Biomedical subjects

Gunther Schadow

Publications and source records attributed to Gunther Schadow.

7 recordsLinked to original sources

PubMed2003

Open Source software in medical informatics--why, how and what.

'Open Source' is a 20-40 year old approach to licensing and distributing software that has recently burst into public view. Against conventional wisdom this approach has been wildly successful in the general software market--probably because the openness lets programmers the world over obtain, critique, use, and build upon the source code without licensing fees. Linux, a UNIX-like operating system, is the best known success. But computer scientists at the University of California, Berkeley began the tradition of software sharing in the mid 1970s with BSD UNIX and distributed the major internet network protocols as source code without a fee. Medical informatics has its own history of Open Source distribution: Massachusetts General's COSTAR and the Veterans Administration's VISTA software have been distributed as source code at no cost for decades. Bioinformatics, our sister field, has embraced the Open Source movement and developed rich libraries of open-source software. Open Source has now gained a tiny foothold in health care (OSCAR GEHR, OpenEMed). Medical informatics researchers and funding agencies should support and nurture this movement. In a world where open-source modules were integrated into operational health care systems, informatics researchers would have real world niches into which they could engraft and test their software inventions. This could produce a burst of innovation that would help solve the many problems of the health care system. We at the Regenstrief Institute are doing our part by moving all of our development to the open-source model.

Database Management Systems↗

PubMed2003

Extracting structured information from free text pathology reports.

We have developed a method that extracts structured information about specimens and their related findings in free-text surgical pathology reports. Our method uses regular expressions that drive a state-automaton on top of XSLT and Java. Text fragments identified are coded against the UMLS. This paper describes the technical approach and reports on a preliminary evaluation study, designed to guide further development. We found that of 275 reviewed reports, 91% were coded at least so that all specimens and their critical pathologic findings were represented in codes.

Databases as Topic↗

PubMed2003

Clinicians' and patients' experiences and satisfaction with unscheduled, nighttime, Internet-based video conferencing for assessing acute medical problems in a nursing facility.

Videoconferencing between patients and their physicians can increase patients' access to healthcare. Unscheduled videoconferencing can benefit patients with acute medical problems but has not been studied extensively. We conducted a clinical trial of unscheduled, nighttime videoconferencing in a nursing home, where on-call physicians usually provide care by telephone from remote locations. Although most calls for medical problems did not lead to videoconferencing, physicians and nursing-home residents were satisfied with videoconferencing when it did occur, and physicians reported that making medical decisions was easier with videoconferencing. Videoconferencing was most often conducted to assess residents with changes in mental status, abnormal laboratory values, or falls. Physicians often lacked immediate access to videoconferencing equipment when medical problems with residents occurred. This application could benefit from improved access and portability of equipment.

Adult↗

PubMed2003

Open-source toolkit for simple XML annotation.

Use of Extensible Markup Language (XML) is increasingly prevalent among medical informatics projects. Many of these projects involve, at some point, the interaction between a researcher and specialized XML documents for the purpose of annotating the XML data. We offer a simple toolkit to assist these researchers. Our solution is a simple, yet fully functional, annotation system that can easily be adapted to the needs of the researcher. All of the materials for this toolkit are freely available.

Algorithms↗

PubMed2002

A successful technique for removing names in pathology reports using an augmented search and replace method.

The ability to access large amounts of de-identified clinical data would facilitate epidemiologic and retrospective research. Previously described de-identification methods require knowledge of natural language processing or have not been made available to the public. We take advantage of the fact that the vast majority of proper names in pathology reports occur in pairs. In rare cases where one proper name is by itself, it is preceded or followed by an affix that identifies it as a proper name (Mrs., Dr., PhD). We created a tool based on this observation using substitution methods that was easy to implement and was largely based on publicly available data sources. We compiled a Clinical and Common Usage Word (CCUW) list as well as a fairly comprehensive proper name list. Despite the large overlap between these two lists, we were able to refine our methods to achieve accuracy similar to previous attempts at de-identification. Our method found 98.7% of 231 proper names in the narrative sections of pathology reports. Three single proper names were missed out of 1001 pathology reports (0.3%, no first name/last name pairs). It is unlikely that identification could be implied from this information. We will continue to refine our methods, specifically working to improve the quality of our CCUW and proper name lists to obtain higher levels of accuracy.

Algorithms↗

PubMed2002

Conducting a study of Internet-based video conferencing for assessing acute medical problems in a nursing facility.

We expect the use of real-time, interactive video conferencing to grow, due to more affordable technology and new health policies. Building and implementing portable systems to enable conferencing between physicians and patients requires durable equipment, committed staff, reliable service, and adequate protection and capture of data. We are studying the use of Internet-based conferencing between on-call physicians and patients residing in a nursing facility. We describe the challenges we experienced in constructing the study. Initiating and orchestrating unscheduled conferences needs to be easy, and requirements for training staff in using equipment should be minimal. Studies of health outcomes should include identification of medical conditions most amenable to benefit from conferencing, and outcomes should include positive as well as negative effects.

Acute Disease↗

PubMed2002

Secure HL7 transactions using Internet mail (Internet draft).

The document describes the applicability of the Internet standardisation efforts on secure electronic data interchange (EDI) transactions for Health Level-7 (HL7), an EDI standard for Healthcare used world-wide. The document heavily relies on the work in progress by the IETF EDIINT working group. It is in most parts a restatement of the EDIINTs requirements document and application statement 1 (AS#1) tailored to the needs of the HL7 audience. The authors tried to make the document as self consistent as possible. The goal is to give to the reader who is not a security or Internet standards expert enough foundational and detail information to enable him to build communication software that complies to the Internet standards. Even though the authors rely on and promote the respective Internet standards and drafts, they did not withstand from commenting on and criticising the work where they see upcoming problems in use with HL7 or other EDI protocols that have not been in the initial focus of the EDIINT working group. The authors make suggestions to add parameters to the specification of the MIME type for EDI messages in RFC 1767 in order to enhance functionality. The authors give use cases for a larger subset of disposition types and modifiers of message disposition notifications. One key issue where the document goes beyond the current EDIINT drafts is the concept of non-repudiation of commitment to an EDI transaction. Secure EDI transactions should be regarded as "distributed contracts," i.e. not only the sending and receiving of single messages should be non-refutable but also the connection between messages interchanges. In anticipation of this requirement HL7 usually requires a response message to be sent to acknowledge every transaction. The authors therefore have the requirement to securely couple an EDI response message to its request message. Given the current shape of RFC 1767 this is generally possible only if a response message is coupled with an MDN receipt and the combination of both signed by the responder. The document describes a protocol to bundle MDN and response that uses the MIME multi-part/related content type in RFC 2112.

Computer Security↗