<p>I have been extracted number of abstracts from pubmed. now I am having a bunch of abstracts of pubmed articles now from this abstracts I need to extract gene names which are included in abstracts.</p>

CC BY-SA 4.0
2019-03-14T13:45:03.980Z
What you need is a list of genes a priori. In my opinion the problem is there are often no "markers" to alert a text finding algorithm that XXX is gene or a protein, i.e. often no labelled as gene or protein. I could be wrong however.
M__
CC BY-SA 4.0
2019-03-14T14:08:33.923Z
Welcome to Bioinformatics.StackExchange @VenkataraoMannem! Please take a look at our Help Center, in particular [how to ask a good question](https://bioinformatics.stackexchange.com/help/how-to-ask). Specifically, please tell us what you have tried so far and why it is not working. There is a lot of published literature on text mining of biomedical literature. Are you having trouble finding this literature? (Have you even made an attempt?) Have you found a strategy but now need help running it?  Please use the `[edit]` button to update your post with these details so we can better help you!
Daniel Standage
CC BY-SA 4.0
2019-03-14T20:50:42.280Z
Cross-posted from Biostars: https://www.biostars.org/p/368251/#368431
Alex Reynolds
<python><text-processing><text-mining>
extracting gene names from pubmed abstracts
# extracting gene names from pubmed abstracts

(Asked by: username_0 on 2019-03-14)

I have been extracted number of abstracts from pubmed. now I am having a bunch of abstracts of pubmed articles now from this abstracts I need to extract gene names which are included in abstracts.

**Tags:** python, text-processing, text-mining
> **Comments:**
> **username_1**: What you need is a list of genes a priori. In my opinion the problem is there are often no "markers" to alert a text finding algorithm that XXX is gene or a protein, i.e. often no labelled as gene or protein. I could be wrong however.  
> **username_2**: Welcome to Bioinformatics.StackExchange @VenkataraoMannem! Please take a look at our Help Center, in particular [how to ask a good question](https://bioinformatics.stackexchange.com/help/how-to-ask). Specifically, please tell us what you have tried so far and why it is not working. There is a lot of published literature on text mining of biomedical literature. Are you having trouble finding this literature? (Have you even made an attempt?) Have you found a strategy but now need help running it?  Please use the `[edit]` button to update your post with these details so we can better help you!  
> **username_3**: Cross-posted from Biostars: https://www.biostars.org/p/368251/#368431  

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## 0 answers

