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How to export regulation table from MetaCyc

asked 2018-10-25 15:30:01 -0500

mikeaalv gravatar image

By regulation, I mean all allosteric regulation, as shown in MetaCyc (I can't post link sorry). It is not species specific or contain information from all species.

I know the "STRUCTURED ADVANCED QUERY PAGE" though I find this is not totally what I want. The two volume that I really need is compound(ID or name) and reaction (ID or name). As this is clearly presented in both the web and local version, there probably be a way to export that.

I look through table file for the flatfile page though not much found (there should be a link here though I cannot post link).

What should be the way to export the regulation table include compound and reactions?

Thank you.

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answered 2018-10-26 00:49:35 -0500

Suzanne Paley gravatar image

updated 2018-10-26 00:57:34 -0500

Will this give you what you want? image description

I get a table that looks like this (you can also request it in tab-delimited text format): image description

The following will give you the reaction frame ids instead of the equations (unfortunately, you have to specify a condition for a field in order to get a variable with which to refer to it to specify result columns, but you can specify a condition that will always be true, like in my example): image description

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Thank you. That seems exactly what I need. I try it on the "STRUCTURED ADVANCED QUERY PAGE" but didn't find the way to formulate the table exactly as you show me.

mikeaalv gravatar imagemikeaalv ( 2018-10-26 06:11:45 -0500 )edit

Although I find it can partially be done by smart table. I can select the pathway I want, convert to reaction, and the substrate regulator. There is one problem with this approach, that I cannot load all reactions into a smart table for some unkown reason.

mikeaalv gravatar imagemikeaalv ( 2018-10-26 06:15:10 -0500 )edit

Unfortunately, in order to get the most out of the advanced query features, you need to both really understand the underlying schema, and the quirks of the tool (I have the former, still struggle with the latter!). I could also get something similar using smart tables by starting from the special table of all reactions in MetaCyc.

Suzanne Paley gravatar imageSuzanne Paley ( 2018-10-26 11:06:55 -0500 )edit

Is it possible that you send me a link of the advanced query that works as the figure above? So that I can figure out how to set it.

mikeaalv gravatar imagemikeaalv ( 2018-10-26 11:27:15 -0500 )edit

We can't create links to the SAQP with fields already filled out. That's why I included the first screenshot, so you'd see how to do it yourself. The biovelo query string that this generated (that you can enter into the freeform AQP) is at the top of the results screenshot.

Suzanne Paley gravatar imageSuzanne Paley ( 2018-10-27 00:19:58 -0500 )edit

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Asked: 2018-10-25 15:30:01 -0500

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Last updated: Oct 26 '18