{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,9,22]],"date-time":"2026-09-22T14:17:55Z","timestamp":1790086675463,"version":"4.0.1"},"reference-count":28,"publisher":"World Scientific Pub Co Pte Lt","issue":"06","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["J. Bioinform. Comput. Biol."],"published-print":{"date-parts":[[2007,12]]},"abstract":"<jats:p> Rich information on point mutation studies is scattered across heterogeneous data sources. This paper presents an automated workflow for mining mutation annotations from full-text biomedical literature using natural language processing (NLP) techniques as well as for their subsequent reuse in protein structure annotation and visualization. This system, called mSTRAP (Mutation extraction and STRucture Annotation Pipeline), is designed for both information aggregation and subsequent brokerage of the mutation annotations. It facilitates the coordination of semantically related information from a series of text mining and sequence analysis steps into a formal OWL-DL ontology. The ontology is designed to support application-specific data management of sequence, structure, and literature annotations that are populated as instances of object and data type properties. mSTRAPviz is a subsystem that facilitates the brokerage of structure information and the associated mutations for visualization. For mutated sequences without any corresponding structure available in the Protein Data Bank (PDB), an automated pipeline for homology modeling is developed to generate the theoretical model. With mSTRAP, we demonstrate a workable system that can facilitate automation of the workflow for the retrieval, extraction, processing, and visualization of mutation annotations \u2014 tasks which are well known to be tedious, time-consuming, complex, and error-prone. The ontology and visualization tool are available at . <\/jats:p>","DOI":"10.1142\/s0219720007003119","type":"journal-article","created":{"date-parts":[[2007,12,31]],"date-time":"2007-12-31T05:56:01Z","timestamp":1199080561000},"page":"1319-1337","source":"Crossref","is-referenced-by-count":18,"title":["A WORKFLOW FOR MUTATION EXTRACTION AND STRUCTURE ANNOTATION"],"prefix":"10.1142","volume":"05","author":[{"given":"RAJARAMAN","family":"KANAGASABAI","sequence":"first","affiliation":[{"name":"Department of Data Mining, Institute for Infocomm Research, 21 Heng Mui Keng Terrace, Singapore 119613, Singapore"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"KHAR HENG","family":"CHOO","sequence":"additional","affiliation":[{"name":"Department of Data Mining, Institute for Infocomm Research, 21 Heng Mui Keng Terrace, Singapore 119613, Singapore"},{"name":"Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, 8 Medical Drive, Singapore 117597, Singapore"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"SHOBA","family":"RANGANATHAN","sequence":"additional","affiliation":[{"name":"Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, 8 Medical Drive, Singapore 117597, Singapore"},{"name":"Department of Chemistry and Biomolecular Sciences &amp;, Biotechnology Research Institute, Macquarie University, NSW 2109, Australia"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"CHRISTOPHER J. 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