View source for DNA extension Version2

This document contains information on removed, changed and new elements in the second version of the DNA extension for ABCD. The new version is not in use yet and will be published in October 2013. We will keep you informed about the ongoing process.

=Removed elements=
Most of deleted elements in the DNA extension has been moved to the core ABCD2.06. See details below

{{ABCD-Change
|element = Preservation
|status = Removed
|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 <code>/DataSets/DataSet/Units/Unit/SpecimenUnit/Preservations/Preservation</code>
}}

{{ABCD-Change
|element = ExtractionStaff
|status = Removed
|type = xs:string
|min = 0
|documentation = Person who carried out DNA extraction
|path = /DNASample/ExtractionStaff
|comments = moved to core ABCD2.06 <code>/DataSets/DataSet/Units/Unit/SpecimenUnit/Preperation/PreparationAgent/Person/FullName</code>
}}

{{ABCD-Change
|element = ExtractionDate
|status = Removed
|type = xs:date
|min = 0
|documentation = Date of DNA extraction
|path = /DNASample/ExtractionDate
|comments = moved to core ABCD2.06 <code>/DataSets/DataSet/Units/Unit/SpecimenUnit/Preperation/PreparationDate</code>
}}

{{ABCD-Change
|element = ExtractionMethod
|status = Removed
|type = xs:string
|min = 0
|documentation = Method or extraction protocol applied
|path = /DNASample/ExtractionMethod
|comments = moved to core ABCD2.06 <code>/DataSets/DataSet/Units/Unit/SpecimenUnit/Preperation/PreparationProcess</code>
}}

{{ABCD-Change
|element = BlockedUntil
|status = Removed
|type = xs:date
|min = 0
|documentation = Date until ordering of DNA samples is blocked
|path = /DNASample/BlockedUntil
|comments = moved to core ABCD2.06 <code>/DataSets/DataSet/Units/Unit/LoanRestriction/BlockedUntil</code>
}}

{{ABCD-Change
|element = ProvidedBy
|status = Removed
|type = xs:string
|min = 0
|documentation = Outside person or company which delivered or donated the DNA sample
|path = /DNASample/ProvidedBy
|comments = moved to core ABCD2.06 <code>Unit/SpecimenUnit/Acquisition/AcquiredFrom</code>
}}

{{ABCD-Change
|element = AmplificationPrimerForward
|status = Removed
|type = Container
|min = 0
|documentation = Container element for information about the amplification forward primer
|path = /DNASample/Amplifications/Amplification/AmplificationPrimers/AmplificationPrimerForward
|comments = deleted; instead 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 = Removed
|type = xs:string
|min = 0
|documentation = Name of the forward primer
|path = /DNASample/Amplifications/Amplification/AmplificationPrimers/AmplificationPrimerForward/PrimerName
|comments = deleted; instead use of a more generic <code>Primer</code> elements, see details in part New elements
}}

{{ABCD-Change
|element = PrimerSequence
|status = Removed
|type = xs:string
|min = 0
|documentation = DNA sequence of the forward primer (5' to 3')
|path = /DNASample/Amplifications/Amplification/AmplificationPrimers/AmplificationPrimerForward/PrimerSequence
|comments = deleted; instead use of a more generic <code>Primer</code> elements, see details in part New elements
}}

{{ABCD-Change
|element = PrimerReferenceCitation
|status = Removed
|type = xs:string
|min = 0
|documentation = First reference of the forward primer
|path = /DNASample/Amplifications/Amplification/AmplificationPrimers/AmplificationPrimerForward/PrimerReferenceCitation
|comments = deleted; instead use of a more generic <code>Primer</code> elements, see details in part New elements
}}

{{ABCD-Change
|element = PrimerReferenceLink
|status = Removed
|type = xs:string
|min = 0
|documentation = Link to the first reference of the forward primer
|path = /DNASample/Amplifications/Amplification/AmplificationPrimers/AmplificationPrimerForward/PrimerReferenceLink
|comments = deleted; instead use of a more generic <code>Primer</code> elements, see details in part New elements
}}

{{ABCD-Change
|element = AmplificationPrimerReverse
|status = Removed
|type = Container
|min = 0
|documentation = Container element for information about the amplification reverse primer
|path = /DNASample/Amplifications/Amplification/AmplificationPrimers/AmplificationPrimerReverse
|comments = deleted; instead 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 = Removed
|type = xs:string
|min = 0
|documentation = Name of the reverse primer
|path = /DNASample/Amplifications/Amplification/AmplificationPrimers/AmplificationPrimerReverse/PrimerName
|comments = deleted; instead use of a more generic <code>Primer</code> elements, see details in part New elements
}}

{{ABCD-Change
|element = PrimerSequence
|status = Removed
|type = xs:string
|min = 0
|documentation = DNA sequence of the reverse primer (5' to 3')
|path = /DNASample/Amplifications/Amplification/AmplificationPrimers/AmplificationPrimerReverse/PrimerSequence
|comments = deleted; instead use of a more generic <code>Primer</code> elements, see details in part New elements
}}

{{ABCD-Change
|element = PrimerReferenceCitation
|status = Removed
|type = xs:string
|min = 0
|documentation = First reference of the reverse primer
|path = /DNASample/Amplifications/Amplification/AmplificationPrimers/AmplificationPrimerReverse/PrimerReferenceCitation
|comments = deleted; instead use of a more generic <code>Primer</code> elements, see details in part New elements
}}

{{ABCD-Change
|element = PrimerReferenceLink
|status = Removed
|type = xs:string
|min = 0
|documentation = Link to the first reference of the reverse primer
|path = /DNASample/Amplifications/Amplification/AmplificationPrimers/AmplificationPrimerReverse/PrimerReferenceLink
|comments = deleted; instead use of a more generic <code>Primer</code> elements, see details in part New elements
}}


{{ABCD-Change
|element = Chromatograms
|status = Removed
|type = Container
|min = 0
|documentation = Container element for chromatograms of an individual DNA sequence
|path = /DNASample/Amplifications/Amplification/Amplification/Sequencings/Sequencing/SingleSequencings/SingleSequencing
|comments = deleted; per single read (single sequencing) only one chromatogram required
}}

=Changed elements=
{{ABCD-Change
|element = Quality
|status = Changed
|type = xs:string
|min = 0
|documentation = DNA or tissue quality estimation
|path = /DNASample/Quality
|comments = type changed to xs:string; vocabulary deleted
}}

{{ABCD-Change
|element = ChromatogramFireURI
|status = Changed
|type = xs:anyURI
|min = 0
|documentation = Link to the chromatogram of an individual DNA sequence (single read)
|path = /DNASample/Amplifications/Amplification/Sequencings/Sequencing/SingleSequencings/SingleSequencing
|comments = changed to minOccure = "0" (no longer unbounded)
}}

=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
}}

{{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
|content = Image+
}}

{{ABCD-Change
|element = Image
|status = New
|type = Container
|min = 1
|max = unbounded
|documentation = Container element for information on images of the DNA sample (e.g. agarose gel images)
|path = /DNASample/Images/Image
|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 = Primer
|min = 1
|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 = PrimerSequence?, PrimerName?, PrimerReferenceCitation?, PrimerReferenceLink?
}}

{{ABCD-Change
|element = CloningPrimers
|status = New
|type = Container
|min = 1
|max = unbounded
|documentation = Container element for cloning primers
|path = /DNASample/Amplifications/Amplification/Sequencings/Sequencing/CloningPrimers
|content = CloningPrimer+
}}

{{ABCD-Change
|element = CloningPrimer
|status = New
|type = Primer
|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 = PrimerSequence?, PrimerName?, PrimerReferenceCitation?, PrimerReferenceLink?
}}

{{ABCD-Change
|element = SequencingPrimer
|status = Changed
|type = Primer
|min = 1
|max = unbounded
|documentation = Container element for an individual sequencing primer
|path = /DNASample/Amplifications/Amplification/Sequencings/Sequencing/SingleSequencings/SingleSequencing/SequencingPrimers/SequencingPrimer
|comments = uses the generic element <code>Primer</code> now
|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
}}

[[Category: Terms documentations]]