<?xml version="1.0"?>

<!--
TISSUE MICROARRAY  ** TISSUE MICRO ARRAY  **  TISSUE ARRAY

First draft of Tissue Microarray DTD open for comment:

Version 1.0 November 15, 2001

Data elements provided by the API TMA Users Group

DTD design by Jules J. Berman

The Association for Pathology Informatics has promoted two Tissue
Microarray Data Exchange Standards Workshops.  The first was held
May 30, 2001 (AIMCL, Ann Arbor, MI), and the second was held Oct. 6
(APIII, Pittsburgh, PA).  The second meeting was cosponsored by the
NCI.  Workshop summaries will be distributed as separate documents.

The most recent meeting (October 6) was organized by Dr. Mary Edgerton.
During the workshop portion of the meeting, the proposed common data
elements for the data exchange standard were reviewed and modified as
per group discussion.

There was agreement that the elements would be used in an XML format,
and that a DTD would be required.

During the past month, I designed a very simple DTD
(api-tma.xml  attached).  I used three publicly available
strategies to determine that the DTD is well-formed and valid:

1. Validating service at:http://www.stg.brown.edu/service/xmlvalid/
2. Validating service at:http://www.hcrc.ed.ac.uk/~richard/xml-check.html
3. IE5 XML compatibility


Some of the features of the DTD design are here described:

1. The DTD can be divided into the following general sections:

histo_file            general information about the file (filename,
                      creation date, etc.)
histo_file_creator    contact information for the person or entity
                      submitting the file
histo_file_ip         intellectual property information
                      (copyright, or restrictions  as may apply)
histo_block           information about the paraffin block from
                      which the TMA slide was cut
histo_slide           information about the TMA slide prepared
                      from the block
histo_core            information regarding each core on the slide
                      (includes clinical/pathology data, stain results,
                      image data)

2. The format permits files to be submitted with information limited
to groups elements of a tissue microarray.

For instance, you could submit a TMA file that only include information
about the TMA paraffin block.  You could prepare a TMA file for a plain
old single tissue glass slide (i.e. the special case where the number
of core elements = 1).   This way, anyone can use the TMA data exchange
format for exchanging a wide range of TMA-specific or TMA-nonspecific
(e.g. regular slides) pathology data.

3. There are no attributes for any elements and no required data
elements at this time.  This permits maximum flexibility for improving
the data structure in the future.

6. The major categories of data elements have been give "namespace"
elements.  The concept of "namespace" elements has been borrowed from
RDF and RELAX.  Basically, it allows users to specify a unique location
where the data related to a group of data elements resides (somewhere
on the web or in a retrievable file).  Invoking the namespace option
eliminates the need to include data that might need to be repeated in
related files produced from the same lab, block, or TMA slide.  Besides
eliminating redunancy, judicious use of namespaces allows TMA designers
to "correct" errors even after the TMA file has been submitted and
distributed to parties unknown.  Also, using namespaces can greatly
facilitate sharing data between heterogeneous databases.

This document is public domain.

Jules J. Berman, Ph.D., M.D.
Program Director, Pathology Informatics
Cancer Diagnosis Program, DCTD, NCI, NIH
EPN - Room 6028
6130 Executive Blvd.
Rockville, MD 20892
email: bermanj@mail.nih.gov
voice: 301-496-7147
fax: 301-402-7819

BEGIN XML FILE HERE
-->

<!DOCTYPE histo
[
<!ELEMENT histo
(
histo_file?,
histo_file_namespace?,
histo_file_name?,
histo_file_type?,
histo_file_creation_date?,
histo_file_url?,
histo_file_version_number?,
histo_file_identification_number?,
histo_file_version_creation_date?
)>
<!ELEMENT histo_file                                   (#PCDATA)>
<!ELEMENT histo_file_namespace
   (
   histo_file_namespace_pointer?,
   histo_file_namespace_id?
   )>
<!ELEMENT histo_file_namespace_pointer                 (#PCDATA)>
<!ELEMENT histo_file_namespace_id                      (#PCDATA)>
<!ELEMENT histo_file_name                              (#PCDATA)>
<!ELEMENT histo_file_type                              (#PCDATA)>
<!ELEMENT histo_file_creation_date                     (#PCDATA)>
<!ELEMENT histo_file_url                               (#PCDATA)>
<!ELEMENT histo_file_version_number                    (#PCDATA)>
<!ELEMENT histo_file_identification_number             (#PCDATA)>
<!ELEMENT histo_file_version_creation_date             (#PCDATA)>
<!ELEMENT histo_file_creator
(
histo_file_creator_namespace?,
histo_file_creator_last_name?,
histo_file_creator_first_name?,
histo_file_creator_middle_name?,
histo_file_creator_title?,
histo_file_creator_department?,
histo_file_creator_organization?,
histo_file_creator_street?,
histo_file_creator_city?,
histo_file_creator_state?,
histo_file_creator_country?,
histo_file_creator_post_code?,
histo_file_creator_phone?,
histo_file_creator_fax?,
histo_file_creator_email?,
histo_file_creator_webpage?
)>
<!ELEMENT histo_file_creator_namespace
(
histo_file_creator_namespace_pointer?,
histo_file_creator_namespace_id?
)>
<!ELEMENT histo_file_creator_namespace_pointer         (#PCDATA)>
<!ELEMENT histo_file_creator_namespace_id              (#PCDATA)>
<!ELEMENT histo_file_creator_last_name                 (#PCDATA)>
<!ELEMENT histo_file_creator_first_name                (#PCDATA)>
<!ELEMENT histo_file_creator_middle_name               (#PCDATA)>
<!ELEMENT histo_file_creator_title                     (#PCDATA)>
<!ELEMENT histo_file_creator_department                (#PCDATA)>
<!ELEMENT histo_file_creator_organization              (#PCDATA)>
<!ELEMENT histo_file_creator_street                    (#PCDATA)>
<!ELEMENT histo_file_creator_city                      (#PCDATA)>
<!ELEMENT histo_file_creator_state                     (#PCDATA)>
<!ELEMENT histo_file_creator_country                   (#PCDATA)>
<!ELEMENT histo_file_creator_post_code                 (#PCDATA)>
<!ELEMENT histo_file_creator_phone                     (#PCDATA)>
<!ELEMENT histo_file_creator_fax                       (#PCDATA)>
<!ELEMENT histo_file_creator_email                     (#PCDATA)>
<!ELEMENT histo_file_creator_webpage                   (#PCDATA)>
<!ELEMENT histo_file_ip
(
histo_file_ip_namespace?,
histo_file_ip_public_domain?,
histo_file_ip_allowed_uses?,
histo_file_ip_restrictions?,
histo_file_ip_charges?,
histo_file_ip_copyright_info?,
histo_file_ip_license_info?
)>
<!ELEMENT histo_file_ip_namespace
(
histo_file_ip_namespace_pointer?,
histo_file_ip_namespace_id?
)>
<!ELEMENT histo_file_ip_namespace_pointer              (#PCDATA)>
<!ELEMENT histo_file_ip_namespace_id                   (#PCDATA)>
<!ELEMENT histo_file_ip_public_domain                  (#PCDATA)>
<!ELEMENT histo_file_ip_allowed_uses                   (#PCDATA)>
<!ELEMENT histo_file_ip_restrictions                   (#PCDATA)>
<!ELEMENT histo_file_ip_charges                        (#PCDATA)>
<!ELEMENT histo_file_ip_copyright_info                 (#PCDATA)>
<!ELEMENT histo_file_ip_license_info                   (#PCDATA)>
<!ELEMENT histo_block
(
histo_block_namespace?,
histo_block_description?,
histo_block_related_blocks?,
histo_block_creator?,
histo_block_creation_date?,
histo_block_identification_number?,
histo_block_protocol?,
histo_block_size_of_cores?,
histo_block_number_of_cores?,
histo_block_core_spacing?,
histo_block_QA?,
histo_block_status?,
histo_block_array?,
histo_block_array_namespace?,
histo_block_array_namespace_pointer?,
histo_block_array_namespace_identifier?,
histo_block_array_hash?
)>
<!ELEMENT histo_block_namespace
(
histo_block_namespace_pointer?,
histo_block_id?
)>
<!ELEMENT histo_block_namespace_pointer                (#PCDATA)>
<!ELEMENT histo_block_id                               (#PCDATA)>
<!ELEMENT histo_block_description                      (#PCDATA)>
<!ELEMENT histo_block_related_blocks                   (#PCDATA)>
<!ELEMENT histo_block_creator                          (#PCDATA)>
<!ELEMENT histo_block_creation_date                    (#PCDATA)>
<!ELEMENT histo_block_identification_number            (#PCDATA)>
<!ELEMENT histo_block_protocol                         (#PCDATA)>
<!ELEMENT histo_block_size_of_cores                    (#PCDATA)>
<!ELEMENT histo_block_number_of_cores                  (#PCDATA)>
<!ELEMENT histo_block_core_spacing                     (#PCDATA)>
<!ELEMENT histo_block_QA                               (#PCDATA)>
<!ELEMENT histo_block_status                           (#PCDATA)>
<!ELEMENT histo_block_array                            (#PCDATA)>
<!ELEMENT histo_block_array_namespace                  (#PCDATA)>
<!ELEMENT histo_block_array_namespace_pointer          (#PCDATA)>
<!ELEMENT histo_block_array_namespace_identifier       (#PCDATA)>
<!ELEMENT histo_block_array_hash                       (#PCDATA)>
<!ELEMENT histo_slide
(
histo_slide_namespace?,
histo_slide_identification_number?,
histo_slide_type?,
histo_slide_creator?,
histo_slide_cut_date?,
histo_slide_thickness?,
histo_slide_level?,
histo_slide_section_identifier?,
histo_slide_sectioning_protocol?,
histo_slide_test_date?,
histo_slide_test_category?,
histo_slide_test_protocol?,
histo_slide_test_feature?,
histo_slide_test_control?
)>
<!ELEMENT histo_slide_namespace
(
histo_slide_namespace_pointer?,
histo_slide_id?
)>
<!ELEMENT histo_slide_namespace_pointer                (#PCDATA)>
<!ELEMENT histo_slide_id                               (#PCDATA)>
<!ELEMENT histo_slide_identification_number            (#PCDATA)>
<!ELEMENT histo_slide_type                             (#PCDATA)>
<!ELEMENT histo_slide_creator                          (#PCDATA)>
<!ELEMENT histo_slide_cut_date                         (#PCDATA)>
<!ELEMENT histo_slide_thickness                        (#PCDATA)>
<!ELEMENT histo_slide_level                            (#PCDATA)>
<!ELEMENT histo_slide_section_identifier               (#PCDATA)>
<!ELEMENT histo_slide_sectioning_protocol              (#PCDATA)>
<!ELEMENT histo_slide_test_date                        (#PCDATA)>
<!ELEMENT histo_slide_test_category                    (#PCDATA)>
<!ELEMENT histo_slide_test_protocol                    (#PCDATA)>
<!ELEMENT histo_slide_test_feature                     (#PCDATA)>
<!ELEMENT histo_slide_test_control                     (#PCDATA)>
<!ELEMENT histo_core
(
histo_core_namespace?,
histo_core_array_identifier?,
histo_core_tissue_fixative?,
histo_core_organism?,
histo_core_demographics?,
histo_core_demographics_namespace?,
histo_core_demographics_namespace_pointer?,
histo_core_demographics_namespace_identifier?,
histo_core_demographics_record?,
histo_core_anatomic_site?,
histo_core_organ?,
histo_core_QA?,
histo_core_clinical_info?,
histo_core_clinical_info_namespace?,
histo_core_clinical_info_available_info?,
histo_core_repository?,
histo_core_repository_namespace?,
histo_core_repository_specimen_diagnosis?,
histo_core_repository_donor_block_diagnosis?,
histo_core_repository_donor_block_drill_site?,
histo_core_results?,
histo_core_results_method_of_reading_data?,
histo_core_results_number_of_nuclei_counted?,
histo_core_results_cell_type_staining?,
histo_core_results_tissue_intensity?,
histo_core_results_percent_tissue_staining?,
histo_core_results_compartment_staining?,
histo_core_results_staining_pattern?,
histo_core_image?,
histo_core_image_namespace?,
histo_core_image_algorithm?,
histo_core_image_checksum?,
histo_core_image_magnification?,
histo_core_image_pixel_size?,
histo_core_image_info?
)>
<!ELEMENT histo_core_namespace
(
histo_core_namespace_pointer?,
histo_core_id?
)>
<!ELEMENT histo_core_namespace_pointer                 (#PCDATA)>
<!ELEMENT histo_core_id                                (#PCDATA)>
<!ELEMENT histo_core_array_identifier                  (#PCDATA)>
<!ELEMENT histo_core_tissue_fixative                   (#PCDATA)>
<!ELEMENT histo_core_organism                          (#PCDATA)>
<!ELEMENT histo_core_demographics                      (#PCDATA)>
<!ELEMENT histo_core_demographics_namespace            (#PCDATA)>
<!ELEMENT histo_core_demographics_namespace_pointer    (#PCDATA)>
<!ELEMENT histo_core_demographics_namespace_identifier (#PCDATA)>
<!ELEMENT histo_core_demographics_record               (#PCDATA)>
<!ELEMENT histo_core_anatomic_site                     (#PCDATA)>
<!ELEMENT histo_core_organ                             (#PCDATA)>
<!ELEMENT histo_core_QA                                (#PCDATA)>
<!ELEMENT histo_core_clinical_info                     (#PCDATA)>
<!ELEMENT histo_core_clinical_info_namespace
(
histo_core_clinical_info_pointer?,
histo_core_clinical_info_id?
)>
<!ELEMENT histo_core_clinical_info_pointer             (#PCDATA)>
<!ELEMENT histo_core_clinical_info_id                  (#PCDATA)>
<!ELEMENT histo_core_clinical_info_available_info      (#PCDATA)>
<!ELEMENT histo_core_repository                        (#PCDATA)>
<!ELEMENT histo_core_repository_namespace
(
histo_core_repository_namespace_pointer?,
histo_core_repository_namespace_identifier?
)>
<!ELEMENT histo_core_repository_namespace_pointer      (#PCDATA)>
<!ELEMENT histo_core_repository_namespace_identifier   (#PCDATA)>
<!ELEMENT histo_core_repository_specimen_diagnosis     (#PCDATA)>
<!ELEMENT histo_core_repository_donor_block_diagnosis  (#PCDATA)>
<!ELEMENT histo_core_repository_donor_block_drill_site (#PCDATA)>
<!ELEMENT histo_core_results                           (#PCDATA)>
<!ELEMENT histo_core_results_method_of_reading_data    (#PCDATA)>
<!ELEMENT histo_core_results_number_of_nuclei_counted  (#PCDATA)>
<!ELEMENT histo_core_results_cell_type_staining        (#PCDATA)>
<!ELEMENT histo_core_results_tissue_intensity          (#PCDATA)>
<!ELEMENT histo_core_results_percent_tissue_staining   (#PCDATA)>
<!ELEMENT histo_core_results_compartment_staining      (#PCDATA)>
<!ELEMENT histo_core_results_staining_pattern          (#PCDATA)>
<!ELEMENT histo_core_image                             (#PCDATA)>
<!ELEMENT histo_core_image_namespace
(
histo_core_image_pointer?,
histo_core_image_identifier?
)>
<!ELEMENT histo_core_image_pointer                     (#PCDATA)>
<!ELEMENT histo_core_image_identifier                  (#PCDATA)>
<!ELEMENT histo_core_image_algorithm                   (#PCDATA)>
<!ELEMENT histo_core_image_checksum                    (#PCDATA)>
<!ELEMENT histo_core_image_magnification               (#PCDATA)>
<!ELEMENT histo_core_image_pixel_size                  (#PCDATA)>
<!ELEMENT histo_core_image_info                        (#PCDATA)>
]>
<histo>
<histo_file_url>
www.mged.org
</histo_file_url>
</histo>


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