class="py-line"> <tt class="py-string">"HSSP"</tt><tt class="py-op">:</tt> <tt class="py-string">"x-hssp"</tt><tt class="py-op">,</tt> </tt>
<a name="L40"></a><tt class="py-lineno"> 40</tt> <tt class="py-line"> <tt class="py-string">"MAIZE-2DPAGE"</tt><tt class="py-op">:</tt> <tt class="py-string">"x-maize"</tt><tt class="py-op">,</tt> </tt>
<a name="L41"></a><tt class="py-lineno"> 41</tt> <tt class="py-line"> <tt class="py-string">"MAIZEDB"</tt><tt class="py-op">:</tt> <tt class="py-string">"x-maizedb"</tt><tt class="py-op">,</tt> </tt>
<a name="L42"></a><tt class="py-lineno"> 42</tt> <tt class="py-line"> <tt class="py-string">"MENDEL"</tt><tt class="py-op">:</tt> <tt class="py-string">"x-mendel"</tt><tt class="py-op">,</tt> </tt>
<a name="L43"></a><tt class="py-lineno"> 43</tt> <tt class="py-line"> <tt class="py-string">"MGD"</tt><tt class="py-op">:</tt> <tt class="py-string">"mgd"</tt><tt class="py-op">,</tt> <tt class="py-comment"># (in GO)</tt> </tt>
<a name="L44"></a><tt class="py-lineno"> 44</tt> <tt class="py-line"> <tt class="py-string">"MIM"</tt><tt class="py-op">:</tt> <tt class="py-string">"x-mim"</tt><tt class="py-op">,</tt> </tt>
<a name="L45"></a><tt class="py-lineno"> 45</tt> <tt class="py-line"> <tt class="py-string">"PDB"</tt><tt class="py-op">:</tt> <tt class="py-string">"x-pdb"</tt><tt class="py-op">,</tt> <tt class="py-comment"># Protein Data Bank</tt> </tt>
<a name="L46"></a><tt class="py-lineno"> 46</tt> <tt class="py-line"> <tt class="py-string">"PFAM"</tt><tt class="py-op">:</tt> <tt class="py-string">"x-pfam"</tt><tt class="py-op">,</tt> </tt>
<a name="L47"></a><tt class="py-lineno"> 47</tt> <tt class="py-line"> <tt class="py-string">"PIR"</tt><tt class="py-op">:</tt> <tt class="py-string">"pir"</tt><tt class="py-op">,</tt> <tt class="py-comment"># GO</tt> </tt>
<a name="L48"></a><tt class="py-lineno"> 48</tt> <tt class="py-line"> <tt class="py-string">"PROSITE"</tt><tt class="py-op">:</tt> <tt class="py-string">"x-prosite"</tt><tt class="py-op">,</tt> </tt>
<a name="L49"></a><tt class="py-lineno"> 49</tt> <tt class="py-line"> <tt class="py-string">"REBASE"</tt><tt class="py-op">:</tt> <tt class="py-string">"x-rebase"</tt><tt class="py-op">,</tt> </tt>
<a name="L50"></a><tt class="py-lineno"> 50</tt> <tt class="py-line"> <tt class="py-string">"SGD"</tt><tt class="py-op">:</tt> <tt class="py-string">"sgd"</tt><tt class="py-op">,</tt> <tt class="py-comment"># GO</tt> </tt>
<a name="L51"></a><tt class="py-lineno"> 51</tt> <tt class="py-line"> <tt class="py-string">"STYGENE"</tt><tt class="py-op">:</tt> <tt class="py-string">"x-stygene"</tt><tt class="py-op">,</tt> </tt>
<a name="L52"></a><tt class="py-lineno"> 52</tt> <tt class="py-line"> <tt class="py-string">"SUBTILIST"</tt><tt class="py-op">:</tt> <tt class="py-string">"x-subtilist"</tt><tt class="py-op">,</tt> </tt>
<a name="L53"></a><tt class="py-lineno"> 53</tt> <tt class="py-line"> <tt class="py-string">"SWISS-2DPAGE"</tt><tt class="py-op">:</tt> <tt class="py-string">"x-swiss"</tt><tt class="py-op">,</tt> </tt>
<a name="L54"></a><tt class="py-lineno"> 54</tt> <tt class="py-line"> <tt class="py-string">"TIGR"</tt><tt class="py-op">:</tt> <tt class="py-string">"tigr"</tt><tt class="py-op">,</tt> <tt class="py-comment"># GO</tt> </tt>
<a name="L55"></a><tt class="py-lineno"> 55</tt> <tt class="py-line"> <tt class="py-string">"TRANSFAC"</tt><tt class="py-op">:</tt> <tt class="py-string">"x-transfac"</tt><tt class="py-op">,</tt> </tt>
<a name="L56"></a><tt class="py-lineno"> 56</tt> <tt class="py-line"> <tt class="py-string">"WORMPEP"</tt><tt class="py-op">:</tt> <tt class="py-string">"x-wormpep"</tt><tt class="py-op">,</tt> </tt>
<a name="L57"></a><tt class="py-lineno"> 57</tt> <tt class="py-line"> <tt class="py-string">"YEPD"</tt><tt class="py-op">:</tt> <tt class="py-string">"x-yepd"</tt><tt class="py-op">,</tt> </tt>
<a name="L58"></a><tt class="py-lineno"> 58</tt> <tt class="py-line"> <tt class="py-string">"ZFIN"</tt><tt class="py-op">:</tt> <tt class="py-string">"x-zfin"</tt><tt class="py-op">,</tt> </tt>
<a name="L59"></a><tt class="py-lineno"> 59</tt> <tt class="py-line"> <tt class="py-op">}</tt><tt class="py-op">,</tt> </tt>
<a name="L60"></a><tt class="py-lineno"> 60</tt> <tt class="py-line"> <tt class="py-string">"go"</tt><tt class="py-op">:</tt> <tt class="py-op">{</tt><tt class="py-string">"CGEN"</tt><tt class="py-op">:</tt> <tt class="py-string">"cgen"</tt><tt class="py-op">,</tt> <tt class="py-comment"># Compugen, Inc.</tt> </tt>
<a name="L61"></a><tt class="py-lineno"> 61</tt> <tt class="py-line"> <tt class="py-string">"DDB"</tt><tt class="py-op">:</tt> <tt class="py-string">"ddb"</tt><tt class="py-op">,</tt> <tt class="py-comment"># DictyBase (Dictyostelium discoideum)</tt> </tt>
<a name="L62"></a><tt class="py-lineno"> 62</tt> <tt class="py-line"> <tt class="py-string">"DDBJ"</tt><tt class="py-op">:</tt> <tt class="py-string">"ddbj"</tt><tt class="py-op">,</tt> <tt class="py-comment"># DNA Database of Japan</tt> </tt>
<a name="L63"></a><tt class="py-lineno"> 63</tt> <tt class="py-line"> <tt class="py-string">"EC"</tt><tt class="py-op">:</tt> <tt class="py-string">"ec"</tt><tt class="py-op">,</tt> <tt class="py-comment"># Enzyme Commission</tt> </tt>
<a name="L64"></a><tt class="py-lineno"> 64</tt> <tt class="py-line"> <tt class="py-string">"EMBL"</tt><tt class="py-op">:</tt> <tt class="py-string">"embl"</tt><tt class="py-op">,</tt> <tt class="py-comment"># EMBL Nucleotide Sequence Data Library</tt> </tt>
<a name="L65"></a><tt class="py-lineno"> 65</tt> <tt class="py-line"> <tt class="py-string">"ENSEMBL"</tt><tt class="py-op">:</tt> <tt class="py-string">"ensembl"</tt><tt class="py-op">,</tt> <tt class="py-comment"># ENSEMBL</tt> </tt>
<a name="L66"></a><tt class="py-lineno"> 66</tt> <tt class="py-line"> <tt class="py-string">"ENZYME"</tt><tt class="py-op">:</tt> <tt class="py-string">"enzyme"</tt><tt class="py-op">,</tt> <tt class="py-comment"># ENZYME</tt> </tt>
<a name="L67"></a><tt class="py-lineno"> 67</tt> <tt class="py-line"> <tt class="py-string">"FB"</tt><tt class="py-op">:</tt> <tt class="py-string">"fb"</tt><tt class="py-op">,</tt> <tt class="py-comment"># FlyBase</tt> </tt>
<a name="L68"></a><tt class="py-lineno"> 68</tt> <tt class="py-line"> <tt class="py-string">"GB"</tt><tt class="py-op">:</tt> <tt class="py-string">"gb"</tt><tt class="py-op">,</tt> <tt class="py-comment"># GenBank</tt> </tt>
<a name="L69"></a><tt class="py-lineno"> 69</tt> <tt class="py-line"> <tt class="py-string">"GO"</tt><tt class="py-op">:</tt> <tt class="py-string">"go"</tt><tt class="py-op">,</tt> <tt class="py-comment"># Gene Ontology</tt> </tt>
<a name="L70"></a><tt class="py-lineno"> 70</tt> <tt class="py-line"> <tt class="py-string">"GXD"</tt><tt class="py-op">:</tt> <tt class="py-string">"gxd"</tt><tt class="py-op">,</tt> <tt class="py-comment"># Gene Expression Database (mouse)</tt> </tt>
<a name="L71"></a><tt class="py-lineno"> 71</tt> <tt class="py-line"> <tt class="py-string">"IPR"</tt><tt class="py-op">:</tt> <tt class="py-string">"ipr"</tt><tt class="py-op">,</tt> <tt class="py-comment"># InterPro</tt> </tt>
<a name="L72"></a><tt class="py-lineno"> 72</tt> <tt class="py-line"> <tt class="py-string">"ISBN"</tt><tt class="py-op">:</tt> <tt class="py-string">"isbn"</tt><tt class="py-op">,</tt> <tt class="py-comment"># International Standard Book Number</tt> </tt>
<a name="L73"></a><tt class="py-lineno"> 73</tt> <tt class="py-line"> <tt class="py-string">"IUBMB"</tt><tt class="py-op">:</tt> <tt class="py-string">"iubmb"</tt><tt class="py-op">,</tt> <tt class="py-comment"># International Union of Biochemistry</tt> </tt>
<a name="L74"></a><tt class="py-lineno"> 74</tt> <tt class="py-line"> <tt class="py-comment"># and Molecular Biology</tt> </tt>
<a name="L75"></a><tt class="py-lineno"> 75</tt> <tt class="py-line"> <tt class="py-string">"IUPAC"</tt><tt class="py-op">:</tt> <tt class="py-string">"iupac"</tt><tt class="py-op">,</tt> <tt class="py-comment"># International Union of Pure and Applied</tt> </tt>
<a name="L76"></a><tt class="py-lineno"> 76</tt> <tt class="py-line"> <tt class="py-comment"># Chemistry</tt> </tt>
<a name="L77"></a><tt class="py-lineno"> 77</tt> <tt class="py-line"> <tt class="py-string">"MEDLINE"</tt><tt class="py-op">:</tt> <tt class="py-string">"medline"</tt><tt class="py-op">,</tt> <tt class="py-comment"># MEDLINE</tt> </tt>
<a name="L78"></a><tt class="py-lineno"> 78</tt> <tt class="py-line"> <tt class="py-string">"MGD"</tt><tt class="py-op">:</tt> <tt class="py-string">"mgd"</tt><tt class="py-op">,</tt> <tt class="py-comment"># Mouse Genome Database</tt> </tt>
<a name="L79"></a><tt class="py-lineno"> 79</tt> <tt class="py-line"> <tt class="py-string">"MGI"</tt><tt class="py-op">:</tt> <tt class="py-string">"mgi"</tt><tt class="py-op">,</tt> <tt class="py-comment"># Mouse Genome Informatics</tt> </tt>
<a name="L80"></a><tt class="py-lineno"> 80</tt> <tt class="py-line"> <tt class="py-string">"NC-IUBMB"</tt><tt class="py-op">:</tt> <tt class="py-string">"NC-IUBMB"</tt><tt class="py-op">,</tt> </tt>
<a name="L81"></a><tt class="py-lineno"> 81</tt> <tt class="py-line"> <tt class="py-comment"># Nomenclature Committee of the International</tt> </tt>
<a name="L82"></a><tt class="py-lineno"> 82</tt> <tt class="py-line"> <tt class="py-comment"># Union of Biochemistry and Molecular Biology</tt> </tt>
<a name="L83"></a><tt class="py-lineno"> 83</tt> <tt class="py-line"> <tt class="py-string">"PIR"</tt><tt class="py-op">:</tt> <tt class="py-string">"pir"</tt><tt class="py-op">,</tt> <tt class="py-comment"># PIR</tt> </tt>
<a name="L84"></a><tt class="py-lineno"> 84</tt> <tt class="py-line"> <tt class="py-string">"PMID"</tt><tt class="py-op">:</tt> <tt class="py-string">"pmid"</tt><tt class="py-op">,</tt> <tt class="py-comment"># PubMed</tt> </tt>
<a name="L85"></a><tt class="py-lineno"> 85</tt> <tt class="py-line"> <tt class="py-string">"Pombase"</tt><tt class="py-op">:</tt> <tt class="py-string">"pombase"</tt><tt class="py-op">,</tt> <tt class="py-comment"># Schizosaccharomyces pombe</tt> </tt>
<a name="L86"></a><tt class="py-lineno"> 86</tt> <tt class="py-line"> <tt class="py-string">"Pompep"</tt><tt class="py-op">:</tt> <tt class="py-string">"pompep"</tt><tt class="py-op">,</tt> <tt class="py-comment"># Schizosaccharomyces pombe Protein</tt> </tt>
<a name="L87"></a><tt class="py-lineno"> 87</tt> <tt class="py-line"> <tt class="py-comment"># Sequence Database</tt> </tt>
<a name="L88"></a><tt class="py-lineno"> 88</tt> <tt class="py-line"> <tt class="py-string">"RESID"</tt><tt class="py-op">:</tt> <tt class="py-string">"resid"</tt><tt class="py-op">,</tt> <tt class="py-comment"># RESID (protein post-translational modifications)</tt> </tt>
<a name="L89"></a><tt class="py-lineno"> 89</tt> <tt class="py-line"> <tt class="py-string">"SGD"</tt><tt class="py-op">:</tt> <tt class="py-string">"sgd"</tt><tt class="py-op">,</tt> <tt class="py-comment"># Saccharomyces Genome Database</tt> </tt>
<a name="L90"></a><tt class="py-lineno"> 90</tt> <tt class="py-line"> <tt class="py-string">"SP"</tt><tt class="py-op">:</tt> <tt class="py-string">"sp"</tt><tt class="py-op">,</tt> <tt class="py-comment"># SWISS-PROT</tt> </tt>
<a name="L91"></a><tt class="py-lineno"> 91</tt> <tt class="py-line"> <tt class="py-string">"SWALL"</tt><tt class="py-op">:</tt> <tt class="py-string">"swall"</tt><tt class="py-op">,</tt> <tt class="py-comment"># SWISS-PROT + TrEMBL + TrEMBLnew</tt> </tt>
<a name="L92"></a><tt class="py-lineno"> 92</tt> <tt class="py-line"> <tt class="py-string">"TAIR"</tt><tt class="py-op">:</tt> <tt class="py-string">"tair"</tt><tt class="py-op">,</tt> <tt class="py-comment"># The Arabidopsis Information Resource</tt> </tt>
<a name="L93"></a><tt class="py-lineno"> 93</tt> <tt class="py-line"> <tt class="py-string">"taxonID"</tt><tt class="py-op">:</tt> <tt class="py-string">"taxonid"</tt><tt class="py-op">,</tt> <tt class="py-comment"># Taxonomy ID</tt> </tt>
<a name="L94"></a><tt class="py-lineno"> 94</tt> <tt class="py-line"> <tt class="py-string">"TC"</tt><tt class="py-op">:</tt> <tt class="py-string">"tc"</tt><tt class="py-op">,</tt> <tt class="py-comment"># Transport Commission</tt> </tt>
<a name="L95"></a><tt class="py-lineno"> 95</tt> <tt class="py-line"> <tt class="py-string">"TIGR"</tt><tt class="py-op">:</tt> <tt class="py-string">"tigr"</tt><tt class="py-op">,</tt> <tt class="py-comment"># The Institute of Genome Research</tt> </tt>
<a name="L96"></a><tt class="py-lineno"> 96</tt> <tt class="py-line"> <tt class="py-string">"TR"</tt><tt class="py-op">:</tt> <tt class="py-string">"tr"</tt><tt class="py-op">,</tt> <tt class="py-comment"># TrEMBL</tt> </tt>
<a name="L97"></a><tt class="py-lineno"> 97</tt> <tt class="py-line"> <tt class="py-string">"WB"</tt><tt class="py-op">:</tt> <tt class="py-string">"wb"</tt><tt class="py-op">,</tt> <tt class="py-comment"># WormBase (Caenorhabditis elegans)</tt> </tt>
<a name="L98"></a><tt class="py-lineno"> 98</tt> <tt class="py-line"> <tt class="py-op">}</tt><tt class="py-op">,</tt> </tt>
<a name="L99"></a><tt class="py-lineno"> 99</tt> <tt class="py-line"> <tt class="py-comment"># http://www.ncbi.nlm.nih.gov/collab/db_xref.html</tt> </tt>
<a name="L100"></a><tt class="py-lineno">100</tt> <tt class="py-line"> <tt class="py-string">"genbank"</tt><tt class="py-op">:</tt> <tt class="py-op">{</tt> </tt>
<a name="L101"></a><tt class="py-lineno">101</tt> <tt class="py-line"> <tt class="py-string">"ATCC"</tt><tt class="py-op">:</tt> <tt class="py-string">"x-atcc"</tt><tt class="py-op">,</tt> <tt class="py-comment"># American Type Culture Collection database</tt> </tt>
<a name="L102"></a><tt class="py-lineno">102</tt> <tt class="py-line"> <tt class="py-comment"># /db_xref="ATCC:123456"</tt> </tt>
<a name="L103"></a><tt class="py-lineno">103</tt> <tt class="py-line"> <tt class="py-string">"ATCC(in host)"</tt><tt class="py-op">:</tt> <tt class="py-string">"x-atcc-host"</tt><tt class="py-op">,</tt> <tt class="py-comment"># See above</tt> </tt>
<a name="L104"></a><tt class="py-lineno">104</tt> <tt class="py-line"> <tt class="py-string">"ATCC(dna)"</tt><tt class="py-op">:</tt> <tt class="py-string">"x-atcc-dna"</tt><tt class="py-op">,</tt> <tt class="py-comment"># See above</tt> </tt>
<a name="L105"></a><tt class="py-lineno">105</tt> <tt class="py-line"> </tt>
<a name="L106"></a><tt class="py-lineno">106</tt> <tt class="py-line"> <tt class="py-string">"BDGP_EST"</tt><tt class="py-op">:</tt> <tt class="py-string">"x-bdgp-est"</tt><tt class="py-op">,</tt> <tt class="py-comment"># Berkeley Drosophila Genome Project</tt> </tt>
<a name="L107"></a><tt class="py-lineno">107</tt> <tt class="py-line"> <tt class="py-comment"># EST database</tt> </tt>
<a name="L108"></a><tt class="py-lineno">108</tt> <tt class="py-line"> <tt class="py-comment"># /db_xref="BDGP_EST:123456"</tt> </tt>
<a name="L109"></a><tt class="py-lineno">109</tt> <tt class="py-line"> </tt>
<a name="L110"></a><tt class="py-lineno">110</tt> <tt class="py-line"> <tt class="py-string">"BDGP_INS"</tt><tt class="py-op">:</tt> <tt class="py-string">"x-bdgp-ins"</tt><tt class="py-op">,</tt> <tt class="py-comment"># Berkeley Drosophila Genome Project</tt> </tt>
<a name="L111"></a><tt class="py-lineno">111</tt> <tt class="py-line"> <tt class="py-comment"># database -- Insertion</tt> </tt>
<a name="L112"></a><tt class="py-lineno">112</tt> <tt class="py-line"> <tt class="py-comment"># /db_xref="BDGP_INS:123456"</tt> </tt>
<a name="L113"></a><tt class="py-lineno">113</tt> <tt class="py-line"> </tt>
<a name="L114"></a><tt class="py-lineno">114</tt> <tt class="py-line"> </tt>
<a name="L115"></a><tt class="py-lineno">115</tt> <tt class="py-line"> <tt class="py-string">"dbEST"</tt><tt class="py-op">:</tt> <tt class="py-string">"x-dbest"</tt><tt class="py-op">,</tt> <tt class="py-comment"># EST database maintained at the NCBI.</tt> </tt>
<a name="L116"></a><tt class="py-lineno">116</tt> <tt class="py-line"> <tt class="py-comment"># /db_xref="dbEST:123456"</tt> </tt>
<a name="L117"></a><tt class="py-lineno">117</tt> <tt class="py-line"> </tt>
<a name="L118"></a><tt class="py-lineno">118</tt> <tt class="py-line"> <tt class="py-string">"dbSNP"</tt><tt class="py-op">:</tt> <tt class="py-string">"x-dbsnp"</tt><tt class="py-op">,</tt> <tt class="py-comment"># Variation database maintained at the NCBI.</tt> </tt>
<a name="L119"></a><tt class="py-lineno">119</tt> <tt class="py-line"> <tt class="py-comment"># /db_xref="dbSNP:4647"</tt> </tt>
<a name="L120"></a><tt class="py-lineno">120</tt> <tt class="py-line"> </tt>
<a name="L121"></a><tt class="py-lineno">121</tt> <tt class="py-line"> <tt class="py-string">"dbSTS"</tt><tt class="py-op">:</tt> <tt class="py-string">"x-dbsts"</tt><tt class="py-op">,</tt> <tt class="py-comment"># STS database maintained at the NCBI.</tt> </tt>
<a name="L122"></a><tt class="py-lineno">122</tt> <tt class="py-line"> <tt class="py-comment"># /db_xref="dbSTS:456789"</tt> </tt>
<a name="L123"></a><tt class="py-lineno">123</tt> <tt class="py-line"> </tt>
<a name="L124"></a><tt class="py-lineno">124</tt> <tt class="py-line"> <tt class="py-string">"ENSEMBL"</tt><tt class="py-op">:</tt> <tt class="py-string">"ensembl"</tt><tt class="py-op">,</tt> <tt class="py-comment"># Database of automatically annotated genomic data</tt> </tt>
<a name="L125"></a><tt class="py-lineno">125</tt> <tt class="py-line"> <tt class="py-comment"># /db_xref="ENSEMBL:HUMAN-Clone-AC005612"</tt> </tt>
<a name="L126"></a><tt class="py-lineno">126</tt> <tt class="py-line"> <tt class="py-comment"># /db_xref="ENSEMBL:HUMAN-Gene-ENSG00000007102" </tt> </tt>
<a name="L127"></a><tt class="py-lineno">127</tt> <tt class="py-line"> </tt>
<a name="L128"></a><tt class="py-lineno">128</tt> <tt class="py-line"> <tt class="py-string">"ESTLIB"</tt><tt class="py-op">:</tt> <tt class="py-string">"x-estlib"</tt><tt class="py-op">,</tt> <tt class="py-comment"># EBI's EST library identifier #'</tt> </tt>
<a name="L129"></a><tt class="py-lineno">129</tt> <tt class="py-line"> <tt class="py-comment"># /db_xref="ESTLIB:1200"</tt> </tt>
<a name="L130"></a><tt class="py-lineno">130</tt> <tt class="py-line"> </tt>
<a name="L131"></a><tt class="py-lineno">131</tt> <tt class="py-line"> <tt class="py-string">"FANTOM_DB"</tt><tt class="py-op">:</tt> <tt class="py-string">"x-fantom-db"</tt><tt class="py-op">,</tt> <tt class="py-comment"># Database of Functional Annotation of Mouse</tt> </tt>
<a name="L132"></a><tt class="py-lineno">132</tt> <tt class="py-line"> <tt class="py-comment"># /db_xref="FANTOM_DB:0610005A07"</tt> </tt>
<a name="L133"></a><tt class="py-lineno">133</tt> <tt class="py-line"> </tt>
<a name="L134"></a><tt class="py-lineno">134</tt> <tt class="py-line"> <tt class="py-string">"FLYBASE"</tt><tt class="py-op">:</tt> <tt class="py-string">"fb"</tt><tt class="py-op">,</tt> <tt class="py-comment"># Database of Genetic and molecular data of Drosophila.</tt> </tt>
<a name="L135"></a><tt class="py-lineno">135</tt> <tt class="py-line"> <tt class="py-comment"># /db_xref="FLYBASE:FBgn0000024"</tt> </tt>
<a name="L136"></a><tt class="py-lineno">136</tt> <tt class="py-line"> </tt>
<a name="L137"></a><tt class="py-lineno">137</tt> <tt class="py-line"> <tt class="py-string">"GDB"</tt><tt class="py-op">:</tt> <tt class="py-string">"x-gdb"</tt><tt class="py-op">,</tt> <tt class="py-comment"># Human Genome Database accession numbers.</tt> </tt>
<a name="L138"></a><tt class="py-lineno">138</tt> <tt class="py-line"> <tt class="py-comment"># /db_xref="GDB:G00-128-600"</tt> </tt>
<a name="L139"></a><tt class="py-lineno">139</tt> <tt class="py-line"> </tt>
<a name="L140"></a><tt class="py-lineno">140</tt> <tt class="py-line"> <tt class="py-string">"GI"</tt><tt class="py-op">:</tt> <tt class="py-string">"x-gi"</tt><tt class="py-op">,</tt> <tt class="py-comment"># GenInfo identifier, used as a unique sequence</tt> </tt>
<a name="L141"></a><tt class="py-lineno">141</tt> <tt class="py-line"> <tt class="py-comment"># identifier for nucleotide and proteins.</tt> </tt>
<a name="L142"></a><tt class="py-lineno">142</tt> <tt class="py-line"> <tt class="py-comment"># /db_xref="GI:1234567890"</tt> </tt>
<a name="L143"></a><tt class="py-lineno">143</tt> <tt class="py-line"> </tt>
<a name="L144"></a><tt class="py-lineno">144</tt> <tt class="py-line"> <tt class="py-string">"GO"</tt><tt class="py-op">:</tt> <tt class="py-string">"go"</tt><tt class="py-op">,</tt> <tt class="py-comment"># Gene Ontology Database identifier</tt> </tt>
<a name="L145"></a><tt class="py-lineno">145</tt> <tt class="py-line"> <tt class="py-comment"># /db_xref="GO:123"</tt> </tt>
<a name="L146"></a><tt class="py-lineno">146</tt> <tt class="py-line"> </tt>
<a name="L147"></a><tt class="py-lineno">147</tt> <tt class="py-line"> <tt class="py-string">"IMGT/LIGM"</tt><tt class="py-op">:</tt> <tt class="py-string">"x-imgt-ligm"</tt><tt class="py-op">,</tt> <tt class="py-comment"># Immunogenetics database, immunoglobulins</tt> </tt>
<a name="L148"></a><tt class="py-lineno">148</tt> <tt class="py-line"> <tt class="py-comment"># and T-cell receptors</tt> </tt>
<a name="L149"></a><tt class="py-lineno">149</tt> <tt class="py-line"> <tt class="py-comment"># /db_xref="IMGT/LIGM:U03895"</tt> </tt>
<a name="L150"></a><tt class="py-lineno">150</tt> <tt class="py-line"> </tt>
<a name="L151"></a><tt class="py-lineno">151</tt> <tt class="py-line"> <tt class="py-string">"IMGT/HLA"</tt><tt class="py-op">:</tt> <tt class="py-string">"x-imgt-hla"</tt><tt class="py-op">,</tt> <tt class="py-comment"># Immunogenetics database, human MHC</tt> </tt>
<a name="L152"></a><tt class="py-lineno">152</tt> <tt class="py-line"> <tt class="py-comment"># /db_xref="IMGT/HLA:HLA00031"</tt> </tt>
<a name="L153"></a><tt class="py-lineno">153</tt> <tt class="py-line"> </tt>
<a name="L154"></a><tt class="py-lineno">154</tt> <tt class="py-line"> </tt>
<a name="L155"></a><tt class="py-lineno">155</tt> <tt class="py-line"> <tt class="py-string">"LocusID"</tt><tt class="py-op">:</tt> <tt class="py-string">"x-locus-id"</tt><tt class="py-op">,</tt> <tt class="py-comment"># NCBI LocusLink ID.</tt> </tt>
<a name="L156"></a><tt class="py-lineno">156</tt> <tt class="py-line"> <tt class="py-comment"># /db_xref="LocusID:51199"</tt> </tt>
<a name="L157"></a><tt class="py-lineno">157</tt> <tt class="py-line"> </tt>
<a name="L158"></a><tt class="py-lineno">158</tt> <tt class="py-line"> <tt class="py-string">"MaizeDB"</tt><tt class="py-op">:</tt> <tt class="py-string">"x-maizedb"</tt><tt class="py-op">,</tt> <tt class="py-comment"># Maize Genome Database unique identifiers.</tt> </tt>
<a name="L159"></a><tt class="py-lineno">159</tt> <tt class="py-line"> <tt class="py-comment"># /db_xref="MaizeDB:Probe/79847"</tt> </tt>
<a name="L160"></a><tt class="py-lineno">160</tt> <tt class="py-line"> </tt>
<a name="L161"></a><tt class="py-lineno">161</tt> <tt class="py-line"> <tt class="py-string">"MGD"</tt><tt class="py-op">:</tt> <tt class="py-string">"mgd"</tt><tt class="py-op">,</tt> <tt class="py-comment"># Mouse Genome Database accession numbers.</tt> </tt>
<a name="L162"></a><tt class="py-lineno">162</tt> <tt class="py-line"> <tt class="py-comment"># /db_xref="MGD:123456"</tt> </tt>
<a name="L163"></a><tt class="py-lineno">163</tt> <tt class="py-line"> </tt>
<a name="L164"></a><tt class="py-lineno">164</tt> <tt class="py-line"> <tt class="py-string">"MGI"</tt><tt class="py-op">:</tt> <tt class="py-string">"mgi"</tt><tt class="py-op">,</tt> <tt class="py-comment"># Medicago Genome Initiative</tt> </tt>
<a name="L165"></a><tt class="py-lineno">165</tt> <tt class="py-line"> <tt class="py-comment"># /db_xref="MGI:S:20819"</tt> </tt>
<a name="L166"></a><tt class="py-lineno">166</tt> <tt class="py-line"> </tt>
<a name="L167"></a><tt class="py-lineno">167</tt> <tt class="py-line"> <tt class="py-string">"MIM"</tt><tt class="py-op">:</tt> <tt class="py-string">"x-mim"</tt><tt class="py-op">,</tt> <tt class="py-comment"># Mendelian Inheritance in Man numbers.</tt> </tt>
<a name="L168"></a><tt class="py-lineno">168</tt> <tt class="py-line"> <tt class="py-comment"># /db_xref="MIM:123456"</tt> </tt>
<a name="L169"></a><tt class="py-lineno">169</tt> <tt class="py-line"> </tt>
<a name="L170"></a><tt class="py-lineno">170</tt> <tt class="py-line"> <tt class="py-string">"niaEST"</tt><tt class="py-op">:</tt> <tt class="py-string">"x-niaEST"</tt><tt class="py-op">,</tt> <tt class="py-comment"># NIA Mouse cDNA Project</tt> </tt>
<a name="L171"></a><tt class="py-lineno">171</tt> <tt class="py-line"> <tt class="py-comment"># /db_xref="niaEST:L0304H12-3"</tt> </tt>
<a name="L172"></a><tt class="py-lineno">172</tt> <tt class="py-line"> </tt>
<a name="L173"></a><tt class="py-lineno">173</tt> <tt class="py-line"> <tt class="py-string">"PIR"</tt><tt class="py-op">:</tt> <tt class="py-string">"pir"</tt><tt class="py-op">,</tt> <tt class="py-comment"># Protein Information Resource accession numbers.</tt> </tt>
<a name="L174"></a><tt class="py-lineno">174</tt> <tt class="py-line"> <tt class="py-comment"># /db_xref="PIR:S12345"</tt> </tt>
<a name="L175"></a><tt class="py-lineno">175</tt> <tt class="py-line"> </tt>
<a name="L176"></a><tt class="py-lineno">176</tt> <tt class="py-line"> <tt class="py-string">"PSEUDO"</tt><tt class="py-op">:</tt> <tt class="py-string">"x-pseudo-embl"</tt><tt class="py-op">,</tt> <tt class="py-comment"># EMBL pseudo protein identifier</tt> </tt>
<a name="L177"></a><tt class="py-lineno">177</tt> <tt class="py-line"> <tt class="py-comment"># /db_xref="PSEUDO:CAC44644.1"</tt> </tt>
<a name="L178"></a><tt class="py-lineno">178</tt> <tt class="py-line"> </tt>
<a name="L179"></a><tt class="py-lineno">179</tt> <tt class="py-line"> <tt class="py-string">"RATMAP"</tt><tt class="py-op">:</tt> <tt class="py-string">"x-ratmap"</tt><tt class="py-op">,</tt> <tt class="py-comment"># Rat Genome Database </tt> </tt>
<a name="L180"></a><tt class="py-lineno">180</tt> <tt class="py-line"> <tt class="py-comment"># /db_xref="RATMAP:5"</tt> </tt>
<a name="L181"></a><tt class="py-lineno">181</tt> <tt class="py-line"> </tt>
<a name="L182"></a><tt class="py-lineno">182</tt> <tt class="py-line"> <tt class="py-string">"RiceGenes"</tt><tt class="py-op">:</tt> <tt class="py-string">"x-ricegenes"</tt><tt class="py-op">,</tt> <tt class="py-comment"># Rice database accession numbers.</tt> </tt>
<a name="L183"></a><tt class="py-lineno">183</tt> <tt class="py-line"> <tt class="py-comment"># /db_xref="RiceGenes:AA231856"</tt> </tt>
<a name="L184"></a><tt class="py-lineno">184</tt> <tt class="py-line"> </tt>
<a name="L185"></a><tt class="py-lineno">185</tt> <tt class="py-line"> <tt class="py-string">"REMTREMBL"</tt><tt class="py-op">:</tt> <tt class="py-string">"x-remtrembl"</tt><tt class="py-op">,</tt> </tt>
<a name="L186"></a><tt class="py-lineno">186</tt> <tt class="py-line"> <tt class="py-comment"># Computer-annotated protein sequence database containing</tt> </tt>
<a name="L187"></a><tt class="py-lineno">187</tt> <tt class="py-line"> <tt class="py-comment"># the translations of those codings sequences (CDS) present</tt> </tt>
<a name="L188"></a><tt class="py-lineno">188</tt> <tt class="py-line"> <tt class="py-comment"># in the EMBL Nucleotide Sequence Database that won't be '</tt> </tt>
<a name="L189"></a><tt class="py-lineno">189</tt> <tt class="py-line"> <tt class="py-comment"># included in SWISS-PROT. These include: immunoglobulins and</tt> </tt>
<a name="L190"></a><tt class="py-lineno">190</tt> <tt class="py-line"> <tt class="py-comment"># T-cell receptors, synthetic sequences, patent application</tt> </tt>
<a name="L191"></a><tt class="py-lineno">191</tt> <tt class="py-line"> <tt class="py-comment"># sequences, small fragments, CDS not coding for real </tt> </tt>
<a name="L192"></a><tt class="py-lineno">192</tt> <tt class="py-line"> <tt class="py-comment"># proteins and truncated proteins.</tt> </tt>
<a name="L193"></a><tt class="py-lineno">193</tt> <tt class="py-line"> <tt class="py-comment"># example: /db_xref="REMTREMBL:CAC01666"</tt> </tt>
<a name="L194"></a><tt class="py-lineno">194</tt> <tt class="py-line"> </tt>
<a name="L195"></a><tt class="py-lineno">195</tt> <tt class="py-line"> <tt class="py-string">"RZPD"</tt><tt class="py-op">:</tt> <tt class="py-string">"x-rzpd"</tt><tt class="py-op">,</tt> <tt class="py-comment"># Resource Centre Primary Database Clone Identifiers</tt> </tt>
<a name="L196"></a><tt class="py-lineno">196</tt> <tt class="py-line"> <tt class="py-comment"># /db_xref="RZPD:IMAGp998I142450Q6"</tt> </tt>
<a name="L197"></a><tt class="py-lineno">197</tt> <tt class="py-line"> </tt>
<a name="L198"></a><tt class="py-lineno">198</tt> <tt class="py-line"> <tt class="py-string">"SGD"</tt><tt class="py-op">:</tt> <tt class="py-string">"sgd"</tt><tt class="py-op">,</tt> <tt class="py-comment"># Saccharomyces Genome Database accession numbers.</tt> </tt>
<a name="L199"></a><tt class="py-lineno">199</tt> <tt class="py-line"> <tt class="py-comment"># /db_xref="SGD:L0000470"</tt> </tt>
<a name="L200"></a><tt class="py-lineno">200</tt> <tt class="py-line"> </tt>
<a name="L201"></a><tt class="py-lineno">201</tt> <tt class="py-line"> <tt class="py-string">"SoyBase"</tt><tt class="py-op">:</tt> <tt class="py-string">"x-soybase"</tt><tt class="py-op">,</tt> <tt class="py-comment"># Glycine max Genome Database </tt> </tt>
<a name="L202"></a><tt class="py-lineno">202</tt> <tt class="py-line"> <tt class="py-comment"># /db_xref="SoyBase:Satt005"</tt> </tt>
<a name="L203"></a><tt class="py-lineno">203</tt> <tt class="py-line"> </tt>
<a name="L204"></a><tt class="py-lineno">204</tt> <tt class="py-line"> <tt class="py-string">"SPTREMBL"</tt><tt class="py-op">:</tt> <tt class="py-string">"x-sptrembl"</tt><tt class="py-op">,</tt> <tt class="py-comment"># is this the same as "swall" ?</tt> </tt>
<a name="L205"></a><tt class="py-lineno">205</tt> <tt class="py-line"> <tt class="py-comment"># Computer-annotated protein sequence database </tt> </tt>
<a name="L206"></a><tt class="py-lineno">206</tt> <tt class="py-line"> <tt class="py-comment"># supplementing SWISS-PROT and containing the </tt> </tt>
<a name="L207"></a><tt class="py-lineno">207</tt> <tt class="py-line"> <tt class="py-comment"># translations of all coding sequences (CDS) </tt> </tt>
<a name="L208"></a><tt class="py-lineno">208</tt> <tt class="py-line"> <tt class="py-comment"># present in the EMBL Nucleotide Sequence </tt> </tt>
<a name="L209"></a><tt class="py-lineno">209</tt> <tt class="py-line"> <tt class="py-comment"># Database not yet integrated in SWISS-PROT. </tt> </tt>
<a name="L210"></a><tt class="py-lineno">210</tt> <tt class="py-line"> <tt class="py-comment"># /db_xref="SPTREMBL:Q00177" </tt> </tt>
<a name="L211"></a><tt class="py-lineno">211</tt> <tt class="py-line"> </tt>
<a name="L212"></a><tt class="py-lineno">212</tt> <tt class="py-line"> <tt class="py-string">"SWISS-PROT"</tt><tt class="py-op">:</tt> <tt class="py-string">"sp"</tt><tt class="py-op">,</tt> <tt class="py-comment"># Swiss-Prot protein database accession numbers.</tt> </tt>
<a name="L213"></a><tt class="py-lineno">213</tt> <tt class="py-line"> <tt class="py-comment"># /db_xref="SWISS-PROT:P12345"</tt> </tt>
<a name="L214"></a><tt class="py-lineno">214</tt> <tt class="py-line"> </tt>
<a name="L215"></a><tt class="py-lineno">215</tt> <tt class="py-line"> <tt class="py-string">"taxon"</tt><tt class="py-op">:</tt> <tt class="py-string">"taxonid"</tt><tt class="py-op">,</tt> <tt class="py-comment"># NCBI taxonomic identifier.</tt> </tt>
<a name="L216"></a><tt class="py-lineno">216</tt> <tt class="py-line"> <tt class="py-comment"># /db_xref="taxon:4932"</tt> </tt>
<a name="L217"></a><tt class="py-lineno">217</tt> <tt class="py-line"> <tt class="py-op">}</tt><tt class="py-op">,</tt> </tt>
<a name="L218"></a><tt class="py-lineno">218</tt> <tt class="py-line"><tt class="py-op">}</tt> </tt>
<a name="L219"></a><tt class="py-lineno">219</tt> <tt class="py-line"> </tt>
<a name="from_parser"></a><div id="from_parser-def"><a name="L220"></a><tt class="py-lineno">220</tt> <a class="py-toggle" href="#" id="from_parser-toggle" onclick="return toggle('from_parser');">-</a><tt class="py-line"><tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.DBXRef-module.html#from_parser">from_parser</a><tt class="py-op">(</tt><tt class="py-param">dbname_style</tt><tt class="py-op">,</tt> <tt class="py-param">dbname</tt><tt class="py-op">,</tt> <tt class="py-param">idtype</tt><tt class="py-op">,</tt> <tt class="py-param">dbid</tt><tt class="py-op">,</tt> <tt class="py-param">negate</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="from_parser-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="from_parser-expanded"><a name="L221"></a><tt class="py-lineno">221</tt> <tt class="py-line"> <tt class="py-keyword">try</tt><tt class="py-op">:</tt> </tt>
<a name="L222"></a><tt class="py-lineno">222</tt> <tt class="py-line"> <tt class="py-name">dbname</tt> <tt class="py-op">=</tt> <tt id="link-14" class="py-name"><a title="Bio.DBXRef.dbname_conversions" class="py-name" href="#" onclick="return doclink('link-14', 'dbname_conversions', 'link-11');">dbname_conversions</a></tt><tt class="py-op">[</tt><tt class="py-name">dbname_style</tt><tt class="py-op">]</tt><tt class="py-op">[</tt><tt class="py-name">dbname</tt><tt class="py-op">]</tt> </tt>
<a name="L223"></a><tt class="py-lineno">223</tt> <tt class="py-line"> <tt class="py-keyword">except</tt> <tt class="py-name">KeyError</tt><tt class="py-op">:</tt> </tt>
<a name="L224"></a><tt class="py-lineno">224</tt> <tt class="py-line"> <tt class="py-name">dbname</tt> <tt class="py-op">=</tt> <tt class="py-string">"x-unknown2-%s--%s"</tt> <tt class="py-op">%</tt> <tt class="py-op">(</tt><tt class="py-name">dbname_style</tt><tt class="py-op">,</tt> <tt class="py-name">dbname</tt><tt class="py-op">)</tt> </tt>
<a name="L225"></a><tt class="py-lineno">225</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt id="link-15" class="py-name" targets="Module Bio.DBXRef=Bio.DBXRef-module.html,Class Bio.DBXRef.DBXRef=Bio.DBXRef.DBXRef-class.html"><a title="Bio.DBXRef
Bio.DBXRef.DBXRef" class="py-name" href="#" onclick="return doclink('link-15', 'DBXRef', 'link-15');">DBXRef</a></tt><tt class="py-op">(</tt><tt class="py-name">dbname</tt><tt class="py-op">,</tt> <tt id="link-16" class="py-name"><a title="Bio.Std.dbid" class="py-name" href="#" onclick="return doclink('link-16', 'dbid', 'link-0');">dbid</a></tt><tt class="py-op">,</tt> <tt class="py-name">idtype</tt><tt class="py-op">,</tt> <tt class="py-name">negate</tt><tt class="py-op">)</tt> </tt>
</div><a name="L226"></a><tt class="py-lineno">226</tt> <tt class="py-line"> </tt><script type="text/javascript">
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