caTIES: a grid based system for coding and retrieval of surgical pathology reports and tissue specimens in support of translational research

Crowley, Rebecca S.; Castine, Melissa; Mitchell, Kevin J.; Chavan, Girish; McSherry, Tara; Feldman, Michael D.

doi:10.1136/jamia.2009.002295

Cited by 79 publications

(78 citation statements)

References 14 publications

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“…Many NLP applications for automatically mapping from clinical text concepts to terms in a standardized vocabulary have been reported, such as MedLEE [9], MetaMap [10], OpenNLP [11], and caTIES [12].…”

Section: B Nature Language Processing In Medicinementioning

confidence: 99%

An entry generation pipeline for converting free-text medical document into Clinical Document Architecture document with entry-level

Lin¹,

Lai²,

Lee³

et al. 2014

IEEE-EMBS International Conference on Biomedical and Health Informatics (BHI)

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The Clinical Document Architecture (CDA) is a widely adopted international standard for clinical documents design; the CDA document with coded entries increases the semantic interoperability in the course of clinical document exchange. This study developed a CDA entry generation pipeline for converting free-text documents into CDA documents with entry-level. The results showed that CDA entry coding could be accomplished using natural language processing.

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Section: B Nature Language Processing In Medicinementioning

confidence: 99%

An entry generation pipeline for converting free-text medical document into Clinical Document Architecture document with entry-level

Lin¹,

Lai²,

Lee³

et al. 2014

IEEE-EMBS International Conference on Biomedical and Health Informatics (BHI)

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“…These results were an improvement on current related work in the bioinformatics field (Barbosa-Silva et al, , Corney et al, 2004, Meurs et al, 2011, chemistry field (Na et al, 2010, Yamashita et al, 2011) and the biomedical field (Bundschus et al, 2008, Crowley et al, 2010, Pestian et al, 2007 using similar techniques.…”

Section: Analysis and Discussionmentioning

confidence: 56%

“…Information extraction methods applied to extract structured data from publications have been studied extensively in the past in fields that include biology (BarbosaSilva et al, 2010, Corney et al, 2004, Meurs et al, 2011, chemistry (Na et al, 2010, Yamashita et al, 2011, biomedicine (Bundschus et al, 2008, Crowley et al, 2010, Pestian et al, 2007, text summarisation (Lin and Hovy, 2000) and e-learning (Monachesi et al, 2009). A review of these previous efforts is provided in this section.…”

Section: Related Workmentioning

confidence: 99%

“…Furthermore, similar approaches (ontology-based GATE gazetteer and relation extraction using pre-defined rules, and machine-learning) have been applied with mixed success to publications in the bioinformatics field (Barbosa-Silva et al, , Bundschus et al, 2008, Corney et al, 2004, Crowley et al, 2010, Meurs et al, 2011, Na et al, 2010, Pestian et al, 2007, Yamashita et al, 2011. Further examples are provided in the following paragraphs.…”

Section: Related Workmentioning

confidence: 99%

“…Access to the search page and some example queries are available via the Web portal (20thcpaint, 2012a). , Bundschus et al, 2008, Corney et al, 2004, Crowley et al, 2010, Meurs et al, 2011, Na et al, 2010, Pestian et al, 2007, Yamashita et al, 2011.…”

Section: System Architecturementioning

confidence: 99%

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A Semantic e-Science Platform for 20th Century Paint Conservation

Odat¹

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Throughout the twentieth century, artists in Australia and across the Southeast AsiaPacific region have enthusiastically embraced new materials (synthetic media, new pigments, dyes and additives). But compared to traditional artists' paints, these new materials have affected paint handling and paint stability. These new materials have also resulted in a lack of understanding of the preservation issues associated with the resulting artworks. As a result, today's collectors, curators and conservators are confronted with significant material-based preservation questions associated with 20 th century art/paint preservation -but they lack the sustained and integrated knowledge-base to inform their decision making.In order to understand the causes of paint degradation and the best preservation and treatment approaches, conservators need access to a wide range of distributed and cross-disciplinary datasets.  Use a number of case studies to evaluate OPPRA's ability to capture the detailed workflows and outputs associated with paint conservation experiments (e.g., sampling method, experimental processes and characterisation data); Apply and optimise a combination of semantic tagging and machine learning approaches to extract structured knowledge (compliant with OPPRA) from freetext publications on paint conservation -so it can be shared, integrated, compared and re-used; Evaluate OPPRA's ability to integrate experimental datasets, structured knowledge extracted from free-text publications and external public relevant databases (e.g., on paint chemistry), to answer a set of advanced, exemplar (SPARQL) queries specified by art conservators; Evaluate OWL-DL for inferencing and extracting new facts from the integrated knowledge base (generated from integrating experimental data capture, structured knowledge extracted from past publications and public relevant databases) in order to answer advanced queries specified by art conservators.4

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Population-Based Analysis of Histologically Confirmed Melanocytic Proliferations Using Natural Language Processing

et al. 2018

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IMPORTANCE Population-based information on the distribution of histologic diagnoses associated with skin biopsies is unknown. Electronic medical records (EMRs) enable automated extraction of pathology report data to improve our epidemiologic understanding of skin biopsy outcomes, specifically those of melanocytic origin.OBJECTIVE To determine population-based frequencies and distribution of histologically confirmed melanocytic lesions. DESIGN, SETTING, AND PARTICIPANTSA natural language processing (NLP)-based analysis of EMR pathology reports of adult patients who underwent skin biopsies at a large integrated health care delivery system in the US Pacific Northwest from January 1, 2007, through December 31, 2012.EXPOSURES Skin biopsy procedure. MAIN OUTCOMES AND MEASURESThe primary outcome was histopathologic diagnosis, obtained using an NLP-based system to process EMR pathology reports. We determined the percentage of diagnoses classified as melanocytic vs nonmelanocytic lesions. Diagnoses classified as melanocytic were further subclassified using the Melanocytic Pathology Assessment Tool and Hierarchy for Diagnosis (MPATH-Dx) reporting schema into the following categories: class I (nevi and other benign proliferations such as mildly dysplastic lesions typically requiring no further treatment), class II (moderately dysplastic and other low-risk lesions that may merit narrow reexcision with <5-mm margins), class III (eg, melanoma in situ and other higher-risk lesions warranting reexcision with 5-mm to 1-cm margins), and class IV/V (invasive melanoma requiring wide reexcision with Ն1-cm margins and potential adjunctive therapy). Health system cancer registry data were used to define the percentage of invasive melanoma cases within MPATH-Dx class IV (stage T1a) vs V (Նstage T1b).RESULTS A total of 80 368 skin biopsies, performed on 47 529 patients, were examined. Nearly 1 in 4 skin biopsies were of melanocytic lesions (23%; n = 18 715), which were distributed according to MPATH-Dx categories as follows: class I, 83.1% (n = 15 558); class II, 8.3% (n = 1548); class III, 4.5% (n = 842); class IV, 2.2% (n = 405); and class V, 1.9% (n = 362). CONCLUSIONS AND RELEVANCEApproximately one-quarter of skin biopsies resulted in diagnoses of melanocytic proliferations. These data provide the first population-based estimates across the spectrum of melanocytic lesions ranging from benign through dysplastic to malignant. These results may serve as a foundation for future research seeking to understand the epidemiology of melanocytic proliferations and optimization of skin biopsy utilization.

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caTIES: a grid based system for coding and retrieval of surgical pathology reports and tissue specimens in support of translational research

Cited by 79 publications

References 14 publications

An entry generation pipeline for converting free-text medical document into Clinical Document Architecture document with entry-level

An entry generation pipeline for converting free-text medical document into Clinical Document Architecture document with entry-level

A Semantic e-Science Platform for 20th Century Paint Conservation

Population-Based Analysis of Histologically Confirmed Melanocytic Proliferations Using Natural Language Processing

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