Tissue Microarray Data Standards

1
Tissue MicroarrayData Standards

• Jules J. Berman, Ph.D., M.D.Program Director,
  Pathology InformaticsCancer Diagnosis
  ProgramNational Cancer InstituteAll opinions
  herein are Dr. Bermans 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 lt?xml
version"1.0"?gt ltdocument name"letter"gt ltstyle
name"block"gtlt/stylegt ltcreation_dategtJuly 14,
2000lt/creation_dategt ltaddresseegtJoe
Doelt/addresseegt ltaddressee_addressgt1234 Main
Street Hometown, CO 80000lt/addressee_addressgt ltsal
utationgtDear Mr. Doelt/salutationgt ltletter_bodygt W
hen 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. lt/letter_bodygt ltclosinggtSincer
ely,lt/closinggt ltsender_namegtAnn
Wrightlt/sender_namegt ltsender_titlegtStyle Guide
Editorlt/sender_titlegt lt/documentgt
4
Other letter data elements may include ltccgt ltsend
er addressgt ltdate_receivedgt lttime_receivedgt lttime_
sentgt lttime_receivedgt lttypistgt lthidden commentgt
(lt!--)
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 XMLParser p1 new
XMLParser(Style gt 'Debug') p1-gtparsefile('xml
short.xml') exit
7
C\newinfogtperl 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\newinfogt
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

• ltdate_of_birthgt10/17/00lt/date_of_birthgt

11
CDEs become self-attributing XML tags

• ltdate_of_birth defnhttp//www.cde.orggt10/17/00
  lt/date_of_birthgt

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