ArticleDatabase : the journal of biological databases and curation2016
Extraction of chemical-induced diseases using prior knowledge and textual information.
Article in Database : the journal of biological databases and curation, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 17 papers.
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Who cites it
17 citing papers in PubMed.
- Identification of Chemical-Disease Associations Through Integration of Molecular Fingerprint, Gene Ontology and Pathway Information.Interdisciplinary sciences, computational life sciences · 2022Article
- Biomedical relation extraction via knowledge-enhanced reading comprehension.BMC bioinformatics · 2022Article
- Chinese-Named Entity Recognition From Adverse Drug Event Records: Radical Embedding-Combined Dynamic Embedding-Based BERT in a Bidirectional Long Short-term Conditional Random Field (Bi-LSTM-CRF) Model.JMIR medical informatics · 2021Article
- CID-GCN: An Effective Graph Convolutional Networks for Chemical-Induced Disease Relation Extraction.Frontiers in genetics · 2021Article
- Document-Level Biomedical Relation Extraction Using Graph Convolutional Network and Multihead Attention: Algorithm Development and Validation.JMIR medical informatics · 2020Article
- Broad-coverage biomedical relation extraction with SemRep.BMC bioinformatics · 2020Article
- Chemical-induced disease relation extraction via attention-based distant supervision.BMC bioinformatics · 2019Article
- Knowledge-guided convolutional networks for chemical-disease relation extraction.BMC bioinformatics · 2019Article
- Hierarchical sequence labeling for extracting BEL statements from biomedical literature.BMC medical informatics and decision making · 2019Article
- A general approach for improving deep learning-based medical relation extraction using a pre-trained model and fine-tuning.Database : the journal of biological databases and curation · 2019Article
- Combining relation extraction with function detection for BEL statement extraction.Database : the journal of biological databases and curation · 2019Article
- A document level neural model integrated domain knowledge for chemical-induced disease relations.BMC bioinformatics · 2018Article
- Leveraging prior knowledge for protein-protein interaction extraction with memory network.Database : the journal of biological databases and curation · 2018Article
- LPTK: a linguistic pattern-aware dependency tree kernel approach for the BioCreative VI CHEMPROT task.Database : the journal of biological databases and curation · 2018Article
- Extracting chemical-protein relations using attention-based neural networks.Database : the journal of biological databases and curation · 2018Article
- Automatic extraction of gene-disease associations from literature using joint ensemble learning.PloS one · 2018Article
- Chemical-induced disease relation extraction via convolutional neural network.Database : the journal of biological databases and curation · 2017Article
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6 authors.
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Abstract
We describe our approach to the chemical-disease relation (CDR) task in the BioCreative V challenge. The CDR task consists of two subtasks: automatic disease-named entity recognition and normalization (DNER), and extraction of chemical-induced diseases (CIDs) from Medline abstracts. For the DNER subtask, we used our concept recognition tool Peregrine, in combination with several optimization steps. For the CID subtask, our system, which we named RELigator, was trained on a rich feature set, comprising features derived from a graph database containing prior knowledge about chemicals and diseases, and linguistic and statistical features derived from the abstracts in the CDR training corpus. We describe the systems that were developed and present evaluation results for both subtasks on the CDR test set. For DNER, our Peregrine system reached anF-score of 0.757. For CID, the system achieved anF-score of 0.526, which ranked second among 18 participating teams. Several post-challenge modifications of the systems resulted in substantially improvedF-scores (0.828 for DNER and 0.602 for CID). RELigator is available as a web service athttp://biosemantics.org/index.php/software/religator.
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