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2020 – today

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2024
[c43]
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  - conf/acl-clinicalnlp/YimAFSXYK24
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Wen-wai Yim, Asma Ben Abacha, Yujuan Fu, Zhaoyi Sun, Fei Xia, Meliha Yetisgen, Martin Krallinger:
Overview of the MEDIQA-M3G 2024 Shared Task on Multilingual Multimodal Medical Answer Generation. ClinicalNLP@NAACL 2024: 581-589
[c42]
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Anastasios Nentidis, Georgios Katsimpras, Anastasia Krithara, Salvador Lima-López, Eulàlia Farré-Maduell, Martin Krallinger, Natalia V. Loukachevitch, Vera Davydova, Elena Tutubalina, Georgios Paliouras:
Overview of BioASQ 2024: The Twelfth BioASQ Challenge on Large-Scale Biomedical Semantic Indexing and Question Answering. CLEF (2) 2024: 3-27
[c41]
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Salvador Lima-López, Eulàlia Farré-Maduell, Jan Rodríguez-Miret, Miguel Rodríguez-Ortega, Livia Lilli, Jacopo Lenkowicz, Giovanna Ceroni, Jonathan Kossof, Anoop Shah, Anastasios Nentidis, Anastasia Krithara, Georgios Katsimpras, Georgios Paliouras, Martin Krallinger:
Overview of MultiCardioNER task at BioASQ 2024 on Medical Specialty and Language Adaptation of Clinical NER Systems for Spanish, English and Italian. CLEF (Working Notes) 2024: 8-27
[c40]
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Anastasios Nentidis, Anastasia Krithara, Georgios Paliouras, Martin Krallinger, Luis Gascó Sánchez, Salvador Lima-López, Eulàlia Farré, Natalia V. Loukachevitch, Vera Davydova, Elena Tutubalina:
BioASQ at CLEF2024: The Twelfth Edition of the Large-Scale Biomedical Semantic Indexing and Question Answering Challenge. ECIR (5) 2024: 490-497
[c39]
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Fernando Gallego Donoso, Guillermo López-García, Luis Gascó Sánchez, Martin Krallinger, Francisco J. Veredas:
ClinLinker: Medical Entity Linking of Clinical Concept Mentions in Spanish. ICCS (5) 2024: 266-280
[i7]
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  - journals/corr/abs-2404-06367
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Fernando Gallego Donoso, Guillermo López-García, Luis Gascó Sánchez, Martin Krallinger, Francisco J. Veredas:
ClinLinker: Medical Entity Linking of Clinical Concept Mentions in Spanish. CoRR abs/2404.06367 (2024)
2023
[j31]
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  - journals/biodb/MirandaEscaladaMLEGPVK23
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Antonio Miranda-Escalada, Farrokh Mehryary, Jouni Luoma, Darryl Estrada-Zavala, Luis Gascó, Sampo Pyysalo, Alfonso Valencia, Martin Krallinger:
Overview of DrugProt task at BioCreative VII: data and methods for large-scale text mining and knowledge graph generation of heterogenous chemical-protein relations. Database J. Biol. Databases Curation 2023 (2023)
[j30]
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Salvador Lima-López, Eulàlia Farré-Maduell, Vicent Brivá-Iglesias, Luis Gascó Sánchez, Martin Krallinger:
MEDDOPLACE Shared Task overview: recognition, normalization and classification of locations and patient movement in clinical texts. Proces. del Leng. Natural 71: 301-311 (2023)
[c38]
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Salvador Lima-López, Eulàlia Farré-Maduell, Luis Gascó, Anastasios Nentidis, Anastasia Krithara, Georgios Katsimpras, Georgios Paliouras, Martin Krallinger:
Overview of MedProcNER Task on Medical Procedure Detection and Entity Linking at BioASQ 2023. CLEF (Working Notes) 2023: 1-18
[c37]
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Anastasios Nentidis, Georgios Katsimpras, Anastasia Krithara, Salvador Lima-López, Eulàlia Farré-Maduell, Luis Gascó, Martin Krallinger, Georgios Paliouras:
Overview of BioASQ 2023: The Eleventh BioASQ Challenge on Large-Scale Biomedical Semantic Indexing and Question Answering. CLEF 2023: 227-250
[c36]
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Anastasios Nentidis, Anastasia Krithara, Georgios Paliouras, Eulàlia Farré-Maduell, Salvador Lima-López, Martin Krallinger:
BioASQ at CLEF2023: The Eleventh Edition of the Large-Scale Biomedical Semantic Indexing and Question Answering Challenge. ECIR (3) 2023: 577-584
[i6]
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  - journals/corr/abs-2307-05131
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Anastasios Nentidis, Georgios Katsimpras, Anastasia Krithara, Salvador Lima-López, Eulàlia Farré-Maduell, Luis Gascó, Martin Krallinger, Georgios Paliouras:
Overview of BioASQ 2023: The eleventh BioASQ challenge on Large-Scale Biomedical Semantic Indexing and Question Answering. CoRR abs/2307.05131 (2023)
2022
[j29]
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  - journals/biodb/Chatr-aryamontri22
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Andrew Chatr-aryamontri, Lynette Hirschman, Karen E. Ross, Rose Oughtred, Martin Krallinger, Kara Dolinski, Mike Tyers, Tonia Korves, Cecilia N. Arighi:
Overview of the COVID-19 text mining tool interactive demonstration track in BioCreative VII. Database J. Biol. Databases Curation 2022(2022) (2022)
[j28]
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  - journals/biodb/Gonzalez-Hernandez22
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Graciela Gonzalez-Hernandez, Martin Krallinger, Monica A. Muñoz, Raul Rodriguez-Esteban, Özlem Uzuner, Lynette Hirschman:
Challenges and opportunities for mining adverse drug reactions: perspectives from pharma, regulatory agencies, healthcare providers and consumers. Database J. Biol. Databases Curation 2022(2022) (2022)
[j27]
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Antonio Miranda-Escalada, Eulàlia Farré-Maduell, Salvador Lima-López, Darryl Estrada, Luis Gascó, Martin Krallinger:
Mention detection, normalization & classification of species, pathogens, humans and food in clinical documents: Overview of the LivingNER shared task and resources. Proces. del Leng. Natural 69: 241-253 (2022)
[c35]
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Antonio Miranda-Escalada, Luis Gascó, Salvador Lima-López, Eulàlia Farré-Maduell, Darryl Estrada, Anastasios Nentidis, Anastasia Krithara, Georgios Katsimpras, Georgios Paliouras, Martin Krallinger:
Overview of DisTEMIST at BioASQ: Automatic detection and normalization of diseases from clinical texts: results, methods, evaluation and multilingual resources. CLEF (Working Notes) 2022: 179-203
[c34]
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Anastasios Nentidis, Georgios Katsimpras, Eirini Vandorou, Anastasia Krithara, Antonio Miranda-Escalada, Luis Gascó, Martin Krallinger, Georgios Paliouras:
Overview of BioASQ 2022: The Tenth BioASQ Challenge on Large-Scale Biomedical Semantic Indexing and Question Answering. CLEF 2022: 337-361
[c33]
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  - conf/coling/SanchezEFLMK22
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Luis Gascó Sánchez, Darryl Estrada-Zavala, Eulàlia Farré-Maduell, Salvador Lima-López, Antonio Miranda-Escalada, Martin Krallinger:
The SocialDisNER shared task on detection of disease mentions in health-relevant content from social media: methods, evaluation, guidelines and corpora. SMM4H@COLING 2022: 182-189
[c32]
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  - conf/coling/WeissenbacherBD22
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Davy Weissenbacher, Juan M. Banda, Vera Davydova, Darryl Estrada-Zavala, Luis Gascó Sánchez, Yao Ge, Yuting Guo, Ari Z. Klein, Martin Krallinger, Mathias Leddin, Arjun Magge, Raul Rodriguez-Esteban, Abeed Sarker, Ana Lucía Schmidt, Elena Tutubalina, Graciela Gonzalez-Hernandez:
Overview of the Seventh Social Media Mining for Health Applications (#SMM4H) Shared Tasks at COLING 2022. SMM4H@COLING 2022: 221-241
[c31]
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Anastasios Nentidis, Anastasia Krithara, Georgios Paliouras, Luis Gascó, Martin Krallinger:
BioASQ at CLEF2022: The Tenth Edition of the Large-scale Biomedical Semantic Indexing and Question Answering Challenge. ECIR (2) 2022: 429-435
[c30]
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  - conf/wmt/NevesJSRTNYWNVGBELFKGN22
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Mariana Neves, Antonio Jimeno-Yepes, Amy Siu, Roland Roller, Philippe Thomas, Maika Vicente Navarro, Lana Yeganova, Dina Wiemann, Giorgio Maria Di Nunzio, Federica Vezzani, Christel Gérardin, Rachel Bawden, Darryl Estrada, Salvador Lima-López, Eulàlia Farré-Maduell, Martin Krallinger, Cristian Grozea, Aurélie Névéol:
Findings of the WMT 2022 Biomedical Translation Shared Task: Monolingual Clinical Case Reports. WMT 2022: 694-723
[i5]
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  - journals/corr/abs-2210-06852
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Anastasios Nentidis, Georgios Katsimpras, Eirini Vandorou, Anastasia Krithara, Antonio Miranda-Escalada, Luis Gascó, Martin Krallinger, Georgios Paliouras:
Overview of BioASQ 2022: The tenth BioASQ challenge on Large-Scale Biomedical Semantic Indexing and Question Answering. CoRR abs/2210.06852 (2022)
2021
[j26]
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  - journals/frma/HobbsGMSLKSMNJG21
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Elizabeth T. Hobbs, Stephen M. Goralski, Ashley Mitchell, Andrew Simpson, Dorjan Leka, Emmanuel Kotey, Matt Sekira, James B. Munro, Suvarna Nadendla, Rebecca Jackson, Aitor Gonzalez-Agirre, Martin Krallinger, Michelle G. Giglio, Ivan Erill:
ECO-CollecTF: A Corpus of Annotated Evidence-Based Assertions in Biomedical Manuscripts. Frontiers Res. Metrics Anal. 6: 674205 (2021)
[j25]
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  - journals/pdln/Lima-LopezFMBK21
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Salvador Lima-López, Eulàlia Farré-Maduell, Antonio Miranda-Escalada, Vicent Brivá-Iglesias, Martin Krallinger:
NLP applied to occupational health: MEDDOPROF shared task at IberLEF 2021 on automatic recognition, classification and normalization of professions and occupations from medical texts. Proces. del Leng. Natural 67: 243-256 (2021)
[c29]
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  - conf/clef/GascoNKEMPBPK21
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Luis Gascó, Anastasios Nentidis, Anastasia Krithara, Darryl Estrada-Zavala, Renato Toshiyuki Murasaki, Elena Primo-Peña, Cristina Bojo-Canales, Georgios Paliouras, Martin Krallinger:
Overview of BioASQ 2021-MESINESP track. Evaluation of advance hierarchical classification techniques for scientific literature, patents and clinical trials. CLEF (Working Notes) 2021: 165-187
[c28]
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Anastasios Nentidis, Georgios Katsimpras, Eirini Vandorou, Anastasia Krithara, Luis Gascó, Martin Krallinger, Georgios Paliouras:
Overview of BioASQ 2021: The Ninth BioASQ Challenge on Large-Scale Biomedical Semantic Indexing and Question Answering. CLEF 2021: 239-263
[c27]
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Anastasia Krithara, Anastasios Nentidis, Georgios Paliouras, Martin Krallinger, Antonio Miranda:
BioASQ at CLEF2021: Large-Scale Biomedical Semantic Indexing and Question Answering. ECIR (2) 2021: 624-630
[c26]
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Antonio Miranda-Escalada, Eulàlia Farré-Maduell, Salvador Lima-López, Luis Gascó, Vicent Brivá-Iglesias, Marvin M. Agüero-Torales, Martin Krallinger:
The ProfNER shared task on automatic recognition of occupation mentions in social media: systems, evaluation, guidelines, embeddings and corpora. SMM4H@NAACL-HLT 2021: 13-20
[c25]
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Arjun Magge, Ari Z. Klein, Antonio Miranda-Escalada, Mohammed Ali Al-Garadi, Ilseyar Alimova, Zulfat Miftahutdinov, Eulàlia Farré, Salvador Lima-López, Ivan Flores, Karen O'Connor, Davy Weissenbacher, Elena Tutubalina, Abeed Sarker, Juan M. Banda, Martin Krallinger, Graciela Gonzalez-Hernandez:
Overview of the Sixth Social Media Mining for Health Applications (#SMM4H) Shared Tasks at NAACL 2021. SMM4H@NAACL-HLT 2021: 21-32
[e3]
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Arjun Magge, Ari Z. Klein, Antonio Miranda-Escalada, Mohammed Ali Al-garadi, Ilseyar Alimova, Zulfat Miftahutdinov, Eulàlia Farré-Maduell, Salvador Lima-López, Ivan Flores, Karen O'Connor, Davy Weissenbacher, Elena Tutubalina, Abeed Sarker, Juan M. Banda, Martin Krallinger, Graciela Gonzalez-Hernandez:
Proceedings of the Sixth Social Media Mining for Health Workshop and Shared Task, SMM4H@NAACL-HLT 2021, Mexico City, Mexico, June 10, 2021. Association for Computational Linguistics 2021, ISBN 978-1-954085-31-2 [contents]
[i4]
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  - journals/corr/abs-2106-14618
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Anastasios Nentidis, Anastasia Krithara, Konstantinos Bougiatiotis, Martin Krallinger, Carlos Rodríguez Penagos, Marta Villegas, Georgios Paliouras:
Overview of BioASQ 2020: The eighth BioASQ challenge on Large-Scale Biomedical Semantic Indexing and Question Answering. CoRR abs/2106.14618 (2021)
[i3]
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  - journals/corr/abs-2106-14885
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Anastasios Nentidis, Georgios Katsimpras, Eirini Vandorou, Anastasia Krithara, Luis Gascó, Martin Krallinger, Georgios Paliouras:
Overview of BioASQ 2021: The ninth BioASQ challenge on Large-Scale Biomedical Semantic Indexing and Question Answering. CoRR abs/2106.14885 (2021)
[i2]
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  - journals/corr/abs-2109-07765
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Casimiro Pio Carrino, Jordi Armengol-Estapé, Ona De Gibert Bonet, Asier Gutiérrez-Fandiño, Aitor Gonzalez-Agirre, Martin Krallinger, Marta Villegas:
Spanish Biomedical Crawled Corpus: A Large, Diverse Dataset for Spanish Biomedical Language Models. CoRR abs/2109.07765 (2021)
2020
[c24]
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Antonio Miranda-Escalada, Aitor Gonzalez-Agirre, Jordi Armengol-Estapé, Martin Krallinger:
Overview of Automatic Clinical Coding: Annotations, Guidelines, and Solutions for non-English Clinical Cases at CodiEsp Track of CLEF eHealth 2020. CLEF (Working Notes) 2020
[c23]
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Anastasios Nentidis, Anastasia Krithara, Konstantinos Bougiatiotis, Martin Krallinger, Carlos Rodríguez Penagos, Marta Villegas, Georgios Paliouras:
Overview of BioASQ 2020: The Eighth BioASQ Challenge on Large-Scale Biomedical Semantic Indexing and Question Answering. CLEF 2020: 194-214
[c22]
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Lorraine Goeuriot, Hanna Suominen, Liadh Kelly, Antonio Miranda-Escalada, Martin Krallinger, Zhengyang Liu, Gabriella Pasi, Gabriela González Sáez, Marco Viviani, Chenchen Xu:
Overview of the CLEF eHealth Evaluation Lab 2020. CLEF 2020: 255-271
[c21]
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Carlos Rodríguez Penagos, Anastasios Nentidis, Aitor Gonzalez-Agirre, Alejandro Asensio, Jordi Armengol-Estapé, Anastasia Krithara, Marta Villegas, Georgios Paliouras, Martin Krallinger:
Overview of MESINESP, a Spanish Medical Semantic Indexing Task within BioASQ 2020. CLEF (Working Notes) 2020
[c20]
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  - conf/ecir/CoutoK20a
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Francisco M. Couto, Martin Krallinger:
Report of the First International Workshop on Semantic Indexing and Information Retrieval for Health from heterogeneous content types and languages. SIIRH@ECIR 2020
[c19]
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Martin Krallinger, Anastasia Krithara, Anastasios Nentidis, Georgios Paliouras, Marta Villegas:
BioASQ at CLEF2020: Large-Scale Biomedical Semantic Indexing and Question Answering. ECIR (2) 2020: 550-556
[c18]
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Hanna Suominen, Liadh Kelly, Lorraine Goeuriot, Martin Krallinger:
CLEF eHealth Evaluation Lab 2020. ECIR (2) 2020: 587-594
[c17]
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Francisco M. Couto, Martin Krallinger:
Proposal of the First International Workshop on Semantic Indexing and Information Retrieval for Health from Heterogeneous Content Types and Languages (SIIRH). ECIR (2) 2020: 654-659
[c16]
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Elizabeth T. Hobbs, Stephen M. Goralski, Ashley Mitchell, Andrew Simpson, Dorjan Leka, Emmanuel Kotey, Matt Sekira, James B. Munro, Suvarna Nadendla, Rebecca Jackson, Aitor Gonzalez-Agirre, Martin Krallinger, Michelle G. Giglio, Ivan Erill:
Corpora as Evolving Entities: Embedding Corpora in Biomedical Ontologies. ICBO/ODLS 2020: 1-11
[c15]
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Antonio Miranda-Escalada, Eulàlia Farré, Martin Krallinger:
Named Entity Recognition, Concept Normalization and Clinical Coding: Overview of the Cantemist Track for Cancer Text Mining in Spanish, Corpus, Guidelines, Methods and Results. IberLEF@SEPLN 2020: 303-323
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Francisco M. Couto, Martin Krallinger:
Proceedings of the Workshop on Semantic Indexing and Information Retrieval for Health from heterogeneous content types and languages co-located with 42nd European Conference on Information Retrieval, SIIRH@ECIR 2020, Lisbon, Portugal, April 14, 2020. CEUR Workshop Proceedings 2619, CEUR-WS.org 2020 [contents]

2010 – 2019

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2019
[j24]
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Martín Pérez-Pérez, Gael Pérez Rodríguez, Aitor Blanco-Míguez, Florentino Fdez-Riverola, Alfonso Valencia, Martin Krallinger, Anália Lourenço:
Next generation community assessment of biomedical entity recognition web servers: metrics, performance, interoperability aspects of BeCalm. J. Cheminformatics 11(1): 42:1-42:16 (2019)
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Aitor Gonzalez-Agirre, Montserrat Marimon, Ander Intxaurrondo, Obdulia Rabal, Marta Villegas, Martin Krallinger:
PharmaCoNER: Pharmacological Substances, Compounds and proteins Named Entity Recognition track. BioNLP-OST@EMNLP-IJNCLP 2019: 1-10
[c13]
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Montserrat Marimon, Aitor Gonzalez-Agirre, Ander Intxaurrondo, Heidy Rodriguez, Jose Lopez Martin, Marta Villegas, Martin Krallinger:
Automatic De-identification of Medical Texts in Spanish: the MEDDOCAN Track, Corpus, Guidelines, Methods and Evaluation of Results. IberLEF@SEPLN 2019: 618-638
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Rachel Bawden, Kevin Bretonnel Cohen, Cristian Grozea, Antonio Jimeno-Yepes, Madeleine Kittner, Martin Krallinger, Nancy Mah, Aurélie Névéol, Mariana L. Neves, Felipe Soares, Amy Siu, Karin Verspoor, Maika Vicente Navarro:
Findings of the WMT 2019 Biomedical Translation Shared Task: Evaluation for MEDLINE Abstracts and Biomedical Terminologies. WMT (3) 2019: 29-53
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Felipe Soares, Martin Krallinger:
BSC Participation in the WMT Translation of Biomedical Abstracts. WMT (3) 2019: 175-178
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Miguel Ángel García Cumbreras, Julio Gonzalo, Eugenio Martínez Cámara, Raquel Martínez-Unanue, Paolo Rosso, Jorge Carrillo-de-Albornoz, Soto Montalvo, Luis Chiruzzo, Sandra Collovini, Yoan Gutiérrez, Salud M. Jiménez-Zafra, Martin Krallinger, Manuel Montes-y-Gómez, Reynier Ortega-Bueno, Aiala Rosá:
Proceedings of the Iberian Languages Evaluation Forum co-located with 35th Conference of the Spanish Society for Natural Language Processing, IberLEF@SEPLN 2019, Bilbao, Spain, September 24th, 2019. CEUR Workshop Proceedings 2421, CEUR-WS.org 2019 [contents]
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Felipe Soares, Martin Krallinger:
BVS Corpus: A Multilingual Parallel Corpus of Biomedical Scientific Texts. CoRR abs/1905.01712 (2019)
2018
[j23]
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Jesus Santamaría, Martin Krallinger:
Construcción de recursos terminológicos médicos para el espa˜nol: el sistema de extracción de términos CUTEXT y los repositorios de términos biomédicos. Proces. del Leng. Natural 61: 49-56 (2018)
[c10]
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Ander Intxaurrondo, Montserrat Marimon, Aitor Gonzalez-Agirre, Jose Antonio López-Martín, Heidy Rodriguez, Jesus Santamaría, Marta Villegas, Martin Krallinger:
Finding Mentions of Abbreviations and Their Definitions in Spanish Clinical Cases: The BARR2 Shared Task Evaluation Results. IberEval@SEPLN 2018: 280-289
2017
[j22]
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Andrés Cañada, Salvador Capella-Gutiérrez, Obdulia Rabal, Julen Oyarzabal, Alfonso Valencia, Martin Krallinger:
LimTox: a web tool for applied text mining of adverse event and toxicity associations of compounds, drugs and genes. Nucleic Acids Res. 45(Webserver-Issue): W484-W489 (2017)
[j21]
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Marta Villegas, Santiago de la Peña, Ander Intxaurrondo, Jesus Santamaría, Martin Krallinger:
Esfuerzos para fomentar la minería de textos en biomedicina más allá del inglés: el plan estratégico nacional español para las tecnologías del lenguaje. Proces. del Leng. Natural 59: 141-144 (2017)
[c9]
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Ander Intxaurrondo, Martín Pérez-Pérez, Gael Pérez Rodríguez, Jose Antonio López-Martín, Jesus Santamaría, Santiago de la Peña, Marta Villegas, Saber Ahmad Akhondi, Alfonso Valencia, Anália Lourenço, Martin Krallinger:
The Biomedical Abbreviation Recognition and Resolution (BARR) Track: Benchmarking, Evaluation and Importance of Abbreviation Recognition Systems Applied to Spanish Biomedical Abstracts. IberEval@SEPLN 2017: 230-246
[c8]
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Ander Intxaurrondo, Martin Krallinger:
CNIO at BARR IberEval 2017: Exploring Three Biomedical Abbreviation Identifiers for Spanish Biomedical Publications. IberEval@SEPLN 2017: 278-285
2016
[j20]
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Martín Pérez-Pérez, Gael Pérez Rodríguez, Obdulia Rabal, Miguel Vazquez, Julen Oyarzabal, Florentino Fdez-Riverola, Alfonso Valencia, Martin Krallinger, Anália Lourenço:
The Markyt visualisation, prediction and benchmark platform for chemical and gene entity recognition at BioCreative/CHEMDNER challenge. Database J. Biol. Databases Curation 2016 (2016)
[c7]
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Jose Camilla Sammartino, Martin Krallinger, Alfonso Valencia:
Annotation Process, Guidelines and Text Corpus of Small Non-Coding RNA Molecules: the MiNCor for MicroRNA Annotations. SMBM 2016: 56-63
2015
[j19]
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Jonathan G. Lees, Jean-Karim Hériché, Ian Morilla, José María Fernández, Priit Adler, Martin Krallinger, Jaak Vilo, Alfonso Valencia, Jan Ellenberg, Juan A. G. Ranea, Christine A. Orengo:
FUN-L: gene prioritization for RNAi screens. Bioinform. 31(12): 2052-2053 (2015)
[j18]
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Martin Krallinger, Florian Leitner, Obdulia Rabal, Miguel Vazquez, Julen Oyarzabal, Alfonso Valencia:
CHEMDNER: The drugs and chemical names extraction challenge. J. Cheminformatics 7(S-1): S1 (2015)
[j17]
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Martin Krallinger, Obdulia Rabal, Florian Leitner, Miguel Vazquez, David Salgado, Zhiyong Lu, Robert Leaman, Yanan Lu, Donghong Ji, Daniel M. Lowe, Roger A. Sayle, Riza Theresa Batista-Navarro, Rafal Rak, Torsten Huber, Tim Rocktäschel, Sérgio Matos, David Campos, Buzhou Tang, Hua Xu, Tsendsuren Munkhdalai, Keun Ho Ryu, S. V. Ramanan, P. Senthil Nathan, Slavko Zitnik, Marko Bajec, Lutz Weber, Matthias Irmer, Saber A. Akhondi, Jan A. Kors, Shuo Xu, Xin An, Utpal Kumar Sikdar, Asif Ekbal, Masaharu Yoshioka, Thaer M. Dieb, Miji Choi, Karin Verspoor, Madian Khabsa, C. Lee Giles, Hongfang Liu, Ravikumar Komandur Elayavilli, Andre Lamurias, Francisco M. Couto, Hong-Jie Dai, Richard Tzong-Han Tsai, Caglar Ata, Tolga Can, Anabel Usie, Rui Alves, Isabel Segura-Bedmar, Paloma Martínez, Julen Oyarzabal, Alfonso Valencia:
The CHEMDNER corpus of chemicals and drugs and its annotation principles. J. Cheminformatics 7(S-1): S2 (2015)
2014
[j16]
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Cecilia N. Arighi, Cathy H. Wu, Kevin Bretonnel Cohen, Lynette Hirschman, Martin Krallinger, Alfonso Valencia, Zhiyong Lu, W. John Wilbur, Thomas C. Wiegers:
BioCreative-IV virtual issue. Database J. Biol. Databases Curation 2014 (2014)
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Martin Krallinger, Florian Leitner, Alfonso Valencia:
Retrieval and Discovery of Cell Cycle Literature and Proteins by Means of Machine Learning, Text Mining and Network Analysis. PACBB 2014: 285-292
2013
[j15]
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Cecilia N. Arighi, Ben Carterette, K. Bretonnel Cohen, Martin Krallinger, W. John Wilbur, Petra Fey, Robert J. Dodson, Laurel Cooper, Ceri E. Van Slyke, Wasila M. Dahdul, Paula M. Mabee, Donghui Li, Bethany R. Harris, Marc Gillespie, Silvia Jimenez, Phoebe M. Roberts, Lisa Matthews, Kevin G. Becker, Harold J. Drabkin, Susan M. Bello, Luana Licata, Andrew Chatr-aryamontri, Mary L. Schaeffer, Julie Park, Melissa A. Haendel, Kimberly Van Auken, Yuling Li, Juancarlos Chan, Hans-Michael Müller, Hong Cui, James P. Balhoff, Chi-Yang Wu, Zhiyong Lu, Chih-Hsuan Wei, Catalina O. Tudor, Kalpana Raja, Suresh Subramani, Jeyakumar Natarajan, Juan Miguel Cejuela, Pratibha Dubey, Cathy H. Wu:
An overview of the BioCreative 2012 Workshop Track III: interactive text mining task. Database J. Biol. Databases Curation 2013 (2013)
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Donald C. Comeau, Rezarta Islamaj Dogan, Paolo Ciccarese, Kevin Bretonnel Cohen, Martin Krallinger, Florian Leitner, Zhiyong Lu, Yifan Peng, Fabio Rinaldi, Manabu Torii, Alfonso Valencia, Karin Verspoor, Thomas C. Wiegers, Cathy H. Wu, W. John Wilbur:
BioC: a minimalist approach to interoperability for biomedical text processing. Database J. Biol. Databases Curation 2013 (2013)
[c5]
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Roser Morante, Martin Krallinger, Alfonso Valencia, Walter Daelemans:
Machine Reading of Biomedical Texts about Alzheimer's Disease. CLEF (Working Notes) 2013
2012
[j13]
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Lynette Hirschman, Gully A. P. C. Burns, Martin Krallinger, Cecilia N. Arighi, K. Bretonnel Cohen, Alfonso Valencia, Cathy H. Wu, Andrew Chatr-aryamontri, Karen G. Dowell, Eva Huala, Anália Lourenço, Robert S. Nash, Anne-Lise Veuthey, Thomas C. Wiegers, Andrew G. Winter:
Text mining for the biocuration workflow. Database J. Biol. Databases Curation 2012 (2012)
[j12]
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Martin Krallinger, Florian Leitner, Miguel Vazquez, David Salgado, Christophe Marcelle, Mike Tyers, Alfonso Valencia, Andrew Chatr-aryamontri:
How to link ontologies and protein-protein interactions to literature: text-mining approaches and the BioCreative experience. Database J. Biol. Databases Curation 2012 (2012)
[j11]
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Cathy H. Wu, Cecilia N. Arighi, Kevin Bretonnel Cohen, Lynette Hirschman, Martin Krallinger, Zhiyong Lu, Carolyn J. Mattingly, Alfonso Valencia, Thomas C. Wiegers, W. John Wilbur:
BioCreative-2012 Virtual Issue. Database J. Biol. Databases Curation 2012 (2012)
[j10]
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David Salgado, Martin Krallinger, Marc Depaule, Elodie Drula, Ashish V. Tendulkar, Florian Leitner, Alfonso Valencia, Christophe Marcelle:
MyMiner: a web application for computer-assisted biocuration and text annotation. Bioinform. 28(17): 2285-2287 (2012)
[c4]
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Roser Morante, Martin Krallinger, Alfonso Valencia, Walter Daelemans:
Machine Reading of Biomedical Texts about Alzheimer's Disease. CLEF (Online Working Notes/Labs/Workshop) 2012
2011
[j9]
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Cecilia N. Arighi, Zhiyong Lu, Martin Krallinger, Kevin Bretonnel Cohen, W. John Wilbur, Alfonso Valencia, Lynette Hirschman, Cathy H. Wu:
Overview of the BioCreative III Workshop. BMC Bioinform. 12(S-8): S1 (2011)
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Martin Krallinger, Miguel Vazquez, Florian Leitner, David Salgado, Andrew Chatr-aryamontri, Andrew G. Winter, Livia Perfetto, Leonardo Briganti, Luana Licata, Marta Iannuccelli, Luisa Castagnoli, Gianni Cesareni, Mike Tyers, Gerold Schneider, Fabio Rinaldi, Robert Leaman, Graciela Gonzalez, Sérgio Matos, Sun Kim, W. John Wilbur, Luis M. Rocha, Hagit Shatkay, Ashish V. Tendulkar, Shashank Agarwal, Feifan Liu, Xinglong Wang, Rafal Rak, Keith Noto, Charles Elkan, Zhiyong Lu:
The Protein-Protein Interaction tasks of BioCreative III: classification/ranking of articles and linking bio-ontology concepts to full text. BMC Bioinform. 12(S-8): S3 (2011)
[j7]
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Cecilia N. Arighi, Phoebe M. Roberts, Shashank Agarwal, Sanmitra Bhattacharya, Gianni Cesareni, Andrew Chatr-aryamontri, Simon Clematide, Pascale Gaudet, Michelle G. Giglio, Ian Harrow, Eva Huala, Martin Krallinger, Ulf Leser, Donghui Li, Feifan Liu, Zhiyong Lu, Lois J. Maltais, Naoaki Okazaki, Livia Perfetto, Fabio Rinaldi, Rune Sætre, David Salgado, Padmini Srinivasan, Philippe E. Thomas, Luca Toldo, Lynette Hirschman, Cathy H. Wu:
BioCreative III interactive task: an overview. BMC Bioinform. 12(S-8): S4 (2011)
2010
[j6]
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Martin Krallinger, Ashish V. Tendulkar, Florian Leitner, Andrew Chatr-aryamontri, Alfonso Valencia:
The PPI affix dictionary (PPIAD) and BioMethod Lexicon: importance of affixes and tags for recognition of entity mentions and experimental protein interactions. BMC Bioinform. 11(S-5): O1 (2010)
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Florian Leitner, Scott A. Mardis, Martin Krallinger, Gianni Cesareni, Lynette Hirschman, Alfonso Valencia:
An Overview of BioCreative II.5. IEEE ACM Trans. Comput. Biol. Bioinform. 7(3): 385-399 (2010)
[c3]
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Martin Krallinger:
Importance of negations and experimental qualifiers in biomedical literature. NeSp-NLP@ACL 2010: 46-49

2000 – 2009

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2009
[j4]
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Martin Krallinger, José M. G. Izarzugaza, Carlos Rodríguez Penagos, Alfonso Valencia:
Extraction of human kinase mutations from literature, databases and genotyping studies. BMC Bioinform. 10(S-8): 1 (2009)
[j3]
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Martin Krallinger, Carlos Rodríguez Penagos, Ashish V. Tendulkar, Alfonso Valencia:
PLAN2L: a web tool for integrated text mining and literature-based bioentity relation extraction. Nucleic Acids Res. 37(Web-Server-Issue): 160-165 (2009)
2006
[c2]
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Helen L. Johnson, William A. Baumgartner Jr., Martin Krallinger, K. Bretonnel Cohen, Lawrence Hunter:
Refactoring Corpora. BioNLP@NAACL-HLT 2006: 116-117
2005
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Christian Blaschke, Eduardo Andrés León, Martin Krallinger, Alfonso Valencia:
Evaluation of BioCreAtIvE assessment of task 2. BMC Bioinform. 6(S-1) (2005)
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Martin Krallinger, Maria Padron, Alfonso Valencia:
A sentence sliding window approach to extract protein annotations from biomedical articles. BMC Bioinform. 6(S-1) (2005)
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Martin Krallinger, Alfonso Valencia:
Applications of Text Mining in Molecular Biology, from Name Recognition to Protein Interaction Maps. Data Analysis and Visualization in Genomics and Proteomics 2005: 41-59
2004
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Martin Krallinger, Maria Padron, Christian Blaschke, Alfonso Valencia:
Assessing the Correlation between Contextual Patterns and Biological Entity Tagging. NLPBA/BioNLP 2004

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