[R] String based chemical name identification
Jason.Law at portlandoregon.gov
Thu Jul 4 00:21:59 CEST 2013
Might be better off using a web service like ChemSpider to do the matching for you <http://www.chemspider.com/AboutServices.aspx?>. The idea that you can identify the synonyms by name is probably optimistic unless they are exact matches.
Here's some python code that seems to make it pretty easy: https://github.com/mcs07/ChemSpiPy. Search the names, extract the InChI for the best match and then you can match them in R via the InChI. Might require some fixing by hand afterwards.
From: r-help-bounces at r-project.org [mailto:r-help-bounces at r-project.org] On Behalf Of Zsurzsa Laszlo
Sent: Wednesday, July 03, 2013 7:28 AM
To: r-help at r-project.org
Subject: [R] String based chemical name identification
The problem is the following:
I have two big databases one look like this:
2-Methyl-4-trimethylsilyloxyoct-5-yne Benzoic acid, methyl ester Benzoic
acid, 2-methyl-, methyl ester Acetic acid, phenylmethyl ester
The second one looks like this:
Name: D-Tagatose 1,6-bisphosphate Name: 1-Phosphatidyl-D-myo-inositol;:
1,2-Diacyl-sn-glycero-3-phosphoinositol;: Phosphatidylinositol Name:
Androstenedione;: Androst-4-ene-3,17-dione;: 4-Androstene-3,17-dione Name:
Spermine;: N,N'-Bis(3-aminopropyl)-1,4-butanediamine Name: H+;: Hydron Name:
Both of them have more then 3000 lines. Matching their name by hand is not an option because I don't know chemistry.
*Possible solution I came up with*:
Go through all the names of the first database and then try to match with the other one. I'm using *regexec *and *strsplit *functions for the matching. Basically I split the name into small chunks and try to get some hit in the other database.
I can supply code If needed but I did not want to spam in the first mail.
Any solution is welcome! It can be in pseudo-cod also or in any type of logical arguing. It does not matter.
Msc. Informatics, Technical University Munchen
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