<!-- ********************************************************************* -->
<!--   AGAVE - Architecture for Genomic Annotation, Visualization and      -->
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<!-- AGAVE is designed to offer the life sciences community a              -->
<!-- comprehensive, extensible and open format for sharing genomic         -->
<!-- annotations. Information on AGAVE can be found at                     -->
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<!--                                                                       -->
<!--                                                                       -->
<!--   History:                                                            -->
<!--                                                                       -->
<!--   Jun. 30, 2000 version 2.0 Released with Prophecy 1.0                -->
<!--   Aug. 25, 2000 version 2.1 Released with Prophecy 1.1.2              --> 
<!--   Nov. 13, 2000 version 2.2 Released with Prophecy 2.0                -->
<!--   Jul.  3, 2001 version 2.3 Released with Propehcy 3.0                --> 
<!--                                                                       -->
<!-- ********************************************************************* -->

<!--                                                                       -->
<!-- sciobj - The XML document root.                                       -->
<!--                                                                       -->
<!-- The version is incremented when an incompatible change is made.       -->
<!-- The release changes to indicate compatible changes within a           -->
<!-- version.  An incompatible change causes a "fatal error" in an XML     -->
<!-- compliant parser when parsing data files formatted to a previous      -->
<!-- version of the DTD.  Compatible changes may cause non-fatal errors    -->
<!-- or warnings.                                                          -->
<!--                                                                       -->
<!-- Attributes:                                                           -->
<!--                                                                       -->
<!-- version: incremented to indicate incompatible changes.                -->
<!-- release: incremented to indicate compatible changes.                  -->
<!-- date:    The date this document was created.  The date does not       -->
<!--          specify when the data in the document was created, only      -->
<!--          when the data was assembled into this document. The date     -->
<!--          format is YYYY-MM-DD on the Gregorian calendar, as           -->
<!--          specified in W3C technical report                            -->
<!--          http://www.w3.org/TR/NOTE-datetime-970915                    -->
<!--                                                                       -->
<!ELEMENT sciobj  (bio_sequence* , contig* , computation* , chromosome*)>
<!ATTLIST sciobj  version  NMTOKEN "2" 
                  release  NMTOKEN "3" 
                  date     CDATA   #IMPLIED >

<!-- ********************************************************************* -->
<!--  Basic elements                                                       -->
<!--                                                                       -->
<!-- ********************************************************************* -->

<!--                                                                       -->
<!-- db_id is an identifier for an object in its source database.          -->
<!--                                                                       -->
<!-- Attributes:                                                           -->
<!--                                                                       -->
<!-- id:       a data identifier such as GenBank accession or PID.         -->
<!-- db_code:  a code for the data source, e.g. GenBank is "gb".           --> 
<!-- version:  version of the associated data.                             -->
<!--                                                                       -->
<!ELEMENT db_id EMPTY>
<!ATTLIST db_id  id       CDATA  #REQUIRED
                 version  CDATA  #IMPLIED
                 db_code  CDATA  #REQUIRED >

<!--                                                                       -->
<!-- element_id contains an IDREF.  Use when need to have an IDREF in an   -->
<!-- ELEMENT content model.  Useful for alternation of db_id or            -->
<!-- element_id                                                            -->
<!--                                                                       -->
<!-- Attributes:                                                           -->
<!--                                                                       -->
<!-- id: the XML ID of another ELEMENT                                     -->
<!--                                                                       -->
<!ELEMENT element_id EMPTY>
<!ATTLIST element_id  id IDREF  #REQUIRED >

<!--                                                                       -->
<!-- A user added note.                                                    -->
<!--                                                                       -->
<!ELEMENT note (#PCDATA )>


<!--                                                                       -->
<!-- A dataset name and version that identifies a set of annotations,      -->
<!-- for example                                                           -->
<!--                                                                       -->
<!--    dataset name="Prophecy" version="1.1.1"                            -->
<!--                                                                       -->
<!-- Attributes:                                                           -->
<!--                                                                       -->
<!-- name:    a dataset name                                               -->
<!-- version: version of the dataset                                       -->
<!--                                                                       -->
<!ELEMENT dataset EMPTY>
<!ATTLIST dataset name     CDATA   #REQUIRED
                  version  NMTOKEN #REQUIRED >


<!--                                                                       -->
<!-- related_annot relates sequence annotations and specifies the          -->
<!-- relationship type.  This allows relationships other than              -->
<!-- containment.  For example, a link between overlapping features can    -->
<!-- be created.                                                           -->
<!--                                                                       -->
<!-- Attributes:                                                           -->
<!--                                                                       -->
<!-- rel:   a relationship type name                                       -->
<!-- score: a score representing the strength of the relationship. Score   -->
<!--        is scaled to an integer from 0-100                             -->
<!--                                                                       -->
<!-- Content:                                                              -->
<!--                                                                       -->
<!-- element_id: A reference to a comp_result or seq_feature in the same   -->
<!--             document. Multiple references can be used because         -->
<!--             more than one annotation may be in the same               -->
<!--             relationship.                                             -->
<!-- property:   A property of the relationship such as a score or         -->
<!--             a description.                                            -->
<!--                                                                       -->
<!--                                                                       -->  
<!ELEMENT related_annot (element_id+, sci_property*)>
<!ATTLIST related_annot rel   CDATA  #REQUIRED
                        score CDATA  #IMPLIED>

<!--                                                                       -->
<!-- sci_property is a name-value pair.                                    -->
<!--                                                                       -->
<!-- We use SQL types to specify the data_type because they are a well     -->
<!-- established standard.  Using a diffent datatype set such as Java      -->
<!-- datatypes would be equally valid.                                     -->
<!--                                                                       -->
<!--                                                                       -->
<!-- Attributes:                                                           -->
<!--                                                                       -->
<!-- prop_type: The type of the property                                   -->                                             
<!-- data_type: indicates if the content should be interpreted as a        -->
<!--            number or a string                                         --> 
<!--                                                                       -->
<!ELEMENT sci_property  (#PCDATA )>
<!ATTLIST sci_property  prop_type  CDATA  #REQUIRED
                        data_type  (NUMBER | VARCHAR | LONG )  'NUMBER' >

<!--                                                                       -->
<!-- An assignment of type from a classification system.  For example,     -->
<!-- an element may be classified as a "gene" with id "BCHE" which is a    -->
<!-- concept in the HUGO classifcation system. This would be written as    -->
<!--                                                                       -->
<!-- classification code="HUGO"                                            -->
<!--                id="BCHE"                                              -->
<!--                type="gene"                                            -->
<!--                assigned_by="locuslink"                                -->
<!--                                                                       -->
<!-- Attributes:                                                           -->
<!--                                                                       -->
<!-- system: the classification system, e.g. "HUGO"                        -->
<!-- id:   the type id in the classification system.  For example, a       -->
<!--       gene label.                                                     -->
<!-- type: a type assignment such as "gene".                               -->
<!--                                                                       -->
<!-- assiged_by: person, organization, or algorithm who determined the     -->
<!--             classification.                                           -->
<!--                                                                       -->
<!--                                                                       -->
<!ELEMENT classification (description? , id_alias* , evidence? )> 
<!ATTLIST classification system      CDATA  #REQUIRED
                         id          CDATA  #REQUIRED
                         type        CDATA  #REQUIRED 
                         assigned_by CDATA  #IMPLIED >
<!--                                                                       -->
<!-- alternate ids in a classification                                     -->
<!--                                                                       -->
<!-- Attributes:                                                           -->
<!--                                                                       -->
<!-- id:   a type id in the classification system.                         -->
<!-- type: The reason for the alias, such as "withdrawn", "misspelling",   -->
<!--       "former".                                                       -->
<!--                                                                       -->
<!ELEMENT id_alias EMPTY>
<!ATTLIST id_alias id   CDATA #REQUIRED 
                   type CDATA #IMPLIED >

<!--                                                                       -->
<!-- Description.                                                          -->
<!--                                                                       -->
<!ELEMENT description  (#PCDATA )>


<!--                                                                       -->
<!-- A view is the range in a chromosome or contig which contains all      -->
<!-- available annotations.  Since the number of annotations in a          -->
<!-- chromosome or contig may be large, we have views to allow the         -->
<!-- annotations to be divided among different documents.                  -->
<!--                                                                       -->
<!-- Attributes:                                                           -->
<!--                                                                       -->
<!-- start:  the start position in the container's coordinate system.      -->
<!--         Must be an integer.                                           -->
<!-- length: The length of the view.                                       -->
<!--                                                                       -->
<!ELEMENT view  EMPTY>
<!ATTLIST view  start  CDATA #REQUIRED
                length CDATA #REQUIRED >
                  

<!-- ********************************************************************* -->
<!--   Computational results elements.                                     -->
<!--                                                                       -->
<!-- ********************************************************************* -->

<!--                                                                       -->
<!-- a computation element represents a particular run of an analysis      -->
<!-- algorithm.  A computation contains comp_input, comp_results, and      -->
<!-- possible comp_error if the computation fails.                         -->
<!--                                                                       -->
<!-- comp_results can contain sub comp_results in a result_group.          -->
<!--                                                                       -->
<!-- Attributes:                                                           -->
<!--                                                                       -->
<!-- element_id:        an XML ID for this ELEMENT                         -->
<!-- computation_id:    a unique key for database storage                  -->
<!-- algorithm:         Algorithm/program type                             -->
<!-- algorithm_version: The algorithm/program version                      -->
<!-- parameters:        Parameters that were used to run the program.      -->
<!-- target_database:   Database type that was used to perform             -->
<!--                    computation                                        -->
<!--                                                                       -->
<!--                                                                       -->
<!ELEMENT computation (comp_input? , dataset? , (comp_error | result_group | results)*)>
<!ATTLIST computation  element_id        ID       #IMPLIED
                       computation_id    NMTOKEN  #IMPLIED
                       algorithm         CDATA    #REQUIRED
                       algorithm_version CDATA    #IMPLIED
                       parameters        CDATA    #IMPLIED
                       target_database   CDATA    #IMPLIED >

<!--                                                                       -->
<!-- Computational Input element                                           -->
<!--                                                                       -->
<!-- This takes one or more db_ids or biosequences as input.               -->
<!-- Biosequences could be used when we want to include more info other    -->
<!-- than the identifier (e.g. species or the sequence itself).            -->
<!--                                                                       -->
<!ELEMENT comp_input (db_id | bio_sequence)+>

<!--                                                                       -->
<!-- For storing error messages from programs                              -->
<!-- The error message is the contents of the comp_error tag               -->
<!--                                                                       -->
<!-- Attributes:                                                           -->
<!--                                                                       -->
<!-- program:    name of program called                                    -->
<!-- arguments:  arguments of program                                      -->
<!-- errno:      formal error number (if available)                        -->
<!-- returncode: OS return code (if available)                             -->
<!-- source:     source of error (for multi-layer reporting)               -->
<!-- time:       time of error                                             -->
<!--                                                                       -->
<!ELEMENT comp_error (#PCDATA)>
<!ATTLIST comp_error   program     CDATA    #IMPLIED
                       arguments   CDATA    #IMPLIED
                       errorno     CDATA    #IMPLIED
                       returncode  CDATA    #IMPLIED
                       source      CDATA    #IMPLIED
                       time        CDATA    #IMPLIED>

<!--                                                                       -->
<!-- comp_result contains result alignments, scores, and other             -->
<!-- properties.  comp_results can be nested using a result_group          -->
<!--                                                                       -->
<!-- Attributes:                                                           -->
<!--                                                                       -->
<!-- element_id:   an XML ID for this ELEMENT                              -->
<!-- result_id:    a unique key for database storage                       -->
<!-- group_order:  is the order of a result when it appears inside a       --> 
<!--               group. The group_order is only needed as a database     -->
<!--               storage id.                                             -->
<!-- result_type:  a result type code, for example grail_exon for a        -->
<!--               Grail predicted Exon                                    -->
<!-- feature_type: an assignment of the computed result_type to a          -->
<!--               GenBank feature type.  Use "*alignment" for             -->
<!--               feature_type if the result is an alignment not          -->
<!--               interpreted as a feature.                               -->
<!--                                                                       -->
<!-- on_complement_strand: true when match is on complementary strand      -->
<!--                                                                       -->
<!-- confidence: an integer in the range 0-100.  It expresses the          -->
<!--             confidence in the result, and is usually a rough          --> 
<!--             summary of the algorithm scores.  Applications can use    -->
<!--             the confidence score for filtering, querying, and         -->
<!--             sorting.  We use an integer rather than a floating        -->
<!--             point because as a rough estimate there is no useful      -->
<!--             difference between an integral and a fractional score     -->
<!--             in this range.                                            -->
<!--                                                                       -->
<!-- align_length: the length of the alignment in the alignment units      -->
<!-- align_units:  the alignment length units                              -->
<!--                                                                       -->
<!ELEMENT comp_result  (note? , match_desc? , match_align? , query_region? , 
                        match_region? , result_property* , result_group* , 
                        related_annot*)>
<!ATTLIST comp_result  element_id           ID       #IMPLIED
                       result_id            NMTOKEN  #IMPLIED
                       group_order          NMTOKEN  #IMPLIED
                       result_type          CDATA    #REQUIRED
                       feature_type         CDATA    #IMPLIED
                       on_complement_strand  (true | false )  'false'
                       confidence           NMTOKEN  #IMPLIED 
                       align_length         NMTOKEN  #IMPLIED
                       align_units          (bp | AA) #IMPLIED >
<!--                                                                       -->
<!-- result_group is an association class that holds the group_id          -->
<!-- of a group of comp_results                                            -->
<!--                                                                       -->
<!-- Attributes:                                                           -->
<!--                                                                       -->
<!-- group_order: a unique key for database storage                        -->
<!--                                                                       -->
<!ELEMENT result_group  (comp_result+ )>
<!ATTLIST result_group  group_order NMTOKEN  '0' >

<!--                                                                       -->
<!--  results contain comp_results that are not grouped.                   -->
<!--                                                                       -->
<!ELEMENT results  (comp_result+ )>

<!--                                                                       -->
<!-- result_property holds result values such as blast P scores            -->
<!--                                                                       -->
<!-- We use SQL types to specify the data_type because they are a well     -->
<!-- established standard.  Using a diffent datatype set such as Java      -->
<!-- datatypes would be equally valid.                                     -->
<!--                                                                       -->
<!--                                                                       -->
<!-- Attributes:                                                           -->
<!--                                                                       -->
<!-- prop_type: The type of the property                                   -->                                             
<!-- data_type: indicates if the content should be interpreted as a        -->
<!--            number or a string                                         --> 
<!--                                                                       -->
<!ELEMENT result_property  (#PCDATA )>
<!ATTLIST result_property  prop_type  CDATA  #REQUIRED
                           data_type  (NUMBER | VARCHAR | LONG )  'NUMBER' >

<!-- description of an alignment               -->
<!--                                           -->
<!ELEMENT match_desc  (#PCDATA )>

<!-- the text representation of an alignment   -->
<!--                                           -->
<!ELEMENT match_align  (#PCDATA )>

<!-- query_region is the region of the query sequence described by a       --> 
<!-- comp_result.                                                          -->
<!--                                                                       -->
<!-- Attributes:                                                           -->
<!--                                                                       -->
<!-- start: start point on the query sequence                              -->                                                        
<!-- end:   end point on the query sequence                                -->
<!--                                                                       -->
<!ELEMENT query_region  (db_id? )>
<!ATTLIST query_region  start CDATA  #REQUIRED
                        end   CDATA  #REQUIRED >

<!-- match_region is the region of the match or hit sequence described     --> 
<!-- by a comp_result.  The match can be identified by db_id, an           -->
<!-- element_id containing an IDREF to a bio_sequence, or the              -->
<!-- match_region can contain a bio_sequence that represents the match.    -->
<!--                                                                       -->
<!-- Note that the IDREF should refer to a bio_sequence defined earlier    -->
<!-- the document to make it easy to use a SAX parser.                     -->
<!--                                                                       -->
<!-- Attributes:                                                           -->
<!--                                                                       -->
<!-- start: start point on the match sequence                              -->                                                        
<!-- end:   end point on the match sequence                                --> 
<!--                                                                       -->
<!ELEMENT match_region  (db_id | element_id | bio_sequence)? >
<!ATTLIST match_region  start CDATA  #REQUIRED
                        end   CDATA  #REQUIRED >

<!-- ********************************************************************* -->
<!-- Sequence related elements.                                            -->
<!--                                                                       -->
<!-- ********************************************************************* -->

<!--                                                                       -->
<!-- The chromosome element contains sub-assemblies of DNA such as         -->
<!-- contigs or BACs.                                                      -->
<!--                                                                       -->
<!-- Attributes:                                                           -->
<!--                                                                       -->
<!-- number:      The chromosome identifier, for example, "1", "2", "X".   -->
<!-- length:      THe base pair length of the chromosome                   -->
<!-- view_start:  The view_start and view_length specify the range of      -->
<!--              contig annotations that are included in this document.   -->
<!--              The view coordinates define a window on the contig       -->
<!--              data.                                                    -->
<!-- view_length: length of the view from view_start                       -->
<!--                                                                       -->
<!-- Content:                                                              -->
<!--                                                                       -->
<!-- view:   the range of the chromosome in which all available            -->
<!--         annotations are included in this document.                    -->
<!-- contig: an assembled DNA sequence.                                    -->
<!--                                                                       -->
<!ELEMENT chromosome (view? , contig*)>
<!ATTLIST chromosome number      CDATA    #IMPLIED 
                     length      NMTOKEN  #IMPLIED > 

<!--                                                                       -->
<!-- A bio_sequence represents a linear molecule such as DNA, RNA,         -->
<!-- or a protein. The bio_sequence element contains a primary identifier, -->
<!-- sequence, alternate identifiers, and cross references.                -->
<!--                                                                       -->
<!-- Attributes:                                                           -->
<!--                                                                       -->
<!-- element_id:  an XML ID for this ELEMENT                               -->
<!-- sequence_id: a unique key for database storage                        --> 
<!-- seq_length:  The length of the sequence                               -->
<!-- molecule_type: The sequence molecule type                             -->
<!-- organism_name: The organism name in form Genus Species                -->
<!-- taxon_id:      NCBI Taxonomy database identifier                      -->
<!-- clone_id:      Identifier of the clone from which this sequence was   -->
<!--                derived                                                -->
<!-- clone_library: the clone library                                      -->
<!-- chromosome:    the chromosome name                                    -->
<!-- map_position:  Cytogenetic Map position where sequence comes from     -->
<!-- ec_number:     The Enzyme commision number which serves to            -->
<!--                characterize the enzymatic activity of proteins        -->
<!--                using a hierarchical classification scheme             -->
<!-- create_date:   The date that the sequence was "created" or placed     -->
<!--                in the original source database. Not currently used.   -->
<!-- update_date:   date that sequence or annotation was updated.  Not     -->
<!--                currently used.                                        -->
<!--                                                                       -->
<!-- Content:                                                              -->
<!--                                                                       -->
<!-- xrefs:         cross-references to other sequences or annotations.    -->
<!-- map_location:  location of the sequence within a larger sequence      -->
<!--                such as a chromosome or contig.                        -->
<!--                                                                       -->
<!ELEMENT bio_sequence  (db_id , note? , description?, keyword*, sequence? , 
                         alt_ids? , xrefs? ,  sequence_map*, map_location* , 
                         classification*)>
<!ATTLIST bio_sequence  element_id    ID       #IMPLIED
                        sequence_id   NMTOKEN  #IMPLIED
                        seq_length    NMTOKEN  #IMPLIED
                        molecule_type  (DNA | mRNA | rRNA | tRNA | cDNA | AA )  #IMPLIED
                        organism_name CDATA    #IMPLIED
                        taxon_id      CDATA    #IMPLIED
                        clone_id      CDATA    #IMPLIED
                        clone_library CDATA    #IMPLIED
                        chromosome    CDATA    #IMPLIED
                        map_position  CDATA    #IMPLIED
                        ec_number     CDATA    #IMPLIED
                        create_date   CDATA    #IMPLIED
                        update_date   CDATA    #IMPLIED >

<!--                                                                       -->
<!-- seq_location contains a sequence location in GenBank format           -->
<!--                                                                       -->
<!-- the location format is defined on the NCBI web site. The location     -->
<!-- may have ambiguous start and end points, and it may be a join of      -->
<!-- many intervals.  For convenience applications may parse out the       -->
<!-- least start point and greatest end point and store them in the        -->
<!-- seq_location attributes.                                              -->
<!--                                                                       -->
<!-- Attributes:                                                           -->
<!--                                                                       -->
<!-- is_on_complement: true when feature is on complementary strand        -->
<!--                                                                       -->
<!-- least_start:  the smallest start point of the location.  For          -->
<!--               example, the least_start of "(<25.50)..100" is 25.      -->
<!-- greatest_end: the greatest end point of the location.  The            -->
<!--               greatest_end of "50..(100.110)" is 110.                 -->
<!--                                                                       -->
<!ELEMENT seq_location  (#PCDATA )>
<!ATTLIST seq_location is_on_complement (true | false )  #IMPLIED
                       least_start      NMTOKEN #IMPLIED
                       greatest_end     NMTOKEN #IMPLIED >

<!--                                                                       -->
<!-- A keyword.  Used in bio_sequence.                                     -->
<!--                                                                       -->
<!ELEMENT keyword  (#PCDATA )>

<!--                                                                       -->
<!-- A sequence of symbols representing a linear molecule such as DNA or   -->
<!-- a protein.                                                            -->
<!--                                                                       -->
<!-- Attributes:                                                           -->
<!--                                                                       -->
<!-- start: index of the first symbol in the sequence when the sequence    -->
<!--        is partial.  This is used in case there is a partial           -->
<!--        sequence, such as sequence data within a view.                 -->
<!--                                                                       -->
<!ELEMENT sequence  (#PCDATA )>
<!ATTLIST sequence  start NMTOKEN #IMPLIED>

<!--                                                                       -->
<!-- Alternate identifiers.  Used in bio_sequence.                         -->
<!--                                                                       -->
<!ELEMENT alt_ids  (db_id+ )>

<!--                                                                       -->
<!-- A list of cross references.                                           -->
<!--                                                                       -->
<!ELEMENT xrefs  (db_id | xref)+> 

<!--                                                                       -->
<!-- xref is a cross reference.  It optionally includes a relationship     -->
<!-- descriptor, e.g. protein, and a list of properties.                   -->
<!--                                                                       -->
<!--                                                                       -->
<!-- Attributes:                                                           -->
<!--                                                                       -->
<!-- relationship: The relationship between the cross-referenced           -->
<!--               bio_sequences                                           -->
<!--                                                                       -->  
<!ELEMENT xref (db_id, xref_property*)>
<!ATTLIST xref relationship  CDATA #IMPLIED>

<!--                                                                       -->
<!-- xref_property holds any data related to a cross reference             -->
<!--                                                                       -->
<!-- Attributes:                                                           -->
<!--                                                                       -->
<!-- prop_type: The type of the property                                   -->                                             
<!-- data_type: indicates if the content should be interpreted as a        -->
<!--            number or a string                                         -->
<!--                                                                       -->
<!ELEMENT xref_property  (#PCDATA )>
<!ATTLIST xref_property  prop_type  CDATA  #REQUIRED
                         data_type  (NUMBER | VARCHAR | LONG )  'VARCHAR' >


<!--                                                                       -->
<!-- The seq_feature element describes a feature of a bio_sequence region. -->
<!--                                                                       -->
<!--                                                                       -->
<!-- Attributes:                                                           -->
<!--                                                                       -->
<!-- element_id:   an XML ID for this ELEMENT                              -->
<!-- feature_type: The type of the feature.  Usually a GenBank feature     -->
<!--               type such as "exon".                                    -->
<!-- label:        a descriptive name used to refer to the feature.        -->
<!--               Usually corresponds to a GenBank /gene or /label        -->
<!--               qualifier.  Can be assigned by the user.                -->
<!-- Content:                                                              -->
<!--                                                                       -->
<!-- xrefs:         cross-references to annotations.                       -->
<!--                                                                       -->
<!ELEMENT seq_feature  (classification* , note? , seq_location , xrefs? , 
                        evidence? , qualifier* ,  seq_feature* , related_annot*)>
<!ATTLIST seq_feature element_id   ID     #IMPLIED
                      feature_type CDATA  #REQUIRED
                      label        CDATA  #IMPLIED >

<!--                                                                       -->
<!-- The gene element inherits the content and attributes of a seq_feature -->
<!-- and adds classifications and transcripts.                             -->
<!--                                                                       -->
<!--                                                                       -->
<!-- Content:                                                              -->
<!--                                                                       -->
<!-- classification: classification of the gene.  Element order is not     -->
<!--                 significant.                                          -->
<!--                                                                       -->
<!-- xrefs:      cross-references to annotations.                          -->
<!-- transcript: alternate splice forms of the gene.  The first            -->
<!--             transcript is the primary transcript.  The order of the   -->
<!--             following transcripts is not significant.                 -->
<!--                                                                       -->
<!ELEMENT gene (classification* , note? , seq_location , xrefs? , 
                evidence? , qualifier* , seq_feature* , related_annot* , 
                transcript*)>
<!ATTLIST gene  element_id   ID     #IMPLIED
                label        CDATA  #IMPLIED >

<!--                                                                       -->
<!-- The transcript element is a subset of exons from a gene model along   -->
<!-- with the possible translation of those exons into cds, mrna, and a    -->
<!-- predicted_protein                                                     -->
<!--                                                                       -->
<!ELEMENT transcript (exons , cds? , mrna? , predicted_protein?)>

<!--                                                                       -->
<!-- The exons element contains a subset of exons from a gene model that   -->
<!-- constitute a transcript.                                              -->
<!--                                                                       -->
<!-- Content:                                                              -->
<!--                                                                       -->
<!-- Each element_id refers to an exon seq_feature within the same gene.   -->
<!--                                                                       -->
<!ELEMENT exons (element_id+)>

<!--                                                                       -->
<!-- The cds element represents a CDS. We put bio_sequence here to support -->
<!-- annotation of the CDS. For example, the CDS could be annotated with   -->  
<!-- SNPs.                                                                 -->
<!--                                                                       -->
<!ELEMENT cds (bio_sequence)>

<!--                                                                       -->
<!-- The mrna element represents an mRNA. The bio_sequence supports        -->
<!-- annotation of the mRNA.  For example, the mRNA could be annotated     -->
<!-- to tell where cDNA starts and ends.                                   -->
<!--                                                                       -->
<!ELEMENT mrna (bio_sequence)>

<!--                                                                       -->
<!-- The predicted_protein element contains the translation of a           -->
<!-- transcript into a protein.  The bio_sequence allows annotation        -->
<!-- of the protein and cross references to known proteins.                -->
<!--                                                                       -->
<!ELEMENT predicted_protein (bio_sequence)>

<!--                                                                       -->
<!-- A qualifier-value pair.  Corresponds to GenBank feature qualifiers.   -->
<!--                                                                       -->
<!-- Attributes:                                                           -->
<!--                                                                       -->
<!-- qualifier_type: The type of the qualifier.  Usually a GenBank         --> 
<!--                 feature qualifier.                                    -->
<!--                                                                       -->                                            
<!-- data_type: indicates if the content should be interpreted as a        -->
<!--            number or a string                                         -->
<!--                                                                       -->
<!ELEMENT qualifier  (#PCDATA )>
<!ATTLIST qualifier  qualifier_type CDATA  #REQUIRED
                     data_type  (NUMBER | VARCHAR | LONG )  'VARCHAR' >

<!--                                                                       -->
<!-- The evidence element contains comp_results.  A computational result   -->
<!-- may be the evidence for the existence of a feature.  The evidence     -->
<!-- element may contain other types of evidence later.                    -->
<!--                                                                       -->
<!ELEMENT evidence  (element_id | comp_result)+>

<!-- ********************************************************************* -->
<!-- Sequence mapping elements                                             -->
<!--                                                                       -->
<!-- ********************************************************************* -->

<!--                                                                       --> 
<!-- A contig is an assembly of sequence fragments that may have come      -->
<!-- from a contiguous source sequence.  A contig may represent a          -->
<!-- Bacterial Artificial Chromosome (BAC).  contigs may be partially      -->
<!-- ordered, so a contig contains ordered and unordered fragments.        -->
<!--                                                                       -->
<!-- Attributes:                                                           -->
<!--                                                                       -->
<!-- length: the length is the sum of the lengths of all the contained     -->
<!--         sequences.                                                    -->
<!--                                                                       -->
<!-- Content:                                                              -->
<!--                                                                       -->
<!-- db_id: The identifier of the contig in its source database.           -->
<!-- view:  the range of the chromosome in which all available             -->
<!--        annotations are included in this document.                     -->
<!-- note:  A user added note.                                             -->
<!--                                                                       -->
<!-- fragment_order: depreacted. Use assembly instead.                     -->
<!--                                                                       -->
<!-- unordered_fragments: deprecated.  Use assembly instead.               -->
<!--                                                                       -->
<!-- assembly:     an assembly or ordering of segments such as BACs to     -->
<!--               make up the contig.  Use the bio_sequence               -->
<!--               map_location to provide a position for the segments     -->
<!--               within the contig.                                      -->
<!--                                                                       -->
<!-- bio_sequence: sub-sequences of the contig.                            -->
<!--                                                                       -->
<!-- map_location:  location of the sequence within a larger sequence      -->
<!--                such as a chromosome or contig.                        -->
<!--                                                                       -->
<!ELEMENT contig (db_id , view? , note? , fragment_order* , unordered_fragments? ,  assembly? , 
                  sequence? , sequence_map* ,  map_location* )>
<!ATTLIST contig length NMTOKEN  #REQUIRED >


<!--                                                                       -->
<!-- fragment_order is a container for fragments that have a relative      -->
<!-- ordering.  The ordering may have been determined computationally.     -->
<!--                                                                       -->
<!-- Attributes:                                                           -->
<!--                                                                       -->
<!-- group_id: a unique key for database storage                           -->
<!--                                                                       -->
<!-- Content:                                                              -->
<!--                                                                       -->
<!-- fragment_orientation is deprecated.  Use of bio_sequence with a       -->
<!-- map_location is more flexible.                                        -->
<!--                                                                       -->
<!-- bio_sequence: a sequence fragment within the group of ordered         -->
<!--               fragments.  It can be positioned relative to the        -->
<!--               group by its map_location.                              -->
<!--                                                                       -->
<!-- map_location:  location of the fragment_order within a larger         -->
<!--                sequence such as a contig.                             -->
<!--                                                                       --> 
<!ELEMENT fragment_order ((fragment_orientation+ | bio_sequence+) , map_location?) >
<!ATTLIST fragment_order group_id CDATA   #IMPLIED 
                         length   NMTOKEN #IMPLIED >

<!--                                                                       -->
<!-- unordered_fragments is a container for fragments that have no known   -->
<!-- relative ordering,                                                    -->
<!--                                                                       --> 
<!ELEMENT unordered_fragments  (bio_sequence+ )>

<!--                                                                       -->
<!-- contains the assembled bio_sequences in a contig.  Assembled          -->
<!-- sequences are contiguous and positioned within the contig.            --> 
<!--                                                                       --> 
<!ELEMENT assembly (bio_sequence | fragment_order)+ >
 
<!--                                                                       -->
<!-- fragment_orientation defines the orientation of a sequence fragment   -->
<!-- within an ordering.                                                   -->
<!--                                                                       -->
<!-- Attributes:                                                           -->
<!--                                                                       -->
<!-- on_complement_strand: true when match is on complementary strand      -->
<!-- has_5prime_end:       true if 5 prime end has BAC contamination       -->
<!-- has_3prime_end:       true if 3 prime end has BAC contamination       -->
<!-- is_all_BAC_vect:      true if the entire fragment is BAC              -->
<!--                       contamination.                                  -->
<!--                                                                       -->
<!-- Content:                                                              -->
<!--                                                                       -->        
<!--                                                                       -->
<!ELEMENT fragment_orientation (bio_sequence , map_location?)>
<!ATTLIST fragment_orientation on_complement_strand    (true | false ) 'false'                                             
                               has_5prime_end          (true | false ) #IMPLIED
                               has_3prime_end          (true | false ) #IMPLIED
                               is_all_BAC_vect         (true | false ) #IMPLIED>

<!--                                                                       --> 
<!-- A sequence_map is a set of annotations on a bio_sequence.  An         -->
<!-- annotation is a seq_feature or a comp_result.                         -->
<!--                                                                       -->
<!--                                                                       -->
<!-- Attributes:                                                           -->
<!--                                                                       -->
<!-- label: an identifying name for the map.  Usually an algorithm name.   -->
<!--                                                                       -->
<!ELEMENT sequence_map  (note? , computation? , annotations? )>
<!ATTLIST sequence_map label        CDATA #IMPLIED >

<!--                                                                       --> 
<!-- annotations is a container for sequence annotations.                  -->
<!--                                                                       -->
<!ELEMENT annotations       (seq_feature | gene | comp_result )+ >

<!--                                                                       --> 
<!-- map_location is the location of a bio_sequence within a larger        -->
<!-- sequence such as a chromosome. A location may be a single position    -->
<!-- or a location within an interval.                                     -->
<!--                                                                       --> 
<!-- Attributes:                                                           -->
<!--                                                                       -->
<!-- map_type:   map type such as cytogentic, RH, or physical              --> 
<!-- source:     the source of the map, i.e. who made it                   -->
<!-- units:      units of measurement for the contained position.          -->
<!-- chromosome: chromosome assignment                                     -->
<!--                                                                       -->
<!-- subseq_start: the start of the interval.  For example, the            -->
<!--             starting position on a BAC which makes up a contig.       -->
<!--             Must be an integer.                                       -->
<!--                                                                       -->
<!-- orientation: indicates the orientation within the larger sequence     -->
<!--                                                                       -->
<!-- Content:                                                              -->
<!--                                                                       -->
<!-- map_position:  a single position or the start of an interval          -->
<!-- map_position?: the end of an interval                                 -->  
<!--                                                                       -->
<!ELEMENT map_location (map_position, map_position?)>
<!ATTLIST map_location map_type     CDATA                           #REQUIRED
                       source       CDATA                           #IMPLIED
                       units        ( band | cR | cM | kb | bp )    #REQUIRED
                       chromosome   CDATA                           #IMPLIED 
                       subseq_start CDATA                           '1'
                       orientation  ( forward | complement | none ) #IMPLIED >

<!--                                                                       --> 
<!-- A position relative to a genomic sequence such as a contig or         -->
<!-- chromosome                                                            --> 
<!--                                                                       --> 
<!-- Attributes:                                                           -->
<!--                                                                       -->
<!-- pos: map position such as "13.2" or "7q11" measured in the units of   -->
<!--      the containing map_location                                      -->
<!-- Content:                                                              -->
<!--                                                                       -->
<!-- db_id: reference to the object that this position is on. We allow     -->
<!--        multiples for aliases of the same object.                      -->
<!--                                                                       -->
<!ELEMENT map_position (db_id*)>
<!ATTLIST map_position pos CDATA  #REQUIRED>