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<div>Hi there,</div>
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<div>I have been working with the BioPax level 2 formatted LycoCyc 2.0. I have found considerable difference in the online database statistics that is at the following web location and the one that is in the BioPax file available to download form the LycoCyc
FTP. </div>
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<a href="http://pathway.gramene.org/LYCO/organism-summary?">http://pathway.gramene.org/LYCO/organism-summary?</a>
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<div><a href="http://pathway.gramene.org/LYCO/NEW-IMAGE?object=Pathways">Pathways:</a>338 Enzymatic Reactions:1793
<a href="http://pathway.gramene.org/LYCO/NEW-IMAGE?object=Transport-Reactions">Transport Reactions:</a>12
<a href="http://pathway.gramene.org/LYCO/NEW-IMAGE?object=Polypeptides">Polypeptides:</a>20964
<a href="http://pathway.gramene.org/LYCO/NEW-IMAGE?object=Protein-Complexes">Protein Complexes:</a>2 Enzymes:5216 Transporters:137
<a href="http://pathway.gramene.org/LYCO/NEW-IMAGE?object=Compounds">Compounds:</a>1379
<a href="http://pathway.gramene.org/LYCO/NEW-IMAGE?object=Transcription-Units">Transcription Units:</a>0
<a href="http://pathway.gramene.org/LYCO/NEW-IMAGE?object=tRNAs">tRNAs:</a>0</div>
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<div>Below is the statistics from the Biopax file. </div>
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<div style="margin-top: 0cm; margin-right: 0cm; margin-left: 0cm; margin-bottom: 0.0001pt; font-size: 12pt; font-family: 'Times New Roman', serif; ">
<span style="font-size: 11pt; font-family: Calibri, sans-serif; color: rgb(31, 73, 125); ">[root@Lyco ~]# grep -c \<bp:biochemicalReaction lycocyc_2.0.biopax.owl<o:p></o:p></span></div>
<div style="margin-top: 0cm; margin-right: 0cm; margin-left: 0cm; margin-bottom: 0.0001pt; font-size: 12pt; font-family: 'Times New Roman', serif; ">
<span style="font-size: 11pt; font-family: Calibri, sans-serif; color: rgb(31, 73, 125); ">1613<o:p></o:p></span></div>
<div style="margin-top: 0cm; margin-right: 0cm; margin-left: 0cm; margin-bottom: 0.0001pt; font-size: 12pt; font-family: 'Times New Roman', serif; ">
<span style="font-size: 11pt; font-family: Calibri, sans-serif; color: rgb(31, 73, 125); ">[root@Lyco ~]# grep -c \<bp:catalysis lycocyc_2.0.biopax.owl<o:p></o:p></span></div>
<div style="margin-top: 0cm; margin-right: 0cm; margin-left: 0cm; margin-bottom: 0.0001pt; font-size: 12pt; font-family: 'Times New Roman', serif; ">
<span style="font-size: 11pt; font-family: Calibri, sans-serif; color: rgb(31, 73, 125); ">7505<o:p></o:p></span></div>
<div style="margin-top: 0cm; margin-right: 0cm; margin-left: 0cm; margin-bottom: 0.0001pt; font-size: 12pt; font-family: 'Times New Roman', serif; ">
<span style="font-size: 11pt; font-family: Calibri, sans-serif; color: rgb(31, 73, 125); ">[root@Lyco ~]# grep -c \<bp:smallMolecule lycocyc_2.0.biopax.owl<o:p></o:p></span></div>
<div style="margin-top: 0cm; margin-right: 0cm; margin-left: 0cm; margin-bottom: 0.0001pt; font-size: 12pt; font-family: 'Times New Roman', serif; ">
<span style="font-size: 11pt; font-family: Calibri, sans-serif; color: rgb(31, 73, 125); ">1487<o:p></o:p></span></div>
<div style="margin-top: 0cm; margin-right: 0cm; margin-left: 0cm; margin-bottom: 0.0001pt; font-size: 12pt; font-family: 'Times New Roman', serif; ">
<span style="font-size: 11pt; font-family: Calibri, sans-serif; color: rgb(31, 73, 125); ">[root@Lyco ~]# grep -c \<bp:transport lycocyc_2.0.biopax.owl<o:p></o:p></span></div>
<div style="margin-top: 0cm; margin-right: 0cm; margin-left: 0cm; margin-bottom: 0.0001pt; font-size: 12pt; font-family: 'Times New Roman', serif; ">
<span style="font-size: 11pt; font-family: Calibri, sans-serif; color: rgb(31, 73, 125); ">12<o:p></o:p></span></div>
<div style="margin-top: 0cm; margin-right: 0cm; margin-left: 0cm; margin-bottom: 0.0001pt; font-size: 12pt; font-family: 'Times New Roman', serif; ">
<span style="font-size: 11pt; font-family: Calibri, sans-serif; color: rgb(31, 73, 125); ">[root@Lyco ~]# grep -c \<bp:protein lycocyc_2.0.biopax.owl<o:p></o:p></span></div>
<div style="margin-top: 0cm; margin-right: 0cm; margin-left: 0cm; margin-bottom: 0.0001pt; font-size: 12pt; font-family: 'Times New Roman', serif; ">
<span style="font-size: 11pt; font-family: Calibri, sans-serif; color: rgb(31, 73, 125); ">4551<o:p></o:p></span></div>
<div style="margin-top: 0cm; margin-right: 0cm; margin-left: 0cm; margin-bottom: 0.0001pt; font-size: 12pt; font-family: 'Times New Roman', serif; ">
<span style="font-size: 11pt; font-family: Calibri, sans-serif; color: rgb(31, 73, 125); ">[root@Lyco ~]# grep -c \<bp:pathway\ lycocyc_2.0.biopax.owl<o:p></o:p></span></div>
<div style="margin-top: 0cm; margin-right: 0cm; margin-left: 0cm; margin-bottom: 0.0001pt; font-size: 12pt; font-family: 'Times New Roman', serif; ">
<span style="font-size: 11pt; font-family: Calibri, sans-serif; color: rgb(31, 73, 125); ">372</span></div>
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<div>Could you please comment on why is there a difference and which statistics I should rely more ? </div>
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<div>If I am using an older version of Biopax formatted LycoCyc, could you please provide me the latest online version of LycoCyc in the Biopax format.</div>
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<div>Many thanks. </div>
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<div>Best regards,<br>
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-Pooja<br>
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