Final CFP SYMPTEMIST (BioCreative VIII @ AMIA 2023): Named entity recognition & linking of symptoms (incl. multilingual dataset)
Martin Krallinger via Corpora <[email protected]> Tue, 5 Sep 2023 09:54:10 +0200
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--===============8110693326003649420== Content-Type: multipart/alternative; boundary="000000000000561c9b060497ef75" --000000000000561c9b060497ef75 Content-Type: text/plain; charset="UTF-8" Content-Transfer-Encoding: quoted-printable (Apologies for cross-posting) Final CFP: SYMPTEMIST Shared Task (BioCreative VIII run with AMIA 2023) NER and entity linking of symptoms https://temu.bsc.es/SYMPTEMIST/ <https://temu.bsc.es/distemist/> The SYMPTEMIST focuses on the detection of mentions of symptoms (NER) and mapping to concept identifiers in clinical case reports in Spanish (entity linking). Also a multilingual version of the dataset will be released including versions in English, French, Italian, Dutch, Portuguese, Romanian and Swedish. Key information: - Web: https://temu.bsc.es/symptemist - Data: <https://doi.org/10.5281/zenodo.6408476> https://zenodo.org/record/8223654 - Annotation guidelines: https://zenodo.org/record/8246440 - BioCreative web: https://biocreative.bioinformatics.udel.edu - Registration form (Track 2- SYMPTEMIST): <https://temu.bsc.es/distemist/registration/> https://docs.google.com/forms/d/e/1FAIpQLScoSNulOoxRju3c8v9Q-CSv-w5jJcXu= 93G7A7v343AWfonpPw/viewform Motivation Systems able to detect and normalize clinical symptom mentions from medical texts are crucial for almost any healthcare data mining, AI, medical analytics or predictive application. As opposed to other clinical information types, such as diagnoses (diseases/procedures), lab test results or even medications, clinical symptoms can only be recovered directly from written clinical narratives. Due to the high complexity, variability and difficulty in generating annotated corpora for clinical symptoms, only few large manually annotated data collections have been constructed so far, with certain underlying limitations in terms of a) entity linking / normalization of the symptom mentions to controlled vocabularies and b) a lack of attempts to promote the development of multilingual solutions and b) provide detailed annotation criteria and guidelines. To address these issues, we have posed the SYMPTEMIST track at the upcoming BioCreative VIII initiative, which will be run in the context of the prestigious AMIA 2023 conference, which received over 1400 submissions this year. Automatic detection of symptoms mentions are key for a range of clinical use cases and real world applications like: - Predictive modeling of diseases - Differential diagnosis of complex diseases - Rare disease characterization & analysis - Selection of appropriate treatment & therapy - Study of disease-symptom associations - Early detection of disease outbreaks & epidemiological surveillance - Extraction of phenotypes - Drug repurposing & off label indications The SYMPTEMIST organizers will also release multilingual resources to foster the development of multilingual tools and generate systems not only for Spanish but also for content in English and Romance languages (French, Portuguese, Italian, Romanian and Catalan) as well as versions in Dutch, Swedish and Czech. Inspired by previous initiatives (e.g. n2c2, CLEF or TREC) and shared tasks (CANTEMIST, PharmaCoNER, or CodiEsp), we are launching the SYMPTEMIST share= d task as part of the BioCreative 2023 evaluation initiative, with the following three sub-tracks: - SYMPTEMIST-entities: automatic detection of mentions of symptoms. - SYMPTEMIST-linking: finding mentions of symptoms and normalizing them to their Snomed-CT concept identifiers. - SYMPTEMIST-multilingual: automatic detection of mentions of symptoms in versions of the corpus generated in English, French, Italian, Portuguese= , Romanian, Catalan, Dutch, Swedish and Czech. Tentative schedule - SympTEMIST Annotation Guidelines Release August 8th 2023 - SympTEMIST Train Set Subtask 1 (NER) Release August 8th, 2023 - SympTEMIST Train Set Subtask 2 (Linking) Release September 12th, 2023 - SympTEMIST Gazetteer Release September 12th, 2023 - SympTEMIST Test Set Release September 30th 2023 - Participants Test Predictions Deadline October 5th 2023 - Participants Evaluation Results Release October 10th 2023 - Submission of Participant Papers Deadline October 22nd 2023 - Notification of Acceptance Participant Papers October 30th 2023 - Submission of Camera-ready Participant Papers Deadline November 1st 2023 - BioCreative VIII @ AMIA 2023 November 11-15 2023 BioCreative proceedings and AMIA workshop Teams participating in SYMPTEMIST will be invited to contribute a systems description paper for the BioCreative 2023 Working Notes proceedings and a flash presentation of their approach at the BioCreative 2023 session. The BioCreative VIII workshop will run with AMIA 2023, November 11-15, 2023, In New Orleans, LA. See: https://amia.org/education-events/amia-2023-annual-symposium Workshop Proceedings and Special Issue: The BioCreative VIII Proceedings will host all the submissions from participating teams, and it will be freely available by the time of the workshop. In addition, we are happy to announce that the journal Database will host the BioCreative VIII special issue for work that has passed their peer-review process. Invitation to submit will be sent after the workshop. All BioCreative VIII tracks Track 1: BioRED (Biomedical Relation Extraction Dataset) *Track 2: SYMPTEMIST (Symptom TExt Mining Shared Task) Track 3: Genetic Phenotype Extraction and Normalization from Dysmorphology Physical Examination Entries Track 4: Clinical Annotation Tool Track Main Organizers - Martin Krallinger, Barcelona Supercomputing Center, Spain - Eul=C3=A0lia Farr=C3=A9-Maduell, Barcelona Supercomputing Center, Spain - Luis Gasc=C3=B3, Barcelona Supercomputing Center, Spain - Salvador Lima, Barcelona Supercomputing Center, Spain - Jan Rodriguez, Barcelona Supercomputing Center, Spain =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D Martin Krallinger, Dr. Head of NLP for Biomedical Information Analysis Unit Barcelona Supercomputing Center (BSC-CNS) https://www.linkedin.com/in/martin-krallinger-85495920/ =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D --000000000000561c9b060497ef75 Content-Type: text/html; charset="UTF-8" Content-Transfer-Encoding: quoted-printable <div dir=3D"ltr"><div dir=3D"ltr"><span id=3D"m_-5654700342234366369gmail-d= ocs-internal-guid-7fba9f1a-7fff-bd34-385e-916fca66a844"><p dir=3D"ltr" styl= e=3D"line-height:1.38;margin-top:0pt;margin-bottom:0pt"><span style=3D"font= -size:11pt;font-family:Arial,sans-serif;color:rgb(0,0,0);background-color:t= ransparent;font-variant-numeric:normal;font-variant-east-asian:normal;font-= variant-alternates:normal;vertical-align:baseline">(Apologies for cross-pos= ting)</span></p><br><p dir=3D"ltr" style=3D"line-height:1.44;text-align:cen= ter;margin-top:10pt;margin-bottom:10pt"><span style=3D"font-size:10pt;font-= family:Calibri,sans-serif;color:rgb(0,0,0);background-color:transparent;fon= t-weight:700;font-variant-numeric:normal;font-variant-east-asian:normal;fon= t-variant-alternates:normal;vertical-align:baseline"><span class=3D"gmail-i= l">Final CFP</span>:=C2=A0<span class=3D"gmail-il">SYMPTEMIST</span>=C2=A0S= hared Task (BioCreative VIII run with AMIA 2023)=C2=A0</span></p><p dir=3D"= ltr" style=3D"line-height:1.44;text-align:center;margin-top:0pt;margin-bott= om:0pt"><span style=3D"font-size:10pt;font-family:Calibri,sans-serif;color:= rgb(0,0,0);background-color:transparent;font-weight:700;font-variant-numeri= c:normal;font-variant-east-asian:normal;font-variant-alternates:normal;vert= ical-align:baseline">NER and entity linking of symptoms</span></p><p dir=3D= "ltr" style=3D"line-height:1.44;text-align:center;margin-top:0pt;margin-bot= tom:0pt;padding:0pt 0pt 10pt"><a href=3D"https://temu.bsc.es/distemist/" ta= rget=3D"_blank" style=3D"text-decoration-line:none"><span style=3D"font-siz= e:10pt;font-family:Calibri,sans-serif;background-color:transparent;font-var= iant-numeric:normal;font-variant-east-asian:normal;font-variant-alternates:= normal;text-decoration-line:underline;vertical-align:baseline">https://temu= .bsc.es/<span class=3D"gmail-il">SYMPTEMIST</span>/</span></a></p><p dir=3D= "ltr" style=3D"line-height:1.44;text-align:center;margin-top:0pt;margin-bot= tom:0pt"><span style=3D"font-size:11pt;font-family:Arial,sans-serif;color:r= gb(0,0,0);background-color:transparent;font-variant-numeric:normal;font-var= iant-east-asian:normal;font-variant-alternates:normal;vertical-align:baseli= ne">=C2=A0</span></p><p dir=3D"ltr" style=3D"line-height:1.44;text-align:ju= stify;margin-top:0pt;margin-bottom:0pt;padding:10pt 0pt"><span style=3D"fon= t-size:10pt;font-family:Calibri,sans-serif;color:rgb(0,0,0);background-colo= r:transparent;font-variant-numeric:normal;font-variant-east-asian:normal;fo= nt-variant-alternates:normal;vertical-align:baseline">The=C2=A0<span class= =3D"gmail-il">SYMPTEMIST</span>=C2=A0focuses on the detection of mentions o= f symptoms (NER) and mapping to concept identifiers in clinical case report= s in Spanish (entity linking). Also a multilingual version of the dataset w= ill be released including versions in English, French, Italian, Dutch, Port= uguese, Romanian and Swedish.</span></p><p dir=3D"ltr" style=3D"line-height= :1.44;margin-top:0pt;margin-bottom:0pt"><span style=3D"font-size:10pt;font-= family:Calibri,sans-serif;color:rgb(0,0,0);background-color:transparent;fon= t-weight:700;font-variant-numeric:normal;font-variant-east-asian:normal;fon= t-variant-alternates:normal;vertical-align:baseline">Key information:</span= ></p><ul style=3D"margin-top:0px;margin-bottom:0px"><li dir=3D"ltr" style= =3D"margin-left:11pt;list-style-type:disc;font-size:10pt;font-family:Arial,= sans-serif;color:rgb(0,0,0);background-color:transparent;font-variant-numer= ic:normal;font-variant-east-asian:normal;font-variant-alternates:normal;ver= tical-align:baseline"><p dir=3D"ltr" role=3D"presentation" style=3D"line-he= ight:1.38;margin-top:0pt;margin-bottom:0pt"><span style=3D"font-size:10pt;f= ont-family:Calibri,sans-serif;background-color:transparent;font-weight:700;= font-variant-numeric:normal;font-variant-east-asian:normal;font-variant-alt= ernates:normal;vertical-align:baseline">Web</span><span style=3D"font-size:= 10pt;font-family:Calibri,sans-serif;background-color:transparent;font-varia= nt-numeric:normal;font-variant-east-asian:normal;font-variant-alternates:no= rmal;vertical-align:baseline">: <a href=3D"https://temu.bsc.es/symptemist" = target=3D"_blank">https://temu.bsc.es/<span class=3D"gmail-il">symptemist</= span></a></span></p></li><li dir=3D"ltr" style=3D"margin-left:11pt;list-sty= le-type:disc;font-size:10pt;font-family:Arial,sans-serif;color:rgb(0,0,0);b= ackground-color:transparent;font-variant-numeric:normal;font-variant-east-a= sian:normal;font-variant-alternates:normal;vertical-align:baseline"><p dir= =3D"ltr" role=3D"presentation" style=3D"line-height:1.38;margin-top:0pt;mar= gin-bottom:0pt"><span style=3D"font-size:10pt;font-family:Calibri,sans-seri= f;background-color:transparent;font-weight:700;font-variant-numeric:normal;= font-variant-east-asian:normal;font-variant-alternates:normal;vertical-alig= n:baseline">Data</span><span style=3D"font-size:10pt;font-family:Calibri,sa= ns-serif;background-color:transparent;font-variant-numeric:normal;font-vari= ant-east-asian:normal;font-variant-alternates:normal;vertical-align:baselin= e">:</span><a href=3D"https://doi.org/10.5281/zenodo.6408476" target=3D"_bl= ank" style=3D"text-decoration-line:none"><span style=3D"font-size:10pt;font= -family:Calibri,sans-serif;color:rgb(0,0,0);background-color:transparent;fo= nt-variant-numeric:normal;font-variant-east-asian:normal;font-variant-alter= nates:normal;vertical-align:baseline"> </span></a><span style=3D"font-size:= 10pt;font-family:Calibri,sans-serif;color:rgb(17,85,204);background-color:t= ransparent;font-variant-numeric:normal;font-variant-east-asian:normal;font-= variant-alternates:normal;text-decoration-line:underline;vertical-align:bas= eline"><a href=3D"https://zenodo.org/record/8223654" target=3D"_blank">http= s://zenodo.org/record/8223654</a></span></p></li><li dir=3D"ltr" style=3D"m= argin-left:11pt;list-style-type:disc;font-size:10pt;font-family:Arial,sans-= serif;color:rgb(0,0,0);background-color:transparent;font-variant-numeric:no= rmal;font-variant-east-asian:normal;font-variant-alternates:normal;vertical= -align:baseline"><p dir=3D"ltr" role=3D"presentation" style=3D"line-height:= 1.38;margin-top:0pt;margin-bottom:0pt"><span style=3D"font-size:10pt;font-f= amily:Calibri,sans-serif;background-color:transparent;font-weight:700;font-= variant-numeric:normal;font-variant-east-asian:normal;font-variant-alternat= es:normal;vertical-align:baseline">Annotation guidelines</span><span style= =3D"font-size:10pt;font-family:Calibri,sans-serif;background-color:transpar= ent;font-variant-numeric:normal;font-variant-east-asian:normal;font-variant= -alternates:normal;vertical-align:baseline">: <a href=3D"https://zenodo.org= /record/8246440" target=3D"_blank">https://zenodo.org/record/8246440</a></s= pan></p></li><li dir=3D"ltr" style=3D"margin-left:11pt;list-style-type:disc= ;font-size:10pt;font-family:Calibri,sans-serif;color:rgb(0,0,0);background-= color:transparent;font-variant-numeric:normal;font-variant-east-asian:norma= l;font-variant-alternates:normal;vertical-align:baseline"><p dir=3D"ltr" ro= le=3D"presentation" style=3D"line-height:1.38;margin-top:0pt;margin-bottom:= 0pt"><span style=3D"font-size:10pt;background-color:transparent;font-weight= :700;font-variant-numeric:normal;font-variant-east-asian:normal;font-varian= t-alternates:normal;vertical-align:baseline">BioCreative web</span><span st= yle=3D"font-size:10pt;background-color:transparent;font-variant-numeric:nor= mal;font-variant-east-asian:normal;font-variant-alternates:normal;vertical-= align:baseline">: </span><a href=3D"https://biocreative.bioinformatics.udel= .edu/" target=3D"_blank" style=3D"text-decoration-line:none"><span style=3D= "font-size:10pt;background-color:transparent;font-variant-numeric:normal;fo= nt-variant-east-asian:normal;font-variant-alternates:normal;text-decoration= -line:underline;vertical-align:baseline">https://biocreative.bioinformatics= .udel.edu</span></a></p></li><li dir=3D"ltr" style=3D"margin-left:11pt;list= -style-type:disc;font-size:10pt;font-family:Calibri,sans-serif;color:rgb(0,= 0,0);background-color:transparent;font-variant-numeric:normal;font-variant-= east-asian:normal;font-variant-alternates:normal;vertical-align:baseline"><= p dir=3D"ltr" role=3D"presentation" style=3D"line-height:1.38;margin-top:0p= t;margin-bottom:0pt"><span style=3D"font-size:10pt;background-color:transpa= rent;font-weight:700;font-variant-numeric:normal;font-variant-east-asian:no= rmal;font-variant-alternates:normal;vertical-align:baseline">Registration f= orm (</span><span style=3D"font-size:10pt;color:rgb(32,33,36);font-weight:7= 00;font-variant-numeric:normal;font-variant-east-asian:normal;font-variant-= alternates:normal;vertical-align:baseline">Track 2- <span class=3D"gmail-il= ">SYMPTEMIST</span></span><span style=3D"font-size:10pt;background-color:tr= ansparent;font-weight:700;font-variant-numeric:normal;font-variant-east-asi= an:normal;font-variant-alternates:normal;vertical-align:baseline">)</span><= span style=3D"font-size:10pt;background-color:transparent;font-variant-nume= ric:normal;font-variant-east-asian:normal;font-variant-alternates:normal;ve= rtical-align:baseline">:</span><a href=3D"https://temu.bsc.es/distemist/reg= istration/" target=3D"_blank" style=3D"text-decoration-line:none"><span sty= le=3D"font-size:10pt;color:rgb(0,0,0);background-color:transparent;font-var= iant-numeric:normal;font-variant-east-asian:normal;font-variant-alternates:= normal;vertical-align:baseline"> </span></a><a href=3D"https://docs.google.= com/forms/d/e/1FAIpQLScoSNulOoxRju3c8v9Q-CSv-w5jJcXu93G7A7v343AWfonpPw/view= form" target=3D"_blank" style=3D"text-decoration-line:none"><span style=3D"= font-size:10pt;background-color:transparent;font-variant-numeric:normal;fon= t-variant-east-asian:normal;font-variant-alternates:normal;text-decoration-= line:underline;vertical-align:baseline">https://docs.google.com/forms/d/e/1= FAIpQLScoSNulOoxRju3c8v9Q-CSv-w5jJcXu93G7A7v343AWfonpPw/viewform</span></a>= </p></li></ul><p dir=3D"ltr" style=3D"line-height:1.44;text-align:justify;m= argin-top:10pt;margin-bottom:0pt;padding:0pt 0pt 10pt"><span style=3D"font-= size:10pt;font-family:Calibri,sans-serif;color:rgb(17,85,204);background-co= lor:transparent;font-variant-numeric:normal;font-variant-east-asian:normal;= font-variant-alternates:normal;text-decoration-line:underline;vertical-alig= n:baseline"><br></span><span style=3D"font-size:10pt;font-family:Calibri,sa= ns-serif;color:rgb(0,0,0);background-color:transparent;font-weight:700;font= -variant-numeric:normal;font-variant-east-asian:normal;font-variant-alterna= tes:normal;vertical-align:baseline">Motivation</span><span style=3D"font-si= ze:10pt;font-family:Calibri,sans-serif;color:rgb(0,0,0);background-color:tr= ansparent;font-weight:700;font-variant-numeric:normal;font-variant-east-asi= an:normal;font-variant-alternates:normal;vertical-align:baseline"><br></spa= n><span style=3D"font-size:10pt;font-family:Calibri,sans-serif;color:rgb(0,= 0,0);background-color:transparent;font-variant-numeric:normal;font-variant-= east-asian:normal;font-variant-alternates:normal;vertical-align:baseline">S= ystems able to detect and normalize clinical symptom mentions from medical = texts are crucial for almost any healthcare data mining, AI, medical analyt= ics or predictive application. As opposed to other clinical information typ= es, such as diagnoses (diseases/procedures), lab test results or even medic= ations, clinical symptoms can only be recovered directly from written clini= cal narratives. Due to the high complexity, variability and difficulty in g= enerating annotated corpora for clinical symptoms, only few large manually = annotated data collections have been constructed so far, with certain under= lying limitations in terms of a) entity linking / normalization of the symp= tom mentions to controlled vocabularies and b) a lack of attempts to promot= e the development of multilingual solutions and b) provide detailed annotat= ion criteria and guidelines. To address these issues, we have posed the=C2= =A0<span class=3D"gmail-il">SYMPTEMIST</span>=C2=A0track at the upcoming Bi= oCreative VIII initiative, which will be run in the context of the prestigi= ous AMIA 2023 conference, which received over 1400 submissions this year.</= span></p><p dir=3D"ltr" style=3D"line-height:1.44;text-align:justify;margin= -top:0pt;margin-bottom:10pt"><span style=3D"font-size:10pt;font-family:Cali= bri,sans-serif;color:rgb(0,0,0);background-color:transparent;font-variant-n= umeric:normal;font-variant-east-asian:normal;font-variant-alternates:normal= ;vertical-align:baseline">Automatic detection of symptoms mentions are key = for a range of clinical use cases and real world applications like:</span><= /p><ul style=3D"margin-top:0px;margin-bottom:0px"><li dir=3D"ltr" style=3D"= margin-left:15px;list-style-type:disc;font-size:10pt;font-family:Calibri,sa= ns-serif;color:rgb(0,0,0);background-color:transparent;font-variant-numeric= :normal;font-variant-east-asian:normal;font-variant-alternates:normal;verti= cal-align:baseline"><p dir=3D"ltr" role=3D"presentation" style=3D"line-heig= ht:1.38;margin-top:0pt;margin-bottom:0pt"><span style=3D"font-size:10pt;bac= kground-color:transparent;font-variant-numeric:normal;font-variant-east-asi= an:normal;font-variant-alternates:normal;vertical-align:baseline">Predictiv= e modeling of diseases</span></p></li><li dir=3D"ltr" style=3D"margin-left:= 15px;list-style-type:disc;font-size:10pt;font-family:Calibri,sans-serif;col= or:rgb(0,0,0);background-color:transparent;font-variant-numeric:normal;font= -variant-east-asian:normal;font-variant-alternates:normal;vertical-align:ba= seline"><p dir=3D"ltr" role=3D"presentation" style=3D"line-height:1.38;marg= in-top:0pt;margin-bottom:0pt"><span style=3D"font-size:10pt;background-colo= r:transparent;font-variant-numeric:normal;font-variant-east-asian:normal;fo= nt-variant-alternates:normal;vertical-align:baseline">Differential diagnosi= s of complex diseases</span></p></li><li dir=3D"ltr" style=3D"margin-left:1= 5px;list-style-type:disc;font-size:10pt;font-family:Calibri,sans-serif;colo= r:rgb(0,0,0);background-color:transparent;font-variant-numeric:normal;font-= variant-east-asian:normal;font-variant-alternates:normal;vertical-align:bas= eline"><p dir=3D"ltr" role=3D"presentation" style=3D"line-height:1.38;margi= n-top:0pt;margin-bottom:0pt"><span style=3D"font-size:10pt;background-color= :transparent;font-variant-numeric:normal;font-variant-east-asian:normal;fon= t-variant-alternates:normal;vertical-align:baseline">Rare disease character= ization & analysis</span></p></li><li dir=3D"ltr" style=3D"margin-left:= 15px;list-style-type:disc;font-size:10pt;font-family:Calibri,sans-serif;col= or:rgb(0,0,0);background-color:transparent;font-variant-numeric:normal;font= -variant-east-asian:normal;font-variant-alternates:normal;vertical-align:ba= seline"><p dir=3D"ltr" role=3D"presentation" style=3D"line-height:1.38;marg= in-top:0pt;margin-bottom:0pt"><span style=3D"font-size:10pt;background-colo= r:transparent;font-variant-numeric:normal;font-variant-east-asian:normal;fo= nt-variant-alternates:normal;vertical-align:baseline">Selection of appropri= ate treatment & therapy</span></p></li><li dir=3D"ltr" style=3D"margin-= left:15px;list-style-type:disc;font-size:10pt;font-family:Calibri,sans-seri= f;color:rgb(0,0,0);background-color:transparent;font-variant-numeric:normal= ;font-variant-east-asian:normal;font-variant-alternates:normal;vertical-ali= gn:baseline"><p dir=3D"ltr" role=3D"presentation" style=3D"line-height:1.38= ;margin-top:0pt;margin-bottom:0pt"><span style=3D"font-size:10pt;background= -color:transparent;font-variant-numeric:normal;font-variant-east-asian:norm= al;font-variant-alternates:normal;vertical-align:baseline">Study of=C2=A0 d= isease-symptom associations</span></p></li><li dir=3D"ltr" style=3D"margin-= left:15px;list-style-type:disc;font-size:10pt;font-family:Calibri,sans-seri= f;color:rgb(0,0,0);background-color:transparent;font-variant-numeric:normal= ;font-variant-east-asian:normal;font-variant-alternates:normal;vertical-ali= gn:baseline"><p dir=3D"ltr" role=3D"presentation" style=3D"line-height:1.38= ;margin-top:0pt;margin-bottom:0pt"><span style=3D"font-size:10pt;background= -color:transparent;font-variant-numeric:normal;font-variant-east-asian:norm= al;font-variant-alternates:normal;vertical-align:baseline">Early detection = of disease outbreaks & epidemiological surveillance</span></p></li><li = dir=3D"ltr" style=3D"margin-left:15px;list-style-type:disc;font-size:10pt;f= ont-family:Calibri,sans-serif;color:rgb(0,0,0);background-color:transparent= ;font-variant-numeric:normal;font-variant-east-asian:normal;font-variant-al= ternates:normal;vertical-align:baseline"><p dir=3D"ltr" role=3D"presentatio= n" style=3D"line-height:1.38;margin-top:0pt;margin-bottom:0pt"><span style= =3D"font-size:10pt;background-color:transparent;font-variant-numeric:normal= ;font-variant-east-asian:normal;font-variant-alternates:normal;vertical-ali= gn:baseline">Extraction of phenotypes</span></p></li><li dir=3D"ltr" style= =3D"margin-left:15px;list-style-type:disc;font-size:10pt;font-family:Calibr= i,sans-serif;color:rgb(0,0,0);background-color:transparent;font-variant-num= eric:normal;font-variant-east-asian:normal;font-variant-alternates:normal;v= ertical-align:baseline"><p dir=3D"ltr" role=3D"presentation" style=3D"line-= height:1.38;margin-top:0pt;margin-bottom:0pt"><span style=3D"font-size:10pt= ;background-color:transparent;font-variant-numeric:normal;font-variant-east= -asian:normal;font-variant-alternates:normal;vertical-align:baseline">Drug = repurposing & off label indications=C2=A0</span></p></li></ul><br><p di= r=3D"ltr" style=3D"line-height:1.44;margin-top:0pt;margin-bottom:12pt"><spa= n style=3D"font-size:10pt;font-family:Calibri,sans-serif;color:rgb(0,0,0);b= ackground-color:transparent;font-variant-numeric:normal;font-variant-east-a= sian:normal;font-variant-alternates:normal;vertical-align:baseline">The=C2= =A0<span class=3D"gmail-il">SYMPTEMIST</span>=C2=A0organizers will also rel= ease multilingual resources to foster the development of multilingual tools= and generate systems not only for Spanish but also for content in English = and Romance languages (French, Portuguese, Italian, Romanian and Catalan) a= s well as versions in Dutch, Swedish and Czech.</span></p><p dir=3D"ltr" st= yle=3D"line-height:1.44;margin-top:0pt;margin-bottom:12pt"><span style=3D"f= ont-size:10pt;font-family:Calibri,sans-serif;color:rgb(0,0,0);background-co= lor:transparent;font-variant-numeric:normal;font-variant-east-asian:normal;= font-variant-alternates:normal;vertical-align:baseline">Inspired by previou= s initiatives (e.g. n2c2, CLEF or TREC) and shared tasks (CANTEMIST, Pharma= CoNER, or CodiEsp), we are launching the=C2=A0<span class=3D"gmail-il">SYMP= TEMIST</span>=C2=A0shared task as part of the BioCreative 2023 evaluation i= nitiative, with the following three sub-tracks:</span></p><ul style=3D"marg= in-top:0px;margin-bottom:0px"><li dir=3D"ltr" style=3D"margin-left:11pt;lis= t-style-type:disc;font-size:10pt;font-family:Arial,sans-serif;color:rgb(0,0= ,0);background-color:transparent;font-variant-numeric:normal;font-variant-e= ast-asian:normal;font-variant-alternates:normal;vertical-align:baseline"><p= dir=3D"ltr" role=3D"presentation" style=3D"line-height:1.38;margin-top:0pt= ;margin-bottom:0pt"><span style=3D"font-size:10pt;font-family:Calibri,sans-= serif;background-color:transparent;font-weight:700;font-variant-numeric:nor= mal;font-variant-east-asian:normal;font-variant-alternates:normal;vertical-= align:baseline"><span class=3D"gmail-il">SYMPTEMIST</span>-entities:</span>= <span style=3D"font-size:10pt;font-family:Calibri,sans-serif;background-col= or:transparent;font-variant-numeric:normal;font-variant-east-asian:normal;f= ont-variant-alternates:normal;vertical-align:baseline"> automatic detection= of mentions of symptoms.</span></p></li></ul><ul style=3D"margin-top:0px;m= argin-bottom:0px"><li dir=3D"ltr" style=3D"margin-left:11pt;list-style-type= :disc;font-size:10pt;font-family:Arial,sans-serif;color:rgb(0,0,0);backgrou= nd-color:transparent;font-variant-numeric:normal;font-variant-east-asian:no= rmal;font-variant-alternates:normal;vertical-align:baseline"><p dir=3D"ltr"= role=3D"presentation" style=3D"line-height:1.38;margin-top:0pt;margin-bott= om:0pt"><span style=3D"font-size:10pt;font-family:Calibri,sans-serif;backgr= ound-color:transparent;font-weight:700;font-variant-numeric:normal;font-var= iant-east-asian:normal;font-variant-alternates:normal;vertical-align:baseli= ne"><span class=3D"gmail-il">SYMPTEMIST</span>-linking</span><span style=3D= "font-size:10pt;font-family:Calibri,sans-serif;background-color:transparent= ;font-variant-numeric:normal;font-variant-east-asian:normal;font-variant-al= ternates:normal;vertical-align:baseline">: finding mentions of symptoms and= normalizing them to their Snomed-CT concept identifiers.</span></p></li><l= i dir=3D"ltr" style=3D"margin-left:11pt;list-style-type:disc;font-size:10pt= ;font-family:Arial,sans-serif;color:rgb(0,0,0);background-color:transparent= ;font-variant-numeric:normal;font-variant-east-asian:normal;font-variant-al= ternates:normal;vertical-align:baseline"><p dir=3D"ltr" role=3D"presentatio= n" style=3D"line-height:1.38;margin-top:0pt;margin-bottom:0pt"><span style= =3D"font-size:10pt;font-family:Calibri,sans-serif;background-color:transpar= ent;font-weight:700;font-variant-numeric:normal;font-variant-east-asian:nor= mal;font-variant-alternates:normal;vertical-align:baseline"><span class=3D"= gmail-il">SYMPTEMIST</span>-multilingual</span><span style=3D"font-size:10p= t;font-family:Calibri,sans-serif;background-color:transparent;font-variant-= numeric:normal;font-variant-east-asian:normal;font-variant-alternates:norma= l;vertical-align:baseline">: automatic detection of mentions of symptoms in= versions of the corpus generated in English, French, Italian, Portuguese, = Romanian, Catalan, Dutch, Swedish and Czech.</span></p></li></ul><p dir=3D"= ltr" style=3D"line-height:1.44;margin-top:0pt;margin-bottom:0pt"><span styl= e=3D"font-size:10pt;font-family:Calibri,sans-serif;color:rgb(0,0,0);backgro= und-color:transparent;font-variant-numeric:normal;font-variant-east-asian:n= ormal;font-variant-alternates:normal;vertical-align:baseline"><br></span><s= pan style=3D"font-size:10pt;font-family:Calibri,sans-serif;color:rgb(0,0,0)= ;background-color:transparent;font-variant-numeric:normal;font-variant-east= -asian:normal;font-variant-alternates:normal;vertical-align:baseline"><br><= /span><span style=3D"font-size:10pt;font-family:Calibri,sans-serif;color:rg= b(0,0,0);background-color:transparent;font-weight:700;font-variant-numeric:= normal;font-variant-east-asian:normal;font-variant-alternates:normal;vertic= al-align:baseline">Tentative schedule</span></p><p dir=3D"ltr" style=3D"lin= e-height:1.44;margin-top:0pt;margin-bottom:0pt"></p><ul><li><span style=3D"= background-color:transparent;color:rgb(0,0,0);font-family:Calibri,sans-seri= f;font-size:10pt">SympTEMIST Annotation Guidelines Release August 8th 2023<= /span></li><li><span style=3D"background-color:transparent;color:rgb(0,0,0)= ;font-family:Calibri,sans-serif;font-size:10pt">SympTEMIST Train Set Subtas= k 1 (NER) Release August 8th, 2023</span></li><li><span style=3D"background= -color:transparent;color:rgb(0,0,0);font-family:Calibri,sans-serif;font-siz= e:10pt">SympTEMIST Train Set Subtask 2 (Linking) Release September 12th, 20= 23</span></li><li><span style=3D"background-color:transparent;color:rgb(0,0= ,0);font-family:Calibri,sans-serif;font-size:10pt">SympTEMIST Gazetteer Rel= ease September 12th, 2023</span></li><li><span style=3D"background-color:tr= ansparent;color:rgb(0,0,0);font-family:Calibri,sans-serif;font-size:10pt">S= ympTEMIST Test Set Release September 30th 2023</span></li><li><span style= =3D"background-color:transparent;color:rgb(0,0,0);font-family:Calibri,sans-= serif;font-size:10pt">Participants Test Predictions Deadline October 5th 20= 23</span></li><li><span style=3D"background-color:transparent;color:rgb(0,0= ,0);font-family:Calibri,sans-serif;font-size:10pt">Participants Evaluation = Results Release October 10th 2023</span></li><li><span style=3D"background-= color:transparent;color:rgb(0,0,0);font-family:Calibri,sans-serif;font-size= :10pt">Submission of Participant Papers Deadline October 22nd 2023</span></= li><li><span style=3D"background-color:transparent;color:rgb(0,0,0);font-fa= mily:Calibri,sans-serif;font-size:10pt">Notification of Acceptance Particip= ant Papers October 30th 2023</span></li><li><span style=3D"background-color= :transparent;color:rgb(0,0,0);font-family:Calibri,sans-serif;font-size:10pt= ">Submission of Camera-ready Participant Papers Deadline November 1st 2023<= /span></li><li><span style=3D"background-color:transparent;color:rgb(0,0,0)= ;font-family:Calibri,sans-serif;font-size:10pt">BioCreative VIII @ AMIA 202= 3 November 11-15 2023</span></li></ul><p></p><p dir=3D"ltr" style=3D"line-h= eight:1.44;margin-top:0pt;margin-bottom:0pt"><span style=3D"font-size:10pt;= font-family:Calibri,sans-serif;color:rgb(0,0,0);background-color:transparen= t;font-variant-numeric:normal;font-variant-east-asian:normal;font-variant-a= lternates:normal;vertical-align:baseline"><br></span></p><p dir=3D"ltr" sty= le=3D"line-height:1.44;margin-top:0pt;margin-bottom:0pt"><span style=3D"fon= t-size:10pt;font-family:Calibri,sans-serif;color:rgb(0,0,0);background-colo= r:transparent;font-weight:700;font-variant-numeric:normal;font-variant-east= -asian:normal;font-variant-alternates:normal;vertical-align:baseline">BioCr= eative proceedings and AMIA workshop</span></p><p dir=3D"ltr" style=3D"line= -height:1.44;margin-top:0pt;margin-bottom:0pt"><span style=3D"font-size:10p= t;font-family:Calibri,sans-serif;color:rgb(0,0,0);background-color:transpar= ent;font-weight:700;font-variant-numeric:normal;font-variant-east-asian:nor= mal;font-variant-alternates:normal;vertical-align:baseline"><br></span><spa= n style=3D"font-size:10pt;font-family:Calibri,sans-serif;color:rgb(0,0,0);b= ackground-color:transparent;font-variant-numeric:normal;font-variant-east-a= sian:normal;font-variant-alternates:normal;vertical-align:baseline">Teams p= articipating in=C2=A0<span class=3D"gmail-il">SYMPTEMIST</span>=C2=A0will b= e invited to contribute a systems description paper for the BioCreative=C2= =A0 2023 Working Notes proceedings and a flash presentation of their approa= ch at the BioCreative 2023 session. The BioCreative VIII workshop will run = with AMIA 2023, November 11-15, 2023, In New Orleans, LA. See:=C2=A0<a href= =3D"https://amia.org/education-events/amia-2023-annual-symposium" target=3D= "_blank">https://amia.org/education-events/amia-2023-annual-symposium</a></= span></p><br><br><p dir=3D"ltr" style=3D"line-height:1.44;margin-top:0pt;ma= rgin-bottom:0pt"><span style=3D"font-size:10pt;font-family:Calibri,sans-ser= if;color:rgb(0,0,0);background-color:transparent;font-weight:700;font-varia= nt-numeric:normal;font-variant-east-asian:normal;font-variant-alternates:no= rmal;vertical-align:baseline">Workshop Proceedings and Special Issue</span>= <span style=3D"font-size:10pt;font-family:Calibri,sans-serif;color:rgb(0,0,= 0);background-color:transparent;font-variant-numeric:normal;font-variant-ea= st-asian:normal;font-variant-alternates:normal;vertical-align:baseline">:</= span></p><br><p dir=3D"ltr" style=3D"line-height:1.44;margin-top:0pt;margin= -bottom:0pt"><span style=3D"font-size:10pt;font-family:Calibri,sans-serif;c= olor:rgb(0,0,0);background-color:transparent;font-variant-numeric:normal;fo= nt-variant-east-asian:normal;font-variant-alternates:normal;vertical-align:= baseline">The BioCreative VIII Proceedings will host all the submissions fr= om participating teams, and it will be freely available by the time of the = workshop. In addition, we are happy to announce that the journal Database w= ill host the BioCreative VIII special issue for work that has passed their = peer-review process. Invitation to submit will be sent after the workshop.= =C2=A0</span></p><p dir=3D"ltr" style=3D"line-height:1.44;margin-top:0pt;ma= rgin-bottom:0pt"><span style=3D"font-size:10pt;font-family:Calibri,sans-ser= if;color:rgb(0,0,0);background-color:transparent;font-variant-numeric:norma= l;font-variant-east-asian:normal;font-variant-alternates:normal;vertical-al= ign:baseline"><br><br></span></p><p dir=3D"ltr" style=3D"line-height:1.44;m= argin-top:0pt;margin-bottom:0pt"><span style=3D"font-size:10pt;font-family:= Calibri,sans-serif;color:rgb(0,0,0);background-color:transparent;font-weigh= t:700;font-variant-numeric:normal;font-variant-east-asian:normal;font-varia= nt-alternates:normal;vertical-align:baseline">All BioCreative VIII tracks</= span></p><p dir=3D"ltr" style=3D"line-height:1.44;margin-top:0pt;margin-bot= tom:0pt"><span style=3D"font-size:10pt;font-family:Calibri,sans-serif;color= :rgb(0,0,0);background-color:transparent;font-variant-numeric:normal;font-v= ariant-east-asian:normal;font-variant-alternates:normal;vertical-align:base= line">Track 1: BioRED (Biomedical Relation Extraction Dataset)</span></p><p= dir=3D"ltr" style=3D"line-height:1.44;margin-top:0pt;margin-bottom:0pt"><s= pan style=3D"font-size:10pt;font-family:Calibri,sans-serif;color:rgb(0,0,0)= ;background-color:transparent;font-variant-numeric:normal;font-variant-east= -asian:normal;font-variant-alternates:normal;vertical-align:baseline">*Trac= k 2:=C2=A0<span class=3D"gmail-il">SYMPTEMIST</span>=C2=A0(Symptom TExt Min= ing Shared Task)</span></p><p dir=3D"ltr" style=3D"line-height:1.44;margin-= top:0pt;margin-bottom:0pt"><span style=3D"font-size:10pt;font-family:Calibr= i,sans-serif;color:rgb(0,0,0);background-color:transparent;font-variant-num= eric:normal;font-variant-east-asian:normal;font-variant-alternates:normal;v= ertical-align:baseline">Track 3: Genetic Phenotype Extraction and Normaliza= tion from Dysmorphology Physical Examination Entries</span></p><p dir=3D"lt= r" style=3D"line-height:1.44;margin-top:0pt;margin-bottom:0pt"><span style= =3D"font-size:10pt;font-family:Calibri,sans-serif;color:rgb(0,0,0);backgrou= nd-color:transparent;font-variant-numeric:normal;font-variant-east-asian:no= rmal;font-variant-alternates:normal;vertical-align:baseline">Track 4: Clini= cal Annotation Tool Track</span></p><br><p dir=3D"ltr" style=3D"line-height= :1.44;margin-top:0pt;margin-bottom:0pt"><span style=3D"font-size:10pt;font-= family:Calibri,sans-serif;color:rgb(0,0,0);background-color:transparent;fon= t-variant-numeric:normal;font-variant-east-asian:normal;font-variant-altern= ates:normal;vertical-align:baseline"><br></span><span style=3D"font-size:10= pt;font-family:Calibri,sans-serif;color:rgb(0,0,0);background-color:transpa= rent;font-weight:700;font-variant-numeric:normal;font-variant-east-asian:no= rmal;font-variant-alternates:normal;vertical-align:baseline">Main Organizer= s</span></p><ul style=3D"margin-top:0px;margin-bottom:0px"><li dir=3D"ltr" = style=3D"margin-left:11pt;list-style-type:disc;font-size:10pt;font-family:A= rial,sans-serif;color:rgb(0,0,0);background-color:transparent;font-variant-= numeric:normal;font-variant-east-asian:normal;font-variant-alternates:norma= l;vertical-align:baseline"><p dir=3D"ltr" role=3D"presentation" style=3D"li= ne-height:1.38;margin-top:0pt;margin-bottom:0pt"><span style=3D"font-size:1= 0pt;font-family:Calibri,sans-serif;background-color:transparent;font-varian= t-numeric:normal;font-variant-east-asian:normal;font-variant-alternates:nor= mal;vertical-align:baseline">Martin Krallinger, Barcelona Supercomputing Ce= nter, Spain</span></p></li><li dir=3D"ltr" style=3D"margin-left:11pt;list-s= tyle-type:disc;font-size:10pt;font-family:Arial,sans-serif;color:rgb(0,0,0)= ;background-color:transparent;font-variant-numeric:normal;font-variant-east= -asian:normal;font-variant-alternates:normal;vertical-align:baseline"><p di= r=3D"ltr" role=3D"presentation" style=3D"line-height:1.38;margin-top:0pt;ma= rgin-bottom:0pt"><span style=3D"font-size:10pt;font-family:Calibri,sans-ser= if;background-color:transparent;font-variant-numeric:normal;font-variant-ea= st-asian:normal;font-variant-alternates:normal;vertical-align:baseline">Eul= =C3=A0lia Farr=C3=A9-Maduell, Barcelona Supercomputing Center, Spain</span>= </p></li><li dir=3D"ltr" style=3D"margin-left:11pt;list-style-type:disc;fon= t-size:10pt;font-family:Arial,sans-serif;color:rgb(0,0,0);background-color:= transparent;font-variant-numeric:normal;font-variant-east-asian:normal;font= -variant-alternates:normal;vertical-align:baseline"><p dir=3D"ltr" role=3D"= presentation" style=3D"line-height:1.38;margin-top:0pt;margin-bottom:0pt"><= span style=3D"font-size:10pt;font-family:Calibri,sans-serif;background-colo= r:transparent;font-variant-numeric:normal;font-variant-east-asian:normal;fo= nt-variant-alternates:normal;vertical-align:baseline">Luis Gasc=C3=B3, Barc= elona Supercomputing Center, Spain</span></p></li><li dir=3D"ltr" style=3D"= margin-left:11pt;list-style-type:disc;font-size:10pt;font-family:Calibri,sa= ns-serif;color:rgb(0,0,0);background-color:transparent;font-variant-numeric= :normal;font-variant-east-asian:normal;font-variant-alternates:normal;verti= cal-align:baseline"><p dir=3D"ltr" role=3D"presentation" style=3D"line-heig= ht:1.38;margin-top:0pt;margin-bottom:0pt"><span style=3D"font-size:10pt;bac= kground-color:transparent;font-variant-numeric:normal;font-variant-east-asi= an:normal;font-variant-alternates:normal;vertical-align:baseline">Salvador = Lima, Barcelona Supercomputing Center, Spain</span></p></li><li dir=3D"ltr"= style=3D"margin-left:11pt;list-style-type:disc;font-size:10pt;font-family:= Calibri,sans-serif;color:rgb(0,0,0);background-color:transparent;font-varia= nt-numeric:normal;font-variant-east-asian:normal;font-variant-alternates:no= rmal;vertical-align:baseline"><p dir=3D"ltr" role=3D"presentation" style=3D= "line-height:1.38;margin-top:0pt;margin-bottom:0pt"><span style=3D"font-siz= e:10pt;background-color:transparent;font-variant-numeric:normal;font-varian= t-east-asian:normal;font-variant-alternates:normal;vertical-align:baseline"= >Jan Rodriguez, Barcelona Supercomputing Center, Spain</span></p></li></ul>= <br><br></span><div><br></div><div dir=3D"ltr" class=3D"gmail_signature"><d= iv dir=3D"ltr"><div dir=3D"ltr"><div dir=3D"ltr"><div dir=3D"ltr"><div dir= =3D"ltr"><div dir=3D"ltr"><div dir=3D"ltr"><div dir=3D"ltr"><div>=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D<br>Martin Krallinger, Dr.<br><span style= =3D"font-family:arial,helvetica,sans-serif">Head of NLP for Biomedical Info= rmation Analysis Unit<br></span><span style=3D"font-family:arial,helvetica,= sans-serif">Barcelona Supercomputing Center (BSC-CNS)</span></div><div><fon= t face=3D"arial, helvetica, sans-serif"><a href=3D"https://www.linkedin.com= /in/martin-krallinger-85495920/" target=3D"_blank">https://www.linkedin.com= /in/martin-krallinger-85495920/</a><br></font>=C2=A0=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D</div></div></div></div></div></div></div></div></div>= </div></div></div> --000000000000561c9b060497ef75-- --===============8110693326003649420== Content-Type: text/plain; charset="us-ascii" MIME-Version: 1.0 Content-Transfer-Encoding: 7bit Content-Disposition: inline _______________________________________________ Corpora mailing list -- [email protected] https://list.elra.info/mailman3/postorius/lists/corpora.list.elra.info/ To unsubscribe send an email to [email protected] --===============8110693326003649420==--