Overview of the CDISC2RDF ontologies and a first overview of the import/transformation for standards-as-is into machine processable OWL/RDF. See also http://cdisc2rdf.com/
This document discusses linked open data, which organizes data using URIs and RDF triples so that the data can be connected across sources. It provides examples of datasets that use linked open data principles like DBpedia, Wikidata, and Schema.org. The document outlines the semantic web stack for linked data, including RDF, RDF Schema, and OWL. It discusses benefits like preparing data for unknown future uses and enabling automation through linking related information.
2010-dec-08 HL7 Detailed Clinical Modelling and ArchitectureMichael van der Zel
Michael van der Zel presented on detailed clinical models (DCM). He discussed where DCM fits within different architecture frameworks like Gartner's component model and RM-ODP. He then explained what a DCM is and the specifics of a DCM information model and toolset for creating, validating, exporting, and transforming DCMs. Finally, he discussed granularity issues around DCMs and provided an example case on propensity to adverse reactions.
Digital Imaging and Communications in Medicine (DICOM) is a standard for handling, storing, printing, and transmitting information in medical imaging. It includes a file format definition and a network communications protocol. The communication protocol is an application protocol that uses TCP/IP to communicate between systems. DICOM files can be exchanged between two entities that are capable of receiving image and patient data in DICOM format.
DICOM enables the integration of scanners, servers, workstations, printers, and network hardware from multiple manufacturers into a picture archiving and communication system (PACS). The different devices come with DICOM conformance statements which clearly state the DICOM classes they support. DICOM has been widely adopted by hospitals and is making inroads in smaller applications like dentists' and doctors' offices.
A copyright protection technology for 3 d printing models (john choi)MecklerMedia
1. The document discusses copyright protection technologies for 3D printing models, including a clearing center for copyrighted 3D models, feature extraction from 3D models, shape estimation to match models, and THz detection.
2. It describes potential solutions such as encryption of 3D model files, feature extraction for fingerprinting, and using a clearing center to manage licensing and monitor for illegal distribution of copyrighted 3D models.
3. The key technologies proposed are extracting features from 3D models, analyzing model structures through skeleton extraction, and estimating the original model shape based on the skeleton to enable digital forensics of 3D models.
A Database Management System (DBMS) is software that allows for the storage, retrieval, and management of data in a database. A DBMS provides data independence, efficient data access, data integrity, security, and concurrency control. It uses data models like the relational model to define the conceptual, logical, and physical schemas for databases.
A simulation model of ieee 802.15.4 gts mechanism and gtswissem hammouda
This document presents a simulation model of the IEEE 802.15.4 GTS mechanism and known GTS attacks developed in OMNeT++. The model includes a GTS management scheme model that implements beacon transmission, PAN association, GTS slot allocation and data transmission during GTS slots. It also includes a GTS attacks model that simulates five known GTS attack variants. The models were integrated to provide a comprehensive simulation of both normal GTS operation and attacks against the mechanism. The document describes the architecture, parameters and operation of the models in detail.
This document discusses linked open data, which organizes data using URIs and RDF triples so that the data can be connected across sources. It provides examples of datasets that use linked open data principles like DBpedia, Wikidata, and Schema.org. The document outlines the semantic web stack for linked data, including RDF, RDF Schema, and OWL. It discusses benefits like preparing data for unknown future uses and enabling automation through linking related information.
2010-dec-08 HL7 Detailed Clinical Modelling and ArchitectureMichael van der Zel
Michael van der Zel presented on detailed clinical models (DCM). He discussed where DCM fits within different architecture frameworks like Gartner's component model and RM-ODP. He then explained what a DCM is and the specifics of a DCM information model and toolset for creating, validating, exporting, and transforming DCMs. Finally, he discussed granularity issues around DCMs and provided an example case on propensity to adverse reactions.
Digital Imaging and Communications in Medicine (DICOM) is a standard for handling, storing, printing, and transmitting information in medical imaging. It includes a file format definition and a network communications protocol. The communication protocol is an application protocol that uses TCP/IP to communicate between systems. DICOM files can be exchanged between two entities that are capable of receiving image and patient data in DICOM format.
DICOM enables the integration of scanners, servers, workstations, printers, and network hardware from multiple manufacturers into a picture archiving and communication system (PACS). The different devices come with DICOM conformance statements which clearly state the DICOM classes they support. DICOM has been widely adopted by hospitals and is making inroads in smaller applications like dentists' and doctors' offices.
A copyright protection technology for 3 d printing models (john choi)MecklerMedia
1. The document discusses copyright protection technologies for 3D printing models, including a clearing center for copyrighted 3D models, feature extraction from 3D models, shape estimation to match models, and THz detection.
2. It describes potential solutions such as encryption of 3D model files, feature extraction for fingerprinting, and using a clearing center to manage licensing and monitor for illegal distribution of copyrighted 3D models.
3. The key technologies proposed are extracting features from 3D models, analyzing model structures through skeleton extraction, and estimating the original model shape based on the skeleton to enable digital forensics of 3D models.
A Database Management System (DBMS) is software that allows for the storage, retrieval, and management of data in a database. A DBMS provides data independence, efficient data access, data integrity, security, and concurrency control. It uses data models like the relational model to define the conceptual, logical, and physical schemas for databases.
A simulation model of ieee 802.15.4 gts mechanism and gtswissem hammouda
This document presents a simulation model of the IEEE 802.15.4 GTS mechanism and known GTS attacks developed in OMNeT++. The model includes a GTS management scheme model that implements beacon transmission, PAN association, GTS slot allocation and data transmission during GTS slots. It also includes a GTS attacks model that simulates five known GTS attack variants. The models were integrated to provide a comprehensive simulation of both normal GTS operation and attacks against the mechanism. The document describes the architecture, parameters and operation of the models in detail.
IRJET- Enhanced Density Based Method for Clustering Data StreamIRJET Journal
The document presents a new incremental density-based algorithm called Enhanced Density-based Data Stream (EDDS) for clustering data streams. EDDS modifies the traditional DBSCAN algorithm to represent clusters using only surface core points. It detects clusters and outliers in incoming data chunks, merges new clusters with existing ones, and filters outliers for the next round. The algorithm prunes internal core points using heuristics and removes aged core points/outliers using a fading function. It was evaluated on datasets and found to improve clustering correctness with time complexity comparable to existing methods.
Distributed Systems: How to connect your real-time applicationsJaime Martin Losa
This document provides an overview of distributed systems and how to connect real-time applications using the Data Distribution Service (DDS) standard. It introduces DDS and its architecture, including topics, instances, keys, quality of service policies. It then demonstrates how to create a basic "hello world" publisher/subscriber example in both eProsima Fast RTPS and RTI Connext DDS middleware in 3 steps: defining the data type, generating code, and building/running the publisher and subscriber.
Hw09 Hadoop Based Data Mining Platform For The Telecom IndustryCloudera, Inc.
The document summarizes a parallel data mining platform called BC-PDM developed by China Mobile Communication Corporation to address the challenges of analyzing their large scale telecom data. Key points:
- BC-PDM is based on Hadoop and designed to perform ETL and data mining algorithms in parallel to enable scalable analysis of datasets exceeding hundreds of terabytes.
- The platform implements various ETL operations and data mining algorithms using MapReduce. Initial experiments showed a 10-50x speedup over traditional solutions.
- Future work includes improving data security, migrating online systems to the platform, and enhancing the user interface.
Professor Jon Patrick
Health Information Technology Research Laboratory (HITRL - www.it.usyd.edu.au/~hitru)
School of Information Technologies
University of Sydney
(P39, 17/10/08, Systems & Methods stream, 1.50pm)
Distributing your pandas ETL job using Modin and Ray.pdfAndrew Li
This document discusses using Ray and Modin to distribute pandas ETL jobs. It introduces Ray and Modin, their architectures, and how they can be used to handle two common cases: processing many small datasets that share logic, and handling out-of-core datasets without rewriting ETL scripts. Key aspects of Ray include its global control store, bottom-up scheduler, in-memory object store, and handling dependencies. Modin supports pandas APIs through eager execution and various partitioning schemes, while defaulting to pandas for unsupported APIs.
System on Chip Design and Modelling Dr. David J GreavesSatya Harish
The document provides an overview of a course on system on chip design and modeling techniques. The course covers topics like register transfer language, SystemC components, basic SoC components, assertion-based design, network on chip structures, and architectural design exploration. It aims to cover the front end of the design automation process, including specification, modeling at different levels of abstraction, and logic synthesis. A running example evolves over the lectures to demonstrate a simple SoC.
Sparse feature analysis for detection of clustered microcalcifications in mam...Wesley De Neve
This document analyzes the use of sparse feature analysis for detecting clustered microcalcifications in mammogram images. It compares different feature types, combinations of features, and dictionary construction techniques for sparse representation based classification (SRC) of mammogram images. The experimental results show that texture features like Laws' texture features (LAW) are more effective than shape/morphology features. SRC using LAW features alone or combined with local binary patterns (LBP) achieved high performance. Larger dictionaries containing more atoms resulted in higher discriminative power for the SRC-based detection system.
A comparison of Simulation and Operational ArchitecturesSimware
This whitepaper presents a comparison between simulation and operational architectures. Presented at the Simulation Interoperability Standards Organization (SISO) 2012 Fall Simulation Interoperability Workshop in Orlando, FL, USA. The paper is co-authored with Thales and Prismtech.
This document provides an overview of the Intel x86 architecture, including its registers, instructions, memory management, interrupts and exceptions, task management, and input/output capabilities. It describes the basic execution environment including memory management registers and control registers. It explains the operation modes of protected mode and real mode, and the memory models. It also summarizes the general purpose instructions, system instructions, privilege levels, basic program execution registers, and memory addressing in the x86 architecture.
IJCER (www.ijceronline.com) International Journal of computational Engineeri...ijceronline
The document proposes implementing register files in the processor hardware to improve context switching performance in hard real-time systems. Conventionally, context switching involves saving processor registers to external memory, which takes 50-80 clock cycles. The proposed approach saves contexts to register files within the processor, requiring only 4 clock cycles. Software and a small operating system were modified to use new "save context" and "restore context" instructions. Simulation results showed contexts being saved and restored from an internal register file in 2 clock cycles each. Two test applications demonstrated the performance improvement from using internal register files versus external memory for context switching.
This document evaluates several XML compression tools. It examines 11 compressors, including 3 general text compressors and 8 XML-aware compressors. The compressors are evaluated on 57 XML documents from different domains, measuring compression ratio, compression time, and decompression time on two different computing environments. The results show that XML-aware compressors generally achieve better compression ratios than general text compressors, with ratios ranging from 0.07 to 0.24 on structural documents and 0.12 to 0.22 on original documents.
EUGM 2014 - Brock Luty (Dart Neuroscience): A ChemAxon/KNIME based tool for ...ChemAxon
This document summarizes the development of a chemical library design tool at Dart NeuroScience. It describes the goals of creating an easy to use tool to standardize calculations, reactions, and simplify workflows. The tool was developed using KNIME with ChemAxon services and utilizes a service oriented architecture. Key features of the tool include reactant selection, reaction enumeration, property calculations, clustering, and exporting designs to Spotfire and ELNs. The tool has been iteratively improved over several years of development and testing.
The document discusses remote function call (RFC) specifications between different systems for various analysis processes in a project called Landscape. It states that the same RFC name should be used when transmitting data from the Analysis system to either the Statistics or Reference system as is specified in the Control system. It provides examples of RFC names for Clearing Analysis, Upgrade Change Impact Analysis, and Change and Transport System Analysis. It also notes that the target and statistics systems are typically the same for CTS analysis.
This document provides an overview of the DirectPath subsystems, including the Internet delivery subsystem, TV delivery and MPEG platform subsystems, volume and file access subsystems, and content transfer engine subsystem. It describes the components, functions, and interactions between the subsystems to deliver digital content over the Internet and to TVs. The document also explains how the subsystems support applications like hospitality video-on-demand and cable TV ad insertion.
1. The document introduces Cisco's Software Defined Data Center (SDDC) technology strategy. It discusses the trends of BiModal IT and the emergence of Mode 1 and Mode 2 IT.
2. It describes the SDDC architecture including Software Defined Computing (SDC) using Cisco UCS, Software Defined Storage (SDS) using Cisco HyperFlex, and Software Defined Networking (SDN) using Cisco ACI.
3. Case studies show that implementing SDDC with SDx technologies from Cisco can improve agility, reduce costs, and help organizations deploy both Mode 1 and Mode 2 applications.
The application of STDM in a no-profit and disease specific organisation - CD...Angelo Tinazzi
This document summarizes a presentation given by Angelo Tinazzi at the 2008 CDISC Italian-Speaking User Group Meeting in Milan. The presentation discusses the application of SDTM at SENDO Tech, a non-profit clinical research organization focused on oncology drug development. SENDO implements SDTM using a hybrid approach, applying some SDTM standards within their clinical database and performing additional transformations and mappings in SAS post-processing to fully comply with SDTM. The presentation outlines SENDO's SDTM implementation challenges due to the heterogeneity of oncology data and describes their methods for mapping clinical data to SDTM domains and variables. It also provides examples of new domains SENDO has
The document provides an introduction to Cadence design flow, outlining the typical steps involved in integrated circuit design from schematic capture and simulation to layout and fabrication. These steps include creating schematics using a process design kit, performing layout with design rules in mind, extracting parasitic components, and verifying the design through simulation and layout vs schematic checks before finalizing the layout file for fabrication. Key software tools used in the Cadence design flow are also outlined.
This document provides an overview of JTAG (Joint Test Action Group) devices, including their basic chip architecture, capabilities, and common system configurations. It describes the JTAG standard architecture which defines boundary-scan cells and a test access port. It also summarizes common JTAG instructions, the TAP controller state machine, typical JTAG interfaces and connectors, BSDL description files, and how JTAG devices can be daisy-chained to form a scan chain for testing connections between components.
1. The document summarizes Kerstin Forsberg's presentation on semantics and linked data at AstraZeneca R&D. It discusses (1) an internal competitive intelligence tool called CI360, (2) public pre-competitive projects like Open PHACTS and standards bodies, (3) AstraZeneca's Linked Data Community of Practice, and (4) ongoing work on study identifiers and APIs.
2. It provides an overview of Kerstin Forsberg's background and goal of improving the utility of clinical trial data through semantic interoperability. It also outlines some of AstraZeneca's collaborations and contributions to linked data initiatives.
3. The presentation highlights AstraZeneca
Linked Data efforts for data standards in biopharma and healthcareKerstin Forsberg
1) The document discusses efforts to represent biomedical data standards like CDISC, HL7 FHIR, MeSH, ICD-11, and others in semantic web formats like RDF and OWL to make them machine-processable.
2) It describes projects that have converted various standards to RDF through the work of groups like CDISC2RDF and PhUSE, and efforts to engage traditional standards bodies.
3) However, it notes that pushing standards organizations to adopt semantic web approaches requires ongoing knowledge sharing and community building, and that spreadsheets still see significant use.
IRJET- Enhanced Density Based Method for Clustering Data StreamIRJET Journal
The document presents a new incremental density-based algorithm called Enhanced Density-based Data Stream (EDDS) for clustering data streams. EDDS modifies the traditional DBSCAN algorithm to represent clusters using only surface core points. It detects clusters and outliers in incoming data chunks, merges new clusters with existing ones, and filters outliers for the next round. The algorithm prunes internal core points using heuristics and removes aged core points/outliers using a fading function. It was evaluated on datasets and found to improve clustering correctness with time complexity comparable to existing methods.
Distributed Systems: How to connect your real-time applicationsJaime Martin Losa
This document provides an overview of distributed systems and how to connect real-time applications using the Data Distribution Service (DDS) standard. It introduces DDS and its architecture, including topics, instances, keys, quality of service policies. It then demonstrates how to create a basic "hello world" publisher/subscriber example in both eProsima Fast RTPS and RTI Connext DDS middleware in 3 steps: defining the data type, generating code, and building/running the publisher and subscriber.
Hw09 Hadoop Based Data Mining Platform For The Telecom IndustryCloudera, Inc.
The document summarizes a parallel data mining platform called BC-PDM developed by China Mobile Communication Corporation to address the challenges of analyzing their large scale telecom data. Key points:
- BC-PDM is based on Hadoop and designed to perform ETL and data mining algorithms in parallel to enable scalable analysis of datasets exceeding hundreds of terabytes.
- The platform implements various ETL operations and data mining algorithms using MapReduce. Initial experiments showed a 10-50x speedup over traditional solutions.
- Future work includes improving data security, migrating online systems to the platform, and enhancing the user interface.
Professor Jon Patrick
Health Information Technology Research Laboratory (HITRL - www.it.usyd.edu.au/~hitru)
School of Information Technologies
University of Sydney
(P39, 17/10/08, Systems & Methods stream, 1.50pm)
Distributing your pandas ETL job using Modin and Ray.pdfAndrew Li
This document discusses using Ray and Modin to distribute pandas ETL jobs. It introduces Ray and Modin, their architectures, and how they can be used to handle two common cases: processing many small datasets that share logic, and handling out-of-core datasets without rewriting ETL scripts. Key aspects of Ray include its global control store, bottom-up scheduler, in-memory object store, and handling dependencies. Modin supports pandas APIs through eager execution and various partitioning schemes, while defaulting to pandas for unsupported APIs.
System on Chip Design and Modelling Dr. David J GreavesSatya Harish
The document provides an overview of a course on system on chip design and modeling techniques. The course covers topics like register transfer language, SystemC components, basic SoC components, assertion-based design, network on chip structures, and architectural design exploration. It aims to cover the front end of the design automation process, including specification, modeling at different levels of abstraction, and logic synthesis. A running example evolves over the lectures to demonstrate a simple SoC.
Sparse feature analysis for detection of clustered microcalcifications in mam...Wesley De Neve
This document analyzes the use of sparse feature analysis for detecting clustered microcalcifications in mammogram images. It compares different feature types, combinations of features, and dictionary construction techniques for sparse representation based classification (SRC) of mammogram images. The experimental results show that texture features like Laws' texture features (LAW) are more effective than shape/morphology features. SRC using LAW features alone or combined with local binary patterns (LBP) achieved high performance. Larger dictionaries containing more atoms resulted in higher discriminative power for the SRC-based detection system.
A comparison of Simulation and Operational ArchitecturesSimware
This whitepaper presents a comparison between simulation and operational architectures. Presented at the Simulation Interoperability Standards Organization (SISO) 2012 Fall Simulation Interoperability Workshop in Orlando, FL, USA. The paper is co-authored with Thales and Prismtech.
This document provides an overview of the Intel x86 architecture, including its registers, instructions, memory management, interrupts and exceptions, task management, and input/output capabilities. It describes the basic execution environment including memory management registers and control registers. It explains the operation modes of protected mode and real mode, and the memory models. It also summarizes the general purpose instructions, system instructions, privilege levels, basic program execution registers, and memory addressing in the x86 architecture.
IJCER (www.ijceronline.com) International Journal of computational Engineeri...ijceronline
The document proposes implementing register files in the processor hardware to improve context switching performance in hard real-time systems. Conventionally, context switching involves saving processor registers to external memory, which takes 50-80 clock cycles. The proposed approach saves contexts to register files within the processor, requiring only 4 clock cycles. Software and a small operating system were modified to use new "save context" and "restore context" instructions. Simulation results showed contexts being saved and restored from an internal register file in 2 clock cycles each. Two test applications demonstrated the performance improvement from using internal register files versus external memory for context switching.
This document evaluates several XML compression tools. It examines 11 compressors, including 3 general text compressors and 8 XML-aware compressors. The compressors are evaluated on 57 XML documents from different domains, measuring compression ratio, compression time, and decompression time on two different computing environments. The results show that XML-aware compressors generally achieve better compression ratios than general text compressors, with ratios ranging from 0.07 to 0.24 on structural documents and 0.12 to 0.22 on original documents.
EUGM 2014 - Brock Luty (Dart Neuroscience): A ChemAxon/KNIME based tool for ...ChemAxon
This document summarizes the development of a chemical library design tool at Dart NeuroScience. It describes the goals of creating an easy to use tool to standardize calculations, reactions, and simplify workflows. The tool was developed using KNIME with ChemAxon services and utilizes a service oriented architecture. Key features of the tool include reactant selection, reaction enumeration, property calculations, clustering, and exporting designs to Spotfire and ELNs. The tool has been iteratively improved over several years of development and testing.
The document discusses remote function call (RFC) specifications between different systems for various analysis processes in a project called Landscape. It states that the same RFC name should be used when transmitting data from the Analysis system to either the Statistics or Reference system as is specified in the Control system. It provides examples of RFC names for Clearing Analysis, Upgrade Change Impact Analysis, and Change and Transport System Analysis. It also notes that the target and statistics systems are typically the same for CTS analysis.
This document provides an overview of the DirectPath subsystems, including the Internet delivery subsystem, TV delivery and MPEG platform subsystems, volume and file access subsystems, and content transfer engine subsystem. It describes the components, functions, and interactions between the subsystems to deliver digital content over the Internet and to TVs. The document also explains how the subsystems support applications like hospitality video-on-demand and cable TV ad insertion.
1. The document introduces Cisco's Software Defined Data Center (SDDC) technology strategy. It discusses the trends of BiModal IT and the emergence of Mode 1 and Mode 2 IT.
2. It describes the SDDC architecture including Software Defined Computing (SDC) using Cisco UCS, Software Defined Storage (SDS) using Cisco HyperFlex, and Software Defined Networking (SDN) using Cisco ACI.
3. Case studies show that implementing SDDC with SDx technologies from Cisco can improve agility, reduce costs, and help organizations deploy both Mode 1 and Mode 2 applications.
The application of STDM in a no-profit and disease specific organisation - CD...Angelo Tinazzi
This document summarizes a presentation given by Angelo Tinazzi at the 2008 CDISC Italian-Speaking User Group Meeting in Milan. The presentation discusses the application of SDTM at SENDO Tech, a non-profit clinical research organization focused on oncology drug development. SENDO implements SDTM using a hybrid approach, applying some SDTM standards within their clinical database and performing additional transformations and mappings in SAS post-processing to fully comply with SDTM. The presentation outlines SENDO's SDTM implementation challenges due to the heterogeneity of oncology data and describes their methods for mapping clinical data to SDTM domains and variables. It also provides examples of new domains SENDO has
The document provides an introduction to Cadence design flow, outlining the typical steps involved in integrated circuit design from schematic capture and simulation to layout and fabrication. These steps include creating schematics using a process design kit, performing layout with design rules in mind, extracting parasitic components, and verifying the design through simulation and layout vs schematic checks before finalizing the layout file for fabrication. Key software tools used in the Cadence design flow are also outlined.
This document provides an overview of JTAG (Joint Test Action Group) devices, including their basic chip architecture, capabilities, and common system configurations. It describes the JTAG standard architecture which defines boundary-scan cells and a test access port. It also summarizes common JTAG instructions, the TAP controller state machine, typical JTAG interfaces and connectors, BSDL description files, and how JTAG devices can be daisy-chained to form a scan chain for testing connections between components.
1. The document summarizes Kerstin Forsberg's presentation on semantics and linked data at AstraZeneca R&D. It discusses (1) an internal competitive intelligence tool called CI360, (2) public pre-competitive projects like Open PHACTS and standards bodies, (3) AstraZeneca's Linked Data Community of Practice, and (4) ongoing work on study identifiers and APIs.
2. It provides an overview of Kerstin Forsberg's background and goal of improving the utility of clinical trial data through semantic interoperability. It also outlines some of AstraZeneca's collaborations and contributions to linked data initiatives.
3. The presentation highlights AstraZeneca
Linked Data efforts for data standards in biopharma and healthcareKerstin Forsberg
1) The document discusses efforts to represent biomedical data standards like CDISC, HL7 FHIR, MeSH, ICD-11, and others in semantic web formats like RDF and OWL to make them machine-processable.
2) It describes projects that have converted various standards to RDF through the work of groups like CDISC2RDF and PhUSE, and efforts to engage traditional standards bodies.
3) However, it notes that pushing standards organizations to adopt semantic web approaches requires ongoing knowledge sharing and community building, and that spreadsheets still see significant use.
Linked data presentation for who umc 21 jan 2015Kerstin Forsberg
This document discusses the semantic web and linked data. It provides an overview of Web 1.0, Web 2.0, and Web 3.0 (semantic web) and how the semantic web uses RDF triples to represent data as a web of linked data. It also discusses how AstraZeneca is engaging with the semantic web through projects involving drug discovery and clinical research standards.
Slides to be presented at a webinar arranged by Metasolution as part of a Vinnova project http://metasolutions.se/2014/03/webbinarium-med-kerstin-forsberg-om-lankade-data-i-lakemedelsforskningen/
Pushing back, standards and standard organizations in a Semantic Web enabled ...Kerstin Forsberg
1. Kerstin Forsberg encourages standard organizations to represent their standards using semantic web standards for sustainability and trustability.
2. She provides examples of engaging with organizations like NCI and MedDRA to represent their terminologies in RDF using SKOS.
3. A project represented clinical trial data exchange standards like CDISC in RDF and linked the different standards fragments to each other.
CDISC2RDF started as a cross-industry project to demonstrate Semantic Web standards and Linked Data principles, and is now part of several working groups focusing on semantic interoperability for clinical research and patient safety. It transforms CDISC standards documentation from human-readable formats like PDFs and Excel into machine-processable linked data using RDF triples, uniquely identifying each part of the standards and linking related parts to each other. The RDF triples can then be serialized into formats like XML, JSON, and CSV.
This document provides an example of spending data from Lichfield District Council in the UK. It describes a payment with a unique identifier and standardized classifications for the payment type, amount, and payer using linked data formats. The UK government takes a top-down approach to standardizing the semantics of spending data using published ontologies for payments and statistical data.
Semantic models for cdisc based standards and metadata management (1)Kerstin Forsberg
This document discusses semantic models for integrating CDISC standards, metadata, and information models. It proposes using semantic web standards like RDF, OWL, and SKOS to build a knowledge base and information architecture for CDISC. This would provide a consistent framework and address issues around maturity and consistency across CDISC standards. The approach is demonstrated in a metadata repository implemented at Roche that uses semantic technologies to support clinical trial processes from protocol to submission.
Semantic models for cdisc based standards and metadata managementKerstin Forsberg
The document discusses using semantic web standards and linked data principles to manage CDISC standards and metadata. It provides two examples of how AstraZeneca and Roche are applying these techniques. Roche has built a biomedical metadata repository that integrates CDISC standards and other metadata. It uses semantic modeling tools to publish the standards and enable integrated knowledge and data management. The semantic approaches allow for linking diverse sources of clinical research data and standards.
The document discusses the potential for using linked data principles to help address complexity in pharmaceutical research and development. It provides examples of existing linked data projects like DBpedia, Wikidata, and Schema.org and describes how applying semantic web standards like RDF, RDF schemas, and SKOS can help organize disparate data sources. The principles of linked data - using URIs, HTTP URIs, providing useful information at URIs, and including links between URIs - are outlined. Existing linked open data clouds and enterprise implementations are briefly noted as encouragement for applying linked data to improve associations between data and enable greater automation in life sciences and healthcare.
The document introduces linked data and describes how applying linked data principles such as using URIs and HTTP to identify and link pieces of data can improve the research and commercial utility of information. Examples are given of how linked data has been applied to clinical trial metadata and government spending data. The benefits of a top-down approach to standardization using shared vocabularies and ontologies are also discussed.
Designing and launching the Clinical Reference LibraryKerstin Forsberg
Presentation for the European Clinical Data Forum conference, 24 May, 2011. Describing the business problems and drivers behind the design of a ISO11179 based metadata registry for clinical data. And also introducing the features of the CRL application.
The document discusses linking clinical data standards to the Semantic Web. It begins by explaining the difference between the traditional web of documents and the emerging web of linked data. It then provides examples of linked open government data from the UK and US. The presentation considers opportunities for applying linked data principles to linking clinical study metadata and data across the industry. Pragmatic first steps discussed include learning from other projects, expressing CDISC standards as linked data using URIs, and publishing trial summary parameters as RDF.
This document discusses how linked data and semantic web technologies can help mitigate complexity in pharmaceutical research and development. It notes that making sense of all the associated data from areas like pathophysiology, targets, phenotypes, biomarkers, costs and quality of life has become too complex a task. Linked data principles and semantic web standards can improve the research utility of shared datasets by organizing data for associations, preparing it for undefined future uses, and enabling computers to automate tasks and work alongside researchers. A pragmatic and iterative process is recommended to apply linked data management including using linked data principles, semantic web standards, and open ontologies.
"Linked Data, an opportunity to mitigate complexity pharmaceutical research and development" A poster accapted for first international workshop on linked web data management in Uppsala, 25 March, 2011
1. We want to push back to CDISC and NCI, and other
CDISC2RDF public and internal standard groups, and show in
practice how to: “Use (semantic web) standards for
standards”
CDISC2RDF Schemas
(based on the core of ISO11179)
Human readable documentation Directly machine computable
of different CDISC’s data and queryable Linked Clinical
standards Data Standards
Project team:
Frederik Malfait (IMOS consulting, working for Roche), Charlie
Mead and Eric Prud’hommeaux (W3C HCLS), Phil Ashworth (Top
Quadrant), Sam Hume (Clinical Standard Governance
Organisation, AstraZeneca, and CDISC ODM team), Laura Hollink
(Vrije Universiteit, Amsterdam, and EUREKA projekt)
Sponsors:
Jonathan Chainey (Data Standard Office, Roche), Tom Plaster
(Integrative Informatics Semantic Framework, AstraZeneca), Frank
van Harmelen (Vrije Universiteit, Amsterdam) and Irene Polikoff
(TopQuadrant).
Blog: http://cdisc2rdf.com/
Google Code: https://code.google.com/p/cdisc2rdf/ (under Source)
2. CDISC2RDF
CDISC2RDF Schemas
(based on the core of ISO11179)
Human readable documentation Directly machine computable
of different CDISC’s data and queryable Linked Clinical
standards Data Standards Example: ”DRUG INTERRUPTED” in
Codelist ”ACN” (Action Taken with
Study Treatment)
Example: --ACN
Screenshots from the ontology tool:
Example: AEACN
TopBraid Composer
3. CDISC2RDF
Overview of Ontologies: Schemas
Meta model schema (mms)
(Data definition, the core part of ISO 11179)
SDTM 1.2 schema (sdtms)
(Classifiers: Data Element roles
and types)
Controlled Terminology schema (cts)
(a few additional properties
from the NCI Thesaurus export)
SDTM 3.1.2 IG schema
(sdtmigs)
(a few additional properties)
4. CDISC2RDF
Overview of Ontologies: Schemas and Standards
Meta model schema (mms)
(Data definition, the core part of ISO 11179)
CDASH CT
value sets
SDTM 1.2 schema (sdtms) SDTM 1.2
(classificiers: Data Element roles
and types)
model
ADaM CT Controlled Terminology schema (cts)
(a few additional properties
value sets
from the NCI Thesaurus export)
SDTM IG 3.1.2
SDTM 3.1.2 IG schema
domains
SDTM CT (sdtmigs)
(a few additional properties)
value sets
5. CDISC2RDF
SDTM Model 1.2
Example: --ACN
Meta model schema (mms)
(Data definition, the core part of ISO 11179)
SDTM 1.2 schema (sdtms)
SDTM 1.2
(Classifiers: Data Element
Compliance, Roles and Types) model
Screenshots from the ontology tool:
TopBraid Composer
6. CDISC2RDF
SDTM Model 1.2 + IG 3.1.2
Example: --ACN
Meta model schema (mms)
(Data definition, the core part of ISO 11179)
SDTM 1.2 schema (sdtms)
SDTM 1.2
(Classifiers: Data Element
Compliance, Roles and Types) model
SDTM IG 3.1.2
SDTM 3.1.2 IG schema
domains
(sdtmigs)
(a few additional properties)
Example: AEACN
Screenshots from the ontology tool:
TopBraid Composer
7. CDISC2RDF
CT Schema and CT:s
Meta model schema (mms)
(Data definition, the core part of ISO 11179)
Controlled Terminology schema (cts) SDTM CT
(a few additional properties
from the NCI Thesaurus export)
value sets
Example: ”DRUG INTERRUPTED” in
Codelist ”ACN” (Action Taken with
Study Treatment)
Screenshots from the ontology tool:
TopBraid Composer
8. CDISC2RDF
Annotation of SDTM CT Excel using CDISC2RDF schemas
SDTM CT original format
Import file: SDTM Codelist, annotated to map the CDISC2RDF schema for Controlled Terminologies
Meta model schema (mms)
(data definition, the core part of ISO 11179)
Controlled Terminology schema (cts)
(structure of CDISC’s value sets
drawn from NCI Thesaurus)
Import file: SDTM Codelist Elements annotated to map CDISC2RDF schema for Controlled Terminologies
9. CDISC2RDF
Import / Transform SDTM CT in Annotated Excel to a SDTM CT ontology
Import file: SDTM Codelist, annotated to map the CDISC2RDF schema for Controlled Terminologies
TopBraid Composer Import
Import file: SDTM Codelist Elements annotated to map CDISC2RDF schema for Controlled Terminologies
SDTM CT
value sets
Screenshots from the ontology tool:
TopBraid Composer
10. CDISC2RDF
From SDTM Implementation Guideline (IG) in PDF/Excel to OWL/RDF
Meta model schema (mms)
(data definition, the core part of ISO 11179)
SDTM 1.2 schema (sdtms) SDTM 1.2
(classifications: Data Element
roles and types)
model
SDTM 3.1.2 IG schema
(sdtmigs)
(a few additional properties)
This one is yet not published
Annotations Import file: SDTM IG 3.1.2 annotated
using CDISC2RDF SDTM IG Schema
Import/Transform
using TopBraid
Composer
SDTM IG 3.1.2
SDTM CT domains
value sets