Tissue Microarray Data Standards

1. Tissue MicroarrayData Standards • Jules J. Berman, Ph.D., M.D.Program Director, Pathology InformaticsCancer Diagnosis ProgramNational Cancer Institute*All opinions herein are Dr. Berman’s and do not represent those of any federal agency.

2. Letter Format from U of Colorado at Boulder Style Guide LETTERHEAD HERE July 14, 2000 Joe Doe 1234 Main Street Hometown, CO 80000 Dear Mr. Doe: When typing formal letters on CU letterhead, leave at least one inch of white space below the letterhead and use one-inch margins on the left, right, and bottom sides. Align all type flush left with no paragraph indentations. Double space between paragraphs. As for other spacing, it's traditional to triple space between the date and the address block, double space between the address block and the salutation, double space after the salutation, and leave four lines for the signature. However, it's fine to only double space after the date, especially if doing do will save the letter from running on to a second page. This block style is the current business letter writing style standard and has been approved by efficiency experts because it saves keystrokes. To readers, this flush left style looks more contemporary than the indented paragraph style. Finally, adopting this style will help convey a consistent image for all CU correspondence. Sincerely, Ann Wright Style Guide Editor

3. Valid XML document for letter <?xml version="1.0"?> <document name="letter"> <style name="block"></style> <creation_date>July 14, 2000</creation_date> <addressee>Joe Doe</addressee> <addressee_address>1234 Main Street Hometown, CO 80000</addressee_address> <salutation>Dear Mr. Doe:</salutation> <letter_body> When typing formal letters on CU letterhead, leave at least one inch of white space below the letterhead and use one-inch margins on the left, right, and bottom sides. Align all type flush left with no paragraph indentations. Double space between paragraphs. </letter_body> <closing>Sincerely,</closing> <sender_name>Ann Wright</sender_name> <sender_title>Style Guide Editor</sender_title> </document>

4. Other letter data elements may include: <cc> <sender address> <date_received> <time_received> <time_sent> <time_received> <typist> <hidden comment> (<!--)

5. There will be two dominant uses of XML parsers: 1. To parse on any valid XML document in order to find the Common Data Elements 2. To process specific XML document types: Example: Gene array XML documents Tissue Microarray XML documents Surgical Pathology Report XML documents

6. #!/usr/bin/perl -w use XML::Parser; $p1 = new XML::Parser(Style => 'Debug'); $p1->parsefile('xmlshort.xml'); exit;

7. C:\newinfo>perl xmlshort.pl \\ (name letter) document || #10; document \\ (name block) document // document || #10; document \\ () document creation_date || July 14, 2000 document // document || #10; document \\ () document addressee || Joe Doe document // document || #10; document \\ () document addressee_address || 1234 Main Street Hometown, CO 80000 document // document || #10; document \\ () document salutation || Dear Mr. Doe: document // document || #10; document \\ () document letter_body || #10; document letter_body || When typing formal letters on CU letterhead, leave at le ast one inch of white space below the letterhead and use one-inch margins on the left, right, and bottom sides. Align all type flush left with no paragraph inde ntations. Double space between paragraphs. document letter_body || #10; document // document || #10; document \\ () document closing || Sincerely, document // document || #10; document \\ () document sender_name || Ann Wright document // document || #10; document \\ () document sender_title || Style Guide Editor document // document || #10; // C:\newinfo>

8. CDE for Date of Birth • |birthdate| September 15, 1970 • |birthday| September 15, 1970 • |D.O.B.| September 15, 1970 • |d.o.b.| September 15, 1970 • |date of birth| September 15, 1970 • |date of birth| September 15, 1970 • |date-of-birth| September 15, 1970 • |date_of_birth| September 15, 1970 • |dob| September 15, 1970 • |DOB| September 15, 1970

9. Representation of CDE • |date_of_birth| September 15, 1970 • |date_of_birth| 15, September, 1970 • |date_of_birth| 9/15/70 • |date_of_birth| 15/9/70 • |date_of_birth| 15/09/70 • |date_of_birth| 9/15/1970 • |date_of_birth| 9.15.70 • |date_of_birth| 9,15,70 • |date_of_birth| some delta time

10. CDEs become XML tags • <date_of_birth>10/17/00</date_of_birth>

11. CDEs become self-attributing XML tags • <date_of_birth defn=“http://www.cde.org”>10/17/00 </date_of_birth>

12. The difference between Uniform Standards and Uniform Requirements 1. Standards are about giving people an opportunity to cooperate and share. All good standards are publicly available and free. 2. Requirements are about forcing people to act a certain way.

13. Minimum information about a [GENE] microarray experiment - MIAME Draft March 21, 2001, based on November 17, 2000 The goal of the MIAME is to specify the minimum information that must be reported about a microarray (or any DNA array) based gene expression monitoring experiment in order to ensure the interpretability, as well as potential verification of the results by third parties. The background aim is to facilitate the establishing public repositories and data exchange format for microarray based gene expression data. The MGED group will be encouraging the scientific journals and funding agencies to adopt policies requiring data submissions to repositories, once MIAME compliant repositories are established.

14. a.array related information unique ID as used in part 1 (for commercial or standard arrays a unique ID given by the provider may be used) array design name (e.g., "Stanford Human 10K set") platform type: insitu synthesized or spotted array provider (source) surface type: glass, membrane, other surface type name array support (e.g. slide) dimensions number of elements on the array a reference system allowing to locate each element (spot) on the array (in the simplest case the number of columns and rows is sufficient) production protocol (obligatory if applicable) optional "qualifier, value, source" list (see Introduction)

15. Good things about standards