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  1. Software

    An ontology-driven tool for structured data acquisition using Web forms

    Structured data acquisition is a common task that is widely performed in biomedicine. However, current solutions for this task are far from providing a means to structure data in such a way that it can be auto...

    Rafael S. Gonçalves, Samson W. Tu, Csongor I. Nyulas, Michael J. Tierney and Mark A. Musen

    Journal of Biomedical Semantics 2017 8:26

    Published on: 1 August 2017

  2. Research

    Towards a more molecular taxonomy of disease

    Disease taxonomies have been designed for many applications, but they tend not to fully incorporate the growing amount of molecular-level knowledge of disease processes, inhibiting research efforts. Understand...

    Jisoo Park, Benjamin J. Hescott and Donna K. Slonim

    Journal of Biomedical Semantics 2017 8:25

    Published on: 27 July 2017

  3. Research

    Ontological interpretation of biomedical database content

    Biological databases store data about laboratory experiments, together with semantic annotations, in order to support data aggregation and retrieval. The exact meaning of such annotations in the context of a d...

    Filipe Santana da Silva, Ludger Jansen, Fred Freitas and Stefan Schulz

    Journal of Biomedical Semantics 2017 8:24

    Published on: 26 June 2017

  4. Research

    NCBO Ontology Recommender 2.0: an enhanced approach for biomedical ontology recommendation

    Ontologies and controlled terminologies have become increasingly important in biomedical research. Researchers use ontologies to annotate their data with ontology terms, enabling better data integration and in...

    Marcos Martínez-Romero, Clement Jonquet, Martin J. O’Connor, John Graybeal, Alejandro Pazos and Mark A. Musen

    Journal of Biomedical Semantics 2017 8:21

    Published on: 7 June 2017

  5. Software

    Literature evidence in open targets - a target validation platform

    We present the Europe PMC literature component of Open Targets - a target validation platform that integrates various evidence to aid drug target identification and validation. The component identifies target-...

    Şenay Kafkas, Ian Dunham and Johanna McEntyre

    Journal of Biomedical Semantics 2017 8:20

    Published on: 6 June 2017

  6. Software

    Dead simple OWL design patterns

    Bio-ontologies typically require multiple axes of classification to support the needs of their users. Development of such ontologies can only be made scalable and sustainable by the use of inference to automat...

    David Osumi-Sutherland, Melanie Courtot, James P. Balhoff and Christopher Mungall

    Journal of Biomedical Semantics 2017 8:18

    Published on: 5 June 2017

  7. Research

    Building a semantic web-based metadata repository for facilitating detailed clinical modeling in cancer genome studies

    Detailed Clinical Models (DCMs) have been regarded as the basis for retaining computable meaning when data are exchanged between heterogeneous computer systems. To better support clinical cancer data capturing...

    Deepak K. Sharma, Harold R. Solbrig, Cui Tao, Chunhua Weng, Christopher G. Chute and Guoqian Jiang

    Journal of Biomedical Semantics 2017 8:19

    Published on: 5 June 2017

  8. 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

  9. 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

  10. 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

  11. 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 Jr, Durre Zehra, Stefan Decker and Dietrich Rebholz-Schuhmann

    Journal of Biomedical Semantics 2017 8:13

    Published on: 15 March 2017

  12. 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

  13. 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

  14. 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

  15. 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

  16. 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

  17. 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

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