DermO; an ontology for the description of dermatologic disease

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

FALDO: a semantic standard for describing the location of nucleotide and protein feature annotation

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

Overlap in drug-disease associations between clinical practice guidelines and drug structured product label indications

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

PhenoImageShare: an image annotation and query infrastructure

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

A corpus of potentially contradictory research claims from cardiovascular research abstracts

Research literature in biomedicine and related fields contains a huge number of claims, such as the effectiveness of treatments. These claims are not always consistent and may even contradict each other. Being...

Authors: Abdulaziz Alamri and Mark Stevenson

The Orthology Ontology: development and applications

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

The Proteasix Ontology

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

Generation of open biomedical datasets through ontology-driven transformation and integration processes

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

Erratum to: Towards exergaming commons: composing the exergame ontology for publishing open game data

Authors: Giorgos Bamparopoulos, Evdokimos Konstantinidis, Charalampos Bratsas and Panagiotis D. Bamidis

The BioHub Knowledge Base: Ontology and Repository for Sustainable Biosourcing

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

Ontology-based collection, representation and analysis of drug-associated neuropathy adverse events

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

Inferring gene-to-phenotype and gene-to-disease relationships at Mouse Genome Informatics: challenges and solutions

Inferring gene-to-phenotype and gene-to-human disease model relationships from annotated mouse phenotypes and disease associations is critical when researching gene function and identifying candidate disease g...

Authors: Susan M. Bello and Janan T. Eppig

The cellular microscopy phenotype ontology

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

Trivalent influenza vaccine adverse symptoms analysis based on MedDRA terminology using VAERS data in 2011

Trivalent Influenza Virus Vaccine (FLU3) is a traditional flu vaccine to protect people against three different flu viruses, including influenza A H1N1 virus, an influenza A H3N2 virus and one B virus.

Authors: Jingcheng Du, Yi Cai, Yong Chen and Cui Tao

Filtering large-scale event collections using a combination of supervised and unsupervised learning for event trigger classification

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

OmniSearch: a semantic search system based on the Ontology for MIcroRNA Target (OMIT) for microRNA-target gene interaction data

As a special class of non-coding RNAs (ncRNAs), microRNAs (miRNAs) perform important roles in numerous biological and pathological processes. The realization of miRNA functions depends largely on how miRNAs re...

Authors: Jingshan Huang, Fernando Gutierrez, Harrison J. Strachan, Dejing Dou, Weili Huang, Barry Smith, Judith A. Blake, Karen Eilbeck, Darren A. Natale, Yu Lin, Bin Wu, Nisansa de Silva, Xiaowei Wang, Zixing Liu, Glen M. Borchert, Ming Tan…

Extracting a stroke phenotype risk factor from Veteran Health Administration clinical reports: an information content analysis

In the United States, 795,000 people suffer strokes each year; 10–15 % of these strokes can be attributed to stenosis caused by plaque in the carotid artery, a major stroke phenotype risk factor. Studies compa...

Authors: Danielle L. Mowery, Brian E. Chapman, Mike Conway, Brett R. South, Erin Madden, Salomeh Keyhani and Wendy W. Chapman

Publication of nuclear magnetic resonance experimental data with semantic web technology and the application thereof to biomedical research of proteins

The nuclear magnetic resonance (NMR) spectroscopic data for biological macromolecules archived at the BioMagResBank (BMRB) provide a rich resource of biophysical information at atomic resolution. The NMR data ...

Authors: Masashi Yokochi, Naohiro Kobayashi, Eldon L. Ulrich, Akira R. Kinjo, Takeshi Iwata, Yannis E. Ioannidis, Miron Livny, John L. Markley, Haruki Nakamura, Chojiro Kojima and Toshimichi Fujiwara

The Non-Coding RNA Ontology (NCRO): a comprehensive resource for the unification of non-coding RNA biology

In recent years, sequencing technologies have enabled the identification of a wide range of non-coding RNAs (ncRNAs). Unfortunately, annotation and integration of ncRNA data has lagged behind their identificat...

Authors: Jingshan Huang, Karen Eilbeck, Barry Smith, Judith A. Blake, Dejing Dou, Weili Huang, Darren A. Natale, Alan Ruttenberg, Jun Huan, Michael T. Zimmermann, Guoqian Jiang, Yu Lin, Bin Wu, Harrison J. Strachan, Yongqun He, Shaojie Zhang…

Modularising ontology and designing inference patterns to personalise health condition assessment: the case of obesity

The public health initiatives for obesity prevention are increasingly exploiting the advantages of smart technologies that can register various kinds of data related to physical, physiological, and behavioural...

Authors: Aleksandra Sojic, Walter Terkaj, Giorgia Contini and Marco Sacco

OBIB-a novel ontology for biobanking

Biobanking necessitates extensive integration of data to allow data analysis and specimen sharing. Ontologies have been demonstrated to be a promising approach in fostering better semantic integration of bioba...

Authors: Mathias Brochhausen, Jie Zheng, David Birtwell, Heather Williams, Anna Maria Masci, Helena Judge Ellis and Christian J. Stoeckert Jr.

miRiaD: A Text Mining Tool for Detecting Associations of microRNAs with Diseases

MicroRNAs are increasingly being appreciated as critical players in human diseases, and questions concerning the role of microRNAs arise in many areas of biomedical research. There are several manually curated...

Authors: Samir Gupta, Karen E. Ross, Catalina O. Tudor, Cathy H. Wu, Carl J. Schmidt and K. Vijay-Shanker

Active learning for ontological event extraction incorporating named entity recognition and unknown word handling

Biomedical text mining may target various kinds of valuable information embedded in the literature, but a critical obstacle to the extension of the mining targets is the cost of manual construction of labeled ...

Authors: Xu Han, Jung-jae Kim and Chee Keong Kwoh

VICO: Ontology-based representation and integrative analysis of Vaccination Informed Consent forms

Although signing a vaccination (or immunization) informed consent form is not a federal requirement in the US and Canada, such a practice is required by many states and pharmacies. The content and structures o...

Authors: Yu Lin, Jie Zheng and Yongqun He

Erratum to: Extracting drug-enzyme relation from literature as evidence for drug drug interaction

Authors: Yaoyun Zhang, Heng-Yi Wu, Jingcheng Du, Jun Xu, Jingqi Wang, Cui Tao, Lang Li and Hua Xu