PMCC PMCC

Search tips
Search criteria

Advanced
Results 1-25 (1048789)

Clipboard (0)
None

Related Articles

1.  Semantic-JSON: a lightweight web service interface for Semantic Web contents integrating multiple life science databases 
Nucleic Acids Research  2011;39(Web Server issue):W533-W540.
Global cloud frameworks for bioinformatics research databases become huge and heterogeneous; solutions face various diametric challenges comprising cross-integration, retrieval, security and openness. To address this, as of March 2011 organizations including RIKEN published 192 mammalian, plant and protein life sciences databases having 8.2 million data records, integrated as Linked Open or Private Data (LOD/LPD) using SciNetS.org, the Scientists' Networking System. The huge quantity of linked data this database integration framework covers is based on the Semantic Web, where researchers collaborate by managing metadata across public and private databases in a secured data space. This outstripped the data query capacity of existing interface tools like SPARQL. Actual research also requires specialized tools for data analysis using raw original data. To solve these challenges, in December 2009 we developed the lightweight Semantic-JSON interface to access each fragment of linked and raw life sciences data securely under the control of programming languages popularly used by bioinformaticians such as Perl and Ruby. Researchers successfully used the interface across 28 million semantic relationships for biological applications including genome design, sequence processing, inference over phenotype databases, full-text search indexing and human-readable contents like ontology and LOD tree viewers. Semantic-JSON services of SciNetS.org are provided at http://semanticjson.org.
doi:10.1093/nar/gkr353
PMCID: PMC3125761  PMID: 21632604
2.  Nursing Routine Data as a Basis for Association Analysis in the Domain of Nursing Knowledge 
This paper describes the data mining method of association analysis within the framework of Knowledge Discovery in Databases (KDD) with the aim to identify standard patterns of nursing care. The approach is application-oriented and used on nursing routine data of the method LEP nursing 2. The increasing use of information technology in hospitals, especially of nursing information systems, requires the storage of large data sets, which hitherto have not always been analyzed adequately. Three association analyses for the days of admission, surgery and discharge, have been performed. The results of almost 1.5 million generated association rules indicate that it is valid to apply association analysis to nursing routine data. All rules are semantically trivial, since they reflect existing knowledge from the domain of nursing. This may be due either to the method LEP Nursing 2, or to the nursing activities themselves. Nonetheless, association analysis may in future become a useful analytical tool on the basis of structured nursing routine data.
PMCID: PMC3799158  PMID: 24199122
3.  Semantics-based composition of EMBOSS services 
Journal of Biomedical Semantics  2011;2(Suppl 1):S5.
Background
More than in other domains the heterogeneous services world in bioinformatics demands for a methodology to classify and relate resources in a both human and machine accessible manner. The Semantic Web, which is meant to address exactly this challenge, is currently one of the most ambitious projects in computer science. Collective efforts within the community have already led to a basis of standards for semantic service descriptions and meta-information. In combination with process synthesis and planning methods, such knowledge about types and services can facilitate the automatic composition of workflows for particular research questions.
Results
In this study we apply the synthesis methodology that is available in the Bio-jETI workflow management framework for the semantics-based composition of EMBOSS services. EMBOSS (European Molecular Biology Open Software Suite) is a collection of 350 tools (March 2010) for various sequence analysis tasks, and thus a rich source of services and types that imply comprehensive domain models for planning and synthesis approaches. We use and compare two different setups of our EMBOSS synthesis domain: 1) a manually defined domain setup where an intuitive, high-level, semantically meaningful nomenclature is applied to describe the input/output behavior of the single EMBOSS tools and their classifications, and 2) a domain setup where this information has been automatically derived from the EMBOSS Ajax Command Definition (ACD) files and the EMBRACE Data and Methods ontology (EDAM). Our experiments demonstrate that these domain models in combination with our synthesis methodology greatly simplify working with the large, heterogeneous, and hence manually intractable EMBOSS collection. However, they also show that with the information that can be derived from the (current) ACD files and EDAM ontology alone, some essential connections between services can not be recognized.
Conclusions
Our results show that adequate domain modeling requires to incorporate as much domain knowledge as possible, far beyond the mere technical aspects of the different types and services. Finding or defining semantically appropriate service and type descriptions is a difficult task, but the bioinformatics community appears to be on the right track towards a Life Science Semantic Web, which will eventually allow automatic service composition methods to unfold their full potential.
doi:10.1186/2041-1480-2-S1-S5
PMCID: PMC3105497  PMID: 21388574
4.  Why are organisations that provide healthcare services fuzzy? 
The Australasian Medical Journal  2013;6(11):542-548.
Background
Healthcare organisations are an enigma to many people inand outside the service. Organisational fuzziness is a common state, characterised by a lack of clarity, lack of awareness, lack of organisational knowledge, and the reliance on practice and custom instead of transparency.
Aims
The objective of this study was to obtain a better understanding of what causes this fuzziness and provide an actionable description of fuzzy organisations. Such a description is essential to managing and preventing organisational fuzziness.
Method
We used a longitudinal case study in an integrated healthand social care organisation to obtain a thorough understanding of how the organisation functions. These indepth insights allowed the identification of three generators of fuzziness.
Results
We found that the three main generators of organisational fuzziness are change, informal organisation and complexity. Organisational fuzziness is thus partly due to the inherent complexities of human systems. However, also continuous change and the inability of the system to adapt its formal structures resulted in structures deteriorating or no longer being appropriate.
Conclusion
Existing approaches to explain unclear or absent structures in healthcare organisations by describing these organisations as complex adaptive systems (CAS) are too simplistic. While aspects relating to people and their interactions are indeed complex, fuzziness of structural aspects are often the result of continuous change and insufficient organisational capacity to adapt to it.
doi:10.4066/AMJ.2013.1857
PMCID: PMC3858607  PMID: 24348870
Complexity; change; healthcare services; complex adaptive systems; healthcare organisations; service design
5.  Partnering with diabetes educators to improve patient outcomes 
Diabetes is a chronic, progressive disease that affects millions worldwide. The paradigm of diabetes management has shifted to focus on empowering the person with diabetes to manage the disease successfully and to improve their quality of life. Diabetes self-management education is a collaborative process through which people with diabetes gain the knowledge and skills needed to modify their behavior and to self-manage successfully the disease and its related conditions. Diabetes educators are health care professionals who apply in-depth knowledge and skills in the biological and social sciences, communication, counseling, and pedagogy to enable patients to manage daily and future challenges. Diabetes educators are integral in providing individualized education and promoting behavior change, using a framework of seven self-care behaviors known as the AADE7 Self-Care Behaviors™, developed by the American Association of Diabetes Educators. The iterative process of promoting behavior change includes assessment, goal setting, planning, implementation, evaluation, and documentation. Diabetes educators work as part of the patient’s health care team to engage with the patient in informed, shared decision making. The increasing prevalence of diabetes and the growing focus on its prevention require strategies for providing people with knowledge, skills, and strategies they need and can use. The diabetes educator is the logical facilitator of change. Access to diabetes education is critically important; incorporating diabetes educators into more and varied practice settings will serve to improve clinical and quality of life outcomes for persons with diabetes.
doi:10.2147/DMSO.S40036
PMCID: PMC3926770  PMID: 24550679
diabetes educator; diabetes self-management education; healthcare team; behavior change
6.  Selected papers from the 13th Annual Bio-Ontologies Special Interest Group Meeting 
Journal of Biomedical Semantics  2011;2(Suppl 2):I1.
Over the years, the Bio-Ontologies SIG at ISMB has provided a forum for discussion of the latest and most innovative research in the application of ontologies and more generally the organisation, presentation and dissemination of knowledge in biomedicine and the life sciences. The ten papers selected for this supplement are extended versions of the original papers presented at the 2010 SIG. The papers span a wide range of topics including practical solutions for data and knowledge integration for translational medicine, hypothesis based querying , understanding kidney and urinary pathways, mining the pharmacogenomics literature; theoretical research into the orthogonality of biomedical ontologies, the representation of diseases, the representation of research hypotheses, the combination of ontologies and natural language processing for an annotation framework, the generation of textual definitions, and the discovery of gene interaction networks.
doi:10.1186/2041-1480-2-S2-I1
PMCID: PMC3102888  PMID: 21624154
7.  Large-scale data integration framework provides a comprehensive view on glioblastoma multiforme 
Genome Medicine  2010;2(9):65.
Background
Coordinated efforts to collect large-scale data sets provide a basis for systems level understanding of complex diseases. In order to translate these fragmented and heterogeneous data sets into knowledge and medical benefits, advanced computational methods for data analysis, integration and visualization are needed.
Methods
We introduce a novel data integration framework, Anduril, for translating fragmented large-scale data into testable predictions. The Anduril framework allows rapid integration of heterogeneous data with state-of-the-art computational methods and existing knowledge in bio-databases. Anduril automatically generates thorough summary reports and a website that shows the most relevant features of each gene at a glance, allows sorting of data based on different parameters, and provides direct links to more detailed data on genes, transcripts or genomic regions. Anduril is open-source; all methods and documentation are freely available.
Results
We have integrated multidimensional molecular and clinical data from 338 subjects having glioblastoma multiforme, one of the deadliest and most poorly understood cancers, using Anduril. The central objective of our approach is to identify genetic loci and genes that have significant survival effect. Our results suggest several novel genetic alterations linked to glioblastoma multiforme progression and, more specifically, reveal Moesin as a novel glioblastoma multiforme-associated gene that has a strong survival effect and whose depletion in vitro significantly inhibited cell proliferation. All analysis results are available as a comprehensive website.
Conclusions
Our results demonstrate that integrated analysis and visualization of multidimensional and heterogeneous data by Anduril enables drawing conclusions on functional consequences of large-scale molecular data. Many of the identified genetic loci and genes having significant survival effect have not been reported earlier in the context of glioblastoma multiforme. Thus, in addition to generally applicable novel methodology, our results provide several glioblastoma multiforme candidate genes for further studies.
Anduril is available at http://csbi.ltdk.helsinki.fi/anduril/
The glioblastoma multiforme analysis results are available at http://csbi.ltdk.helsinki.fi/anduril/tcga-gbm/
doi:10.1186/gm186
PMCID: PMC3092116  PMID: 20822536
8.  Clever generation of rich SPARQL queries from annotated relational schema: application to Semantic Web Service creation for biological databases 
BMC Bioinformatics  2013;14:126.
Background
In recent years, a large amount of “-omics” data have been produced. However, these data are stored in many different species-specific databases that are managed by different institutes and laboratories. Biologists often need to find and assemble data from disparate sources to perform certain analyses. Searching for these data and assembling them is a time-consuming task. The Semantic Web helps to facilitate interoperability across databases. A common approach involves the development of wrapper systems that map a relational database schema onto existing domain ontologies. However, few attempts have been made to automate the creation of such wrappers.
Results
We developed a framework, named BioSemantic, for the creation of Semantic Web Services that are applicable to relational biological databases. This framework makes use of both Semantic Web and Web Services technologies and can be divided into two main parts: (i) the generation and semi-automatic annotation of an RDF view; and (ii) the automatic generation of SPARQL queries and their integration into Semantic Web Services backbones. We have used our framework to integrate genomic data from different plant databases.
Conclusions
BioSemantic is a framework that was designed to speed integration of relational databases. We present how it can be used to speed the development of Semantic Web Services for existing relational biological databases. Currently, it creates and annotates RDF views that enable the automatic generation of SPARQL queries. Web Services are also created and deployed automatically, and the semantic annotations of our Web Services are added automatically using SAWSDL attributes. BioSemantic is downloadable at http://southgreen.cirad.fr/?q=content/Biosemantic.
doi:10.1186/1471-2105-14-126
PMCID: PMC3680174  PMID: 23586394
9.  Finding Complex Biological Relationships in Recent PubMed Articles Using Bio-LDA 
PLoS ONE  2011;6(3):e17243.
The overwhelming amount of available scholarly literature in the life sciences poses significant challenges to scientists wishing to keep up with important developments related to their research, but also provides a useful resource for the discovery of recent information concerning genes, diseases, compounds and the interactions between them. In this paper, we describe an algorithm called Bio-LDA that uses extracted biological terminology to automatically identify latent topics, and provides a variety of measures to uncover putative relations among topics and bio-terms. Relationships identified using those approaches are combined with existing data in life science datasets to provide additional insight. Three case studies demonstrate the utility of the Bio-LDA model, including association predication, association search and connectivity map generation. This combined approach offers new opportunities for knowledge discovery in many areas of biology including target identification, lead hopping and drug repurposing.
doi:10.1371/journal.pone.0017243
PMCID: PMC3063155  PMID: 21448266
10.  The BioIntelligence Framework: a new computational platform for biomedical knowledge computing 
Breakthroughs in molecular profiling technologies are enabling a new data-intensive approach to biomedical research, with the potential to revolutionize how we study, manage, and treat complex diseases. The next great challenge for clinical applications of these innovations will be to create scalable computational solutions for intelligently linking complex biomedical patient data to clinically actionable knowledge. Traditional database management systems (DBMS) are not well suited to representing complex syntactic and semantic relationships in unstructured biomedical information, introducing barriers to realizing such solutions. We propose a scalable computational framework for addressing this need, which leverages a hypergraph-based data model and query language that may be better suited for representing complex multi-lateral, multi-scalar, and multi-dimensional relationships. We also discuss how this framework can be used to create rapid learning knowledge base systems to intelligently capture and relate complex patient data to biomedical knowledge in order to automate the recovery of clinically actionable information.
doi:10.1136/amiajnl-2011-000646
PMCID: PMC3555311  PMID: 22859646
Database management systems (L01.224.900.280); access to information (L01.143.024); knowledge (L01.535); data; information; knowledge; bioinformatics; databases; research; computer; science; biomedical; informatics; trent1952; genomics; knowledge; hypergraph; cancer; database
11.  Towards Semantic e-Science for Traditional Chinese Medicine 
BMC Bioinformatics  2007;8(Suppl 3):S6.
Background
Recent advances in Web and information technologies with the increasing decentralization of organizational structures have resulted in massive amounts of information resources and domain-specific services in Traditional Chinese Medicine. The massive volume and diversity of information and services available have made it difficult to achieve seamless and interoperable e-Science for knowledge-intensive disciplines like TCM. Therefore, information integration and service coordination are two major challenges in e-Science for TCM. We still lack sophisticated approaches to integrate scientific data and services for TCM e-Science.
Results
We present a comprehensive approach to build dynamic and extendable e-Science applications for knowledge-intensive disciplines like TCM based on semantic and knowledge-based techniques. The semantic e-Science infrastructure for TCM supports large-scale database integration and service coordination in a virtual organization. We use domain ontologies to integrate TCM database resources and services in a semantic cyberspace and deliver a semantically superior experience including browsing, searching, querying and knowledge discovering to users. We have developed a collection of semantic-based toolkits to facilitate TCM scientists and researchers in information sharing and collaborative research.
Conclusion
Semantic and knowledge-based techniques are suitable to knowledge-intensive disciplines like TCM. It's possible to build on-demand e-Science system for TCM based on existing semantic and knowledge-based techniques. The presented approach in the paper integrates heterogeneous distributed TCM databases and services, and provides scientists with semantically superior experience to support collaborative research in TCM discipline.
doi:10.1186/1471-2105-8-S3-S6
PMCID: PMC1892103  PMID: 17493289
12.  e-Science and biological pathway semantics 
BMC Bioinformatics  2007;8(Suppl 3):S3.
Background
The development of e-Science presents a major set of opportunities and challenges for the future progress of biological and life scientific research. Major new tools are required and corresponding demands are placed on the high-throughput data generated and used in these processes. Nowhere is the demand greater than in the semantic integration of these data. Semantic Web tools and technologies afford the chance to achieve this semantic integration. Since pathway knowledge is central to much of the scientific research today it is a good test-bed for semantic integration. Within the context of biological pathways, the BioPAX initiative, part of a broader movement towards the standardization and integration of life science databases, forms a necessary prerequisite for its successful application of e-Science in health care and life science research. This paper examines whether BioPAX, an effort to overcome the barrier of disparate and heterogeneous pathway data sources, addresses the needs of e-Science.
Results
We demonstrate how BioPAX pathway data can be used to ask and answer some useful biological questions. We find that BioPAX comes close to meeting a broad range of e-Science needs, but certain semantic weaknesses mean that these goals are missed. We make a series of recommendations for re-modeling some aspects of BioPAX to better meet these needs.
Conclusion
Once these semantic weaknesses are addressed, it will be possible to integrate pathway information in a manner that would be useful in e-Science.
doi:10.1186/1471-2105-8-S3-S3
PMCID: PMC1892100  PMID: 17493286
13.  Large Scale Application of Neural Network Based Semantic Role Labeling for Automated Relation Extraction from Biomedical Texts 
PLoS ONE  2009;4(7):e6393.
To reduce the increasing amount of time spent on literature search in the life sciences, several methods for automated knowledge extraction have been developed. Co-occurrence based approaches can deal with large text corpora like MEDLINE in an acceptable time but are not able to extract any specific type of semantic relation. Semantic relation extraction methods based on syntax trees, on the other hand, are computationally expensive and the interpretation of the generated trees is difficult. Several natural language processing (NLP) approaches for the biomedical domain exist focusing specifically on the detection of a limited set of relation types. For systems biology, generic approaches for the detection of a multitude of relation types which in addition are able to process large text corpora are needed but the number of systems meeting both requirements is very limited. We introduce the use of SENNA (“Semantic Extraction using a Neural Network Architecture”), a fast and accurate neural network based Semantic Role Labeling (SRL) program, for the large scale extraction of semantic relations from the biomedical literature. A comparison of processing times of SENNA and other SRL systems or syntactical parsers used in the biomedical domain revealed that SENNA is the fastest Proposition Bank (PropBank) conforming SRL program currently available. 89 million biomedical sentences were tagged with SENNA on a 100 node cluster within three days. The accuracy of the presented relation extraction approach was evaluated on two test sets of annotated sentences resulting in precision/recall values of 0.71/0.43. We show that the accuracy as well as processing speed of the proposed semantic relation extraction approach is sufficient for its large scale application on biomedical text. The proposed approach is highly generalizable regarding the supported relation types and appears to be especially suited for general-purpose, broad-scale text mining systems. The presented approach bridges the gap between fast, cooccurrence-based approaches lacking semantic relations and highly specialized and computationally demanding NLP approaches.
doi:10.1371/journal.pone.0006393
PMCID: PMC2712690  PMID: 19636432
14.  Ontologies as integrative tools for plant science 
American journal of botany  2012;99(8):1263-1275.
Premise of the study
Bio-ontologies are essential tools for accessing and analyzing the rapidly growing pool of plant genomic and phenomic data. Ontologies provide structured vocabularies to support consistent aggregation of data and a semantic framework for automated analyses and reasoning. They are a key component of the semantic web.
Methods
This paper provides background on what bio-ontologies are, why they are relevant to botany, and the principles of ontology development. It includes an overview of ontologies and related resources that are relevant to plant science, with a detailed description of the Plant Ontology (PO). We discuss the challenges of building an ontology that covers all green plants (Viridiplantae).
Key results
Ontologies can advance plant science in four keys areas: (1) comparative genetics, genomics, phenomics, and development; (2) taxonomy and systematics; (3) semantic applications; and (4) education.
Conclusions
Bio-ontologies offer a flexible framework for comparative plant biology, based on common botanical understanding. As genomic and phenomic data become available for more species, we anticipate that the annotation of data with ontology terms will become less centralized, while at the same time, the need for cross-species queries will become more common, causing more researchers in plant science to turn to ontologies.
doi:10.3732/ajb.1200222
PMCID: PMC3492881  PMID: 22847540
bio-ontologies; genome annotation; OBO Foundry; phenomics; plant anatomy; plant genomics; Plant Ontology; plant systematics; semantic web
15.  Design and implementation of a generalized laboratory data model 
BMC Bioinformatics  2007;8:362.
Background
Investigators in the biological sciences continue to exploit laboratory automation methods and have dramatically increased the rates at which they can generate data. In many environments, the methods themselves also evolve in a rapid and fluid manner. These observations point to the importance of robust information management systems in the modern laboratory. Designing and implementing such systems is non-trivial and it appears that in many cases a database project ultimately proves unserviceable.
Results
We describe a general modeling framework for laboratory data and its implementation as an information management system. The model utilizes several abstraction techniques, focusing especially on the concepts of inheritance and meta-data. Traditional approaches commingle event-oriented data with regular entity data in ad hoc ways. Instead, we define distinct regular entity and event schemas, but fully integrate these via a standardized interface. The design allows straightforward definition of a "processing pipeline" as a sequence of events, obviating the need for separate workflow management systems. A layer above the event-oriented schema integrates events into a workflow by defining "processing directives", which act as automated project managers of items in the system. Directives can be added or modified in an almost trivial fashion, i.e., without the need for schema modification or re-certification of applications. Association between regular entities and events is managed via simple "many-to-many" relationships. We describe the programming interface, as well as techniques for handling input/output, process control, and state transitions.
Conclusion
The implementation described here has served as the Washington University Genome Sequencing Center's primary information system for several years. It handles all transactions underlying a throughput rate of about 9 million sequencing reactions of various kinds per month and has handily weathered a number of major pipeline reconfigurations. The basic data model can be readily adapted to other high-volume processing environments.
doi:10.1186/1471-2105-8-362
PMCID: PMC2194795  PMID: 17897463
16.  Managing Requirement Volatility in an Ontology-Driven Clinical LIMS Using Category Theory 
Requirement volatility is an issue in software engineering in general, and in Web-based clinical applications in particular, which often originates from an incomplete knowledge of the domain of interest. With advances in the health science, many features and functionalities need to be added to, or removed from, existing software applications in the biomedical domain. At the same time, the increasing complexity of biomedical systems makes them more difficult to understand, and consequently it is more difficult to define their requirements, which contributes considerably to their volatility. In this paper, we present a novel agent-based approach for analyzing and managing volatile and dynamic requirements in an ontology-driven laboratory information management system (LIMS) designed for Web-based case reporting in medical mycology. The proposed framework is empowered with ontologies and formalized using category theory to provide a deep and common understanding of the functional and nonfunctional requirement hierarchies and their interrelations, and to trace the effects of a change on the conceptual framework.
doi:10.1155/2009/917826
PMCID: PMC2662492  PMID: 19343191
17.  Biomedical semantics in the Semantic Web 
Journal of Biomedical Semantics  2011;2(Suppl 1):S1.
The Semantic Web offers an ideal platform for representing and linking biomedical information, which is a prerequisite for the development and application of analytical tools to address problems in data-intensive areas such as systems biology and translational medicine. As for any new paradigm, the adoption of the Semantic Web offers opportunities and poses questions and challenges to the life sciences scientific community: which technologies in the Semantic Web stack will be more beneficial for the life sciences? Is biomedical information too complex to benefit from simple interlinked representations? What are the implications of adopting a new paradigm for knowledge representation? What are the incentives for the adoption of the Semantic Web, and who are the facilitators? Is there going to be a Semantic Web revolution in the life sciences?
We report here a few reflections on these questions, following discussions at the SWAT4LS (Semantic Web Applications and Tools for Life Sciences) workshop series, of which this Journal of Biomedical Semantics special issue presents selected papers from the 2009 edition, held in Amsterdam on November 20th.
doi:10.1186/2041-1480-2-S1-S1
PMCID: PMC3105493  PMID: 21388570
18.  S3QL: A distributed domain specific language for controlled semantic integration of life sciences data 
BMC Bioinformatics  2011;12:285.
Background
The value and usefulness of data increases when it is explicitly interlinked with related data. This is the core principle of Linked Data. For life sciences researchers, harnessing the power of Linked Data to improve biological discovery is still challenged by a need to keep pace with rapidly evolving domains and requirements for collaboration and control as well as with the reference semantic web ontologies and standards. Knowledge organization systems (KOSs) can provide an abstraction for publishing biological discoveries as Linked Data without complicating transactions with contextual minutia such as provenance and access control.
We have previously described the Simple Sloppy Semantic Database (S3DB) as an efficient model for creating knowledge organization systems using Linked Data best practices with explicit distinction between domain and instantiation and support for a permission control mechanism that automatically migrates between the two. In this report we present a domain specific language, the S3DB query language (S3QL), to operate on its underlying core model and facilitate management of Linked Data.
Results
Reflecting the data driven nature of our approach, S3QL has been implemented as an application programming interface for S3DB systems hosting biomedical data, and its syntax was subsequently generalized beyond the S3DB core model. This achievement is illustrated with the assembly of an S3QL query to manage entities from the Simple Knowledge Organization System. The illustrative use cases include gastrointestinal clinical trials, genomic characterization of cancer by The Cancer Genome Atlas (TCGA) and molecular epidemiology of infectious diseases.
Conclusions
S3QL was found to provide a convenient mechanism to represent context for interoperation between public and private datasets hosted at biomedical research institutions and linked data formalisms.
doi:10.1186/1471-2105-12-285
PMCID: PMC3155508  PMID: 21756325
S3DB; Linked Data; KOS; RDF; SPARQL; knowledge organization system, policy
19.  Using semantic web rules to reason on an ontology of pseudogenes 
Bioinformatics  2010;26(12):i71-i78.
Motivation: Recent years have seen the development of a wide range of biomedical ontologies. Notable among these is Sequence Ontology (SO) which offers a rich hierarchy of terms and relationships that can be used to annotate genomic data. Well-designed formal ontologies allow data to be reasoned upon in a consistent and logically sound way and can lead to the discovery of new relationships. The Semantic Web Rules Language (SWRL) augments the capabilities of a reasoner by allowing the creation of conditional rules. To date, however, formal reasoning, especially the use of SWRL rules, has not been widely used in biomedicine.
Results: We have built a knowledge base of human pseudogenes, extending the existing SO framework to incorporate additional attributes. In particular, we have defined the relationships between pseudogenes and segmental duplications. We then created a series of logical rules using SWRL to answer research questions and to annotate our pseudogenes appropriately. Finally, we were left with a knowledge base which could be queried to discover information about human pseudogene evolution.
Availability: The fully populated knowledge base described in this document is available for download from http://ontology.pseudogene.org. A SPARQL endpoint from which to query the dataset is also available at this location.
Contact: matthew.holford@yale.edu; mark.gerstein@yale.edu
doi:10.1093/bioinformatics/btq173
PMCID: PMC2881358  PMID: 20529940
20.  Integrating patient safety into the clinical microsystem 
Quality & safety in health care  2004;13(Suppl 2):ii34-ii38.
Healthcare institutions continue to face challenges in providing safe patient care in increasingly complex organisational and regulatory environments while striving to maintain financial viability. The clinical microsystem provides a conceptual and practical framework for approaching organisational learning and delivery of care. Tensions exist between the conceptual theory and the daily practical applications of providing safe and effective care within healthcare systems. Healthcare organisations are often complex, disorganised, and opaque systems to their users and their patients. This disorganisation may lead to patient discomfort and harm as well as much waste. Healthcare organisations are in some sense conglomerates of smaller systems, not coherent monolithic organisations. The microsystem unit allows organisational leaders to embed quality and safety into a microsystem's developmental journey. Leaders can set the stage for making safety a priority for the organisation while allowing individual microsystems to create innovative strategies for improvement.
doi:10.1136/qshc.2003.009571
PMCID: PMC1765806  PMID: 15576690
21.  Annotation of SBML models through rule-based semantic integration 
Journal of Biomedical Semantics  2010;1(Suppl 1):S3.
Background
The creation of accurate quantitative Systems Biology Markup Language (SBML) models is a time-intensive, manual process often complicated by the many data sources and formats required to annotate even a small and well-scoped model. Ideally, the retrieval and integration of biological knowledge for model annotation should be performed quickly, precisely, and with a minimum of manual effort.
Results
Here we present rule-based mediation, a method of semantic data integration applied to systems biology model annotation. The heterogeneous data sources are first syntactically converted into ontologies, which are then aligned to a small domain ontology by applying a rule base. We demonstrate proof-of-principle of this application of rule-based mediation using off-the-shelf semantic web technology through two use cases for SBML model annotation. Existing tools and technology provide a framework around which the system is built, reducing development time and increasing usability.
Conclusions
Integrating resources in this way accommodates multiple formats with different semantics, and provides richly-modelled biological knowledge suitable for annotation of SBML models. This initial work establishes the feasibility of rule-based mediation as part of an automated SBML model annotation system.
Availability
Detailed information on the project files as well as further information on and comparisons with similar projects is available from the project page at http://cisban-silico.cs.ncl.ac.uk/RBM/.
doi:10.1186/2041-1480-1-S1-S3
PMCID: PMC2903722  PMID: 20626923
22.  The Learning Organisation and Health Care Education 
The ‘Learning Organisation’ is a concept first described by Peter Senge as an organisation where people continuously learn and enhance their capabilities to create. It consists of five main disciplines: team learning, shared vision, mental models, personal mastery and systems thinking. These disciplines are dynamic and interact with each other. System thinking is the cornerstone of a true learning organisation and is described as the discipline used to implement the disciplines. In a learning organisation, health care education aims to educate its members with up to date knowledge to produce competent and safe personnel, who can promote quality in health care services. In addition, there are some educational concepts and theoretical models, which are of relevance to the learning organisation, and can provide a framework for managerial decisions. The stages required to achieve the principles of a learning organisation will be described in detail. Moreover, in a proper culture which supports the learning organisation, members continuously learn to improve the environment and never remain passive recipients.
PMCID: PMC3074888  PMID: 21748105
Learning organisation; Healthcare education; Leadership
23.  Understanding life together: A brief history of collaboration in biology 
Endeavour  2013;37(3):162-171.
The history of science shows a shift from single-investigator ‘little science’ to increasingly large, expensive, multinational, interdisciplinary and interdependent ‘big science’. In physics and allied fields this shift has been well documented, but the rise of collaboration in the life sciences and its effect on scientific work and knowledge has received little attention. Research in biology exhibits different historical trajectories and organisation of collaboration in field and laboratory – differences still visible in contemporary collaborations such as the Census of Marine Life and the Human Genome Project. We employ these case studies as strategic exemplars, supplemented with existing research on collaboration in biology, to expose the different motives, organisational forms and social dynamics underpinning contemporary large-scale collaborations in biology and their relations to historical patterns of collaboration in the life sciences. We find the interaction between research subject, research approach as well as research organisation influencing collaboration patterns and the work of scientists.
doi:10.1016/j.endeavour.2013.03.001
PMCID: PMC3878597  PMID: 23578694
24.  Towards ontology-driven navigation of the lipid bibliosphere 
BMC Bioinformatics  2008;9(Suppl 1):S5.
Background
The indexing of scientific literature and content is a relevant and contemporary requirement within life science information systems. Navigating information available in legacy formats continues to be a challenge both in enterprise and academic domains. The emergence of semantic web technologies and their fusion with artificial intelligence techniques has provided a new toolkit with which to address these data integration challenges. In the emerging field of lipidomics such navigation challenges are barriers to the translation of scientific results into actionable knowledge, critical to the treatment of diseases such as Alzheimer's syndrome, Mycobacterium infections and cancer.
Results
We present a literature-driven workflow involving document delivery and natural language processing steps generating tagged sentences containing lipid, protein and disease names, which are instantiated to custom designed lipid ontology. We describe the design challenges in capturing lipid nomenclature, the mandate of the ontology and its role as query model in the navigation of the lipid bibliosphere. We illustrate the extent of the description logic-based A-box query capability provided by the instantiated ontology using a graphical query composer to query sentences describing lipid-protein and lipid-disease correlations.
Conclusion
As scientists accept the need to readjust the manner in which we search for information and derive knowledge we illustrate a system that can constrain the literature explosion and knowledge navigation problems. Specifically we have focussed on solving this challenge for lipidomics researchers who have to deal with the lack of standardized vocabulary, differing classification schemes, and a wide array of synonyms before being able to derive scientific insights. The use of the OWL-DL variant of the Web Ontology Language (OWL) and description logic reasoning is pivotal in this regard, providing the lipid scientist with advanced query access to the results of text mining algorithms instantiated into the ontology. The visual query paradigm assists in the adoption of this technology.
doi:10.1186/1471-2105-9-S1-S5
PMCID: PMC2259406  PMID: 18315858
25.  Enhancing medical database semantics. 
Medical Databases deal with dynamic, heterogeneous and fuzzy data. The modeling of such complex domain demands powerful semantic data modeling methodologies. This paper describes GSM-Explorer a Case Tool that allows for the creation of relational databases using semantic data modeling techniques. GSM Explorer fully incorporates the Generic Semantic Data Model-GSM enabling knowledge engineers to model the application domain with the abstraction mechanisms of generalization/specialization, association and aggregation. The tool generates a structure that implements persistent database-objects through the automatic generation of customized SQL ANSI scripts that sustain the semantics defined in the higher lever. This paper emphasizes the system architecture and the mapping of the semantic model into relational tables. The present status of the project and its further developments are discussed in the Conclusions.
PMCID: PMC2579102  PMID: 8563288

Results 1-25 (1048789)