Difference between revisions of "DNA extension Version2"

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Line 1: Line 1:
 +
=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 10:35, 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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