Question: Which Are Stable Text Mining Solution For Biologists.
8
gravatar for Andra Waagmeester
3.2 years ago by
Maastricht, the Netherlands
Andra Waagmeester3.0k wrote:

I am working on integrating pathway relations into a pathway diagram. I have two text mining solutions that I use to find interactions. I am looking for new suggestions. The idea is that I provide a pathway entity (ie. gene/protein, metabolite) and all relations based on the literature are returned.

ADD COMMENTlink modified 10 months ago by Charles Warden2.3k • written 3.2 years ago by Andra Waagmeester3.0k
1

I am using Whatizit: http://www.ebi.ac.uk/webservices/whatizit/info.jsf and Phasar: http://www.phasar.cs.ru.nl/. The first works decently, the second has issues with performance and accessibility.

ADD REPLYlink written 3.2 years ago by Andra Waagmeester3.0k

Could you please tell us which are the two text mining solutions that you already have?

ADD REPLYlink written 3.2 years ago by Lars Juhl Jensen8.6k

I need to add Chilibot (http://www.chilibot.net/) and Agilents literature plugin for Cytoscape to this question/answer serie (http://www.agilent.be/labs/research/litsearch.html)

ADD REPLYlink written 3.1 years ago by Andra Waagmeester3.0k
7
gravatar for Lars Juhl Jensen
3.2 years ago by
Copenhagen, Denmark
Lars Juhl Jensen8.6k wrote:

You might want to take a look at STITCH. It is a database that allows you to query with a gene/protein or a small molecule (e.g. a metabolite) and retrieve the interaction partners. A very large part of the evidence in STITCH comes from text mining, and if you really want to, you can turn off all the other evidence types to exclusively get the results obtained through text mining.

Edit:

If you are using Whatizit, I would suggest that you take a look at the REST API of Reflect. It is designed for speed, so you do not need to worry about hammering the API. If you send too many requests at the same time, some of them will simply be rejected and you will get an error code back.

ADD COMMENTlink modified 3.2 years ago • written 3.2 years ago by Lars Juhl Jensen8.6k
6
gravatar for Casey Bergman
3.2 years ago by
Casey Bergman15k
Manchester, UK
Casey Bergman15k wrote:

For gene/protein interactions, try iHop, which has an API described here.

ADD COMMENTlink written 3.2 years ago by Casey Bergman15k
3
gravatar for Egon Willighagen
3.2 years ago by
Maastricht
Egon Willighagen4.6k wrote:

There is Oscar which knows about chemical structures, and used in ChemicalTagger for detecting biological roles, such as solvent roles in this demo, created in a collaboration with the ChEBI team.

ADD COMMENTlink written 3.2 years ago by Egon Willighagen4.6k
1
gravatar for Dominique Noel
3.1 years ago by
Dominique Noel10 wrote:

You might want to have a look into BER (Biological Entities and Relationships) developed by Temis which provides relationships (including interactions) between proteins/genes aswell as relationships between these and other biological entities (disorders, cells and tissues, treatments, chemical entities, etc....). This solution can be tuned to find relationships only between those entities you are iterested in and/or for the selection of relationship types which you are interested in, and can integrate Oscar if desired. You will find more about Temis at www.temis.com and can contact yoann at yoann.marsac@temis.com for more information on functionalities and deployment.

ADD COMMENTlink written 3.1 years ago by Dominique Noel10
1
gravatar for Andra Waagmeester
3.1 years ago by
Maastricht, the Netherlands
Andra Waagmeester3.0k wrote:

Since I have asked this question, I also (re)found the following text mining apps: Chilibot chilibot.net) and Agilents literature plugin for Cytoscape to this question/answer serie agilent.be/labs/research/litsearch.html

ADD COMMENTlink written 3.1 years ago by Andra Waagmeester3.0k
1
gravatar for enunvillafer
10 months ago by
enunvillafer60
enunvillafer60 wrote:

Other text mining tools are: SciMiner, EbiMed FASTA+ GoPubMed iHOP

;)

ADD COMMENTlink written 10 months ago by enunvillafer60
0
gravatar for Charles Warden
10 months ago by
Charles Warden2.3k
Los Angeles, CA
Charles Warden2.3k wrote:

Yeah, iHOP would be one of my top open-source tools. PolySearch is another one (it is a little more buggy, but more flexible in the types of queries that it can handle).

http://www.ihop-net.org/UniPub/iHOP/

http://wishart.biology.ualberta.ca/polysearch/

If you have a license, IPA is also an excellent tool for mining the literature (and probably my favorite)

http://www.ingenuity.com/

ADD COMMENTlink written 10 months ago by Charles Warden2.3k
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