DNA extension Version2

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Revision as of 09:43, 18 September 2013 by WikiSysop (talk | contribs) (→‎Deleted elements)
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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

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


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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