<directory>
  <urn name="urn:open-bio.org:alphabet:dna">
    <description>
The DNA alphabet. DNA is composed from four nucleotides. Read a biochemistry
or genetics introductory textbook to find out more. Commonly, the nucleotides
are reprsented by the four letters a, g, c and t. However, this is not a
formal requirement for a resource to declare this alphabet as its type.
    </description>
  </urn>
  <urn name="urn:open-bio.org:alphabet">
    <description>
A namespace within which to store alphabet identifiers. Alphabets should
represent URNs that represent objects of the type identified by
urn:open-bio.org:type:alphabet, and any useage outside of this is not supported.
    </description>
  </urn>
  <urn name="urn:open-bio.org:alphabet:protein">
    <description>
The protein alphabet. Proteins are composed from amino-acids. To find out more,
read a biochemistry or genetics text book. It is common for protein sequences
to be represented by characters, but this is not a formal requirement for
a resource to publish an alphabet equal to this identifier.
    </description>
  </urn>
  <urn name="urn:open-bio.org:alphabet:rna">
    <description>
The RNA alphabet. RNA is composed from four nucleotides. Read a biochemistry
or genetics introductory textbook to find out more. Commonly, the nucleotides
are reprsented by the four letters a, g, c and u. However, this is not a
formal requirement for a resource to declare this alphabet as its type.
    </description>
  </urn>
  <urn name="urn:open-bio.org:format:embl">
    <description>
The EMBL file format associated with entries in the EMBL sequence database.
    </description>
  </urn>
  <urn name="urn:open-bio.org:format:enzyme">
    <description>
The Enzyme database entry format. The enzyme database can be downloaded from
the ebi at:

  ftp://ftp.ebi.ac.uk/pub/databases/enzyme/

For an example of a file in this format, see:

  ftp://ftp.ebi.ac.uk/pub/databases/enzyme/enzyme.dat

The format is described more fully in

  ftp://ftp.ebi.ac.uk/pub/databases/enzyme/enzyser.txt
    </description>
  </urn>
  <urn name="urn:open-bio.org:format:genbank">
    <description>
The GENBANK file format associated with the GENBANK sequence database.
    </description>
  </urn>
  <urn name="urn:open-bio.org:format">
    <description>
A namespace for OBDA URNs that define formats. All URNs within this namespace
must be of the type urn:open-bio.org:type:format. Any URN in this namespace that
is not of that type is not a valid OBDA URN.
    </description>
  </urn>
  <urn name="urn:open-bio.org:format:swissprot">
    <description>
The SWISSPROT file format as used in the SWISSPROT sequence database.
    </description>
  </urn>
  <urn name="urn:open-bio.org">
    <description>
This is the root namespace for all OBDA URNs. All OBDA URNs should be prefixed
by urn:open-bio.org as described in the file naming/open-bio_urns.txt in the
module obda-specs in the cvs repository located at
pub.open-bio.org:/home/repository/obf-common.
    </description>
  </urn>
  <urn name="urn:open-bio.org:type:alphabet">
    <description>
A biological sequence alphabet. Biological sequences are often represented as
strings of characters. However, in differnt circumstances, the same characters
can represent different things. For example, in DNA, the 't' character
represents tyrosine. In Protein, this same character represents tryptophan.

Associating alphabets with these sequences disambiguates their interpretation.
Alphabets do not define a mapping to or from strings, but should be used
wherever the type of the content of a sequence needs to be stated.
    </description>
  </urn>
  <urn name="urn:open-bio.org:type:format">
    <description>
A file format. Many file formats are used in bioinformatics. Entities of this
type identify a format. The format can be used to choose how to treat a file.
The format is not expected to be resolvable to a formal deffinition of the
file structure using OBDA-supplied functionality. Different applications may
chose to process a stream with the same format URN in different ways. This
type of URN is purely there to identify the format of the stream, not the
manner in which it should be processed.
    </description>
  </urn>
  <urn name="urn:open-bio.org:type">
    <description>
The namespace for URNs that identify data types. It is expected that the types
that are given IDs will be very general in nature, such as Sequence and
File Format. All types are of type urn:open-bio.org:type:type. Any URN in the
type namespace that is not of this type is not conforming to the OBDA
specification for this namespace.
    </description>
  </urn>
  <urn name="urn:open-bio.org:type:type">
    <description>
The OBDA URN that identifies the concept of 'type'. In a given language, this
may map to the types of data structures, or objects. Alternativel, it may
map to a particular set of keys being present in a map, or a term in an
ontology. This is not important. The important thing is that we have unique
identifiers for common types that all projects use and interact with.
    </description>
  </urn>
</directory>
