Question: Best Practice For Extracting Gene Names From Pubmed Abstracts
2
gravatar for gundalav
6.4 years ago by
gundalav270
La La Land
gundalav270 wrote:

I have a collection of several hundreds of Pubmed Abstracts. What I want to do is to extract all the gene names reported there.

What's the best way to go about it programmatically? Later I'd simply create a hash with pubmed ID as keys and gene names as its members.

pubmed • 3.4k views
ADD COMMENTlink modified 5.3 years ago by Pierre Lindenbaum120k • written 6.4 years ago by gundalav270
5
gravatar for Pierre Lindenbaum
6.4 years ago by
France/Nantes/Institut du Thorax - INSERM UMR1087
Pierre Lindenbaum120k wrote:

There is a webservice for whatizit: http://www.ebi.ac.uk/webservices/whatizit/helpws.jsp

it comes with an example:

String pipelineName = "whatizitSwissprot";
String pmid = "9879"; // The number is a Pubmed accession key
String xml = whatizit.queryPmid(pipelineName, pmid);
System.out.println(xml);
ADD COMMENTlink written 6.4 years ago by Pierre Lindenbaum120k
5
gravatar for Casey Bergman
6.4 years ago by
Casey Bergman18k
Athens, GA, USA
Casey Bergman18k wrote:

You can get a list of NCBI Gene IDs based on Pubmed IDs using the GNAT webservice: http://textmining.ls.manchester.ac.uk:8081/. To call this webservice, provide a PMID list to the base URL with the pmid parameter as follows:

http://textmining.ls.manchester.ac.uk:8081/?pmid=21483786,21483692

For more information about this webservice, see this paper.

ADD COMMENTlink modified 4.6 years ago • written 6.4 years ago by Casey Bergman18k

Hi Thanks, Casey. Do you have any version that also recognize miRNA?

ADD REPLYlink written 6.4 years ago by gundalav270
1

At the time we made this version of the NCBI gene name dictionaries, mirna's were included in the Entrez gene. It looks like they are now though, so we should consider this in the next version of the GNAT dictionaries that are built.

ADD REPLYlink modified 4.6 years ago • written 6.4 years ago by Casey Bergman18k
4
gravatar for aidan-budd
6.4 years ago by
aidan-budd1.9k
Germany
aidan-budd1.9k wrote:

Reflect http://reflect.ws/ can be used programatically, and is designed to extract biological (and chemical) entities from text. It has a huge dictionary of synonyms sitting behind it, and could be useful for you - check out the "About" page REFLECT webpage for more info.

ADD COMMENTlink written 6.4 years ago by aidan-budd1.9k
1
gravatar for Pappu
6.4 years ago by
Pappu1.9k
Pappu1.9k wrote:

There are several papers out there on pubmed text mining i.e. papers which report protein-protein interactions. DId you check the pubmed/google before posting?

Once you have a list of gene names, you can easily make a dictionary out of PMID and gene names in abstracts in python. Also have a look at Pubmed API.

ADD COMMENTlink written 6.4 years ago by Pappu1.9k
1
gravatar for Evangelos
6.4 years ago by
Evangelos10
Crete Greece
Evangelos10 wrote:

+1 to aidan-budd! +1 to the Reflect API developers for providing us with such a stable service

In the "About" page of Reflect you may find a link to the Reflect's REST API (http://reflect.ws/REST_API.html) "GetEntities" invoked with the "pmid" parameters provide you with a solution.

ADD COMMENTlink written 6.4 years ago by Evangelos10

you should add this as a comment to the post

ADD REPLYlink written 6.4 years ago by Istvan Albert ♦♦ 80k
0
gravatar for Pierre Lindenbaum
5.3 years ago by
France/Nantes/Institut du Thorax - INSERM UMR1087
Pierre Lindenbaum120k wrote:

(Added Feb 2014) http://www.ncbi.nlm.nih.gov/pubmed/23736528

Bioinformatics. 2013 Aug 1;29(15):1915-6. doi:

10.1093/bioinformatics/btt317. Epub 2013 Jun 4. BeCAS: biomedical concept recognition services and visualization. Nunes T1, Campos D,

Matos S, Oliveira JL.

it provides a nice REST-API: http://bioinformatics.ua.pt/becas

ADD COMMENTlink written 5.3 years ago by Pierre Lindenbaum120k
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