Ir-Man: An Information Retrieval Framework for Marine Animal Necropsy Analysis

A Carmichael, Deepayan Bhowmik, Johanna Baily, Andrew Brownlow, GJ Gunn, A Reeves

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Abstract

This paper proposes Ir-Man (Information Retrieval for Marine Animal Necropsies), a framework for retrieving discrete information from marine mammal post-mortem reports for statistical analysis. When a marine mammal is reported dead after stranding in Scotland, the carcass is examined by the Scottish Marine Animal Strandings Scheme (SMASS) to establish the circumstances of the animal's death. This involves the creation of a 'post-mortem' (or necropsy) report, which systematically describes the body. These semi-structured reports record lesions (damage or abnormalities to anatomical regions) as well as other observations. Observations embedded within these texts are used to determine cause of death. While a cause of death is recorded separately, many other descriptions may be of pathological and epidemiological significance when aggregated and analysed collectively. As manual extraction of these descriptions is costly, time consuming and at times erroneous, there is a need for an automated information retrieval mechanism which is a non-trivial task given the wide variety of possible descriptions, pathologies and species. The Ir-Man framework consists of a new ontology, a lexicon of observations and anatomical terms and an entity relation engine for information retrieval and statistics generation from a pool of necropsy reports. We demonstrate the effectiveness of our framework by creating a rule-based binary classifier for identifying bottlenose dolphin attacks (BDA) in harbour porpoise gross pathology reports and achieved an accuracy of 83.4%.
Original languageEnglish
Title of host publicationACM Conference on Bioinformatics, Computational Biology, and Health Informatics (ACM BCB 2020)
PublisherAssociation for Computing Machinery (ACM)
Number of pages9
ISBN (Electronic) 978-1-4503-7964-9/20/09
DOIs
Publication statusAccepted/In press - Sep 2020
Event11th ACM International Conference on Bioinformatics, Computational Biology and Health Informatics (BCB ’20) - Virtual Event, New York, United States
Duration: 21 Sep 202024 Sep 2020

Conference

Conference11th ACM International Conference on Bioinformatics, Computational Biology and Health Informatics (BCB ’20)
CountryUnited States
CityNew York
Period21/09/2024/09/20

Keywords

  • Marine mammals
  • Information extraction
  • Post Mortem
  • Text mining

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  • Cite this

    Carmichael, A., Bhowmik, D., Baily, J., Brownlow, A., Gunn, GJ., & Reeves, A. (Accepted/In press). Ir-Man: An Information Retrieval Framework for Marine Animal Necropsy Analysis. In ACM Conference on Bioinformatics, Computational Biology, and Health Informatics (ACM BCB 2020) Association for Computing Machinery (ACM). https://doi.org/10.1145/3388440.3412417