Notes:
Release Notes
MAGE-OM API
Version 1.5
(from $Name: v1_5_deploy-stage_build_31 $)
$Date: 2007/02/27 17:56:36 $
National Cancer Institute Center for Bioinformatics
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Contents
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1.0 caArray Introduction
2.0 Release History
3.0 New Features and Updates
4.0 Bugs Fixed Since Last Release
5.0 Known Issues/Defects
6.0 Bug Reports, Feature Requests, and Support
7.0 Documentation and Files
8.0 NCICB Web Pages
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1.0 MAGE-OM API Version 1.5 - Introduction
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The caArray (http://caarray.nci.nih.gov/) software has been developed by the NCI Center for
Bioinformatics (NCICB) to create an information-sharing network modeled on the World Wide
Web. caArray consists of a microarray database and microarray data visualization and analysis
tools. caArray is an open source project, and the source code and APIs are available in the
caArray Informatics page of the NCICB website. The goals of the project are to make microarray
data publicly available, and to develop and bring together open source tools to analyze these
data. Existing caArray documentation can be found on the caArray page of the NCICB website:
http://caarray.nci.nih.gov/caARRAY/devdoc/caarraydbdocs.
The caArray MAGE-OM API is a set of Java objects that adhere to the object model defined by
OMG's Gene Expression v1.1. The caArray MAGE-OM API objects provide access to data in
the caArray database via Remote Method Invocation (RMI) call issued to a dedicated MAGE
server at NCI or any other site with an accessible MAGE-OM server installation. There are two
primary types of objects defined in the API:
1. MAGE-OM-compliant interfaces
2. Custom MAGE-OM Impl (implementation) objects
The MAGE-compliant objects are defined as Java interfaces, which the custom MAGE-OM Impl
Java classes implement. This ensures the custom MAGE-OM Impl provide a MAGE-OM
compliant API. The MGED Society web site is an excellent source for supplemental material on
the MAGE object model.
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2.0 Release History
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MAGE-OM API v1.0 for caArray Version 1.3 -- October 20, 2005
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3.0 New Features and Updates
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- MAGE-OM API:
- Provided enhanced capability to search for Experiments by
- "tissue type"
- "Chip/Platform type"
- DesignElement.name
- DesignElement.identifier
- "investigator name"
- "organism name"
- Experiment.name
- "PubMed Id"
- Provided enhanced capability to search for MeasuredBioAssays by
- Experiment.id
- Experiment.name
- BioSource.name
- BioSource.identifier
- Provided enhanced capability to search for DerivedBioAssays by
- Experiment.id
- Experiment.name
- BioSource.name
- BioSource.identifier
- Provided enhanced capability to search for ArrayDesign and Reporter data
as an aggregated result into a ArrayDesignReporterSummary type by
- ArrayDesign.id
- ArrayDesign.name
- Reporter.name
- "Chromosome value"
- "gb4 value"
- "kb position value"
- Improved BioDataCube support for various BioAssayData types from vendors
(CEL, CHP, Imagene, Genepix, see caArray Portal Release notes for further information.
- no longer requires NetCDF; no longer supports BioAssayDataNum from before.
- Improved performance of DesignElementDimensions' DesignElements retrieval
(includes FeatureDimension.containFeatures, ReporterDimension.reporters,
CompositeSequenceDimension.compositeSequences)
- Improved adherence of the Domain classes to the specification;
- IdentifiableImpl, ExtendableImpl, ContactImpl, BioMaterialImpl, ConfidenceIndicatorImpl, QuantitationTypeImpl, StandardQuantitationTypeImpl
are now abstract classes
- Order is now guarenteed for QuantitationTypeDimension.quantitationTypes
-
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4.0 Defects Fixed Since Last Release
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- NONE (see GForge for report)
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5.0 Known Issues/Defects
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- See GForge for existing open bugs and feature requests,
http://gforge.nci.nih.gov/tracker/?group_id=82
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6.0 Bug Reports, Feature Requests, and Support
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Send email to ncicb@pop.nci.nih.gov to request support or
report a bug or request a new feature. Existing requests and
resolution may be viewed at the caArray GForge URL:
http://gforge.nci.nih.gov/tracker/?group_id=82
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7.0 Documentation and Files
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All documentation and files are bundled with the distribution.
Documentation can be found in the docs subdirectory of this
distribution.
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8.0 NCICB Web Pages
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The NCI Center for Bioinformatics
-- http://ncicb.nci.nih.gov/
NCICB Application Support
-- http://ncicb.nci.nih.gov/NCICB/support
NCICB Download Center
-- http://ncicb.nci.nih.gov/download/
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