
<!-- 4.      MAML DTD  from http://cgi.omg.org/cgi-bin/doc?lifesci/00-11-16.pdf -->

<!-------------------------------------------------------------------->

<!-- MAML DOCUMENT CLUSTER                                          -->


<!ELEMENT  maml          (analysis_list?,

                         array_platform_list?,

                         contact_list?,

                         creation_info,

                         data_set_list?,

                         experiment_set_list?,

                         hardware_list?,

                         protocol_list?,

                         sample_list?,

                         software_list?,

                         publication_list) >


<!-------------------------------------------------------------------->

<!-- CREATION INFORMATION                                           -->

<!--                    A description of the creator of the XML

                        document (human, software, hardware)        -->


<!ELEMENT  creation_info EMPTY >


<!--                    date is an ISO date string                  -->

<!ATTLIST  creation_info                  

              date        CDATA                             #REQUIRED

              contact_id  IDREF                             #IMPLIED

              software_id IDREF                             #IMPLIED  >


<!--                    Contact can specify either an individual

                        researcher or an organization               -->

<!ELEMENT  contact_list  (contact+) >

<!ELEMENT  protocol_list (protocol+) >

<!ELEMENT  hardware_list (hardware+) >

<!ELEMENT  software_list (software+) >

                                     
<!ELEMENT  contact       (parameter*) >

<!ATTLIST  contact

              id             ID                             #REQUIRED

              last_name      CDATA                          #IMPLIED

              first_name     CDATA                          #IMPLIED

              middle_name    CDATA                          #IMPLIED

              type           CDATA                          #IMPLIED

              lab            CDATA                          #IMPLIED

              department     CDATA                          #IMPLIED

              organization   CDATA                          #IMPLIED

              street         CDATA                          #IMPLIED

              city           CDATA                          #IMPLIED

              province_state CDATA                          #IMPLIED

              country        CDATA                          #IMPLIED

              postal_code    CDATA                          #IMPLIED

              phone          CDATA                          #IMPLIED

              fax            CDATA                          #IMPLIED

              email          CDATA                          #IMPLIED

              uri            CDATA                          #IMPLIED  >


<!--                    Can represent PCR, scanner, array printer,

                        etc.                                        -->

<!ELEMENT  hardware      (description?,

                         parameter*) >

<!ATTLIST  hardware

              id            ID                              #REQUIRED

              contact_id    IDREF                           #IMPLIED

              type          CDATA                           #IMPLIED

              make          CDATA                           #IMPLIED

              model         CDATA                           #IMPLIED

              serial_number CDATA                           #IMPLIED

              year          CDATA                           #IMPLIED

              uri           CDATA                           #IMPLIED  >


<!ELEMENT  software      (description?,

                         parameter*) >

<!ATTLIST  software                         

              id               ID                           #REQUIRED

              contact_id       IDREF                        #IMPLIED

              hardware_ids     IDREFS                       #IMPLIED

              type             CDATA                        #IMPLIED

              name             CDATA                        #REQUIRED

              version          CDATA                        #IMPLIED

              year             CDATA                        #IMPLIED

              operating_system CDATA                        #IMPLIED

              uri              CDATA                        #IMPLIED  >


<!-- III     Protocols                                              -->

<!ELEMENT  protocol     (standard_protocol, 

                         db_xref?, 

                         protocol_deviations?,

                         protocol_abstract?) >

<!ATTLIST  protocol

              id        ID                                  #REQUIRED

              name      CDATA                               #IMPLIED

              type      CDATA                               #IMPLIED  >


<!ELEMENT  protocol_abstract (#PCDATA) >

<!ATTLIST  protocol_abstract

              xml:space preserve                            #FIXED    >


<!ELEMENT  standard_protocol (#PCDATA) >

<!ATTLIST  standard_protocol

              xml:space preserve                            #FIXED    >


<!ELEMENT  protocol_deviations (#PCDATA) >

<!ATTLIST  protocol_deviations

              xml:space preserve                            #FIXED    >


<!-- IV      Data                                                   -->

<!ELEMENT  data_set_list (data_set+) >


<!--                    for each grouping the first item in the

                        pair is the rows of the matrix, and the

                        second element is columns                   -->

<!ELEMENT  data_set      ((matrix_axes, 

                          matrix_data), 

                         (tagged_data_internal| 

                          tagged_data_external)) >

<!ATTLIST  data_set

              id          ID                                #REQUIRED

              name        CDATA                             #IMPLIED

              description CDATA                             #IMPLIED  >


<!ELEMENT  matrix_data  (ascii_data_internal | 

                         ascii_data_external |

                         binary_data_external)*                       >


<!ELEMENT  matrix_axes  (matrix_row_list, 

                         matrix_column_list, 

                         matrix_stack) >

<!ELEMENT  matrix_row_list (matrix_row+) >

<!ELEMENT  matrix_row   EMPTY >

<!ATTLIST  matrix_row

              element_id      IDREF                         #IMPLIED

              image_id        IDREF                         #IMPLIED

              quantitation_id IDREF                         #IMPLIED  >


<!ELEMENT  matrix_column_list (matrix_column+) >

<!ELEMENT  matrix_column EMPTY >

<!ATTLIST  matrix_column

             element_id      IDREF                          #IMPLIED

             image_id        IDREF                          #IMPLIED

             quantitation_id IDREF                          #IMPLIED  >


<!ELEMENT  matrix_stack (matrix+) >

<!ELEMENT  matrix       EMPTY >

<!ATTLIST  matrix

             element_id      IDREF                          #IMPLIED

             image_id        IDREF                          #IMPLIED

             quantitation_id IDREF                          #IMPLIED  >


<!--                    axis_key refers to either an <element>:id or

                        <composite_element>:id; or an <image>:id or 

                        <composite_image>:id; or a <quantitation>:id or 

                        <composite_quantitation>:id this is intended to

                        reference the missing third dimension of the data

                        matrix                                      -->

<!-- 

Data stored internally should be treated as a white

space delimited matrix where null values are specified

as 'NULL'. Carriage returns to delineate the ends of

rows are not necessary.

 -->

<!ELEMENT  ascii_data_internal (#PCDATA) >

<!ATTLIST  ascii_data_internal

              id         ID                                 #REQUIRED

              type       CDATA                              #REQUIRED

              derivation CDATA                              #REQUIRED >


<!-- 

Data stored externally should be treated as a white

space delimited matrix where null values are specified

as 'NULL'. Carriage returns to delineate the ends of

rows are not necessary.

 -->

<!ELEMENT  ascii_data_external EMPTY >

<!ATTLIST  ascii_data_external

              id        ID                                  #REQUIRED

              type      CDATA                               #REQUIRED

              file_uri  CDATA                               #REQUIRED >


<!ELEMENT  tagged_data_internal (tagged_data+) >

<!ATTLIST  tagged_data_internal

              id        ID                                  #REQUIRED

              type      CDATA                               #REQUIRED >


<!ELEMENT  tagged_data_external (tagged_data+) >

<!ATTLIST  tagged_data_external

              id        ID                                  #REQUIRED

              type      CDATA                               #REQUIRED >


<!ELEMENT  tagged_data EMPTY >

<!ATTLIST  tagged_data

              element_id      IDREF                         #REQUIRED

              image_id        IDREF                         #REQUIRED

              quantitation_id IDREF                         #REQUIRED

              data            CDATA                         #REQUIRED >


<!ELEMENT  binary_data_external EMPTY >

<!ATTLIST  binary_data_external

              id        ID                                  #REQUIRED

              axis_key  IDREF                               #REQUIRED

              type      CDATA                               #REQUIRED

              file_uri  CDATA                               #REQUIRED >


<!ELEMENT  parameter EMPTY >

<!ATTLIST  parameter

              name      CDATA                               #REQUIRED

              value     CDATA                               #REQUIRED >


<!-- V       Analysis -->

<!ELEMENT  analysis_list  (analysis+) >

<!ELEMENT  analysis (quantitation_list,

                    composite_image_list,

                    composite_quantitation_list,

                    composite_element_list) >


<!--                    For primary <quantitation> the 'name'

                        should be the same as the column name

                        provided by the scanner software           -->

<!--                    For a primary <quantitation> the

                        'software_id' really ought to be required

                        and should refer to the scanner software

                        that produced the data                     -->

<!ELEMENT  quantitation_list (quantitation+) >

<!ELEMENT  quantitation EMPTY >

<!ATTLIST  quantitation

              id          ID                                #REQUIRED

              name        CDATA                             #REQUIRED

              software_id IDREF                             #IMPLIED

              protocol_id IDREF                             #IMPLIED  >


<!ELEMENT  composite_element_list (composite_element+) >

<!ELEMENT  composite_element EMPTY >

<!ATTLIST  composite_element

              id          ID                                #REQUIRED

              element_ids IDREFS                            #REQUIRED >


<!ELEMENT  composite_image_list (composite_image+) >

<!ELEMENT  composite_image EMPTY >

<!--                    protocol_id references a protocol that

                        describes the method used to create the

                        composite elements from the primary

                        measurements                               -->

<!ATTLIST  composite_image

              id          ID                                #REQUIRED

              image_ids   IDREFS                            #REQUIRED

              protocol_id IDREF                             #IMPLIED

              software_id IDREF                             #IMPLIED  >


<!ELEMENT  composite_quantitation_list (composite_quantitation)+>


<!ELEMENT  composite_quantitation EMPTY >

<!--                    protocol_id references a protocol that

                        describes the method used to create the

                        composite  from the primary

                        measurements                               -->

<!--                    We're not sure that software_id is useful

                        in this context                            -->

<!ATTLIST  composite_quantitation

             id              ID                             #REQUIRED

             quantitaion_ids IDREFS                         #REQUIRED

             protocol_id     IDREF                          #IMPLIED

             software_id     IDREF                          #IMPLIED  >


<!-- VIII    Experiment Set -->

<!ELEMENT  experiment_set_list (experiment_set+) >

<!ELEMENT  experiment_set (experimental_design, 

                           extract_list, 

                           hybridization_list, 

                           control_element_list, 

                           labeled_extract_list,

                           sample_list) >

<!ATTLIST  experiment_set

              local_accession_number CDATA                  #IMPLIED

              experiment_type        CDATA                  #IMPLIED

              publication_id         IDREF                  #IMPLIED

              contact_id             CDATA                  #IMPLIED

              submission_date        CDATA                  #IMPLIED

              release_date           CDATA                  #IMPLIED

              experiment_date        CDATA                  #IMPLIED  >


<!ELEMENT  experimental_design (biology_description,

                                analysis_description,

                                experimental_factors, 

                                quality) >


<!ELEMENT  biology_description (#PCDATA) >

<!ATTLIST  biology_description

              xml:space preserved                           #FIXED >

<!ELEMENT  analysis_description (#PCDATA) >

<!ATTLIST  analysis_description

              xml:space preserved                           #FIXED >


<!ELEMENT  experimental_factors (#PCDATA) >

<!ATTLIST  experimental_factors

              xml:space preserved                           #FIXED >


<!--                    We understand that this is limited and

                        insufficient, but we believe that quality

                        control is an important issue              -->

<!ELEMENT  quality (replicates, quality_info*) >

<!ATTLIST  quality

              has_replicates (true|false)                    #REQUIRED >

              peer_reviewed  (true|false)                    false     >


<!ELEMENT  replicates (description?) >


<!ELEMENT  quality_info (#PCDATA) >


<!ELEMENT  control_element_list (control_element+) >

<!ELEMENT  control_element EMPTY >

<!ATTLIST  control_element

             id              ID                             #REQUIRED

             expected_value  CDATA                          #REQUIRED

             quantitation_id IDREF                          #REQUIRED

             element_id      IDREF                          #REQUIRED >


<!ELEMENT  hybridization_list (hybridization+) >

<!ELEMENT  hybridization (image+) >

<!ATTLIST  hybridization

             name                CDATA                      #REQUIRED

             protocol_ids        IDREFS                     #IMPLIED

             labeled_extract_ids IDREFS                     #REQUIRED

             control_element_ids IDREFS                     #REQUIRED

             array_id            IDREF                      #REQUIRED

             id                  ID                         #REQUIRED >


<!ELEMENT  image EMPTY >

<!ATTLIST  image

              protocol_id         IDREF                     #REQUIRED

              labeled_extract_ids IDREFS                    #REQUIRED

              software_id         IDREF                     #REQUIRED

              hardware_id         IDREF                     #REQUIRED

              file_uri            CDATA                     #REQUIRED

              file_header         CDATA                     #IMPLIED

              microns_per_pixel   CDATA                     #IMPLIED

              image_identifier    CDATA                     #REQUIRED >


<!ELEMENT  sample_list   (primary_sample|

                          derived_sample)+ >


<!ELEMENT  derived_sample (treatment+) >

<!ATTLIST  derived_sample

              id                ID                          #REQUIRED

              parent_sample_ids IDREFS                      #REQUIRED >


<!ELEMENT  treatment (measurement) >

<!ATTLIST  treatment

              action      CDATA                             #REQUIRED

              object      CDATA                             #IMPLIED

              protocol_id IDREF                             #IMPLIED

              order       CDATA                             #REQUIRED >


<!--   We don't yet have a full ontology so the primary sample

       should include the following kinds of values:


       organism_ncbi

       organism_other                   

       cell_source                      

       cell_type                        

       sex                              

       age                              

       development_stage                

       organism_part (tissue)           

       strain_or_line                   

       genetic_variation                

       individual                       

       genotype                         

       disease_state                    

       target_cell_type                 

       cell_line_and_source             

       in_vivo_treatments               

       in_vitro_treatments              

       treatment_type                   

       compound                         

       separation_technique             -->

<!ELEMENT  primary_sample (parameter|generic_measure)* >

<!ATTLIST  primary_sample

              id        ID                                  #REQUIRED >


<!ELEMENT  extract_list (extract+) >

<!ELEMENT  extract (description?,parameter*) >

<!ATTLIST  extract

              id          ID                                #REQUIRED

              protocol_id IDREF                             #REQUIRED

              type        (total_rna|mrna|dna)              #REQUIRED

              sample_ids  IDREFS                            #REQUIRED

              label_name  CDATA                             #REQUIRED

              name        CDATA                             #IMPLIED  >


<!ELEMENT  labeled_extract_list (labeled_extract+) >

 
<!ELEMENT  labeled_extract (description?,parameter*) >

<!ATTLIST  labeled_extract

              id          ID                                #REQUIRED

              protocol_id IDREF                             #REQUIRED

              extract_ids IDREFS                            #REQUIRED

              name        CDATA                             #IMPLIED  >


<!-------------------------------------------------------------------->

<!-- DESCRIPTIONS                                                   -->


<!ELEMENT  description  CDATA                                         >


<!-------------------------------------------------------------------->

<!-- MEASUREMENT CLUSTER                                            -->


<!ELEMENT  time         EMPTY >


<!ATTLIST  time                           

              value      CDATA                              #REQUIRED

              unit       (years |

                          months |

                          weeks |

                          d |

                          h |

                          m |

                          s |

                          ms |

                          us |

                          other)                            #REQUIRED

              other_unit CDATA                              #IMPLIED   >


<!ELEMENT  vector       (distance+) >

<!ELEMENT  distance     EMPTY >

<!ATTLIST  distance     

              value      CDATA                              #REQUIRED

              unit       (fm |

                          pm |

                          nm |

                          um |

                          mm |

                          cm |

                          m |

                          other)                            #REQUIRED

              other_unit CDATA                              #IMPLIED   >


<!ELEMENT  temperature  EMPTY >

<!ATTLIST  temperature             

              value     CDATA                               #REQUIRED

              unit      (C|F)                               #REQUIRED >


<!ELEMENT  mass         EMPTY >

<!ATTLIST  mass                            

              value      CDATA                              #REQUIRED

              unit       (kg |

                          g |

                          mg |

                          ug |

                          ng |

                          pg |

                          fg |

                          other)                            #REQUIRED

              other_unit CDATA                              #IMPLIED  >


<!ELEMENT  volume        EMPTY >

<!ATTLIST  volume                          

              value     CDATA                               #REQUIRED

              unit      (mL |

                         cc |

                         dL |

                         L  |

                         uL |

                         nL |

                         pL |

                         fL |

                         other)                             #REQUIRED

              other_unit CDATA                              #IMPLIED   >


<!ELEMENT  concentration EMPTY >

<!ATTLIST  concentration                   

              value      CDATA                              #REQUIRED

              unit       (M |

                          mM |

                          uM |

                          nM |

                          pM |

                          fM |

                          mg_per_mL |

                          mL_per_L |

                          g_per_L |

                          g_percent |

                          other)                            #REQUIRED

              other_unit CDATA                              #IMPLIED   >


<!ELEMENT  quantity     EMPTY >

<!ATTLIST  quantity

              value      CDATA                              #REQUIRED

              unit       ( mol|

                          amol|

                          fmol|

                          pmol|

                          nmol|

                          umol|

                          mmol|

                          molecule)                         #REQUIRED >


<!ELEMENT  generic_measure EMPTY >

<!ATTLIST  generic_measure              

              name      CDATA                               #REQUIRED

              value     CDATA                               #REQUIRED

              unit      CDATA                               #REQUIRED >


<!ELEMENT  measurement  (time |

                         distance |

                         vector |

                         quantity |

                         temperature |

                         mass |

                         volume |

                         concentration |

                         generic_measure) >

<!ATTLIST  measurement     

              type      (absolute | change)                 #IMPLIED  >


<!-------------------------------------------------------------------->

<!-- RELATIONSHIPS                                                  -->


<!ELEMENT  reference    (db_xref*,description?) >


<!--                    Date is an ISO date string, and is

                        intended to be used to specify the date

                        that the reference was made, not the date

                        the database was released                   -->

<!ELEMENT  db_xref      (parameter*) >

<!ATTLIST  db_xref

              database          CDATA                       #IMPLIED

              database_version  CDATA                       #IMPLIED

              date              CDATA                       #IMPLIED

              accession         CDATA                       #IMPLIED

              accession_version CDATA                       #IMPLIED

              uri               CDATA                       #IMPLIED  >


<!-------------------------------------------------------------------->

<!-- PUBLICATION                                                    -->


<!ELEMENT  publication_list (publication+) >

<!ELEMENT  publication  (citation | reference) >

<!ATTLIST  publication

              id        ID                                  #REQUIRED >


<!ELEMENT  citation     (abstract?) >

<!ATTLIST  citation                  

              journal   CDATA                               #IMPLIED

              year      CDATA                               #IMPLIED

              volume    CDATA                               #IMPLIED

              issue     CDATA                               #IMPLIED

              page      CDATA                               #IMPLIED

              authors   CDATA                               #IMPLIED

              publisher CDATA                               #IMPLIED

              editor    CDATA                               #IMPLIED

              uri       CDATA                               #IMPLIED  >


<!ELEMENT  abstract     (#PCDATA) >


<!-------------------------------------------------------------------->

<!-- ARRAY PLATFORM                                                 -->

<!--   changes:                                                     -->

<!--      1) 'array_def': exchanged 'type' attribute with           -->

<!--         'surface_type' and 'reporter_type'                     -->

<!--      2) 'reporter' element converted into Paul's               -->

<!--         suggested 'element' element                            -->


<!ELEMENT  array        (description?) >

<!ATTLIST  array

              id                ID                          #REQUIRED

              name              CDATA                       #REQUIRED

              array_platform_id IDREF                       #REQUIRED >


<!ELEMENT  array_platform_list (array_platform|

                                array)+ >


<!ELEMENT  array_platform (array_def) >


<!ATTLIST  array_platform

              id        ID                                  #REQUIRED >


<!ELEMENT  array_def    (description?,

                         reference*,

                         parameter*,

                         element*) >


<!ATTLIST  array_def                     

              name               CDATA                      #REQUIRED

              contact_id         CDATA                      #REQUIRED

              protocol_id        CDATA                      #REQUIRED

              in_situ_synthesis  (true|false)               #REQUIRED

              spotted            (true|false)               #REQUIRED

              surface_type       (non-absorptive|

                                  absorptive)               #REQUIRED

              surface_type_name  CDATA                      #REQUIRED

              other_surface_type CDATA                      #IMPLIED

              number_of_elements CDATA                      #IMPLIED

              short_axis_length  CDATA                      #IMPLIED

              long_axis_length   CDATA                      #IMPLIED

              element_type       (single-multimer |

                                  multiple-oligomer |

                                  other)                    #REQUIRED

              model_name         CDATA                      #IMPLIED

              version            CDATA                      #IMPLIED

              uri                CDATA                      #IMPLIED  >


<!-------------------------------------------------------------------->

<!-- ELEMENT                                                        -->

<!ELEMENT  element     ((bio_seq|

                         ref_bio_seq|

                         ref_clone)+,

                        gene*,

                        parameter*,

                        measurement*,

                        description?) >


<!--                    sequence_length can be approximate         -->

<!--                    diameter can be approximate                -->

<!--                    empty elements should have an empty

                        <bio_seq>                                  -->

<!ATTLIST  element                     

              id                ID                          #REQUIRED

              attachment_method CDATA                       #IMPLIED

              strandedness      (single|double)             #IMPLIED

              type              (empty|

                                 pcr|

                                 synthesized_oligo|

                                 intact_plasmid|

                                 colony)                    #REQUIRED

              diameter          CDATA                       #IMPLIED

              sequence_length   CDATA                       #IMPLIED

              location          CDATA                       #IMPLIED

              protocol_id       CDATA                       #IMPLIED

              row               CDATA                       #IMPLIED

              column            CDATA                       #IMPLIED

              block             CDATA                       #IMPLIED

              x_microns         CDATA                       #IMPLIED

              y_microns         CDATA                       #IMPLIED

              name              CDATA                       #IMPLIED  >


<!ELEMENT  bio_seq      (#PCDATA|db_xref) >

<!ELEMENT  ref_bio_seq  (#PCDATA|db_xref) >

<!ELEMENT  gene         (#PCDATA|db_xref) >

<!ELEMENT  ref_clone    (#PCDATA|db_xref) >