DNA extension Version2: Difference between revisions
Jump to navigation
Jump to search
No edit summary |
|||
| Line 1: | Line 1: | ||
=Deleted elements= | =Deleted elements= | ||
Most of deleted elements in the DNA extension has been moved to the core ABCD2.06. See details below | |||
{{ABCD-Change | {{ABCD-Change | ||
| Line 49: | Line 49: | ||
|documentation = Container element for information about the amplification forward primer | |documentation = Container element for information about the amplification forward primer | ||
|path = /DNASample/Amplifications/Amplification/AmplificationPrimers/AmplificationPrimerForward | |path = /DNASample/Amplifications/Amplification/AmplificationPrimers/AmplificationPrimerForward | ||
|comments = deleted; | |comments = deleted; instead use of a more generic <code>Primer</code> elements, see details in part New elements | ||
|content = PrimerName?, PrimerSequence?, PrimerReferenceCitation?, PrimerReferenceLink? | |content = PrimerName?, PrimerSequence?, PrimerReferenceCitation?, PrimerReferenceLink? | ||
}} | }} | ||
| Line 60: | Line 60: | ||
|documentation = Name of the forward primer | |documentation = Name of the forward primer | ||
|path = /DNASample/Amplifications/Amplification/AmplificationPrimers/AmplificationPrimerForward/PrimerName | |path = /DNASample/Amplifications/Amplification/AmplificationPrimers/AmplificationPrimerForward/PrimerName | ||
|comments = deleted; | |comments = deleted; instead use of a more generic <code>Primer</code> elements, see details in part New elements | ||
}} | }} | ||
| Line 70: | Line 70: | ||
|documentation = DNA sequence of the forward primer (5' to 3') | |documentation = DNA sequence of the forward primer (5' to 3') | ||
|path = /DNASample/Amplifications/Amplification/AmplificationPrimers/AmplificationPrimerForward/PrimerSequence | |path = /DNASample/Amplifications/Amplification/AmplificationPrimers/AmplificationPrimerForward/PrimerSequence | ||
|comments = deleted; | |comments = deleted; instead use of a more generic <code>Primer</code> elements, see details in part New elements | ||
}} | }} | ||
| Line 80: | Line 80: | ||
|documentation = First reference of the forward primer | |documentation = First reference of the forward primer | ||
|path = /DNASample/Amplifications/Amplification/AmplificationPrimers/AmplificationPrimerForward/PrimerReferenceCitation | |path = /DNASample/Amplifications/Amplification/AmplificationPrimers/AmplificationPrimerForward/PrimerReferenceCitation | ||
|comments = deleted; | |comments = deleted; instead use of a more generic <code>Primer</code> elements, see details in part New elements | ||
}} | }} | ||
| Line 90: | Line 90: | ||
|documentation = Link to the first reference of the forward primer | |documentation = Link to the first reference of the forward primer | ||
|path = /DNASample/Amplifications/Amplification/AmplificationPrimers/AmplificationPrimerForward/PrimerReferenceLink | |path = /DNASample/Amplifications/Amplification/AmplificationPrimers/AmplificationPrimerForward/PrimerReferenceLink | ||
|comments = deleted; | |comments = deleted; instead use of a more generic <code>Primer</code> elements, see details in part New elements | ||
}} | }} | ||
| Line 101: | Line 101: | ||
|documentation = Container element for information about the amplification reverse primer | |documentation = Container element for information about the amplification reverse primer | ||
|path = /DNASample/Amplifications/Amplification/AmplificationPrimers/AmplificationPrimerReverse | |path = /DNASample/Amplifications/Amplification/AmplificationPrimers/AmplificationPrimerReverse | ||
|comments = deleted; | |comments = deleted; instead use of a more generic <code>Primer</code> elements, see details in part New elements | ||
|content = PrimerName?, PrimerSequence?, PrimerReferenceCitation?, PrimerReferenceLink? | |content = PrimerName?, PrimerSequence?, PrimerReferenceCitation?, PrimerReferenceLink? | ||
}} | }} | ||
| Line 112: | Line 112: | ||
|documentation = Name of the reverse primer | |documentation = Name of the reverse primer | ||
|path = /DNASample/Amplifications/Amplification/AmplificationPrimers/AmplificationPrimerReverse/PrimerName | |path = /DNASample/Amplifications/Amplification/AmplificationPrimers/AmplificationPrimerReverse/PrimerName | ||
|comments = deleted; | |comments = deleted; instead use of a more generic <code>Primer</code> elements, see details in part New elements | ||
}} | }} | ||
| Line 122: | Line 122: | ||
|documentation = DNA sequence of the reverse primer (5' to 3') | |documentation = DNA sequence of the reverse primer (5' to 3') | ||
|path = /DNASample/Amplifications/Amplification/AmplificationPrimers/AmplificationPrimerReverse/PrimerSequence | |path = /DNASample/Amplifications/Amplification/AmplificationPrimers/AmplificationPrimerReverse/PrimerSequence | ||
|comments = deleted; | |comments = deleted; instead use of a more generic <code>Primer</code> elements, see details in part New elements | ||
}} | }} | ||
| Line 132: | Line 132: | ||
|documentation = First reference of the reverse primer | |documentation = First reference of the reverse primer | ||
|path = /DNASample/Amplifications/Amplification/AmplificationPrimers/AmplificationPrimerReverse/PrimerReferenceCitation | |path = /DNASample/Amplifications/Amplification/AmplificationPrimers/AmplificationPrimerReverse/PrimerReferenceCitation | ||
|comments = deleted; | |comments = deleted; instead use of a more generic <code>Primer</code> elements, see details in part New elements | ||
}} | }} | ||
| Line 142: | Line 142: | ||
|documentation = Link to the first reference of the reverse primer | |documentation = Link to the first reference of the reverse primer | ||
|path = /DNASample/Amplifications/Amplification/AmplificationPrimers/AmplificationPrimerReverse/PrimerReferenceLink | |path = /DNASample/Amplifications/Amplification/AmplificationPrimers/AmplificationPrimerReverse/PrimerReferenceLink | ||
|comments = deleted; | |comments = deleted; instead use of a more generic <code>Primer</code> elements, see details in part New elements | ||
}} | }} | ||
=New elements= | =New elements= | ||
Revision as of 09:36, 18 September 2013
Deleted elements
Most of 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; instead 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; instead 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; instead 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; instead use of a more generic
Primer elements, see details in part New elements
PrimerReferenceLink(link)
| Core | Deleted | xs:string | minOccurs: 0 | maxOccurs: 1 |
Link to the first reference of the forward primer
Element Path:
/DNASample/Amplifications/Amplification/AmplificationPrimers/AmplificationPrimerForward/PrimerReferenceLink
Comments:
deleted; instead 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; instead 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; instead 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; instead 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; instead use of a more generic
Primer elements, see details in part New elements
PrimerReferenceLink(link)
| Core | Deleted | xs:string | minOccurs: 0 | maxOccurs: 1 |
Link to the first reference of the reverse primer
Element Path:
/DNASample/Amplifications/Amplification/AmplificationPrimers/AmplificationPrimerReverse/PrimerReferenceLink
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