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Hi Michelle,<div><br></div><div>I have put the compound files of RiceCyc and SorghumCyc on our ftp site ( <a href="ftp://ftp.gramene.org/pub/gramene/pathways/ricecyc/">ftp://ftp.gramene.org/pub/gramene/pathways/ricecyc/</a> and <a href="ftp://ftp.gramene.org/pub/gramene/pathways/sorghumcyc/">ftp://ftp.gramene.org/pub/gramene/pathways/sorghumcyc/</a> ). The format is the same as the one from AraCyc.</div><div><br></div><div>Please let me know if you have any questions about the files.</div><div><br></div><div>Regards,</div><div><br></div><div>Liya</div><div><br></div><div><br></div><div><div><div>On Jan 15, 2009, at 1:44 PM, LACY, MICHELLE [AG/1000] wrote:</div><br class="Apple-interchange-newline"><blockquote type="cite"> <span><image001.gif></span><!--[if gte mso 9]><xml> <v:background id="_x0000_s1025" o:bwmode="white" o:targetscreensize="800,600"> <v:fill src="cid:image001.gif@01C9770E.FA2C6230" o:title="strbkgde" type="frame" /> </v:background></xml><![endif]--> <div class="Section1"><p class="MsoNormal"><span style="font-size:11.0pt;color:navy">Good Afternoon,<o:p></o:p></span></p><p class="MsoNormal"><span style="font-size:11.0pt;color:navy"><o:p> </o:p></span></p><p class="MsoNormal"><span style="font-size:11.0pt;color:navy"><o:p> </o:p></span></p><p class="MsoNormal"><span style="font-size:11.0pt;color:navy">Is it possible to download a table delimited file with compound information from Ricecyc and SorghumCyc. I noticed that TAIR supplies a file called aracyc_compounds.20080611 and plantcyc_compounds.20080616, which is a tab delimited text file that contains the following fields:<o:p></o:p></span></p><p class="MsoNormal"><span style="font-size:11.0pt;color:navy"><o:p> </o:p></span></p><p class="MsoNormal"><span style="font-size:10.0pt;font-family:"Courier New"; color:windowtext">aracyc_compounds contains all compounds found in AraCyc pathways:<o:p></o:p></span></p><p class="MsoNormal"><span style="font-size:10.0pt;font-family:"Courier New"; color:windowtext">1. compound common name. The common name of the compound.<o:p></o:p></span></p><p class="MsoNormal"><span style="font-size:10.0pt;font-family:"Courier New"; color:windowtext">2. compound synonyms. The synonyms of the compound, joint by *.<o:p></o:p></span></p><p class="MsoNormal"><span style="font-size:10.0pt;font-family:"Courier New"; color:windowtext">3. chemical formula. The chemical formula of the compound.<o:p></o:p></span></p><p class="MsoNormal"><span style="font-size:10.0pt;font-family:"Courier New"; color:windowtext">4. smiles. The smiles string of the compound.<o:p></o:p></span></p><p class="MsoNormal"><span style="font-size:10.0pt;font-family:"Courier New"; color:windowtext">5. links. Links to other databases for the compound, such as CAS. <o:p></o:p></span></p><p class="MsoNormal"><span style="font-size:10.0pt;font-family:"Courier New"; color:windowtext">6. EC. EC number of the reaction which contains this compound either as a reactant or a product. If no EC number, the AraCyc frame name for the reaction is given.<o:p></o:p></span></p><p class="MsoNormal"><span style="font-size:10.0pt;font-family:"Courier New"; color:windowtext">7. reaction equation. The equation of the reaction.<o:p></o:p></span></p><p class="MsoNormal"><span style="font-family:"Times New Roman","serif"; color:windowtext">8. pathway. The common name of the pathway which contains the reaction. One pathway per line.</span><span style="font-family:"Times New Roman","serif";color:windowtext"><o:p></o:p></span></p><p class="MsoNormal"><span style="font-family:"Times New Roman","serif"; color:windowtext"><o:p> </o:p></span></p><p class="MsoNormal"><span style="font-family:"Times New Roman","serif"; color:windowtext"><o:p> </o:p></span></p><p class="MsoNormal"><span style="font-size:11.0pt;color:navy">I would like to have similar information from Ricecyc and SorghumCyc.</span><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:navy"><o:p></o:p></span></p><p class="MsoNormal"><span style="font-size:11.0pt;color:navy"><o:p> </o:p></span></p><p class="MsoNormal"><span style="font-size:11.0pt;color:navy">Thanks,<o:p></o:p></span></p><p class="MsoNormal"><span style="font-size:11.0pt;color:navy"><o:p> </o:p></span></p><p class="MsoNormal"><span style="font-size:13.5pt;font-family:"Monotype Corsiva"; color:navy">Michelle Lacy</span><span style="font-size:11.0pt;color:navy"><o:p></o:p></span></p><p class="MsoNormal"><span style="font-size:13.5pt;font-family:"Monotype Corsiva"; color:navy">Monsanto Company</span><span style="font-size:11.0pt;color:navy"><o:p></o:p></span></p><p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif"; color:navy"><o:p> </o:p></span></p> </div> <div align="left"><p><font face="Arial" size="2"><em>This e-mail message may contain privileged and/or confidential information, and is intended to be received only by persons entitled to receive such information. If you have received this e-mail in error, please notify the sender immediately. Please delete it and all attachments from any servers, hard drives or any other media. Other use of this e-mail by you is strictly prohibited.</em></font></p><p><font face="Arial" size="2"><em>All e-mails and attachments sent and received are subject to monitoring, reading and archival by Monsanto, including its subsidiaries. The recipient of this e-mail is solely responsible for checking for the presence of "Viruses" or other "Malware". Monsanto, along with its subsidiaries, accepts no liability for any damage caused by any such code transmitted by or accompanying this e-mail or any attachment.</em></font></p> </div> <span><image001.gif></span><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">_______________________________________________</div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">Gramene mailing list</div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><a href="mailto:Gramene@brie4.cshl.edu">Gramene@brie4.cshl.edu</a></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><a href="http://mail.gramene.org/mailman/listinfo/gramene">http://mail.gramene.org/mailman/listinfo/gramene</a></div> </blockquote></div><br></div><br><br><div> <span class="Apple-style-span" style="border-collapse: separate; border-spacing: 0px 0px; color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; text-align: auto; -khtml-text-decorations-in-effect: none; text-indent: 0px; -apple-text-size-adjust: auto; text-transform: none; orphans: 2; white-space: normal; widows: 2; word-spacing: 0px; "><div>Liya Ren </div><div><br class="khtml-block-placeholder"></div><div>www.gramene.org</div><div><a href="mailto:ren@cshl.edu">ren@cshl.edu</a></div><div>Cold Spring Harbor Laboratory</div><div><br class="khtml-block-placeholder"></div><br class="Apple-interchange-newline"></span> </div><br></body></html>