From 70c14705beeec3b821757fb755a18d7d1692f3ef Mon Sep 17 00:00:00 2001 From: jprocter Date: Mon, 22 May 2006 15:50:20 +0000 Subject: [PATCH] post-meeting refinements and commenting. git-svn-id: https://svn.lifesci.dundee.ac.uk/svn/repository/trunk@221 be28352e-c001-0410-b1a7-c7978e42abec --- schemas/vamsas.xsd | 1202 ++++++++++++++++++++++++++++++++++++-------- schemas/vamsasDocument.xsd | 1 + 2 files changed, 999 insertions(+), 204 deletions(-) diff --git a/schemas/vamsas.xsd b/schemas/vamsas.xsd index 25ccc55..e735b8b 100644 --- a/schemas/vamsas.xsd +++ b/schemas/vamsas.xsd @@ -1,164 +1,480 @@ - - - - Specify positions and/or regions on the principle dimension of some associated vamsas object - TODO: this is abstract. should provide context to scope the range of ids for each use - 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 - - - - + + + + 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 + + + + Primary Key for vamsas object referencing + + - objects with modifiable=false will not be modified by a vamsas client update + + + + 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 - + + 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 + + + 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 + + - objects with modifiable=false will not be modified by a vamsas client update + + + + 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 + + - objects with modifiable=false will not be modified by a vamsas client update + + + + objects with modifiable=false will not be + modified by a vamsas client update + + - + - - 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 + + + + + + + + + + + Primitive labelled URI object + + + - - 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 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 + + + + + + + - provenance contains source of annotation - polymorphism for having collection of single points, - or ordered set of regions with polarity (start.lt.end or end.lt.start) + + 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. + - - - - - - Note:These are mutable so an application should check them each time. - + + + + 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 + + + Primary Key for vamsas object referencing + + + + + + + objects with modifiable=false will not be + modified by a vamsas client update + + - - 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 + + - - Annotation with the same non-empty group name are grouped together - - - + + - Specifies a named and typed value used to perform some data transformation. + Specifies a named and typed value used to perform + some data transformation. - LATER: experiment with xml validation of property set prototypes for services + 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 + + + - - + + + + - Selects all or part of a collection of vamsas objects as a named input to some transformation process. + 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 + + + - + - 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. - Who - With which application - Did what - When - additional information - parameter for the action - bioinformatic objects input to action + + + + Who + + + + + + + With which application + + + + + + + Did what + + + + + + + When + + + + + + + additional information + + + + + + + parameter for the action + + + + + + + bioinformatic objects input to + action + + + - Primary Key for vamsas object referencing + + + + Primary Key for vamsas object + referencing + + @@ -167,225 +483,703 @@ - A collection of sequences, alignments, trees and other things. + + + A collection of sequences, alignments, trees and + other things. + + - 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 + + + + - + + + + + + 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 + + + + + + + - - - - Primary Key for vamsas object referencing + + + + 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 + + + + Primary Key for vamsas + object referencing + + + + + + + symbol class for sequence + + - symbol class for sequence - + - Annotate over positions and regions of dataset sequences + + + Annotate over positions and regions of a + dataset sequence + - - - annotation may be associated with a particular sequence lying within the same reference frame as the rangeType's objRef + + + + + + + + annotation is associated + with a particular dataset + sequence + + - + - - Annotate over positions and regions of the alignment - - - - annotation may be associated with a particular sequence lying within the same reference frame as the rangeType's objRef - - - - + - TODO: hard to distinguish this from the alignment features element. Do we merge them and leave the applications + This is annotation over the + coordinate frame defined by all + the columns in the alignment. - - - - - - - - Primary Key for vamsas object referencing - + + + + + + + + + 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 sequences in the alignment - TODO: have to remove id rangeSpec or require it to be the same as dataset sequence reference - - + + + + + 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 alignment score objects - - + + + + typical properties may be + additional alignment score + objects + + + + - - - 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 + + + + 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 + + - 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 - true means the annotation element appears between the specified position and the next - Primary Key for vamsas object referencing + + + + 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 + + + + + + + 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 + + + - - - - - 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 - - - - + + + + + + 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 + + + + + + - - + + diff --git a/schemas/vamsasDocument.xsd b/schemas/vamsasDocument.xsd index 17547c7..2834313 100644 --- a/schemas/vamsasDocument.xsd +++ b/schemas/vamsasDocument.xsd @@ -19,6 +19,7 @@ + -- 1.7.10.2