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2006 Annual Meeting Posters
Poster # |
Title of Poster |
Short Summary
|
Poster Thumbnail(click the image for large view) |
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07 |
Paraffin-Embedded Tissue Archive | The Paraffin-Embedded Tissue Archive project is converting Surgical Pathology
Reports (SPRs) for paraffin-embedded cancer tissue blocks from microfiche
into a caTIES/De-ID-parsed format for uploading into the caTIES database.
Through the caTIES query interface these tissue samples will be exposed
to the caBIG™ community. |
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| 08 | Microsoft Excel caBIG™ Smart Client Joining the Fight Against
Cancer |
For over a decade, Microsoft Office (MS) Excel has been the primary tool, especially in terms of statistical analysis and visualization, used by biomedical scientists for analyzing cancer research data. Scientists traditionally analyzed a limited set of data collected in their labs or made available by select collaborators. Through caBIG™, scientists will have access to data from researchers around the world. |  |
| 09 | caAdapter (HL7 SDK) | caAdapter (HL7 SDK) The caAdapter is an open source tool set that facilitates HL7 version 3 message building, parsing, and validation based on specific message definitions. It has the capability to perform vocabulary validation and integrates with NCICB caCORE components. |  |
| 10 | Firebird (Federated Investigator Registry) | Firebird (Federated Investigator Registry) Firebird is the first module implemented to achieve the vision of the Clinical Research Information Exchange (CRIX) infrastructure. Firebird will automate the submission of the FDA Form 1572 and enable investigators to register online with NCI and other sponsors, including pharmaceutical companies, thus removing paper-based latencies and infrastructure costs and allowing investigators to maintain and manage 1,572 registrations. |  |
| 13 | QARC’s Digital Image Management System Supporting Cancer Clinical Trials | QARC is an active data management organization with a clinical service and interactive mission. The key objective is to insure the quality of the data and compliance to study for the clinical cooperative groups in order to secure a uniform study population for outcome analysis. Improving study compliance and providing uniform data format promotes the validation of study endpoints. |  |
| 14 | Leveraging caBIG™ Technology for Diseases Other than Cancer | The SLE Biomarkers Consortium is a cross-sector, multi-institutional effort to identify, develop, and validate biomarkers for Systemic Lupus Erythematosus. SLE is a relatively rare (~250,000 patients in the United States) multisystem disorder affecting mainly women of child-bearing age. It has diverse clinical and laboratory manifestations, waxes and wanes over time, and may involve essentially any organ system. The consortium goals are to identify biomarkers of lupus disease activity, to validate them so that they can be used by the FDA as indicators in clinical trials, and to facilitate the development of new safe and effective treatments for SLE. |  |
| 16 | Automated Peak Identification in a TOF-MS Spectrum | The high-throughput capability, and capability of providing a variety of chemical and structural information, have made mass spectrometry a standard tool for proteome and biomarker discovery research using bio-fluid samples such as blood serum and digested protein samples. A bottleneck is that modern mass spectrometers (e.g., MALDI/SELDI), as a result of improved resolving power, produce very large raw data sets containing hundreds of peaks for these complex biological samples. Hence these spectra must be preprocessed to identify mass peaks from background noise for further analysis. |  |
| 17 | Janus/CRIX Pilot | NCI, FDA, CTIS, and IBM have been conducting an effort to develop a pilot for a clinical trial data facility based on JANUS for use by the FDA for review and analysis and by the NCI to help address a set of the CRIX objectives, including: More efficient submissions based on standards; -Reproducible, custom datasets for analysis; -Reusable tools for analysis and review; -Less data redundancy; -Less time on orientation to data by reviewers; -Less ambiguity in communications of information; -More auditable data; -Less manual, paper processing; -Use of common standards across the entire community (government, industry, academia); and Interoperability with other caBIG™ data sets, tools, capabilities. |  |
| 20 | The Mouse/Human Anatomy Ontology Mapping Project | Mouse Genome Informatics (MGI) and the National Cancer Institute (NCI) have developed extensive anatomy ontologies for the adult mouse and human to facilitate the standardized description and integration of data for the respective species. The objective of the Mouse/Human Anatomy Ontology Mapping Project is to harmonize and map anatomical descriptors used for the mouse and human. |  |
| 21 | The Challenge of Integrating caGrid in the Cancer Center Environment | The service-oriented integration approach is quickly changing the way applications can be integrated. In the caBIG™ world, caGrid will provide a preferred environment for delivering services by coordinating independent cancer center resources. However, caGrid also introduces challenges that cancer centers might never have faced before, which may significantly impact their tools and integration strategies. |  |
| 22 | Financial Billing Infrastructure Model for Cancer Centers | caBIG™ Clinical Trials Financial Billing Architecture: A Multi-Tiered Model Approach. The CTMS Financial Billing Special Interest Group will present what it has mapped to be the outline for Financial Billing in a Cancer Clinical Trials Environment. A workflow representation for Financial Billing will demonstrate our approach in defining this model and its components. |  |
| 24 | The Advanced Technology QA Consortium (ATC) | The Advanced Technology QA Consortium (ATC), an NCI sponsored organization, combines the efforts of the nation quality assurance (QA) organizations responsible for radiation therapy QA for cooperative group clinical trials. ATC includes the Quality Assurance Review Center (QARC), Radiological Physics Center (RPC), American College of Radiology/Radiation Therapy Oncology Group (RTOG), Image Guided Therapy QA Center (ITC), and the Resource Center for Emerging Technologies (RCET). |  |
| 25 | Placing Reactome into the caBIG™ Grid | Reactome is a curated database of human biological pathways and reactions. The information in this database is authored by biological experts, maintained by the Reactome editorial staff, and cross-referenced with PubMed, Gene Ontology, UniProt, OMIM and other databases. Reactome provides high values to bench and computational biologists as well as biological students because of its high quality, rich contents and sophisticated data model. |  |
| 26 | A Web-based Tissue Gene Expression Visualization Tool Developed on the caCORE Cancer Research Informatics Platform | The National Cancer Institute has developed an informatics infrastructure called caCORE to facilitate data and application sharing among cancer research institutes. We have evaluated it in our data warehouse project and have established the need for compatibility for tools development, to share data with external organizations, and also as a gateway to access data in the public domain. |  |
| 27 | CDS (Clinical Data System) | The Clinical Data System (CDS) is an independent and stand alone data submission infrastructure (electronic) at NCICB to serve as the primary data resource for NCI sponsored clinical trials. Data is submitted either as an electronic file submission or via a Web-based interface. The system also provides a mechanism to access data to stakeholders including cancer centers, cooperative groups, and single institutions via a data analysis interface. This interface enables users to view and generate reports about various aspects of the clinical trial process. |  |
| 29 | Docu-MART | Docu-MART is a system of software applications utilizing both desktop and Web technologies developed to assist in the authoring, review, and tracking of clinical trial protocol documents. Protocols can be authored using predefined structured protocol representations using XML templates. |  |
| 30 | caArray: A Standards-Based and caBIG™-Compliant Microarray Data Management System at the National Cancer Institute (NCI) Center for Bioinformatics | caArray database is a standards-based, Web-accessible open source data management system. It has been developed following the caBIG™-compatibility guidelines that highlight the use of controlled vocabularies, common data elements (CDEs), well-documented APIs and UML model. It is an open-development, open-source, and open-access system that seeks to facilitate cross system, cross platform sharing of cancer research data. |  |
| 32 | Grid Enablement of Protein Information Resource (gridPIR) | The Protein Information Resource (PIR) is an integrated bioinformatics resource that provides protein databases and analysis tools to support genomic and proteomic research. As a participant in the Integrative Cancer Research (ICR) workspace of caBIG™, PIR developed gridPIR in collaboration with the adopter from the Biomedical Informatics Facility (BMIF) for the Abramson Cancer Center at the University of Pennsylvania. |  |
| 33 | Initial Vocabulary and Common Data Element Compatibility Review Process | Elements of a Compatibility Review process are described which support the reuse of well defined Common Data Elements (CDEs) that can be used to join data sets across institutions and systems. The Compatibility Review process aims to be consistent, transparent and scalable. The Silver Level Compatibility Review is performed to ensure consistency between UML models and CDEs stored in the NCI cancer Data Standards Repository (caDSR). |
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| 35 | Cancer Clinical Central Participant Registry (C3PR) Adopter | C3PR is a component of NCI’s Cancer Centralized Clinical Database System (C3DS). It is an open source Web-based application that provides a central repository for participant information across studies, sites, systems, and organizations. |  |
| 36 | Cancer Models Database 2.0 | The NCI Center for Bioinformatics (NCICB) and NCI™ Mouse Models of Human Cancers Consortium (MMHCC) released a new version of the Cancer Models Database (caMOD) in December 2005. Cancer models that recapitulate many aspects of the genesis, progression, and clinical course of human cancers are valuable resources to cancer researchers engaged in a variety of basic, translational, clinical, and epidemiological investigations. |  |
| 37 | caBIG™ Data (CDE) Standards Development | Over the past year, the caBIG™ Vocabulary and Common Data Element workspace has facilitated the review, adoption and deployment of data standards. caBIG™ success is dependent on use of these data standards in the development of caBIG™ models and applications. Reuse of standard common data elements (CDEs) by developers is the key to semantic and syntactic interoperability, and has the additional benefit of time savings for modelers and developers. |  |
| 38 | VISDA: A caBIG™ Analytical Tool for Clustering and Beyond | VISDA (Visual Statistical Data Analyzer) is a caBIG™ analytical tool for cluster modeling, visualization, and discovery. Being statistically-principled and visually-insightful, VISDA exploits the human gift for pattern recognition and allows users to discover hidden clustered data structures within high dimensional and complex biomedical data sets. |  |
| 39 | RProteomics: An Application for Analyzing Mass Spectrometry Proteomics Data | In this poster, we describe the RProteomics application, which comprises a set of low-level and high-level statistical methods for analyzing MALDI and SELDI MS and LC-MS mass spectrometry proteomics data. Currently available routines include background removal, denoising, normalization, alignment, and calibration. |  |
| 40 | cPath: Pathway Database Software for Systems Biology | cPath is open-source pathway database software that eases data integration
from multiple sources. It currently supports the BioPAX pathway exchange
language and the PSI-MI protein interaction exchange format. It can be locally
installed and can connect with Cytoscape for network visualization and analysis. |
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| 42 | Implementing a Learning Management System (LMS) to Maximize caBIG™ Training Benefits | To effectively manage training programs offered as part of the caBIG™ initiative, NCICB is implementing Training Partner, a Learning Management System (LMS). This system will enable the caBIG™ Training Workspace to set up and maintain a central portal for publicizing training programs, registering and communicating with trainees, recording progress, and evaluating course/program success. |  |
| 43 | CTMS Best Practices SIG | The CTMS Best Practices SIG was founded to focus on establishing and fostering relevant clinical trial management best practices for clinical trials within the caBIG™ community. The identification and possible adoption of Best Practices are presented to the group from member experiences or developed as a combination of proven techniques or processes. |  |
| 44 | Introducing caBIG™ Documentation and Training—Requirements, Processes, and Resources | This poster will introduce the guidelines, templates, and support resources
that the Training Workspace has developed related to documentation and training.
It will provide an overview of the documentation and training requirements
and templates, and where they can be found; it will introduce the documentation/
training mentoring program; and it will outline the steps involved with
registering a project, requesting a documentation/training mentor, and submitting
documentation and training modules for review. |
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| 46 | caElmer—The MMHCC Pre-Clinical Trials Laboratory Information Management System | The NCI Mouse Models of Human Cancers Consortium (MMHCC) has been given the task of studying and validating mouse models of human cancers. In preparation for pre-clinical trials, a Pre-clinical Trials Working Group was appointed by the MMHCC II Informatics Committee and tasked with developing a Pre-Clinical Trials Data Assessment Survey, which showed that the majority of the laboratories did not store their data in a retrievable digital format. |  |
| 52 | A Validation Framework for Biological Pathways | Biological Pathway Exchange (BioPAX) is an ontology developed to describe biological pathway data. It uses OWL (Web ontology language), which is part of the W3C effort with regard to the semantic Web. We have developed a Java based tool, the BioPAX validator, that validates any pathway data expressed in BioPAX. The BioPAX ontology, which is expressed in OWL, also captures comments for each BioPAX object as defined in BioPAX. |
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| 53 | A Diagnostic Test Suite for the RProteomics Statistical Routines | We present a statistical testing suite developed as part of our test strategy as caBIG™ adopters of the RProteomics statistical routines developed by Duke Comprehensive Cancer Center. RProteomics was developed in the open source statistical programming environment R, and consists of multiple processing routines for each step of the low-level analysis of proteomics data. |  |
| 55 | The CAP Cancer Checklist Model and Common Data Elements—An Emerging Standard in Tissue Banking and Pathology Tool | Background: An important aspect of caBIG™ pilot is the development of consistent practices for data standards development, using a multi-tier approach that facilitates semantic interoperability of systems. The Tissue Banking and Pathology Tools (TBPT) Workspace has identified the College of American Pathologists (CAP) cancer checklists as one important standard set of standardized data elements in our domain. |  |
| 56 | Translational Informatics Model for SPECS and SPORES | The SPECS in Lung Cancer involves a consortium of institutions, including SPORES from UCLA, Colorado, UTSW/MDA, Pittsburgh, Dana Farber, Vanderbilt, and non SPORES sites such as USC, Duke, Dartmouth, UC Davis, Michigan, as well as the SWOG, and Spanish Lung Cancer Cooperative groups. Many with their own substantive Bioinformatics operations. |  |
| 57 | mzHDF for High-Throughput Proteomics Data |
We have been developing the open source mzHDF format and associated utilities for storing, accessing, exchanging and computing on very large proteomics data sets using the established Hierarchical Data Format (HDF) developed by the NCSA. The current implementations of mzXML have serious limitations for typical proteomic or metabolomic datasets, which are often larger than a terabyte. |  |
| 58 | BreastCancerTrials.org: Feasibility of a caMATCH Tool to Match Breast Cancer Patients to Clinical Trials | BreastCancerTrials.org (BCT) is a patient-centered clinical trial matching tool, piloted by caMATCH. Launched June 2006 in Northern California, efforts are underway to study acceptance, usability, and data quality. Patients registering with BCT self-report a detailed Personal Health Record (PHR) that is matched to trial eligibility criteria. Matches are displayed in a password-contolled Message Center with a trial summary and contact information. Patients can contact research staff directly or use the Message Center to send their PHR to selected sites. |  |
| 59 | BRIDG: A Model of the Shared Semantics of Clinical Trials Research | In this poster, we will provide an update to the BRIDG project, a formal
representation of the shared semantics of clinical trials research. We will
describe some of the organizational changes made to the model in response
to feedback from the caBIG™, HL7, and CDISC communities, and highlight
some of the harmonization efforts to include CTOM, adverse event reporting,
and the SDTM standard for the submission of data to the FDA. The BRIDG project
is intended to support a Model Driven Architecture (MDA) and provides the
shared semantics across various stakeholders. |
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| 60 | Sharing Cancer Microarray Data is Associated with Increased Citation Rate | Background Sharing research data on the caBIG™ grid will provide clear benefit to patients and to the researchers who use that data. For the researcher who makes his or her data available, the benefits are less obvious. In this study we used citation analysis to study the impact of sharing cancer microarray data on citation rates for authors. |  |
| 61 | Integration Strategies and Methods for Legacy Systems to be caBIG™ Silver Compatible | For many cancer centers, the ultimate goal of participating in caBIG™ is to achieve caGrid availability by sharing their data resources onto the grid. The first step is to enable the legacy systems to be silver compatible. However, tremendous resources available at many cancer centers are still embedded in legacy databases. This poster will document the strategies Kimmel Cancer Center applied to fill the gap of moving our breast cancer tissue system to be caBIG™ silver compatible in caTISSUE CORE context. |
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| 63 | NCI-60 Dataset Evaluation for the caBIG™ Initiative | A panel of 60 human tumor cell lines (NCI-60) have been used extensively as a standard set of biological reagents for compound screening. The Genomics and Bioinformatics Group, Laboratory of Molecular Pharmacology, NCI, has assembled a set of high throughput data generated on the NCI-60 set, and subsequently provided it to the caBIG™ initiative. |  |
| 64 | The Impact of caBIG™ Products on the Cancer Patient’s Experience | This poster will highlight the impact of caBIG™ products on the
cancer patients experience. We will illustrate an individuals experience
through diagnosis and treatment and show how caBIG™ products will
influence their care. The caBIG™ initiative is developing an interconnected
biomedical informatics grid that will facilitate the successful sharing
of data, which will lead to more rapid translation of basic research to
improve cancer patient care. |
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| 65 | A Grid-Enabled Array Annotator Implementation | This poster will describe the implementation of a Grid-enabled application, called ArrayAnnotator. The application supports the data management and analyses processes for annotation of each clone of microarray chips to design custom arrays for DMH experiments in a P50 project studying epigenetic mechanisms in ovarian cancer. |
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| 66 | Model Driven Design Approach to Extending Clinical Annotation Collection at the University of Pittsburgh | caTISSUE Clinical Annotation Engine (CAE) was developed using the caCore SDK Framework to provide a tool for integrating data from existing clinical and research systems. It provides XML-based batch import, a user interface for entering annotations manually and a query interface for finding cases with specific clinical characteristics. Both the batch and interactive modes of adding data to the system enforce the use of caBIG™-standard values as specified in Common Data Elements (CDEs) in the caDSR. The user interface for query is driven off the same CDEs. |  |
| 67 | Model Driven Development of the caBIG™ CTMS Adverse Events Reporting System (caAERS) Prototype | The objective of the caAERS project is to capture adverse events and report as required to individuals and organizations responsible for trial conduct and for patient safety. CaAERS is envisioned as a flexible set of 12 integrated modules that will be configurable to meet the needs of cancer centers with little or no data management systems, as well as those with robust systems supplemented by selected modules. |  |
| 68 | Clinical Trials Object Model (CTOM) | The Clinical Trials Object Model (CTOM) is an initiative within NCICB
to model the Clinical Trials arena and offer patient de-identified clinical
trials data for research purposes. The UML classes designed in CTOM will
be implemented into Java objects using the caCORE tool set. CTOM is a CDE
driven UML class diagram and the CDE mappings have been captured in the
model. It is intended to be a reference implementation of the BRIDG model. |
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| 70 | Clinical Trials Laboratory Data: A Real-World Application of the BRIDG Model | The BRIDG model is a formal representation of the shared semantics of clinical trials research. The majority of data collected in clinical trials originates in the laboratory; clinical laboratory systems are thus key source systems, and there is a pressing need for reusable interfaces between clinical laboratory systems and clinical trials systems. |  |
| 71 | The Disease Ontology and Browser | We have been developing the open source Disease Ontology (DO) (http://diseaseontology.sourceforge.net) for several years, with the current release, version 3, based on UMLS concepts from unrestricted vocabularies that have been organized into a directed acyclic graph (DAG). The graph has been organized according to OBO principles of being open, machine computable, and the concepts are organized so that the path to the top is always true. |  |
| 72 | Scalable, Federated, caBIG™-Compatible Clinical Trials—Technology in Use | A technology model delivering a unique infrastructure that has been developed and operationalized across multiple institutions in cancer clinical research is presented and discussed. This model provides collaborative clinical research across ten major research institutions and delivers caBIG™ compatible research services to the network, called the PCC (Prostate Cancer Consortium) Network. |  |
| 73 | Cancer Experimental Protocol Assessment Tool: PADRE | In genomics, proteomics, and metabolomics, molecular-based experimental protocols usually introduce noisy variations in the high throughput data. Thus, manufactures have incorporated some naive statistics methodologies (e.g., GCRMA) to normalize the data. However, it is not enough to eliminate experimental-protocol-specific noisy variations, and the downstream analysis algorithms may produce misleading results for discovery. |  |
| 83 | The Past and Future of DWD in caBIG™ | Distance Weighted Discrimination (DWD) has become a workhorse method for combining micro-array data sets. An old question as to why its empirical performance has proven to be better than PAM and other mean based methods, is resolved through the study of varying subpopulation sizes. Further examples illustrate some situations where conventional DWD may fail. |  |
| 85 | Clinical Research Information Exchange (CRIX) Initiative | In early 2003, the National Cancer Institute (NCI) and the Food and Drug Administration (FDA) formed the Inter-Agency Operational Task Force (IOTF) with the goals to: Speed new research discoveries to the public; and Implement a common, standards based electronic infrastructure for regulatory data and document submission, review and analysis. | |
| 86 | Regulatory Requirements for Records and Signatures | Regulatory requirements for records and signatures are central to assuring data veracity, authenticity, and non-repudiation of records and/or information submitted to FDA for regulatory review. Title 21 Regulations & ICH Guidelines address the record and signature requirements for pre-clinical, pharmacogenomic, clinical research trials, as well as pharmcosurveillance. |  |
| 87 | InforSense LLC | Inforsense Ltd., working in collaboration with the Windber Research Institute, is building a next generation medical informatics solution to bring the power of translational medicine to the fight against breast cancer. At the foundation of the solution is a patient centric data warehouse that integrates a wide array of traditionally siloed data sources. From genotypes to pathology, PET scans to proteomics, data from the clinic and the lab are made available to researchers and care givers alike. |
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| 88 | Nutrition Ontology | A nutritional ontology was developed that integrates into the Thesaurus of the National Cancer Institute (NCI) to facilitate collaboration and data sharing as part of the caBIG™ project. Several agencies provide useful information about dietary components, including the US Department of Agriculture. The International Network of Food Data Systems (InFoods) of the UNFAO provides an administrative framework for the development of standards and guidelines for collection, compilation, and reporting of food component data. |  |
last modified
06-04-2007 12:32 PM
