Question: Biocuration of plant compounds - software related
0
gravatar for Priya Saravanan
9 months ago by
Priya Saravanan0 wrote:

I am doing Biocuration for Plant compounds of many different species (Nearly 3000) with their properties (Structure, Mol. Weight, assay data, etc) in Excel (Each species in different sheets of excel). I want to combine this data and access it. Is there any software available for this?

software error • 206 views
ADD COMMENTlink modified 9 months ago by Michael Dondrup47k • written 9 months ago by Priya Saravanan0
1

To forego the comment, I am guessing you have experienced the approach of doing bioinformatics in Excel, unfortunately with that many documents you hit the wall pretty hard when trying to deal with them. You didn't describe what you are going to do with the data, and what your data volume actually is, but I am assuming you wish to do some sort of queries? I would first try to convert the data into a proper database format, e.g. an SQLite database, or an Access database (ignoring 'propper' ;) ). This process has to be scripted using an Excel parser capable of reading your data and converting it to text.

For further guidance, you will have to provide example data and exemplary queries.

ADD REPLYlink modified 9 months ago • written 9 months ago by Michael Dondrup47k

I need to know whether there is any existing application to compile(Just to access the data) this data. Thank You.

ADD REPLYlink written 9 months ago by Priya Saravanan0

I don't think there is. Excel can't handle it without some serious scripting, and I don't know if Access is able to import a bunch of Excel files automatically. Possibly googling for "importing many excel files into Access" is your best bet. If I, personally, would have do this, I would:

  • use R's excel importer to parse the files and convert to CSV format
  • check whether all files have the same structure, hopefully they do, if not the whole process will become more costly
  • write up the unique structure and create the database definition for a SQLite DB, deliberately do this manually
  • import the files into SQLite3

would take about 0.5- several hours depending on data complexity and consistency.

  • query SQLite using SQL

(piece of cake;)

ADD REPLYlink modified 9 months ago • written 9 months ago by Michael Dondrup47k

Its a great help for us, Thank you : )

ADD REPLYlink written 9 months ago by Priya Saravanan0

Btw, why did you use the tag software error. the only error I see is using Excel ;)

ADD REPLYlink written 9 months ago by Michael Dondrup47k
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