From: jprocter Date: Thu, 18 May 2006 17:01:14 +0000 (+0000) Subject: current vamsas type document. Still being worked on and refined. X-Git-Tag: Release_0.2~301 X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=6944ad87af9e39a36c8dc42c077f836bee01599a;p=vamsas.git current vamsas type document. Still being worked on and refined. git-svn-id: https://svn.lifesci.dundee.ac.uk/svn/repository/trunk@219 be28352e-c001-0410-b1a7-c7978e42abec --- diff --git a/schemas/vamsas.xsd b/schemas/vamsas.xsd index 4511438..bf17ca3 100644 --- a/schemas/vamsas.xsd +++ b/schemas/vamsas.xsd @@ -2,17 +2,49 @@ + + + Specify positions and/or regions on the principle dimension of some associated vamsas objects + 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 + + + + + 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 @@ -20,27 +52,116 @@ - + + 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 + + + + + + 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) + + + + + + + + + + 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 + + + annotation may be associated with a particular sequence lying within the same reference frame as the rangeType's objRef + + + + + + + + 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. + + + + + + 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 + @@ -48,45 +169,51 @@ + A collection of sequences, alignments, trees and other things. + a primary or secondary sequence record from which all other sequences may be derived + + + - + Primary Key for vamsas object referencing + - - + Primary Key for vamsas object referencing + + symbol class for sequence - - - - - - - - - - - + Annotate over positions and regions of dataset sequences + + + + + + Annotate over positions and regions of the alignment + + + @@ -96,7 +223,8 @@ - + Primary Key for vamsas object referencing + @@ -104,53 +232,90 @@ - + + + + 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 + + + + + + + Primary Key for vamsas object referencing + + + typical properties may be 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 + @@ -158,20 +323,55 @@ + Data available to just a particular user + + + + + + + + + + + + + Data available to just a specific instance of the 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 + + + + +