BioCreative VII

Overview

BioCreative VII

Programme: Independent Projects

SEEK ID: https://fairdomhub.org/projects/259

Public web page: Not specified

Organisms: No Organisms specified

FAIRDOM PALs: No PALs for this Project

Project created: 11th Oct 2021

Related items

Sucheta Ghosh

Projects: COVID-19 Disease Map, BioCreative VII

Institutions: Heidelberg Institute for Theoretical Studies (HITS gGmbH)

https://orcid.org/0000-0002-2896-4552
Bettina Heinlein

Projects: BioCreative VII

Institutions: Heidelberg Institute for Theoretical Studies (HITS gGmbH)

Olga Krebs adminproject_administratorasset_housekeeperasset_gatekeeperprogramme_administrator

Projects: SysMO DB, FAIRDOM, ICYSB 2015 - International Practical Course in Systems Biology, ZucAt, SysMO-LAB, Kinetics on the move - Workshop 2016, Example use cases, FAIRDOM user meeting, ErasysApp Funders, EraCoBiotech 2 nd call proposal preparation, Service to URV Tarragona, Spain with respect to their Safety Assessment of Endocrine Disrupting Chemicals model (Active NOW), FAIRDOM & LiSyM & de.NBI Data Structuring Training, MESI-STRAT, INCOME, Multiscale modelling of state transitions in the host-microbiome-brain network, BESTER, TRALAMINOL, Sustainable co-production, INDIE - Biotechnological production of sustainable indole, Extremophiles metabolsim, PoLiMeR - Polymers in the Liver: Metabolism and Regulation, GB-XMap: Assessing the risk of gut-brain cross-diseases Investigating the gut-brain-axis, NAD COMPARTMENTATION, HOTSOLUTE, Stress granules, FAIRDOM Community Workers, GMDS Project Group "FAIRe Dateninfrastrukturen für die Biomedizinische Informatik", Mechanism based modeling viral disease ( COVID-19 ) dynamics in human population, COVID-19 Disease Map, AquaHealth (ERA-BlueBio), LiSyM Core Infrastructure and Management (LiSyM-PD), Early Metabolic Injury (LiSyM-EMI - Pillar I), Regeneration and Repair in Acute-on-Chronic Liver Failure (LiSyM-ACLF - Pillar III), Chronic Liver Disease Progression (LiSyM-DP - Pillar II), Liver Function Diagnostics (LiSyM-LiFuDi - Pillar IV), The Hedgehog Signalling Pathway (LiSyM-JGMMS), Multi-Scale Models for Personalized Liver Function Tests (LiSyM-MM-PLF), Model Guided Pharmacotherapy In Chronic Liver Disease (LiSyM-MGP), Molecular Steatosis - Imaging & Modeling (LiSyM-MSIM), Modelling COVID-19 epidemics, SNAPPER: Synergistic Neurotoxicology APP for Environmental Regulation, SCyCode The Autotrophy-Heterotrophy Switch in Cyanobacteria: Coherent Decision-Making at Multiple Regulatory Layers, SASKit: Senescence-Associated Systems diagnostics Kit for cancer and stroke, CC-TOP, BioCreative VII

Institutions: Heidelberg Institute for Theoretical Studies (HITS gGmbH), FAIRDOM User meeting, Norwegian University of Science and Technology, University of Rostock

https://orcid.org/0000-0003-3540-0402
Lukrécia Mertová

Projects: FAIRDOM, BioCreative VII

Institutions: Heidelberg Institute for Theoretical Studies (HITS gGmbH)

Ghadeer Mobasher

Projects: PoLiMeR - Polymers in the Liver: Metabolism and Regulation, BioCreative VII

Institutions: Heidelberg Institute for Theoretical Studies (HITS gGmbH)

https://orcid.org/0000-0003-4026-6965
Wolfgang Müller project_administratorasset_housekeeperasset_gatekeeperprogramme_administrator

Projects: SysMO DB, FAIRDOM, ICYSB 2015 - International Practical Course in Systems Biology, de.NBI-SysBio, Regeneration and Repair in Acute-on-Chronic Liver Failure (LiSyM-ACLF - Pillar III), Early Metabolic Injury (LiSyM-EMI - Pillar I), Chronic Liver Disease Progression (LiSyM-DP - Pillar II), LiSyM Core Infrastructure and Management (LiSyM-PD), Liver Function Diagnostics (LiSyM-LiFuDi - Pillar IV), Molecular Steatosis - Imaging & Modeling (LiSyM-MSIM), Multi-Scale Models for Personalized Liver Function Tests (LiSyM-MM-PLF), Model Guided Pharmacotherapy In Chronic Liver Disease (LiSyM-MGP), The Hedgehog Signalling Pathway (LiSyM-JGMMS), Kinetics on the move - Workshop 2016, Example use cases, SBEpo - Systems Biology of Erythropoietin, FAIRDOM & LiSyM & de.NBI Data Structuring Training, MESI-STRAT, INCOME, EnzymeML, PoLiMeR - Polymers in the Liver: Metabolism and Regulation, MS_DILI, GMDS Project Group "FAIRe Dateninfrastrukturen für die Biomedizinische Informatik", COMBINE Multicellular Modelling, COVID-19 Disease Map, COVID-19 related studies and tools in Germany, nfdi4health - German National Research Data Infrastructure for Personal Health Data, NMTrypI - New Medicines for Trypanosomatidic Infections, ModeleXchange initiative, SNAPPER: Synergistic Neurotoxicology APP for Environmental Regulation, BioCreative VII

Institutions: Heidelberg Institute for Theoretical Studies (HITS gGmbH)

https://orcid.org/0000-0002-4980-3512
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Combining dictionary- and rule-based approximate entity linking with tuned BioBERT
BioCreative VII

Abstract (Expand)

Chemical named entity recognition (NER) is a significant step for many downstream applications like entity linking for the chemical text-mining pipeline. However, the identification of chemical entities … in a biomedical text is a challenging task due to the diverse morphology of chemical entities and the different types of chemical nomenclature. In this work, we describe our approach that was submitted for BioCreative version 7 challenge Track 2, focusing on the ‘Chemical Identification’ task for identifying chemical entities and entity linking, using MeSH. For this purpose, we have applied a two-stage approach as follows (a) usage of fine-tuned BioBERT for identification of chemical entities (b) semantic approximate search in MeSH and PubChem databases for entity linking. There was some friction between the two approaches, as our rule-based approach did not harmonise optimally with partially recognized words forwarded by the BERT component. For our future work, we aim to resolve the issue of the artefacts arising from BERT tokenizers and develop joint learning of chemical named entity recognition and entity linking using pre-trained transformer-based models and compare their performance with our preliminary approach. Next, we will improve the efficiency of our approximate search in reference databases during entity linking. This task is non-trivial as it entails determining similarity scores of large sets of trees with respect to a query tree. Ideally, this will enable flexible parametrization and rule selection for the entity linking search.

Authors: Ghadeer Mobasher, Lukrécia Mertová, Sucheta Ghosh, Olga Krebs, Bettina Heinlein, Wolfgang Müller

Date Published: 11th Nov 2021

Publication Type: Proceedings

Combining dictionary- and rule-based approximate entity linking with tuned BioBERT
BioCreative VII
No description specified

Creators: Lukrécia Mertová, Ghadeer Mobasher

Submitter: Lukrécia Mertová

Combining dictionary- and rule-based approximate entity linking with tuned BioBERT
BioCreative VII
No description specified

Creators: Lukrécia Mertová, Ghadeer Mobasher

Submitter: Lukrécia Mertová

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