[Gramene] LycoCyc Feedback: Difference in the database stats BioPax level 2 (LycoCyc 2.0) and Online LycoCyc.

[Jain, Pooja]

Hi there,

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.

http://pathway.gramene.org/LYCO/organism-summary?

Pathways:<http://pathway.gramene.org/LYCO/NEW-IMAGE?object=Pathways>338 Enzymatic Reactions:1793 Transport Reactions:<http://pathway.gramene.org/LYCO/NEW-IMAGE?object=Transport-Reactions>12 Polypeptides:<http://pathway.gramene.org/LYCO/NEW-IMAGE?object=Polypeptides>20964 Protein Complexes:<http://pathway.gramene.org/LYCO/NEW-IMAGE?object=Protein-Complexes>2 Enzymes:5216 Transporters:137 Compounds:<http://pathway.gramene.org/LYCO/NEW-IMAGE?object=Compounds>1379 Transcription Units:<http://pathway.gramene.org/LYCO/NEW-IMAGE?object=Transcription-Units>0 tRNAs:<http://pathway.gramene.org/LYCO/NEW-IMAGE?object=tRNAs>0

Below is the statistics from the Biopax file.

[root at Lyco ~]# grep -c \<bp:biochemicalReaction lycocyc_2.0.biopax.owl
1613
[root at Lyco ~]# grep -c \<bp:catalysis lycocyc_2.0.biopax.owl
7505
[root at Lyco ~]# grep -c \<bp:smallMolecule lycocyc_2.0.biopax.owl
1487
[root at Lyco ~]# grep -c \<bp:transport lycocyc_2.0.biopax.owl
12
[root at Lyco ~]# grep -c \<bp:protein lycocyc_2.0.biopax.owl
4551
[root at Lyco ~]# grep -c \<bp:pathway\  lycocyc_2.0.biopax.owl
372

Could you please comment on why is there a difference and which statistics I should rely more ?


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.

Many thanks.

Best regards,

-Pooja



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