Phylogenetics Workflows

The dataset presents input/output data of the TGOWLeR framework. TGOWLeR abstracts general patterns from workflow sequences previously extracted from texts. It comprises two modules –a workflow extractor and a pattern miner– both relying on a specific domain ontology.The input of the first module is an RDF/ZIPPED ontology (tgowler_resource_ontologies_PHAGE_1.0.rdf.zip) and a set of un-annotated articles (e.g., datastore_2018_2019.zip). The proposed pipeline (implemented in GATE 8.1) produces annotated texts (e.g., annotated_2018_2019.zip) and their corresponding workflows (e.g., WFMiner_WF_2018_2019.xml).The input of the second module is the serialized ontology ... Publications:Halioui, Ahmed, et al. "Ontology-based workflow pattern mining: Application to bioinformatics expertise acquisition." Proceedings of the Symposium on Applied Computing. ACM, 2017.Halioui, Ahmed, Petko Valtchev, and Abdoulaye Baniré Diallo. "Bioinformatic Workflow Extraction from Scientific Texts based on Word Sense Disambiguation." IEEE/ACM transactions on computational biology and bioinformatics 15.6 (2018): 1979-1990.