X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=schemas%2Fvamsas.xsd;h=e735b8b1ee34abd504218d74115d205c4a2ea019;hb=b0e8ba054e5c3d3cd256f78d3a7310e6e263630e;hp=26b9bd17dd721938c8f2dded710f43699135bae7;hpb=5fb0ffd7883f1723b9461a318c107b64a24de3f3;p=vamsas.git diff --git a/schemas/vamsas.xsd b/schemas/vamsas.xsd index 26b9bd1..e735b8b 100644 --- a/schemas/vamsas.xsd +++ b/schemas/vamsas.xsd @@ -1,46 +1,481 @@ - + + + + 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 + + + @@ -48,134 +483,703 @@ + + + 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 + + + - - - - - - - - - - - - - - - - + + + +