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caBIG™ Silver Compatibility Review Process
Introduction
The majority of developer projects in caBIG™ are developing to Silver level compatibility. The four criteria defining caBIG™ compatibility are Messaging Interfaces/APIs, Common Data Elements (CDEs), Vocabularies and Information Models as definied in the caBIG™ Compatibility Guidelines. The Vocabulary and Common Data Elements (VCDE) and Architecture (ARCH) Workspaces are responsible for ensuring that development projects satisfy the silver level criteria for caBIG™ compatibility. The VCDE WS is responsible for reviewing CDEs and vocabularies, while the Architecture WS is responsible for Messaging Interfaces. Both ARCH and VCDE Workspaces need to review the UML model as that is the source for the API and CDEs. In order to carry out this mission, the Crosscutting Workspaces (VCDE and ARCH) have developed a Compatibility Review process. The purpose of this document is to define the compatibility review process and provide detailed information on the documentation that a developer will need to submit to the Crosscutting Workspaces for review.
Silver Compatibility Review Process (zip file)
Silver Level Reviews - Members of the caBIG™ community from the Architecture and VCDE workspaces serve on compatibility review teams.
Silver Compatible Products (passed review)
| Product | Description | Status | Materials |
|---|---|---|---|
| BioConductor | Description: Bioconductor is a collection of open-source software components based on the R programming language. Bioconductor is used for gene expression and other high-throughput analysis in molecular biology. R packages are collections of algorithms grouped to facilitate particular analyses. This module allows R package developers to expose the functionality of their package as analytic services on caGrid. The focus of this effort is the development of tools for converting existing Bioconductor packages to caGrid analytic services. This is in contrast to other modules, which may focus on providing specific functionality as analytic services. |
Passed Review | Submission Material Review Docs |
| caBIO | caBIO is an object oriented data system that supplies bioinformatics data with a 'gene centric' view. | Passed Review | Submission Material Review Docs |
| caIntegrator/Rembrandt | caIntegrator is a caBIG™ compatible generic framework that allows retrieval and transformation of data from a variety of heterogeneous data sources that house microarray, genomic, tissue array, imaging and clinic data. | Passed Review | Presentation Review Docs |
| caMOD v2.1 | The cancer models database (caMOD) is a web-based resource that provides information about animal models for human cancer to the public research community. | Passed Review | Presentation Review Docs |
| caTIES | caTIES is the Cancer Tissue Information Extraction System that has the ability to perform concept coding, indexing, and searching of de-identified free text pathology reports. | Passed Review | Submission Material Review Docs |
| caTIES v2.0 | The goals of caTIES v2.0 are to extract encoded information from Surgical Pathology Reports, to provide research with the ability to query and browse annotated tissue data, and to allow a space in which researchers may construct and manage retrospective tissue distribution protocols. | Passed Review | Submission Material Review Docs |
| caTissue Core v.1.2 | caTissue Core version 1.1 was tested by the adopters, and based on their feedback, some of the features were identified as critical enhancements. These features which would improve the usability for the biospecimen bank staff to successfully use caTissue Core in production are:
|
Passed Review | Submission Material
Review Docs |
| caTissue Core v1.0 | caTISSUE Core is a tissue banking and biospecimen management tool that is used by pathologists, scientists, and clinicians. | Passed Review | Submission Material Review Docs |
| caTRIP | Description: caTRIP allows users to query across a number of caBIG data services, join on common data elements (CDEs), and view their results in a user-friendly interface. Having as its initial focus the enabling of outcomes analysis, caTRIP allows clinicians to query across data from existing patients with similar characteristics to find treatments that were administered with success. In doing so, caTRIP can help inform treatment and improve patient care, as well as enable the searching of available tumor tissue, locating patients for clinical trials, and investigating the association between multiple predictors and their corresponding outcomes such as survival (https://cabig.nci.nih.gov/tools/caTRIP). | Passed Review | Submission Material Review Docs |
| caXchange | The Laboratory Integration Hub is an open source software tool used to collect, process and report laboratory data gathered during a clinical trial (https://cabig.nci.nih.gov/tools/LabIntegrationHub). | Passed Review | Submission Material ARCH Review Docs VCDE Review Docs |
| Function Express | The caBIG™ Function Express Server (caFE Server) is an automated Gene Annotation Datawarehouse that utilizes a web based query interface. | Passed Review | Submission Material VCDE Compatibility Review Results API Compatibility Review Results caFE Kick-off Meeting Notes |
| GenePattern | GenePattern is a flexible analysis platform developed to support multidisciplinary biomedical research. GenePattern puts the power of sophisticated computational methods into the hands of non-programming users. It also provides an environment for rapid development and deployment of new analytic techniques. GenePattern has a modular architecture that allows the inclusion of additional analytic or visualization modules. To be integrated into GenePattern, modules must provide a command-line interface allowing them to be called and have parameters passed to them from a normal command line. This facilitates the independent development and testing of Modules external to the GenePattern environment.The GenePattern Grid Extensions project’s goal is to integrate the GenePattern environment into caGrid both as a consumer and as a producer of analytic services on caGrid. |
Passed Review | Submission Material Review Docs |
| PIR | PIR is an integrated protein informatics resource for genomic/proteomic research. One of the major goals of the project is to provide methods to query and retrieve protein related information for the cancer research community. | Passed Review | Submission Material PIR Silver Level Review |
| ProteomicsLIMS | ProtLIMS is a laboratory management system dedicated to studies in the realm of proteomics. The goal of the prototype version is to develop the system to the point in the analytical workflow where samples are prepared for mass spectroscopy. This entails recording of biological sample data, sample preparation, protein separation/resolution, and isolated protein sample preparation. | Passed Review | Submission Material protLIMS API Package Review Docs |
| Reactome | A curated database of fundamental biological pathways in humans that uses strict rules of assertion and evidence tracking to ensure a consistent high quality product. This database will be made compatible with the pathways exchanges standard identified by caBIG™. | Passed Review | Submission Material Review Docs |
| RProteomics | A system that aids cancer researchers in the processing of matrix-assisted laser desorption/ionization-time of flight (MALDI-TOF) data. These R (a software language for statistical computing and graphics) libraries will be developed and incorporated into a caBIG™- compliant system that will aid cancer researchers in post-processing of their mass spectrometry data (available on G-Forge). | Passed Review | Submission Material Review Docs |
| SEED | A framework that supports peer-to-peer annotation of genomes, and enables investigators to work independently on their instances of the SEED database and synchronize their work when desired, or update code versions quickly via the network. | Passed Review | Submission Material Review Docs |
| TrAPPS | A system of several tools that aid scientists in searching for the genetic mutation(s) that cause a defect or disease. The system allows the researcher to create and prioritize a large list of candidate genes, select order, manage primer pairs, and predict secondary structure. | Passed Review | Submission Docs Review Docs |
Under review for Silver Level Compatibility
| Product | Description | Status | Materials |
|---|---|---|---|
| Annotation and Image Markup (AIM) | Description: Annotation and Image Markup (AIM) schema offers a method, using existing XML and DICOM standards, to capture image annotation and markup information relevant to images. An annotation is explanatory or descriptive information, generated by humans or machines. A markup is graphical symbols or textual descriptions placed on an image. AIM project has produced AIM information model or schema, AIM library and a validation and transformation tool. AIM library is written in standard C++, using DCMTK and Xerces for DICOM and XML creations and manipulations. The library has two logical parts, implementation of AIM Schema as an object model and a defined set of operations, which can be performed on the AIM object model. ANIVATR tool is used for validating AIM annotations and transcoding between AIM XML, DICOM SR and HL7 CDA. | Under Review | Submission Material |
| geWorkbench | Description: geWorkbench provides an innovative, open-source software platform for genomic data integration, bringing together analysis and visualization tools for gene expression, sequences, pathways, and other biomedical data. It gives scientists transparent access to a number of external data sources and algorithmic services, combining these with many built-in tools for analysis and visualization (at present more than 40 distinct analysis and visualization modules are part of the platform). | Under Review | Submission Material |
| geWorkbench-ANOVA | Description: geWorkbench-ANOVA is a component of geWorkbench that provides a statistical analysis function to determine significance between the means of independent groups of data using the analysis of variance algorithm. In geWorkbench, each group comprises gene expression microarray measurements from various samples, and one is interested in identifying genes whose mean expression is significantly different across the various groups. | Under Review | Submission Material |
| In Vivo Imaging Middleware | Description: The caBIG IVI middleware development has the overarching goals of providing interoperability, ensuring performance, and simplifying usage. There are 3 primary objectives for the middleware: DICOM interoperability; bulk data transport and dynamic service deployment; and grid service and application development support SDK. | Under Review | Submission Material |
| NCIA | Description: The National Cancer Imaging Archive (NCIA) is a searchable repository of in vivo cancer images in DICOM format. In addition to images, NCIA contains non-image files (PDF, image markup) and annotation data rpovided by a curator. | Under Review | Presentation |
| Patient Study Calendar | Description: The Patient Study Calendar (PSC) is an open source, standards-compliant software application that can be used by organizations that manage patients on clinical trials. The PSC is a stand-alone, Web-based application providing the ability to create and edit study calendar templates, generate and view prospective calendars of patient activities, track activities as they occur, and manage patient calendars as they change during a study. The PSC accommodates epidemiological/population studies, observational studies and interventional studies, and facilitates easy management of the screening process, registration, active monitoring, and long-term follow-up. | Under Review | Submission Material |
last modified
09-17-2008 08:47 AM
