[DAS2] sources.rnc

Andrew Dalke dalke at dalkescientific.com
Wed Nov 8 01:36:50 UTC 2006

> I have nothing substantial to change in sources.rnc.  Just clean up the
> notes and comments:
> ** Can this note be improved?
>   # NOTE: the segments capability has optional 'coordinates'
>   # element to state that it implements the given coordinate
>   # system.  I could not figure out how to do that in Relax-NG.
> ##attribute coordinates { text },

   # NOTE: the segments capability has an optional 'coordinates'
   # element describing the supported coordinate system.  Because
   # of the 'attribute *' a few lines above there is an ambiguity.
   # Any capability element may have a 'coordiantes' attribute
   # so there's no need for an explicit schema declaration.
   #attribute coordinates { text }?,

> ** Several references to "At present...." should be removed

At present those have been removed.

> ** Can this note be cleaned-up?  Which Andreas?  Is this the
> ** full list of reserved words?

I listed Andreas earlier, regarding his use of "das1:types",
etc. in a capability 'type'.  I've added those as reserved

As to the one for
> # 'Chromosome', 'Clone', 'Contig', 'Scaffold', etc.

I've updated that to

   # For a full list of the "authority" and "source" values see
   #    http://das.sanger.ac.uk/registry/help_coordsys.jsp

   # This refers to the "physical dimension" of the annotated data.
   # The following names are reserved: "Chromosome", "Clone",
   #   "Contig", "Gene_ID", "NT_Contig", "Protein Sequence",
   #   "Protein Structure", "Scaffold", "Volume Map".
   # The 'source' attribute corresponds to the coordinate
   # system 'type' in the DAS registry.
   attribute source { text },

   # The name of an authority/institution that defines the accession
   # codes of a coordinate system or that provides a gene-build.
   # See the DAS registry help for a full list of reserved names.
   # A partial list is: "BDGP", "EMBL", "Entrez", "KEGG", "MGI", "NCBI",
   #  "PDBresnum", "SDG" and "UniProt" and "ZFISH".
   attribute authority { text },

Changes made and das2_schemas.rnc has been checked in.

					dalke at dalkescientific.com

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