DNA extension Version2: Difference between revisions

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=Deleted elements=
Deleted elements in the DNA extension has been moved to the core ABCD2.06. See details below
{{ABCD-Change
{{ABCD-Change
|element = test123
|element = Preservation
|status = Deleted
|type = xs:string
|min = 0
|documentation = Form of conservation or fixation in which the tissue was available for extraction
|path = /DNASample/Preservation
|comments = moved to core ABCD2.06
}}
 
{{ABCD-Change
|element = ExtractionStaff
|status = Deleted
|type = xs:string
|min = 0
|documentation = Person who carried out DNA extraction
|path = /DNASample/ExtractionStaff
|comments = moved to core ABCD2.06
}}
 
{{ABCD-Change
|element = ExtractionDate
|status = Deleted
|type = xs:date
|min = 0
|documentation = Date of DNA extraction
|path = /DNASample/ExtractionDate
|comments = moved to core ABCD2.06
}}
 
{{ABCD-Change
|element = ExtractionMethod
|status = Deleted
|type = xs:string
|min = 0
|documentation = Method or extraction protocol applied
|path = /DNASample/ExtractionMethod
|comments = moved to core ABCD2.06
}}
 
{{ABCD-Change
|element = AmplificationPrimerForward
|status = Deleted
|type = Container
|min = 0
|documentation = Container element for information about the amplification forward primer
|path = /DNASample/Amplifications/Amplification/AmplificationPrimers/AmplificationPrimerForward
|comments = deleted; insted use of a more generic <code>Primer</code> elements, see details in part New elements
|content = PrimerName?, PrimerSequence?, PrimerReferenceCitation?, PrimerReferenceLink?
}}
 
{{ABCD-Change
|element = PrimerName
|status = Deleted
|type = xs:string
|min = 0
|documentation = Name of the forward primer
|path = /DNASample/Amplifications/Amplification/AmplificationPrimers/AmplificationPrimerForward/PrimerName
|comments = deleted; insted use of a more generic <code>Primer</code> elements, see details in part New elements
}}
 
{{ABCD-Change
|element = PrimerSequence
|status = Deleted
|type = xs:string
|min = 0
|documentation = DNA sequence of the forward primer (5' to 3')
|path = /DNASample/Amplifications/Amplification/AmplificationPrimers/AmplificationPrimerForward/PrimerSequence
|comments = deleted; insted use of a more generic <code>Primer</code> elements, see details in part New elements
}}
 
{{ABCD-Change
|element = PrimerReferenceCitation
|status = Deleted
|type = xs:string
|min = 0
|documentation = First reference of the forward primer
|path = /DNASample/Amplifications/Amplification/AmplificationPrimers/AmplificationPrimerForward/PrimerReferenceCitation
|comments = deleted; insted use of a more generic <code>Primer</code> elements, see details in part New elements
}}
 
{{ABCD-Change
|element = PrimerReferenceLink
|status = Deleted
|type = xs:string
|min = 0
|documentation = Link to the first reference of the forward primer
|path = /DNASample/Amplifications/Amplification/AmplificationPrimers/AmplificationPrimerForward/PrimerReferenceLink
|comments = deleted; insted use of a more generic <code>Primer</code> elements, see details in part New elements
}}
 
 
{{ABCD-Change
|element = AmplificationPrimerReverse
|status = Deleted
|type = Container
|min = 0
|documentation = Container element for information about the amplification reverse primer
|path = /DNASample/Amplifications/Amplification/AmplificationPrimers/AmplificationPrimerReverse
|comments = deleted; insted use of a more generic <code>Primer</code> elements, see details in part New elements
|content = PrimerName?, PrimerSequence?, PrimerReferenceCitation?, PrimerReferenceLink?
}}
 
{{ABCD-Change
|element = PrimerName
|status = Deleted
|type = xs:string
|min = 0
|documentation = Name of the reverse primer
|path = /DNASample/Amplifications/Amplification/AmplificationPrimers/AmplificationPrimerReverse/PrimerName
|comments = deleted; insted use of a more generic <code>Primer</code> elements, see details in part New elements
}}
 
{{ABCD-Change
|element = PrimerSequence
|status = Deleted
|type = xs:string
|min = 0
|documentation = DNA sequence of the reverse primer (5' to 3')
|path = /DNASample/Amplifications/Amplification/AmplificationPrimers/AmplificationPrimerReverse/PrimerSequence
|comments = deleted; insted use of a more generic <code>Primer</code> elements, see details in part New elements
}}
 
{{ABCD-Change
|element = PrimerReferenceCitation
|status = Deleted
|type = xs:string
|min = 0
|documentation = First reference of the reverse primer
|path = /DNASample/Amplifications/Amplification/AmplificationPrimers/AmplificationPrimerReverse/PrimerReferenceCitation
|comments = deleted; insted use of a more generic <code>Primer</code> elements, see details in part New elements
}}
 
{{ABCD-Change
|element = PrimerReferenceLink
|status = Deleted
|type = xs:string
|min = 0
|documentation = Link to the first reference of the reverse primer
|path = /DNASample/Amplifications/Amplification/AmplificationPrimers/AmplificationPrimerReverse/PrimerReferenceLink
|comments = deleted; insted use of a more generic <code>Primer</code> elements, see details in part New elements
}}
 
 
 
=New elements=
 
{{ABCD-Change
|element = QualityCheckMethod
|status = New
|type = xs:string
|min = 0
|documentation = Method used for determination of DNA or tissue quality parameters
|path = /DNASample/QualityCheckMethod
|comments = check again, as well as the other Quality fields!
}}
 
{{ABCD-Change
|element = Images
|status = Changed
|type = Container
|min = 0
|documentation = Container element for information on images of the DNA sample (e.g. agarose gel images)
|path = /DNASample/Images
|comments = changed documentation
}}
 
{{ABCD-Change
|element = Images
|status = Changed
|status = Changed
|type = xs:tring
|type = Container
|min = 1
|min = 0
|documentation = Container element for information on images of the DNA sample (e.g. agarose gel images)
|path = /DNASample/Images
|comments = changed documentation
|content = Image+
}}
 
 
{{ABCD-Change
|element = Image
|status = New
|type = Container
|min = 0
|max = unbounded
|max = unbounded
|documentation = A reference to or the text of a permit related to the gathering
|documentation = Container element for information on images of the DNA sample (e.g. agarose gel images)
|path = /DataSets/DataSet/Units/Unit/Gathering/Permits/Permit/Permit
|path = /DNASample/Images/Image
|comments = unbounded due to backwards compatibility; documentation added
|content = FileURI?, GelVoltage?, GelConcentration?, GelDuration?, GelLadder?
}}
 
{{ABCD-Change
|element = FileURI
|status = Changed
|type = StringType
|min = 0
|documentation = Link to an DNA sample image (e.g. agarose gel image)
|path = /DNASample/Images/Image/FileURI
|comments = no longer unbounded
}}
 
{{ABCD-Change
|element = GelVoltage
|status = New
|type = xs:string
|min = 0
|path = /DNASample/Images/Image/GelVoltage
}}
 
{{ABCD-Change
|element = GelConcentration
|status = New
|type = xs:string
|min = 0
|path = /DNASample/Images/Image/GelConcentration
}}
 
{{ABCD-Change
|element = GelDuration
|status = New
|type = xs:string
|min = 0
|path = /DNASample/Images/Image/GelDuration
}}
 
{{ABCD-Change
|element = GelLadder
|status = New
|type = xs:string
|min = 0
|path = /DNASample/Images/Image/GelLadder
}}
 
{{ABCD-Change
|element = Marker
|status = Changed
|type = xs:string
|min = 0
|documentation = Marker, genetic locus or DNA fragment amplified by PCR (e.g. "CO1", "ITS")
|path = /DNASample/Amplifications/Amplification
|comments = changed element name, was <code>GeneticLocus</code> before
}}
 
{{ABCD-Change
|element = AmplificationSuccess
|status = New
|type = xs:boolean
|min = 0
|documentation = true/false or yes/no whether the ampliciation was sucessful in general
|path = /DNASample/Amplifications/Amplification/AmplificationSuccess
}}
 
{{ABCD-Change
|element = AmplificationSuccessDetails
|status = New
|type = xs:string
|min = 0
|documentation = details about the amplification, e.g. including why it has failed
|path = /DNASample/Amplifications/Amplification/AmplificationSuccessDetails
}}
 
{{ABCD-Change
|element = AmplificationMethod
|status = New
|type = xs:string
|min = 0
|documentation = Method used for amplification
|path = /DNASample/Amplifications/Amplification/AmplificationMethod
}}
 
{{ABCD-Change
|element = AmplificationPrimer
|status = New
|type = Container
|min = 0
|max = unbounded
|documentation = Container element for an individual amplification primer
|path = /DNASample/Amplifications/Amplification/AmplificationPrimers/AmplificationPrimer
|comments = uses the generic element <code>Primer</code>
|content = Primer+
}}
 
{{ABCD-Change
|element = CloningPrimers
|status = New
|type = Container
|min = 0
|documentation = Container element for cloning primers
|path = /DNASample/Amplifications/Amplification/Sequencings/Sequencing/CloningPrimers
|content = CloningPrimer+
}}
 
{{ABCD-Change
|element = CloningPrimer
|status = New
|type = Container
|min = 0
|documentation = Container element for an individual cloning primer
|path = /DNASample/Amplifications/Amplification/Sequencings/Sequencing/CloningPrimers/CloningPrimer
|comments = uses the generic element <code>Primer</code>
|content = Primer+
}}
 
{{ABCD-Change
|element = SequencingPrimer
|status = Changed
|type = Container
|min = 0
|max = unbounded
|documentation = Container element for an individual sequencing primer
|path = /DNASample/Amplifications/Amplification/Sequencings/Sequencing/SequencingPrimers/SequencingPrimer
|comments = uses the generic element <code>Primer</code> now
|content = Primer+
}}
 
{{ABCD-Change
|element = Primer
|status = Changed
|type = Container
|min = 0
|documentation = Container element for information of a sequencing, cloning, or amplification primer
|path = /DNASample/Amplifications/Amplification/Sequencings/Sequencing/SequencingPrimers/SequencingPrimer/Primer
|comments = changed name of element
|content = PrimerSequence?, PrimerName?, PrimerReferenceCitation?, PrimerReferenceLink?
}}
 
{{ABCD-Change
|element = Haplotype
|status = New
|type = xs:string
|min = 0
|documentation = Name of the haplotype
|path = /DNASample/Amplifications/Amplification/Sequencings/Sequencing/Haplotype
}}
 
{{ABCD-Change
|element = GeneticAccessionNumber
|status = Changed
|type = xs:string
|min = 0
|documentation = Definite number or ID under which the DNA sequence is deposited in a public database (e.g. GenBank accession number)
|path = /DNASample/Amplifications/Amplification/Sequencings/Sequencing/GeneticAccessionNumber
|comments = changed name of element
}}
 
{{ABCD-Change
|element = GeneticAccessionNumber-URI
|status = Changed
|type = xs:string
|min = 0
|documentation = Link to the related record in a public database (e.g. link to a GenBank or EMBL record)
|path = /DNASample/Amplifications/Amplification/Sequencings/Sequencing/GeneticAccessionNumber-URI
|comments = changed name of element
}}
 
{{ABCD-Change
|element = BOLDProcessID
|status = New
|type = xs:string
|min = 0
|documentation = Definite number or ID under which the DNA sequence is deposited in the BOLD database
|path = /DNASample/Amplifications/Amplification/Sequencings/Sequencing/BOLDProcessID
|comments = separated from the <code>GeneticAccessionNumber</code> element, no URI element required (only one BOLD instance)
}}
 
{{ABCD-Change
|element = SequenceLength
|status = New
|type = xs:string
|min = 0
|documentation = Length of the single sequence/read
|path = /DNASample/Amplifications/Amplification/Sequencings/Sequencing/SingleSequencings/SingleSequencing/SequenceLength
}}
}}

Revision as of 09:35, 18 September 2013

Deleted elements

Deleted elements in the DNA extension has been moved to the core ABCD2.06. See details below

Preservation(link)
Core Deleted xs:string minOccurs: 0 maxOccurs: 1
Form of conservation or fixation in which the tissue was available for extraction
Element Path:
/DNASample/Preservation
Comments:
moved to core ABCD2.06


ExtractionStaff(link)
Core Deleted xs:string minOccurs: 0 maxOccurs: 1
Person who carried out DNA extraction
Element Path:
/DNASample/ExtractionStaff
Comments:
moved to core ABCD2.06


ExtractionDate(link)
Core Deleted xs:date minOccurs: 0 maxOccurs: 1
Date of DNA extraction
Element Path:
/DNASample/ExtractionDate
Comments:
moved to core ABCD2.06


ExtractionMethod(link)
Core Deleted xs:string minOccurs: 0 maxOccurs: 1
Method or extraction protocol applied
Element Path:
/DNASample/ExtractionMethod
Comments:
moved to core ABCD2.06


AmplificationPrimerForward(link)
Core Deleted Container minOccurs: 0 maxOccurs: 1
Container element for information about the amplification forward primer
Element Path:
/DNASample/Amplifications/Amplification/AmplificationPrimers/AmplificationPrimerForward
Content:
PrimerName?, PrimerSequence?, PrimerReferenceCitation?, PrimerReferenceLink?
Comments:
deleted; insted use of a more generic Primer elements, see details in part New elements


PrimerName(link)
Core Deleted xs:string minOccurs: 0 maxOccurs: 1
Name of the forward primer
Element Path:
/DNASample/Amplifications/Amplification/AmplificationPrimers/AmplificationPrimerForward/PrimerName
Comments:
deleted; insted use of a more generic Primer elements, see details in part New elements


PrimerSequence(link)
Core Deleted xs:string minOccurs: 0 maxOccurs: 1
DNA sequence of the forward primer (5' to 3')
Element Path:
/DNASample/Amplifications/Amplification/AmplificationPrimers/AmplificationPrimerForward/PrimerSequence
Comments:
deleted; insted use of a more generic Primer elements, see details in part New elements


PrimerReferenceCitation(link)
Core Deleted xs:string minOccurs: 0 maxOccurs: 1
First reference of the forward primer
Element Path:
/DNASample/Amplifications/Amplification/AmplificationPrimers/AmplificationPrimerForward/PrimerReferenceCitation
Comments:
deleted; insted use of a more generic Primer elements, see details in part New elements




AmplificationPrimerReverse(link)
Core Deleted Container minOccurs: 0 maxOccurs: 1
Container element for information about the amplification reverse primer
Element Path:
/DNASample/Amplifications/Amplification/AmplificationPrimers/AmplificationPrimerReverse
Content:
PrimerName?, PrimerSequence?, PrimerReferenceCitation?, PrimerReferenceLink?
Comments:
deleted; insted use of a more generic Primer elements, see details in part New elements


PrimerName(link)
Core Deleted xs:string minOccurs: 0 maxOccurs: 1
Name of the reverse primer
Element Path:
/DNASample/Amplifications/Amplification/AmplificationPrimers/AmplificationPrimerReverse/PrimerName
Comments:
deleted; insted use of a more generic Primer elements, see details in part New elements


PrimerSequence(link)
Core Deleted xs:string minOccurs: 0 maxOccurs: 1
DNA sequence of the reverse primer (5' to 3')
Element Path:
/DNASample/Amplifications/Amplification/AmplificationPrimers/AmplificationPrimerReverse/PrimerSequence
Comments:
deleted; insted use of a more generic Primer elements, see details in part New elements


PrimerReferenceCitation(link)
Core Deleted xs:string minOccurs: 0 maxOccurs: 1
First reference of the reverse primer
Element Path:
/DNASample/Amplifications/Amplification/AmplificationPrimers/AmplificationPrimerReverse/PrimerReferenceCitation
Comments:
deleted; insted use of a more generic Primer elements, see details in part New elements




New elements

QualityCheckMethod(link)
Core New xs:string minOccurs: 0 maxOccurs: 1
Method used for determination of DNA or tissue quality parameters
Element Path:
/DNASample/QualityCheckMethod
Comments:
check again, as well as the other Quality fields!


Images(link)
Core Changed Container minOccurs: 0 maxOccurs: 1
Container element for information on images of the DNA sample (e.g. agarose gel images)
Element Path:
/DNASample/Images
Comments:
changed documentation


Images(link)
Core Changed Container minOccurs: 0 maxOccurs: 1
Container element for information on images of the DNA sample (e.g. agarose gel images)
Element Path:
/DNASample/Images
Content:
Image+
Comments:
changed documentation



Image(link)
Core New Container minOccurs: 0 maxOccurs: unbounded
Container element for information on images of the DNA sample (e.g. agarose gel images)
Element Path:
/DNASample/Images/Image
Content:
FileURI?, GelVoltage?, GelConcentration?, GelDuration?, GelLadder?


FileURI(link)
Core Changed StringType minOccurs: 0 maxOccurs: 1
Link to an DNA sample image (e.g. agarose gel image)
Element Path:
/DNASample/Images/Image/FileURI
Comments:
no longer unbounded


GelVoltage(link)
Core New xs:string minOccurs: 0 maxOccurs: 1
Element Path:
/DNASample/Images/Image/GelVoltage


GelConcentration(link)
Core New xs:string minOccurs: 0 maxOccurs: 1
Element Path:
/DNASample/Images/Image/GelConcentration


GelDuration(link)
Core New xs:string minOccurs: 0 maxOccurs: 1
Element Path:
/DNASample/Images/Image/GelDuration


GelLadder(link)
Core New xs:string minOccurs: 0 maxOccurs: 1
Element Path:
/DNASample/Images/Image/GelLadder


Marker(link)
Core Changed xs:string minOccurs: 0 maxOccurs: 1
Marker, genetic locus or DNA fragment amplified by PCR (e.g. "CO1", "ITS")
Element Path:
/DNASample/Amplifications/Amplification
Comments:
changed element name, was GeneticLocus before


AmplificationSuccess(link)
Core New xs:boolean minOccurs: 0 maxOccurs: 1
true/false or yes/no whether the ampliciation was sucessful in general
Element Path:
/DNASample/Amplifications/Amplification/AmplificationSuccess


AmplificationSuccessDetails(link)
Core New xs:string minOccurs: 0 maxOccurs: 1
details about the amplification, e.g. including why it has failed
Element Path:
/DNASample/Amplifications/Amplification/AmplificationSuccessDetails


AmplificationMethod(link)
Core New xs:string minOccurs: 0 maxOccurs: 1
Method used for amplification
Element Path:
/DNASample/Amplifications/Amplification/AmplificationMethod


AmplificationPrimer(link)
Core New Container minOccurs: 0 maxOccurs: unbounded
Container element for an individual amplification primer
Element Path:
/DNASample/Amplifications/Amplification/AmplificationPrimers/AmplificationPrimer
Content:
Primer+
Comments:
uses the generic element Primer


CloningPrimers(link)
Core New Container minOccurs: 0 maxOccurs: 1
Container element for cloning primers
Element Path:
/DNASample/Amplifications/Amplification/Sequencings/Sequencing/CloningPrimers
Content:
CloningPrimer+


CloningPrimer(link)
Core New Container minOccurs: 0 maxOccurs: 1
Container element for an individual cloning primer
Element Path:
/DNASample/Amplifications/Amplification/Sequencings/Sequencing/CloningPrimers/CloningPrimer
Content:
Primer+
Comments:
uses the generic element Primer


SequencingPrimer(link)
Core Changed Container minOccurs: 0 maxOccurs: unbounded
Container element for an individual sequencing primer
Element Path:
/DNASample/Amplifications/Amplification/Sequencings/Sequencing/SequencingPrimers/SequencingPrimer
Content:
Primer+
Comments:
uses the generic element Primer now


Primer(link)
Core Changed Container minOccurs: 0 maxOccurs: 1
Container element for information of a sequencing, cloning, or amplification primer
Element Path:
/DNASample/Amplifications/Amplification/Sequencings/Sequencing/SequencingPrimers/SequencingPrimer/Primer
Content:
PrimerSequence?, PrimerName?, PrimerReferenceCitation?, PrimerReferenceLink?
Comments:
changed name of element


Haplotype(link)
Core New xs:string minOccurs: 0 maxOccurs: 1
Name of the haplotype
Element Path:
/DNASample/Amplifications/Amplification/Sequencings/Sequencing/Haplotype


GeneticAccessionNumber(link)
Core Changed xs:string minOccurs: 0 maxOccurs: 1
Definite number or ID under which the DNA sequence is deposited in a public database (e.g. GenBank accession number)
Element Path:
/DNASample/Amplifications/Amplification/Sequencings/Sequencing/GeneticAccessionNumber
Comments:
changed name of element


GeneticAccessionNumber-URI(link)
Core Changed xs:string minOccurs: 0 maxOccurs: 1
Link to the related record in a public database (e.g. link to a GenBank or EMBL record)
Element Path:
/DNASample/Amplifications/Amplification/Sequencings/Sequencing/GeneticAccessionNumber-URI
Comments:
changed name of element


BOLDProcessID(link)
Core New xs:string minOccurs: 0 maxOccurs: 1
Definite number or ID under which the DNA sequence is deposited in the BOLD database
Element Path:
/DNASample/Amplifications/Amplification/Sequencings/Sequencing/BOLDProcessID
Comments:
separated from the GeneticAccessionNumber element, no URI element required (only one BOLD instance)


SequenceLength(link)
Core New xs:string minOccurs: 0 maxOccurs: 1
Length of the single sequence/read
Element Path:
/DNASample/Amplifications/Amplification/Sequencings/Sequencing/SingleSequencings/SingleSequencing/SequenceLength


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