Transcript www.julesberman.info

API Imaging Working Group
Jules J. Berman and Ulysses J. Balis, Co-Chairs
Laboratory Digital Imaging Project
APIII, 2006
Vancouver, British Columbia
Thursday, August 17, 2006
11:30 A.M. To 1:00 P.M.
Jules J. Berman, Ph.D., M.D.
President, Association for Pathology Informatics
Purpose of LDIP image specification
1. To permit image users to annotate a pathology image with relevant
technical, pathologic, and clinical information and to convey this
information with the image file.
2. To provide a file that is self-describing, containing well-defined
metadata for all data values, and that uses a standard, generic syntax
that is easy to understand and implement.
3. To produce image files that can be integrated with other image
standards and other types of data expressed in the same syntax.
Specific goals of LDIP
1. Develop an RDF schema for LDIP that employs well-defined
metadata from existing standards (HL7, DICOM, OME, CytometryML,
MISFISHIE, GO).
2. Keep it simple (should not require more than 5 minutes to learn if
you know anything about RDF; 8 minutes if you don't)
3. Publish easily emulated examples of the LDIP schema being used
with HL7, DICOM, jpeg, OME, surgical pathology reports, etc.
4. Follow our progress at: www.ldip.org
Problems with existing standards (including
DICOM)
1. Too complex, hard to understand and implement.
2. Not generic (won't merge with datasets using other standards)
3. Made with non-standard (often obsolete) methodologies (not
XML/RDF, even ascii)
4. Lack the metadata (data descriptors) needed by pathologists.
Government and Standards Organizations often bet
on the the wrong horse.
I3C – Dozens of industry and government leaders united to develop
health care interoperability
Sun Microsystems' Informatics Advisory Council
IBM
Apple
Oracle
Federal Government:
National Cancer Institute
National Human Genome Research Institute
Now defunct: Impression is that the group conceded effort to the W3C
which has a generic approach embodied under the semantic web.
LDIP is a way of specifying an image and is not a
standard.
LDIP simply uses generic W3C standards to create a simple way
of expressing image information.
You can learn the basics of RDF in a few minutes.
Methods used here can (and should) be extended to other
biomedical domains.
LDIP uses RDF, a existing generic simple syntax
recommended by the W3C
RDF files are collections of statements expressed as data triples
<identified subject><metadata><data>
“Jules Berman” “blood glucose level” “85”
“Mary Smith” “eye color” “brown”
“Samuel Rice” “eye color” “blue”
“Jules Berman” “eye color” “brown”
When you bind a key/value pair to a specified object, you're moving from
the realm of data structure into the realm of data meaning.
RDF permits data to be merged between different files
Medical file:
“Jules Berman” “blood glucose level” “85”
“Mary Smith” “eye color” “brown”
“Samuel Rice” “eye color” “blue”
“Jules Berman” “eye color” “brown”
Merged Jules Berman database:
“Jules Berman” “blood glucose level” “85”
“Jules Berman” “eye color” “brown”
“Jules Berman” “hat size” “9”
Hat file:
“Sally Frann” “hat size” “8”
“Jules Berman” “hat size” “9”
“Fred Garfield” “hat size” “9”
“Fred Garfield” “hat_type” “bowler”
"The image is a squamous cell carcinoma of the floor of the mouth.
It was taken by Jules Berman, on February 2, 2002. The
microscope was an Olympus model 3453. The lens objective was 40x
The camera was a Sony model 342. The image dimensions are
524 by 429 pixels. The microscope and camera were
not calibrated. The specimen Baltimore Hospital Center
S-3456-2001, specimen 2, block 3. The specimen was logged in
8/15/01 and processed using the standard protocol for H&E that
was in place for that day. The patient is Sam Someone, medical
identifier 4357 The tissue was received in formalin. The
specimen shows a moderately differentiated, invasive squamous
carcinoma. The patient has a 30 year history of oral tobacco
use. The image is kept in jpeg (Joint Photographic Experts Group)
file format and named y49w3p2.jpg and kept
in the pathology subdirectory of the hospital's server. It's URL
is https://baltohosp.org/pathology/y49w3p2.jpg The image file
has an md_5 hash value of 84027730gjsj350489 The image has no
watermark Copyright is held by Baltimore Hospital Center, and
all rights are reserved."
[file:image.n3 @prefix :]
[<http://www.pathologyinformatics.org/image_schema.rdf#>.]
[@prefix rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#>.]
[:Baltimore_Hospital_Center rdf:type "Hospital".]
[:Baltimore_Hospital_Center_4357 rdf:type"Unique_medical_identifier".]
[:Baltimore_Hospital_Center_4357 :patient_name "Sam_Someone".]
[:Baltimore_Hospital_Center_4357 :surgical_pathology_specimen "S3456_2001".]
[:S_3456_2001 rdf:type "Surgical_pathology_specimen".]
[:S_3456_2001 :image <https://baltohosp.org/pathology/y49w3p2.jpg>.]
[:S_3456_2001:log_in_date "2001-08-15".]
[:S_3456_2001 :clinical_history "30_years_oral_tobacco_use".]
[<https://baltohosp.org/pathology/y49w3p2.jpg> rdf:type "Medical_image".]
[<https://baltohosp.org/pathology/y49w3p2.jpg> :surgical_pathology_accession_number "S3456-2001".]
[<https://baltohosp.org/pathology/y49w3p2.jpg> :specimen "2".]
[<https://baltohosp.org/pathology/y49w3p2.jpg> :block "3".]
[<https://baltohosp.org/pathology/y49w3p2.jpg> :format "jpeg".]
[<https://baltohosp.org/pathology/y49w3p2.jpg> :width "524_pixels".]
[<https://baltohosp.org/pathology/y49w3p2.jpg> :height "429_pixels".]
[<https://baltohosp.org/pathology/y49w3p2.jpg> :hash_value "84027730gjsj350489".]
[<https://baltohosp.org/pathology/y49w3p2.jpg> :hash_type "md_5".]
[<https://baltohosp.org/pathology/y49w3p2.jpg> :watermark "none".]
[<https://baltohosp.org/pathology/y49w3p2.jpg> :camera "Sony".]
[<https://baltohosp.org/pathology/y49w3p2.jpg> :camera_model "342".]
[<https://baltohosp.org/pathology/y49w3p2.jpg> :capture_date "2002-02-02".]
[<https://baltohosp.org/pathology/y49w3p2.jpg> :diagnosis "squamous_cell_carcinoma".]
[<https://baltohosp.org/pathology/y49w3p2.jpg> :topography "floor_of_mouth".]
[<https://baltohosp.org/pathology/y49w3p2.jpg> :has "Intellectual_property_restriction".]
[<https://baltohosp.org/pathology/y49w3p2.jpg> :copyright "all_rights_reserved".]
[<https://baltohosp.org/pathology/y49w3p2.jpg> :copyright_holder "Baltimore_Hospital_Center".]
[<https://baltohosp.org/pathology/y49w3p2.jpg> :microscope "Olympus".]
[<https://baltohosp.org/pathology/y49w3p2.jpg> :microscope_model "3453".]
[<https://baltohosp.org/pathology/y49w3p2.jpg> :microscope_objective_power "40X".]
[<https://baltohosp.org/pathology/y49w3p2.jpg> :photographer_name "Jules_Berman".]
Logic of the RDF syntax
“Jules Berman”
A specified object
“blood glucose level”
well-defined metada
“85”
datatyping
1. Unique identifiers for unique objects:
URIs, LSIDs, other identification systems
2. Class identifiers for class objects:
examples.... image class, person class, report class, event class
3. Formal Common Data elements protected in namespaces
example..... chem:blood_glucose ldip:imaging_device
4. Datatyping using xsd for data types
examples.... integer, string literal, one of an enumeration list
CDEs in RDF are either classes or properties. The LDIP model for CDEs
is designed to support automatic transformation into an RDF schema:
The format for classes is:
Class Label (in standard XML tag format, uppercase 1st letter):
Registration Authority: Association for Pathology Informatics
Cardinality: (default is "/[0-9]+/"):
Comment (must include detailed definition):
subClassOf:
Contributor (your consistent first-name last-name):
Date of your contribution (/[\d]{2}\-[\d{2}]\-[\d]{4}]/):
The format for properties is:
Property Label (in standard XML tag format, lowercase 1st letter):
Registration Authority: Association for Pathology Informatics
Cardinality (default is "/[0-9]+/"):
Datatype (can be "literal", a list or a regex; default is "literal"):
Comment (must include detailed definition):
Domain (comma-delimited if multiple):
Range (default is "literal"):
Contributor (your consistent first-name last-name):
Date of your contribution (/[\d]{2}\-[\d{2}]\-[\d]{4}/):
Example: CDE for Instrument
Class Label:Instrument
versionInfo (required): 0.1
Registration Authority (required): Association for Pathology Informatics
Language:en
Cardinality (required):/[0-9]+/
Datatype: Literal
comment: All the instruments used in preparing, viewing,
and imaging a specimen. Includes: microscope, camera.
subClassOf:Class
Contributor:Bill Moore
Date_of_contribution:05-15-2006
The plain-text list of CDEs can be automatically converted into RDF schema and
xsd user-defined datatypes.
Purpose of today's workshop
1. To explain what LDIP is trying to accomplish
2. To review work done in LDIP
3. To encourage participation in LDIP effort.