Vorba ID - Vamsas Object Request Broker Address ID (name
needs to be worked on): Suggest it could be of the form
documentRoot/datasetName/SequenceUID for a dataset sequence.
Alignment sequence:
documentRoot/datasetName/AlignmentId/SequenceUID for an
aligned form of a dataset sequence
contains unassociated trees and a number of analysis
sets
Primary Key for vamsas object referencing
objects with modifiable=false will not be
modified by a vamsas client update
Properties. Generally, these are mutable so an application
should check them each time. This may change depending on
the context of the property
Contains a named collection of trees
TODO: define
way of referencing leaves of global tree for any
sequence/alignment object.
SUggestion 1: Each named tree leafnode has a unique id (which may be unique in combination with trees own vorba ID).
Dataset sequences can be tagged with a property "vamsas:tree_leaf"
Primary Key for vamsas
object referencing
objects with
modifiable=false will not be
modified by a vamsas client
update
Primary Key for vamsas object referencing
objects with modifiable=false will not be
modified by a vamsas client update
Named and typed property string
The type specifies how the property will
be parsed. Empty property strings are
allowed, and can be used to prototype
the input to a document. TODO: specify
allowed types
Primitive labelled URI object
The URI
Specify an ordered set of positions and/or regions on the principle
dimension of some associated vamsas object
Keeping to jaxb-1.0 specification for the moment - this
choice should become a substitution group when we use
jaxb-2.0 capable bindings
a position within the associated object's
coordinate system
a region from start to end, with flag for
inclusivity of terminii
when false, a consecutive range like
'start=1, end=2' means the region lying
after position 1 and before position 2
Annotation for a rangeSpec - values can be attached for the whole specification, and to each position within the spec. following the orientation specified by the ordered set of rangeSpec (pos, seg) elements.
Short, meaningful name for the annotation - if this is absent, then the type string should be used in its place.
Human readable description of the annotation
TODO: specify this - we have considered taking the GO evidence codes as a model for assessing a measure of quality to an annotation.
Annotation Element position maps to
ordered positions defined by the
sequence of rangeType pos positions or
concatenated seg start/end segments.
Ordered set of optionally named float
values for the whole annotation
Note:These are mutable so an application
should check them each time.
Primary Key for vamsas object referencing
objects with modifiable=false will not be
modified by a vamsas client update
Annotation with the same non-empty group
name are grouped together
A Das Feature has both a type and a Type ID.
We go the route of requiring the type string
to be taken from a controlled vocabulary if
an application expects others to make sense
of it.
The type may qualified - so uniprot:CHAIN is a valid type name,
and considered distinct from someotherDB:CHAIN
Specifies a named and typed value used to perform
some data transformation.
LATER: experiment with xml validation of property
set prototypes for services
Named and typed property string
The type specifies how the property will
be parsed. Empty property strings are
allowed, and can be used to prototype
the input to a document. TODO: specify
allowed types
Selects all or part of a collection of vamsas
objects as a named input to some transformation
process. Many inputs with the same name imply a
group input (such as a collection of sequences)
Reference Frame for rangeType
specfication
Defines the origin and series of operations applied
directly to the object that references it.
Who
With which application
Did what
When
additional information
parameter for the action
bioinformatic objects input to
action
Primary Key for vamsas object
referencing
A collection of sequences, alignments, trees and
other things.
a primary or secondary sequence record
from which all other sequences may be
derived
Store a list of database
references for this
sequence record - with
optional mapping from
database sequence to the
given sequence record
Offset
to
first
position
in
dataset
sequence
record
that
this
database
entry
maps
to
Offset
to
last
position
in
dataset
sequence
record
that
this
database
entry
maps
to
Offset
to first
last
position
in
database
entry
that
first
(or
offset)
position
in
sequence
maps to
Offset
to last
position
in
database
entry
that
last
(offset)
position
in
sequence
maps to
TODO Database
Naming
Convention:
either start
using LSID (so
change type to
URI) or leave
this as an
uncontrolled/unspecified
string ID
Version must be
specified -
TODO: make some
specification of
the database
field from which
this accessionId
is taken from -
should that be a
special property
of the dbRef
object ?
Primary Key for
vamsas object
referencing
Primary Key for vamsas
object referencing
symbol class for sequence
Annotate over positions and regions of a
dataset sequence
annotation is associated
with a particular dataset
sequence
This is annotation over the
coordinate frame defined by all
the columns in the alignment.
TODO: decide if
this flag is
redundant - when
true it would
suggest that the
annotationElement
values together
form a graph
Annotate
over
positions
and
regions
of the
ungapped
sequence
in the
context
of the
alignment
TODO:
decide
if
this
flag
is
redundant
-
when
true
it
would
suggest
that
the
annotationElement
values
together
form
a
graph
Primary Key for
vamsas object
referencing
Dataset Sequence
from which this
alignment
sequence is
taken from
typical properties may be
additional alignment score
objects
Primary Key for vamsas object
referencing
objects with modifiable=false will
not be modified by a vamsas client
update
Primary Key for vamsas object referencing
per-site symbolic and/or quantitative annotation
SecondaryStructure and display character (from
Jalview) have been subsumed into the glyph element
Free text at this position
Discrete symbol - possibly graphically
represented
specifies the symbol
dictionary for this glyph -
eg utf8 (the default),
aasecstr_3 or
kd_hydrophobicity - the
content is not validated so
applications must ensure
they gracefully deal with
invalid entries here
TODO: specify a minimum list
of glyph dictionaries to get
us started and provide a way
for the vamsasClient to
validate their content if
regexes are specified
Ordered set of float values - an application
may treat the values together as a vector
with common support for a set of annotation
elements - but this is, again, not validated
so applications should deal gracefully with
varying numbers of dimensions
position with respect to the coordinate frame
defined by a rangeType specification
true means the annotation element appears
between the specified position and the next
Primary Key for vamsas object referencing
additional typed properties
Data specific to a particular type and version of
vamsas application
Data available to just a
particular user
Data available to just a
specific instance of the
application
VAMSAS/Pierre: Is this
data volatile ?
Application instances
may not be accessible
after the session has
closed - the user may
have to be presented
with the option of
picking up the data in
that instance
Version string describing the application specific data storage version used
Canonical name of application
General data container to attach a typed
data object to any vamsas object
true implies data will be decompresses
with Zip before presenting to
application
Type of arbitrary data - TODO: decide
format - use (extended) MIME types ?
Object the arbitrary data is associated
with
Primary Key for vamsas object
referencing