PEDL+: Protein-centered relation extraction from PubMed at your fingertip
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Item Type: | Article |
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Title: | PEDL+: Protein-centered relation extraction from PubMed at your fingertip |
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Creators Name: | Weber, L. and Barth, F. and Lorenz, L. and Konrath, F. and Huska, K. and Wolf, J. and Leser, U. |
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Abstract: | Relation extraction (RE) from large text collections is an important tool for database curation, pathway reconstruction, or functional omics data analysis. In practice, RE often is part of a complex data analysis pipeline requiring specific adaptations like restricting the types of relations or the set of proteins to be considered. However, current systems are either non-programmable web sites or research code with fixed functionality. We present PEDL+, a user-friendly tool for extracting protein-protein and protein-chemical associations from PubMed articles. PEDL+ combines state-of-the-art NLP technology with adaptable ranking and filtering options and can easily be integrated into analysis pipelines. We evaluated PEDL+ in two pathway curation projects and found that 59% to 80% of its extractions were helpful. |
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Keywords: | Factual Databases, PubMed, Software |
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Source: | Bioinformatics |
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ISSN: | 1367-4803 |
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Publisher: | Oxford University Press |
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Volume: | 39 |
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Number: | 11 |
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Page Range: | btad603 |
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Date: | November 2023 |
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Official Publication: | https://doi.org/10.1093/bioinformatics/btad603 |
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PubMed: | View item in PubMed |
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