Difference between revisions of "XORT"

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(New page: <nowiki> Chado-XML ========= Chado-XML is a direct mapping of the Chado relational schema into XML. Currently the only tool for performing this mapping is XML::XORT, which can du...)
 
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{{Tool data
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|name=XORT
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|status=mature
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|dev=maintenance
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|support=active
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|type=Database tools, Middleware
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|platform=linux, unix
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|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]].
  
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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."
  
<nowiki>
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|open source=Yes
Chado-XML
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|language=Perl
=========
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|audience=private
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|contact=[mailto:zhou@morgan.harvard.edu Pinglei Zhou]
Chado-XML is a direct mapping of the Chado relational schema into
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}}
XML. Currently the only tool for performing this mapping is XML::XORT,
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<!-- To change the contents of this page, please go to http://gmod.org/wiki/XORT/tool_data -->
which can dump or save Chado-XML to and from a chado db.
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{{ :XORT/tool_data | template = Template:ToolDisplay }}
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Contents:
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---
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chado-xml
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        README
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        xsl/                    -- useful transforms
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        dtd/                    -- DTDs/XSDs defining the xml model
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        examples/              -- example XML files
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        doc/                    -- documentation
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---
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Documentation in asciidoc - can use asciidoc.py to convert to HTML,
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PDF, RTF etc
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See:
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        SourceForge: http://sourceforge.net/projects/asciidoc/
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        Main website: http://www.methods.co.nz/asciidoc/
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Macros
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------
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The basic chado-xml expansion can be extremely verbose - this is
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because chado-xml uses the unique keys from the chado db, yet it does
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not database internal foreign keys.
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Macros can be used to capture repeated nodes in the xml and give them
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XML IDs that are valid within a particular document.
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See also
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--------
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gmod/XML-XORT
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</nowiki>
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[[Category:GMOD Components]]
 
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[[Category:XORT]]
* [[Chado-xml doc]]
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[[Category:XML]]
* [[XORT Usage]]
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{{SemanticLink
 
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|linkurl=http://sourceforge.net/projects/gmod/files/OldFiles/
 
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|linktype=download
 
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}}
 
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{{InteroperableComponent
Chris suggested the inclusion of the chado-xml docs from the schema--I did that.
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|relationship=reads from and writes to
 
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|object=Chado
 
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}}
 
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I should also mention that this README and the child page with chado-xml documentation are dynamically pulled in an included from the sourceforge cvs. While this means it will always be up to date with respect to what is in cvs, it also give an additional point of failure if SF's cvs server is down.
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Latest revision as of 21:22, 16 October 2013



Status
  • Mature release
  • Development: maintenance
  • Support: active
Resources


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



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

FlyBase at Harvard

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

Facts about "XORT"RDF feed
Available on platformlinux + and unix +
Has URLhttp://sourceforge.net/projects/gmod/files/OldFiles/ +
Has descriptionXORT is a utility written in Perl that canXORT 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 statusmaintenance +
Has download URLhttp://sourceforge.net/projects/gmod/files/OldFiles/ +
Has software maturity statusmature +
Has support statusactive +
Has topicXORT +
Has websitehttp://gmod.org/wiki/XORT +
Interaction typereads from and writes to +
InteractorXORT +
Interacts withChado +
Is open sourceYes +
Link typedownload +
Tool functionality or classificationDatabase tools + and Middleware +
Written in languagePerl +
Has subobjectThis property is a special property in this wiki.XORT#http://sourceforge.net/projects/gmod/files/OldFiles/ + and XORT +