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Assessing the Utility of Automatic Cancer Registry Notifications Data Extraction from Free-Text Pathology Reports

Anthony N Nguyen, Julie Moore, John O'Dwyer, Shoni Philpot
2015 AMIA Annual Symposium Proceedings  
A system for automatic extraction of cancer data from HL7 electronic free-text pathology reports has been proposed to improve the workflow efficiency of the Cancer Registry.  ...  The system is currently processing an incoming trickle feed of HL7 electronic pathology reports from across the state of Queensland in Australia to produce an electronic cancer notification.  ...  Background There has been a number of clinical language processing systems or studies relating to the extraction of key cancer characteristics from pathology free-text.  ... 
pmid:26958232 pmcid:PMC4765645 fatcat:scprtgnukrhhtbob4jrc7zf7sa

Automated Cancer Registry Notifications: Validation of a Medical Text Analytics System for Identifying Patients with Cancer from a State-Wide Pathology Repository

Anthony N Nguyen, Julie Moore, John O'Dwyer, Shoni Philpot
2017 AMIA Annual Symposium Proceedings  
A corpus of 45.3 million pathology HL7 messages (including 119,581 histology and cytology reports) from a Queensland pathology repository for the year of 2009 was analysed by Medtex for cancer notification  ...  The paper assesses the utility of Medtex on automating Cancer Registry notifications from narrative histology and cytology reports from the Queensland state-wide pathology information system.  ...  The authors acknowledge Stephen Armstrong and Nilesh Mendis from QCCAT for data access as well as help in getting Medtex deployed on the Department of Health's infrastructure.  ... 
pmid:28269893 pmcid:PMC5333242 fatcat:ue6tcwq45zh7lnjuv77lvmfcm4

Classification of cancer-related death certificates using machine learning

Luke Butt
2013 Australasian Medical Journal  
In this paper, approaches for the automatic detection of notifiable cancer cases as the cause of death from free-text death certificates supplied to Cancer Registries are investigated.  ...  However, the abstraction and classification of cancer from the free-text of pathology reports and other relevant documents, such as death certificates, exist as complex and time-consuming activities.  ...  ACKNOWLEDGEMENTS The authors would like to thank the Australian e--Health Research Centre and Cancer Institute NSW for their support of this research.  ... 
doi:10.4066/amj.2013.1654 pmid:23745151 pmcid:PMC3674421 fatcat:z2hbsgrfm5erfggmhffjakfftq

Tumour Classification and Analysis from Breast Cancer Pathology Reports using Natural Language Processing

G. Johanna Johnsi Rani, D. Gladis, Joy John Mammen, Marie Therese Manipadam
2015 Indian Journal of Science and Technology  
One such report is the Pathology report which has natural language narrations of the conditions of patients.  ...  Breast Cancer is the prime cause of death in Indian women. Hospitals in India use electronic means of collection and reporting of data.  ...  The authors would like to thank the Department of Pathology, Christian Medical College & Hospital, Vellore for providing with the sample data for their study.  ... 
doi:10.17485/ijst/2015/v8i29/86268 fatcat:kykrxuby7fhqrdrt3ielgxeuju

Tumour Classification and Analysis from Breast Cancer Pathology Reports using Natural Language Processing

G. Johanna Johnsi Rani, D. Gladis, Joy John Mammen, Marie Therese Manipadam
2015 Indian Journal of Science and Technology  
One such report is the Pathology report which has natural language narrations of the conditions of patients.  ...  Breast Cancer is the prime cause of death in Indian women. Hospitals in India use electronic means of collection and reporting of data.  ...  The authors would like to thank the Department of Pathology, Christian Medical College & Hospital, Vellore for providing with the sample data for their study.  ... 
doi:10.17485/ijst/2015/v8i1/84414 fatcat:iiokgftewvgyjlq4bkulyrw5ei

Text mining of cancer-related information: Review of current status and future directions

Irena Spasić, Jacqueline Livsey, John A. Keane, Goran Nenadić
2014 International Journal of Medical Informatics  
Results: A range of studies have proven the feasibility of TM for extracting structured information from clinical narratives such as those found in pathology or radiology reports.  ...  In addition, there is a need for a comprehensive cancer ontology that would enable semantic representation of textual information found in narrative reports.  ...  to automatic extraction from freetext colonoscopy and pathology reports [5] .  ... 
doi:10.1016/j.ijmedinf.2014.06.009 pmid:25008281 fatcat:c3ifkrjacjgghdm6kz65flh434

Automated determination of metastases in unstructured radiology reports for eligibility screening in oncology clinical trials

Valentina I Petkov, Lynne T Penberthy, Bassam A Dahman, Andrew Poklepovic, Chris W Gillam, James H McDermott
2013 Experimental biology and medicine  
One approach to meet these accrual challenges is to utilize technology to automatically screen patients for clinical trial eligibility.  ...  This manuscript reports on the evaluation of different automated approaches to determine the metastatic status from unstructured radiology reports using the Clinical Trials Eligibility Database Integrated  ...  Acknowledgment Services in support of the research project were provided by the VCU Cancer Research Informatics and Services Shared Resource, supported, in part, with the funding from NIH-NCI Cancer Center  ... 
doi:10.1177/1535370213508172 pmid:24108448 pmcid:PMC4358809 fatcat:hsv3fdnupvfgvoz77dukoixkoa

CAPABLE D5.2: Framework Defined (Including Patients' Needs) Based on Available Data and Modelling Approaches

Flora Gilboa-Solomon, Silvana Quaglini, Alexandra Kogan, Ronald Cornet, Savannah Glaser, Ella Barkan, Aneta Lisowska, Konrad Śniatała, Szymon Wilk, David Glasspool
2021 Zenodo  
This document describes the means by which the AI framework supports the requirements of melanoma and renal cancer patients, their caregivers, and physicians.  ...  The aim of this deliverable is to describe a framework that is part of the CAPABLE system architecture.  ...  The NLP pipeline and the results achieved shows an example of an automatically extracted keywords set for pancreatic cancer and prostate cancer posts.  ... 
doi:10.5281/zenodo.5159166 fatcat:o3ozlwru4jflbj6iygnfhdkq6i

Temporal representation of care trajectories of cancer patients using data from a regional information system: an application in breast cancer

Gautier Defossez, Alexandre Rollet, Olivier Dameron, Pierre Ingrand
2014 BMC Medical Informatics and Decision Making  
We developed an algorithm for extracting temporally represented care trajectories from coded information collected routinely by the general cancer Registry in Poitou-Charentes region, France.  ...  Dissimilarities between sequences were mainly due to the absence of certain pathology reports and to coding anomalies in hospitalisation data.  ...  Acknowledgments The authors would like to thanks all the all the pathologists, departments of medical data processing in public and private hospitals, oncologists, and medical practitioners for their valuable  ... 
doi:10.1186/1472-6947-14-24 pmid:24690482 pmcid:PMC3983896 fatcat:kulc2f4i5bd2nkvm6j6zmtzlvq

Customization of Medical Report Data

Bruce I. Reiner
2010 Journal of digital imaging  
Structured reporting offers a number of theoretical advantages, perhaps the most important of which is creation of standardized report databases.  ...  In addition, these referenceable report databases can be used to facilitate the practice of evidence based medicine, through data-driven meta-analysis and determination of best practice guidelines.  ...  Communication Table 2 . 2 Different Versions of Report Presentation for Mammography Report A: Conventional Free Text (Prose) Report Report B: Anatomical Structured Text (data classified according to  ... 
doi:10.1007/s10278-010-9307-4 pmid:20567993 pmcid:PMC3046662 fatcat:3wsav3vps5h2vobnzezr5ib5fm

Defining key design elements of registry-based randomised controlled trials: a scoping review

Bill Karanatsios, Khic-Houy Prang, Ebony Verbunt, Justin M. Yeung, Margaret Kelaher, Peter Gibbs
2020 Trials  
The search strategy included MeSH and text words related to RRCT. We identified 2369 articles of which 75 were selected for full-text screening.  ...  Four databases were searched for articles published from inception to June 2018: Medline; Embase; the Cumulative Index to Nursing and Allied Health Literature and; Scopus.  ...  BK, KP and EV screened titles, abstracts and full-text for relevance. BK, KP and EV extracted the data from the full-text. BK and KP drafted the manuscript.  ... 
doi:10.1186/s13063-020-04459-z pmid:32571382 fatcat:hxt7ygjxw5gvzalvhyrle5tuty

Analysis and Curation of the Database of a Colo-Rectal Cancer Screening Program [chapter]

Rocio Aznar-Gimeno, Patricia Carrera-Lasfuentes, Vega Rodrigalvarez-Chamarro, Rafael del-Hoyo-Alonso, Angel Lanas, Manuel Doblare
2021 Data Integrity and Quality [Working Title]  
With the aim of improving the redesign of a regional CRC screening program platform, we performed an exhaustive analysis of the data collected, proposing a set of recommendations for its correct maintenance  ...  It is necessary therefore to establish "good practice" guidelines for data collection, management and analysis.  ...  Acknowledgements We acknowledge the help provided by the Department of Health of the Aragón Government for allowing us the access to anonymized patient data and to the EU Program for Employment and Social  ... 
doi:10.5772/intechopen.95899 fatcat:jhcngoha45bw3ifs3mabjug2e4

Methods and Trends in Information Retrieval in Big Data Genomic Research

2019 VOLUME-8 ISSUE-10, AUGUST 2019, REGULAR ISSUE  
There was a surge of genomic information from the different literature and the production of genome datasets that catapulted the development of several tools for analyzing and presenting new found knowledge  ...  This paper described information retrieval (IR) and the common methods of finding, extracting, and mining information in genomic research through text mining, and natural language processing (NLP).  ...  Text-mining methods were also employed for genes in microarray to automatically link the information of gene to articles in databases.  ... 
doi:10.35940/ijitee.i1109.0789s219 fatcat:j2uramagd5a75jusrcor75w7ue

Supplemental Material, sj-pdf-6-vet-10.1177_03009858211013712 - International Guidelines for Veterinary Tumor Pathology: A Call to Action

Donald J. Meuten, Frances M. Moore, Taryn A. Donovan, Christof A. Bertram, Robert Klopfleisch, Robert A. Foster, Rebecca C. Smedley, Michael J. Dark, Milan Milovancev, Paul Stromberg, Bruce H. Williams, Marc Aubreville (+29 others)
2021 Figshare  
Supplemental Material, sj-pdf-6-vet-10.1177_03009858211013712 for International Guidelines for Veterinary Tumor Pathology: A Call to Action by Donald J. Meuten, Frances M. Moore, Taryn A.  ...  Mark Simpson, Harold Tvedten and Derick Whitley in Veterinary Pathology  ...  The addition of free text fields associated with standardized options would allow for customization of reports while retaining standardization for further applications.  ... 
doi:10.25384/sage.15028859.v1 fatcat:vhyl7ugagvfofhhryj4oq5dwcq

Informatics

2015 Laboratory Investigation  
Manual scores were extracted from the diagnostic pathology reports and compared to the automated image analysis scores.  ...  We have also been able to establish an automated filtration and reporting pipeline that allows the identification and reporting of regions of LOH harboring important cancer genes such as CDKN2A and JAK2  ...  KingMed Diagnostics is the largest independent pathology laboratory in China. Since 2012, UPMC and KingMed have established an international telepathology consultation service for Chinese patients.  ... 
doi:10.1038/labinvest.2015.17 fatcat:74eygyy7o5gkrhizoootoyfol4
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