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  1. Research

    Modulated evaluation metrics for drug-based ontologies

    Research for ontology evaluation is scarce. If biomedical ontological datasets and knowledgebases are to be widely used, there needs to be quality control and evaluation for the content and structure of the on...

    Muhammad Amith and Cui Tao

    Journal of Biomedical Semantics 2017 8:17

    Published on: 24 April 2017

  2. Research

    Learning from biomedical linked data to suggest valid pharmacogenes

    A standard task in pharmacogenomics research is identifying genes that may be involved in drug response variability, i.e., pharmacogenes. Because genomic experiments tended to generate many false positives, co...

    Kevin Dalleau, Yassine Marzougui, Sébastien Da Silva, Patrice Ringot, Ndeye Coumba Ndiaye and Adrien Coulet

    Journal of Biomedical Semantics 2017 8:16

    Published on: 20 April 2017

  3. Research

    SNPPhenA: a corpus for extracting ranked associations of single-nucleotide polymorphisms and phenotypes from literature

    Single Nucleotide Polymorphisms (SNPs) are among the most important types of genetic variations influencing common diseases and phenotypes. Recently, some corpora and methods have been developed with the purpo...

    Behrouz Bokharaeian, Alberto Diaz, Nasrin Taghizadeh, Hamidreza Chitsaz and Ramyar Chavoshinejad

    Journal of Biomedical Semantics 2017 8:14

    Published on: 7 April 2017

  4. Research

    BioFed: federated query processing over life sciences linked open data

    Biomedical data, e.g. from knowledge bases and ontologies, is increasingly made available following open linked data principles, at best as RDF triple data. This is a necessary step towards unified access to b...

    Ali Hasnain, Qaiser Mehmood, Syeda Sana e Zainab, Muhammad Saleem, Claude Warren, Durre Zehra, Stefan Decker and Dietrich Rebholz-Schuhmann

    Journal of Biomedical Semantics 2017 8:13

    Published on: 15 March 2017

  5. Research

    Therapeutic indications and other use-case-driven updates in the drug ontology: anti-malarials, anti-hypertensives, opioid analgesics, and a large term request

    The Drug Ontology (DrOn) is an OWL2-based representation of drug products and their ingredients, mechanisms of action, strengths, and dose forms. We originally created DrOn for use cases in comparative effecti...

    William R. Hogan, Josh Hanna, Amanda Hicks, Samira Amirova, Baxter Bramblett, Matthew Diller, Rodel Enderez, Timothy Modzelewski, Mirela Vasconcelos and Chris Delcher

    Journal of Biomedical Semantics 2017 8:10

    Published on: 3 March 2017

  6. Research

    12 years on – Is the NLM medical text indexer still useful and relevant?

    Facing a growing workload and dwindling resources, the US National Library of Medicine (NLM) created the Indexing Initiative project in 1996. This cross-library team’s mission is to explore indexing methodolog...

    James Mork, Alan Aronson and Dina Demner-Fushman

    Journal of Biomedical Semantics 2017 8:8

    Published on: 23 February 2017

  7. Research

    Building a model for disease classification integration in oncology, an approach based on the national cancer institute thesaurus

    Identifying incident cancer cases within a population remains essential for scientific research in oncology. Data produced within electronic health records can be useful for this purpose. Due to the multiplici...

    Vianney Jouhet, Fleur Mougin, Bérénice Bréchat and Frantz Thiessard

    Journal of Biomedical Semantics 2017 8:6

    Published on: 7 February 2017

  8. Research

    SAFE: SPARQL Federation over RDF Data Cubes with Access Control

    Several query federation engines have been proposed for accessing public Linked Open Data sources. However, in many domains, resources are sensitive and access to these resources is tightly controlled by stake...

    Yasar Khan, Muhammad Saleem, Muntazir Mehdi, Aidan Hogan, Qaiser Mehmood, Dietrich Rebholz-Schuhmann and Ratnesh Sahay

    Journal of Biomedical Semantics 2017 8:5

    Published on: 1 February 2017

  9. Research

    Developing a knowledge base to support the annotation of ultrasound images of ectopic pregnancy

    Ectopic pregnancy is a frequent early complication of pregnancy associated with significant rates of morbidly and mortality. The positive diagnosis of this condition is established through transvaginal ultraso...

    Ferdinand Dhombres, Paul Maurice, Stéphanie Friszer, Lucie Guilbaud, Nathalie Lelong, Babak Khoshnood, Jean Charlet, Nicolas Perrot, Eric Jauniaux, Davor Jurkovic and Jean-Marie Jouannic

    Journal of Biomedical Semantics 2017 8:4

    Published on: 31 January 2017

  10. Research

    Consolidating drug data on a global scale using Linked Data

    Drug product data is available on the Web in a distributed fashion. The reasons lie within the regulatory domains, which exist on a national level. As a consequence, the drug data available on the Web are inde...

    Milos Jovanovik and Dimitar Trajanov

    Journal of Biomedical Semantics 2017 8:3

    Published on: 21 January 2017

  11. Research

    An ontological analysis of medical Bayesian indicators of performance

    Biomedical ontologies aim at providing the most exhaustive and rigorous representation of reality as described by biomedical sciences. A large part of medical reasoning deals with diagnosis and is essentially ...

    Adrien Barton, Jean-François Ethier, Régis Duvauferrier and Anita Burgun

    Journal of Biomedical Semantics 2017 8:1

    Published on: 3 January 2017

  12. Research

    tESA: a distributional measure for calculating semantic relatedness

    Semantic relatedness is a measure that quantifies the strength of a semantic link between two concepts. Often, it can be efficiently approximated with methods that operate on words, which represent these conce...

    Maciej Rybinski and José Francisco Aldana-Montes

    Journal of Biomedical Semantics 2016 7:67

    Published on: 28 December 2016

  13. Short Report

    Thematic issue of the Second combined Bio-ontologies and Phenotypes Workshop

    This special issue covers selected papers from the 18th Bio-Ontologies Special Interest Group meeting and Phenotype Day, which took place at the Intelligent Systems for Molecular Biology (ISMB) conference in D...

    Karin Verspoor, Anika Oellrich, Nigel Collier, Tudor Groza, Philippe Rocca-Serra, Larisa Soldatova, Michel Dumontier and Nigam Shah

    Journal of Biomedical Semantics 2016 7:66

    Published on: 12 December 2016

  14. Research

    The flora phenotype ontology (FLOPO): tool for integrating morphological traits and phenotypes of vascular plants

    The systematic analysis of a large number of comparable plant trait data can support investigations into phylogenetics and ecological adaptation, with broad applications in evolutionary biology, agriculture, c...

    Robert Hoehndorf, Mona Alshahrani, Georgios V. Gkoutos, George Gosline, Quentin Groom, Thomas Hamann, Jens Kattge, Sylvia Mota de Oliveira, Marco Schmidt, Soraya Sierra, Erik Smets, Rutger A. Vos and Claus Weiland

    Journal of Biomedical Semantics 2016 7:65

    Published on: 14 November 2016

  15. Research

    TNM-O: ontology support for staging of malignant tumours

    Objectives of this work are to (1) present an ontological framework for the TNM classification system, (2) exemplify this framework by an ontology for colon and rectum tumours, and (3) evaluate this ontology b...

    Martin Boeker, Fábio França, Peter Bronsert and Stefan Schulz

    Journal of Biomedical Semantics 2016 7:64

    Published on: 14 November 2016

  16. Research

    Supporting the analysis of ontology evolution processes through the combination of static and dynamic scaling functions in OQuaRE

    The biomedical community has now developed a significant number of ontologies. The curation of biomedical ontologies is a complex task and biomedical ontologies evolve rapidly, so new versions are regularly an...

    Astrid Duque-Ramos, Manuel Quesada-Martínez, Miguela Iniesta-Moreno, Jesualdo Tomás Fernández-Breis and Robert Stevens

    Journal of Biomedical Semantics 2016 7:63

    Published on: 17 October 2016

  17. Research

    Dione: An OWL representation of ICD-10-CM for classifying patients’ diseases

    Systematized Nomenclature of Medicine - Clinical Terms (SNOMED CT) has been designed as standard clinical terminology for annotating Electronic Health Records (EHRs). EHRs textual information is used to classi...

    María del Mar Roldán-García, María Jesús García-Godoy and José F. Aldana-Montes

    Journal of Biomedical Semantics 2016 7:62

    Published on: 13 October 2016

  18. Research

    TrhOnt: building an ontology to assist rehabilitation processes

    One of the current research efforts in the area of biomedicine is the representation of knowledge in a structured way so that reasoning can be performed on it. More precisely, in the field of physiotherapy, in...

    Idoia Berges, David Antón, Jesús Bermúdez, Alfredo Goñi and Arantza Illarramendi

    Journal of Biomedical Semantics 2016 7:60

    Published on: 4 October 2016

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