Framework for Gene Name Entity Recognition

fjkvfhjkgjkkhfdsd · 05-26-2020, 04:52 PM

Does a framework for gene name entity recognition exists?
Use case: Input a text from a publication and get all gene names from that text.
Many thanks and best regards.

fjkvfhjkgjkkhfdsd · 05-26-2020, 05:12 PM

Does especially a framework exist which was made for developers with no background in biology? I tried to do Named Entity Recognition for gene names. But I think it is a major problem to create a gold standard with no knowledge in biology.

Therefore, I asked my self if a framework exists where one can input a text and get gene names as a result.

Many thanks and best regards.

fjkvfhjkgjkkhfdsd · 05-27-2020, 08:54 AM

Hi,

For those who have a similar problem, I found a solution.
NCBI provides an API which does exactly that job: https://www.ncbi.nlm.nih.gov/research/pubtator/

Best Regards

05-26-2020, 04:52 PM	#1
fjkvfhjkgjkkhfdsd Junior Member Location: Germany Join Date: May 2020 Posts: 6	Framework for Gene Name Entity Recognition Does a framework for gene name entity recognition exists? Use case: Input a text from a publication and get all gene names from that text. Many thanks and best regards.

05-26-2020, 05:12 PM	#2
fjkvfhjkgjkkhfdsd Junior Member Location: Germany Join Date: May 2020 Posts: 6	Does especially a framework exist which was made for developers with no background in biology? I tried to do Named Entity Recognition for gene names. But I think it is a major problem to create a gold standard with no knowledge in biology. Therefore, I asked my self if a framework exists where one can input a text and get gene names as a result. Many thanks and best regards.

05-27-2020, 08:54 AM	#3
fjkvfhjkgjkkhfdsd Junior Member Location: Germany Join Date: May 2020 Posts: 6	Hi, For those who have a similar problem, I found a solution. NCBI provides an API which does exactly that job: https://www.ncbi.nlm.nih.gov/research/pubtator/ Best Regards