Connectionists: Shared task on Medica Named Entity Recnognition and Neural Networks: PharmaCoNER – BioNLP-OST 2019

[Martin Krallinger]

Dear all,




Neural networks are currently considered the most competitive approach for
NLP tasks such as Named Entity Recognition (NER), and a number of

resources and libraries are being implemented to make this track more

efficient (NeuroNER,..etc).


We are currently organizing the first task on chemical and drug mention
recognition from Spanish medical texts, as part of the BioNLP-OST 2019
framework / EMNLP-IJCNLP 2019.


Efficient access to mentions of drugs, medications and chemical entities is
a pressing need shared by biomedical researchers, clinicians and pharma
industry.



I thought you might also be interested in the track, or potentially have
colleagues that might be interested in either participating or the
generated results/approaches used.



I would be very grateful if you would help us spread the call.



Best regards,



Martin





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**** Final Call for Participation PharmaCoNER – BioNLP-OST 2019 ****



*Pharmacological Substances, compounds and proteins and Named Entity
Recognition track at BioNLP-OST 2019 collocated with EMNLP-IJCNLP 2019*

*3 or 4 November 2019 (Hong Kong)*

*http://temu.bsc.es/pharmaconer* <http://temu.bsc.es/pharmaconer>
<http://temu.bsc.es/meddocan>



Plan TL Award  for the PharmaCoNER Track

PharmaCoNER Awards: 3,400€ total



*Task description*

Efficient access to mentions of drugs, medications and chemical entities is
a pressing need shared by biomedical researchers, clinicians,
pharmaceutical industry or even patients. The recognition of pharmaceutical
drugs and chemical entities is a critical step required for the subsequent
detection of drug-related adverse reactions, drug-repositioning, detection
of drug-related fake news, drug-target associations, just to name a few.



The critical importance of chemical and drug name recognition motivated
several-shared tasks in the past, such as the CHEMDNER tracks (Krallinger
et al. 2015) or the i2b2 medication challenge (Uzuner et al. 2010), with a
considerable number of participants and impact in the field. The
publications, corpora and participating systems of these tracks represent
influential results for the community working in biomedical and clinical
text mining.



As part of the BioNLP-OST framework (https://2019.bionlp-ost.org/home),
following the outline of previous chemical and drug NER efforts, we organize*
the first task on chemical and drug mention recognition from Spanish
medical texts*. This task will address the automatic extraction of
chemical, drug, gene/protein mentions from clinical case studies written in
Spanish.



Spanish is a language spoken by more than 572 million people in the world
today, either as a native, second or foreign language. It is the second
language in the world by number of native speakers with more than 477
million people. According to results derived from WHO statistics, just in
Spain there are over 180 thousand practicing physicians, more than 247
thousand nursing and midwifery personnel or 55 thousand pharmaceutical
personnel





The PharmaCoNER task will be structured into *two sub-tracks*:

1) Track 1: NER offset and entity classification.

2) Track 2: Concept indexing.

*Publications*

As a venue to compile the results of the follow-up investigation, a journal
special issue will be organized to be published a few months after the
workshop. The specific journal will be announced. More information at the
<https://2019.bionlp-ost.org/>BioNLP-OST 2019 <https://2019.bionlp-ost.org/>
webpage.



*Important Dates*



●      March 18, 2019           Sample set and Evaluation script released.

●      March 26, 2019           Training set released.

●      March 26, 2019           Development set released.

●      May 31, 2019              Test set released (includes background
set).

●      June 25, 2019             End of evaluation period (system
submissions).

●      July 1, 2019                 Results posted and Test set with GS
annotations released.

●      July 19, 2019               Working notes paper submission.

●      TBD                             Notification of acceptance
(peer-reviews).

●      TBD                             Camera ready paper submission.

●      November, 2019          BioNLP-OST 2019 Workshop (to be collocated
with EMNLP-IJCNLP 2019, Hong Kong)



Additional information is available at:

·       http://temu.bsc.es/pharmaconer

·       https://2019.bionlp-ost.org

·



Best regards,



            Martin Krallinger




-- 
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Martin Krallinger, Dr.
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Head of Biological Text Mining Unit
Barcelona Supercomputing Center (BSC-CNS)
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Oficina Técnica General (OTG) del Plan TL en el
área de Biomedicina de la
*Secretaría de Estado *
*para* el Avance Digital

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