API Imaging Working Group

Jules J. Berman and Ulysses J. Balis, Co-ChairsLaboratory Digital Imaging Project

APIII, 2006Vancouver, British ColumbiaThursday, August 17, 200611:30 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 CouncilIBMAppleOracleFederal 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.

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”

RDF permits data to be merged between different files

"The image is a squamous cell carcinoma of the floor of the mouth.It was taken by Jules Berman, on February 2, 2002. Themicroscope was an Olympus model 3453. The lens objective was 40xThe camera was a Sony model 342. The image dimensions are524 by 429 pixels. The microscope and camera werenot calibrated. The specimen Baltimore Hospital CenterS-3456-2001, specimen 2, block 3. The specimen was logged in8/15/01 and processed using the standard protocol for H&E thatwas in place for that day. The patient is Sam Someone, medicalidentifier 4357 The tissue was received in formalin. Thespecimen shows a moderately differentiated, invasive squamouscarcinoma. The patient has a 30 year history of oral tobaccouse. The image is kept in jpeg (Joint Photographic Experts Group)file format and named y49w3p2.jpg and keptin the pathology subdirectory of the hospital's server. It's URLis https://baltohosp.org/pathology/y49w3p2.jpg The image filehas an md_5 hash value of 84027730gjsj350489 The image has nowatermark Copyright is held by Baltimore Hospital Center, andall 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” “blood glucose level” “85”A specified object well-defined metada 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 namespacesexample..... chem:blood_glucose ldip:imaging_device

4. Datatyping using xsd for data typesexamples.... 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 InformaticsCardinality: (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 InformaticsCardinality (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:InstrumentversionInfo (required): 0.1Registration Authority (required): Association for Pathology InformaticsLanguage:enCardinality (required):/[0-9]+/Datatype: Literalcomment: All the instruments used in preparing, viewing, and imaging a specimen. Includes: microscope, camera.subClassOf:ClassContributor:Bill MooreDate_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.