Dataset Information

SATORI: a system for ontology-guided visual exploration of biomedical data repositories.

ABSTRACT: Motivation:The ever-increasing number of biomedical datasets provides tremendous opportunities for re-use but current data repositories provide limited means of exploration apart from text-based search. Ontological metadata annotations provide context by semantically relating datasets. Visualizing this rich network of relationships can improve the explorability of large data repositories and help researchers find datasets of interest. Results:We developed SATORI-an integrative search and visual exploration interface for the exploration of biomedical data repositories. The design is informed by a requirements analysis through a series of semi-structured interviews. We evaluated the implementation of SATORI in a field study on a real-world data collection. SATORI enables researchers to seamlessly search, browse and semantically query data repositories via two visualizations that are highly interconnected with a powerful search interface. Availability and implementation:SATORI is an open-source web application, which is freely available at http://satori.refinery-platform.org and integrated into the Refinery Platform. Contact:nils@hms.harvard.edu. Supplementary information:Supplementary data are available at Bioinformatics online.

SUBMITTER: Lekschas F

PROVIDER: S-EPMC6031061 | biostudies-literature | 2018 Apr

REPOSITORIES: biostudies-literature

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SATORI: a system for ontology-guided visual exploration of biomedical data repositories.

Lekschas Fritz F Gehlenborg Nils N

Bioinformatics (Oxford, England) 20180401 7

<h4>Motivation</h4>The ever-increasing number of biomedical datasets provides tremendous opportunities for re-use but current data repositories provide limited means of exploration apart from text-based search. Ontological metadata annotations provide context by semantically relating datasets. Visualizing this rich network of relationships can improve the explorability of large data repositories and help researchers find datasets of interest.<h4>Results</h4>We developed SATORI-an integrative sea ...[more]

PMID: 29186292

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Project description:There is an urgent need to standardize the semantics of biomedical data values, such as phenotypes, to enable comparative and integrative analyses. However, it is unlikely that all studies will use the same data collection protocols. As a result, retrospective standardization is often required, which involves matching of original (unstructured or locally coded) data to widely used coding or ontology systems such as SNOMED CT (clinical terms), ICD-10 (International Classification of Disease) and HPO (Human Phenotype Ontology). This data curation process is usually a time-consuming process performed by a human expert. To help mechanize this process, we have developed SORTA, a computer-aided system for rapidly encoding free text or locally coded values to a formal coding system or ontology. SORTA matches original data values (uploaded in semicolon delimited format) to a target coding system (uploaded in Excel spreadsheet, OWL ontology web language or OBO open biomedical ontologies format). It then semi- automatically shortlists candidate codes for each data value using Lucene and n-gram based matching algorithms, and can also learn from matches chosen by human experts. We evaluated SORTA's applicability in two use cases. For the LifeLines biobank, we used SORTA to recode 90?000 free text values (including 5211 unique values) about physical exercise to MET (Metabolic Equivalent of Task) codes. For the CINEAS clinical symptom coding system, we used SORTA to map to HPO, enriching HPO when necessary (315 terms matched so far). Out of the shortlists at rank 1, we found a precision/recall of 0.97/0.98 in LifeLines and of 0.58/0.45 in CINEAS. More importantly, users found the tool both a major time saver and a quality improvement because SORTA reduced the chances of human mistakes. Thus, SORTA can dramatically ease data (re)coding tasks and we believe it will prove useful for many more projects. Database URL: http://molgenis.org/sorta or as an open source download from http://www.molgenis.org/wiki/SORTA.

Project description:IntroductionWhile data repositories are well-established in clinical and research enterprises, knowledge repositories with shareable computable biomedical knowledge (CBK) are relatively new entities to the digital health ecosystem. Trustworthy knowledge repositories are necessary for learning health systems, but the policies, standards, and practices to promote trustworthy CBK artifacts and methods to share, and safely and effectively use them are not well studied.MethodsWe conducted an online survey of 24 organizations in the United States known to be involved in the development or deployment of CBK. The aim of the survey was to assess the current policies and practices governing these repositories and to identify best practices. Descriptive statistics methods were applied to data from 13 responding organizations, to identify common practices and policies instantiating the TRUST principles of Transparency, Responsibility, User Focus, Sustainability, and Technology.ResultsAll 13 respondents indicated to different degrees adherence to policies that convey TRUST. Transparency is conveyed by having policies pertaining to provenance, credentialed contributors, and provision of metadata. Repositories provide knowledge in machine-readable formats, include implementation guidelines, and adhere to standards to convey Responsibility. Repositories report having Technology functions that enable end-users to verify, search, and filter for knowledge products. Less common TRUST practices are User Focused procedures that enable consumers to know about user licensing requirements or query the use of knowledge artifacts. Related to Sustainability, less than a majority post describe their sustainability plans. Few organizations publicly describe whether patients play any role in their decision-making.ConclusionIt is essential that knowledge repositories identify and apply a baseline set of criteria to lay a robust foundation for their trustworthiness leading to optimum uptake, and safe, reliable, and effective use to promote sharing of CBK. Identifying current practices suggests a set of desiderata for the CBK ecosystem in its continued evolution.

Project description:The Ontology for Biomedical Investigations (OBI) is an ontology that provides terms with precisely defined meanings to describe all aspects of how investigations in the biological and medical domains are conducted. OBI re-uses ontologies that provide a representation of biomedical knowledge from the Open Biological and Biomedical Ontologies (OBO) project and adds the ability to describe how this knowledge was derived. We here describe the state of OBI and several applications that are using it, such as adding semantic expressivity to existing databases, building data entry forms, and enabling interoperability between knowledge resources. OBI covers all phases of the investigation process, such as planning, execution and reporting. It represents information and material entities that participate in these processes, as well as roles and functions. Prior to OBI, it was not possible to use a single internally consistent resource that could be applied to multiple types of experiments for these applications. OBI has made this possible by creating terms for entities involved in biological and medical investigations and by importing parts of other biomedical ontologies such as GO, Chemical Entities of Biological Interest (ChEBI) and Phenotype Attribute and Trait Ontology (PATO) without altering their meaning. OBI is being used in a wide range of projects covering genomics, multi-omics, immunology, and catalogs of services. OBI has also spawned other ontologies (Information Artifact Ontology) and methods for importing parts of ontologies (Minimum information to reference an external ontology term (MIREOT)). The OBI project is an open cross-disciplinary collaborative effort, encompassing multiple research communities from around the globe. To date, OBI has created 2366 classes and 40 relations along with textual and formal definitions. The OBI Consortium maintains a web resource (http://obi-ontology.org) providing details on the people, policies, and issues being addressed in association with OBI. The current release of OBI is available at http://purl.obolibrary.org/obo/obi.owl.

Project description:BackgroundOntologies 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 interoperability across disparate datasets. However, the number, variety and complexity of current biomedical ontologies make it cumbersome for researchers to determine which ones to reuse for their specific needs. To overcome this problem, in 2010 the National Center for Biomedical Ontology (NCBO) released the Ontology Recommender, which is a service that receives a biomedical text corpus or a list of keywords and suggests ontologies appropriate for referencing the indicated terms.MethodsWe developed a new version of the NCBO Ontology Recommender. Called Ontology Recommender 2.0, it uses a novel recommendation approach that evaluates the relevance of an ontology to biomedical text data according to four different criteria: (1) the extent to which the ontology covers the input data; (2) the acceptance of the ontology in the biomedical community; (3) the level of detail of the ontology classes that cover the input data; and (4) the specialization of the ontology to the domain of the input data.ResultsOur evaluation shows that the enhanced recommender provides higher quality suggestions than the original approach, providing better coverage of the input data, more detailed information about their concepts, increased specialization for the domain of the input data, and greater acceptance and use in the community. In addition, it provides users with more explanatory information, along with suggestions of not only individual ontologies but also groups of ontologies to use together. It also can be customized to fit the needs of different ontology recommendation scenarios.ConclusionsOntology Recommender 2.0 suggests relevant ontologies for annotating biomedical text data. It combines the strengths of its predecessor with a range of adjustments and new features that improve its reliability and usefulness. Ontology Recommender 2.0 recommends over 500 biomedical ontologies from the NCBO BioPortal platform, where it is openly available (both via the user interface at http://bioportal.bioontology.org/recommender , and via a Web service API).

Dataset Information

SATORI: a system for ontology-guided visual exploration of biomedical data repositories.

Publications

SATORI: a system for ontology-guided visual exploration of biomedical data repositories.

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