Publications by authors named "Sampo Pyysalo"

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Annotated textual dataset PV600 of perovskite bandgaps for information extraction from literature.
Matilda Sipilä, Farrokh Mehryary, Sampo Pyysalo, Filip Ginter, Milica Todorović

Sci Data· August 2025

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The STRING database in 2025: protein networks with directionality of regulation.
Damian Szklarczyk, Katerina Nastou, Mikaela Koutrouli, Rebecca Kirsch, Farrokh Mehryary, Sampo Pyysalo

Nucleic Acids Res· January 2025

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LSD600: the first corpus of biomedical abstracts annotated with lifestyle-disease relations.
Esmaeil Nourani, Evangelia-Mantelena Makri, Xiqing Mao, Sampo Pyysalo, Søren Brunak

Database (Oxford)· January 2025

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Lifestyle factors in the biomedical literature: an ontology and comprehensive resources for named entity recognition.
Esmaeil Nourani, Mikaela Koutrouli, Yijia Xie, Danai Vagiaki, Sampo Pyysalo

Bioinformatics· November 2024

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Improving dictionary-based named entity recognition with deep learning.
Katerina Nastou, Mikaela Koutrouli, Sampo Pyysalo, Lars Juhl Jensen

Bioinformatics· September 2024

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RegulaTome: a corpus of typed, directed, and signed relations between biomedical entities in the scientific literature.
Katerina Nastou, Farrokh Mehryary, Tomoko Ohta, Jouni Luoma, Sampo Pyysalo

Database (Oxford)· September 2024

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STRING-ing together protein complexes: corpus and methods for extracting physical protein interactions from the biomedical literature.
Farrokh Mehryary, Katerina Nastou, Tomoko Ohta, Lars Juhl Jensen, Sampo Pyysalo

Bioinformatics· September 2024

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CoNECo: a Corpus for Named Entity recognition and normalization of protein Complexes.
Katerina Nastou, Mikaela Koutrouli, Sampo Pyysalo, Lars Juhl Jensen

Bioinform Adv· August 2024

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Overview of DrugProt task at BioCreative VII: data and methods for large-scale text mining and knowledge graph generation of heterogenous chemical-protein relations.
Antonio Miranda-Escalada, Farrokh Mehryary, Jouni Luoma, Darryl Estrada-Zavala, Luis Gasco, Sampo Pyysalo

Database (Oxford)· November 2023

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S1000: a better taxonomic name corpus for biomedical information extraction.
Jouni Luoma, Katerina Nastou, Tomoko Ohta, Harttu Toivonen, Evangelos Pafilis, Sampo Pyysalo

Bioinformatics· June 2023

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The STRING database in 2023: protein-protein association networks and functional enrichment analyses for any sequenced genome of interest.
Damian Szklarczyk, Rebecca Kirsch, Mikaela Koutrouli, Katerina Nastou, Farrokh Mehryary, Sampo Pyysalo

Nucleic Acids Res· January 2023

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Correction to 'The STRING database in 2021: customizable protein-protein networks, and functional characterization of user-uploaded gene/measurement sets'.
Damian Szklarczyk, Annika L Gable, Katerina C Nastou, David Lyon, Rebecca Kirsch, Sampo Pyysalo

Nucleic Acids Res· October 2021

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The STRING database in 2021: customizable protein-protein networks, and functional characterization of user-uploaded gene/measurement sets.
Damian Szklarczyk, Annika L Gable, Katerina C Nastou, David Lyon, Rebecca Kirsch, Sampo Pyysalo

Nucleic Acids Res· January 2021

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Dependency parsing of biomedical text with BERT.
Jenna Kanerva, Filip Ginter, Sampo Pyysalo

BMC Bioinformatics· December 2020

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LION LBD: a literature-based discovery system for cancer biology.
Sampo Pyysalo, Simon Baker, Imran Ali, Stefan Haselwimmer, Tejas Shah

Bioinformatics· May 2019

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A neural classification method for supporting the creation of BioVerbNet.
Billy Chiu, Olga Majewska, Sampo Pyysalo, Laura Wey, Ulla Stenius

J Biomed Semantics· January 2019

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Neural networks for link prediction in realistic biomedical graphs: a multi-dimensional evaluation of graph embedding-based approaches.
Gamal Crichton, Yufan Guo, Sampo Pyysalo, Anna Korhonen

BMC Bioinformatics· May 2018

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Bio-SimVerb and Bio-SimLex: wide-coverage evaluation sets of word similarity in biomedicine.
Billy Chiu, Sampo Pyysalo, Ivan Vulić, Anna Korhonen

BMC Bioinformatics· February 2018

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Cancer Hallmarks Analytics Tool (CHAT): a text mining approach to organize and evaluate scientific literature on cancer.
Simon Baker, Imran Ali, Ilona Silins, Sampo Pyysalo, Yufan Guo

Bioinformatics· December 2017

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A neural network multi-task learning approach to biomedical named entity recognition.
Gamal Crichton, Sampo Pyysalo, Billy Chiu, Anna Korhonen

BMC Bioinformatics· August 2017

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Overview of the Cancer Genetics and Pathway Curation tasks of BioNLP Shared Task 2013.
Sampo Pyysalo, Tomoko Ohta, Rafal Rak, Andrew Rowley, Hong-Woo Chun

BMC Bioinformatics· February 2016

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Cell line name recognition in support of the identification of synthetic lethality in cancer from text.
Suwisa Kaewphan, Sofie Van Landeghem, Tomoko Ohta, Yves Van de Peer, Filip Ginter, Sampo Pyysalo

Bioinformatics· January 2016

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Generalising semantic category disambiguation with large lexical resources for fun and profit.
Pontus Stenetorp, Sampo Pyysalo, Sophia Ananiadou, Jun'ichi Tsujii

J Biomed Semantics· August 2014

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Anatomical entity mention recognition at literature scale.
Sampo Pyysalo, Sophia Ananiadou

Bioinformatics· March 2014

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A method for integrating and ranking the evidence for biochemical pathways by mining reactions from text.
Makoto Miwa, Tomoko Ohta, Rafal Rak, Andrew Rowley, Douglas B Kell, Sampo Pyysalo

Bioinformatics· July 2013

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