Difference between revisions of "DNA extension Version2"

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This document contains information on removed, changed and new elements in the DNA extension for ABCD. The new extension is not in use yet and will be published in October 2013. We will keep you informed about the ongoing process.
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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=
 
=Removed elements=
Line 42: Line 42:
 
|path = /DNASample/ExtractionMethod
 
|path = /DNASample/ExtractionMethod
 
|comments = moved to core ABCD2.06 <code>/DataSets/DataSet/Units/Unit/SpecimenUnit/Preperation/PreparationProcess</code>
 
|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>
 
}}
 
}}
  
Line 94: Line 114:
 
|comments = deleted; instead use of a more generic <code>Primer</code> elements, see details in part New elements
 
|comments = deleted; instead use of a more generic <code>Primer</code> elements, see details in part New elements
 
}}
 
}}
−
 
  
 
{{ABCD-Change
 
{{ABCD-Change
Line 145: Line 164:
 
|path = /DNASample/Amplifications/Amplification/AmplificationPrimers/AmplificationPrimerReverse/PrimerReferenceLink
 
|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
 
|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)
 
}}
 
}}
  
Line 156: Line 207:
 
|documentation = Method used for determination of DNA or tissue quality parameters
 
|documentation = Method used for determination of DNA or tissue quality parameters
 
|path = /DNASample/QualityCheckMethod
 
|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
 
 
}}
 
}}
  
Line 179: Line 219:
 
|content = Image+
 
|content = Image+
 
}}
 
}}
−
 
  
 
{{ABCD-Change
 
{{ABCD-Change
Line 185: Line 224:
 
|status = New
 
|status = New
 
|type = Container
 
|type = Container
−
|min = 0
+
|min = 1
 
|max = unbounded
 
|max = unbounded
 
|documentation = Container element for information on images of the DNA sample (e.g. agarose gel images)
 
|documentation = Container element for information on images of the DNA sample (e.g. agarose gel images)
Line 274: Line 313:
 
|element = AmplificationPrimer
 
|element = AmplificationPrimer
 
|status = New
 
|status = New
−
|type = Container
+
|type = Primer
−
|min = 0
+
|min = 1
 
|max = unbounded
 
|max = unbounded
 
|documentation = Container element for an individual amplification primer
 
|documentation = Container element for an individual amplification primer
 
|path = /DNASample/Amplifications/Amplification/AmplificationPrimers/AmplificationPrimer
 
|path = /DNASample/Amplifications/Amplification/AmplificationPrimers/AmplificationPrimer
 
|comments = uses the generic element <code>Primer</code>
 
|comments = uses the generic element <code>Primer</code>
−
|content = Primer+
+
|content = PrimerSequence?, PrimerName?, PrimerReferenceCitation?, PrimerReferenceLink?
 
}}
 
}}
  
Line 287: Line 326:
 
|status = New
 
|status = New
 
|type = Container
 
|type = Container
−
|min = 0
+
|min = 1
 +
|max = unbounded
 
|documentation = Container element for cloning primers
 
|documentation = Container element for cloning primers
 
|path = /DNASample/Amplifications/Amplification/Sequencings/Sequencing/CloningPrimers
 
|path = /DNASample/Amplifications/Amplification/Sequencings/Sequencing/CloningPrimers
Line 296: Line 336:
 
|element = CloningPrimer
 
|element = CloningPrimer
 
|status = New
 
|status = New
−
|type = Container
+
|type = Primer
 
|min = 0
 
|min = 0
 
|documentation = Container element for an individual cloning primer
 
|documentation = Container element for an individual cloning primer
 
|path = /DNASample/Amplifications/Amplification/Sequencings/Sequencing/CloningPrimers/CloningPrimer
 
|path = /DNASample/Amplifications/Amplification/Sequencings/Sequencing/CloningPrimers/CloningPrimer
 
|comments = uses the generic element <code>Primer</code>
 
|comments = uses the generic element <code>Primer</code>
−
|content = Primer+
+
|content = PrimerSequence?, PrimerName?, PrimerReferenceCitation?, PrimerReferenceLink?
 
}}
 
}}
  
Line 307: Line 347:
 
|element = SequencingPrimer
 
|element = SequencingPrimer
 
|status = Changed
 
|status = Changed
−
|type = Container
+
|type = Primer
−
|min = 0
+
|min = 1
 
|max = unbounded
 
|max = unbounded
 
|documentation = Container element for an individual sequencing primer
 
|documentation = Container element for an individual sequencing primer
−
|path = /DNASample/Amplifications/Amplification/Sequencings/Sequencing/SequencingPrimers/SequencingPrimer
+
|path = /DNASample/Amplifications/Amplification/Sequencings/Sequencing/SingleSequencings/SingleSequencing/SequencingPrimers/SequencingPrimer
 
|comments = uses the generic element <code>Primer</code> now
 
|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?
 
|content = PrimerSequence?, PrimerName?, PrimerReferenceCitation?, PrimerReferenceLink?
 
}}
 
}}
Line 374: Line 403:
 
|path = /DNASample/Amplifications/Amplification/Sequencings/Sequencing/SingleSequencings/SingleSequencing/SequenceLength
 
|path = /DNASample/Amplifications/Amplification/Sequencings/Sequencing/SingleSequencings/SingleSequencing/SequenceLength
 
}}
 
}}
 +
 +
[[Category: Terms documentations]]

Latest revision as of 11:34, 9 January 2023

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

Preservation(link)
Core Removed 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 /DataSets/DataSet/Units/Unit/SpecimenUnit/Preservations/Preservation

ExtractionStaff(link)
Core Removed xs:string minOccurs: 0 maxOccurs: 1
Person who carried out DNA extraction
Element Path:
/DNASample/ExtractionStaff
Comments:
moved to core ABCD2.06 /DataSets/DataSet/Units/Unit/SpecimenUnit/Preperation/PreparationAgent/Person/FullName

ExtractionDate(link)
Core Removed xs:date minOccurs: 0 maxOccurs: 1
Date of DNA extraction
Element Path:
/DNASample/ExtractionDate
Comments:
moved to core ABCD2.06 /DataSets/DataSet/Units/Unit/SpecimenUnit/Preperation/PreparationDate

ExtractionMethod(link)
Core Removed xs:string minOccurs: 0 maxOccurs: 1
Method or extraction protocol applied
Element Path:
/DNASample/ExtractionMethod
Comments:
moved to core ABCD2.06 /DataSets/DataSet/Units/Unit/SpecimenUnit/Preperation/PreparationProcess

BlockedUntil(link)
Core Removed xs:date minOccurs: 0 maxOccurs: 1
Date until ordering of DNA samples is blocked
Element Path:
/DNASample/BlockedUntil
Comments:
moved to core ABCD2.06 /DataSets/DataSet/Units/Unit/LoanRestriction/BlockedUntil

ProvidedBy(link)
Core Removed xs:string minOccurs: 0 maxOccurs: 1
Outside person or company which delivered or donated the DNA sample
Element Path:
/DNASample/ProvidedBy
Comments:
moved to core ABCD2.06 Unit/SpecimenUnit/Acquisition/AcquiredFrom

AmplificationPrimerForward(link)
Core Removed 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; instead use of a more generic Primer elements, see details in part New elements

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

PrimerSequence(link)
Core Removed 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; instead use of a more generic Primer elements, see details in part New elements

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


AmplificationPrimerReverse(link)
Core Removed 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; instead use of a more generic Primer elements, see details in part New elements

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

PrimerSequence(link)
Core Removed 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; instead use of a more generic Primer elements, see details in part New elements

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



Chromatograms(link)
Core Removed Container minOccurs: 0 maxOccurs: 1
Container element for chromatograms of an individual DNA sequence
Element Path:
/DNASample/Amplifications/Amplification/Amplification/Sequencings/Sequencing/SingleSequencings/SingleSequencing
Comments:
deleted; per single read (single sequencing) only one chromatogram required

Changed elements

Quality(link)
Core Changed xs:string minOccurs: 0 maxOccurs: 1
DNA or tissue quality estimation
Element Path:
/DNASample/Quality
Comments:
type changed to xs:string; vocabulary deleted

ChromatogramFireURI(link)
Core Changed xs:anyURI minOccurs: 0 maxOccurs: 1
Link to the chromatogram of an individual DNA sequence (single read)
Element Path:
/DNASample/Amplifications/Amplification/Sequencings/Sequencing/SingleSequencings/SingleSequencing
Comments:
changed to minOccure = "0" (no longer unbounded)

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

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: 1 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 Primer minOccurs: 1 maxOccurs: unbounded
Container element for an individual amplification primer
Element Path:
/DNASample/Amplifications/Amplification/AmplificationPrimers/AmplificationPrimer
Content:
PrimerSequence?, PrimerName?, PrimerReferenceCitation?, PrimerReferenceLink?
Comments:
uses the generic element Primer

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

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

SequencingPrimer(link)
Core Changed Primer minOccurs: 1 maxOccurs: unbounded
Container element for an individual sequencing primer
Element Path:
/DNASample/Amplifications/Amplification/Sequencings/Sequencing/SingleSequencings/SingleSequencing/SequencingPrimers/SequencingPrimer
Content:
PrimerSequence?, PrimerName?, PrimerReferenceCitation?, PrimerReferenceLink?
Comments:
uses the generic element Primer now

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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