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  1. Medical ontologies are expected to contribute to the effective use of medical information resources that store considerable amount of data. In this study, we focused on disease ontology because the complicated...

    Authors: Kouji Kozaki, Yuki Yamagata, Riichiro Mizoguchi, Takeshi Imai and Kazuhiko Ohe

    Citation: Journal of Biomedical Semantics 2017 8:22

    Content type: Research

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  2. 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...

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

    Citation: Journal of Biomedical Semantics 2017 8:21

    Content type: Research

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  3. 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-...

    Authors: Şenay Kafkas, Ian Dunham and Johanna McEntyre

    Citation: Journal of Biomedical Semantics 2017 8:20

    Content type: Software

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  4. 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...

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

    Citation: Journal of Biomedical Semantics 2017 8:19

    Content type: Research

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  5. 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...

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

    Citation: Journal of Biomedical Semantics 2017 8:18

    Content type: Software

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  6. 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...

    Authors: Muhammad Amith and Cui Tao

    Citation: Journal of Biomedical Semantics 2017 8:17

    Content type: Research

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  7. 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...

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

    Citation: Journal of Biomedical Semantics 2017 8:16

    Content type: Research

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  8. 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...

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

    Citation: Journal of Biomedical Semantics 2017 8:14

    Content type: Research

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  9. 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...

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

    Citation: Journal of Biomedical Semantics 2017 8:13

    Content type: Research

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  10. Integrating multiple sources of pharmacovigilance evidence has the potential to advance the science of safety signal detection and evaluation. In this regard, there is a need for more research on how to integr...

    Authors:

    Citation: Journal of Biomedical Semantics 2017 8:11

    Content type: Software

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  11. 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...

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

    Citation: Journal of Biomedical Semantics 2017 8:10

    Content type: Research

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  12. Analysing public opinions on HPV vaccines on social media using machine learning based approaches will help us understand the reasons behind the low vaccine coverage and come up with corresponding strategies t...

    Authors: Jingcheng Du, Jun Xu, Hsingyi Song, Xiangyu Liu and Cui Tao

    Citation: Journal of Biomedical Semantics 2017 8:9

    Content type: Research

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  13. 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...

    Authors: Vianney Jouhet, Fleur Mougin, Bérénice Bréchat and Frantz Thiessard

    Citation: Journal of Biomedical Semantics 2017 8:6

    Content type: Research

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  14. 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...

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

    Citation: Journal of Biomedical Semantics 2017 8:5

    Content type: Research

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  15. 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...

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

    Citation: Journal of Biomedical Semantics 2017 8:4

    Content type: Research

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  16. 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...

    Authors: Milos Jovanovik and Dimitar Trajanov

    Citation: Journal of Biomedical Semantics 2017 8:3

    Content type: Research

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  17. 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 ...

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

    Citation: Journal of Biomedical Semantics 2017 8:1

    Content type: Research

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  18. 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...

    Authors: Maciej Rybinski and José Francisco Aldana-Montes

    Citation: Journal of Biomedical Semantics 2016 7:67

    Content type: Research

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  19. 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...

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

    Citation: Journal of Biomedical Semantics 2016 7:66

    Content type: Short Report

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  20. 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...

    Authors: 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

    Citation: Journal of Biomedical Semantics 2016 7:65

    Content type: Research

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  21. 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...

    Authors: Martin Boeker, Fábio França, Peter Bronsert and Stefan Schulz

    Citation: Journal of Biomedical Semantics 2016 7:64

    Content type: Research

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  22. 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...

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

    Citation: Journal of Biomedical Semantics 2016 7:63

    Content type: Research

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  23. 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...

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

    Citation: Journal of Biomedical Semantics 2016 7:62

    Content type: Research

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  24. Twitter updates now represent an enormous stream of information originating from a wide variety of formal and informal sources, much of which is relevant to real-world events. They can therefore be highly usef...

    Authors: Nicholas Thapen, Donal Simmie and Chris Hankin

    Citation: Journal of Biomedical Semantics 2016 7:61

    Content type: Research

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  25. 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...

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

    Citation: Journal of Biomedical Semantics 2016 7:60

    Content type: Research

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  26. The process of discovering new drugs is a lengthy, time-consuming and expensive process. Modern day drug discovery relies heavily on the rapid identification of novel ‘targets’, usually proteins that can be mo...

    Authors: Prudence Mutowo, A. Patrícia Bento, Nathan Dedman, Anna Gaulton, Anne Hersey, Jane Lomax and John P. Overington

    Citation: Journal of Biomedical Semantics 2016 7:59

    Content type: Database

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  27. Research on medical vocabulary expansion from large corpora has primarily been conducted using text written in English or similar languages, due to a limited availability of large biomedical corpora in most la...

    Authors: Magnus Ahltorp, Maria Skeppstedt, Shiho Kitajima, Aron Henriksson, Rafal Rzepka and Kenji Araki

    Citation: Journal of Biomedical Semantics 2016 7:58

    Content type: Research

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  28. The Environment Ontology (ENVO; http://​www.​environmentontol​ogy.​org/​), first described in 2013, is a resource and research target for the semantically c...

    Authors: Pier Luigi Buttigieg, Evangelos Pafilis, Suzanna E. Lewis, Mark P. Schildhauer, Ramona L. Walls and Christopher J. Mungall

    Citation: Journal of Biomedical Semantics 2016 7:57

    Content type: Research

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  29. In biomedical applications where the size and complexity of SNOMED CT become problematic, using a smaller subset that can act as a reasonable substitute is usually preferred. In a special class of use cases—li...

    Authors: Pablo López-García and Stefan Schulz

    Citation: Journal of Biomedical Semantics 2016 7:56

    Content type: Research

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  30. Statistics play a critical role in biological and clinical research. However, most reports of scientific results in the published literature make it difficult for the reader to reproduce the statistical analys...

    Authors: Jie Zheng, Marcelline R. Harris, Anna Maria Masci, Yu Lin, Alfred Hero, Barry Smith and Yongqun He

    Citation: Journal of Biomedical Semantics 2016 7:53

    Content type: Research

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  31. Gene Ontology (GO) terms represent the standard for annotation and representation of molecular functions, biological processes and cellular compartments, but a large gap exists between the way concepts are rep...

    Authors: Christopher S. Funk, K. Bretonnel Cohen, Lawrence E. Hunter and Karin M. Verspoor

    Citation: Journal of Biomedical Semantics 2016 7:52

    Content type: Research

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  32. Ontologies are widely used both in the life sciences and in the management of public and private companies. Typically, the different offices in an organization develop their own models and related ontologies t...

    Authors: Giandomenico Pozza, Stefano Borgo, Alessandro Oltramari, Laura Contalbrigo and Stefano Marangon

    Citation: Journal of Biomedical Semantics 2016 7:51

    Content type: Research

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  33. We developed the Apollo Structured Vocabulary (Apollo-SV)—an OWL2 ontology of phenomena in infectious disease epidemiology and population biology—as part of a project whose goal is to increase the use of epide...

    Authors: William R. Hogan, Michael M. Wagner, Mathias Brochhausen, John Levander, Shawn T. Brown, Nicholas Millett, Jay DePasse and Josh Hanna

    Citation: Journal of Biomedical Semantics 2016 7:50

    Content type: Research

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  34. Reasoning over biomedical ontologies using their OWL semantics has traditionally been a challenging task due to the high theoretical complexity of OWL-based automated reasoning. As a consequence, ontology repo...

    Authors: Luke Slater, Georgios V. Gkoutos, Paul N. Schofield and Robert Hoehndorf

    Citation: Journal of Biomedical Semantics 2016 7:49

    Content type: Research

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  35. The increasing number of open-access ontologies and their key role in several applications such as decision-support systems highlight the importance of their validation. Human expertise is crucial for the vali...

    Authors: Asma Ben Abacha, Julio Cesar Dos Reis, Yassine Mrabet, Cédric Pruski and Marcos Da Silveira

    Citation: Journal of Biomedical Semantics 2016 7:48

    Content type: Research

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  36. The Ontology of Medically Related Social Entities (OMRSE) was initially developed in 2011 to provide a framework for modeling demographic data in Resource Description Framework/Web Ontology Language. It is bui...

    Authors: Amanda Hicks, Josh Hanna, Daniel Welch, Mathias Brochhausen and William R. Hogan

    Citation: Journal of Biomedical Semantics 2016 7:47

    Content type: Research

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  37. Open model repositories provide ready-to-reuse computational models of biological systems. Models within those repositories evolve over time, leading to different model versions. Taken together, the underlying...

    Authors: Martin Scharm, Dagmar Waltemath, Pedro Mendes and Olaf Wolkenhauer

    Citation: Journal of Biomedical Semantics 2016 7:46

    Content type: Research

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  38. Neurodegenerative diseases are incurable and debilitating indications with huge social and economic impact, where much is still to be learnt about the underlying molecular events. Mechanistic disease models co...

    Authors: Anandhi Iyappan, Shweta Bagewadi Kawalia, Tamara Raschka, Martin Hofmann-Apitius and Philipp Senger

    Citation: Journal of Biomedical Semantics 2016 7:45

    Content type: Research

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  39. The Cell Ontology (CL) is an OBO Foundry candidate ontology covering the domain of canonical, natural biological cell types. Since its inception in 2005, the CL has undergone multiple rounds of revision and ex...

    Authors: Alexander D. Diehl, Terrence F. Meehan, Yvonne M. Bradford, Matthew H. Brush, Wasila M. Dahdul, David S. Dougall, Yongqun He, David Osumi-Sutherland, Alan Ruttenberg, Sirarat Sarntivijai, Ceri E. Van Slyke, Nicole A. Vasilevsky, Melissa A. Haendel, Judith A. Blake and Christopher J. Mungall

    Citation: Journal of Biomedical Semantics 2016 7:44

    Content type: Database

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  40. The ShARe/CLEF eHealth challenge lab aims to stimulate development of natural language processing and information retrieval technologies to aid patients in understanding their clinical reports. In clinical tex...

    Authors: Danielle L. Mowery, Brett R. South, Lee Christensen, Jianwei Leng, Laura-Maria Peltonen, Sanna Salanterä, Hanna Suominen, David Martinez, Sumithra Velupillai, Noémie Elhadad, Guergana Savova, Sameer Pradhan and Wendy W. Chapman

    Citation: Journal of Biomedical Semantics 2016 7:43

    Content type: Research

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  41. Clinical Natural Language Processing (NLP) systems require a semantic schema comprised of domain-specific concepts, their lexical variants, and associated modifiers to accurately extract information from clini...

    Authors: William Scuba, Melissa Tharp, Danielle Mowery, Eugene Tseytlin, Yang Liu, Frank A. Drews and Wendy W. Chapman

    Citation: Journal of Biomedical Semantics 2016 7:42

    Content type: Software

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  42. Biological sequences, such as proteins, have been provided with annotations that assign functional information. These functional annotations are associations of proteins (or other biological sequences) with de...

    Authors: Hugo P. Bastos, Lisete Sousa, Luka A. Clarke and Francisco M. Couto

    Citation: Journal of Biomedical Semantics 2016 7:41

    Content type: Research

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