in reply to Recognizing protein name

hello pdahal,

unfortunately the Crystal::Ball module is not on CPAN..

It would be an useful module for me to know what are you parsing and for you to find proteines that are good against thrombosis in your texts. But..

If I understand you want to tell between Xa proteine name from Liu Xa a fantasy chinese name.

This is not possible..

I suspect some manual work is needed in your case.

The best I can imagine is the following: given a list of proteine, build up a hash with proteine name as key and an empty array as value. Parse your texts searching proteine names and store in the array some sourronding text: like $prot{Xa}=["the proteine Xa is good for"]

It can happen that you store something $prot{Xa}=["as the famous Liu Xa said to the queen"]

Then choose some human redable dataformat to save your data and clean it by hand: many options are available, YAML among them.

It is still risky because you can parse something like the proteine Xa used in the terapy followed by the text is now considered harmfull

So, because you are working on sensible things, the best will be to store also the name of text and the line number, to check it by hand: like $prot{Xa}=["Necronomicon,42,the proteine Xa is good for"]

L*

There are no rules, there are no thumbs..
Reinvent the wheel, then learn The Wheel; may be one day you reinvent one of THE WHEELS.

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Re^2: Recognizing protein name -- Crystal::Ball
by pdahal (Acolyte) on May 20, 2017 at 12:53 UTC
    hello Discipulus, I have attempted to do something. I read few abstracts and listed out the words that can possibly around the protein name. For example if "Xa" is a protein name then it may appear in the form like "xa inhibitor", "xa activity" and so on. I have listed those words. Can you now suggest me what to do further?
      One example is not enough