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It would be useful to create smart tables from a list of EC numbers

asked 2018-04-19 08:58:04 -0500

Daniel gravatar image

I can paint pathway diagrams with EC numbers as key, but EC numbers are not recognized when I upload a file to create a smart table. For me, being able to create a smart table with all reactions connected to a number of EC numbers would be very useful.

/Daniel

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answered 2018-04-19 13:05:25 -0500

Suzanne Paley gravatar image

I agree that this sounds useful. Unfortunately, EC numbers are not represented as objects in any organism database (we have a separate EC-number database that maps EC numbers to their relevant info), so the current implementation of SmartTables doesn't recognize them, and just treats them as arbitrary strings. I don't see an easy way of getting around that. It is however easy to generate a SmartTable of all EC numbers and their associated reactions in a given organism database, if that would be useful. Go to the Special SmartTables tab and select the table of all reactions in the current organism. From there, click on the green + in the EC-number column -- the result will be a table of EC numbers and the reactions they are linked to.

Also, this is clearly not an intuitive thing to do, but it turns out that if you export the above-mentioned table to a spreadsheet file, and then re-upload it (tell it not to try to interpret the first column as objects), and then classify the reaction column as reactions, you will have a master SmartTable mapping all EC strings to reaction objects (it will look the same as the original SmartTable you downloaded, but will be interpreted by the software slightly differently). If you then create another SmartTable by uploading another file containing just the set of EC#s you are interested in (in the format EC-1.1.1.1), you can take the intersection of the two SmartTables to get a new SmartTable mapping just the EC#s you are interested in to their reactions. I'm aware that this is clearly a fairly awkward set of steps, but it should accomplish what you want, and for the time being (and forseeable future), I can't see a better way of doing it.

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Excellent! (I have nothing against workarounds that work; this will save me a lot of manual work.) /Daniel

Daniel gravatar imageDaniel ( 2018-04-19 14:06:13 -0500 )edit

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Asked: 2018-04-19 08:58:04 -0500

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Last updated: Apr 19

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