Archive for the ‘Pathology Informatics’ Category

Journal of the American Medical Informatics Association (JAMIA)

Sunday, August 5th, 2012

Journal of the American Medical Informatics Association (JAMIA)

Aims and Scope

JAMIA is AMIA‘s premier peer-reviewed journal for biomedical and health informatics. Covering the full spectrum of activities in the field, JAMIA includes informatics articles in the areas of clinical care, clinical research, translational science, implementation science, imaging, education, consumer health, public health, and policy. JAMIA’s articles describe innovative informatics research and systems that help to advance biomedical science and to promote health. Case reports, perspectives and reviews also help readers stay connected with the most important informatics developments in implementation, policy and education.

Another informatics journal to whitelist for searching.

Content is freely available after twelve (12) months.

Cancer, NLP & Kaiser Permanente Southern California (KPSC)

Sunday, August 5th, 2012

Kaiser Permanente Southern California (KPSC) deserves high marks for the research in:

Identifying primary and recurrent cancers using a SAS-based natural language processing algorithm by Justin A Strauss, et. al.


Objective Significant limitations exist in the timely and complete identification of primary and recurrent cancers for clinical and epidemiologic research. A SAS-based coding, extraction, and nomenclature tool (SCENT) was developed to address this problem.

Materials and methods SCENT employs hierarchical classification rules to identify and extract information from electronic pathology reports. Reports are analyzed and coded using a dictionary of clinical concepts and associated SNOMED codes. To assess the accuracy of SCENT, validation was conducted using manual review of pathology reports from a random sample of 400 breast and 400 prostate cancer patients diagnosed at Kaiser Permanente Southern California. Trained abstractors classified the malignancy status of each report.

Results Classifications of SCENT were highly concordant with those of abstractors, achieving κ of 0.96 and 0.95 in the breast and prostate cancer groups, respectively. SCENT identified 51 of 54 new primary and 60 of 61 recurrent cancer cases across both groups, with only three false positives in 792 true benign cases. Measures of sensitivity, specificity, positive predictive value, and negative predictive value exceeded 94% in both cancer groups.

Discussion Favorable validation results suggest that SCENT can be used to identify, extract, and code information from pathology report text. Consequently, SCENT has wide applicability in research and clinical care. Further assessment will be needed to validate performance with other clinical text sources, particularly those with greater linguistic variability.

Conclusion SCENT is proof of concept for SAS-based natural language processing applications that can be easily shared between institutions and used to support clinical and epidemiologic research.

Before I forget:

Data sharing statement SCENT is freely available for non-commercial use and modification. Program source code and requisite support files may be downloaded from:

Topic map promotion point: Application was built to account for linguistic variability, not to stamp it out.

Tools build to fit users are more likely to succeed, don’t you think?

Journal of Pathology Informatics (JPI)

Sunday, August 5th, 2012

Journal of Pathology Informatics (JPI)


The Journal of Pathology Informatics (JPI) is an open access peer-reviewed journal dedicated to the advancement of pathology informatics. This is the official journal of the Association for Pathology Informatics (API). The journal aims to publish broadly about pathology informatics and freely disseminate all articles worldwide. This journal is of interest to pathologists, informaticians, academics, researchers, health IT specialists, information officers, IT staff, vendors, and anyone with an interest in informatics. We encourage submissions from anyone with an interest in the field of pathology informatics. We publish all types of papers related to pathology informatics including original research articles, technical notes, reviews, viewpoints, commentaries, editorials, book reviews, and correspondence to the editors. All submissions are subject to peer review by the well-regarded editorial board and by expert referees in appropriate specialties.

Another site to add to your whitelist of sites to search for informatics information.