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Resource:SMD

Name: Resource:SMD
Description: Database to store, annotate, view, analyze and share microarray data. It provides registered users access to their own data, provides users access to public data, and tools with which to analyze those data, to any public user anywhere in the world.

The GenePattern software package has been incorporated directly into SMD, providing access to many new analysis tools, as well as a plug-in architecture that allows users to directly integrate and share additional tools through SMD. This extension is available with the SMD source code that is fully and freely available to others under an Open Source license, enabling other groups to create a local installation of SMD with an enriched data analysis capability.

SMD search options allow the user to Search By Experiments, Search By Datasets, or Search By Gene Names.

Web services are provided using common standards, such as Simple Object Access Protocol (SOAP). This enables both local and remote researchers to connect to an installation of the database and retrieve data using pre-defined methods, without needing to resort to use of a web browser.[1]
Other Name(s): Stanford Microarray Database
Abbreviation: SMD
Parent Organization: Princeton University; New Jersey; USA
Supporting Agency: NHGRI, NCI, Howard Hughes Medical Institute, Stanford University School of Medicine; California; USA
Grant: R01 HG003469
Resource Type(s): Database, Data repository, Data analysis service
Resource: Resource
URL: http://smd.princeton.edu/
*Id: nlx_94141
PMID: PMID 18953035, 17182626, 15608265, 12519956, 11125075
Related to: Resource:3DVC, Resource:OMICtools, Resource:re3data.org
Availability: Public, Open-source license, The community can contribute to this resource, Acknowledgement requested
Address: Department of Genetics, Stanford University School of Medicine, CA 94305, USA.
Keywords: Data set, microarray, gene, image, gene expression, Adenovirus disease, Apoptosis, Leukemia, Source code, Web service
Link to OWL / RDF: Download this content as OWL/RDF

Categories related to Resource:SMD

Resource:Longhorn Array Database, Resource:Tuberculosis Database

Parts of Resource:SMD

Curation status: Uncurated

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References

  1. Hubble J et al. (2009) Implementation of GenePattern within the Stanford Microarray Database. Nucleic Acids Res 37: D898-901 PubMed

Notes

This page uses this default form:Resource

Xref: OMICS_00870

Old URL: http://genome-www.stanford.edu/microarray/
Old URL: http://smd.stanford.edu/



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*Note: Neurolex imports many terms and their ids from existing community ontologies, e.g., the Gene Ontology. Neurolex, however, is a dynamic site and any content beyond the identifier should not be presumed to reflect the content or views of the source ontology. Users should consult with the authoritative source for each ontology for current information.

Facts about Resource:SMDRDF feed
AbbrevSMD  +
AddressDepartment of Genetics  +, Stanford University School of Medicine  +, CA 94305  +, and USA.  +
AvailabilityPublic  +, Open-source license  +, The community can contribute to this resource  +, and Acknowledgement requested  +
Commentorg-id: smd_stanford Access: Open/Closed
Start date: 2011
Type: Disciplinary
(info provided by re3data.org)
CurationStatuscurated  +
DefiningCitationhttp://smd.princeton.edu/  +
DefinitionDatabase to store, annotate, view, analyze Database to store, annotate, view, analyze and share microarray data. It provides registered users access to their own data, provides users access to public data, and tools with which to analyze those data, to any public user anywhere in the world.

The GenePattern software package has been incorporated directly into SMD, providing access to many new analysis tools, as well as a plug-in architecture that allows users to directly integrate and share additional tools through SMD. This extension is available with the SMD source code that is fully and freely available to others under an Open Source license, enabling other groups to create a local installation of SMD with an enriched data analysis capability. SMD search options allow the user to Search By Experiments, Search By Datasets, or Search By Gene Names.

Web services are provided using common standards, such as Simple Object Access Protocol (SOAP). This enables both local and remote researchers to connect to an installation of the database and retrieve data using pre-defined methods, without needing to resort to use of a web browser.
needing to resort to use of a web browser.
ExampleImageSMD.PNG  +
GrantCategory:R01 HG003469   +
Has default formThis property is a special property in this wiki.Resource  +
Has roleDatabase  +, Data repository  +, and Data analysis service  +
Idnlx_94141  +
Is part ofPrinceton University; New Jersey; USA  +
KeywordsData set  +, Microarray  +, Gene  +, Image  +, Gene expression  +, Adenovirus disease  +, Apoptosis  +, Leukemia  +, Source code  +, and Web service  +
LabelResource:SMD  +
ModifiedDate29 July 2014  +
OldURLhttp://genome-www.stanford.edu/microarray/  +, and http://smd.stanford.edu/  +
PMID18953035, 17182626, 15608265, 12519956, 11125075  +
Page has default formThis property is a special property in this wiki.Resource  +
RelatedToResource:3DVC  +, Resource:OMICtools  +, and Resource:re3data.org  +
SuperCategoryResource  +
Supporting AgencyNational Human Genome Research Institute  +, National Cancer Institute  +, Howard Hughes Medical Institute  +, and Stanford University School of Medicine; California; USA  +
SynonymStanford Microarray Database  +
XrefResource:SMD  +