X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=schemas%2Fvamsas.xsd;h=80f5d91272c45a6b85aa985963fb7b989bb74946;hb=0a868a9601b051aeaf439a8d73f6fc070044a02c;hp=e735b8b1ee34abd504218d74115d205c4a2ea019;hpb=70c14705beeec3b821757fb755a18d7d1692f3ef;p=vamsas.git diff --git a/schemas/vamsas.xsd b/schemas/vamsas.xsd index e735b8b..80f5d91 100644 --- a/schemas/vamsas.xsd +++ b/schemas/vamsas.xsd @@ -1,333 +1,308 @@ - + - - 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 - - + 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 + 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 - + Primary Key for vamsas object referencing + - - Properties. Generally, these are mutable so an application - should check them each time. This may change depending on - the context of the property + 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" - + 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 + Primary Key for vamsas object referencing - + + + + + + + + node identity and mapping data between tree + representations and vamsas document objects + + + + + + + reference to one or more trees containing + the node being described. + + + - - objects with - modifiable=false will not be - modified by a vamsas client - update + String uniquely identifying a particular + node in the referenced tree according to the format of + the tree representation that is referenced. + - + - - + + - - Primary Key for vamsas object referencing - + Primary Key for vamsas object referencing - + + + + + + base type for citing arbitrary links between vamsas objects + + + + - - objects with modifiable=false will not be - modified by a vamsas client update + Optional human readable description of the relationship - - - + + + Primary Key for vamsas object referencing + + + + + + List of one or more vamsas object + references + + + + + + + + + + Short name for this node + + + + + Descriptive text for this node + + + + + Direct associations between this node and any vamsas + objects + + + + + + + Primary Key for vamsas object referencing + + + + - - Named and typed property string - + 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 - + 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 - - - - 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 + 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 position within the associated object's coordinate system - + - + - - a region from start to end, with flag for - inclusivity of terminii - + 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 + 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. - + 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. - + 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 - + 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. - + TODO: specify this - we have considered taking the GO + evidence codes as a model for assessing a measure of quality to an + annotation. - + - - Ordered set of optionally named float - values for the whole 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. - + Note:These are mutable so an application should check + them each time. - - Primary Key for vamsas object referencing + 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 - + - - 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 - + 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 @@ -336,34 +311,22 @@ - - Specifies a named and typed value used to perform - some data transformation. - - - LATER: experiment with xml validation of property - set prototypes for services - + 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 - + 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 - + 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 @@ -373,25 +336,16 @@ - - 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) - + 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 + Reference Frame for rangeType specfication @@ -399,14 +353,11 @@ - - - Defines the origin and series of operations applied - directly to the object that references it. - + Defines the origin and series of operations applied directly to + the object that references it. @@ -414,65 +365,44 @@ - - Who - + Who - - With which application - + With which application - + - - Did what - + Did what - + - - When - + When - + - - additional information - + additional information - + - - parameter for the action - + parameter for the action - + - - bioinformatic objects input to - action + bioinformatic objects input to action - + - - Primary Key for vamsas object - referencing + Primary Key for vamsas object referencing @@ -484,204 +414,114 @@ - - A collection of sequences, alignments, trees and - other things. + A collection of sequences, alignments, trees and other things. + TODO: Add a title field and properties for programs that can + present the user with different distinct datasets For the moment, the program + just presents them as a list and perhaps lets the user work out which dataset it + wants based on the alignments that it contains. (Dominik and Jim 7th June 2007) - - a primary or secondary sequence record - from which all other sequences may be - derived - + 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 - - - + 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 - - - - + + + + the local mapType maps from the parent + sequence coordinate frame to the reference + frame defined by the dbRef element. + The mapped mapType is the mapped range defined + on the dbRef element's reference frame. + Conventionally, the unit attribute defaults to 1, or + will be inferred from the local sequence's + dictionary type and any dictionary type associated + with the database being mapped to. + However, it may be used to avoid ambiguity. + + + + + + + + + - - + + - + - - TODO Database - Naming - Convention: - either start - using LSID (so - change type to - URI) or leave - this as an - uncontrolled/unspecified - string ID - + 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 - - + 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 ? - + 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 + + + explicitly named cross reference to + other objects in the document. + + - + - - Primary Key for vamsas - object referencing + Primary Key for vamsas object referencing - + - - symbol class for sequence + symbol class for sequence @@ -689,145 +529,134 @@ - + - - Annotate over positions and regions of a - dataset sequence - + + A mapping between the specified 'local' and 'mapped' sequence coordinate frames. + The step size between each coordinate frame depends on the sequence + dictionary types, or alternatively specified in the optional unit + attribute on each range element. - + - + - + - - annotation is associated - with a particular dataset - sequence - + Object on which the local + range is defined. + + + Object on which the mapped + range is defined. + + + - + + + + 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. + 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 - + TODO: decide if this flag is + redundant - when true it would suggest that + the annotationElement values together form a + graph + + + annotation is associated with + a range on a particular group of alignment + sequences + + + - - + + - + + + + + Annotate over + positions and regions of the + ungapped sequence in the context of + the alignment + + + + + - - - - 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 - + Primary Key for vamsas object + referencing - + - - Dataset Sequence - from which this - alignment - sequence is - taken from - + Dataset Sequence from which + this alignment sequence is taken from + - + - - typical properties may be - additional alignment score - objects - + 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 + - - + + - - Primary Key for vamsas object referencing - + Primary Key for vamsas object referencing @@ -920,207 +720,147 @@ - - per-site symbolic and/or quantitative annotation - - - SecondaryStructure and display character (from - Jalview) have been subsumed into the glyph element - + 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 - + Free text at this position - + - - Discrete symbol - possibly graphically - represented + 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 - + 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 + 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 - + 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 - + true means the annotation element appears between the + specified position and the next - - Primary Key for vamsas object referencing - + Primary Key for vamsas object referencing - - - - + + + + - - additional typed properties - + additional typed properties - - + + - - Data specific to a particular type and version of - vamsas application - + Data specific to a particular type and version of vamsas + application - + - + - - Data available to just a - particular user - + 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 - + 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 - + + + Version string describing the application specific + data storage version used - + + + + Canonical name of application + + @@ -1130,45 +870,30 @@ - - General data container to attach a typed - data object to any vamsas object - + 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 - + true implies data will be decompresses with Zip + before presenting to application - + - - Type of arbitrary data - TODO: decide - format - use (extended) MIME types ? - + Type of arbitrary data - TODO: decide format - use + (extended) MIME types ? - + - - Object the arbitrary data is associated - with + Object the arbitrary data is associated with - + - - Primary Key for vamsas object - referencing + Primary Key for vamsas object referencing @@ -1178,8 +903,58 @@ - - + + + + + Two sets of ranges defined between objects - usually sequences, indicating which + regions on each are mapped. + + + + + + + + + + + + + + + + + + + + + + + + + number of dictionary symbol widths involved in each + mapped position on this sequence (for example, 3 for a dna sequence exon + region that is being mapped to a protein sequence). This is optional, + since the unit can be usually be inferred from the dictionary type of + each sequence involved in the mapping. + + + + + + + + + Contains lock information: locktype:ApplicationHandle locktype is + 'local' or 'full' A lock is only valid if the ApplicationHandle resolves to a living + application in the vamsas session. A local lock means that the application has + locked changes to all local properties on the object. A full lock means that the + application has locked changes to all properties on the object, and any objects that + it holds references to. + + +