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  1. Article: A Linked Open Data-Based Terminology to Describe Libre/Free and Open-source Software: Incremental Development Study.

    Jahn, Franziska / Ammenwerth, Elske / Dornauer, Verena / Höffner, Konrad / Bindel, Michelle / Karopka, Thomas / Winter, Alfred

    JMIR medical informatics

    2023  Volume 11, Page(s) e38861

    Abstract: Background: There is a variety of libre/free and open-source software (LIFOSS) products for medicine and health care. To support health care and IT professionals select an appropriate software product for given tasks, several comparison studies and web ... ...

    Abstract Background: There is a variety of libre/free and open-source software (LIFOSS) products for medicine and health care. To support health care and IT professionals select an appropriate software product for given tasks, several comparison studies and web platforms, such as Medfloss.org, are available. However, due to the lack of a uniform terminology for health informatics, ambiguous or imprecise terms are used to describe the functionalities of LIFOSS. This makes comparisons of LIFOSS difficult and may lead to inappropriate software selection decisions. Using Linked Open Data (LOD) promises to address these challenges.
    Objective: We describe LIFOSS systematically with the help of the underlying Health Information Technology Ontology (HITO). We publish HITO and HITO-based software product descriptions using LOD to obtain the following benefits: (1) linking and reusing existing terminologies and (2) using Semantic Web tools for viewing and querying the LIFOSS data on the World Wide Web.
    Methods: HITO was incrementally developed and implemented. First, classes for the description of software products in health IT evaluation studies were identified. Second, requirements for describing LIFOSS were elicited by interviewing domain experts. Third, to describe domain-specific functionalities of software products, existing catalogues of features and enterprise functions were analyzed and integrated into the HITO knowledge base. As a proof of concept, HITO was used to describe 25 LIFOSS products.
    Results: HITO provides a defined set of classes and their relationships to describe LIFOSS in medicine and health care. With the help of linked or integrated catalogues for languages, programming languages, licenses, features, and enterprise functions, the functionalities of LIFOSS can be precisely described and compared. We publish HITO and the LIFOSS descriptions as LOD; they can be queried and viewed using different Semantic Web tools, such as Resource Description Framework (RDF) browsers, SPARQL Protocol and RDF Query Language (SPARQL) queries, and faceted searches. The advantages of providing HITO as LOD are demonstrated by practical examples.
    Conclusions: HITO is a building block to achieving unambiguous communication among health IT professionals and researchers. Providing LIFOSS product information as LOD enables barrier-free and easy access to data that are often hidden in user manuals of software products or are not available at all. Efforts to establish a unique terminology of medical and health informatics should be further supported and continued.
    Language English
    Publishing date 2023-01-20
    Publishing country Canada
    Document type Journal Article
    ZDB-ID 2798261-0
    ISSN 2291-9694
    ISSN 2291-9694
    DOI 10.2196/38861
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  2. Conference proceedings: Medicine 2.0, Health 2.0, Health 3.0 – „Buzzwords“ oder Chancen für die medizinische Forschung und die Gesundheitswirtschaft?

    Karopka, Thomas

    2009  , Page(s) 09gmds314

    Event/congress 54. Jahrestagung der Deutschen Gesellschaft für Medizinische Informatik, Biometrie und Epidemiologie (gmds); Essen; Deutsche Gesellschaft für Medizinische Informatik, Biometrie und Epidemiologie; 2009
    Keywords Medizin, Gesundheit ; Web 2.0 ; Medicine 2.0 ; Health 2.0 ; Health 3.0 ; Public Health
    Publishing date 2009-09-02
    Publisher German Medical Science GMS Publishing House; Düsseldorf
    Document type Conference proceedings
    DOI 10.3205/09gmds314
    Database German Medical Science

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  3. Article ; Online: Towards Precise Descriptions of Medical Free/Libre and Open Source Software.

    Jahn, Franziska / Bindel, Michelle / Höffner, Konrad / Ghalandari, Maryam / Schneider, Birgit / Stäubert, Sebastian / Dornauer, Verena / Karopka, Thomas / Ammenwerth, Elske / Winter, Alfred

    Studies in health technology and informatics

    2020  Volume 270, Page(s) 463–468

    Abstract: The web portal Medfloss.org lists over 360 medical free/libre and open source software (MEDFLOSS) projects. These projects are described with the help of a self-developed nomenclature. Due to inconsistencies, the nomenclature shall be replaced by HITO, ... ...

    Abstract The web portal Medfloss.org lists over 360 medical free/libre and open source software (MEDFLOSS) projects. These projects are described with the help of a self-developed nomenclature. Due to inconsistencies, the nomenclature shall be replaced by HITO, the Health IT Ontology. HITO is developed iteratively based on different use cases. This paper aims to describe methods and results of the second HITO use case in which HITO is extended to improve the description, retrieval and comparisons of MEDFLOSS projects on Medfloss.org. We use a mixed-methods approach to add concepts and relationships to describe MEDFLOSS precisely. The resulting HITO version stresses functional descriptions based on features and supported enterprise functions, rather than just describing technical characteristics. However, describing a larger number of MEDFLOSS projects requires the commitment of the community.
    MeSH term(s) Semantics ; Software
    Language English
    Publishing date 2020-06-20
    Publishing country Netherlands
    Document type Journal Article
    ISSN 1879-8365
    ISSN (online) 1879-8365
    DOI 10.3233/SHTI200203
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  4. Article: Free/Libre open source software in health care: a review.

    Karopka, Thomas / Schmuhl, Holger / Demski, Hans

    Healthcare informatics research

    2014  Volume 20, Issue 1, Page(s) 11–22

    Abstract: Objectives: To assess the current state of the art and the contribution of Free/Libre Open Source Software in health care (FLOSS-HC).: Methods: The review is based on a narrative review of the scientific literature as well as sources in the context ... ...

    Abstract Objectives: To assess the current state of the art and the contribution of Free/Libre Open Source Software in health care (FLOSS-HC).
    Methods: The review is based on a narrative review of the scientific literature as well as sources in the context of FLOSS-HC available through the Internet. All relevant available sources have been integrated into the MedFLOSS database and are freely available to the community.
    Results: The literature review reveals that publications about FLOSS-HC are scarce. The largest part of information about FLOSS-HC is available on dedicated websites and not in the academic literature. There are currently FLOSS alternatives available for nearly every specialty in health care. Maturity and quality varies considerably and there is little information available on the percentage of systems that are actually used in health care delivery.
    Conclusions: The global impact of FLOSS-HC is still very limited and no figures on the penetration and usage of FLOSS-HC are available. However, there has been a considerable growth in the last 5 to 10 years. While there where only few systems available a decade ago, in the meantime many systems got available (e.g., more than 300 in the MedFLOSS database). While FLOSS concepts play an important role in most IT related sectors (e.g., telecommunications, embedded devices) the healthcare industry is lagging behind this trend.
    Language English
    Publishing date 2014-01-31
    Publishing country Korea (South)
    Document type Journal Article ; Review
    ZDB-ID 2619923-3
    ISSN 2093-369X ; 2093-3681
    ISSN (online) 2093-369X
    ISSN 2093-3681
    DOI 10.4258/hir.2014.20.1.11
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  5. Article ; Online: Use of some cost-effective technologies for a routine clinical pathology laboratory.

    Vázquez, Mercedes / Anfossi, Laura / Ben-Yoav, Hadar / Diéguez, Lorena / Karopka, Thomas / Della Ventura, Bartolomeo / Abalde-Cela, Sara / Minopoli, Antonio / Di Nardo, Fabio / Shukla, Vikas Kumar / Teixeira, Alexandra / Tvarijonaviciute, Asta / Franco-Martínez, Lorena

    Lab on a chip

    2021  Volume 21, Issue 22, Page(s) 4330–4351

    Abstract: Classically, the need for highly sophisticated instruments with important economic costs has been a major limiting factor for clinical pathology laboratories, especially in developing countries. With the aim of making clinical pathology more accessible, ... ...

    Abstract Classically, the need for highly sophisticated instruments with important economic costs has been a major limiting factor for clinical pathology laboratories, especially in developing countries. With the aim of making clinical pathology more accessible, a wide variety of free or economical technologies have been developed worldwide in the last few years. 3D printing and Arduino approaches can provide up to 94% economical savings in hardware and instrumentation in comparison to commercial alternatives. The vast selection of point-of-care-tests (POCT) currently available also limits the need for specific instruments or personnel, as they can be used almost anywhere and by anyone. Lastly, there are dozens of free and libre digital tools available in health informatics. This review provides an overview of the state-of-the-art on cost-effective alternatives with applications in routine clinical pathology laboratories. In this context, a variety of technologies including 3D printing and Arduino, lateral flow assays, plasmonic biosensors, and microfluidics, as well as laboratory information systems, are discussed. This review aims to serve as an introduction to different technologies that can make clinical pathology more accessible and, therefore, contribute to achieve universal health coverage.
    MeSH term(s) Cost-Benefit Analysis ; Laboratories ; Microfluidics ; Pathology, Clinical ; Point-of-Care Testing
    Language English
    Publishing date 2021-11-09
    Publishing country England
    Document type Journal Article ; Research Support, Non-U.S. Gov't ; Review
    ZDB-ID 2056646-3
    ISSN 1473-0189 ; 1473-0197
    ISSN (online) 1473-0189
    ISSN 1473-0197
    DOI 10.1039/d1lc00658d
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  6. Article ; Online: Free/Libre Open Source Software in Health Care

    Thomas Karopka / Holger Schmuhl / Hans Demski

    Healthcare Informatics Research, Vol 20, Iss 1, Pp 11-

    A Review

    2014  Volume 22

    Abstract: ObjectivesTo assess the current state of the art and the contribution of Free/Libre Open Source Software in health care (FLOSS-HC).MethodsThe review is based on a narrative review of the scientific literature as well as sources in the context of FLOSS-HC ...

    Abstract ObjectivesTo assess the current state of the art and the contribution of Free/Libre Open Source Software in health care (FLOSS-HC).MethodsThe review is based on a narrative review of the scientific literature as well as sources in the context of FLOSS-HC available through the Internet. All relevant available sources have been integrated into the MedFLOSS database and are freely available to the community.ResultsThe literature review reveals that publications about FLOSS-HC are scarce. The largest part of information about FLOSS-HC is available on dedicated websites and not in the academic literature. There are currently FLOSS alternatives available for nearly every specialty in health care. Maturity and quality varies considerably and there is little information available on the percentage of systems that are actually used in health care delivery.ConclusionsThe global impact of FLOSS-HC is still very limited and no figures on the penetration and usage of FLOSS-HC are available. However, there has been a considerable growth in the last 5 to 10 years. While there where only few systems available a decade ago, in the meantime many systems got available (e.g., more than 300 in the MedFLOSS database). While FLOSS concepts play an important role in most IT related sectors (e.g., telecommunications, embedded devices) the healthcare industry is lagging behind this trend.
    Keywords software ; medical informatics ; delivery of health care ; sustainable development ; Computer applications to medicine. Medical informatics ; R858-859.7
    Subject code 302
    Language English
    Publishing date 2014-01-01T00:00:00Z
    Publisher The Korean Society of Medical Informatics
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  7. Conference proceedings: Medfloss.org – Ein umfassendes und offenes Informationsportal zu Open Source im Gesundheitswesen

    Schmuhl, Holger / Demski, Hans / Karopka, Thomas

    2011  , Page(s) 11gmds510

    Event/congress 56. Jahrestagung der Deutschen Gesellschaft für Medizinische Informatik, Biometrie und Epidemiologie (gmds), 6. Jahrestagung der Deutschen Gesellschaft für Epidemiologie (DGEpi); Mainz//2011; Mainz; ; Deutsche Gesellschaft für Epidemiologie; 2011
    Keywords Medizin, Gesundheit ; Open Source ; Freie Software ; FLOSS ; Informationsportal ; Kollaboration
    Publishing date 2011-09-20
    Publisher German Medical Science GMS Publishing House; Düsseldorf
    Document type Conference proceedings
    DOI 10.3205/11gmds510
    Database German Medical Science

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  8. Article: Automatic construction of gene relation networks using text mining and gene expression data.

    Karopka, Thomas / Scheel, Thomas / Bansemer, Sven / Glass, Anne

    Medical informatics and the Internet in medicine

    2004  Volume 29, Issue 2, Page(s) 169–183

    Abstract: Microarray gene expression analysis is a powerful high-throughput technique that enables researchers to monitor the expression of thousands of genes simultaneously. Using this methodology huge amounts of data are produced which have to be analysed. ... ...

    Abstract Microarray gene expression analysis is a powerful high-throughput technique that enables researchers to monitor the expression of thousands of genes simultaneously. Using this methodology huge amounts of data are produced which have to be analysed. Clustering algorithms are used to group genes together based on a predefined distance measure. However, clustering algorithms do not necessarily group the genes in a biological meaningful way. Additional information is needed to improve the identification of disease relevant genes. The primary objective of our project is to support the analysis of microarray gene expression data by construction of gene relation networks (GRNs). Required information can not be found in a structured representation like a database. In contrast, a large number of relations are described in biomedical literature. The main outcome of this project is the implementation of a software system that provides clinicians and researchers with a tool that supports the analysis of microarray gene expression data by mapping known relationships from the biomedical literature to local gene expression experiments.
    MeSH term(s) Abbreviations as Topic ; Abstracting and Indexing as Topic ; Algorithms ; Cluster Analysis ; Databases, Genetic/standards ; Gene Expression Profiling/methods ; Gene Expression Profiling/standards ; Humans ; Information Systems/organization & administration ; Leukemia, Myeloid, Acute/classification ; Leukemia, Myeloid, Acute/genetics ; MEDLINE ; Natural Language Processing ; Neural Networks (Computer) ; Oligonucleotide Array Sequence Analysis/methods ; Oligonucleotide Array Sequence Analysis/standards ; Precursor Cell Lymphoblastic Leukemia-Lymphoma/classification ; Precursor Cell Lymphoblastic Leukemia-Lymphoma/genetics ; User-Computer Interface
    Language English
    Publishing date 2004-06
    Publishing country England
    Document type Journal Article ; Research Support, Non-U.S. Gov't ; Validation Studies
    ZDB-ID 1470814-0
    ISSN 1464-5238 ; 1463-9238
    ISSN (online) 1464-5238
    ISSN 1463-9238
    DOI 10.1080/14639230412331280422
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  9. Conference proceedings: Knowledge Based Analysis of Microarray Gene Expression Data

    Karopka, Thomas / Glass, Änne

    2005  , Page(s) 05gmds064

    Event/congress 50. Jahrestagung der Deutschen Gesellschaft für Medizinische Informatik, Biometrie und Epidemiologie (gmds), 12. Jahrestagung der Deutschen Arbeitsgemeinschaft für Epidemiologie; Freiburg im Breisgau; ; Deutsche Arbeitsgemeinschaft für Epidemiologie; 2005
    Keywords Medizin, Gesundheit
    Publishing date 2005-09-08
    Publisher German Medical Science; Düsseldorf, Köln
    Document type Conference proceedings
    Database German Medical Science

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  10. Article ; Online: The Autoimmune Disease Database: a dynamically compiled literature-derived database.

    Karopka, Thomas / Fluck, Juliane / Mevissen, Heinz-Theodor / Glass, Anne

    BMC bioinformatics

    2006  Volume 7, Page(s) 325

    Abstract: Background: Autoimmune diseases are disorders caused by an immune response directed against the body's own organs, tissues and cells. In practice more than 80 clinically distinct diseases, among them systemic lupus erythematosus and rheumatoid arthritis, ...

    Abstract Background: Autoimmune diseases are disorders caused by an immune response directed against the body's own organs, tissues and cells. In practice more than 80 clinically distinct diseases, among them systemic lupus erythematosus and rheumatoid arthritis, are classified as autoimmune diseases. Although their etiology is unclear these diseases share certain similarities at the molecular level i.e. susceptibility regions on the chromosomes or the involvement of common genes. To gain an overview of these related diseases it is not feasible to do a literary review but it requires methods of automated analyses of the more than 500,000 Medline documents related to autoimmune disorders.
    Results: In this paper we present the first version of the Autoimmune Disease Database which to our knowledge is the first comprehensive literature-based database covering all known or suspected autoimmune diseases. This dynamically compiled database allows researchers to link autoimmune diseases to the candidate genes or proteins through the use of named entity recognition which identifies genes/proteins in the corresponding Medline abstracts. The Autoimmune Disease Database covers 103 autoimmune disease concepts. This list was expanded to include synonyms and spelling variants yielding a list of over 1,200 disease names. The current version of the database provides links to 541,690 abstracts and over 5,000 unique genes/proteins.
    Conclusion: The Autoimmune Disease Database provides the researcher with a tool to navigate potential gene-disease relationships in Medline abstracts in the context of autoimmune diseases.
    MeSH term(s) Autoimmune Diseases/classification ; Autoimmune Diseases/genetics ; Databases, Factual ; Databases, Genetic ; Evaluation Studies as Topic ; Humans ; Internet ; MEDLINE ; Medical Subject Headings ; Systems Integration ; User-Computer Interface ; Vocabulary, Controlled
    Language English
    Publishing date 2006-06-27
    Publishing country England
    Document type Comparative Study ; Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 2041484-5
    ISSN 1471-2105 ; 1471-2105
    ISSN (online) 1471-2105
    ISSN 1471-2105
    DOI 10.1186/1471-2105-7-325
    Database MEDical Literature Analysis and Retrieval System OnLINE

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