missing annotations in gpml files

[Tin Yau Pang]

Hello,

  I tried to extract the database links of the metabolite in the pathways, and I found that some of the labels found on the webpages are not listed in the downloadable gpml files.

  For example, the metabolite '4alpha-methyl zymosterol' is annotated with 'LMST01010202' of lipidmaps, but this labeled cannot be found in the corresponding gpml file. This happens to some but not all the metabolites. Can you please add the lipidmaps and other annotations to the metabolites in the downloadable files? Many thanks.

Yours sincerely,

Tin

link to the Cholesterol metabolism with Bloch and Kandutsch-Russell pathways (Mus musculus)

https://www.wikipathways.org/index.php/Pathway:WP4346

[Kristina Hanspers]

Hi Tin,

I apologize for the late reply. I looked at the gpml of the pathway you mentioned (WP4346), and I'm not sure I understand your question. 

Here is the "4alpha-methyl zymosterol" node in the gpml:

  <DataNode TextLabel="4alpha-methyl zymosterol" GraphId="ec117" Type="Metabolite">
    <Comment>C12CC[C@@]3([H])C(C)[C@@H](O)CC[C@]3(C)C=1CC[C@]1(C)[C@@]([H])([C@@](C)([H])CC/C=C(\C)/C)CC[C]21H</Comment>
    <Graphics CenterX="810.1057346255649" CenterY="940.5615678516264" Width="197.3203410475032" Height="24.50000000000003" ZOrder="32940" FontSize="12" Valign="Middle" Color="0033ff"/>
    <Xref Database="LIPID MAPS" ID="LMST01010202" />
  </DataNode>

The node label, which is what you see in the graphical representation of the pathway, is "4alpha-methyl zymosterol", represented in the gpml as: DataNode TextLabel="4alpha-methyl zymosterol"

The node XRef ID is "LMST01010202", from the LIPID MAPS data source, represented in the gpml as: Xref Database="LIPID MAPS" ID="LMST01010202" 

Can you explain what information you are missing, or give an alternate example? 

Thanks,

Kristina

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[Tin]

Hi Kristina,

Attached is the gpml file for the pathway WP4346 that I downloaded a while ago. It was published probably on 28th July this year. The label 'LMST01010202' can not be found. This label can now be found on the currently downloadable version though. Many thanks.

Yours sincerely,

Tin

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[Kristina Hanspers]

Hi Tin,

That makes sense, if you look at the pathway history, it looks like LIPID MAPS identifiers were added on Nov 24. The diagram and datanode table you see on the default webpage (https://www.wikipathways.org/index.php/Pathway:WP4346) represents the latest revision and will be out of sync with what you see in a gpml downloaded earlier. To see an earlier revision, click "view" for that revision in the History table. 

Regards,

Kristina

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