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Journal of Biomedical Semantics

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https://www.readbyqxmd.com/read/29329592/the-extensible-ontology-development-xod-principles-and-tool-implementation-to-support-ontology-interoperability
#1
REVIEW
Yongqun He, Zuoshuang Xiang, Jie Zheng, Yu Lin, James A Overton, Edison Ong
Ontologies are critical to data/metadata and knowledge standardization, sharing, and analysis. With hundreds of biological and biomedical ontologies developed, it has become critical to ensure ontology interoperability and the usage of interoperable ontologies for standardized data representation and integration. The suite of web-based Ontoanimal tools (e.g., Ontofox, Ontorat, and Ontobee) support different aspects of extensible ontology development. By summarizing the common features of Ontoanimal and other similar tools, we identified and proposed an "eXtensible Ontology Development" (XOD) strategy and its associated four principles...
January 12, 2018: Journal of Biomedical Semantics
https://www.readbyqxmd.com/read/29316970/cuiless2016-a-clinical-corpus-applying-compositional-normalization-of-text-mentions
#2
John D Osborne, Matthew B Neu, Maria I Danila, Thamar Solorio, Steven J Bethard
BACKGROUND: Traditionally text mention normalization corpora have normalized concepts to single ontology identifiers ("pre-coordinated concepts"). Less frequently, normalization corpora have used concepts with multiple identifiers ("post-coordinated concepts") but the additional identifiers have been restricted to a defined set of relationships to the core concept. This approach limits the ability of the normalization process to express semantic meaning. We generated a freely available corpus using post-coordinated concepts without a defined set of relationships that we term "compositional concepts" to evaluate their use in clinical text...
January 10, 2018: Journal of Biomedical Semantics
https://www.readbyqxmd.com/read/29316968/improving-the-interoperability-of-biomedical-ontologies-with-compound-alignments
#3
Daniela Oliveira, Catia Pesquita
BACKGROUND: Ontologies are commonly used to annotate and help process life sciences data. Although their original goal is to facilitate integration and interoperability among heterogeneous data sources, when these sources are annotated with distinct ontologies, bridging this gap can be challenging. In the last decade, ontology matching systems have been evolving and are now capable of producing high-quality mappings for life sciences ontologies, usually limited to the equivalence between two ontologies...
January 9, 2018: Journal of Biomedical Semantics
https://www.readbyqxmd.com/read/29258588/integrating-phenotype-ontologies-with-phenomenet
#4
Miguel Ángel Rodríguez-García, Georgios V Gkoutos, Paul N Schofield, Robert Hoehndorf
BACKGROUND: Integration and analysis of phenotype data from humans and model organisms is a key challenge in building our understanding of normal biology and pathophysiology. However, the range of phenotypes and anatomical details being captured in clinical and model organism databases presents complex problems when attempting to match classes across species and across phenotypes as diverse as behaviour and neoplasia. We have previously developed PhenomeNET, a system for disease gene prioritization that includes as one of its components an ontology designed to integrate phenotype ontologies...
December 19, 2017: Journal of Biomedical Semantics
https://www.readbyqxmd.com/read/29212530/identifying-genotype-phenotype-relationships-in-biomedical-text
#5
Maryam Khordad, Robert E Mercer
BACKGROUND: One important type of information contained in biomedical research literature is the newly discovered relationships between phenotypes and genotypes. Because of the large quantity of literature, a reliable automatic system to identify this information for future curation is essential. Such a system provides important and up to date data for database construction and updating, and even text summarization. In this paper we present a machine learning method to identify these genotype-phenotype relationships...
December 6, 2017: Journal of Biomedical Semantics
https://www.readbyqxmd.com/read/29202830/experiences-from-the-anatomy-track-in-the-ontology-alignment-evaluation-initiative
#6
REVIEW
Zlatan Dragisic, Valentina Ivanova, Huanyu Li, Patrick Lambrix
BACKGROUND: One of the longest running tracks in the Ontology Alignment Evaluation Initiative is the Anatomy track which focuses on aligning two anatomy ontologies. The Anatomy track was started in 2005. In 2005 and 2006 the task in this track was to align the Foundational Model of Anatomy and the OpenGalen Anatomy Model. Since 2007 the ontologies used in the track are the Adult Mouse Anatomy and a part of the NCI Thesaurus. Since 2015 the data in the Anatomy track is also used in the Interactive track of the Ontology Alignment Evaluation Initiative...
December 4, 2017: Journal of Biomedical Semantics
https://www.readbyqxmd.com/read/29197409/matching-disease-and-phenotype-ontologies-in-the-ontology-alignment-evaluation-initiative
#7
Ian Harrow, Ernesto Jiménez-Ruiz, Andrea Splendiani, Martin Romacker, Peter Woollard, Scott Markel, Yasmin Alam-Faruque, Martin Koch, James Malone, Arild Waaler
BACKGROUND: The disease and phenotype track was designed to evaluate the relative performance of ontology matching systems that generate mappings between source ontologies. Disease and phenotype ontologies are important for applications such as data mining, data integration and knowledge management to support translational science in drug discovery and understanding the genetics of disease. RESULTS: Eleven systems (out of 21 OAEI participating systems) were able to cope with at least one of the tasks in the Disease and Phenotype track...
December 2, 2017: Journal of Biomedical Semantics
https://www.readbyqxmd.com/read/29179777/a-document-centric-approach-for-developing-the-tolapc-ontology
#8
Aisha Blfgeh, Jennifer Warrender, Catharien M U Hilkens, Phillip Lord
BACKGROUND: There are many challenges associated with ontology building, as the process often touches on many different subject areas; it needs knowledge of the problem domain, an understanding of the ontology formalism, software in use and, sometimes, an understanding of the philosophical background. In practice, it is very rare that an ontology can be completed by a single person, as they are unlikely to combine all of these skills. So people with these skills must collaborate. One solution to this is to use face-to-face meetings, but these can be expensive and time-consuming for teams that are not co-located...
November 28, 2017: Journal of Biomedical Semantics
https://www.readbyqxmd.com/read/29169408/the-bacterial-interlocked-process-ontology-bipon-a-systemic-multi-scale-unified-representation-of-biological-processes-in-prokaryotes
#9
Vincent J Henry, Anne Goelzer, Arnaud Ferré, Stephan Fischer, Marc Dinh, Valentin Loux, Christine Froidevaux, Vincent Fromion
BACKGROUND: High-throughput technologies produce huge amounts of heterogeneous biological data at all cellular levels. Structuring these data together with biological knowledge is a critical issue in biology and requires integrative tools and methods such as bio-ontologies to extract and share valuable information. In parallel, the development of recent whole-cell models using a systemic cell description opened alternatives for data integration. Integrating a systemic cell description within a bio-ontology would help to progress in whole-cell data integration and modeling synergistically...
November 23, 2017: Journal of Biomedical Semantics
https://www.readbyqxmd.com/read/29132408/using-semantics-for-representing-experimental-protocols
#10
Olga Giraldo, Alexander García, Federico López, Oscar Corcho
BACKGROUND: An experimental protocol is a sequence of tasks and operations executed to perform experimental research in biological and biomedical areas, e.g. biology, genetics, immunology, neurosciences, virology. Protocols often include references to equipment, reagents, descriptions of critical steps, troubleshooting and tips, as well as any other information that researchers deem important for facilitating the reusability of the protocol. Although experimental protocols are central to reproducibility, the descriptions are often cursory...
November 13, 2017: Journal of Biomedical Semantics
https://www.readbyqxmd.com/read/29122012/drug-target-ontology-to-classify-and-integrate-drug-discovery-data
#11
Yu Lin, Saurabh Mehta, Hande Küçük-McGinty, John Paul Turner, Dusica Vidovic, Michele Forlin, Amar Koleti, Dac-Trung Nguyen, Lars Juhl Jensen, Rajarshi Guha, Stephen L Mathias, Oleg Ursu, Vasileios Stathias, Jianbin Duan, Nooshin Nabizadeh, Caty Chung, Christopher Mader, Ubbo Visser, Jeremy J Yang, Cristian G Bologa, Tudor I Oprea, Stephan C Schürer
BACKGROUND: One of the most successful approaches to develop new small molecule therapeutics has been to start from a validated druggable protein target. However, only a small subset of potentially druggable targets has attracted significant research and development resources. The Illuminating the Druggable Genome (IDG) project develops resources to catalyze the development of likely targetable, yet currently understudied prospective drug targets. A central component of the IDG program is a comprehensive knowledge resource of the druggable genome...
November 9, 2017: Journal of Biomedical Semantics
https://www.readbyqxmd.com/read/29122011/entity-recognition-in-the-biomedical-domain-using-a-hybrid-approach
#12
Marco Basaldella, Lenz Furrer, Carlo Tasso, Fabio Rinaldi
BACKGROUND: This article describes a high-recall, high-precision approach for the extraction of biomedical entities from scientific articles. METHOD: The approach uses a two-stage pipeline, combining a dictionary-based entity recognizer with a machine-learning classifier. First, the OGER entity recognizer, which has a bias towards high recall, annotates the terms that appear in selected domain ontologies. Subsequently, the Distiller framework uses this information as a feature for a machine learning algorithm to select the relevant entities only...
November 9, 2017: Journal of Biomedical Semantics
https://www.readbyqxmd.com/read/28982381/querying-clinical-data-in-hl7-rim-based-relational-model-with-morph-rdb
#13
Freddy Priyatna, Raul Alonso-Calvo, Sergio Paraiso-Medina, Oscar Corcho
BACKGROUND: Semantic interoperability is essential when carrying out post-genomic clinical trials where several institutions collaborate, since researchers and developers need to have an integrated view and access to heterogeneous data sources. One possible approach to accommodate this need is to use RDB2RDF systems that provide RDF datasets as the unified view. These RDF datasets may be materialized and stored in a triple store, or transformed into RDF in real time, as virtual RDF data sources...
October 5, 2017: Journal of Biomedical Semantics
https://www.readbyqxmd.com/read/28978337/towards-refactoring-the-molecular-function-ontology-with-a-uml-profile-for-function-modeling
#14
Patryk Burek, Frank Loebe, Heinrich Herre
BACKGROUND: Gene Ontology (GO) is the largest resource for cataloging gene products. This resource grows steadily and, naturally, this growth raises issues regarding the structure of the ontology. Moreover, modeling and refactoring large ontologies such as GO is generally far from being simple, as a whole as well as when focusing on certain aspects or fragments. It seems that human-friendly graphical modeling languages such as the Unified Modeling Language (UML) could be helpful in connection with these tasks...
October 4, 2017: Journal of Biomedical Semantics
https://www.readbyqxmd.com/read/28969675/a-histological-ontology-of-the-human-cardiovascular-system
#15
Claudia Mazo, Liliana Salazar, Oscar Corcho, Maria Trujillo, Enrique Alegre
BACKGROUND: In this paper, we describe a histological ontology of the human cardiovascular system developed in collaboration among histology experts and computer scientists. RESULTS: The histological ontology is developed following an existing methodology using Conceptual Models (CMs) and validated using OOPS!, expert evaluation with CMs, and how accurately the ontology can answer the Competency Questions (CQ). It is publicly available at http://bioportal.bioontology...
October 2, 2017: Journal of Biomedical Semantics
https://www.readbyqxmd.com/read/28962670/analysis-and-visualization-of-disease-courses-in-a-semantically-enabled-cancer-registry
#16
Angel Esteban-Gil, Jesualdo Tomás Fernández-Breis, Martin Boeker
BACKGROUND: Regional and epidemiological cancer registries are important for cancer research and the quality management of cancer treatment. Many technological solutions are available to collect and analyse data for cancer registries nowadays. However, the lack of a well-defined common semantic model is a problem when user-defined analyses and data linking to external resources are required. The objectives of this study are: (1) design of a semantic model for local cancer registries; (2) development of a semantically-enabled cancer registry based on this model; and (3) semantic exploitation of the cancer registry for analysing and visualising disease courses...
September 29, 2017: Journal of Biomedical Semantics
https://www.readbyqxmd.com/read/28962645/simplifying-drug-package-leaflets-written-in-spanish-by-using-word-embedding
#17
Isabel Segura-Bedmar, Paloma Martínez
BACKGROUND: Drug Package Leaflets (DPLs) provide information for patients on how to safely use medicines. Pharmaceutical companies are responsible for producing these documents. However, several studies have shown that patients usually have problems in understanding sections describing posology (dosage quantity and prescription), contraindications and adverse drug reactions. An ultimate goal of this work is to provide an automatic approach that helps these companies to write drug package leaflets in an easy-to-understand language...
September 29, 2017: Journal of Biomedical Semantics
https://www.readbyqxmd.com/read/28938912/semantic-annotation-in-biomedicine-the-current-landscape
#18
REVIEW
Jelena Jovanović, Ebrahim Bagheri
The abundance and unstructured nature of biomedical texts, be it clinical or research content, impose significant challenges for the effective and efficient use of information and knowledge stored in such texts. Annotation of biomedical documents with machine intelligible semantics facilitates advanced, semantics-based text management, curation, indexing, and search. This paper focuses on annotation of biomedical entity mentions with concepts from relevant biomedical knowledge bases such as UMLS. As a result, the meaning of those mentions is unambiguously and explicitly defined, and thus made readily available for automated processing...
September 22, 2017: Journal of Biomedical Semantics
https://www.readbyqxmd.com/read/28938902/large-scale-online-semantic-indexing-of-biomedical-articles-via-an-ensemble-of-multi-label-classification-models
#19
Yannis Papanikolaou, Grigorios Tsoumakas, Manos Laliotis, Nikos Markantonatos, Ioannis Vlahavas
BACKGROUND: In this paper we present the approach that we employed to deal with large scale multi-label semantic indexing of biomedical papers. This work was mainly implemented within the context of the BioASQ challenge (2013-2017), a challenge concerned with biomedical semantic indexing and question answering. METHODS: Our main contribution is a MUlti-Label Ensemble method (MULE) that incorporates a McNemar statistical significance test in order to validate the combination of the constituent machine learning algorithms...
September 22, 2017: Journal of Biomedical Semantics
https://www.readbyqxmd.com/read/29297414/an-automatic-approach-for-constructing-a-knowledge-base-of-symptoms-in-chinese
#20
Tong Ruan, Mengjie Wang, Jian Sun, Ting Wang, Lu Zeng, Yichao Yin, Ju Gao
BACKGROUND: While a large number of well-known knowledge bases (KBs) in life science have been published as Linked Open Data, there are few KBs in Chinese. However, KBs in Chinese are necessary when we want to automatically process and analyze electronic medical records (EMRs) in Chinese. Of all, the symptom KB in Chinese is the most seriously in need, since symptoms are the starting point of clinical diagnosis. RESULTS: We publish a public KB of symptoms in Chinese, including symptoms, departments, diseases, medicines, and examinations as well as relations between symptoms and the above related entities...
September 20, 2017: Journal of Biomedical Semantics
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