This
page
is
part
of
the
FHIR
Specification
(v4.0.1:
R4
(v5.0.0-ballot:
R5
Ballot
-
Mixed
Normative
and
STU
see
ballot
notes
)
in
it's
permanent
home
(it
will
always
be
available
at
this
URL).
).
The
current
version
which
supercedes
this
version
is
5.0.0
.
For
a
full
list
of
available
versions,
see
the
Directory
of
published
versions
.
Page
versions:
R5
R4B
R4
R3
R2
Work
Group
|
Maturity
Level
:
|
|
Nucleic
acids
are
defined
by
three
distinct
elements:
the
base,
sugar
and
linkage.
Individual
substance/moiety
IDs
will
be
created
for
each
of
these
elements.
The
nucleotide
sequence
will
be
always
entered
in
the
5’-3’
direction.
11.24.1
Scope
and
Usage
This
XML
representation
for
a
resource
is
referenced
by
SubstanceSpecification
described
using
this
format:
<name xmlns="http://hl7.org/fhir" (attrA="value")><!-- from Resource: id, meta, implicitRules, and language --> <nameA><!--
1..1 type description of content --><nameA> <nameB[x]><!-- 0..1 type1|type1 description --></nameB[x]> <nameC> <!-- 1..* --> <nameD><!-- 1..1 type>Relevant elements --></nameD> </nameC> <name>
Using this format:
value
attribute,
extension
URLs
in
url
attribute
on
an
extension,
and
id
property
on
)
denotes
that
<?xml
encoding="UTF-8"
?>
)
application/fhir+xml
.
This
page
contains
some
JSON
examples
for
double
stranded
RNA
or
DNA.
The
number
associated
with
the
subunit
followed
by
the
number
associated
to
purposes
of
comparison
between
the
residue
shall
be
specified
in
increasing
order.
two
formats.
The
underscore
“”
shall
be
used
as
separator
as
follows:
“Subunitnumber
Residue”
areaOfHybridisation
:
string
[0..1]
(TBC)
oligoNucleotideType
:
CodeableConcept
[0..1]
Subunit
Index
of
linear
sequences
of
nucleic
acids
in
order
of
decreasing
length.
Sequences
of
formats
page
has
a
comparison
between
the
same
length
will
be
ordered
by
molecular
weight.
Subunits
that
have
identical
sequences
will
be
repeated
XML
and
have
sequential
subscripts
subunit
:
integer
[0..1]
JSON
formats
.
An
element
that
has
a
controlled
vocabulary.
Since
the
sequence
is
represented
from
the
5'
to
maximum
cardinality
of
>1
(e.g.
x..*
in
the
3'
end,
definitions)
may
occur
more
than
once
in
the
5’
prime
nucleotide
instance.
In
XML,
this
is
simply
done
by
repeating
the
letter
at
the
first
position
in
the
sequence.
A
separate
representation
would
be
redundant
fivePrime
:
XML
element
multiple
times.
So
a
CodeableConcept
[0..1]
The
nucleotide
present
at
the
3’
terminal
shall
be
specified
based
on
a
controlled
vocabulary.
Since
the
sequence
is
represented
from
the
5'
to
the
3'
end,
the
5’
prime
nucleotide
is
the
letter
at
the
last
position
in
the
sequence.
A
separate
representation
would
be
redundant
threePrime
:
CodeableConcept
[0..1]
Linkage
The
entity
that
links
the
sugar
residues
together
should
also
be
captured
for
nearly
all
naturally
occurring
nucleic
acid
the
linkage
is
a
phosphate
group.
XML
like
this:
<code>
<coding>
<system value="http://snomed.info/sct"/>
<code value="104934005"/>
</coding>
<coding>
<system value="http://loinc.org"/>
<code value="2947-0"/>
</coding>
</code>
For
many
synthetic
oligonucleotides
phosphorothioate
linkages
are
often
seen.
Linkage
connectivity
is
assumed
to
be
3’-5’.
If
the
linkage
is
either
3’-3’
or
5’-5’
comparison,
In
JSON,
this
should
be
specified
connectivity
:
string
[0..1]
Each
linkage
will
be
registered
as
a
fragment
and
have
is
done
by
using
an
ID
identifier
:
Identifier
[0..1]
Each
linkage
will
be
registered
as
a
fragment
and
have
at
least
one
name.
A
single
name
shall
be
assigned
to
each
linkage
name
:
string
[0..1]
Residues
shall
be
captured
as
described
in
5.3.6.8.3
residueSite
:
string
[0..1]
Sugar
The
Substance
ID
of
the
sugar
or
sugar-like
component
that
make
up
array
type,
also
using
the
nucleotide
identifier
:
Identifier
[0..1]
singular
name:
{
"coding": [
{
"system" : "http://snomed.info/sct",
"code" : "104934005"
},
{
"system" : "http://loinc.org",
"code" : "2947-0"
}
]
}
FHIR
elements
with
primitive
datatypes
are
listed
represented
in
order
of
decreasing
length;
sequences
of
the
same
length
will
be
ordered
by
molecular
weight;
subunits
that
have
identical
sequences
will
be
repeated
multiple
times
subunit
[0..*]
an
XML
Template
element
with
a
value
attribute.
<code value="abc"/> <!-- code --> <date value="1972-11-30"/> <!-- dateTime --> <deceased value="false" /> <!-- boolean --> <count value="23" /> <!-- integer -->
For
comparison,
this
is
represented
in
JSON
Template
as
"code" : "abc", "date" : "1972-11-30", "deceased" : false, "count" : 23
Turtle
Template
If
the
value
has
an
id
attribute,
or
extensions,
then
these
are
represented
as
follows:
<birthDate id="314159" value="1970-03-30" >
<extension url="http://example.org/fhir/StructureDefinition/text">
<valueString value="Easter 1970"/>
</extension>
</birthDate>
Changes
since
R3
This
resource
did
not
exist
in
Release
2
This
analysis
is
available
as
XML
or
The
JSON
.
Structure
representation
is
more
complex:
"birthDate": "1970-03-30",
"_birthDate": {
"id": "314159",
"extension" : [ {
"url" : "http://example.org/fhir/StructureDefinition/text",
"valueString" : "Easter 1970"
}]
}
Complex
datatypes
Nucleic
acids
(types
that
contain
named
elements
of
other
types)
are
defined
by
three
distinct
elements:
the
base,
sugar
and
linkage.
Individual
substance/moiety
IDs
will
be
created
represented
using
an
element
that
containing
an
element
for
each
of
these
elements.
The
nucleotide
sequence
will
be
always
entered
in
the
5’-3’
direction
Elements
defined
element
in
Ancestors:
id
,
meta
,
implicitRules
,
language
,
text
,
contained
,
extension
,
modifierExtension
sequenceType
Σ
0..1
CodeableConcept
The
type
of
the
sequence
shall
be
specified
based
on
a
controlled
vocabulary
numberOfSubunits
Σ
0..1
integer
The
number
of
linear
sequences
of
nucleotides
linked
through
phosphodiester
bonds
shall
be
described.
Subunits
would
be
strands
of
nucleic
acids
that
datatype.
Complex
datatypes
can
have
ids,
which
are
tightly
associated
typically
through
Watson-Crick
base
pairing.
NOTE:
If
not
specified
represented
as
id
attributes,
in
the
reference
source,
the
assumption
is
that
there
is
1
subunit
areaOfHybridisation
Σ
0..1
string
The
area
of
hybridisation
shall
be
same
manner
as
described
if
applicable
for
double
stranded
RNA
or
DNA.
The
number
associated
with
primitives.
For
example:
<Patient xmlns="http://hl7.org/fhir">
<text>
<status value="generated" />
<div xmlns="http://www.w3.org/1999/xhtml"><p>...</p></div>
</text>
<name id="f2">
<use value="official" />
<given value="Karen" />
<family id="a2" value="Van" />
</name>
</Patient>
For comparison, this is represented in JSON as:
{
"resourceType" : "Patient",
"name" : [{
"id" : "f2",
"use" : "official" ,
"given" : [ "Karen" ],
"family" : "Van",
"_family" : {"id" : "a2"}
}],
"text" : {
"status" : "generated" ,
"div" : "<div xmlns=\"http://www.w3.org/1999/xhtml\"><p>...</p></div>"
}
}
Things to note here are:
http://hl7.org/fhir
namespace,
except
for
the
div
element
which
is
in
text
is
represented
directly
as
This
specification
provides
schema
definitions
for
all
the
same
length
will
be
ordered
by
molecular
weight.
Subunits
that
have
identical
sequences
will
be
repeated
resource
and
have
sequential
subscripts
sequence
Σ
datatype
content
models
it
describes.
The
base
schema
is
called
"
fhir-base.xsd
0..1
string
"
and
defines
all
the
datatypes
and
base
infrastructure
types.
In
addition,
there
is
a
schema
for
each
resource
and
a
common
schema
fhir-all.xsd
Actual
nucleotide
sequence
notation
from
5'
to
3'
end
using
standard
that
includes
all
the
resource
schemas.
For
schema
processors
that
do
not
like
circular
includes,
there
is
a
single
letter
codes.
schema
that
contains
everything.
In
addition
to
the
base
sequence,
sugar
and
type
of
phosphate
or
non-phosphate
linkage
should
w3c
schema
files,
this
specification
also
be
captured
length
Σ
0..1
integer
The
length
provides
Schematron
files
that
enforce
most
of
the
sequence
shall
be
captured
sequenceAttachment
Σ
0..1
Attachment
(TBC)
fivePrime
Σ
0..1
CodeableConcept
The
nucleotide
present
at
constraints
defined
for
the
5’
terminal
shall
datatypes
and
resources,
though
some
are
only
expressible
and
validatable
using
FHIRPath
.
These
are
packaged
as
files
for
each
resource.
XML
that
is
exchanged
SHALL
be
specified
based
on
a
controlled
vocabulary.
Since
valid
against
the
sequence
is
represented
from
w3c
schema
and
Schematron,
though
being
valid
against
the
5'
schema
and
Schematron
is
not
sufficient
to
be
a
conformant
instance:
this
specification
makes
several
rules
that
cannot
be
checked
by
either
mechanism.
Operational
systems
may
choose
to
use
schema
tools
to
check
validation,
but
are
not
required
to
do
so.
Exchanged
content
SHALL
NOT
specify
the
3'
end,
schema
or
even
contain
the
5’
prime
nucleotide
is
schema
instance
namespace
in
the
letter
at
resource
itself.
Given
the
first
position
way
extensions
work,
applications
reading
XML
resources
will
never
encounter
unknown
elements.
However,
once
an
application
starts
trading
with
other
applications
that
conform
to
later
versions
of
this
specification,
unknown
XML
elements
may
be
encountered.
Applications
MAY
choose
to
ignore
unknown
elements
to
foster
forwards
compatibility
in
the
sequence.
A
separate
representation
this
regard,
but
may
also
choose
not
to
-
which
would
be
redundant
threePrime
the
normal
behavior
for
schema
generated
applications.
In
addition
to
the
3’
terminal
shall
be
specified
based
on
validation
schema,
this
specification
provides
a
controlled
vocabulary.
Since
the
sequence
is
represented
from
set
of
schemas
suitable
for
code
generation.
These
schemas
describe
the
5'
same
XML
syntax,
but
apply
less
validation
to
create
schemas
that
work
better
with
code
generation
tooling.
Specifically,
these
schemas
are
generated
without
any
xsd:choice
elements,
for
code
generators
that
don't
deal
with
choices
well.
Implementers
that
use
these
schemas
will
need
to
enforce
the
3'
end,
the
5’
prime
nucleotide
is
the
letter
at
the
last
position
in
correct
usage
of
the
sequence.
A
separate
representation
would
be
redundant
linkage
Σ
0..*
BackboneElement
The
linkages
between
sugar
residues
will
also
be
captured
connectivity
Σ
choice
elements
0..1
string
without
schema
support.
Implementers
making
use
of
schema-driven
code
generation
tooling
need
to
consider
how
to
handle
the
decimal
datatype.
The
entity
that
links
the
sugar
residues
together
should
also
be
captured
for
nearly
all
naturally
occurring
nucleic
acid
the
linkage
is
a
phosphate
group.
For
many
synthetic
oligonucleotides
phosphorothioate
linkages
are
often
seen.
Linkage
connectivity
decimal
datatype
is
assumed
defined
to
be
3’-5’.
If
precision
aware
-
that
is,
that
implementers
need
to
preserve
the
linkage
difference
between
"2.0"
and
"2.00"
-
this
is
either
3’-3’
or
5’-5’
ubiquitously
considered
important
in
handling
observed
data
in
healthcare.
Both
schemas
map
this
should
be
specified
identifier
Σ
0..1
Identifier
Each
linkage
will
be
registered
as
datatype
to
a
fragment
union
of
xsd:decimal
and
have
an
ID
name
Σ
0..1
xsd:double
,
but
the
base
W3C
schema
decimal
type
string
Each
linkage
will
is
specified
not
to
be
registered
precision
aware.
Schema
driven
implementations
vary
as
a
fragment
to
how
precision
is
handled.
Implementers
will
need
to
determine
how
their
generated
code
handles
decimals/doubles
and
have
at
least
one
name.
A
single
name
shall
be
assigned
consider
changing
the
type
for
decimal
in
their
schema
from
xsd:decimal/double
to
each
linkage
xsd:string
.
Specifically,
implementers
may
wish
to
change:
<xs:simpleType name="decimal-primitive">
<xs:union memberTypes="xs:decimal xs:double"/>
</xs:simpleType>
to this:
<xs:simpleType name="decimal-primitive">
<xs:restriction base="xs:string">
<xs:pattern value="-?(0|[1-9][0-9]*)(\.[0-9]+)?([eE][+-]?[0-9]+)?"/>
</xs:restriction>
</xs:simpleType>
Note that most code generation frameworks ignore the pattern restriction.
Resources
and/or
Bundles
may
be
captured
as
described
in
5.3.6.8.3
sugar
Σ
0..*
BackboneElement
5.3.6.8.1
Sugar
ID
(Mandatory)
identifier
Σ
digitally
signed
(see
Bundle
0..1
Identifier
and
Provenance
The
Substance
ID
of
).
This
specification
defines
the
sugar
following
method
for
canonicalizing
FHIR
resources,
when
represented
as
XML.
Each
XML
instance
or
sugar-like
component
fragment
that
make
up
the
nucleotide
name
Σ
0..1
string
The
name
is
part
of
the
sugar
or
sugar-like
component
that
make
up
collection
being
signed
SHALL:
'
instead
of
"
)
<?xml
version="1.0"
encoding="UTF-8"?>
http://www.w3.org/2006/12/xml-c14n11
)
This
canonicalization
method
is
identified
by
the
URI
http://hl7.org/fhir/canonicalization/xml
.
The
following
additional
canonicalization
URIs
are
also
defined:
| http://hl7.org/fhir/canonicalization/xml#data |
The
narrative
(
Resource.text
)
Resource.text
,
not
Resource.text.div
)
|
| http://hl7.org/fhir/canonicalization/xml#static |
In
addition
to
narrative
(Resource.text),
the
Resource.meta
element
is
|
| http://hl7.org/fhir/canonicalization/xml#narrative |
The
Resource.id
and
Narrative
(
Resource.text
|
| http://hl7.org/fhir/canonicalization/xml#document |
The
|
These
canonicalization
methods
allow
systems
the
3'
end,
the
5’
prime
nucleotide
is
the
letter
at
flexibility
to
sign
the
last
position
in
various
portions
of
the
sequence.
A
separate
representation
would
be
redundant
threePrime
:
CodeableConcept
[0..1]
Linkage
The
entity
resource
that
links
the
sugar
residues
together
should
also
be
captured
matter
for
nearly
all
naturally
occurring
nucleic
acid
the
linkage
is
a
phosphate
group.
For
many
synthetic
oligonucleotides
phosphorothioate
linkages
are
often
seen.
Linkage
connectivity
is
assumed
to
be
3’-5’.
If
workflow
the
linkage
is
either
3’-3’
or
5’-5’
this
should
be
specified
connectivity
:
string
[0..1]
Each
linkage
signature
serves.
These
canonicalization
algorithms
do
not
work
for
enveloped
signatures.
This
will
be
registered
as
a
fragment
researched
and
have
an
ID
identifier
:
Identifier
[0..1]
Each
linkage
will
be
registered
as
addressed
in
a
fragment
and
have
at
least
one
name.
A
single
name
shall
be
assigned
to
each
linkage
name
:
string
[0..1]
Residues
shall
be
captured
as
described
future
release.
This
specification
may
define
additional
canonicalizations
in
5.3.6.8.3
residueSite
:
string
[0..1]
Sugar
The
Substance
ID
of
the
sugar
or
sugar-like
component
that
make
up
the
nucleotide
identifier
:
Identifier
[0..1]
future,
and
other
specifications
might
also
define
additional
canonicalization
methods.
The nameImplementation Note: One consequence of signing the
sugar or sugar-like component that make up the nucleotide name : string [0..1] The residuesdocument is thatcontain a given sugar willURLs, identifiers and internal references are frozen and cannot becaptured. The order of given residues willchanged. This might becaptured in the 5‘-3‘direction consistent with the base sequences listed above residueSite : string [0..1] The linkages between sugar residues willa desired feature, but it may alsobe captured linkage [0..*] 5.3.6.8.1 Sugar ID (Mandatory) sugarcripple interoperability between closed ecosystems where re-identification[0..*] Subunits are listed in orderfrequently occurs. For this reason, it is recommended that systems consider carefully the impact ofdecreasing length; sequencesany signature processes. The impact ofthe same length will be ordered by molecular weight; subunits that have identical sequences will be repeated multiple times subunit [0..*] XML Template < <!-- from --> <!-- from --> <</sequenceType> < < <</oligoNucleotideType> < < < < <</sequenceAttachment> <</fivePrime> <</threePrime> < < <</identifier> < < </linkage> < <</identifier> < < </sugar> </subunit> </SubstanceNucleicAcid> JSON Template { "resourceType" : "", // from // from " " " " " " " " " " " " " " " " }], " " " " }] }] }signatures on Document bundlesTurtle Templateand their related processes is the most well understood use of digital signatures.@prefix fhir: <http://hl7.org/fhir/> . [ a fhir:; fhir:nodeRole fhir:treeRoot; # if this is the parser root # from # from fhir: fhir: fhir: fhir: fhir: fhir: fhir: fhir: fhir: fhir: fhir: fhir: fhir: fhir: fhir: fhir: ], ...; fhir: fhir: fhir: fhir: ], ...; ], ...; ] Changes since Release 3
This
resource
did
not
exist
Note
that
following
normalization
procedures
in
Release
2
This
analysis
is
available
as
XML
or
JSON
.
See
can
assign
the
Profiles
&
Extensions
same
normalized
text
to
resources
with
slightly
different
meanings,
since
leading
whitespace
matters
in
markdown
text,
and
the
alternate
definitions:
Master
Definition
XML
+
JSON
,
XML
Schema
/
Schematron
+
JSON
Schema
,
ShEx
(for
Turtle
)
+
see
the
extensions
&
representation
serializes
the
dependency
analysis
markdown
datatype
using
attributes.