Forum: Doctor looking fertility for a collaborator for text mining on pubmed
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gravatar for jeromebouaziz
19 months ago by
jeromebouaziz0 wrote:

I m a doctor expert in fertility and especially in endometriosis . I saw good examples on how text mining on pubmed database and genes understanding could help. This disease remains very difficult to understand and the average delay is 8 years .... Anyway I am looking for a partner who can do text mining on pubmed and will be interested to work with me and be a game changer in this terrific disease .

Any ideas where I can find a partner ?

Thanks

ADD COMMENTlink modified 19 months ago by Kevin Blighe44k • written 19 months ago by jeromebouaziz0
2

... changed "partner" to "collaborator" ... :-)

ADD REPLYlink modified 19 months ago • written 19 months ago by Pierre Lindenbaum121k
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I was worried by the title! :) I thought that Biostars had changed to a dating site

ADD REPLYlink modified 19 months ago • written 19 months ago by Kevin Blighe44k
1

That should have been sufficient to trigger all spam filters :-)

ADD REPLYlink written 19 months ago by WouterDeCoster39k

But only in the title :)

ADD REPLYlink written 19 months ago by genomax68k
1

Although it is some thing of privacy concern, it would be better if you could let us know where you are from and preferred places/institute of collaboration. Though cross country/international collaborations are possible and effective now a days, a local collaboration (institute/place/state/country) would be more fruitful (IMO). Biostars in and around your place may collaborate with you in solving scientific problems.

ADD REPLYlink modified 19 months ago • written 19 months ago by cpad011211k
1

If you use the latest Open Targets tool, LINK, and search for endometriosis, these are the results you get. Scroll down to see the connections with genes, drugs, etc...Check Get to know LINK and explore 500+ million relations from PubMed abstracts post for more details.

Besides LINK, you can also use the Open Targets Platform as we have done the text mining for associations between genes and diseases. We mine the abstracts (and full text when they are open source) from EuropePMC, which include PubMed. The current version of our Platform shows just over 1k genes associated with endometriosis, filtered by text mining only. Some of these results are also confirmed by other sources e.g. drugs from ChEMBL, differential RNA expression and GWAS data.

If you remove the filter, you will get 1644 targets associated with endometriosis.

These can perhaps help you (and colleagues) to start off with some hypotheses for further studies/validation.

ADD REPLYlink modified 17 months ago • written 17 months ago by Denise - Open Targets5.0k

Isn't this better referred to as a disorder?

ADD REPLYlink written 19 months ago by genomax68k
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Not sure if 'terrific' is meant to mean 'causing terror' or someone is just a really big fan of endometriosis.

enter image description here

ADD REPLYlink modified 19 months ago • written 19 months ago by jrj.healey12k

How extensive do you want this text mining to be? If you're just looking for keywords, pubmed/NCBI allows you to save searches (with potentially quite complicated syntax such as "Smith, J[author] AND sequencing") and have the searches repeated weekly and delivered straight to your email inbox.

ADD REPLYlink written 19 months ago by jrj.healey12k
1
gravatar for Kevin Blighe
19 months ago by
Kevin Blighe44k
Kevin Blighe44k wrote:

A good literature search typically begins with a review manuscript, and from there you can do follow-up reading on the citations used in the review.

I have already found 3 for you:

The first one is Nature Reviews Endocrinology - start there.

I also have colleagues in the UK working in this area.

Kevin

ADD COMMENTlink written 19 months ago by Kevin Blighe44k
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