PMCC PMCC

Search tips
Search criteria

Advanced
Results 1-25 (779897)

Clipboard (0)
None

Related Articles

1.  COEUS: “semantic web in a box” for biomedical applications 
Background
As the “omics” revolution unfolds, the growth in data quantity and diversity is bringing about the need for pioneering bioinformatics software, capable of significantly improving the research workflow. To cope with these computer science demands, biomedical software engineers are adopting emerging semantic web technologies that better suit the life sciences domain. The latter’s complex relationships are easily mapped into semantic web graphs, enabling a superior understanding of collected knowledge. Despite increased awareness of semantic web technologies in bioinformatics, their use is still limited.
Results
COEUS is a new semantic web framework, aiming at a streamlined application development cycle and following a “semantic web in a box” approach. The framework provides a single package including advanced data integration and triplification tools, base ontologies, a web-oriented engine and a flexible exploration API. Resources can be integrated from heterogeneous sources, including CSV and XML files or SQL and SPARQL query results, and mapped directly to one or more ontologies. Advanced interoperability features include REST services, a SPARQL endpoint and LinkedData publication. These enable the creation of multiple applications for web, desktop or mobile environments, and empower a new knowledge federation layer.
Conclusions
The platform, targeted at biomedical application developers, provides a complete skeleton ready for rapid application deployment, enhancing the creation of new semantic information systems. COEUS is available as open source at http://bioinformatics.ua.pt/coeus/.
doi:10.1186/2041-1480-3-11
PMCID: PMC3554586  PMID: 23244467
Semantic web framework; Rapid application deployment; Linked data; Web services; Biomedical applications; Biomedical semantics
2.  NCBO Technology: Powering semantically aware applications 
Journal of Biomedical Semantics  2013;4(Suppl 1):S8.
As new biomedical technologies are developed, the amount of publically available biomedical data continues to increase. To help manage these vast and disparate data sources, researchers have turned to the Semantic Web. Specifically, ontologies are used in data annotation, natural language processing, information retrieval, clinical decision support, and data integration tasks. The development of software applications to perform these tasks requires the integration of Web services to incorporate the wide variety of ontologies used in the health care and life sciences. The National Center for Biomedical Ontology, a National Center for Biomedical Computing created under the NIH Roadmap, developed BioPortal, which provides access to one of the largest repositories of biomedical ontologies. The NCBO Web services provide programmtic access to these ontologies and can be grouped into four categories; Ontology, Mapping, Annotation, and Data Access. The Ontology Web services provide access to ontologies, their metadata, ontology versions, downloads, navigation of the class hierarchy (parents, children, siblings) and details of each term. The Mapping Web services provide access to the millions of ontology mappings published in BioPortal. The NCBO Annotator Web service “tags” text automatically with terms from ontologies in BioPortal, and the NCBO Resource Index Web services provides access to an ontology-based index of public, online data resources. The NCBO Widgets package the Ontology Web services for use directly in Web sites. The functionality of the NCBO Web services and widgets are incorporated into semantically aware applications for ontology development and visualization, data annotation, and data integration. This overview will describe these classes of applications, discuss a few examples of each type, and which NCBO Web services are used by these applications.
doi:10.1186/2041-1480-4-S1-S8
PMCID: PMC3633000  PMID: 23734708
BioPortal; ontology; web service; REST; Annotator; Resource Index
3.  linkedISA: semantic representation of ISA-Tab experimental metadata 
BMC Bioinformatics  2014;15(Suppl 14):S4.
Background
Reporting and sharing experimental metadata- such as the experimental design, characteristics of the samples, and procedures applied, along with the analysis results, in a standardised manner ensures that datasets are comprehensible and, in principle, reproducible, comparable and reusable. Furthermore, sharing datasets in formats designed for consumption by humans and machines will also maximize their use. The Investigation/Study/Assay (ISA) open source metadata tracking framework facilitates standards-compliant collection, curation, visualization, storage and sharing of datasets, leveraging on other platforms to enable analysis and publication. The ISA software suite includes several components used in increasingly diverse set of life science and biomedical domains; it is underpinned by a general-purpose format, ISA-Tab, and conversions exist into formats required by public repositories. While ISA-Tab works well mainly as a human readable format, we have also implemented a linked data approach to semantically define the ISA-Tab syntax.
Results
We present a semantic web representation of the ISA-Tab syntax that complements ISA-Tab's syntactic interoperability with semantic interoperability. We introduce the linkedISA conversion tool from ISA-Tab to the Resource Description Framework (RDF), supporting mappings from the ISA syntax to multiple community-defined, open ontologies and capitalising on user-provided ontology annotations in the experimental metadata. We describe insights of the implementation and how annotations can be expanded driven by the metadata. We applied the conversion tool as part of Bio-GraphIIn, a web-based application supporting integration of the semantically-rich experimental descriptions. Designed in a user-friendly manner, the Bio-GraphIIn interface hides most of the complexities to the users, exposing a familiar tabular view of the experimental description to allow seamless interaction with the RDF representation, and visualising descriptors to drive the query over the semantic representation of the experimental design. In addition, we defined queries over the linkedISA RDF representation and demonstrated its use over the linkedISA conversion of datasets from Nature' Scientific Data online publication.
Conclusions
Our linked data approach has allowed us to: 1) make the ISA-Tab semantics explicit and machine-processable, 2) exploit the existing ontology-based annotations in the ISA-Tab experimental descriptions, 3) augment the ISA-Tab syntax with new descriptive elements, 4) visualise and query elements related to the experimental design. Reasoning over ISA-Tab metadata and associated data will facilitate data integration and knowledge discovery.
doi:10.1186/1471-2105-15-S14-S4
PMCID: PMC4255742  PMID: 25472428
4.  A journey to Semantic Web query federation in the life sciences 
BMC Bioinformatics  2009;10(Suppl 10):S10.
Background
As interest in adopting the Semantic Web in the biomedical domain continues to grow, Semantic Web technology has been evolving and maturing. A variety of technological approaches including triplestore technologies, SPARQL endpoints, Linked Data, and Vocabulary of Interlinked Datasets have emerged in recent years. In addition to the data warehouse construction, these technological approaches can be used to support dynamic query federation. As a community effort, the BioRDF task force, within the Semantic Web for Health Care and Life Sciences Interest Group, is exploring how these emerging approaches can be utilized to execute distributed queries across different neuroscience data sources.
Methods and results
We have created two health care and life science knowledge bases. We have explored a variety of Semantic Web approaches to describe, map, and dynamically query multiple datasets. We have demonstrated several federation approaches that integrate diverse types of information about neurons and receptors that play an important role in basic, clinical, and translational neuroscience research. Particularly, we have created a prototype receptor explorer which uses OWL mappings to provide an integrated list of receptors and executes individual queries against different SPARQL endpoints. We have also employed the AIDA Toolkit, which is directed at groups of knowledge workers who cooperatively search, annotate, interpret, and enrich large collections of heterogeneous documents from diverse locations. We have explored a tool called "FeDeRate", which enables a global SPARQL query to be decomposed into subqueries against the remote databases offering either SPARQL or SQL query interfaces. Finally, we have explored how to use the vocabulary of interlinked Datasets (voiD) to create metadata for describing datasets exposed as Linked Data URIs or SPARQL endpoints.
Conclusion
We have demonstrated the use of a set of novel and state-of-the-art Semantic Web technologies in support of a neuroscience query federation scenario. We have identified both the strengths and weaknesses of these technologies. While Semantic Web offers a global data model including the use of Uniform Resource Identifiers (URI's), the proliferation of semantically-equivalent URI's hinders large scale data integration. Our work helps direct research and tool development, which will be of benefit to this community.
doi:10.1186/1471-2105-10-S10-S10
PMCID: PMC2755818  PMID: 19796394
5.  Semantic Web repositories for genomics data using the eXframe platform 
Journal of Biomedical Semantics  2014;5(Suppl 1):S3.
Background
With the advent of inexpensive assay technologies, there has been an unprecedented growth in genomics data as well as the number of databases in which it is stored. In these databases, sample annotation using ontologies and controlled vocabularies is becoming more common. However, the annotation is rarely available as Linked Data, in a machine-readable format, or for standardized queries using SPARQL. This makes large-scale reuse, or integration with other knowledge bases very difficult.
Methods
To address this challenge, we have developed the second generation of our eXframe platform, a reusable framework for creating online repositories of genomics experiments. This second generation model now publishes Semantic Web data. To accomplish this, we created an experiment model that covers provenance, citations, external links, assays, biomaterials used in the experiment, and the data collected during the process. The elements of our model are mapped to classes and properties from various established biomedical ontologies. Resource Description Framework (RDF) data is automatically produced using these mappings and indexed in an RDF store with a built-in Sparql Protocol and RDF Query Language (SPARQL) endpoint.
Conclusions
Using the open-source eXframe software, institutions and laboratories can create Semantic Web repositories of their experiments, integrate it with heterogeneous resources and make it interoperable with the vast Semantic Web of biomedical knowledge.
doi:10.1186/2041-1480-5-S1-S3
PMCID: PMC4108874  PMID: 25093072
6.  Semantically Interoperable XML Data 
XML is ubiquitously used as an information exchange platform for web-based applications in healthcare, life sciences, and many other domains. Proliferating XML data are now managed through latest native XML database technologies. XML data sources conforming to common XML schemas could be shared and integrated with syntactic interoperability. Semantic interoperability can be achieved through semantic annotations of data models using common data elements linked to concepts from ontologies. In this paper, we present a framework and software system to support the development of semantic interoperable XML based data sources that can be shared through a Grid infrastructure. We also present our work on supporting semantic validated XML data through semantic annotations for XML Schema, semantic validation and semantic authoring of XML data. We demonstrate the use of the system for a biomedical database of medical image annotations and markups.
doi:10.1142/S1793351X13500037
PMCID: PMC4185431  PMID: 25298789
Biomedical Data Management; XML Database; Data Integration; Semantic Interoperability
7.  Advancing translational research with the Semantic Web 
BMC Bioinformatics  2007;8(Suppl 3):S2.
Background
A fundamental goal of the U.S. National Institute of Health (NIH) "Roadmap" is to strengthen Translational Research, defined as the movement of discoveries in basic research to application at the clinical level. A significant barrier to translational research is the lack of uniformly structured data across related biomedical domains. The Semantic Web is an extension of the current Web that enables navigation and meaningful use of digital resources by automatic processes. It is based on common formats that support aggregation and integration of data drawn from diverse sources. A variety of technologies have been built on this foundation that, together, support identifying, representing, and reasoning across a wide range of biomedical data. The Semantic Web Health Care and Life Sciences Interest Group (HCLSIG), set up within the framework of the World Wide Web Consortium, was launched to explore the application of these technologies in a variety of areas. Subgroups focus on making biomedical data available in RDF, working with biomedical ontologies, prototyping clinical decision support systems, working on drug safety and efficacy communication, and supporting disease researchers navigating and annotating the large amount of potentially relevant literature.
Results
We present a scenario that shows the value of the information environment the Semantic Web can support for aiding neuroscience researchers. We then report on several projects by members of the HCLSIG, in the process illustrating the range of Semantic Web technologies that have applications in areas of biomedicine.
Conclusion
Semantic Web technologies present both promise and challenges. Current tools and standards are already adequate to implement components of the bench-to-bedside vision. On the other hand, these technologies are young. Gaps in standards and implementations still exist and adoption is limited by typical problems with early technology, such as the need for a critical mass of practitioners and installed base, and growing pains as the technology is scaled up. Still, the potential of interoperable knowledge sources for biomedicine, at the scale of the World Wide Web, merits continued work.
doi:10.1186/1471-2105-8-S3-S2
PMCID: PMC1892099  PMID: 17493285
8.  SSWAP: A Simple Semantic Web Architecture and Protocol for semantic web services 
BMC Bioinformatics  2009;10:309.
Background
SSWAP (Simple Semantic Web Architecture and Protocol; pronounced "swap") is an architecture, protocol, and platform for using reasoning to semantically integrate heterogeneous disparate data and services on the web. SSWAP was developed as a hybrid semantic web services technology to overcome limitations found in both pure web service technologies and pure semantic web technologies.
Results
There are currently over 2400 resources published in SSWAP. Approximately two dozen are custom-written services for QTL (Quantitative Trait Loci) and mapping data for legumes and grasses (grains). The remaining are wrappers to Nucleic Acids Research Database and Web Server entries. As an architecture, SSWAP establishes how clients (users of data, services, and ontologies), providers (suppliers of data, services, and ontologies), and discovery servers (semantic search engines) interact to allow for the description, querying, discovery, invocation, and response of semantic web services. As a protocol, SSWAP provides the vocabulary and semantics to allow clients, providers, and discovery servers to engage in semantic web services. The protocol is based on the W3C-sanctioned first-order description logic language OWL DL. As an open source platform, a discovery server running at (as in to "swap info") uses the description logic reasoner Pellet to integrate semantic resources. The platform hosts an interactive guide to the protocol at , developer tools at , and a portal to third-party ontologies at (a "swap meet").
Conclusion
SSWAP addresses the three basic requirements of a semantic web services architecture (i.e., a common syntax, shared semantic, and semantic discovery) while addressing three technology limitations common in distributed service systems: i.e., i) the fatal mutability of traditional interfaces, ii) the rigidity and fragility of static subsumption hierarchies, and iii) the confounding of content, structure, and presentation. SSWAP is novel by establishing the concept of a canonical yet mutable OWL DL graph that allows data and service providers to describe their resources, to allow discovery servers to offer semantically rich search engines, to allow clients to discover and invoke those resources, and to allow providers to respond with semantically tagged data. SSWAP allows for a mix-and-match of terms from both new and legacy third-party ontologies in these graphs.
doi:10.1186/1471-2105-10-309
PMCID: PMC2761904  PMID: 19775460
9.  The BiSciCol Triplifier: bringing biodiversity data to the Semantic Web 
BMC Bioinformatics  2014;15(1):257.
Background
Recent years have brought great progress in efforts to digitize the world’s biodiversity data, but integrating data from many different providers, and across research domains, remains challenging. Semantic Web technologies have been widely recognized by biodiversity scientists for their potential to help solve this problem, yet these technologies have so far seen little use for biodiversity data. Such slow uptake has been due, in part, to the relative complexity of Semantic Web technologies along with a lack of domain-specific software tools to help non-experts publish their data to the Semantic Web.
Results
The BiSciCol Triplifier is new software that greatly simplifies the process of converting biodiversity data in standard, tabular formats, such as Darwin Core-Archives, into Semantic Web-ready Resource Description Framework (RDF) representations. The Triplifier uses a vocabulary based on the popular Darwin Core standard, includes both Web-based and command-line interfaces, and is fully open-source software.
Conclusions
Unlike most other RDF conversion tools, the Triplifier does not require detailed familiarity with core Semantic Web technologies, and it is tailored to a widely popular biodiversity data format and vocabulary standard. As a result, the Triplifier can often fully automate the conversion of biodiversity data to RDF, thereby making the Semantic Web much more accessible to biodiversity scientists who might otherwise have relatively little knowledge of Semantic Web technologies. Easy availability of biodiversity data as RDF will allow researchers to combine data from disparate sources and analyze them with powerful linked data querying tools. However, before software like the Triplifier, and Semantic Web technologies in general, can reach their full potential for biodiversity science, the biodiversity informatics community must address several critical challenges, such as the widespread failure to use robust, globally unique identifiers for biodiversity data.
Electronic supplementary material
The online version of this article (doi:10.1186/1471-2105-15-257) contains supplementary material, which is available to authorized users.
doi:10.1186/1471-2105-15-257
PMCID: PMC4124153  PMID: 25073721
Biocollections; Biodiversity informatics; Darwin core; Linked data; Ontology; RDF; Semantic web; SPARQL
10.  Semantic SenseLab: implementing the vision of the Semantic Web in neuroscience 
Summary
Objective
Integrative neuroscience research needs a scalable informatics framework that enables semantic integration of diverse types of neuroscience data. This paper describes the use of the Web Ontology Language (OWL) and other Semantic Web technologies for the representation and integration of molecular-level data provided by several of SenseLab suite of neuroscience databases.
Methods
Based on the original database structure, we semi-automatically translated the databases into OWL ontologies with manual addition of semantic enrichment. The SenseLab ontologies are extensively linked to other biomedical Semantic Web resources, including the Subcellular Anatomy Ontology, Brain Architecture Management System, the Gene Ontology, BIRNLex and UniProt. The SenseLab ontologies have also been mapped to the Basic Formal Ontology and Relation Ontology, which helps ease interoperability with many other existing and future biomedical ontologies for the Semantic Web. In addition, approaches to representing contradictory research statements are described. The SenseLab ontologies are designed for use on the Semantic Web that enables their integration into a growing collection of biomedical information resources.
Conclusion
We demonstrate that our approach can yield significant potential benefits and that the Semantic Web is rapidly becoming mature enough to realize its anticipated promises. The ontologies are available online at http://neuroweb.med.yale.edu/senselab/
doi:10.1016/j.artmed.2009.11.003
PMCID: PMC3131218  PMID: 20006477
Semantic Web; neuroscience; description logic; ontology mapping; Web Ontology Language; integration
11.  The Semantic Automated Discovery and Integration (SADI) Web service Design-Pattern, API and Reference Implementation 
Background
The complexity and inter-related nature of biological data poses a difficult challenge for data and tool integration. There has been a proliferation of interoperability standards and projects over the past decade, none of which has been widely adopted by the bioinformatics community. Recent attempts have focused on the use of semantics to assist integration, and Semantic Web technologies are being welcomed by this community.
Description
SADI - Semantic Automated Discovery and Integration - is a lightweight set of fully standards-compliant Semantic Web service design patterns that simplify the publication of services of the type commonly found in bioinformatics and other scientific domains. Using Semantic Web technologies at every level of the Web services "stack", SADI services consume and produce instances of OWL Classes following a small number of very straightforward best-practices. In addition, we provide codebases that support these best-practices, and plug-in tools to popular developer and client software that dramatically simplify deployment of services by providers, and the discovery and utilization of those services by their consumers.
Conclusions
SADI Services are fully compliant with, and utilize only foundational Web standards; are simple to create and maintain for service providers; and can be discovered and utilized in a very intuitive way by biologist end-users. In addition, the SADI design patterns significantly improve the ability of software to automatically discover appropriate services based on user-needs, and automatically chain these into complex analytical workflows. We show that, when resources are exposed through SADI, data compliant with a given ontological model can be automatically gathered, or generated, from these distributed, non-coordinating resources - a behaviour we have not observed in any other Semantic system. Finally, we show that, using SADI, data dynamically generated from Web services can be explored in a manner very similar to data housed in static triple-stores, thus facilitating the intersection of Web services and Semantic Web technologies.
doi:10.1186/2041-1480-2-8
PMCID: PMC3212890  PMID: 22024447
12.  iTools: A Framework for Classification, Categorization and Integration of Computational Biology Resources 
PLoS ONE  2008;3(5):e2265.
The advancement of the computational biology field hinges on progress in three fundamental directions – the development of new computational algorithms, the availability of informatics resource management infrastructures and the capability of tools to interoperate and synergize. There is an explosion in algorithms and tools for computational biology, which makes it difficult for biologists to find, compare and integrate such resources. We describe a new infrastructure, iTools, for managing the query, traversal and comparison of diverse computational biology resources. Specifically, iTools stores information about three types of resources–data, software tools and web-services. The iTools design, implementation and resource meta - data content reflect the broad research, computational, applied and scientific expertise available at the seven National Centers for Biomedical Computing. iTools provides a system for classification, categorization and integration of different computational biology resources across space-and-time scales, biomedical problems, computational infrastructures and mathematical foundations. A large number of resources are already iTools-accessible to the community and this infrastructure is rapidly growing. iTools includes human and machine interfaces to its resource meta-data repository. Investigators or computer programs may utilize these interfaces to search, compare, expand, revise and mine meta-data descriptions of existent computational biology resources. We propose two ways to browse and display the iTools dynamic collection of resources. The first one is based on an ontology of computational biology resources, and the second one is derived from hyperbolic projections of manifolds or complex structures onto planar discs. iTools is an open source project both in terms of the source code development as well as its meta-data content. iTools employs a decentralized, portable, scalable and lightweight framework for long-term resource management. We demonstrate several applications of iTools as a framework for integrated bioinformatics. iTools and the complete details about its specifications, usage and interfaces are available at the iTools web page http://iTools.ccb.ucla.edu.
doi:10.1371/journal.pone.0002265
PMCID: PMC2386255  PMID: 18509477
13.  Computational toxicology using the OpenTox application programming interface and Bioclipse 
BMC Research Notes  2011;4:487.
Background
Toxicity is a complex phenomenon involving the potential adverse effect on a range of biological functions. Predicting toxicity involves using a combination of experimental data (endpoints) and computational methods to generate a set of predictive models. Such models rely strongly on being able to integrate information from many sources. The required integration of biological and chemical information sources requires, however, a common language to express our knowledge ontologically, and interoperating services to build reliable predictive toxicology applications.
Findings
This article describes progress in extending the integrative bio- and cheminformatics platform Bioclipse to interoperate with OpenTox, a semantic web framework which supports open data exchange and toxicology model building. The Bioclipse workbench environment enables functionality from OpenTox web services and easy access to OpenTox resources for evaluating toxicity properties of query molecules. Relevant cases and interfaces based on ten neurotoxins are described to demonstrate the capabilities provided to the user. The integration takes advantage of semantic web technologies, thereby providing an open and simplifying communication standard. Additionally, the use of ontologies ensures proper interoperation and reliable integration of toxicity information from both experimental and computational sources.
Conclusions
A novel computational toxicity assessment platform was generated from integration of two open science platforms related to toxicology: Bioclipse, that combines a rich scriptable and graphical workbench environment for integration of diverse sets of information sources, and OpenTox, a platform for interoperable toxicology data and computational services. The combination provides improved reliability and operability for handling large data sets by the use of the Open Standards from the OpenTox Application Programming Interface. This enables simultaneous access to a variety of distributed predictive toxicology databases, and algorithm and model resources, taking advantage of the Bioclipse workbench handling the technical layers.
doi:10.1186/1756-0500-4-487
PMCID: PMC3264531  PMID: 22075173
14.  AlzPharm: integration of neurodegeneration data using RDF 
BMC Bioinformatics  2007;8(Suppl 3):S4.
Background
Neuroscientists often need to access a wide range of data sets distributed over the Internet. These data sets, however, are typically neither integrated nor interoperable, resulting in a barrier to answering complex neuroscience research questions. Domain ontologies can enable the querying heterogeneous data sets, but they are not sufficient for neuroscience since the data of interest commonly span multiple research domains. To this end, e-Neuroscience seeks to provide an integrated platform for neuroscientists to discover new knowledge through seamless integration of the very diverse types of neuroscience data. Here we present a Semantic Web approach to building this e-Neuroscience framework by using the Resource Description Framework (RDF) and its vocabulary description language, RDF Schema (RDFS), as a standard data model to facilitate both representation and integration of the data.
Results
We have constructed a pilot ontology for BrainPharm (a subset of SenseLab) using RDFS and then converted a subset of the BrainPharm data into RDF according to the ontological structure. We have also integrated the converted BrainPharm data with existing RDF hypothesis and publication data from a pilot version of SWAN (Semantic Web Applications in Neuromedicine). Our implementation uses the RDF Data Model in Oracle Database 10g release 2 for data integration, query, and inference, while our Web interface allows users to query the data and retrieve the results in a convenient fashion.
Conclusion
Accessing and integrating biomedical data which cuts across multiple disciplines will be increasingly indispensable and beneficial to neuroscience researchers. The Semantic Web approach we undertook has demonstrated a promising way to semantically integrate data sets created independently. It also shows how advanced queries and inferences can be performed over the integrated data, which are hard to achieve using traditional data integration approaches. Our pilot results suggest that our Semantic Web approach is suitable for realizing e-Neuroscience and generic enough to be applied in other biomedical fields.
doi:10.1186/1471-2105-8-S3-S4
PMCID: PMC1892101  PMID: 17493287
15.  The semantic web in translational medicine: current applications and future directions 
Briefings in Bioinformatics  2013;16(1):89-103.
Semantic web technologies offer an approach to data integration and sharing, even for resources developed independently or broadly distributed across the web. This approach is particularly suitable for scientific domains that profit from large amounts of data that reside in the public domain and that have to be exploited in combination. Translational medicine is such a domain, which in addition has to integrate private data from the clinical domain with proprietary data from the pharmaceutical domain. In this survey, we present the results of our analysis of translational medicine solutions that follow a semantic web approach. We assessed these solutions in terms of their target medical use case; the resources covered to achieve their objectives; and their use of existing semantic web resources for the purposes of data sharing, data interoperability and knowledge discovery. The semantic web technologies seem to fulfill their role in facilitating the integration and exploration of data from disparate sources, but it is also clear that simply using them is not enough. It is fundamental to reuse resources, to define mappings between resources, to share data and knowledge. All these aspects allow the instantiation of translational medicine at the semantic web-scale, thus resulting in a network of solutions that can share resources for a faster transfer of new scientific results into the clinical practice. The envisioned network of translational medicine solutions is on its way, but it still requires resolving the challenges of sharing protected data and of integrating semantic-driven technologies into the clinical practice.
doi:10.1093/bib/bbt079
PMCID: PMC4293377  PMID: 24197933
semantic web; translational medicine; data integration; data sharing; data interoperability; knowledge discovery
16.  Ontology driven integration platform for clinical and translational research 
BMC Bioinformatics  2009;10(Suppl 2):S2.
Semantic Web technologies offer a promising framework for integration of disparate biomedical data. In this paper we present the semantic information integration platform under development at the Center for Clinical and Translational Sciences (CCTS) at the University of Texas Health Science Center at Houston (UTHSC-H) as part of our Clinical and Translational Science Award (CTSA) program. We utilize the Semantic Web technologies not only for integrating, repurposing and classification of multi-source clinical data, but also to construct a distributed environment for information sharing, and collaboration online. Service Oriented Architecture (SOA) is used to modularize and distribute reusable services in a dynamic and distributed environment. Components of the semantic solution and its overall architecture are described.
doi:10.1186/1471-2105-10-S2-S2
PMCID: PMC2646248  PMID: 19208190
17.  TRIAD: The Translational Research Informatics and Data Management Grid 
Applied Clinical Informatics  2011;2(3):331-344.
Objective
Multi-disciplinary and multi-site biomedical research programs frequently require infrastructures capable of enabling the collection, management, analysis, and dissemination of heterogeneous, multi-dimensional, and distributed data and knowledge collections spanning organizational boundaries. We report on the design and initial deployment of an extensible biomedical informatics platform that is intended to address such requirements.
Methods
A common approach to distributed data, information, and knowledge management needs in the healthcare and life science settings is the deployment and use of a service-oriented architecture (SOA). Such SOA technologies provide for strongly-typed, semantically annotated, and stateful data and analytical services that can be combined into data and knowledge integration and analysis “pipelines.” Using this overall design pattern, we have implemented and evaluated an extensible SOA platform for clinical and translational science applications known as the Translational Research Informatics and Data-management grid (TRIAD). TRIAD is a derivative and extension of the caGrid middleware and has an emphasis on supporting agile “working interoperability” between data, information, and knowledge resources.
Results
Based upon initial verification and validation studies conducted in the context of a collection of driving clinical and translational research problems, we have been able to demonstrate that TRIAD achieves agile “working interoperability” between distributed data and knowledge sources.
Conclusion
Informed by our initial verification and validation studies, we believe TRIAD provides an example instance of a lightweight and readily adoptable approach to the use of SOA technologies in the clinical and translational research setting. Furthermore, our initial use cases illustrate the importance and efficacy of enabling “working interoperability” in heterogeneous biomedical environments.
doi:10.4338/ACI-2011-02-RA-0014
PMCID: PMC3631927  PMID: 23616879
Clinical research informatics; data access; data integration; data analysis; standards; workflow; socio-organizational issues
18.  Phylotastic! Making tree-of-life knowledge accessible, reusable and convenient 
BMC Bioinformatics  2013;14:158.
Background
Scientists rarely reuse expert knowledge of phylogeny, in spite of years of effort to assemble a great “Tree of Life” (ToL). A notable exception involves the use of Phylomatic, which provides tools to generate custom phylogenies from a large, pre-computed, expert phylogeny of plant taxa. This suggests great potential for a more generalized system that, starting with a query consisting of a list of any known species, would rectify non-standard names, identify expert phylogenies containing the implicated taxa, prune away unneeded parts, and supply branch lengths and annotations, resulting in a custom phylogeny suited to the user’s needs. Such a system could become a sustainable community resource if implemented as a distributed system of loosely coupled parts that interact through clearly defined interfaces.
Results
With the aim of building such a “phylotastic” system, the NESCent Hackathons, Interoperability, Phylogenies (HIP) working group recruited 2 dozen scientist-programmers to a weeklong programming hackathon in June 2012. During the hackathon (and a three-month follow-up period), 5 teams produced designs, implementations, documentation, presentations, and tests including: (1) a generalized scheme for integrating components; (2) proof-of-concept pruners and controllers; (3) a meta-API for taxonomic name resolution services; (4) a system for storing, finding, and retrieving phylogenies using semantic web technologies for data exchange, storage, and querying; (5) an innovative new service, DateLife.org, which synthesizes pre-computed, time-calibrated phylogenies to assign ages to nodes; and (6) demonstration projects. These outcomes are accessible via a public code repository (GitHub.com), a website (http://www.phylotastic.org), and a server image.
Conclusions
Approximately 9 person-months of effort (centered on a software development hackathon) resulted in the design and implementation of proof-of-concept software for 4 core phylotastic components, 3 controllers, and 3 end-user demonstration tools. While these products have substantial limitations, they suggest considerable potential for a distributed system that makes phylogenetic knowledge readily accessible in computable form. Widespread use of phylotastic systems will create an electronic marketplace for sharing phylogenetic knowledge that will spur innovation in other areas of the ToL enterprise, such as annotation of sources and methods and third-party methods of quality assessment.
doi:10.1186/1471-2105-14-158
PMCID: PMC3669619  PMID: 23668630
Phylogeny; Taxonomy; Hackathon; Web services; Data reuse; Tree of life
19.  Pain Research Forum: application of scientific social media frameworks in neuroscience 
Background: Social media has the potential to accelerate the pace of biomedical research through online collaboration, discussions, and faster sharing of information. Focused web-based scientific social collaboratories such as the Alzheimer Research Forum have been successful in engaging scientists in open discussions of the latest research and identifying gaps in knowledge. However, until recently, tools to rapidly create such communities and provide high-bandwidth information exchange between collaboratories in related fields did not exist.
Methods: We have addressed this need by constructing a reusable framework to build online biomedical communities, based on Drupal, an open-source content management system. The framework incorporates elements of Semantic Web technology combined with social media. Here we present, as an exemplar of a web community built on our framework, the Pain Research Forum (PRF) (http://painresearchforum.org). PRF is a community of chronic pain researchers, established with the goal of fostering collaboration and communication among pain researchers.
Results: Launched in 2011, PRF has over 1300 registered members with permission to submit content. It currently hosts over 150 topical news articles on research; more than 30 active or archived forum discussions and journal club features; a webinar series; an editor-curated weekly updated listing of relevant papers; and several other resources for the pain research community. All content is licensed for reuse under a Creative Commons license; the software is freely available. The framework was reused to develop other sites, notably the Multiple Sclerosis Discovery Forum (http://msdiscovery.org) and StemBook (http://stembook.org).
Discussion: Web-based collaboratories are a crucial integrative tool supporting rapid information transmission and translation in several important research areas. In this article, we discuss the success factors, lessons learned, and ongoing challenges in using PRF as a driving force to develop tools for online collaboration in neuroscience. We also indicate ways these tools can be applied to other areas and uses.
doi:10.3389/fninf.2014.00021
PMCID: PMC3949323  PMID: 24653693
social media; neuropathic pain; content management systems; Drupal
20.  search GenBank: interactive orchestration and ad-hoc choreography of Web services in the exploration of the biomedical resources of the National Center For Biotechnology Information 
BMC Bioinformatics  2013;14:73.
Background
Due to the growing number of biomedical entries in data repositories of the National Center for Biotechnology Information (NCBI), it is difficult to collect, manage and process all of these entries in one place by third-party software developers without significant investment in hardware and software infrastructure, its maintenance and administration. Web services allow development of software applications that integrate in one place the functionality and processing logic of distributed software components, without integrating the components themselves and without integrating the resources to which they have access. This is achieved by appropriate orchestration or choreography of available Web services and their shared functions. After the successful application of Web services in the business sector, this technology can now be used to build composite software tools that are oriented towards biomedical data processing.
Results
We have developed a new tool for efficient and dynamic data exploration in GenBank and other NCBI databases. A dedicated search GenBank system makes use of NCBI Web services and a package of Entrez Programming Utilities (eUtils) in order to provide extended searching capabilities in NCBI data repositories. In search GenBank users can use one of the three exploration paths: simple data searching based on the specified user’s query, advanced data searching based on the specified user’s query, and advanced data exploration with the use of macros. search GenBank orchestrates calls of particular tools available through the NCBI Web service providing requested functionality, while users interactively browse selected records in search GenBank and traverse between NCBI databases using available links. On the other hand, by building macros in the advanced data exploration mode, users create choreographies of eUtils calls, which can lead to the automatic discovery of related data in the specified databases.
Conclusions
search GenBank extends standard capabilities of the NCBI Entrez search engine in querying biomedical databases. The possibility of creating and saving macros in the search GenBank is a unique feature and has a great potential. The potential will further grow in the future with the increasing density of networks of relationships between data stored in particular databases. search GenBank is available for public use at http://sgb.biotools.pl/.
doi:10.1186/1471-2105-14-73
PMCID: PMC3602006  PMID: 23452691
NCBI entrez; Entrez databases; Entrez search engine; Entrez programming utilities; Data exploration; Data searching; Data querying; Web services; Orchestration; Choreography
21.  ADEpedia: A Scalable and Standardized Knowledge Base of Adverse Drug Events Using Semantic Web Technology 
A source of semantically coded Adverse Drug Event (ADE) data can be useful for identifying common phenotypes related to ADEs. We proposed a comprehensive framework for building a standardized ADE knowledge base (called ADEpedia) through combining ontology-based approach with semantic web technology. The framework comprises four primary modules: 1) an XML2RDF transformation module; 2) a data normalization module based on NCBO Open Biomedical Annotator; 3) a RDF store based persistence module; and 4) a front-end module based on a Semantic Wiki for the review and curation. A prototype is successfully implemented to demonstrate the capability of the system to integrate multiple drug data and ontology resources and open web services for the ADE data standardization. A preliminary evaluation is performed to demonstrate the usefulness of the system, including the performance of the NCBO annotator. In conclusion, the semantic web technology provides a highly scalable framework for ADE data source integration and standard query service.
PMCID: PMC3243176  PMID: 22195116
22.  A Semantic Problem Solving Environment for Integrative Parasite Research: Identification of Intervention Targets for Trypanosoma cruzi 
Background
Research on the biology of parasites requires a sophisticated and integrated computational platform to query and analyze large volumes of data, representing both unpublished (internal) and public (external) data sources. Effective analysis of an integrated data resource using knowledge discovery tools would significantly aid biologists in conducting their research, for example, through identifying various intervention targets in parasites and in deciding the future direction of ongoing as well as planned projects. A key challenge in achieving this objective is the heterogeneity between the internal lab data, usually stored as flat files, Excel spreadsheets or custom-built databases, and the external databases. Reconciling the different forms of heterogeneity and effectively integrating data from disparate sources is a nontrivial task for biologists and requires a dedicated informatics infrastructure. Thus, we developed an integrated environment using Semantic Web technologies that may provide biologists the tools for managing and analyzing their data, without the need for acquiring in-depth computer science knowledge.
Methodology/Principal Findings
We developed a semantic problem-solving environment (SPSE) that uses ontologies to integrate internal lab data with external resources in a Parasite Knowledge Base (PKB), which has the ability to query across these resources in a unified manner. The SPSE includes Web Ontology Language (OWL)-based ontologies, experimental data with its provenance information represented using the Resource Description Format (RDF), and a visual querying tool, Cuebee, that features integrated use of Web services. We demonstrate the use and benefit of SPSE using example queries for identifying gene knockout targets of Trypanosoma cruzi for vaccine development. Answers to these queries involve looking up multiple sources of data, linking them together and presenting the results.
Conclusion/Significance
The SPSE facilitates parasitologists in leveraging the growing, but disparate, parasite data resources by offering an integrative platform that utilizes Semantic Web techniques, while keeping their workload increase minimal.
Author Summary
Effective research in parasite biology requires analyzing experimental lab data in the context of constantly expanding public data resources. Integrating lab data with public resources is particularly difficult for biologists who may not possess significant computational skills to acquire and process heterogeneous data stored at different locations. Therefore, we develop a semantic problem solving environment (SPSE) that allows parasitologists to query their lab data integrated with public resources using ontologies. An ontology specifies a common vocabulary and formal relationships among the terms that describe an organism, and experimental data and processes in this case. SPSE supports capturing and querying provenance information, which is metadata on the experimental processes and data recorded for reproducibility, and includes a visual query-processing tool to formulate complex queries without learning the query language syntax. We demonstrate the significance of SPSE in identifying gene knockout targets for T. cruzi. The overall goal of SPSE is to help researchers discover new or existing knowledge that is implicitly present in the data but not always easily detected. Results demonstrate improved usefulness of SPSE over existing lab systems and approaches, and support for complex query design that is otherwise difficult to achieve without the knowledge of query language syntax.
doi:10.1371/journal.pntd.0001458
PMCID: PMC3260319  PMID: 22272365
23.  A unified structural/terminological interoperability framework based on LexEVS: application to TRANSFoRm 
Objective
Biomedical research increasingly relies on the integration of information from multiple heterogeneous data sources. Despite the fact that structural and terminological aspects of interoperability are interdependent and rely on a common set of requirements, current efforts typically address them in isolation. We propose a unified ontology-based knowledge framework to facilitate interoperability between heterogeneous sources, and investigate if using the LexEVS terminology server is a viable implementation method.
Materials and methods
We developed a framework based on an ontology, the general information model (GIM), to unify structural models and terminologies, together with relevant mapping sets. This allowed a uniform access to these resources within LexEVS to facilitate interoperability by various components and data sources from implementing architectures.
Results
Our unified framework has been tested in the context of the EU Framework Program 7 TRANSFoRm project, where it was used to achieve data integration in a retrospective diabetes cohort study. The GIM was successfully instantiated in TRANSFoRm as the clinical data integration model, and necessary mappings were created to support effective information retrieval for software tools in the project.
Conclusions
We present a novel, unifying approach to address interoperability challenges in heterogeneous data sources, by representing structural and semantic models in one framework. Systems using this architecture can rely solely on the GIM that abstracts over both the structure and coding. Information models, terminologies and mappings are all stored in LexEVS and can be accessed in a uniform manner (implementing the HL7 CTS2 service functional model). The system is flexible and should reduce the effort needed from data sources personnel for implementing and managing the integration.
doi:10.1136/amiajnl-2012-001312
PMCID: PMC3756256  PMID: 23571850
Translational Medical Research; Interoperability; Semantics; Terminology; Ontology; LexEVS
24.  The Application of the Open Pharmacological Concepts Triple Store (Open PHACTS) to Support Drug Discovery Research 
PLoS ONE  2014;9(12):e115460.
Integration of open access, curated, high-quality information from multiple disciplines in the Life and Biomedical Sciences provides a holistic understanding of the domain. Additionally, the effective linking of diverse data sources can unearth hidden relationships and guide potential research strategies. However, given the lack of consistency between descriptors and identifiers used in different resources and the absence of a simple mechanism to link them, gathering and combining relevant, comprehensive information from diverse databases remains a challenge. The Open Pharmacological Concepts Triple Store (Open PHACTS) is an Innovative Medicines Initiative project that uses semantic web technology approaches to enable scientists to easily access and process data from multiple sources to solve real-world drug discovery problems. The project draws together sources of publicly-available pharmacological, physicochemical and biomolecular data, represents it in a stable infrastructure and provides well-defined information exploration and retrieval methods. Here, we highlight the utility of this platform in conjunction with workflow tools to solve pharmacological research questions that require interoperability between target, compound, and pathway data. Use cases presented herein cover 1) the comprehensive identification of chemical matter for a dopamine receptor drug discovery program 2) the identification of compounds active against all targets in the Epidermal growth factor receptor (ErbB) signaling pathway that have a relevance to disease and 3) the evaluation of established targets in the Vitamin D metabolism pathway to aid novel Vitamin D analogue design. The example workflows presented illustrate how the Open PHACTS Discovery Platform can be used to exploit existing knowledge and generate new hypotheses in the process of drug discovery.
doi:10.1371/journal.pone.0115460
PMCID: PMC4270790  PMID: 25522365
25.  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

Results 1-25 (779897)