X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=schemas%2Fvamsas.xsd;h=946b609094b646e034a33e72c85be565aece056a;hb=1890f014c0a312a7a2203c878e4802e3eb914e47;hp=cdbc00377adfc387fd8f02258493dfe8f2524c5b;hpb=de558440c776d39285b02d970a21df7002e85a3c;p=vamsas.git diff --git a/schemas/vamsas.xsd b/schemas/vamsas.xsd index cdbc003..946b609 100644 --- a/schemas/vamsas.xsd +++ b/schemas/vamsas.xsd @@ -1,7 +1,10 @@ - + 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 @@ -60,28 +63,27 @@ - - node identity and mapping data between tree representations and vamsas document objects - + node identity and mapping data between tree + representations and vamsas document objects - - reference to one or more trees containing the node being described. - + reference to one or more trees containing + the node being described. - - String uniquely identifying a particular node in the referenced tree according to the format of the tree representation that is referenced. + String uniquely identifying a particular + node in the referenced tree according to the format of + the tree representation that is referenced. - + @@ -99,25 +101,25 @@ - - base type for citing arbitrary links between vamsas objects + base type for citing arbitrary links between vamsas objects - - Optional human readable description of the relationship + Optional human readable description of the relationship - Primary Key for vamsas object referencing + Primary Key for vamsas object referencing + - List of one or more vamsas object references + List of one or more vamsas object + references @@ -137,7 +139,8 @@ - Direct associations between this node and any vamsas objects + Direct associations between this node and any vamsas + objects @@ -266,7 +269,8 @@ - + @@ -374,7 +378,7 @@ Did what - + When @@ -410,7 +414,11 @@ - 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) @@ -433,47 +441,56 @@ - - - From: Offset to first - position in dataset sequence record that - this database entry maps to To: Offset - to last position in dataset sequence - record that this database entry maps to - Start: Offset to first last position in - database entry that first (or offset) - position in sequence maps to End: 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 + 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 + 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 ? @@ -482,17 +499,17 @@ - Primary Key for vamsas object + Primary Key for vamsas object referencing - + - - explicitly named cross reference to other objects in the document. - + explicitly named cross reference to + other objects in the document. @@ -514,20 +531,33 @@ - - - - - - - - - - - - - - + + + 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. + + + + + + + + + Object on which the local + range is defined. + + + + + Object on which the mapped + range is defined. + + + + + @@ -554,7 +584,8 @@ - + This is annotation over the coordinate frame defined by all the columns in the alignment. @@ -566,21 +597,24 @@ - + - TODO: decide if this flag is + 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 + annotation is associated with + a range on a particular group of alignment + sequences - + @@ -591,34 +625,38 @@ - - - - Annotate over + + + + Annotate over positions and regions of the ungapped sequence in the context of the alignment - - - - - - - - - - TODO: + + + + + + + + + + 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 + Primary Key for vamsas object referencing - + - Dataset Sequence from which + Dataset Sequence from which this alignment sequence is taken from @@ -699,7 +738,8 @@ - + specifies the symbol dictionary for this glyph - eg utf8 (the default), aasecstr_3 or @@ -776,8 +816,10 @@ Data available to just a particular user - - + + @@ -865,42 +907,53 @@ - - - - Offset to first position in dataset sequence record that start - position on 'onto' maps to - - - - - Offset to last position in dataset sequence record that end - position on 'onto' maps to - - - - - Offset to first 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 - - + + + 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. - + 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.