Difference between revisions of "XORT"
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− | == | + | {{Tool data |
+ | |name=XORT | ||
+ | |status=mature | ||
+ | |dev=maintenance | ||
+ | |support=active | ||
+ | |type=Database tools, Middleware | ||
+ | |platform=linux, unix | ||
+ | |about=XORT is a utility written in Perl that can be used to read to and write from a [[Glossary#Relational|relational]] [[Glossary#Schema|schema]] using [[Glossary#XML|XML]] as an interchange format. In GMOD XORT is frequently used to transfer data to and from [[Chado]]. | ||
− | XORT | + | XORT’s three major elements are an XML-database schema mapping specification, an XORT language for both data retrieval and data construction, and a collection of tools that are based on the specification to facilitate the mapping and data exchange. The mapping specification specifies the schema requirement, mapping, operation, and object reference mechanism; the XORT language is used to construct the dump specification; the tool collections comprise the data validation, data input, data output and data debug system. Because it originates from the [[Chado]] database, we denote the corresponding XML "Chado XML." |
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+ | |open source=Yes | ||
+ | |language=Perl | ||
+ | |audience=private | ||
+ | |contact=[mailto:zhou@morgan.harvard.edu Pinglei Zhou] | ||
+ | }} | ||
+ | <!-- To change the contents of this page, please go to http://gmod.org/wiki/XORT/tool_data --> | ||
+ | {{ :XORT/tool_data | template = Template:ToolDisplay }} | ||
[[Category:GMOD Components]] | [[Category:GMOD Components]] | ||
+ | [[Category:XORT]] | ||
+ | [[Category:XML]] | ||
+ | {{SemanticLink | ||
+ | |linkurl=http://sourceforge.net/projects/gmod/files/OldFiles/ | ||
+ | |linktype=download | ||
+ | }} | ||
+ | {{InteroperableComponent | ||
+ | |relationship=reads from and writes to | ||
+ | |object=Chado | ||
+ | }} |
Latest revision as of 21:22, 16 October 2013
Contents
About XORT
XORT is a utility written in Perl that can be used to read to and write from a relational schema using XML as an interchange format. In GMOD XORT is frequently used to transfer data to and from Chado.
XORT’s three major elements are an XML-database schema mapping specification, an XORT language for both data retrieval and data construction, and a collection of tools that are based on the specification to facilitate the mapping and data exchange. The mapping specification specifies the schema requirement, mapping, operation, and object reference mechanism; the XORT language is used to construct the dump specification; the tool collections comprise the data validation, data input, data output and data debug system. Because it originates from the Chado database, we denote the corresponding XML "Chado XML."
Visit the XORT website.
Downloads
- Download XORT: http://sourceforge.net/projects/gmod/files/OldFiles/
Using XORT
System Requirements
Documentation
Publications, Tutorials, and Presentations
Presentations
Contacts and Mailing Lists
There is no mailing list for XORT; please direct queries to the GMOD helpdesk or to the XORT developer Pinglei Zhou.
XORT Development
Development team
See also
Note that GMODTools offers an alternative approach to bulk uploads and downloads from a Chado database.
DBStag
The DBStag XML<->SQL API implements the XORT spec for bulkloading of data; it does not support the dump spec
Chado-XML
Chado XML is a direct mapping of the Chado relational schema into XML.
Tools that read and write Chado-XML
go2chadoxml
Distributed as part of go-perl. Takes any obo file and exports as Chado-XML. Can be loaded using XML::Xort or DBStag
Status: Stable
The OBO repository is pre-converted to Chado-XML on a nightly basis.
BioPerl
writes chadoXML
Status: ?
Bio-Chaos
The bio-chaos library reads and writes chaos-xml, which can be converted to and from chado
Status: no longer supported
Macros
The basic chadoXMLl expansion can be extremely verbose - this is because chadoXML uses the unique keys from the chado db, yet it does not use database internal foreign keys. XORT can be configured with macros that can be used to capture repeated nodes in the XML and give them XML IDs that are valid within a particular document.
More on XORT
See Category:XORT
Raw tool data at XORT/tool data
Available on platform | linux + and unix + |
Has URL | http://sourceforge.net/projects/gmod/files/OldFiles/ + |
Has description | XORT is a utility written in Perl that can … XORT is a utility written in Perl that can be used to read to and write from a relational schema using XML as an interchange format. In GMOD XORT is frequently used to transfer data to and from Chado. XORT’s three major elements are an XML-database schema mapping specification, an XORT language for both data retrieval and data construction, and a collection of tools that are based on the specification to facilitate the mapping and data exchange. The mapping specification specifies the schema requirement, mapping, operation, and object reference mechanism; the XORT language is used to construct the dump specification; the tool collections comprise the data validation, data input, data output and data debug system. Because it originates from the Chado database, we denote the corresponding XML "Chado XML." denote the corresponding XML "Chado XML." + |
Has development status | maintenance + |
Has download URL | http://sourceforge.net/projects/gmod/files/OldFiles/ + |
Has software maturity status | mature + |
Has support status | active + |
Has topic | XORT + |
Has website | http://gmod.org/wiki/XORT + |
Interaction type | reads from and writes to + |
Interactor | XORT + |
Interacts with | Chado + |
Is open source | Yes + |
Link type | download + |
Tool functionality or classification | Database tools + and Middleware + |
Written in language | Perl + |
Has subobjectThis property is a special property in this wiki. | XORT#http://sourceforge.net/projects/gmod/files/OldFiles/ + and XORT + |