Bioinformatic Workflow Extraction from Scientific Texts based on Word Sense Disambiguation
| Autor: | Abdoulaye Baniré Diallo, Ahmed Halioui, Petko Valtchev |
|---|---|
| Rok vydání: | 2018 |
| Předmět: |
0301 basic medicine
business.industry Computer science Applied Mathematics Cloud computing 02 engineering and technology Ontology (information science) computer.software_genre Knowledge acquisition Metadata 03 medical and health sciences 030104 developmental biology Workflow 020204 information systems 0202 electrical engineering electronic engineering information engineering Genetics Task analysis Graph (abstract data type) Artificial intelligence business computer Workflow management system Natural language processing Biotechnology |
| Zdroj: | IEEE/ACM Transactions on Computational Biology and Bioinformatics. 15:1979-1990 |
| ISSN: | 2374-0043 1545-5963 |
| DOI: | 10.1109/tcbb.2018.2847336 |
| Popis: | This paper introduces a method for automatic workflow extraction from texts using Process-Oriented Case-Based Reasoning (POCBR). While the current workflow management systems implement mostly different complicated graphical tasks based on advanced distributed solutions (e.g., cloud computing and grid computation), workflow knowledge acquisition from texts using case-based reasoning represents more expressive and semantic case representations. We propose in this context, an ontology-based workflow extraction framework to acquire processual knowledge from texts. Our methodology extends the classic NLP techniques to extract and disambiguate complex tasks and relations in texts. Using a graph-based representation of workflows and a domain ontology, our extraction process uses a context-aware approach to recognize workflow components in texts: data and control flows. We applied our framework in a technical domain in bioinformatics: i.e., phylogenetic analyses. An evaluation based on workflow semantic similarities in a gold standard proves that our approach provides promising results in the process extraction domain. Both data and implementation of our framework are available in: http://labo.bioinfo.uqam.ca/tgowler . |
| Databáze: | OpenAIRE |
| Externí odkaz: |
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