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  1. 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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  2. 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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  3. 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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  4. 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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  5. 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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  6. 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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  7. 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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  8. 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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  9. 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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  10. 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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  11. 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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  12. 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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  13. 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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  14. 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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  15. 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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  16. 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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  17. 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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  18. 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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  19. 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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  20. 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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  21. 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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  22. 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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  23. 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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  24. 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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  25. 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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  26. 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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  27. 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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  28. 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

    Published on:

  29. 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

    Published on:

  30. 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

    Published on:

  31. Nucleotide and protein sequence feature annotations are essential to understand biology on the genomic, transcriptomic, and proteomic level. Using Semantic Web technologies to query biological annotations, the...

    Authors: Jerven T. Bolleman, Christopher J. Mungall, Francesco Strozzi, Joachim Baran, Michel Dumontier, Raoul J. P. Bonnal, Robert Buels, Robert Hoehndorf, Takatomo Fujisawa, Toshiaki Katayama and Peter J. A. Cock

    Citation: Journal of Biomedical Semantics 2016 7:39

    Content type: Research

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  32. There have been repeated initiatives to produce standard nosologies and terminologies for cutaneous disease, some dedicated to the domain and some part of bigger terminologies such as ICD-10. Recently, formall...

    Authors: Hannah M. Fisher, Robert Hoehndorf, Bruno S. Bazelato, Soheil S. Dadras, Lloyd E. King Jr., Georgios V. Gkoutos, John P. Sundberg and Paul N. Schofield

    Citation: Journal of Biomedical Semantics 2016 7:38

    Content type: Research

    Published on:

  33. Clinical practice guidelines (CPGs) recommend pharmacologic treatments for clinical conditions, and drug structured product labels (SPLs) summarize approved treatment indications. Both resources are intended t...

    Authors: Tiffany I. Leung and Michel Dumontier

    Citation: Journal of Biomedical Semantics 2016 7:37

    Content type: Research

    Published on:

  34. High throughput imaging is now available to many groups and it is possible to generate a large quantity of high quality images quickly. Managing this data, consistently annotating it, or making it available to...

    Authors: Solomon Adebayo, Kenneth McLeod, Ilinca Tudose, David Osumi-Sutherland, Tony Burdett, Richard Baldock, Albert Burger and Helen Parkinson

    Citation: Journal of Biomedical Semantics 2016 7:35

    Content type: Software

    Published on:

  35. Computational comparative analysis of multiple genomes provides valuable opportunities to biomedical research. In particular, orthology analysis can play a central role in comparative genomics; it guides estab...

    Authors: Jesualdo Tomás Fernández-Breis, Hirokazu Chiba, María del Carmen Legaz-García and Ikuo Uchiyama

    Citation: Journal of Biomedical Semantics 2016 7:34

    Content type: Research

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  36. The Proteasix Ontology (PxO) is an ontology that supports the Proteasix tool; an open-source peptide-centric tool that can be used to predict automatically and in a large-scale fashion in silico the proteases inv...

    Authors: Mercedes Arguello Casteleiro, Julie Klein and Robert Stevens

    Citation: Journal of Biomedical Semantics 2016 7:33

    Content type: Research

    Published on:

  37. Biomedical research usually requires combining large volumes of data from multiple heterogeneous sources, which makes difficult the integrated exploitation of such data. The Semantic Web paradigm offers a natu...

    Authors: María del Carmen Legaz-García, José Antonio Miñarro-Giménez, Marcos Menárguez-Tortosa and Jesualdo Tomás Fernández-Breis

    Citation: Journal of Biomedical Semantics 2016 7:32

    Content type: Research

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  38. The motivation for the BioHub project is to create an Integrated Knowledge Management System (IKMS) that will enable chemists to source ingredients from bio-renewables, rather than from non-sustainable sources...

    Authors: Warren J. Read, George Demetriou, Goran Nenadic, Noel Ruddock, Robert Stevens and Jerry Winter

    Citation: Journal of Biomedical Semantics 2016 7:30

    Content type: Research

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  39. Neuropathy often occurs following drug treatment such as chemotherapy. Severe instances of neuropathy can result in cessation of life-saving chemotherapy treatment.

    Authors: Abra Guo, Rebecca Racz, Junguk Hur, Yu Lin, Zuoshuang Xiang, Lili Zhao, Jordan Rinder, Guoqian Jiang, Qian Zhu and Yongqun He

    Citation: Journal of Biomedical Semantics 2016 7:29

    Content type: Research

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  40. Phenotypic data derived from high content screening is currently annotated using free-text, thus preventing the integration of independent datasets, including those generated in different biological domains, s...

    Authors: Simon Jupp, James Malone, Tony Burdett, Jean-Karim Heriche, Eleanor Williams, Jan Ellenberg, Helen Parkinson and Gabriella Rustici

    Citation: Journal of Biomedical Semantics 2016 7:28

    Content type: Database

    Published on:

  41. Biomedical event extraction is one of the key tasks in biomedical text mining, supporting various applications such as database curation and hypothesis generation. Several systems, some of which have been appl...

    Authors: Farrokh Mehryary, Suwisa Kaewphan, Kai Hakala and Filip Ginter

    Citation: Journal of Biomedical Semantics 2016 7:27

    Content type: Research

    Published on:

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