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  1. Matching and comparing sequence annotations of different reference sequences is vital to genomics research, yet many annotation formats do not specify the reference sequence types or versions used. This makes ...

    Authors: Zuotian Tatum, Marco Roos, Andrew P Gibson, Peter EM Taschner, Mark Thompson, Erik A Schultes and Jeroen FJ Laros
    Citation: Journal of Biomedical Semantics 2014 5(Suppl 1):S6

    This article is part of a Supplement: Volume 5 Supplement 1

  2. The lack of established standards to describe and annotate biological assays and screening outcomes in the domain of drug and chemical probe discovery is a severe limitation to utilize public and proprietary d...

    Authors: Saminda Abeyruwan, Uma D Vempati, Hande Küçük-McGinty, Ubbo Visser, Amar Koleti, Ahsan Mir, Kunie Sakurai, Caty Chung, Joshua A Bittker, Paul A Clemons, Steve Brudz, Anosha Siripala, Arturo J Morales, Martin Romacker, David Twomey, Svetlana Bureeva…
    Citation: Journal of Biomedical Semantics 2014 5(Suppl 1):S5

    This article is part of a Supplement: Volume 5 Supplement 1

  3. The molecular etiology is still to be identified for about half of the currently described Mendelian diseases in humans, thereby hindering efforts to find treatments or preventive measures. Advances, such as n...

    Authors: Anika Oellrich, Sebastian Koehler, Nicole Washington, Chris Mungall, Suzanna Lewis, Melissa Haendel, Peter N Robinson and Damian Smedley
    Citation: Journal of Biomedical Semantics 2014 5(Suppl 1):S4

    This article is part of a Supplement: Volume 5 Supplement 1

  4. Ontologies encode relationships within a domain in robust data structures that can be used to annotate data objects, including scientific papers, in ways that ease tasks such as search and meta-analysis. Howev...

    Authors: Chayan Chakrabarti, Thomas B Jones, George F Luger, Jiawei F Xu, Matthew D Turner, Angela R Laird and Jessica A Turner
    Citation: Journal of Biomedical Semantics 2014 5(Suppl 1):S2

    This article is part of a Supplement: Volume 5 Supplement 1

  5. Accounts of evidence are vital to evaluate and reproduce scientific findings and integrate data on an informed basis. Currently, such accounts are often inadequate, unstandardized and inaccessible for computat...

    Authors: Christian Bölling, Michael Weidlich and Hermann-Georg Holzhütter
    Citation: Journal of Biomedical Semantics 2014 5(Suppl 1):S1

    This article is part of a Supplement: Volume 5 Supplement 1

  6. Semantic Category Disambiguation (SCD) is the task of assigning the appropriate semantic category to given spans of text from a fixed set of candidate categories, for example Protein to “Fibrin”. SCD is relevant ...

    Authors: Pontus Stenetorp, Sampo Pyysalo, Sophia Ananiadou and Jun’ichi Tsujii
    Citation: Journal of Biomedical Semantics 2014 5:26
  7. Biomedical ontologists to date have concentrated on ontological descriptions of biomedical entities such as gene products and their attributes, phenotypes and so on. Recently, effort has diversified to descrip...

    Authors: James Malone, Andy Brown, Allyson L Lister, Jon Ison, Duncan Hull, Helen Parkinson and Robert Stevens
    Citation: Journal of Biomedical Semantics 2014 5:25
  8. Hospital documents contain free text describing the most important facts relating to patients and their illnesses. These documents are written in specific language containing medical terminology related to hos...

    Authors: Małgorzata Marciniak and Agnieszka Mykowiecka
    Citation: Journal of Biomedical Semantics 2014 5:24
  9. Recently, exchanging data and information has become a significant challenge in medicine. Such data include abnormal states. Establishing a unified representation framework of abnormal states can be a difficul...

    Authors: Yuki Yamagata, Kouji Kozaki, Takeshi Imai, Kazuhiko Ohe and Riichiro Mizoguchi
    Citation: Journal of Biomedical Semantics 2014 5:23
  10. Elucidating disease and developmental dysfunction requires understanding variation in phenotype. Single-species model organism anatomy ontologies (ssAOs) have been established to represent this variation. Mult...

    Authors: Melissa A Haendel, James P Balhoff, Frederic B Bastian, David C Blackburn, Judith A Blake, Yvonne Bradford, Aurelie Comte, Wasila M Dahdul, Thomas A Dececchi, Robert E Druzinsky, Terry F Hayamizu, Nizar Ibrahim, Suzanna E Lewis, Paula M Mabee, Anne Niknejad, Marc Robinson-Rechavi…
    Citation: Journal of Biomedical Semantics 2014 5:21
  11. Multiple models of anatomy have been developed independently and for different purposes. In particular, 3D graphical models are specially useful for visualizing the different organs composing the human body, w...

    Authors: Olivier Palombi, Federico Ulliana, Valentin Favier, Jean-Claude Léon and Marie-Christine Rousset
    Citation: Journal of Biomedical Semantics 2014 5:20
  12. Due to human variations in genetic susceptibility, vaccination often triggers adverse events in a small population of vaccinees. Based on our previous work on ontological modeling of genetic susceptibility to ...

    Authors: Yu Lin and Yongqun He
    Citation: Journal of Biomedical Semantics 2014 5:19
  13. Pharmacovigilance is the activity related to the collection, analysis and prevention of adverse drug reactions (ADRs) induced by drugs. This activity is usually performed within dedicated databases (national, ...

    Authors: Marie Dupuch, Laëtitia Dupuch, Thierry Hamon and Natalia Grabar
    Citation: Journal of Biomedical Semantics 2014 5:18
  14. The 2013 “Vaccine and Drug Ontology Studies” (VDOS 2013) international workshop series focuses on vaccine- and drug-related ontology modeling and applications. Drugs and vaccines have contributed to dramatic i...

    Authors: Cui Tao, Yongqun He and Sivaram Arabandi
    Citation: Journal of Biomedical Semantics 2014 5:16
  15. Over the past 15 years, the biomedical research community has increased its efforts to produce ontologies encoding biomedical knowledge, and to provide the corresponding infrastructure to maintain them. As ont...

    Authors: Robert Hoehndorf, Melissa Haendel, Robert Stevens and Dietrich Rebholz-Schuhmann
    Citation: Journal of Biomedical Semantics 2014 5:15
  16. The Semanticscience Integrated Ontology (SIO) is an ontology to facilitate biomedical knowledge discovery. SIO features a simple upper level comprised of essential types and relations for the rich description ...

    Authors: Michel Dumontier, Christopher JO Baker, Joachim Baran, Alison Callahan, Leonid Chepelev, José Cruz-Toledo, Nicholas R Del Rio, Geraint Duck, Laura I Furlong, Nichealla Keath, Dana Klassen, Jamie P McCusker, Núria Queralt-Rosinach, Matthias Samwald, Natalia Villanueva-Rosales, Mark D Wilkinson…
    Citation: Journal of Biomedical Semantics 2014 5:14
  17. Personalized drug prescription can be benefited from the use of intelligent information management and sharing. International standard classifications and terminologies have been developed in order to provide ...

    Authors: Charalampos Doulaverakis, George Nikolaidis, Athanasios Kleontas and Ioannis Kompatsiaris
    Citation: Journal of Biomedical Semantics 2014 5:13
  18. The Zebrafish Anatomy Ontology (ZFA) is an OBO Foundry ontology that is used in conjunction with the Zebrafish Stage Ontology (ZFS) to describe the gross and cellular anatomy and development of the zebrafish, Dan...

    Authors: Ceri E Van Slyke, Yvonne M Bradford, Monte Westerfield and Melissa A Haendel
    Citation: Journal of Biomedical Semantics 2014 5:12
  19. Experimental research on the automatic extraction of information about mutations from texts is greatly hindered by the lack of consensus evaluation infrastructure for the testing and benchmarking of mutation t...

    Authors: Artjom Klein, Alexandre Riazanov, Matthew M Hindle and Christopher JO Baker
    Citation: Journal of Biomedical Semantics 2014 5:11
  20. Authors of biomedical publications use gel images to report experimental results such as protein-protein interactions or protein expressions under different conditions. Gel images offer a concise way to commun...

    Authors: Tobias Kuhn, Mate Levente Nagy, ThaiBinh Luong and Michael Krauthammer
    Citation: Journal of Biomedical Semantics 2014 5:10
  21. Systematic representation of information related to genetic and non-genetic variations is required to allow large scale studies, data mining and data integration, and to make it possible to reveal novel relati...

    Authors: Mauno Vihinen
    Citation: Journal of Biomedical Semantics 2014 5:9
  22. Lately, ontologies have become a fundamental building block in the process of formalising and storing complex biomedical information. With the currently existing wealth of formalised knowledge, the ability to ...

    Authors: Razan Paul, Tudor Groza, Jane Hunter and Andreas Zankl
    Citation: Journal of Biomedical Semantics 2014 5:8
  23. The Pathway Ontology (PW) developed at the Rat Genome Database (RGD), covers all types of biological pathways, including altered and disease pathways and captures the relationships between them within the hier...

    Authors: Victoria Petri, Pushkala Jayaraman, Marek Tutaj, G Thomas Hayman, Jennifer R Smith, Jeff De Pons, Stanley JF Laulederkind, Timothy F Lowry, Rajni Nigam, Shur-Jen Wang, Mary Shimoyama, Melinda R Dwinell, Diane H Munzenmaier, Elizabeth A Worthey and Howard J Jacob
    Citation: Journal of Biomedical Semantics 2014 5:7
  24. Terminologies that account for variation in language use by linking synonyms and abbreviations to their corresponding concept are important enablers of high-quality information extraction from medical texts. D...

    Authors: Aron Henriksson, Hans Moen, Maria Skeppstedt, Vidas Daudaravičius and Martin Duneld
    Citation: Journal of Biomedical Semantics 2014 5:6
  25. The application of semantic technologies to the integration of biological data and the interoperability of bioinformatics analysis and visualization tools has been the common theme of a series of annual BioHac...

    Authors: Toshiaki Katayama, Mark D Wilkinson, Kiyoko F Aoki-Kinoshita, Shuichi Kawashima, Yasunori Yamamoto, Atsuko Yamaguchi, Shinobu Okamoto, Shin Kawano, Jin-Dong Kim, Yue Wang, Hongyan Wu, Yoshinobu Kano, Hiromasa Ono, Hidemasa Bono, Simon Kocbek, Jan Aerts…
    Citation: Journal of Biomedical Semantics 2014 5:5
  26. Epidemiology is a data-intensive and multi-disciplinary subject, where data integration, curation and sharing are becoming increasingly relevant, given its global context and time constraints. The semantic ann...

    Authors: Catia Pesquita, João D Ferreira, Francisco M Couto and Mário J Silva
    Citation: Journal of Biomedical Semantics 2014 5:4
  27. Identifying phrases that refer to particular concept types is a critical step in extracting information from documents. Provided with annotated documents as training data, supervised machine learning can autom...

    Authors: Manabu Torii, Kavishwar Wagholikar and Hongfang Liu
    Citation: Journal of Biomedical Semantics 2014 5:3
  28. Natural human languages show a power law behaviour in which word frequency (in any large enough corpus) is inversely proportional to word rank - Zipf’s law. We have therefore asked whether similar power law be...

    Authors: Leila R Kalankesh, John P New, Patricia G Baker and Andy Brass
    Citation: Journal of Biomedical Semantics 2014 5:2
  29. The diverse set of human brain structure and function analysis methods represents a difficult challenge for reconciling multiple views of neuroanatomical organization. While different views of organization are...

    Authors: B Nolan Nichols, Jose LV Mejino, Landon T Detwiler, Trond T Nilsen, Maryann E Martone, Jessica A Turner, Daniel L Rubin and James F Brinkley
    Citation: Journal of Biomedical Semantics 2014 5:1
  30. We built the Drug Ontology (DrOn) because we required correct and consistent drug information in a format for use in semantic web applications, and no existing resource met this requirement or could be altered...

    Authors: Josh Hanna, Eric Joseph, Mathias Brochhausen and William R Hogan
    Citation: Journal of Biomedical Semantics 2013 4:44
  31. As biological and biomedical research increasingly reference the environmental context of the biological entities under study, the need for formalisation and standardisation of environment descriptors is growi...

    Authors: Pier Luigi Buttigieg, Norman Morrison, Barry Smith, Christopher J Mungall and Suzanna E Lewis
    Citation: Journal of Biomedical Semantics 2013 4:43
  32. We are developing the Neurological Disease Ontology (ND) to provide a framework to enable representation of aspects of neurological diseases that are relevant to their treatment and study. ND is a representati...

    Authors: Mark Jensen, Alexander P Cox, Naveed Chaudhry, Marcus Ng, Donat Sule, William Duncan, Patrick Ray, Bianca Weinstock-Guttman, Barry Smith, Alan Ruttenberg, Kinga Szigeti and Alexander D Diehl
    Citation: Journal of Biomedical Semantics 2013 4:42
  33. In prior work, we presented the Ontology of Physics for Biology (OPB) as a computational ontology for use in the annotation and representations of biophysical knowledge encoded in repositories of physics-based...

    Authors: Daniel L Cook, Maxwell L Neal, Fred L Bookstein and John H Gennari
    Citation: Journal of Biomedical Semantics 2013 4:41
  34. Licensed human vaccines can induce various adverse events (AE) in vaccinated patients. Due to the involvement of the whole immune system and complex immunological reactions after vaccination, it is difficult t...

    Authors: Erica Marcos, Bin Zhao and Yongqun He
    Citation: Journal of Biomedical Semantics 2013 4:40
  35. Glycoscience is a research field focusing on complex carbohydrates (otherwise known as glycans)a, which can, for example, serve as “switches” that toggle between different functions of a glycoprotein or glycolipi...

    Authors: Kiyoko F Aoki-Kinoshita, Jerven Bolleman, Matthew P Campbell, Shin Kawano, Jin-Dong Kim, Thomas Lütteke, Masaaki Matsubara, Shujiro Okuda, Rene Ranzinger, Hiromichi Sawaki, Toshihide Shikanai, Daisuke Shinmachi, Yoshinori Suzuki, Philip Toukach, Issaku Yamada, Nicolle H Packer…
    Citation: Journal of Biomedical Semantics 2013 4:39
  36. Though the annotation of digital artifacts with metadata has a long history, the bulk of that work focuses on the association of single terms or concepts to single targets. As annotation efforts expand to capt...

    Authors: Kevin M Livingston, Michael Bada, Lawrence E Hunter and Karin Verspoor
    Citation: Journal of Biomedical Semantics 2013 4:38
  37. Provenance is a critical ingredient for establishing trust of published scientific content. This is true whether we are considering a data set, a computational workflow, a peer-reviewed publication or a simple...

    Authors: Paolo Ciccarese, Stian Soiland-Reyes, Khalid Belhajjame, Alasdair JG Gray, Carole Goble and Tim Clark
    Citation: Journal of Biomedical Semantics 2013 4:37
  38. The Rat Genome Database (RGD) (http://​rgd.​mcw.​edu/​) is the premier site for comprehensive data on the different strains of the laboratory rat (Rattus n...

    Authors: Rajni Nigam, Diane H Munzenmaier, Elizabeth A Worthey, Melinda R Dwinell, Mary Shimoyama and Howard J Jacob
    Citation: Journal of Biomedical Semantics 2013 4:36
  39. Large biomedical simulation initiatives, such as the Virtual Physiological Human (VPH), are substantially dependent on controlled vocabularies to facilitate the exchange of information, of data and of models. ...

    Authors: Michaela Gündel, Erfan Younesi, Ashutosh Malhotra, Jiali Wang, Hui Li, Bijun Zhang, Bernard de Bono, Heinz-Theodor Mevissen and Martin Hofmann-Apitius
    Citation: Journal of Biomedical Semantics 2013 4:35
  40. A hierarchical taxonomy of organisms is a prerequisite for semantic integration of biodiversity data. Ideally, there would be a single, expansive, authoritative taxonomy that includes extinct and extant taxa, ...

    Authors: Peter E Midford, Thomas Alex Dececchi, James P Balhoff, Wasila M Dahdul, Nizar Ibrahim, Hilmar Lapp, John G Lundberg, Paula M Mabee, Paul C Sereno, Monte Westerfield, Todd J Vision and David C Blackburn
    Citation: Journal of Biomedical Semantics 2013 4:34
  41. Ontologies are useful in many branches of biomedical research. For instance, in the vaccine domain, the community-based Vaccine Ontology (VO) has been widely used to promote vaccine data standardization, integ...

    Authors: Yuji Zhang, Cui Tao, Yongqun He, Pradip Kanjamala and Hongfang Liu
    Citation: Journal of Biomedical Semantics 2013 4:33
  42. Anatomy ontologies are query-able classifications of anatomical structures. They provide a widely-used means for standardising the annotation of phenotypes and expression in both human-readable and programmati...

    Authors: Marta Costa, Simon Reeve, Gary Grumbling and David Osumi-Sutherland
    Citation: Journal of Biomedical Semantics 2013 4:32
  43. The African clawed frogs Xenopus laevis and Xenopus tropicalis are prominent animal model organisms. Xenopus research contributes to the understanding of genetic, developmental and molecular mechanisms underlying...

    Authors: Erik Segerdell, Virgilio G Ponferrada, Christina James-Zorn, Kevin A Burns, Joshua D Fortriede, Wasila M Dahdul, Peter D Vize and Aaron M Zorn
    Citation: Journal of Biomedical Semantics 2013 4:31
  44. Phenotype ontologies are queryable classifications of phenotypes. They provide a widely-used means for annotating phenotypes in a form that is human-readable, programatically accessible and that can be used to...

    Authors: David Osumi-Sutherland, Steven J Marygold, Gillian H Millburn, Peter A McQuilton, Laura Ponting, Raymund Stefancsik, Kathleen Falls, Nicholas H Brown and Georgios V Gkoutos
    Citation: Journal of Biomedical Semantics 2013 4:30
  45. Large-scale mutagenesis projects are ongoing to improve our understanding about the pathology and subsequently the treatment of diseases. Such projects do not only record the genotype but also report phenotype...

    Authors: Anika Oellrich, Christoph Grabmüller and Dietrich Rebholz-Schuhmann
    Citation: Journal of Biomedical Semantics 2013 4:29
  46. The identification of protein and gene names (PGNs) from the scientific literature requires semantic resources: Terminological and lexical resources deliver the term candidates into PGN tagging solutions and t...

    Authors: Dietrich Rebholz-Schuhmann, Senay Kafkas, Jee-Hyub Kim, Chen Li, Antonio Jimeno Yepes, Robert Hoehndorf, Rolf Backofen and Ian Lewin
    Citation: Journal of Biomedical Semantics 2013 4:28
  47. The increasing amount of textual information in biomedicine requires effective term recognition methods to identify textual representations of domain-specific concepts as the first step toward automating its s...

    Authors: Irena Spasić, Mark Greenwood, Alun Preece, Nick Francis and Glyn Elwyn
    Citation: Journal of Biomedical Semantics 2013 4:27

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