Martin Krallinger

93 papers Misc 1Journal 42Unranked 46
YearRankTypeTitle / Venue / Authors
2026 — conf
BioASQ at CLEF2026: The Fourteenth Edition of the Large-Scale Biomedical Semantic Indexing and Question Answering Challenge.
ECIR (4)
Anastasios Nentidis, Georgios Katsimpras, Anastasia Krithara, Martin Krallinger, Miguel Rodríguez-Ortega, Eduard Rodriguez-López, Natalia V. Loukachevitch, Igor Rozhkov, Elena Tutubalina, Grigorios Tsoumakas, George Giannakoulas, Dimitris Dimitriadis, Alexandra Bekiaridou, Athanasios Samaras, Vasiliki Patsiou, Giorgio Maria Di Nunzio, Nicola Ferro, Stefano Marchesin, Marco Martinelli, Gianmaria Silvello, Georgios Paliouras
2026 J jnl
SynCABEL: Synthetic Contextualized Augmentation for Biomedical Entity Linking.
CoRR
Adam Remaki, Christel Gérardin, Eulàlia Farré-Maduell, Martin Krallinger, Xavier Tannier
2025 — conf
BioASQ at CLEF2025: The Thirteenth Edition of the Large-Scale Biomedical Semantic Indexing and Question Answering Challenge.
ECIR (5)
Anastasios Nentidis, Georgios Katsimpras, Anastasia Krithara, Martin Krallinger, Miguel Rodríguez-Ortega, Natalia V. Loukachevitch, Andrey Sakhovskiy, Elena Tutubalina, Grigorios Tsoumakas, George Giannakoulas, Alexandra Bekiaridou, Athanasios Samaras, Giorgio Maria Di Nunzio, Nicola Ferro, Stefano Marchesin, Laura Menotti, Gianmaria Silvello, Georgios Paliouras
2025 J jnl
Overview of BioASQ 2024: The twelfth BioASQ challenge on Large-Scale Biomedical Semantic Indexing and Question Answering.
CoRR
Anastasios Nentidis, Georgios Katsimpras, Anastasia Krithara, Salvador Lima-López, Eulàlia Farré-Maduell, Martin Krallinger, Natalia V. Loukachevitch, Vera Davydova, Elena Tutubalina, Georgios Paliouras
2025 — conf
Overview of BioASQ 2025: The Thirteenth BioASQ Challenge on Large-Scale Biomedical Semantic Indexing and Question Answering.
CLEF
Anastasios Nentidis, Georgios Katsimpras, Anastasia Krithara, Martin Krallinger, Miguel Rodríguez-Ortega, Eduard Rodriguez-López, Natalia V. Loukachevitch, Andrey Sakhovskiy, Elena Tutubalina, Dimitris Dimitriadis, Grigorios Tsoumakas, George Giannakoulas, Alexandra Bekiaridou, Athanasios Samaras, Giorgio Maria Di Nunzio, Nicola Ferro, Stefano Marchesin, Marco Martinelli, Gianmaria Silvello, Georgios Paliouras
2025 J jnl
Overview of BioASQ 2025: The Thirteenth BioASQ Challenge on Large-Scale Biomedical Semantic Indexing and Question Answering.
CoRR
Anastasios Nentidis, Georgios Katsimpras, Anastasia Krithara, Martin Krallinger, Miguel Rodríguez-Ortega, Eduard Rodriguez-López, Natalia V. Loukachevitch, Andrey Sakhovskiy, Elena Tutubalina, Dimitris Dimitriadis, Grigorios Tsoumakas, George Giannakoulas, Alexandra Bekiaridou, Athanasios Samaras, Giorgio Maria Di Nunzio, Nicola Ferro, Stefano Marchesin, Marco Martinelli, Gianmaria Silvello, Georgios Paliouras
2025 — conf
Overview of MultiClinSum Task at BioASQ 2025: Evaluation of Clinical Case Summarization Strategies for Multiple Languages: Data, Evaluation, Resources and Results.
CLEF (Working Notes)
Miguel Rodríguez-Ortega, Eduard Rodriguez-López, Salvador Lima-López, Carlos Escolano, Audrey Mash, Maite Melero, Lorenzo Pratesi, Laura Vigil-Gimenez, Leticia Fernandez-Lopez, Eulàlia Farré-Maduell, Martin Krallinger
2024 — conf
BioASQ at CLEF2024: The Twelfth Edition of the Large-Scale Biomedical Semantic Indexing and Question Answering Challenge.
ECIR (5)
Anastasios Nentidis, Anastasia Krithara, Georgios Paliouras, Martin Krallinger, Luis Gascó Sánchez, Salvador Lima-López, Eulàlia Farré, Natalia V. Loukachevitch, Vera Davydova, Elena Tutubalina
2024 — conf
ClinLinker: Medical Entity Linking of Clinical Concept Mentions in Spanish.
ICCS (5)
Fernando Gallego Donoso, Guillermo López-García, Luis Gascó Sánchez, Martin Krallinger, Francisco J. Veredas
2024 J jnl
ClinLinker: Medical Entity Linking of Clinical Concept Mentions in Spanish.
CoRR
Fernando Gallego Donoso, Guillermo López-García, Luis Gascó Sánchez, Martin Krallinger, Francisco J. Veredas
2024 J jnl
Exploring the Potential of Neural Machine Translation for Cross-Language Clinical Natural Language Processing (NLP) Resource Generation through Annotation Projection.
Inf.
Jan Rodríguez-Miret, Eulàlia Farré-Maduell, Salvador Lima-López, Laura Vigil, Vicent Brivá-Iglesias, Martin Krallinger
2024 — conf
Overview of BioASQ 2024: The Twelfth BioASQ Challenge on Large-Scale Biomedical Semantic Indexing and Question Answering.
CLEF (2)
Anastasios Nentidis, Georgios Katsimpras, Anastasia Krithara, Salvador Lima-López, Eulàlia Farré-Maduell, Martin Krallinger, Natalia V. Loukachevitch, Vera Davydova, Elena Tutubalina, Georgios Paliouras
2024 — conf
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)
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
2024 — conf
Overview of the MEDIQA-M3G 2024 Shared Task on Multilingual Multimodal Medical Answer Generation.
ClinicalNLP@NAACL
Wen-Wai Yim, Asma Ben Abacha, Yujuan Fu, Zhaoyi Sun, Fei Xia, Meliha Yetisgen, Martin Krallinger
2023 — conf
BioASQ at CLEF2023: The Eleventh Edition of the Large-Scale Biomedical Semantic Indexing and Question Answering Challenge.
ECIR (3)
Anastasios Nentidis, Anastasia Krithara, Georgios Paliouras, Eulàlia Farré-Maduell, Salvador Lima-López, Martin Krallinger
2023 J jnl
MEDDOPLACE Shared Task overview: recognition, normalization and classification of locations and patient movement in clinical texts.
Proces. del Leng. Natural
Salvador Lima-López, Eulàlia Farré-Maduell, Vicent Brivá-Iglesias, Luis Gascó Sánchez, Martin Krallinger
2023 — conf
Overview of BioASQ 2023: The Eleventh BioASQ Challenge on Large-Scale Biomedical Semantic Indexing and Question Answering.
CLEF
Anastasios Nentidis, Georgios Katsimpras, Anastasia Krithara, Salvador Lima-López, Eulàlia Farré-Maduell, Luis Gascó, Martin Krallinger, Georgios Paliouras
2023 J jnl
Overview of BioASQ 2023: The eleventh BioASQ challenge on Large-Scale Biomedical Semantic Indexing and Question Answering.
CoRR
Anastasios Nentidis, Georgios Katsimpras, Anastasia Krithara, Salvador Lima-López, Eulàlia Farré-Maduell, Luis Gascó, Martin Krallinger, Georgios Paliouras
2023 J jnl
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
Antonio Miranda-Escalada, Farrokh Mehryary, Jouni Luoma, Darryl Estrada-Zavala, Luis Gascó, Sampo Pyysalo, Alfonso Valencia, Martin Krallinger
2023 — conf
Overview of MedProcNER Task on Medical Procedure Detection and Entity Linking at BioASQ 2023.
CLEF (Working Notes)
Salvador Lima-López, Eulàlia Farré-Maduell, Luis Gascó, Anastasios Nentidis, Anastasia Krithara, Georgios Katsimpras, Georgios Paliouras, Martin Krallinger
2022 — conf
BioASQ at CLEF2022: The Tenth Edition of the Large-scale Biomedical Semantic Indexing and Question Answering Challenge.
ECIR (2)
Anastasios Nentidis, Anastasia Krithara, Georgios Paliouras, Luis Gascó, Martin Krallinger
2022 J jnl
Challenges and opportunities for mining adverse drug reactions: perspectives from pharma, regulatory agencies, healthcare providers and consumers.
Database J. Biol. Databases Curation
Graciela Gonzalez-Hernandez, Martin Krallinger, Monica A. Muñoz, Raul Rodriguez-Esteban, Özlem Uzuner, Lynette Hirschman
2022 — conf
Findings of the WMT 2022 Biomedical Translation Shared Task: Monolingual Clinical Case Reports.
WMT
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
2022 J jnl
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
Antonio Miranda-Escalada, Eulàlia Farré-Maduell, Salvador Lima-López, Darryl Estrada, Luis Gascó, Martin Krallinger
2022 — conf
Overview of BioASQ 2022: The Tenth BioASQ Challenge on Large-Scale Biomedical Semantic Indexing and Question Answering.
CLEF
Anastasios Nentidis, Georgios Katsimpras, Eirini Vandorou, Anastasia Krithara, Antonio Miranda-Escalada, Luis Gascó, Martin Krallinger, Georgios Paliouras
2022 J jnl
Overview of BioASQ 2022: The tenth BioASQ challenge on Large-Scale Biomedical Semantic Indexing and Question Answering.
CoRR
Anastasios Nentidis, Georgios Katsimpras, Eirini Vandorou, Anastasia Krithara, Antonio Miranda-Escalada, Luis Gascó, Martin Krallinger, Georgios Paliouras
2022 — conf
Overview of DisTEMIST at BioASQ: Automatic detection and normalization of diseases from clinical texts: results, methods, evaluation and multilingual resources.
CLEF (Working Notes)
Antonio Miranda-Escalada, Luis Gascó, Salvador Lima-López, Eulàlia Farré-Maduell, Darryl Estrada, Anastasios Nentidis, Anastasia Krithara, Georgios Katsimpras, Georgios Paliouras, Martin Krallinger
2022 J jnl
Overview of the COVID-19 text mining tool interactive demonstration track in BioCreative VII.
Database J. Biol. Databases Curation
Andrew Chatr-aryamontri, Lynette Hirschman, Karen E. Ross, Rose Oughtred, Martin Krallinger, Kara Dolinski, Mike Tyers, Tonia Korves, Cecilia N. Arighi
2022 — conf
Overview of the Seventh Social Media Mining for Health Applications (#SMM4H) Shared Tasks at COLING 2022.
SMM4H@COLING
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
2022 — conf
The SocialDisNER shared task on detection of disease mentions in health-relevant content from social media: methods, evaluation, guidelines and corpora.
SMM4H@COLING
Luis Gascó Sánchez, Darryl Estrada-Zavala, Eulàlia Farré-Maduell, Salvador Lima-López, Antonio Miranda-Escalada, Martin Krallinger
2021 — conf
BioASQ at CLEF2021: Large-Scale Biomedical Semantic Indexing and Question Answering.
ECIR (2)
Anastasia Krithara, Anastasios Nentidis, Georgios Paliouras, Martin Krallinger, Antonio Miranda
2021 J jnl
ECO-CollecTF: A Corpus of Annotated Evidence-Based Assertions in Biomedical Manuscripts.
Frontiers Res. Metrics Anal.
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
2021 J jnl
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
Salvador Lima-López, Eulàlia Farré-Maduell, Antonio Miranda-Escalada, Vicent Brivá-Iglesias, Martin Krallinger
2021 J jnl
Overview of BioASQ 2020: The eighth BioASQ challenge on Large-Scale Biomedical Semantic Indexing and Question Answering.
CoRR
Anastasios Nentidis, Anastasia Krithara, Konstantinos Bougiatiotis, Martin Krallinger, Carlos Rodríguez Penagos, Marta Villegas, Georgios Paliouras
2021 — conf
Overview of BioASQ 2021-MESINESP track. Evaluation of advance hierarchical classification techniques for scientific literature, patents and clinical trials.
CLEF (Working Notes)
Luis Gascó, Anastasios Nentidis, Anastasia Krithara, Darryl Estrada-Zavala, Renato Toshiyuki Murasaki, Elena Primo-Peña, Cristina Bojo-Canales, Georgios Paliouras, Martin Krallinger
2021 — conf
Overview of BioASQ 2021: The Ninth BioASQ Challenge on Large-Scale Biomedical Semantic Indexing and Question Answering.
CLEF
Anastasios Nentidis, Georgios Katsimpras, Eirini Vandorou, Anastasia Krithara, Luis Gascó, Martin Krallinger, Georgios Paliouras
2021 J jnl
Overview of BioASQ 2021: The ninth BioASQ challenge on Large-Scale Biomedical Semantic Indexing and Question Answering.
CoRR
Anastasios Nentidis, Georgios Katsimpras, Eirini Vandorou, Anastasia Krithara, Luis Gascó, Martin Krallinger, Georgios Paliouras
2021 — conf
Overview of the Sixth Social Media Mining for Health Applications (#SMM4H) Shared Tasks at NAACL 2021.
SMM4H@NAACL-HLT
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
2021 — ed.
Proceedings of the Sixth Social Media Mining for Health Workshop and Shared Task, SMM4H@NAACL-HLT 2021, Mexico City, Mexico, June 10, 2021
SMM4H@NAACL-HLT
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
2021 J jnl
Spanish Biomedical Crawled Corpus: A Large, Diverse Dataset for Spanish Biomedical Language Models.
CoRR
Casimiro Pio Carrino, Jordi Armengol-Estapé, Ona De Gibert Bonet, Asier Gutiérrez-Fandiño, Aitor Gonzalez-Agirre, Martin Krallinger, Marta Villegas
2021 — conf
The ProfNER shared task on automatic recognition of occupation mentions in social media: systems, evaluation, guidelines, embeddings and corpora.
SMM4H@NAACL-HLT
Antonio Miranda-Escalada, Eulàlia Farré-Maduell, Salvador Lima-López, Luis Gascó, Vicent Brivá-Iglesias, Marvin M. Agüero-Torales, Martin Krallinger
2020 — conf
BioASQ at CLEF2020: Large-Scale Biomedical Semantic Indexing and Question Answering.
ECIR (2)
Martin Krallinger, Anastasia Krithara, Anastasios Nentidis, Georgios Paliouras, Marta Villegas
2020 — conf
CLEF eHealth Evaluation Lab 2020.
ECIR (2)
Hanna Suominen, Liadh Kelly, Lorraine Goeuriot, Martin Krallinger
2020 — conf
Corpora as Evolving Entities: Embedding Corpora in Biomedical Ontologies.
ICBO/ODLS
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
2020 — conf
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
Antonio Miranda-Escalada, Eulàlia Farré, Martin Krallinger
2020 — conf
Overview of Automatic Clinical Coding: Annotations, Guidelines, and Solutions for non-English Clinical Cases at CodiEsp Track of CLEF eHealth 2020.
CLEF (Working Notes)
Antonio Miranda-Escalada, Aitor Gonzalez-Agirre, Jordi Armengol-Estapé, Martin Krallinger
2020 — conf
Overview of BioASQ 2020: The Eighth BioASQ Challenge on Large-Scale Biomedical Semantic Indexing and Question Answering.
CLEF
Anastasios Nentidis, Anastasia Krithara, Konstantinos Bougiatiotis, Martin Krallinger, Carlos Rodríguez Penagos, Marta Villegas, Georgios Paliouras
2020 — conf
Overview of MESINESP, a Spanish Medical Semantic Indexing Task within BioASQ 2020.
CLEF (Working Notes)
Carlos Rodríguez Penagos, Anastasios Nentidis, Aitor Gonzalez-Agirre, Alejandro Asensio, Jordi Armengol-Estapé, Anastasia Krithara, Marta Villegas, Georgios Paliouras, Martin Krallinger
2020 — conf
Overview of the CLEF eHealth Evaluation Lab 2020.
CLEF
Lorraine Goeuriot, Hanna Suominen, Liadh Kelly, Antonio Miranda-Escalada, Martin Krallinger, Zhengyang Liu, Gabriella Pasi, Gabriela González Sáez, Marco Viviani, Chenchen Xu
2020 — ed.
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.
SIIRH@ECIR
Francisco M. Couto, Martin Krallinger
2020 — conf
Proposal of the First International Workshop on Semantic Indexing and Information Retrieval for Health from Heterogeneous Content Types and Languages (SIIRH).
ECIR (2)
Francisco M. Couto, Martin Krallinger
2020 — conf
Report of the First International Workshop on Semantic Indexing and Information Retrieval for Health from heterogeneous content types and languages.
SIIRH@ECIR
Francisco M. Couto, Martin Krallinger
2019 — conf
Automatic De-identification of Medical Texts in Spanish: the MEDDOCAN Track, Corpus, Guidelines, Methods and Evaluation of Results.
IberLEF@SEPLN
Montserrat Marimon, Aitor Gonzalez-Agirre, Ander Intxaurrondo, Heidy Rodriguez, Jose Lopez Martin, Marta Villegas, Martin Krallinger
2019 — conf
BSC Participation in the WMT Translation of Biomedical Abstracts.
WMT (3)
Felipe Soares, Martin Krallinger
2019 J jnl
BVS Corpus: A Multilingual Parallel Corpus of Biomedical Scientific Texts.
CoRR
Felipe Soares, Martin Krallinger
2019 — conf
Findings of the WMT 2019 Biomedical Translation Shared Task: Evaluation for MEDLINE Abstracts and Biomedical Terminologies.
WMT (3)
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
2019 J jnl
Next generation community assessment of biomedical entity recognition web servers: metrics, performance, interoperability aspects of BeCalm.
J. Cheminformatics
Martín Pérez-Pérez, Gael Pérez Rodríguez, Aitor Blanco-Míguez, Florentino Fdez-Riverola, Alfonso Valencia, Martin Krallinger, Anália Lourenço
2019 — conf
PharmaCoNER: Pharmacological Substances, Compounds and proteins Named Entity Recognition track.
BioNLP-OST@EMNLP-IJNCLP
Aitor Gonzalez-Agirre, Montserrat Marimon, Ander Intxaurrondo, Obdulia Rabal, Marta Villegas, Martin Krallinger
2019 — ed.
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.
IberLEF@SEPLN
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
2018 J jnl
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
Jesus Santamaría, Martin Krallinger
2018 — conf
Finding Mentions of Abbreviations and Their Definitions in Spanish Clinical Cases: The BARR2 Shared Task Evaluation Results.
IberEval@SEPLN
Ander Intxaurrondo, Montserrat Marimon, Aitor Gonzalez-Agirre, Jose Antonio López-Martín, Heidy Rodriguez, Jesus Santamaría, Marta Villegas, Martin Krallinger
2017 — conf
CNIO at BARR IberEval 2017: Exploring Three Biomedical Abbreviation Identifiers for Spanish Biomedical Publications.
IberEval@SEPLN
Ander Intxaurrondo, Martin Krallinger
2017 J jnl
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
Marta Villegas, Santiago de la Peña, Ander Intxaurrondo, Jesus Santamaría, Martin Krallinger
2017 J jnl
LimTox: a web tool for applied text mining of adverse event and toxicity associations of compounds, drugs and genes.
Nucleic Acids Res.
Andrés Cañada, Salvador Capella-Gutiérrez, Obdulia Rabal, Julen Oyarzabal, Alfonso Valencia, Martin Krallinger
2017 — conf
The Biomedical Abbreviation Recognition and Resolution (BARR) Track: Benchmarking, Evaluation and Importance of Abbreviation Recognition Systems Applied to Spanish Biomedical Abstracts.
IberEval@SEPLN
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
2016 — conf
Annotation Process, Guidelines and Text Corpus of Small Non-Coding RNA Molecules: the MiNCor for MicroRNA Annotations.
SMBM
Jose Camilla Sammartino, Martin Krallinger, Alfonso Valencia
2016 J jnl
The Markyt visualisation, prediction and benchmark platform for chemical and gene entity recognition at BioCreative/CHEMDNER challenge.
Database J. Biol. Databases Curation
Martín Pérez-Pérez, Gael Pérez Rodríguez, Obdulia Rabal, Miguel Vazquez, Julen Oyarzabal, Florentino Fdez-Riverola, Alfonso Valencia, Martin Krallinger, Anália Lourenço
2015 J jnl
CHEMDNER: The drugs and chemical names extraction challenge.
J. Cheminformatics
Martin Krallinger, Florian Leitner, Obdulia Rabal, Miguel Vazquez, Julen Oyarzabal, Alfonso Valencia
2015 J jnl
FUN-L: gene prioritization for RNAi screens.
Bioinform.
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
2015 J jnl
The CHEMDNER corpus of chemicals and drugs and its annotation principles.
J. Cheminformatics
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
2014 J jnl
BioCreative-IV virtual issue.
Database J. Biol. Databases Curation
Cecilia N. Arighi, Cathy H. Wu, Kevin Bretonnel Cohen, Lynette Hirschman, Martin Krallinger, Alfonso Valencia, Zhiyong Lu, W. John Wilbur, Thomas C. Wiegers
2014 Misc conf
Retrieval and Discovery of Cell Cycle Literature and Proteins by Means of Machine Learning, Text Mining and Network Analysis.
PACBB
Martin Krallinger, Florian Leitner, Alfonso Valencia
2013 J jnl
An overview of the BioCreative 2012 Workshop Track III: interactive text mining task.
Database J. Biol. Databases Curation
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
2013 J jnl
BioC: a minimalist approach to interoperability for biomedical text processing.
Database J. Biol. Databases Curation
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
2013 — conf
Machine Reading of Biomedical Texts about Alzheimer's Disease.
CLEF (Working Notes)
Roser Morante, Martin Krallinger, Alfonso Valencia, Walter Daelemans
2012 J jnl
BioCreative-2012 Virtual Issue.
Database J. Biol. Databases Curation
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
2012 J jnl
How to link ontologies and protein-protein interactions to literature: text-mining approaches and the BioCreative experience.
Database J. Biol. Databases Curation
Martin Krallinger, Florian Leitner, Miguel Vazquez, David Salgado, Christophe Marcelle, Mike Tyers, Alfonso Valencia, Andrew Chatr-aryamontri
2012 — conf
Machine Reading of Biomedical Texts about Alzheimer's Disease.
CLEF (Online Working Notes/Labs/Workshop)
Roser Morante, Martin Krallinger, Alfonso Valencia, Walter Daelemans
2012 J jnl
MyMiner: a web application for computer-assisted biocuration and text annotation.
Bioinform.
David Salgado, Martin Krallinger, Marc Depaule, Elodie Drula, Ashish V. Tendulkar, Florian Leitner, Alfonso Valencia, Christophe Marcelle
2012 J jnl
Text mining for the biocuration workflow.
Database J. Biol. Databases Curation
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
2011 J jnl
BioCreative III interactive task: an overview.
BMC Bioinform.
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
2011 J jnl
Overview of the BioCreative III Workshop.
BMC Bioinform.
Cecilia N. Arighi, Zhiyong Lu, Martin Krallinger, Kevin Bretonnel Cohen, W. John Wilbur, Alfonso Valencia, Lynette Hirschman, Cathy H. Wu
2011 J jnl
The Protein-Protein Interaction tasks of BioCreative III: classification/ranking of articles and linking bio-ontology concepts to full text.
BMC Bioinform.
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
2010 J jnl
An Overview of BioCreative II.5.
IEEE ACM Trans. Comput. Biol. Bioinform.
Florian Leitner, Scott A. Mardis, Martin Krallinger, Gianni Cesareni, Lynette Hirschman, Alfonso Valencia
2010 — conf
Importance of negations and experimental qualifiers in biomedical literature.
NeSp-NLP@ACL
Martin Krallinger
2010 J jnl
The PPI affix dictionary (PPIAD) and BioMethod Lexicon: importance of affixes and tags for recognition of entity mentions and experimental protein interactions.
BMC Bioinform.
Martin Krallinger, Ashish V. Tendulkar, Florian Leitner, Andrew Chatr-aryamontri, Alfonso Valencia
2009 J jnl
Extraction of human kinase mutations from literature, databases and genotyping studies.
BMC Bioinform.
Martin Krallinger, José M. G. Izarzugaza, Carlos Rodríguez Penagos, Alfonso Valencia
2009 J jnl
PLAN2L: a web tool for integrated text mining and literature-based bioentity relation extraction.
Nucleic Acids Res.
Martin Krallinger, Carlos Rodríguez Penagos, Ashish V. Tendulkar, Alfonso Valencia
2006 — conf
Refactoring Corpora.
BioNLP@NAACL-HLT
Helen L. Johnson, William A. Baumgartner Jr., Martin Krallinger, K. Bretonnel Cohen, Lawrence Hunter
2005 J jnl
A sentence sliding window approach to extract protein annotations from biomedical articles.
BMC Bioinform.
Martin Krallinger, Maria Padron, Alfonso Valencia
2005 — ch.
Applications of Text Mining in Molecular Biology, from Name Recognition to Protein Interaction Maps.
Data Analysis and Visualization in Genomics and Proteomics
Martin Krallinger, Alfonso Valencia
2005 J jnl
Evaluation of BioCreAtIvE assessment of task 2.
BMC Bioinform.
Christian Blaschke, Eduardo Andrés León, Martin Krallinger, Alfonso Valencia
2004 — conf
Assessing the Correlation between Contextual Patterns and Biological Entity Tagging.
NLPBA/BioNLP
Martin Krallinger, Maria Padron, Christian Blaschke, Alfonso Valencia