Development and implementation of a data parsing protocol for companion animal cancer data

Chiara Palmieri; Matt Taylor; Mike Rickerby; Peter Bennett; Mieghan Bruce; Mark Krockenberger; Philippa McLaren; Thelma Meiring; Kerrie Mengersen; Gabriele Rossi; Anne Peaston; Attracta Roach; Andrew Stent; Ricardo J. Soares Magalhaes

doi:10.1177/03009858251413572

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Development and implementation of a data parsing protocol for companion animal cancer data

Journal article

Open access

Peer reviewed

Development and implementation of a data parsing protocol for companion animal cancer data

Chiara Palmieri, Matt Taylor, Mike Rickerby, Peter Bennett, Mieghan Bruce, Mark Krockenberger, Philippa McLaren, Thelma Meiring, Kerrie Mengersen, Gabriele Rossi, …

Veterinary pathology, p.3009858251413572

2026

DOI: https://doi.org/10.1177/03009858251413572

PMID: 41574631

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Abstract

cancer

cancer registry

cat

data

database

dog

Companion animal cancer diagnostic reports are text-based documents containing essential information on tumor classification and diagnosis. Establishing an animal cancer registry requires integrating and extracting structured data from diverse report formats across multiple providers. This study presents the development of an object-oriented programming approach to standardize and automate cancer data collection for canine and feline patients, enabling the creation of the Australian Companion Animal Registry of Cancers (ACARCinom); Australia’s first national registry of cat and dog cancers. An object-oriented programming approach was developed using the C# language for data processing, tested on sample data from 6 data providers. The initial programming phase focused on designing a parser that identified report sections using regular expressions based on standardized headings. The text was then cleaned to remove unnecessary formatting and HTML tags. Data dictionaries containing preferred terms and synonyms were used to extract key information such as diagnosis, topography, grade, and metastasis, improving consistency and accuracy. A coordinate map of extracted terms was generated to analyze spatial relationships within the report, allowing prioritization of diagnoses. The system also logged parsing decisions and potential issues for expert review. Markup using HTML tags enabled clear visualization of parsed content within the original reports. Extracted data and patient metadata were stored in an intermediary database table, allowing veterinary pathology experts to review and refine entries before final import. This automated solution streamlines data extraction and standardization from diverse sources, enabling the efficient analysis of cancer records and enhancing research and surveillance capacity in veterinary oncology.

Details

Title: Development and implementation of a data parsing protocol for companion animal cancer data
Authors/Creators: Chiara Palmieri - The University of Queensland
Matt Taylor - Sugar Research Australia (Australia)
Mike Rickerby - Sugar Research Australia (Australia)
Peter Bennett - The University of Melbourne
Mieghan Bruce - Murdoch University, Centre for Biosecurity and One Health
Mark Krockenberger - The University of Sydney
Philippa McLaren - IDEXX Laboratories (France)
Thelma Meiring - IDEXX Laboratories (France)
Kerrie Mengersen - Queensland University of Technology
Gabriele Rossi - Murdoch University, Centre for Animal Production and Health
Anne Peaston - The University of Adelaide
Attracta Roach - Gribbles Veterinary Pathology, Clayton, VIC, Australia
Andrew Stent - Gribbles Veterinary Pathology, Clayton, VIC, Australia
Ricardo J. Soares Magalhaes - UQ Children’s Health Research Centre, South Brisbane, QLD, Australia
Publication Details: Veterinary pathology, p.3009858251413572
Publisher: SAGE Publications
Number of pages: 11
Grant note: Australian Research Data Commons (http://data.elsevier.com/vocabulary/SciValFunders/501100020840)
Identifiers: 991005858493807891
Murdoch Affiliation: Centre for Biosecurity and One Health; School of Veterinary Medicine; Centre for Animal Production and Health
Language: English
Resource Type: Journal article

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Collaboration types: Domestic collaboration; International collaboration
Citation topics: No Topic Assigned; No Topic Assigned; No Topic Assigned
Web Of Science research areas: Pathology; Veterinary Sciences
ESI research areas: Plant & Animal Science