Looking for tool recommendations for text mining

Question

[amoroso.lucas92]

Hello guys, is everything alright?

First of all, I apologize for any grammatical errors, I am Brazilian and I have a beginner level English. I come to you looking for recommendations on some tool that can help me in my master's project. We intend to use some text mining tool, which makes it possible to verify the interaction between microorganisms and plants, specifically aimed at beneficial interactions, so I would like to know if there is any tool that I can insert a dictionary of arguments and names of taxa for prospect in databases of scientific literature

Thank you for your attention!

[Ahill]

If you are looking for precomputed gene or protein level interactions from text mining, have you seen iHOP? I've not looked at in quite a while but they did curate from PubMed "28.4 million sentences and 110,000 genes from over 2,700 organisms".

[amoroso.lucas92]

Thanks for the suggestions. I'm looking for ecological interactions, but I'll study on your suggestion to see if I can adapt to my intention, thanks again!

[Kevin Blighe]

Tudo bem aqui, cara. Não se preocupes - tu inglês é ótimo. Já vejo como você já tem respostas. Boa sorte. Valeu.

[amoroso.lucas92]

Obrigado amigo, agradeço pelas palavras!

Answer 1

[manuel.belmadani]

Sounds like there's two components to this: One is identifying/extracting the papers, the other is mining the text information. There's probably a lot of options for the former, whereas the text mining part will likely require more customization from your part.

I know of this project (https://github.com/neurosynth/ACE) which was designed to extract coordinate information from neuro imaging papers. You could modify the code to extract plant and microorganism information instead.

Otherwise you could do a customized pubmed PubMed search and get a list of papers to apply some text mining.

For performing the actual text mining, search if anyone ever attempted that, or even something similar. This is a bit old and I don't know the journal, but this seems relevant: https://www.degruyter.com/view/j/jib.2011.8.issue-2/biecoll-jib-2011-184/biecoll-jib-2011-184.xml, maybe this too.

Consider how much you want to automate this process versus doing manual curation. For example, is it enough for you to have automation of relevant papers and look into them manually or with some scripts, or are you hoping the relevant information will be summarized as well? That'll determine how much you should invest in the text mining part.

[amoroso.lucas92]

Thank you friend. I had read some of these papers, others had not. I will read carefully all the suggestions you have made, thank you again!