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Standardization of the Histopathology Cancer Report: An Ontological Approach

Anna Maria Masci, Shannon McCall, Alessandro Racioppi, Helena Judge Ellis, Jihad S. Obeid, Barry Smith, Christian J. Stoeckert Jr., Jie Zheng
2018 International Conference on Biomedical Ontology  
This prototype for ontological representation of histopathology report is an innovative approach that will facilitate maximal integration of information from various types of cancer reports, leading to  ...  Methods To address the lack of formal terminology and computational resources critical to improving the use of the histopathology reports, we are developing an ontological representation of the required  ... 
dblp:conf/icbo/MasciMREO0S018 fatcat:u7qv5mgijjfdxiahwdeuxq5of4

Whole-exon sequencing insights into pancreatic synovial sarcoma: a case report

Qijiang Mao, Haoqi Pan, Boqiang Liu, Mei Jin, Guoxiang Fu, Huijiang Shao, Xiaoxiao Fan, Yuelong Liang
2021 Gland surgery  
Here, we reported a case of a 66-year-old male patient with an upper abdominal pain for half a month and a previous history of oral cancer.  ...  driver-genes are enriched in the cancer-related pathways.  ...  The histopathological diagnosis of his oral cancer was highgrade differentiated squamous cell carcinoma in the lingual root and tonsil with striated muscle invasion and cancer metastasis in the lymph node  ... 
doi:10.21037/gs-20-680 pmid:34164326 pmcid:PMC8184378 fatcat:jojqytfgvbg3tpudlbjjjpduva

A computable pathology report for precision medicine: extending an observables ontology unifying SNOMED CT and LOINC

Walter S Campbell, Daniel Karlsson, Daniel J Vreeman, Audrey J Lazenby, Geoffrey A Talmon, James R Campbell
2017 JAMIA Journal of the American Medical Informatics Association  
The College of American Pathologists (CAP) introduced the first cancer synoptic reporting protocols in 1998.  ...  However, the objective of a fully computable and machine-readable cancer synoptic report remains elusive due to insufficient definitional content in Systematized Nomenclature of Medicine -Clinical Terms  ...  ACKNOWLEDGMENTS The authors thank collaborators from SNOMED International, Regenstrief Institute Inc., the College of American Pathologists, Rajesh Dash, MD, Alexis Carter, MD, and Mary Kennedy and National  ... 
doi:10.1093/jamia/ocx097 pmid:29024958 fatcat:uvd4v7ta45bbrkq756n5yqebdq

Pattern-based information extraction from pathology reports for cancer registration

Giulio Napolitano, Colin Fox, Richard Middleton, David Connolly
2010 Cancer Causes and Control  
To assess the impact that implementation of pattern-based methods would have on cancer registration completeness.  ...  Objective To evaluate precision and recall rates for the automatic extraction of information from free-text pathology reports.  ...  Acknowledgments The Northern Ireland Cancer Registry was funded by the Department of Health, Social Services and Public Safety Northern Ireland (DHSSPSNI), at the time this study was completed.  ... 
doi:10.1007/s10552-010-9616-4 pmid:20652738 fatcat:2fy5cgwjvrbqfpiadlup2xkpei

Toward good in vitro reporting standards

Thomas Hartung
2019 ALTEX: Alternatives to Animal Experimentation  
The first priority of reporting standards is to ensure the completeness and transparency of the provided information (data focus).  ...  This thinking is fundamentally flawed, as science is an exercise of sharing.  ...  Acknowledgements The enormous effort by Dr Mardas Daneshian in organizing the earlier work by CAAT toward reporting standards is gratefully appreciated.  ... 
doi:10.14573/altex.1812191 fatcat:vznrq7hdgnaatek2lk34brsjzq

D4.8- Report from thematic meeting [article]

2021 Zenodo  
Ambra Morisi, University of Surrey, presented his research in the development of a novel artificial intelligence method applied in veterinary histopathology to improve cancer diagnostic accuracy.  ...  The title of his presentation was "Deep Learning in Digital Pathology to improve cancer diagnosis in humans and animals".  ...   Outline naming conventions used  Outline the approach towards search keyword  Outline the approach for clear versioning  Specify standards for metadata creation (if any).  ... 
doi:10.5281/zenodo.4897367 fatcat:l5aopbiwljha3cyji2lokdlz2y

A Systematic Review of Artificial Intelligence in Prostate Cancer

Derek J Van Booven, Manish Kuchakulla, Raghav Pai, Fabio S Frech, Reshna Ramasahayam, Pritika Reddy, Madhumita Parmar, Ranjith Ramasamy, Himanshu Arora
2021 Research and Reports in Urology  
The diagnosis and management of prostate cancer involves the interpretation of data from multiple modalities to aid in decision making.  ...  By using AI algorithms and reducing the level of subjectivity, it is possible to use fewer resources while improving the overall efficiency and accuracy in prostate cancer diagnosis and management.  ...  Disclosure The authors report no conflicts of interest for this work. Declaration of interests: the authors declare no competing interests.  ... 
doi:10.2147/rru.s268596 pmid:33520879 pmcid:PMC7837533 fatcat:a2eecsaqmza47lmubnfsahs6wq

Leveraging electronic healthcare record standards and semantic web technologies for the identification of patient cohorts

Jesualdo Tomás Fernández-Breis, José Alberto Maldonado, Mar Marcos, María del Carmen Legaz-García, David Moner, Joaquín Torres-Sospedra, Angel Esteban-Gil, Begoña Martínez-Salvador, Montserrat Robles
2013 JAMIA Journal of the American Medical Informatics Association  
In this context, an important problem is the heterogeneity of clinical data sources, which can be overcome with the combined use of standardized information models, Virtual Health Records, and semantic  ...  Materials and Methods We propose to take advantage of the best features of working with EHR standards and ontologies.  ...  Acknowledgments We thank the "Programa de Prevención del Cáncer de Colon y Recto de la Región de Murcia" for providing the data for performing this study.  ... 
doi:10.1136/amiajnl-2013-001923 pmid:23934950 pmcid:PMC3861938 fatcat:xhu3k5mxh5bo3pnnac5kvtis6u

A cognitive virtual microscopic framework for knowlege-based exploration of large microscopic images in breast cancer histopathology

L. Roux, A. Tutac, N. Lomenie, D. Balensi, D. Racoceanu, A. Veillard, Wee-Kheng Leow, J. Klossa, T.C. Putti
2009 2009 Annual International Conference of the IEEE Engineering in Medicine and Biology Society  
The cognitive virtual microscopic framework, through an extended modeling and use of medical knowledge, has the capacity to analyse histopathological images and to perform grading of breast cancer, providing  ...  Histopathological examination is a powerful method for prognosis of major diseases such as breast cancer. Analysis of medical images largely remains the work of human experts.  ...  Defining the outline of a generic cognitive approach for visual exploration and analysis of histopathological images, this general and ambitious objective focuses on the domain of breast cancer grading  ... 
doi:10.1109/iembs.2009.5334739 pmid:19965006 fatcat:3m5ydge4nrfr3kd6rnia456teq

Melanoma proteomics suggests functional differences related to mutational status

Lucía Trilla-Fuertes, Angelo Gámez-Pozo, Guillermo Prado-Vázquez, Andrea Zapater-Moros, Mariana Díaz-Almirón, Claudia Fortes, María Ferrer-Gómez, Rocío López-Vacas, Verónica Parra Blanco, Iván Márquez-Rodas, Ainara Soria, Juan Ángel Fresno Vara (+1 others)
2019 Scientific Reports  
Melanoma is the most lethal cutaneous cancer. New drugs have recently appeared; however, not all patients obtain a benefit of these new drugs.  ...  The aim of this study was to explore the molecular differences between melanoma tumor subtypes, based on BRAF and NRAS mutational status.  ...  The funders had no role in the study design, data collection and analysis, decision to publish or preparation of the manuscript.  ... 
doi:10.1038/s41598-019-43512-z pmid:31076580 pmcid:PMC6510784 fatcat:dcxwn3va2rem5flukdbhakwrlu

IFPA Meeting 2008 Workshops Report

G.E. Lash, T. Ansari, P. Bischof, G.J. Burton, L. Chamley, I. Crocker, V. Dantzer, G. Desoye, S. Drewlo, A. Fazleabas, T. Jansson, S. Keating (+14 others)
2009 Placenta  
This report is a summary of the various topics covered.  ...  Workshops are an important part of the IFPA annual meeting. At the IFPA meeting 2008 diverse topics were discussed in 12 themed workshops.  ...  Several application doses of MSCs without animal serum were produced in a standardized one-step procedure within 2 weeks supporting therapeutic approaches which depend on the fast and safe availability  ... 
doi:10.1016/j.placenta.2008.11.014 pmid:19084270 pmcid:PMC2668143 fatcat:umhr3fbjwnew3mjyrrv3judth4

Meeting Report: EU–US Workshop on Molecular Signatures of DNA damage-induced Stress Responses☆Cortona, Italy, 26–30 September 2003

Miriam Sander, Christian Desaintes, Richard Pelroy, Wouter Ferro, Bennett Van Houten, Sally Amundson, Alan Lehmann, Leon Mullenders, Susanna-Assunta Sansone, Peter Stambrook
2004 Mutation research  
The reporter construct carries an out-offrame reporter gene downstream from an (A 17 ) repeat.  ...  The gene ontology is an example of an established ontology that was developed for annotating genome databases.  ... 
doi:10.1016/j.mrfmmm.2004.02.009 pmid:15228042 fatcat:665kva7sjzfxpc4fgzvhaozkgy

Gene expression profiling of oral submucous fibrosis using oligonucleotide microarray

Xinchun Jian
1994 Oncology Reports  
Our data suggested that gene abnormalities in immune response, inflammatory response and EMT induced by TGF-ß might play an important role in the pathogenesis and malignant transformation of OSF.  ...  Although oral submucous fibrosis (OSF) is the most common precancerous lesion of the oral cavity in Southeast Asia where the habit of betel quid (BQ) chewing is popular, its molecular biological properties  ...  Acknowledgements We are grateful to the Cancer Research Institute and the Research Center of Molecular Biology of Central South University for their expert technical assistance.  ... 
doi:10.3892/or_00000005 fatcat:xsscmsd33fbyro2qwqauc7umvq

Workshop report: Identifying opportunities for global integration of toxicogenomics databases, 26–27 June 2013, Research Triangle Park, NC, USA

Diana M. Hendrickx, Rebecca R. Boyles, Jos C. S. Kleinjans, Allen Dearry
2014 Archives of Toxicology  
Acknowledgments This report is based on the "Workshop on Identifying Opportunities for Global Integration of Toxicogenomics Databases", 26-27 June 2013, hosted at the National Institute of Environmental  ...  Open Access This article is distributed under the terms of the Creative Commons Attribution License which permits any use, distribution, and reproduction in any medium, provided the original author(s)  ...  When considering an approach to these issues, it became obvious that any roadmap must be grounded in the needs of potential users.  ... 
doi:10.1007/s00204-014-1387-3 pmid:25326818 pmcid:PMC4247478 fatcat:ibhun6x3gng5bb6pfswl23v5gu

A Review of Current Standards and the Evolution of Histopathology Nomenclature for Laboratory Animals

2018 ILAR journal  
These efforts led to the establishment of an international rodent pathology nomenclature program.  ...  First initiated by the World Health Organization's International Agency for Research on Cancer for rodents, it has evolved to include pathology of the major species (rats, mice, guinea pigs, nonhuman primates  ...  of the IMPC histopathology ontology within an IMPC center.  ... 
doi:10.1093/ilar/ily005 pmid:30476141 pmcid:PMC6927895 fatcat:lmatrxhlbzbc5dmz43t6e4inve
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