Connectionists: 1st CFP MedProcNER track: Automatic detection of Medical procedures in text (at BioASQ/CLEF2023)

[Martin Krallinger]

1st CFP MedProcNER track: Automatic detection of Medical procedures in text
(BioASQ/CLEF2023)

MedProcNER (Medical Procedure Named Entity Recognition & Linking)

TRAINING SET + ANNOTATION GUIDELINES RELEASE

https://temu.bsc.es/medprocner/


URLs:

   -

   Web: https://temu.bsc.es/medprocner/
   -

   Corpus: https://doi.org/10.5281/zenodo.7817745
   -

   Guidelines: https://doi.org/10.5281/zenodo.7817666
   -

   Registration: https://temu.bsc.es/medprocner/registration/


Description:

The recent use and exploitation of large language models (LLMs) and
transformer-based technologies have resulted in considerable improvements
in clinical NLP & health data processing systems, in particular for content
in English, but also increasingly for other languages. Efficient semantic
annotation strategies/named entity recognition of key clinical concepts,
such as diseases, medications or adverse events are critical for medical
text mining applications, including QA, information extraction, predictive
modeling or even generative AI.

Despite being at the core of clinical practice and healthcare, only limited
attempts focussed on the automatic detection and normalization of medical
procedures from texts. These were often restricted to very specialized
types of procedures (e.g. medical imaging). Some efforts like the Merlot
corpus included medical procedures, but were not exclusively focused on
this key clinical concept type.

Thus, there is a clear need to foster the development of concept
recognition systems for medical procedures, being essential to characterize
existing treatment options, diagnostic procedures of patients as well as
analyzing key aspects of therapeutic or preventive techniques associated
with patient care. Procedures are also relevant for clinical coding efforts
of electronic health records.

To promote the development, evaluation and use of clinical concept
recognition systems of medical procedure from clinical texts we organize
the MedProcNER task as part of the BioASQ/CLEF 2023 evaluation initiative.

For this track a large Gold Standard corpus of clinical case texts in
Spanish manually annotated through a collaborative effort between
clinicians, clinical coding experts and linguists will be released.
Additionally a multilingual Silver Standard version of the MedProcNER
corpus in English and other languages including French, Italian or
Portuguese will be published as well as cross-mappings to ICD-10 and MeSH
codes.

Aligned with different practical end user scenarios three subtasks will be
posed:

   -

   Procedure-NER (Clinical Procedure Recognition Task 1) subtask: requires
   the automatic detection of all clinical procedures mentioned in clinical
   case documents (their start and end character positions).
   -

   Procedure-Norm (Clinical Procedure Normalization Task 2) subtask:
   requires the automatic detection of all clinical procedures mentioned in
   clinical case documents (their start and end character positions) together
   with their corresponding SNOMED CT concept code.
   -

   Procedure-Indexing (Clinical Procedure-based Document Indexing Task 3)
   subtask: similar to semantic indexing or clinical coding tasks, this
   subtask requires teams to automatically assign to each document their
   corresponding list of clinical procedure SNOMED CT codes.


Schedule:

   -

   Train set release Procedure-NER: April 11th, 2023
   -

   Train set release Procedure-Norm/Indexing & : April 21st, 2023
   -

   Test set release (start of evaluation period): April 24th, 2023
   -

   End of evaluation period (system submissions): May 15th, 2023
   -

   Working papers submission: June 5th, 2023
   -

   Notification of acceptance (peer-reviews): June 23rd, 2023
   -

   Camera-ready system descriptions: July 7th, 2023
   -

   BioASQ workshop at CLEF 2023: Thessaloniki, Greece, September 18th-21st,
   2023 (https://clef2023.clef-initiative.eu)


Publications & conference

Following previous BioASQ/CLEF efforts, participating teams will be invited
to contribute a short systems description paper for the CLEF 2023
proceedings, and to give a short presentation of their approach at the
BioASQ workshop at the CLEF 2023 conference (18-21 September, Thessaloniki,
Greece)

Organizers:

   -

   Martin Krallinger, Barcelona Supercomputing Center, Spain
   -

   Salvador Lima, Barcelona Supercomputing Center, Spain
   -

   Eulàlia Farré, Barcelona Supercomputing Center, Spain
   -

   Luis Gascó, Barcelona Supercomputing Center, Spain
   -

   Anastasios Nentidis, National Center for Scientific Research Demokritos,
   Greece
   -

   Anastasia Krithara, National Center for Scientific Research Demokritos,
   Greece
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://mailman.srv.cs.cmu.edu/pipermail/connectionists/attachments/20230411/d7e4f4f0/attachment.html>