SPECIMEN COMMON DATA ELEMENTS.
THIS DOCUMENT HAS NO OFFICIAL STATUS.
DRAFT COPY ONLY.
4/27/2006.

G. William Moore, MD, PhD.

http://www.gwmoore.org/ldip/spcmncde.htm


Send comments and correspondence to: gwmoore@erols.com

DISCLAIMER.



United States Government Work, uncopyrighted, public-domain, DRAFT COPY ONLY. This document does not necessarily represent the views or policies of any United States Government agency. This document is provided "as is", without warranty of any kind, express or implied, including but not limited to the warranties of merchantability, fitness for a particular purpose and non-infringement. In no event shall the authors be liable for any claim, damages or other liability, whether in an action of contract, tort or otherwise, arising from, out of, or in connection with the document or the use or other dealings made with the document..

0. NOTES


0.1. NOTES FROM 4/27/2006.



Specimen CDE provisional RDF Hierarchy for presentation at 4/27/2006, teleconference:
http://www.gwmoore.org/ldip/scderdfh.htm

0.2. NOTES FROM 3/31/2006.



The specimen task group presented their tentative list of data elements. The draft (this document) is currently available for viewing at:
http://www.gwmoore.org/ldip/spcmncde.htm
Dr. Robert Leif indicated that it needs fluroescence and antibody data elements, and that he would work with Dr. Moore to provide these.

Dr. Jules Berman indicated that each element needed to be defined and put into ISO-11179 format. Dr. Moore indicated that he could do that if Dr. Berman sent Dr. Moore a sample case. Dr. Berman sent the following tissue microarray CDEs, at URL:
http://www.pathologyinformatics.org/tma_cde.htm
It was indicated that the specimen element would need to have subspecimen attributes (a specimen can be part of another specimen). There was discussion that we should be using relationships (such as is_a, has_a, is_part_of) that have been used by other biological ontologies. Dr. Moore indicated that he would visit the OBO (open biomedical ontologies) site to get this information, at URL:
OBO main page: http://obo.sourceforge.net/
OBO relationship page: http://cvs.sourceforge.net/viewcvs.py/obo/obo/ontology/OBO_REL/relationship.obo?view=markup
OBO disease ontology page: http://cvs.sourceforge.net/viewcvs.py/obo/obo/ontology/phenotype/DiseaseOntologyV2_1.obo

0.3. ISO 11179 Format:
Specimen Common Data Elements 
                



Person 

 identifier: person
   Version: 0.1
   Registration Authority: Bill Moore.
   Language: en
   Obligation: Required.
   RDF_Category: Class.
   Datatype: Null.
   SubclassOf: Null.
   Maximum Occurrence: Unlimited
   Definition: http://www.gwmoore.org/ldip/person.htm
   has_child: person_name
   has_child: person_social_security_number
   has_child: person_date_of_birth
   has_child: person_gender
   has_child: person_ethnicity
   Comment: Person is defined as a quadruple of person_name, person_social_security_number, person_gender, and person_date_of_birth, with optional person_ethnicity. A person may be a patient, provider, or pathologist.


                



Biopsy_event 

 identifier: biopsy_event
   Version: 0.1
   Registration Authority: Bill Moore.
   Language: en
   Obligation: Required.
   RDF_Category: Class.
   Datatype: Null.
   SubclassOf: Null.
   Maximum Occurrence: Unlimited
   Definition: http://www.gwmoore.org/ldip/biopsy_event.htm
   has_child:


                                   



Person_name 

 identifier: person_name
   Version: 0.1
   Registration Authority: Bill Moore.
   Language: en
   Obligation: Required
   RDF_Category: Property.
   RDF_Domain: Literal.
   RDF_Range: surname|givenname|honorific, where surname, givennames, and honorific, are all character-strings.
   SubclassOf: person
   Maximum Occurrence: One
   Definition: http://www.gwmoore.org/ldip/person_name.htm
   has_child: None
   Comment: Person_name is defined as: surname|givenname|honorific


                                  



Person_social_security_number 

 identifier: person_social_security_number
   Version: 0.1
   Registration Authority: Bill Moore.
   Language: en
   Obligation: Required.
   RDF_Category: Property.
   RDF_Domain: Numeral.
   RDF_Range: nnn-nn-nnnn
   SubclassOf: person
   Maximum Occurrence: One
   Definition: http://www.gwmoore.org/ldip/person_social_security_number.htm
   has_child: None
   Comment:


                              



Person_date_of_birth 

 identifier: person_date_of_birth
   Version: 0.1
   Registration Authority: Bill Moore.
   Language: en
   Obligation: Required
   RDF_Category: Property.
   RDF_Domain: Numeral.
   RDF_Range: ISO 8601 date_time standard.
   SubclassOf: person
   Maximum Occurrence: One
   Definition: http://www.gwmoore.org/ldip/person_date_of_birth.htm
   has_child: None
   Comment:


                                 



Person_gender 

 identifier: person_gender
   Version: 0.1
   Registration Authority: Bill Moore.
   Language: en
   Obligation: Required
   RDF_Category: Property.
   RDF_Domain: Literal.
   RDF_Range: F, M, or U.
   Maximum Occurrence: One
   SubclassOf: person
   Definition: http://www.gwmoore.org/ldip/person_gender.htm
   has_child: None
   Comment:


                             



Person_ethnicity 

 identifier: person_ethnicity
   Version: 0.1
   Registration Authority: Bill Moore.
   Language: en
   Obligation: Optional
   RDF_Category: Property.
   RDF_Domain: Literal.
   RDF_Range: 
 U. S. Office of Management and Budget Statistical Policy Directive 15. 
   Maximum Occurrence: One
   SubclassOf: patient
   Definition: http://www.gwmoore.org/ldip/patient_ethnicity.htm
   has_child: None
   Comment:


                



Patient 

 identifier: patient
   Version: 0.1
   Registration Authority: Bill Moore.
   Language: en
   Obligation: Required.
   RDF_Category: Class.
   SubclassOf: person
   Domain: Null.
   Maximum Occurrence: Unlimited
   Definition: http://www.gwmoore.org/ldip/patient.htm
   has_child: patient_image
   has_child: pathology_report
   is_a: person
   Comment:


                                        



Patient_hospital_id 

 identifier: patient_hospital_id
   Version: 0.1
   Registration Authority: Bill Moore.
   Language: en
   Obligation: Optional
   RDF_Category: Property.
   RDF_Domain: Numeral.
   RDF_Range:
   Maximum Occurrence: One
   SubclassOf: patient
   Definition: http://www.gwmoore.org/ldip/patient_hospital_id.htm
   has_child: None
   Comment:


                



Provider 

 identifier: provider
   Version: 0.1
   Registration Authority: Bill Moore.
   Language: en
   Obligation: Required.
   RDF_Category: Class.
   SubclassOf: person
   Maximum Occurrence: Unlimited
   Definition: http://www.gwmoore.org/ldip/provider.htm
   has_child:
   Comment:


                                        



Provider_credential 

 identifier: provider_credential
   Version: 0.1
   Registration Authority: Bill Moore.
   Language: en
   Obligation: Optional
   RDF_Category: Property.
   RDF_Domain:
   RDF_Range:
   Maximum Occurrence: One
   SubclassOf: provider
   Definition: http://www.gwmoore.org/ldip/provider_credential.htm
   has_child: None
   Comment:







                                        



Patient_image 

 identifier: patient_image
   Version: 0.1
   Registration Authority: Bill Moore.
   Language: en
   Obligation: Optional
   Datatype:
   SubclassOf: patient
   Maximum Occurrence: Unlimited
   Definition: http://www.gwmoore.org/ldip/patient_image.htm
   has_child:
   Comment:


                          



Pathology_accession

 identifier: pathology_accession
   Version: 0.1
   Registration Authority: Bill Moore.
   Language: en
   Obligation: Optional
   RDF_Category: Class.
   SubclassOf: patient
   SubclassOf: provider
   SubclassOf: pathologist
   Domain: Null.
   Maximum Occurrence: Unlimited
   Definition: http://www.gwmoore.org/ldip/pathology_accession.htm
   has_child: pathology_accession_provider
   has_child: pathology_report
   has_child: specimen
   Comment: A pathology accession corresponds to one patient, one day,
 and one provider.
 A pathology accession may consist of one or more specimens, each submitted in a separate specimen_container.
 A pathology accession generates exactly one pathology_report,
 signed out by exactly one pathology_report_pathologist,
 who submits exactly one pathology_report_bill,


                         



Pathology_accession_provider

 identifier: pathology_accession_provider
   Version: 0.1
   Registration Authority: Bill Moore.
   Language: en
   Obligation: Required
   RDF_Category: Class.
   Datatype: 
   SubclassOf: person
   Maximum Occurrence: Unlimited
   Definition: http://www.gwmoore.org/ldip/pathology_accession_provider.htm
   has_child: 
   Comment:


                          



Pathology_report

 identifier: pathology_report
   Version: 0.1
   Registration Authority: Bill Moore.
   Language: en
   Obligation: Required
   RDF_Category: Class
   Datatype: 
   SubclassOf: pathology_accession
   Maximum Occurrence: One
   Definition: http://www.gwmoore.org/ldip/pathology_report.htm
   has_child: pathology_report_time_obtained
   has_child: pathology_report_time_received
   has_child: pathology_report_time_reported
   has_child: pathology_report_time_amended
   has_child: pathology_report_time_supplemented
   has_child: pathology_report_pathologist
   has_child: pathology_report_pathologist
   has_child: pathology_report_billing
   Comment:


                         



Pathology_report_pathologist

 identifier: pathology_report_pathologist
   Version: 0.1
   Registration Authority: Bill Moore.
   Language: en
   Obligation: Required
   RDF_Category: Class
   SubclassOf: person
   Maximum Occurrence: One
   Definition: http://www.gwmoore.org/ldip/pathology_report_pathologist.htm
   has_child:
   Comment:


                                    



Pathology_report_time_obtained

 identifier: pathology_report_time_obtained
   Version: 0.1
   Registration Authority: Bill Moore.
   Language: en
   Obligation: Required
   RDF_Category: Property.
   RDF_Domain: Numeral.
   RDF_Range: ISO 8601 date_time standard.
   SubclassOf: pathology_report
   Maximum Occurrence: One
   Definition: http://www.gwmoore.org/ldip/pathology_report_time_obtained.htm
   has_child: None
   is_a: ISO 8601 date_time
   Comment:


                                    



Pathology_report_time_received

 identifier: pathology_report_time_received
   Version: 0.1
   Registration Authority: Bill Moore.
   Language: en
   Obligation: Required
   RDF_Category: Property.
   RDF_Domain: Numeral.
   RDF_Range: ISO 8601 date_time standard.
   SubclassOf: pathology_report
   Maximum Occurrence: One
   Definition: http://www.gwmoore.org/ldip/pathology_report_time_received.htm
   has_child: None
   is_a: ISO 8601 date/time
   Comment:


                                     



Pathology_report_time_reported

 identifier: pathology_report_time_reported
   Version: 0.1
   Registration Authority: Bill Moore.
   Language: en
   Obligation: Required
   RDF_Category: Property.
   RDF_Domain: Numeral.
   RDF_Range: ISO 8601 date_time standard.
   SubclassOf: pathology_report
   Maximum Occurrence: One
   Definition: http://www.gwmoore.org/ldip/pathology_report_time_reported.htm
   has_child: None
   is_a: ISO 8601 date/time
   Comment:


                                     



Pathology_report_time_amended

 identifier: pathology_report_time_amended
   Version: 0.1
   Registration Authority: Bill Moore.
   Language: en
   Obligation: Optional
   RDF_Category: Property.
   RDF_Domain: Numeral.
   RDF_Range: ISO 8601 date_time standard.
   SubclassOf: pathology_report
   Maximum Occurrence: Unlimited
   Definition: http://www.gwmoore.org/ldip/pathology_report_time_amended.htm
   has_child: None
   is_a: ISO 8601 date/time
   Comment:


                                     



Pathology_report_time_supplemented

 identifier: pathology_report_time_supplemented
   Version: 0.1
   Registration Authority: Bill Moore.
   Language: en
   Obligation: Optional
   RDF_Category: Property.
   RDF_Domain: Numeral.
   RDF_Range: ISO 8601 date_time standard.
   SubclassOf: pathology_report
   Maximum Occurrence: Unlimited
   Definition: http://www.gwmoore.org/ldip/pathology_report_time_supplemented.htm
   has_child: None
   is_a: ISO 8601 date/time
   Comment:


                                     



Pathology_report_billing

 identifier: pathology_report_billing
   Version: 0.1
   Registration Authority: Bill Moore.
   Language: en
   Obligation: Required
   Datatype:
   SubclassOf: pathology_report
   Maximum Occurrence: One
   Definition: http://www.gwmoore.org/ldip/pathology_report_billing.htm
   has_child: pathology_report_billing_technical
   has_child: pathology_report_billing_professional
   is_a: billing_code.htm
   Comment:


                                    



Pathology_report_billing_technical

 identifier: pathology_report_billing_technical
   Version: 0.1
   Registration Authority: Bill Moore.
   Language: en
   Obligation: Required
   Datatype:
   SubclassOf: pathology_report_billing
   Maximum Occurrence: One
   Definition: http://www.gwmoore.org/ldip/pathology_report_billing_technical.htm
   has_child: None
   is_a: billing_code.htm
   Comment:


                                     



Pathology_report_billing_professional

 identifier: pathology_report_billing_professional
   Version: 0.1
   Registration Authority: Bill Moore.
   Language: en
   Obligation: Required
   Datatype:
   SubclassOf: pathology_report_billing
   Maximum Occurrence: One
   Definition: http://www.gwmoore.org/ldip/pathology_report_billing_professional.htm
   has_child: None
   is_a: billing_code.htm
   Comment:


                          



Specimen 

 identifier: specimen
   Version: 0.1
   Registration Authority: Bill Moore.
   Language: en
   Obligation: Required
   Datatype:
   SubclassOf: pathology_accession
   Maximum Occurrence: Unlimited
   Definition: http://www.gwmoore.org/ldip/specimen.htm
   has_child: specimen_name
   has_child: specimen_cui
   has_child: specimen_procedure
   has_child: specimen_organ
   has_child: specimen_diagnosis
   has_child: specimen_unique_identifier
   has_child: specimen_sequence
   has_child: specimen_container
   is_a:
   Comment:


                     



Specimen_name

 identifier: specimen_name
   Version: 0.1
   Registration Authority: Bill Moore.
   Language: en
   Obligation: Required
   Datatype: 
   SubclassOf: specimen
   Maximum Occurrence: One
   Definition: http://www.gwmoore.org/ldip/specimen_name.htm
   has_child:
   is_a: specimen
   Comment:


                      



Specimen_cui

 identifier: specimen_cui
   Version: 0.1
   Registration Authority: Bill Moore.
   Language: en
   Obligation: Required
   Datatype:
   SubclassOf: specimen
   Maximum Occurrence: One
   Definition: http://www.gwmoore.org/ldip/specimen_cui.htm
   has_child: None.
   is_a: specimen_cui
   Comment:


                      



Specimen_procedure

 identifier: specimen_procedure
   Version: 0.1
   Registration Authority: Bill Moore.
   Language: en
   Obligation: Required
   Datatype: 
   SubclassOf: specimen
   Maximum Occurrence: One
   Definition: http://www.gwmoore.org/ldip/specimen_procedure.htm
   has_child: None
   is_a: specimen_procedure
   Comment:


                      



Specimen_organ

 identifier: specimen_organ
   Version: 0.1
   Registration Authority: Bill Moore.
   Language: en
   Obligation: Required
   Datatype:
   SubclassOf: specimen
   Maximum Occurrence: One
   Definition: http://www.gwmoore.org/ldip/specimen_organ.htm
   has_child: specimen_container_block
   is_a: specimen_organ
   Comment:


                      



Specimen_diagnosis

 identifier: specimen_diagnosis
   Version: 0.1
   Registration Authority: Bill Moore.
   Language: en
   Obligation: Required
   Datatype: 
   SubclassOf: specimen
   Maximum Occurrence: Unlimited
   Definition: http://www.gwmoore.org/ldip/specimen_diagnosis.htm
   has_child:
   is_a: specimen_diagnosis
   Comment:


                      



Specimen_gross_description

 identifier: specimen_gross_description
   Version: 0.1
   Registration Authority: Bill Moore.
   Language: en
   Obligation:
   Datatype: 
   SubclassOf: specimen
   Maximum Occurrence: One
   Definition: http://www.gwmoore.org/ldip/specimen_gross_description.htm
   has_child:
   is_a:
   Comment:


                                    



Specimen_unique_identifier

 identifier: specimen_unique_identifier
   Version: 0.1
   Registration Authority: Bill Moore.
   Language: en
   Obligation: Required
   Datatype: 
   SubclassOf: specimen
   Maximum Occurrence: One
   Definition: http://www.gwmoore.org/ldip/specimen_unique_identifier.htm
   has_child: 
   is_a: specimen_unique_identifier
   Comment:


                                    



Specimen_sequence

 identifier: specimen_sequence
   Version: 0.1
   Registration Authority: Bill Moore.
   Language: en
   Obligation: Required
   Datatype: 
   SubclassOf: specimen
   Maximum Occurrence: One
   Definition: http://www.gwmoore.org/ldip/specimen_sequence.htm
   has_child: 
   is_a:
   Comment:


                                 



Specimen_container

 identifier: specimen_container
   Version: 0.1
   Registration Authority: Bill Moore.
   Language: en
   Obligation: Required
   Datatype: 
   SubclassOf: specimen
   Maximum Occurrence: One
   Definition: http://www.gwmoore.org/ldip/specimen_container.htm
   has_child: specimen_container_block
   is_a: specimen_container
   has_child: specimen_container_block
   Comment:


                                     


Specimen_container_block

 identifier: specimen_container_block
   Version: 0.1
   Registration Authority: Bill Moore.
   Language: en
   Obligation: 
   Datatype: 
   SubclassOf: specimen_container
   Maximum Occurrence: Unlimited
   Definition: http://www.gwmoore.org/ldip/specimen_container_block.htm
   has_child: specimen_container_block_slide
   is_a: block
   Comment:


                                  


Specimen_container_block_slide

 identifier: specimen_container_block_slide
   Version: 0.1
   Registration Authority: Bill Moore.
   Language: en
   Obligation: 
   Datatype: 
   SubclassOf: specimen_container_block
   Maximum Occurrence: Unlimited
   Definition: http://www.gwmoore.org/ldip/specimen_container_block_slide.htm
   has_child: specimen_container_block_slide_stain
   is_a: slide
   Comment:


                                   


Specimen_container_block_slide_stain 

 identifier: specimen_container_block_slide_stain
   Version: 0.1
   Registration Authority: Bill Moore.
   Language: en
   Obligation: Optional
   Datatype: 
   Maximum Occurrence: Unlimited
   Definition: http://www.gwmoore.org/ldip/specimen_container_block_slide_stain.htm
   has_child: specimen_container_block_slide_stain_image
   is_a: histologic_stain
   Comment:


                                     


Specimen_container_block_slide_stain_image 

 identifier: specimen_container_block_slide_stain_image
   Version: 0.1
   Registration Authority: Bill Moore.
   Language: en
   Obligation: Optional
   Datatype: 
   Maximum Occurrence: Unlimited
   Definition: http://www.gwmoore.org/ldip/specimen_container_block_slide_stain_image.htm
   has_child: 
   is_a: image
   Comment:


                                     


Tissue_orientation 

 identifier: tissue_orientation
   Version: 0.1
   Registration Authority: Bill Moore.
   Language: en
   Obligation: Optional
   Datatype: 
   Maximum Occurrence: Unlimited
   Definition: http://www.gwmoore.org/ldip/tissue_orientation.htm
   has_child: 
   is_a: http://www.gwmoore.org/ldip/coordinates
   Comment:


                                     


Tissue_fixative 

 identifier: tissue_fixative
   Version: 0.1
   Registration Authority: Bill Moore.
   Language: en
   Obligation: Required
   Datatype: 
   Maximum Occurrence: One
   Definition: http://www.gwmoore.org/ldip/tissue_fixative.htm
   has_child: 
   is_a: fixative
   Comment:


                                     


Histologic_stain 

 identifier: histologic_stain
   Version: 0.1
   Registration Authority: Bill Moore.
   Language: en
   Obligation: Optional
   Datatype: 
   Maximum Occurrence: Unlimited
   Definition: http://www.gwmoore.org/ldip/histologic_stain.htm
   has_child: 
   is_a: histologic_stain
   Comment:


                                     


Histologic_stain_name 

 identifier: histologic_stain_name
   Version: 0.1
   Registration Authority: Bill Moore.
   Language: en
   Obligation: Optional
   Datatype: 
   Maximum Occurrence: Unlimited
   Definition: http://www.gwmoore.org/ldip/histologic_stain_name.htm
   has_child: 
   is_a: histologic_stain
   Comment:


                                     


Histologic_stain_class

 identifier: histologic_stain_class
   Version: 0.1
   Registration Authority: Bill Moore.
   Language: en
   Obligation: Optional
   Datatype: 
   Maximum Occurrence: Unlimited
   Definition: http://www.gwmoore.org/ldip/histologic_stain_class.htm
   has_child: 
   is_a: histologic_stain_class
   Comment:


                                     


Histologic_stain_method

 identifier: histologic_stain_method
   Version: 0.1
   Registration Authority: Bill Moore.
   Language: en
   Obligation: Optional
   Datatype: 
   Maximum Occurrence: Unlimited
   Definition: http://www.gwmoore.org/ldip/histologic_stain_method.htm
   has_child: 
   is_a: histologic_stain_method
   Comment:


                                     


Histologic_stain_manufacturer

 identifier: histologic_stain_manufacturer
   Version: 0.1
   Registration Authority: Bill Moore.
   Language: en
   Obligation: Optional
   Datatype: 
   Maximum Occurrence: Unlimited
   Definition: http://www.gwmoore.org/ldip/histologic_stain_manufacturer.htm
   has_child: 
   is_a: manufacturer
   Comment:


                    



Person 

 identifier: person
   Version: 0.1
   Registration Authority: Bill Moore.
   Language: en
   Obligation: Required.
   Datatype: Null.
   SubclassOf: Null.
   Domain: Null.
   Maximum Occurrence: Unlimited
   Definition: http://www.gwmoore.org/ldip/person.htm
   has_child:
   is_a: person


                    



Provider 

 identifier: provider
   Version: 0.1
   Registration Authority: Bill Moore.
   Language: en
   Obligation: Required.
   Datatype: Null.
   SubclassOf: Null.
   Domain: Null.
   Maximum Occurrence: Unlimited
   Definition: http://www.gwmoore.org/ldip/provider.htm
   has_child:
   is_a: provider


                    



Pathologist 

 identifier: pathologist
   Version: 0.1
   Registration Authority: Bill Moore.
   Language: en
   Obligation: Required.
   RDF_Category: Class.
   SubclassOf: person
   Datatype: Null.
   Domain: Null.
   Range: Null.
   Maximum Occurrence: One.
   Definition: http://www.gwmoore.org/ldip/pathologist.htm
   has_child:


                    



Surname 

 identifier: surname
   Version: 0.1
   Registration Authority: Bill Moore.
   Language: en
   Obligation: Required.
   RDF_Category: Property
   SubclassOf: person
   Datatype: Literal
   Domain: Literal
   Range: Smith, Jones, Williams, ....
   Maximum Occurrence: One.
   Definition: http://www.gwmoore.org/ldip/surname.htm
   has_child:


                    



Givenname 

 identifier: givenname
   Version: 0.1
   Registration Authority: Bill Moore.
   Language: en
   Obligation: Required.
   RDF_Category: Property
   SubclassOf: person
   Datatype: Literal
   Domain: Literal
   Range: Bill, Jack, Sam, George,....
   Maximum Occurrence: One.
   Definition: http://www.gwmoore.org/ldip/givenname.htm
   has_child:


                    



Honorific 

 identifier: honorific
   Version: 0.1
   Registration Authority: Bill Moore.
   Language: en
   Obligation: Required.
   RDF_Category: Property
   SubclassOf: person
   Datatype: Literal
   Domain: Literal
   Range: MD, DO, PhD, MBChB, Jr, Sr, III, IV, PhD(Cantab), PhD(Oxon),....
   Maximum Occurrence: One.
   Definition: http://www.gwmoore.org/ldip/honorific.htm
   has_child:

0.4 OBO FORMAT, adapted from:


http://cvs.sourceforge.net/viewcvs.py/obo/obo/ontology/phenotype/DiseaseOntologyV2_1.obo 
format-version: 1.0
 default-namespace: disease_ontology
 [Term]
 id: DOID:1
 name: Acute conjunctivitis
 rank: 6
 xref_analog:UMLS_CUI:C0155141
 xref_analog:ICD9CM_2005:372.0
 xref_analog:ICD9CM_2005:372.00
 xref_analog:UMLS_ICD9CM_2005_AUI:A0274262
 xref_analog:UMLS_ICD9CM_2005_AUI:A0639449
 has_child:DOID:7
 has_child:DOID:5
 has_child:DOID:4
 has_child:DOID:6
 has_child:DOID:3
 is_a:DOID:2
 exact_synonym: "Acute conjunctivitis, unspecified" [ICD9CM_2005]

0.5. RDF HIERARCHY:



RESOURCE DESCRIPTION FRAMEWORK (RDF) is a hierarchical arrangement of biomedical knowledge, that can be rapidly searched and indexed with web-based resources:
http://www.w3.org/RDF/
The first thing you need is for an RDF project is the NAME OF YOUR PROJECT, which is LDIP for the present project, i.e., Laboratory Digital Imaging Project. Next, you need a comprehensive list of all the MAJOR CLASSES OF KNOWLEDGE in your project. For LDIP, there are SEVEN MAJOR CLASSES, namely: PERSON, REAGENT, DATA_OBJECT, SPECIMEN, INSTRUMENT, TERMINOLOGY, and EVENT.

You should then create a NOMENCLATURE OF TERMS for your knowledge-base. I recommend using strictly lower-case alphabetic characters, with blank spaces replaced by underline (_), and no other punctuation, numerals, or diacritical-marked letters.

You must arrange all concepts in your knowledge base as a HIERARCHY, with a single, ULTIMATE PARENT; and any number of CHILDREN for each PARENT. Every knowledge concept in RDF is either a CLASS or PROPERTY. The ultimate parent is (unfortunately) named Class; and any class may have any number of children, including zero children. Every class, except for the (ultimate) Class, has EXACTLY ONE PARENT, denoted subClassOf:. For example, the seven major Classes, namely, Class:Person, Class:Reagent, Class:Data_object, Class:Specimen, Class:Instrument, Class:Terminology, and Class:Event, have subClassOf:Class. Each of Class:Patient, Class:Clinical_provider, and Class:Pathologist, have subClassOf:Person.

General concepts, such as Class:Patient, Class:Clinical_provider, and Class:Pathologist, are assigned to Class; Specific concepts, such as Property:patient_surname, Property:clinical_provider_surname, Property:pathologist_surname, etc., are assigned to Property. Every property has at least one (but possibly more) Class-parent, denoted Domain:. For example, the property Property:pathologist_surname has Domain:Pathologist. A property may have zero or more Property-parents, denoted subPropertyof:. For example, the property Property:pathologist_surname has subPropertyof:person_surname. ...............

See: http://en.wikipedia.org/wiki/Resource_Description_Framework 
 <?xml version="1.0" ?>
 <rdf:RDF
  xmlns:rdf="http://www.gwmoore.org/ldip/rdf.htm"
  xmlns:dc="http://www.gwmoore.org/ldip/dc.htm"
 <rdf:Description
  rdf:about="http://www.gwmoore.org/ldip/patient.htm"
  <dc:title>patient
  <dc:publisher>Bill_Moore
</rdf:Description>
</rdf:RDF>


 <?xml version="1.0" ?>
 <rdf:RDF
  xmlns:rdf="http://www.gwmoore.org/ldip/rdf.htm"
  xmlns:dc="http://www.gwmoore.org/ldip/dc.htm"
 <rdf:Description
  <rdf:identifier
  <rdf:version
  <rdf:registration_authority
  <rdf:language
  <rdf:obligation
  <rdf:datatype
  <rdf:maximum_occurrence
  <rdf:definition
  <rdf:has_child
  <rdf:is_a
  <rdf:comment
</rdf:Description>
</rdf:RDF>
The RDF METADATA MODEL is based upon the idea of making statements about resources in the form of a subject-predicate-object expression, called a triple in RDF terminology. The subject is the resource, the "thing" being described. The predicate is a trait or aspect about that resource, and often expresses a relationship between the subject and the object. The object is the object of the relationship or value of that trait.

A collection of RDF statements intrinsically represents a LABELLED, DIRECTED PSEUDO-GRAPH. As such, an RDF-based data model is more naturally suited to certain kinds of knowledge representation than the relational model and other ontological models traditionally used in computing today. However, in practice, RDF data is often stored in relational database representations sometimes also called triple stores, and as OWL demonstrates, additional ontologies can be built upon RDF.

An RDF-file is an .XSD file in the form of a hierarchical tree. For the present application, there is a single, ultimate parent, namely, PERSON. Every RDF-element is either a CLASS or a PROPERTY.

All classes have one or more CHILDREN, which may be either classes themselves or properties. All properties have exactly one parent, named SUBCLASSOF, or parent; and a DATATYPE, consisting of a DOMAIN and RANGE. All classes, except for PERSON, have exactly one parent, named SUBCLASSOF, or parent; but no datatype, no domain, and no range.

0.6. OWL FORMAT:



See: http://en.wikipedia.org/wiki/Web_Ontology_Language

Status: temporarily deferred while we set up the RDF-file features.

0.7. SAMPLE GROSS/MICRO DICTATIONS:




Sample Gross Dictation, Skin excision:
THE PATIENT IDENTIFICATION AGREES WITH THE TISSUE EXAMINATION FORM AND ONE CONTAINER.

1. SPECIMEN # 1 IS RECEIVED IN FORMALIN, LABELED WITH THE PATIENT'S IDENTIFICATION AND "LEFT FOREARM EXCISION" ( SPECIMEN_PROCEDURE) THE SPECIMEN CONSISTS OF ONE TAN-PINK ELLIPSE OF SKIN, WITH FOCAL AREAS OF BROWN PIGMENTATION. THE SPECIMEN IS UNORIENTED. THE SPECIMEN IS HAIR-BEARING. THE SPECIMEN MEASURES 3.5 CM IN LENGTH, 1.7 CM IN WIDTH, AND 0.3 CM IN DEPTH. THE DEEP MARGIN IS INKED BLUE. THE TIPS ARE TAKEN AND SUBMITTED IN A SEPARATE CASSETTE. THE SPECIMEN IS FURTHER SERIALLY SECTIONED ALONG ITS SHORT AXIS TO REVEAL A WELL-CIRCUMSCRIBED, LIGHT-TAN LESION, WHICH EXTENDS TO THE DEEP SURFACE. THE SPECIMEN IS SUBMITTED IN TOTO.

SUMMARY OF SECTIONS:
1-1, TIPS, 2 PIECES.
1-2, SKIN, LEFT FOREARM, LESION, 1 PIECE.
1-3, SKIN, LEFT FOREARM, REMAINING 4 PIECES.
Sample Microscopic Dictation:
SKIN,     LEFT FOREARM,     EXCISION:     ACTINIC KERATOSIS.     NO EVIDENCE OF RESIDUAL MALIGNANCY.    

COMMENT: The previous biopsy on this patient has been REVIEWED, and we concur with the original diagnosis.

Sample Gross Dictation, Esophageal biopsy:
THE PATIENT IDENTIFICATION AGREES WITH THE TISSUE EXAMINATION FORM AND ONE CONTAINER.

1. SPECIMEN # 1 IS RECEIVED IN FORMALIN, LABELED WITH THE PATIENT'S IDENTIFICATION AND "ESOPHAGUS, 35 CM" ( SPECIMEN_PROCEDURE) THE SPECIMEN CONSISTS OF THREE PIECES OF TAN-PINK TISSUE, MEASURING 0.5 CM BY 0.4 CM BY 0.3 CM IN AGGREGATE. THE SPECIMEN IS SUBMITTED IN ITS ENTIRETY.

SUMMARY OF SECTIONS:
1-1, ESOPHAGUS, 3 PIECES.

Sample Gross Dictation, Right Hemicolectomy:
THE PATIENT IDENTIFICATION AGREES WITH THE TISSUE EXAMINATION FORM AND ONE CONTAINER.

1. SPECIMEN # 1 IS RECEIVED IN THE FRESH STATE, LABELED WITH THE PATIENT'S IDENTIFICATION AND "RIGHT HEMICOLECTOMY" ( SPECIMEN_PROCEDURE) THE SPECIMEN CONSISTS OF A RIGHT ASCENDING COLON AND TERMINAL ILEUM, MEASURING 39.5 CM IN LENGTH, WITH AN AVERAGE CIRCUMFERENCE OF 4.5 CM. THE SEGMENT OF TERMINAL ILEUM MEASURES 11.2 CM IN LENGTH, WITH AN AVERAGE CIRCUMFERENCE OF 2.8 CM. THE SPECIMEN ALSO CONTAINS A VERMIFORM APPENDIX, MEASURING 10.5 CM IN LENGTH AND 1.8 CM IN DIAMETER. THE COLON HAS BEEN PREVIOUSLY OPENED BY THE SURGEON. THE SEROSAL SURFACES OF THE CECUM, COLON, AND TERMINAL ILEUM ARE GROSSLY UNREMARKABLE. AN ILL-DEFINED, CIRCUMFERENTIAL FRIABLE MASS IS SEEN AT THE PROXIMAL ASCENDING COLON. THE MASS MEASURES 4.4 CM BY 9.1 CM. SECTIONING THROUGH THE MASS REVEALS A DEPTH OF 4.1 CM. THE MASS EXTENDS TO THE PERICOLONIC FAT. IT IS 0.5 CM FROM THE RADIAL MARGIN, 12 CM FROM THE PROXIMAL ILEAL RESECTION MARGIN, AND 28.2 CM FROM THE DISTAL COLONIC MARGIN. TWO PEDUNCULATED POLYPS ARE SEEN WITHIN THE AREA OF THE MASS, MEASURING 2.5 CM BY 1.5 CM BY 0.9 CM; AND 1.5 CM BY 1.1 CM BY 0.8 CM. A THIRD POLYP IS LIKEWISE SEEN, WHICH IS 7.2 CM FROM THE ILEOCECAL VALVE, 15 CM FROM THE PROXIMAL ILEAL RESECTION MARGIN, AND 26 CM FROM THE DISTAL COLONIC RESECTION MARGIN. THE REMAINDER OF THE COLONIC MUCOSA DISPLAYS NORMAL RUGATION AND NORMAL COLOR. THE ILEAL MUCOSA IS UNREMARKABLE. THE SEROSAL SURFACE OF THE APPENDIX DISPLAYS A COBBLESTONED APPEARANCE; BUT THE MUCOSAL SURFACE IS UNREMARKABLE. FOURTEEN LYMPH NODE CANDIDATES ARE IDENTIFIED, RANGING IN MEASUREMENT FROM 0.3 CM TO 1.2 CM. REPRESENTATIVE SECTIONS ARE SUBMITTED.

SUMMARY OF SECTIONS:


1-1, ILEAL MARGIN, 1 PIECE.

1-2, DISTAL COLONIC MARGIN, 1 PIECE.

1-3, SECTION OF MASS AND CIRCUMFERENTIAL MARGIN, 1 PIECE.

1-4, SECTION OF MASS AND CIRCUMFERENTIAL MARGIN, 1 PIECE.

1-5, SECTION OF MASS AND CIRCUMFERENTIAL MARGIN, 1 PIECE.

1-6, MASS AND MARGIN, 1 PIECE.

1-7, MASS AND MARGIN, 1 PIECE.

1-8, POLYP #1, 2 PIECES.

1-9, POLYP #1, 1 PIECE.

1-10, POLYP #2, 2 PIECES.

1-11, POLYP #3, 1 PIECE.

1-12, NORMAL COLON AT 5 CM. 1 PIECE.

1-13, NORMAL COLON AT 10 CM. 1 PIECE.

1-14, NORMAL COLON AT 15 CM. 1 PIECE.

1-15, LYMPH NODE CANDIDATES, 6 PIECES.

1-16, LYMPH NODE CANDIDATES, 4 PIECES.

1-17, ONE LYMPH NODE, BISECTED, 2 PIECES.

1-18, THREE LYMPH NODES, 3 PIECES.

1-19, APPENDIX, TIP AND CROSS SECTION, 3 PIECES.

1-20, SUSPICIOUS APPENDIX SEROSA, 1 PIECE.

1-21, NORMAL ILEAL MUCOSA, 1 PIECE.
Sample Microscopic Dictation:
RIGHT COLON,     RIGHT HEMICOLECTOMY:    COLON AND CECUM:    INFILTRATING, MODERATELY DIFFERENTIATED ADENOCARCINOMA , EXTENDING TO SUBSEROSA.
MAXIMUM TUMOR DIMENSION: 9.1 CM.
MARGINS OF RESECTION: UNINVOLVED.
TWELVE LYMPH NODES WITH NO EVIDENCE OF MALIGNANCY.
THREE TUBULAR ADENOMAS.
ILEUM: NO SIGNIFICANT PATHOLOGIC ABNORMALITY.
VERMIFORM APPENDIX: FIBRINOUS SEROSITIS.
VERMIFORM APPENDIX: FECALITH.
VERMIFORM APPENDIX: MESOTHELIAL INCLUSION CYSTS.

AJCC/UICC PROTOCOL.

MACROSCOPIC:
SPECIMEN TYPE: RIGHT HEMICOLECTOMY
TUMOR SITE: ASCENDING COLON
TUMOR CONFIGURATION: ANNULAR.

MICROSCOPIC:
HISTOLOGIC TYPE: ADENOCARCINOMA.
HISTOLOGIC GRADE: LOW-GRADE, MODERATELY DIFFERENTIATED.
PROXIMAL MARGIN: UNINVOLVED.
DISTAL MARGIN: UNINVOLVED.
CIRCUMFERENTIAL MARGIN: UNINVOLVED.
LYMPHATIC INVASION: ABSENT
VENOUS INVASION: ABSENT
PERINEURAL INVASION: ABSENT
ADDITIONAL PATHOLOGIC FINDINGS: TUBULAR ADENOMA.
LYMPH NODE STATUS: TWELVE LYMPH NODES WITH NO EVIDENCE OF MALIGNANCY.
PATHOLOGIC STAGING: T3N0MX.   

Sample Gross Dictation, Right Nephrectomy:
THE PATIENT IDENTIFICATION AGREES WITH THE TISSUE EXAMINATION FORM AND ONE CONTAINER.

1. SPECIMEN # 1 IS RECEIVED IN FORMALIN, LABELED WITH THE PATIENT'S IDENTIFICATION AND "RIGHT NEPHRECTOMY" ( SPECIMEN_PROCEDURE) THE SPECIMEN CONSISTS OF ONE RIGHT NEPHRECTOMY SPECIMEN, WEIGHING 1,235 GRAMS AND MEASURING 19.0 CM BY 18.5 CM BY 8.2 CM. THE SPECIMEN HAS ABUNDANT PERINEPHRIC ADIPOSE TISSUE. GEROTA'S FASCIA IS INTACT. 2.5 CM. THE URETERAL MARGINS AND VASCULAR MARGINS ARE IDENTIFIED AND TAKEN AS SHAVE MARGINS. THE OUTER SURFACE OF THE SPECIMEN IS INKED BLACK. THE RIGHT ADRENAL GLAND IS IDENTIFIED IN THE SUPRARENAL FAT. THE RIGHT ADRENAL GLAND MEASURES 6.0 CM BY 4.2 CM BY 2.5 CM. THE SPECIMEN IS SERIALLY SECTIONED TO REVEAL A BRIGHT YELLOW-TO-ORANGE, LOBULATED, GLANDULAR SURFACE, WITH NO FOCAL NODULES IDENTIFIED. THE ADRENAL GLAND DOES NOT APPEAR TO BE INVOLVED BY THE TUMOR. REPRESENTATIVE SECTIONS ARE SUBMITTED. OPENING THE RENAL VEIN ALONG ITS LONGITIDINAL AXIS REVEALS A PATENT LUMEN THAT IS UNREMARKABLE AND UNINVOLVED BY THE TUMOR. BI-VALVING THE KIDNEY AT THE PELVIS REVEALS A BRIGHT YELLOW-TO-ORANGE, VARIGATED, ILL-DEFINED MASS, WHICH APPEARS TO INVOLVE THE RENAL PELVIS, THE ENTIRE SUPERIOR POLE, AND ONE QUARTER OF THE INFERIOR POLE. THE MASS MEASURES 12.2 CM IN THE MEDIAL TO LATERAL DIMENSION, 8.7 CM IN THE SUPERIOR TO INFERIOR DIMENSION AND 7.7 CM FROM ANTERIOR TO POSTERIOR. THE PERIRENAL FAT DOES NOT APPEAR TO BE INVOLVED BY THE TUMOR. THE TUMOR DOES NOT APPEAR TO PENETRATE THE RENAL CAPSULE, BUT DOES APPEAR TO ABUT IT. THE TUMOR SHOWS EXTENSIVE NECROSIS AND HEMORRHAGE. THERE ARE TWO DISTINCT AREAS WITHIN THE TUMOR, ONE WHICH IS MORE YELLOW THAN RED, AND FIRM; THE OTHER WHICH IS MORE HETEROGENEOUS AND NECROTIC. TWO SIMPLE CYSTS ARE IDENTIFIED WITHIN THE RENAL CORTEX. THEY MEASURE 0.5 AND 1.2 CM IN DIAMETER. NO LYMPH NODE CANDIDATES ARE IDENTIFIED NEAR THE RENAL PELVIS. REPRESENTATIVE SECTIONS ARE SUBMITTED.

SUMMARY OF SECTION:

1-1, VASCULAR AND URETERAL MARGINS, 3 PIECES.

1-2, ADRENAL GLAND, 1 PIECE.

1-3, FAT OVERLYING TUMOR, 2 PIECES.

1-4, TUMOR AND CAPSULE, 2 PIECES.

1-5, TUMOR TO NORMAL, 1 PIECE.

1-6, TUMOR, 2 PIECES.

1-7, NORMAL, 2 PIECES.

1-8, CYST, 2 PIECES.

RIGHT KIDNEY, NEPHRECTOMY: RENAL CELL CARCINOMA, CLEAR CELL TYPE, WITH EXTENSIVE NECROSIS AND HEMORRHAGE. VASCULAR ARE UNINVOLVED. URETERAL MARGINS ARE UNINVOLVED. ADRENAL GLAND IS UNINVOLVED.

AJCC/UICC PROTOCOL.

MACROSCOPIC:
SPECIMEN TYPE: RIGHT NEPRECTOMY
TUMOR SITE: SUPERIOR POLE, RIGHT KIDNEY. PELVIS, 12.2 X 8.7 X 7.7 CM, UNIFOCAL. EXTENT OF TUMOR: LIMITED TO KIDNEY.

MICROSCOPIC:
HISTOLOGIC TYPE: RENAL CELL CARCINOMA, CLEAR CELL TYPE.
HISTOLOGIC GRADE: FUHRMAN'S NUCLEAR GRADE 3.
MARGINS: UNINVOLVED. ADRENAL GLAND: UNINVOLVED BY TUMOR.
VENOUS, LYMPHATIC IVASION: ABSENT
ADDITIONAL PATHOLOGIC FINDINGS: EXTENSIVE NECROSIS AND HEMORRHAGE.
PATHOLOGIC STAGING (pTNM): T2NXMX
COMMENT: Above are four samples of gross/microscopic dictations, which have been partitioned into BOLDFACE_HIGHLIGHTED phrases and unbolded_unhighlighted phrases. The BOLDFACE_HIGHLIGHTED phrases, or KEYTERMS, all map into members of the proposed LDIP The remaining phrases, of low information content, are called "stopwords".

STOPWORDS are words of low information content, typically, articles, conjunctions, prepositions, and auxiliary verbs. In all major written and spoken languages on earty, there are a few hundred stopwords that account for over half the utterances and writings of that language. In written English: and, of, the, to, at, for,.... In spoken English, the most common stopword is I. A sequence of words with a stopword at start and end is a STOPTERM.

KEYWORDS are words of moderate or high information content.... A sequence of words with a keyword at start and end is a KEYTERM.

We propose a TRANSLATOR, written in Perl, that points a syntactically-correct dicatation into keyterms and stopwords.

0.8. PROPOSED CONSISTENCY TESTS.



0. The reason for Zulu times is that it is conceivable that, at some time in the future, a pathology test may be reported within one hour, in an earlier time zone that when it was obtained from the patient. This would cause consistency test #1 to fail falsely.

1. Pathology_report_time_obtained < Pathology_report_time_reported < Pathology_report_time_supplemented

Pathology_report_time_obtained < Pathology_report_time_reported < Pathology_report_time_amended

2. Zulu offset correct for where the pathology department is located.

3. FORMAL LOGICAL CONSISTENCY. Part of the specimen cde (or a local copy of the specimen cde) might contain pairs of mutually exclusive elements in a rulebase. Logical consistency is the assertion that no binary statement is both true and false at the same time (or for the same case).

4. Parsing the gross description for consistency and completeness of required scientifically validated data elements (SVDEs), as required by the College of American Pathologists / American College of Surgeons for accreditation as a certified Cancer Center.

5. Minimize the use of AND and IT, THEY, THEM in the gross description, since the vagueness confuses the translator.

1. TABLE OF CONTENTS.


0. Notes.
1. Table of Contents.
2. Abstract.
3. Introduction.
4. Spelling and punctuation.
5. Primary classification.
6. Proposed existing standard: image annotation on the semantic web.
7. Existing standard: Stains on CAP-ANP Inspection Checklist.
8. Existing standard: VistA® Data Definition.
9. Existing standard: Date/time convention, ISO 8601.
10. Existing standard: CAP/AJCC/UICC Specimen Checklists.
11. Detailed classification.
12. Consistency tests.
13. References.
14. Glossary.

2. ABSTRACT.



Herewith is a working draft of a proposed specimen common data element hierarchy (CDEH). ................

3. INTRODUCTION.



Anatomic pathologists are notorious packrats, and many experienced pathologists have large collections of glass slides and kodachromes, showing lesions of clinicopathologic or educational interest. Some of these old collections have now been digitized, but this process only exacerbates an already existing problem: how to file the images so that one can find them again when you want them. In computer science parlance, the images themselves are called DATA (Latin: things given), and the text-descriptions of these images, used for filing and retrieval, are called METADATA (Greek: μετα = after or beyond). There are two levels of metadata: LOW-LEVEL METADATA (features such as color, brightness, contrast, etc.) and HIGH-LEVEL METADATA, pathologic features. Low-level metadata are largely the province of image technology experts, but high-level metadata creation requires domain expertise in pathology.

The simplest approach is to use free-text metadata, but anyone who has ever tried this approach knows that it degenerates quickly into a blizzard of SMALL CELL CARCINOMA LUNG #1, SMALL CELL CARCINOMA LUNG #2, etc., or SMALL CELL CARCINOMA LUNG 8/10/2003, SMALL CELL CARCINOMA LUNG 9/18/2005, and you still can't remember which small cell carcinoma lung is the one you really want. Free text also has no spelling or completeness enforcement, so it is possible to write SMAL CEL CA, forgetting to include the body-site, and then never be able to find the case again. These problems deteriorate rapidly for large-sized collections.

Herewith is a working draft of a proposed common data element hierarchy (CDEH) for pathology specimens. The CDEH is not a requirement or a prescription, but rather a framework into which pathology metadata can be placed, for easy retrieval. The basic principles of this CDEH are:
1. Simplicity in design.
2. Simple spelling/syntax conventions.
3. Comprehensiveness.
4. Use of existing standards, where possible.
5. Convertability to rdf/owl format.
6. Logical consistency.
7. Public-domain demonstration computer scripts.
The specimen CDEH is a simple hierarchical tree, with a single, common ancestor, or ORIGIN. Each PARENT has any number of CHILDREN, denoted by carriage_return and indentation. Every new concept has a distinct name, which is expressible exclusively as lower_case letters and underlines (_). An attempt should be made at COMPREHENSIVENESS, by eventually storing all vocabulary and syntax at a community website, with a simple mechanism for updating.

The reason for public-domain demonstration computer scripts is so that potential users can get a feel for how these CDEH principles function in their own work environment, before making a big or irrevocable commitment to a particular system or vendor.

4. SPELLING AND PUNCTUATION.



Spelling/punctuation conventions.
1. American-English spelling.
2. All lower case.
3. Blank_space and hyphen replaced with underline (_).
4. No apostrophe or apostrophe_s. All nouns singular.
5. Inheritance denoted by carriage-return and indentation.
6. Existing standards used, where applicable and freely available.
7. Date/time convention compliant with International Standards Organization, ISO 8601.
8. ... denotes "repeat previous parent-line" (for clarity only).
9. : denotes carriage-return and indentation (parenthood, see below), where clear from context.
10. , denotes carriage-return only (sibship, see below), where clear from context.
11. For names of histologic stains and methods, all stopwords or barrierwords (prepositions, conjunctions, articles, pronouns, auxiliary verbs, and method, modified, stain, solution, and technique) are removed or placed at the end of the phrase. For example, alizarin stain for calcium becomes alizarin_calcium_stain.
For formal tests of consistency, completeness, and non-redundancy, carriage-return-indentation denotes if...then and carriage-return-only denotes inclusive_or.

5. PRIMARY CLASSIFICATION.

The major classification headings are as follows: 
 patient
    patient_image
    pathology_report
       specimen
          specimen_container
             specimen_container_tissue_block
                specimen_container_tissue_block_slide
                   specimen_container_tissue_block_slide_stain
                      specimen_container_tissue_block_slide_stain_image
 tissue_orientation
 histologic_stain
    histologic_stain_name
    histologic_stain_class
    histologic_stain_method
    histologic_stain_manufacturer
 tissue_fixative
 image
In colon/comma notation, this primary hierarchy can be presented more compactly (but less readably) as:
0:patient, tissue_orientation, histologic_stain, tissue_fixative, image.
patient: patient_image, pathology_report.
pathology_report: specimen: specimen_container: specimen_container_tissue_block: specimen_container_tissue_block_slide: specimen_container_tissue_block_slide_stain: specimen_container_tissue_block_slide_stain_image.
histologic_stain: histologic_stain_name, histologic_stain_class, histologic_stain_method, histologic_stain_manufacturer.
That is, the origin, 0, has five children, namely, patient, tissue_orientation, histologic_stain, tissue_fixative, image. In turn, the patient has two children, namely, patient_image, pathology_report. The specimen has any number of containers, specimen_container_1, specimen_container_2, specimen_container_3, specimen_container_4,.... The specimen_container has any number of tissue_blocks, namely specimen_container_tissue_block_1, specimen_container_tissue_block_2, specimen_container_tissue_block_3, specimen_container_tissue_block_4,..., etc.

A Perl program can be used to convert this hierarchy into the corresponding rdf format, as for example: 
 <rdf:RDF xml:base="http://www.netautopsy.org/ldip/
  xmlns="http://www.netautopsy.org/ldip/
  xmlns.dc="http://www.netautopsy.org/ldip/spcmncde.htm
  xmlns.rdf="http://www.netautopsy.org/ldip/spcmncde.htm
                             
  <rdf:Description rdf:about="spcmncde.htm"/>
   <dc:title> Specimen CDE Hierarchy</dc:title> 
   <dc:creator> G. William Moore, MD, PhD</dc:title> 
                             
 <rdf:Hierarchy/>
   <dc:patient>
     <dc:patient.image> </dc:patient.image>
       <dc:patient.report>
         <dc:patient.report.specimen>
           <dc:patient.report.specimen.container>
             <dc:patient.report.specimen.container.tissue_block>
               <dc:patient.report.specimen.container.tissue_block.slide>
                   ................
               </dc:patient.report.specimen.container.tissue_block.slide>
             </dc:patient.report.specimen.container.tissue_block>
           </dc:patient.report.specimen.container>
         </dc:patient.report.specimen>
       </dc:patient.report>
     </dc:patient>
 </rdf:RDF>

6. PROPOSED EXISTING STANDARD:
IMAGE ANNOTATION ON THE SEMANTIC WEB.
W3C WORKING DRAFT 22 MARCH 2006.



The Worldwide Web Consortium (WC3) has proposed a standard for image annotation, based upon semantic web languages, such as RDF and OWL.

The first working draft was issued on March 22, 2006, and was brought to the LDIP committee by Dr. Robert Leif. Both the editorial staff and the document content itself are weak in domain specialists for biomedicine.
http://www.w3.org/TR/2006/WD-swbp-image-annotation-20060322/
AVAILABLE TOOLS FOR IMAGE ANNOTATION.
1. Type of Content.
2. Type of Metadata.
3. Format of Metadata.
4. Annotation Level: proffered vocabulary and free text.
5. Client-side requirement.
6. License conditions.
7. Collaborative or individual.
8. Granularity: segment-based versus file-based.
9. Threaded versus unthreaded.
10. Access control.

7. EXISTING STANDARD:
STAINS LISTED ON CAP-ANP INSPECTION CHECKLIST.



The following stains are listed on the inspection checklist for the College of American Pathologists (CAP), in the ANP (=anatomic pathology) and CYP (=cytopathology) sections:

QUESTION: ANP.21450 PHASE II:
1. Acid fast organisms;
2. Iron;
3. Bacteria;
4. Elastic tissues;
5. Fungi or pneumocystis;
6. Mucin;
7. Connective tissue;
8. Myelin;
9. Nerve fibers;
10. Periodic acid Schiff.
11. Glycogen;
12. Reticulin fibers;
13. Amyloid;
14. Methyl green-pyronine.

8. EXISTING STANDARD:
VistA® DATA DEFINITION.



See: VistA FileManager data definition:
http://www.netautopsy.org/axsop/axsop233.htm#ap233s42
for U. S. Tissue Examination Form (U. S. Standard Form 515):
http://www.netautopsy.org/axsop/ussf515.pdf
As follows: 
 .01       DATE/TIME SPECIMEN TAKEN (MRDXO), [0;1]
 .011      SPECIMEN SUBMITTED BY (F), [0;5]
 .012      SPECIMEN (Multiple-63.812), [.1;0]
           .01  SPECIMEN (MRF), [0;1]
           .02  SURGICAL WORKLOAD PROFILE (*P60'), [0;2]
           .03  GROSS DESCRIPTION/CUTTING DATE (D), [0;3]
           .04  GROSS DESCRIPTION/CUTTING TYPE (S), [0;4]
           .05  GROSS DESCRIPTION COUNTED (S), [0;5]
           1    PARAFFIN BLOCK (Multiple-63.8121), [1;0]
                .01  PARAFFIN BLOCK ID (MFX), [0;1]
                .02  DATE/TIME BLOCK PREPARED (D), [0;2]
                .03  BLOCK COUNTED (S), [0;3]
                1    STAIN/PROCEDURE (Multiple-63.8122), [1;0]
                     .01  STAIN/PROCEDURE (M*P60'X), [0;1]
                     .02  SLIDES PREPARED (#) (NJ3,0), [0;2]
                     .03  CONTROL SLIDES (#) (NJ2,0), [0;3]
                     .04  DATE/TIME SLIDES STAINED (DX), [0;4]
                     .05  DATE/TIME SLIDES EXAMINED (DX), [0;5]
                     .06  SLIDES COUNTED (#) (NJ3,0), [0;6]
                     .07  LABELS TO PRINT (NJ2,0), [0;7]
                     .09  NON-CONTROL SLIDES COUNTED (NJ3,0), [0;9]
           2    PLASTIC BLOCK (Multiple-63.822), [2;0]
                .01  PLASTIC  BLOCK ID (MFX), [0;1]
                .02  DATE/TIME BLOCK PREPARED (D), [0;2]
                .03  BLOCK COUNTED (S), [0;3]
                1    PLASTIC STAIN/PROCEDURE (Multiple-63.823), [1;0]
                     .01  PLASTIC STAIN/PROCEDURE (M*P60'X), [0;1]
                     .02  PLASTIC SLIDES PREPARED (#) (NJ3,0), [0;2]
                     .03  CONTROL SLIDES (#) (NJ2,0), [0;3]
                     .04  DATE/TIME SLIDES STAINED (DX), [0;4]
                     .05  DATE/TIME SLIDES EXAMINED (DX), [0;5]
                     .06  SLIDES COUNTED (#) (NJ3,0), [0;6]
                     .07  LABELS TO PRINT (NJ2,0), [0;7]
                     .09  NON-CONTROL SLIDES COUNTED (NJ3,0), [0;9]
           3    FROZEN TISSUE BLOCK (Multiple-63.824), [3;0]
                .01  FROZEN  TISSUE ID (MFX), [0;1]
                .02  DATE/TIME FROZEN PREPARED (D), [0;2]
                .03  FROZEN COUNTED (S), [0;3]
                .04  FROZEN TISSUE BLOCK TYPE (RS), [0;4]
                1    STAIN/PROCEDURE (Multiple-63.825), [1;0]
                     .01  STAIN/PROCEDURE (M*P60'X), [0;1]
                     .02  SLIDES PREPARED (#) (NJ3,0), [0;2]
                     .03  CONTROL SLIDES (#) (NJ2,0), [0;3]
                     .04  DATE/TIME SLIDES STAINED (DX), [0;4]
                     .05  DATE/TIME SLIDES EXAMINED (DX), [0;5]
                     .06  SLIDES COUNTED (#) (NJ3,0), [0;6]
                     .07  LABELS TO PRINT (NJ2,0), [0;7]
                     .09  NON-CONTROL SLIDES COUNTED (NJ3,0), [0;9]
 .013      BRIEF CLINICAL HISTORY (Multiple-63.813), [.2;0]
           .01  BRIEF CLINICAL HISTORY (W), [0;1]
 .014      PREOPERATIVE DIAGNOSIS (Multiple-63.814), [.3;0]
           .01  PREOPERATIVE DIAGNOSIS (W), [0;1]
 .015      OPERATIVE FINDINGS (Multiple-63.815), [.4;0]
           .01  OPERATIVE FINDINGS (W), [0;1]
 .016      POSTOPERATIVE DIAGNOSIS (Multiple-63.816), [.5;0]
           .01  POSTOPERATIVE DIAGNOSIS (W), [0;1]
 .02       PATHOLOGIST (*P200'X), [0;2]
 .021      RESIDENT PATHOLOGIST (*P200'X), [0;4]
 .03       DATE REPORT COMPLETED (DX), [0;3]
 .06       SURGICAL PATH ACC # (RFIX), [0;6]
 .07       SURGEON/PHYSICIAN (*P200'X), [0;7]
 .08       PATIENT LOCATION (F), [0;8]
 .09       TYPIST (F), [0;9]
 .1        DATE/TIME SPECIMEN RECEIVED (RDX), [0;10]
 .11       REPORT RELEASE DATE/TIME (DIX), [0;11]
 .13       RELEASED BY (P200'), [0;13]
 .14       TC CODE (S), [0;14]
 .15       ORIGINAL RELEASE DATE (D), [0;15]
 .97       DELAYED REPORT COMMENT (Multiple-63.0897), [97;0]
           .01  DELAYED REPORT COMMENT (MFX), [0;1]
 .99       COMMENT (Multiple-63.98), [99;0]
           .01  COMMENT (MFX), [0;1]
 1         GROSS DESCRIPTION (Multiple-63.81), [1;0]
           .01  GROSS DESCRIPTION (W), [0;1]
 1.1       MICROSCOPIC DESCRIPTION (Multiple-63.811), [1.1;0]
           .01  MICROSCOPIC DESCRIPTION (W), [0;1]
 1.2       SUPPLEMENTARY REPORT (Multiple-63.817), [1.2;0]
           .01  SUPPLEMENTARY REPORT DATE/TIME (D), [0;1]
           .02  RELEASE SUPPLEMENTARY REPORT (S), [0;2]
           1    DESCRIPTION (Multiple-63.818), [1;0]
                .01  DESCRIPTION (W), [0;1]
           2    SUPPLEMENTARY REPORT MODIFIED (Multiple-63.8172), [2;0]
                .01  SUPPLEMENTARY REPORT MODIFIED (D), [0;1]
                .02  PERSON MODIFYING TEXT (P200'), [0;2]
                1    PREMODIFICATION TEXT (Multiple-63.81721), [1;0]
                     .01  PREMODIFICATION TEXT (W), [0;1]
 1.3       FROZEN SECTION (Multiple-63.801), [1.3;0]
           .01  FROZEN SECTION (W), [0;1]
 1.4       SURGICAL PATH DIAGNOSIS (Multiple-63.802), [1.4;0]
           .01  SURGICAL PATH DIAGNOSIS (W), [0;1]
 4         DATE MICROSCOPIC EXAM MODIFIED (Multiple-63.84), [4;0]
           .01  DATE MICROSCOPIC EXAM MODIFIED (MD), [0;1]
           .02  PERSON MODIFYING TEXT (P200'), [0;2]
           1    PREMODIFICATION TEXT (Multiple-63.841), [1;0]
                .01  PREMODIFICATION TEXT (W), [0;1]
 5         DATE DIAGNOSIS MODIFIED (Multiple-63.085), [5;0]
           .01  DATE DIAGNOSIS MODIFIED (MD), [0;1]
           .02  PERSON MODIFYING TEXT (P200'), [0;2]
           1    PREMODIFICATION TEXT (Multiple-63.0851), [1;0]
                .01  PREMODIFICATION TEXT (W), [0;1]
 6         DATE FROZEN SECTION MODIFIED (Multiple-63.086), [6;0]
           .01  DATE FROZEN SECTION MODIFIED (MD), [0;1]
           .02  PERSON MODIFYING TEXT (P200'), [0;2]
           1    PREMODIFICATION TEXT (Multiple-63.0861), [1;0]
                .01  PREMODIFICATION TEXT (W), [0;1]
 7         DATE GROSS DESCRIPTION CHANGED (Multiple-63.087), [7;0]
           .01  DATE GROSS DESCRIPTION CHANGED (MD), [0;1]
           .02  PERSON MODIFYING TEXT (P200'), [0;2]
           1    PREMODIFICATION TEXT (Multiple-63.0871), [1;0]
                .01  PREMODIFICATION TEXT (W), [0;1]
 9         QA CODE (Multiple-63.089), [9;0]
           .01  QA CODE (M*P62.5'X), [0;1]
 10        ORGAN/TISSUE (Multiple-63.12), [2;0]
           .001 NUMBER (NJ2,0), [ ]
           .01  ORGAN/TISSUE (M*P61'X), [0;1]
           1    FUNCTION (Multiple-63.85), [3;0]
                .01  FUNCTION (M*P61.3'X), [0;1]
           1.5  PROCEDURE (Multiple-63.82), [4;0]
                .01  PROCEDURE (M*P61.5'X), [0;1]
                .02  RESULT (S), [0;2]
           2    WEIGHT (gm) (NJ8,3X), [0;3]
           3    DISEASE (Multiple-63.15), [1;0]
                .01  DISEASE (M*P61.4'X), [0;1]
           4    MORPHOLOGY (Multiple-63.16), [2;0]
                .01  MORPHOLOGY (M*P61.1'X), [0;1]
                1    ETIOLOGY (Multiple-63.17), [1;0]
                     .01  ETIOLOGY (M*P61.2'X), [0;1]
           5    SPECIAL STUDIES (Multiple-63.819), [5;0]
                .01  SPECIAL STUDIES (MS), [0;1]
                .02  DATE (RD), [0;2]
                .03  ID # (F), [0;3]
                1    DESCRIPTION (Multiple-63.821), [1;0]
                     .01  DESCRIPTION (W), [0;1]
 80        ICD DIAGNOSIS (Multiple-63.88), [3;0]
           .01  ICD DIAGNOSIS (MP80'X), [0;1]
 2005      IMAGE (Multiple-63.82005), [2005;0]
           .01  IMAGE (MP2005'), [0;1]
           .02  SPECIMEN (NJ2,0), [0;2]

9. EXISTING STANDARD:
DATE/TIME CONVENTION, ISO 8601.

VistA® DATE/TIME CONVENTION. The Veterans' Affairs VistA® date/time convention, as modified, consistently allows all dates to one-second accuracy, including approximate dates and times. This modified VistA® date/time notation is consistent with the International Standards Organization standard, ISO 8601. The system employs the Gregorian Calendar, starting at year 0, corresponding to 1 B.C. ("Before Christ") or 1 B.C.E. ("Before Common Era") in the usual reckoning. Historically, the Gregorian calendar was developed in the late 16th century, named after Pope Gregory the Great (Gregory XIII), in order to stabilize the date of Easter in the Roman Catholic Church.

The format is: ±yyyymmdd.hhmmssZ±hhmm where yyyy is the four-digit year; the first mm is the month; dd is day; first hh is hours; the second mm is minutes; ss is seconds; Z denotes Zulu, or Greenwich Mean Time (GMT); ± is the direction of offset for the local time zone (+ for west of Greenwich, including Berlin, Moscow, Beijing, Tokyo, etc; - for east of Greenwich, including Baltimore, Chicago, Denver, Los Angeles, etc.); the second hh is hour offset for the local time zone; and the third mm is minutes offset for the local time zone (+0100 for Berlin; +0000 for London; -0500 for Baltimore, -0600 for Chicago, -0700 for Denver, -0800 for Los Angeles, etc., during winter). (Minute offsets are necessary, since Nova Scotia, Canada, and Eastern Australia have half-hour offsets.) Note that the offset changes during daylight savings time, which occurs at different dates in different political jurisdictions. All dates between 10,000 B.C.E. and 9,999 C.E. and the present are uniquely representable by this standard. (Earlier times would require more leading zeros.) See:
http://en.wikipedia.org/wiki/ISO_8601
For approximate date/time information, substitute zeros. For example, Abraham Lincoln's birthdate is February 12, 1809, but we do not know what time of day he was born. Therefore, his modified Vista® birthdate is: 18090212.000000Z-0500, since Kentucky is in the Eastern Standard Time zone (Zulu offset minus five hours) during winter. Believe it or not, there are some patients who only know their year of birth. For Abraham Lincoln, this would be: 18090000.000000Z-0500

For example, consider four patients, each of whom has a specimen taken at 6 PM local time, March 15, 2006, in each of the four time zones of the continental USA. Assuming that we use the Microsoft® convention for midnight (see below), then we have:
HospitalPlaceTime ZoneLocal Date/Time Greenwich Date/TimeISO_8601 Date
Baltimore Veterans Affairs
Medical Center 		Baltimore, MDEastern March 15, 2006, 18:00 March 15, 2006, 23:00 +200603152300.000000Z-0500
Edward Hines, Jr, Veterans Affairs
Medical Center 		Hines, ILCentral March 15, 2006, 18:00 March 16, 2006, 00:00 +200603160000.000000Z-0600
Denver Veterans Affairs
Medical Center 		Denver, CO Mountain March 15, 2006, 18:00 March 16, 2006, 01:00 +200603160100.000000Z-0700
West Los Angeles Veterans Affairs
Medical Center 		Los Angeles, CAPacific March 15, 2006, 18:00 March 16, 2006, 02:00 +200603160200.000000Z-0800
That is, 6 PM Baltimore, MD, time, March 15, 2006, is 11 PM, March 15, 2006, in Greenwich, England; 6 PM Hines, IL, time, March 15, 2006, is midnight, March 16, 2006, in Greenwich, England, assuming that midnight belongs to the following day; 6 PM Denver, CO, time, March 15, 2006, is 1 AM, March 16, 2006, in Greenwich, England; and 6 PM Denver, CO, time, March 15, 2006, is 2 AM, March 16, 2006, in Greenwich, England.


Traditionally, MIDNIGHT BELONGS TO THE PREVIOUS DAY, i.e., the twenty-four clock includes 24:00 BUT NOT 0:00. However, in Microsoft® software, MIDNIGHT BELONGS TO THE FOLLOWING DAY, i.e., the twenty-four clock includes 0:00 BUT NOT 24:00. I couldn't figure out which option is preferred by International Standards Organization, ISO 8601, based upon the Wikipedia writeup. Since a great deal of computer systems employ Microsoft® software, I believe that the Microsoft® standard has become de-facto. Actually, the point is somewhat moot, since, say, +20060315.2400Z+0500 (i.e.,ÿ20exactly 7 PM, March 15, 2006, in Baltimore, MD) is equivalent to +20060316.0000Z+0500 (also exactly 7 PM, March 15, 2006, in Baltimore, MD). However, the first notation corresponds to the last moment of March 15, 2006, in Greenwich, England; and the second notation corresponds to the first moment of March 16, 2006, in Greenwich, England. It is merely an esthetic issue that there should be a unique representation for the exact same moment.


Furthermore, this dating notation provides an internal CONSISTENCY TEST for the specimen common data elements. For example, the pathology_report_lab_identifier_address and specimen_time_obtained suffice to determine if the Zulu-offset is consistent.

Consider the following interesting examples from history. I have no idea how the dates were calculated for B.C.E. events, such as the founding of Rome or Qin Shi-Huang's death. For the death of Julius Caesar, the point is moot, because there is less than a one-day offset for events occuring in the first century B.C.E. Julian or Gregorian calendar, regardless, Julius Caesar still died on the Ides of March (i.e., March 15, 44 B.C.E.).
EventPlaceConventional Date Gregorian DateISO_8601 Date
First Autopsy. India5000 B.C.E5000 B.C.E. -49990000.000000Z+0600
Death of Ramesses II,
Greatest Egyptian Pharoah. 		Egypt 1212 B.C.E. 1212 B.C.E. -12110000.000000Z+0200.
Founding of Rome. Rome, Italy. April 21, 753 B.C.E. April 21, 753 B.C.E. -07520421.000000Z+0100
Death of Qin Shi-Huang,
First Emperor of China. 		Eastern China September 10, 210 B.C.E. September 10, 210 B.C.E. -02090910.000000Z+0800.
Death of Julius Caesar,
First Emperor of Rome. 		Rome, Italy. March 15, 44 B.C.E. March 15, 44 B.C.E. -00430315.000000Z+0100
Signing of Magna Carta. Runnymede, England. June 15, 1215. June 22, 1215. +12150622.000000Z+0000
Second Failed Invasion
of Japan by Mongols. 		Hakata Bay, Japan August 15, 1281. August 22, 1281. +12810822.000000Z+0900
Arrival of Johannes Kepler
at Tycho Brahe's Laboratory. 		Prague, Czech Republic. January 1, 1600. January 11, 1600. +16000111.000000Z+0100
Death of Miguel de Cervantes-Saavedra. Madrid, Spain. April 23, 1616. April 23, 1616. +16160423.000000Z+0100
Death of William Shakespeare. Stratford, England. April 23, 1616. May 3, 1616. +16160503.000000Z+0000
Birth of Sir Isaac Newton. Lincolnshire, England. December 25, 1642. January 4, 1643. +16430104.000000Z+0000
Birth of Prof. Rudolf Virchow. Schivelbein, Germany. October 13, 1821. October 13, 1821. +18211013.000000Z+0100
Birth of Prof. Elie Metchnikoff. Kharkiv, Ukraine. May 16, 1845. May 29, 1845. +18450328.000000Z+0200
The Gregorian calendar was adopted on October 15, 1582, in Roman Catholic Spain, Portugal, and most of Italy; but not until September 2, 1752, in Protestant England and Scotland. Thus, Cervantes died on April 23, 1616, in Roman Catholic Spain, and likewise on April 23, 1616, on the Gregorian Calendar. However, Shakespeare died ten days later on April 23, 1616 (the traditional date of Shakespeare's death), on the Julian Calendar in Protestant Great Britain, corresponding to May 3, 1616, on the Gregorian Calendar. The Gregorian Calendar was never adopted by the Russian Empire, and was adopted after the October, 1918, revolution, that formed the Soviet Union. By that time, the Julian Calendar had fallen 13 days behind the Gregorian calendar. Note the offset in Metchnikoff's birthdate.

10. EXISTING STANDARD:
CAP/AJCC/UICC CANCER CHECKLISTS.



CAP/AJCC/UICC CHECKLISTS: "The College of American Pathologists (CAP) produces cancer protocols as a resource to pathologists in effectively delivering the information necessary to provide quality patient care. The protocols consist of cancer case summaries (checklists) accompanied by background documentation. The background documentation includes detailed outlines, explanatory notes, and references, and it is presented to you for information only. The American College of Surgeons Commission on Cancer (ACS CoC) has recognized the value of the CAP cancer checklists in caring for cancer patients. Starting January 1, 2004, it mandated that pathologists at CoC-approved cancer programs include only the scientifically validated or regularly used data elements of the checklists in their surgical pathology reports on cancer specimens.

"Beginning January 1, 2004, the American College of Surgeons Commission on Cancer mandated new standards through its approvals program. New ACS CoC standards have been published and are available through the ACS CoC. One new standard requires that pathologists at CoC-approved cancer programs include all scientifically validated or regularly used data elements of the checklists in their reports for each site and specimen. The required data elements are the non-asterisked elements in the checklists. The ACS standard does not require the actual use of the CAP checklist. The ACS mandate also does not require a specific format for pathology reports. Further, the data elements mandated by the ACS CoC are not exclusive of any other data, but are the minimum requirement for inclusion in the pathology report.

"Not all elements of each checklist are scientifically and peer validated or regularly used in patient care; therefore, some elements are not required as part of the ACS mandate. Elements that are not scientifically validated or regularly used in patient care are marked with an asterisk on the checklists. Although the asterisked elements are not yet fully validated or regularly used, they may be clinically important and are, therefore, included in the checklists as suggested elements of the pathology report."

See: http://www.cap.org

11. DETAILED CLASSIFICATION.



Proposed specimen CDE table: 
 patient
    patient_name
    patient_social_security_number
    patient_date_of_birth
    patient_hospital_id
    patient_gender
    patient_ethnicity
    patient_image
       patient_image_number
       patient_image_time
       patient_image_method
       patient_image_manufacturer
       patient_specimen_container_tissue_block_slide_histologic_stain_image_number
    pathology_report
       pathology_report_accession
       pathology_report_lab_identifier
          pathology_report_lab_identifier_name
          pathology_report_lab_identifier_address
       pathology_report_time
          pathology_report_time_obtained
          pathology_report_time_received
          pathology_report_time_reported
          pathology_report_time_amended
          pathology_report_time_supplemented
       pathology_report_submission
          pathology_report_submission_physician
          pathology_report_submission_service
          pathology_report_submission_patient_location
       pathology_report_clinical
          pathology_report_clinical_brief_clinical_history
          pathology_report_clinical_preoperative_diagnosis
          pathology_report_clinical_operative_findings
          pathology_report_clinical_postoperative_diagnosis
       pathology_report_pathologist
       pathology_report_procedure
          pathology_report_procedure_name
          pathology_report_procedure_cui
       pathology_report_billing
          pathology_report_billing_technical
          pathology_report_billing_professional
             pathology_report_billing_professional_surg_path_level_1
                ...gross only (tooth, prosthesis, foreign body, bunion, ....)
             pathology_report_billing_professional_surg_path_level_2
                ...microscopic_simple (vas deferens, incidental appendix, atheromatous plaque, ....)
             pathology_report_billing_professional_surg_path_level_3
                ...microscopic_routine (gallbladder, inflamed appendix, colostomy stoma, ....)
             pathology_report_billing_professional_surg_path_level_4
                ...microscopic_biopsy_diagnosis (cervix, colon, lymph node, larynx, lung,....)
             pathology_report_billing_professional_surg_path_level_5
                ...microscopic_excision_ordinary (mastectomy no tumor, colectomy no tumor, cervical cone, ....)
             pathology_report_billing_professional_surg_path_level_6
                ...microscopic_excision_complex (mastectomy for tumor, colectomy for tumor, lung lobectomy, ....)


       specimen
          specimen_name
          specimen_cui
          specimen_organ
             ...cardiovascular
                ...heart
                   ...atrium
                      ...right_atrium
                      ...left_atrium
                   ...ventricle
                      ...right_ventricle
                      ...left_ventricle
                   ...atrioventricular_valve
                   ...semilunar_valve
                ...great_vessel
                   ...great_artery
                      ...aorta
                      ...pulmonary_artery
                   ...great_vein
                      ...inferior_vena_cava
                      ...superior_vena_cava
                      ...pulmonary_vein
                ...artery
                ...capillary
                ...vein
             ...respiratory
                ...mainstem_bronchus
                ...left_main_bronchus
                ...right_main_bronchus
                ...lung
                   ...right_lung
                   ...left_lung
             ...gastrointestinal
                ...tubular
                   ...esophagus
                   ...stomach
                   ...duodenum
                   ...jejunum
                   ...ileum
                   ...cecum
                   ...appendix
                   ...ascending_colon
                   ...transverse_colon
                   ...descending_colon
                   ...sigmoid_colon
                   ...rectum
                   ...anus
                ...hepatobiliary
                   ...liver
                   ...gallbladder
                   ...bile_duct
                      ...right_hepatic_duct
                      ...left_hepatic_duct
                      ...common_bile_duct
                   ...pancreas
                   ...ampulla_vater
             ...genitourinary
                   ...kidney
                      ...renal_cortex
                         ...renal_cortex_upper_pole
                         ...renal_cortex_middle
                         ...renal_cortex_lower_pole
                      ...renal_medulla
                      ...renal_pelvis
                   ...ureter
                      ...ureter_right
                      ...ureter_left
                   ...urinary_bladder
                   ...male
                      ...urethra
                         ...prostatic_urethra
                         ...penile_urethra
                      ...penis
                      ...testis
                   ...female
                      ...urethra
                      ...ovary
                      ...ovarian_tube
                      ...uterus
                         ...cornu_uteri
                         ...corpus_uteri
                         ...cervix_uteri
                      ...vagina
                         ...upper_third
                         ...lower_two_thirds
                      ...vulva
             ...endocrine
                ...pituitary
                ...thyroid
                ...parathyroid
                ...endocrine_pancreas
                ...adrenal
                ...female
                   ...ovary
                ...male
                   ...testis
             ...integumentary
             ...lymphoreticular
                ...spleen
                ...lymph_node
                ...afferent_lymphatic
             ...central_nervous_system
             ...musculoskeletal
          specimen_unique_identifier
          specimen_container
             specimen_container_number
             specimen_container_label
             specimen_container_gross
                specimen_container_gross_collected
                   specimen_container_gross_collected_time
                   specimen_container_gross_collected_surgical_biopsy
                   specimen_container_gross_collected_surgical_excision
                   specimen_container_gross_collected_aspiration
                specimen_container_gross_description
                specimen_container_gross_lesion_size
                specimen_container_gross_specimen_size
                specimen_container_gross_specimen_orientation
                specimen_container_gross_pieces
                   specimen_container_gross_pieces_number
                      ...one
                      ...two
                      ...three
                      ...four
                      ...multiple
                   specimen_container_gross_pieces_dimension
             specimen_container_tissue_block
                specimen_container_tissue_block_number
                specimen_container_tissue_block_name
                specimen_container_tissue_block_site
                   specimen_container_tissue_block_site_organ
                   specimen_container_tissue_block_site_within_organ
                specimen_container_tissue_block_processing
                   ...standard_paraffin
                   ...microwave
                   ...other_tissue_block_processing
                specimen_container_tissue_block_primary_fixative
                   specimen_container_tissue_block_primary_fixative_name
                   specimen_container_tissue_block_primary_fixative_duration
                specimen_container_tissue_block_secondary_fixative
                   specimen_container_tissue_block_secondary_fixative_name
                   specimen_container_tissue_block_secondary_fixative_duration
                specimen_container_tissue_block_slide
                   specimen_container_tissue_block_slide_number
                   specimen_container_tissue_block_slide_thickness
                   specimen_container_tissue_block_slide_histologic_stain
                         ...name
                         ...pretreatment.
                            ...mordant_routine_stain.
                            ...hierarchical_immunostain.
                         ...special_protocol.
                         ...unstained
                         ...hematoxylin_eosin.
                         ...acid_fast_organism.
                         ...iron.
                         ...bacteria.
                         ...elastic_tissue.
                         ...fungi_pneumocystis.
                         ...mucin.
                         ...connective_tissue.
                         ...myelin.
                         ...nerve_fiber.
                         ...periodic_acid_schiff.
                         ...glycogen.
                         ...reticulin_fiber.
                         ...amyloid.
                         ...methyl_green_pyronine.
                      specimen_container_tissue_block_slide_histologic_stain_time
                         specimen_container_tissue_block_slide_histologic_stain_time_cut
                         specimen_container_tissue_block_slide_histologic_stain_time_stained
                      specimen_container_tissue_block_slide_histologic_stain_method
                      specimen_container_tissue_block_slide_histologic_stain_manufacturer
                      specimen_container_tissue_block_slide_histologic_stain_lot_number
                      specimen_container_tissue_block_slide_histologic_stain_image                 
                         specimen_container_tissue_block_slide_histologic_stain_image_number                
                         specimen_container_tissue_block_slide_histologic_stain_image_slide_number
                         specimen_container_tissue_block_slide_histologic_stain_image_time
                         specimen_container_tissue_block_slide_histologic_stain_image_method
                         specimen_container_tissue_block_slide_histologic_stain_image_manufacturer
                         specimen_container_tissue_block_slide_histologic_stain_image_tissue_coordinates                   
                                                                                                    ...center_gravity      
                                                                                                       ...abscissa         
                                                                                                       ...ordinate         
                                                                                                    ...width               
                                                                                                    ...height              
                                                                                                    ...tissue_orientation  
                         specimen_container_tissue_block_slide_histologic_stain_image_lesion_coordinates                   
                                                                                                    ...center_gravity      
                                                                                                       ...abscissa         
                                                                                                       ...ordinate         
                                                                                                    ...width               
                                                                                                    ...height              
                                                                                                    ...tissue_orientation  


 tissue_orientation
    tissue_orientation_epithelial_surface
       ...surface_horizontal_tissue_below=0_radian.
       ...surface_horizontal_tissue_above=pi_radian.
       ...includes: skin, tubular_gi_tract, bronchi, ducts.
    tissue_orientation_conventional
       ...kidney:glomerulus_vertical
       ...brain:leptomeningeal_surface_above
       ...bone:periosteum_above
       ...vessel:endothelium_above
       ...adrenal:cortex_above
       ...lymphnode:cortex_above


 histologic_stain
    histologic_stain_name
       ...acid_fast_organism.
       ...amyloid
       ...bacteria.
       ...connective_tissue
       ...elastic_tissue.
       ...fungi_or_pneumocystis.
       ...glycogen
       ...hematoxylin_eosin.
       ...iron.
       ...methyl_green_pyronine.
       ...mucin
       ...myelin
       ...nerve_fibers
       ...periodic_acid_schiff
       ...reticulin_fiber
       ...unstained.
    histologic_stain_method
       ...10%_formal_saline.
       ...3_aminopropyltriethoxysilane_treated_slides.
       ...4%_paraformaldehyde.
       ...aceto_orcein_fast_green.
       ...acetyl_cholinesterase.
       ...acid_fast_mycobacteria_stain.
       ...acid_fast_stain.
       ...acid_phosphatase.
       ...acid_picro_mallory.
       ...adenosine_triphosphatase.
       ...aec_substrate.
       ...alcian_blue_pas.
       ...alcian_blue_pas_stain.
       ...alcian_blue_stain.
       ...alcian_blue_technique.
       ...alizarin_calcium_stain.
       ...alkaline_congo_red_technique.
       ...alkaline_phosphatase.
       ...auramine_rhodamine_fluorescent_stain.
       ...avidin/biotin_technique.
       ...benhold_amyloid_congo_red_method.
       ...bielschowsky_method.
       ...bile_stain.
       ...bodian_stain.
       ...brown_brenn_gram_positive_bacteria_method.
       ...carazzi_hematoxylin.
       ...carbohydrate_mucoprotein_method.
       ...celestine_blue_solution.
       ...chrome_gelatinized_slide.
       ...colloidal_iron_stain_
       ...congo_red_alkaline_technique.
       ...congo_red_stain.
       ...copper_stain.
       ...cresyl_fast_violet_nissl_method.
       ...cross_palmgrens_method.
       ...cytochrome_oxidase_technique.
       ...dab_substrate.
       ...decalcification.
       ...diastase_digestion_method.
       ...diff_quik_stain.
       ...elastic_van_gieson.
       ...elastic_weigert_resorcin_fuchsin_method.
       ...feulgen_dna_reaction.
       ...fite_acid_fast_method.
       ...fontana_masson.
       ...fontana_masson_melanin_stain.
       ...fouchet_method.
       ...fraser_lendrum_stain.
       ...gallyas_technique.
       ...giemsa_helicobacter_pylori.
       ...giemsa_may_gruenwald_hematopoietic_stain.
       ...gill_hematoxylin.
       ...gimenez_stain.
       ...gomori_iron_method.
       ...gomori_trichrome.
       ...gordon_sweet_reticulin_method.
       ...gram_brown_brenn_stain.
       ...gram_stain.
       ...gridley_ameba_stain.
       ...grimelius.
       ...grimelius_argyrophil_pascual_method.
       ...grocott_fungi_method.
       ...grocott_methenamine_silver_stain.
       ...haga_yamagchi_methenamine_silver_technique.
       ...harris_hematoxylin.
       ...hematoxylin_eosin.
       ...hematoxylin_van_gieson.
       ...high_iron_diamine.
       ...highmans_congo_red.
       ...holzer_glial_fiber_stain.
       ...hortega_pineal_stain.
       ...hyaluronidase_digestion_alcian_blue.
       ...hyaluronidase_digestion_method.
       ...immunohistochemical_stain.
       ...immunoperoxidase_stain.
       ...indirect_peroxidase_technique.
       ...iron_prussian_blue_stain.
       ...iron_turnbull_blue_stain.
       ...jones_methenamine_silver.
       ...jones_silver_stain.
       ...lactase.
       ...leucine_amino_peptidase.
       ...lieb_amyloid_crystal_violet_method.
       ...luxol_fast_blue_stain.
       ...masson_fontana.
       ...masson_trichrome_stain.
       ...may_grunwald_giemsa_method._
       ...mayer_mucicarmine_stain.
       ...melanin_bleach.
       ...methenamine_silver_fungi_pneumocystis.
       ...methyl_green_pyronine_stain.
       ...millers_elastic_stain.
       ...modified_elastic_van_gieson_stain.
       ...mowry_colloidal_iron_stain_acid_mucopolysaccharide.
       ...mucicarmine_stain.
       ...myodenylate_deaminase.
       ...nadh_diaphorase.
       ...nissl_stain.
       ...non_specific_esterase.
       ...oil_red_o_propylene_gycol_method.
       ...oil_red_o_stain.
       ...orange_g_stain.
       ...orcein_stain.
       ...papanicolaou_stain.
       ...periodic_acid_schiff_digested_stain.
       ...periodic_acid_schiff_orange_g.
       ...periodic_acid_schiff_stain.
       ...perl_technique.
       ...peroxidase_anti_peroxidase_technique.
       ...phloxine_tartrazine.
       ...phosphorylase.
       ...phosphotungstic_acid_hematoxylin.
       ...poly_l_lysine_coated_slide.
       ...potassium_ferrocyanide_hydrochloric_acid_solution.
       ...removal_of_formalin_pigment.
       ...resin_embedding_high_resolution_morphology.
       ...resin_processing_bone.
       ...resin_staining_methods.
       ...reticulin_stain.
       ...reticulum_hortega_modified.
       ...rubeanic_acid_technique.
       ...schmorl_technique.
       ...shikata_technique.
       ...solochrome_cyanin_technique.
       ...southgates_mucicarmine.
       ...spirochete_steiner_steiner_method.
       ...succinate_dehydrogenase.
       ...sucrase.
       ...sudan_black_b_fat_stain.
       ...sudan_black_b_lipochrome_stain.
       ...thioflavin_s_amyloid_tissue_stain.
       ...thioflavin_s_senile_plaque_modified_stain.
       ...toluidine_blue.
       ...toluidine_blue_mast_cell_stain.
       ...toluidine_blue_sorenson_buffer.
       ...trichrome_masson_method.
       ...trichrome_microwave_method.
       ...trypsin_digestion.
       ...unstained.
       ...urate_crystal_stain.
       ...van_gieson.
       ...van_gieson_collagen_fiber.
       ...verhoeff_elastic_stain.
       ...von_kossa.
       ...vonkossa_calcium_stain.
       ...warthin_starry_method.
       ...weigert_resorcin_fuchsin_elastic_method.
       ...weil_myelin_stain.
       ...wilder_reticulum_method.
       ...ziehl_neelsen_carbol_fuchsin_solution.
                        
 tissue_fixative.
   ...fresh
   ...frozen
   ...10%_neutral_phosphate-buffered_formalin
   ...2_propanol.
   ...95%_alcoholic_bouin_solution.
   ...acetone.
   ...b_5_fixative_formol_sublimate.
   ...bouin_solution.
   ...buffered_10%_formalin.
   ...buffered_formol_acetone.
   ...carnoy_fixative.
   ...chloroform.
   ...clearing_solvent_xylene_substitute.
   ...cytoprep_fixative.
   ...davidson_fixative.
   ...decalcifier.
   ...dichromate_orth_fixative
   ...ethyl_alcohol.
   ...ethylene_glycol_monoethyl_ether.
   ...formaldehyde/zinc_fixative.
   ...formaldehyde_histologic_grade.
   ...formalin_neutral_buffered_10%_acetate_buffer.
   ...formalin_neutral_buffered_10%_phosphate_buffer.
   ...fresh.
   ...frozen.
   ...glutaraldehyde_karnovsky_fixative.
   ...hartman_fixative.
   ...histochoice_molecular_biology_fixative.
   ...hollande_fixative.
   ...immunogold_fixative.
   ...isopropyl_alcohol.
   ...methanol.
   ...methanol_acetone
   ...orth_dichromate_fixative
   ...xylene.
   ...xylene_substitute.
   ...zenker_fluid.
                                
 histologic_stain_manufacturer
   ...anaerobe_systems
   ...arlinton_scientific_inc
   ...aseptic_control_products
   ...basic_medical_industries
   ...bd_biosciences
   ...binax
   ...bio_plas
   ...biochemical_sciences
   ...biomed
   ...boehringer_mannheim
   ...boekel_instruments
   ...cargille
   ...chase_scientific_glass
   ...clearview_unipath
   ...copan
   ...decon_laboratories
   ...denka_seiken
   ...em_diagnostics_systems
   ...ertco
   ...excel_scientific
   ...fisher_scientific
   ...globe_scientific
   ...greiner_vacuette_north_america
   ...hardy_diagnostics
   ...healthlink
   ...hema_resource
   ...hematronix_biorad
   ...hycor_biomedical
   ...hygiena
   ...immucor_gamma_biologicals
   ...isolyzer
   ...kendall_healthcare_products
   ...lab_line_instruments
   ...labnet
   ...medi_flex
   ...medical_action
   ...medical_chemical_corporation
   ...medical_packaging_corporation
   ...medtek_diagnostics
   ...meridian_diagnostics
   ...meridian_diagnostics
   ...microbiological_specialties
   ...microbiologics
   ...microflex
   ...microgenics_corporation
   ...nasco
   ...national_scientific_supply_company
   ...new_horizons
   ...novaone
   ...nunc
   ...organon_teknika
   ...oxoid
   ...parter_medical
   ...pdi_prep_pads
   ...pfb_interapparel
   ...polymedco
   ...propper
   ...puritan_hardwood
   ...quantimetrix
   ...quidel
   ...richard_allan_scientific
   ...samco_corning
   ...scientific_products
   ...seradyn_alexon_trend
   ...sharps_compliance
   ...sherwood_monoject
   ...simport_plastics
   ...simport_plastics_ltd
   ...sps_medical
   ...star_publishing
   ...starplex
   ...thermo_dma
   ...triangle_biomedical_sciences
   ...tuttanauer
   ...valtech_diagnostics
   ...vanguard
   ...volu_sol
   ...wampole
 image
   ...type
      ...digital
      ...analog
   ...relation_depicts
   ...creator
   ...technique
      ...scanning
   ...measurements
   ...format
   ...resolution
      ...n × n pixels.
   ...idnumber
   ...current_repository
   ...rights
                                
 large_specimen_cancer
    large_specimen_cancer_colorectum
    large_specimen_cancer_breast
    large_specimen_cancer_anus
    large_specimen_cancer_esophagus
    large_specimen_cancer_liver
    large_specimen_cancer_gallbladder
    large_specimen_cancer_pancreas
    large_specimen_cancer_small_intestine
    large_specimen_cancer_stomach
    large_specimen_cancer_kidney
    large_specimen_cancer_prostate
    large_specimen_cancer_testis
    large_specimen_cancer_urinary_bladder
    large_specimen_cancer_hysterectomy
    large_specimen_cancer_ovary
    large_specimen_cancer_trophoblastic_tumor
    large_specimen_cancer_uterine_cervix
    large_specimen_cancer_vagina
    large_specimen_cancer_vulva
    large_specimen_cancer_thyroid
    large_specimen_cancer_upper_aerodigestive_tract
    large_specimen_cancer_gastrointestinal_lymphoma
    large_specimen_cancer_hodgkin_lymphoma
    large_specimen_cancer_nonhodgkin_lymphoma
    large_specimen_cancer_skin_carcinoma
    large_specimen_cancer_skin_melanoma
    large_specimen_cancer_lung
    large_specimen_cancer_peripheral_neurectodermal_tumor_ewing_sarcoma
                           
    large_specimen_cancer_colon
       large_specimen_cancer_colon_procedure
          ...right_hemicolectomy
          ...transverse_colectomy
          ...left_hemicolectomy
          ...rectosigmoid_colectomy
          ...total_abdominal_colectomy
          ...sigmoid_colectomy
          ...abdominoperineal_resection
          ...other_large_specimen_cancer_colon_procedure
       large_specimen_cancer_colon_tumor_site
          ...cecum
          ...ascending_colon
          ...hepatic_flexure
          ...transverse_colon
          ...splenic_flexure
          ...descending_colon
          ...sigmoid_colon
          ...rectosigmoid_colon
          ...rectum
          ...colon_nos
       large_specimen_cancer_colon_tumor_configuration
          ...plaque_like
          ...annular
          ...ulcerating
          ...infiltrative
       large_specimen_cancer_colon_tumor_size
       large_specimen_cancer_colon_tumor_histologic_type
          ...adenocarcinoma
          ...adenocarcinoma_mucinous
             ...>50%_mucinous
          ...signet_ring_cell_carcinoma
          ...small_cell_carcinoma
          ...medullary_carcinoma
          ...undifferentiated_carcinoma
          ...large_specimen_cancer_colon_tumor_histologic_type_other
       large_specimen_cancer_colon_tumor_histologic_grade
          ...low_grade
          ...high_grade
          ...nos
       large_specimen_cancer_colon_tumor_margin
          large_specimen_cancer_colon_tumor_margin_proximal
             ...involved
             ...uninvolved
          large_specimen_cancer_colon_tumor_margin_distal
             ...involved
             ...uninvolved
          large_specimen_cancer_colon_tumor_margin_circumferential
             ...involved
             ...uninvolved
       large_specimen_cancer_colon_tumor_invasion
          large_specimen_cancer_colon_tumor_invasion_lymphatic
             ...absent
             ...present
             ...indeterminate
          large_specimen_cancer_colon_tumor_invasion_venous
             ...absent
             ...present
             ...indeterminate
          large_specimen_cancer_colon_tumor_invasion_perineural
             ...absent
             ...present
          large_specimen_cancer_colon_tumor_other_finding
             ...ulcerative_proctocolitis
             ...dysplasia
             ...hyperplastic_polyp
             ...crohn_disease
             ...adenoma
                ...adenoma_tubular
                ...adenoma_tubulovillous
                ...adenoma_villous
          large_specimen_cancer_colon_tumor_stage
             large_specimen_cancer_colon_tumor_stage_TX
                ...indeterminate
             large_specimen_cancer_colon_tumor_stage_T0
                ...absent_primary_tumor
             large_specimen_cancer_colon_tumor_stage_TIS
                ...carcinoma_in_situ
             large_specimen_cancer_colon_tumor_stage_T1
                ...tumor_invades_submucosa
             large_specimen_cancer_colon_tumor_stage_T2
                ...tumor_invades_muscularis_propria
             large_specimen_cancer_colon_tumor_stage_T3
                ...tumor_invades_subserosa
             large_specimen_cancer_colon_tumor_stage_T4
                ...tumor_invades_other_organs
                ...tumor_invades_visceral_peritoneum
          large_specimen_cancer_colon_nodal_stage
             large_specimen_cancer_colon_nodal_stage_number_counted
             large_specimen_cancer_colon_nodal_stage_number_positive
          large_specimen_cancer_colon_metastatic_stage
             ...absent
             ...present
             ...indeterminate
                      
    large_specimen_cancer_breast
       large_specimen_cancer_breast_procedure
       large_specimen_cancer_breast_tumor_site
       large_specimen_cancer_breast_tumor_configuration
       large_specimen_cancer_breast_tumor_size
       large_specimen_cancer_breast_tumor_histologic_type
       large_specimen_cancer_breast_tumor_histologic_grade
       large_specimen_cancer_breast_tumor_margin
       large_specimen_cancer_breast_tumor_invasion
       large_specimen_cancer_breast_tumor_invasion_lymphatic
       large_specimen_cancer_breast_tumor_invasion_venous
       large_specimen_cancer_breast_tumor_invasion_perineural
       large_specimen_cancer_breast_tumor_other_finding
       large_specimen_cancer_breast_tumor_stage
          large_specimen_cancer_breast_tumor_stage_TX
          large_specimen_cancer_breast_tumor_stage_T0
          large_specimen_cancer_breast_tumor_stage_TIS
          large_specimen_cancer_breast_tumor_stage_T1
          large_specimen_cancer_breast_tumor_stage_T2
          large_specimen_cancer_breast_tumor_stage_T3
          large_specimen_cancer_breast_tumor_stage_T4
       large_specimen_cancer_breast_nodal_stage
       large_specimen_cancer_breast_metastatic_stage
                            
    large_specimen_cancer_prostate
       large_specimen_cancer_prostate_procedure
       large_specimen_cancer_prostate_tumor_site
       large_specimen_cancer_prostate_tumor_configuration
       large_specimen_cancer_prostate_tumor_size
       large_specimen_cancer_prostate_tumor_histologic_type
       large_specimen_cancer_prostate_tumor_histologic_grade
       large_specimen_cancer_prostate_tumor_margin
       large_specimen_cancer_prostate_tumor_invasion
       large_specimen_cancer_prostate_tumor_invasion_lymphatic
       large_specimen_cancer_prostate_tumor_invasion_venous
       large_specimen_cancer_prostate_tumor_invasion_perineural
       large_specimen_cancer_prostate_tumor_other_finding
       large_specimen_cancer_prostate_tumor_stage
          large_specimen_cancer_prostate_tumor_stage_TX
          large_specimen_cancer_prostate_tumor_stage_T0
          large_specimen_cancer_prostate_tumor_stage_TIS
          large_specimen_cancer_prostate_tumor_stage_T1
          large_specimen_cancer_prostate_tumor_stage_T2
          large_specimen_cancer_prostate_tumor_stage_T3
          large_specimen_cancer_prostate_tumor_stage_T4
       large_specimen_cancer_prostate_nodal_stage
       large_specimen_cancer_prostate_metastatic_stage
                           
    large_specimen_cancer_lung
       large_specimen_cancer_lung_procedure
       large_specimen_cancer_lung_tumor_site
       large_specimen_cancer_lung_tumor_configuration
       large_specimen_cancer_lung_tumor_size
       large_specimen_cancer_lung_tumor_histologic_type
       large_specimen_cancer_lung_tumor_histologic_grade
       large_specimen_cancer_lung_tumor_margin
       large_specimen_cancer_lung_tumor_invasion
          large_specimen_cancer_lung_tumor_invasion_lymphatic
          large_specimen_cancer_lung_tumor_invasion_venous
          large_specimen_cancer_lung_tumor_invasion_perineural
       large_specimen_cancer_lung_tumor_other_finding
       large_specimen_cancer_lung_tumor_stage
          large_specimen_cancer_lung_tumor_stage_TX
          large_specimen_cancer_lung_tumor_stage_T0
          large_specimen_cancer_lung_tumor_stage_TIS
          large_specimen_cancer_lung_tumor_stage_T1
          large_specimen_cancer_lung_tumor_stage_T2
          large_specimen_cancer_lung_tumor_stage_T3
          large_specimen_cancer_lung_tumor_stage_T4
       large_specimen_cancer_lung_nodal_stage
       large_specimen_cancer_lung_metastatic_stage

12. CONSISTENCY TESTS.



TIME-EVENT CONSISTENCY.


Several CONSISTENCY TESTS may be performed on the basis of this data-structure. The most obvious tests are time comparisons. For example, the various pathology_report_times should always always occur in temporal sequence, as follows:
pathology_report_time_obtained < pathology_report_time_received
pathology_report_time_received < pathology_report_time_reported
pathology_report_time_reported < pathology_report_time_amended
pathology_report_time_reported < pathology_report_time_supplemented
Furthermore, obviously patient_date_of_birth < pathology_report_time_obtained.

ZULU OFFSET CONSISTENCY.


Secondly, pathology_report_lab_identifier_address specifies a time zone, and specimen_time_obtained determines whether Daylight Savings Time is in force in that time zone. These two pieces of information suffice to determine if the Zulu-offset is consistent.

It is possible that the specimen_obtained_address is different from the pathology_report_lab_identifier_address, for example, if a patient was biopsied at one location, and his/her biopsy was sent in consultation to another location. Thus, the Zulu-offset may not be the same for all date/times in the pathology report.

FORMAL LOGICAL CONSISTENCY.


The above data-structure may be viewed as a RULEBASE in the sense of Artificial Intelligence (AI), i.e., collection of statements in formal logic, where the hierarchical form: 
   X
      X_Y1
      X_Y2
      X_Y3....
corresponds to the formal logic expression:
X ⇒ ( X_Y1 ∨ X_Y2 ∨ X_Y3 ∨ ...),
where ⇒ denotes if...then and ∨ denotes logical-or. The latter expressions may be solved for completeness, consistency, and redundancy of expressions, using automated / computerized logic-solvers.

13. REFERENCES.



1. Moore GW, Berman JJ.
Anatomic Pathology Data Mining.
Chapter 4. In: Cios KJ. Medical Data Mining and Knowledge Discovery.
Berlin: Springer Verlag. 2000;4:61-107.
ISBN: 3-7908-1340-0, 502 pages.
Published within the series: "Studies in Fuzziness and Soft Computing", Physica-Verlag Heidelberg, a Springer-Verlag Company.
Full Text of Article:
http://www.medparse.com/ldip/apdmchap.htm

2. VistA Filemanager specification.
http://www.netautopsy.org/axsop/axsop233.htm#ap233s42

3. CAP inspection questions:
http://www.cap.org
Click on: ACCREDITATION AND LABORATORY IMPROVEMENT (tab in the upper right of screen).
Under: ACCREDITATION AND INSPECTION INFORMATION (lower left right of screen).
Click on: INSPECTION CHECKLISTS (about halfway down the list).
Go to the most recent sections entitled ANATOMIC PATHOLOGY (ANP) and CYTOPATHOLOGY (CYP).
See:
QUESTION: CYP.03300 PHASE: II
Are all specimens properly and adequately identified (i.e., patient's name or other unique and complete identifier on frosted or labeled slide)?
QUESTION: CYP.03400 PHASE: II
Does the cytopathology requisition include space for the name of the patient, the date of birth or age, the date of specimen collection, the source of the cytologic material, the submitting physician's name, and pertinent clinical information?
QUESTION: ANP.21450 PHASE: II
Are the following special stains of high quality, and do they satisfactorily demonstrate (on each day of use), the tissue characteristics for which they were designed:
1. acid fast organisms;
2. iron;
3. bacteria;
4. elastic tissues;
5. fungi or pneumocystis;
6. mucin;
7. connective tissue;
8. myelin;
9. nerve fibers;
10. periodic acid Schiff (PAS);
11. glycogen;
12. reticulin fibers;
13. amyloid;
14. methyl green-pyronine (MGP).



4. Symbolic logic solver. Each expression of the form X ⇒ ( X_Y1 ∨ X_Y2 ∨ X_Y3 ∨ ...), where ⇒ denotes if...then, ~ denotes logical-not, and ∨ denotes logical-or, may be converted to a NAND EXPRESSION (nand = logical not-and), of the form: {X, ~X_Y1, ~X_Y2, ~X_Y3, ...}. In turn, nand-expressions may be combined in an addition-like procedure.

For example, if there are two expressions in the rulebase of the form, X ⇒ ( X_Y1 ∨ X_Y2) and X ⇒ ( X_Y1 ∨ X_Y2 ∨ X_Y3), then either the first expression is incomplete or the second expression is redundant. This incompleteness/redundancy question can easily be examined automatically by computer.

Another property of this logical formalism is that W ⇒ X and X ⇒ ( X_Y1 ∨ X_Y2) implies W ⇒ X ⇒ ( X_Y1 ∨ X_Y2). Therefore, one can isolate parts of a large rulebase for easier reading and overview.

See:
4.1. Quine WV.
Theory of Deduction.
Cambridge, MA: Harvard Cooperative Society. 1948;:65-81.

4.2. Quine WV.
Methods of Logic.
New York: Henry Holt & Co. 1950.

4.3. Quine WV.
The problem of simplifying truth functions.
Am Math Monthly 59:521-531, l952.

4.4. Quine WV.
A way to simplify truth functions.
Am Math Monthly 1955;62:627-631.

4.5. McCluskey EJ jr.
Minimization of Boolean Functions.
Bell Syst Tech J 1956;36:1417-1444.


5. Geller SA.
A Short History of the Autopsy. Chapter 2.
In: Collins KA, Hutchins GM. Autopsy Performance & Reporting. Northfield, IL: College of American Pathologists. 2003;2:13-16.
ISBN 0-930304-78-0, 397 pages.
"...Susruta, in approximately 5000 BC in India during the Brahmin period, is the first person credited with performing [an autopsy]." (page 13).

6. Histologic stain websites.


University of Buffalo, Buffalo, NY, Department of Pathology.
http://www.smbs.buffalo.edu/path/techniques.htm

University of Arizona, Department of Cell Biology and Anatomy.
http://www.cba.arizona.edu/histo/stains.html

University of Florida, Department of Dental Histology.
http://medinfo.ufl.edu/~dental/denhisto/stains.html

Protocol-Online.
http://www.protocol-online.org/prot/Histology/Staining/

Florida State University, COllege of Medicine.
http://medlib.med.utah.edu/WebPath/webpath.html
Click on Anatomy-Histology. Click on Histology Procedure Manual.

University of Nottingham, Pathology Laboratory, Nottingham, UK.
http://www.nottingham.ac.uk/pathology/default.html

University of Florida, Department of Animal Science.
http://www.animal.ufl.edu/hansen/protocols.shtml

National Institutes of Health. National Cancer Institute.
http://mammary.nih.gov/tools/histological/Histology/index.html

Dako USA.
http://www.dakocytomation.us/

Histology.to
http://www.histology.to/eosin.html

University Bristol, Department of Veterinary Pathology, Bristol, UK.
http://www.bris.ac.uk/Depts/PathAndMicro/CPL/

Bioww.net
http://biowww.net/detail-781.html


7. Moore GW, Miller RE, and Hutchins GM.
Indexing by MeSH titles of natural language pathology phrases identified on first encounter using the barrier word method.
Lab Invest 58: 110A, 1988.

8. Moore GW, Miller RE, Hutchins GM.
Indexing by MeSH titles of natural language pathology phrases identified on first encounter using the barrier word method.
In, Scherrer JR, Côté RA, and Mandil SH, eds., Computerized Natural Medical Language Processing for Knowledge Representation. North-Holland, Amsterdam, 1989.

9. Tersmette KWF, Scott AF, Moore GW, Matheson NW, Miller RE.
Barrier word method for detecting molecular biology multiple word terms.
Proc Annu Symp Comput Appl Med Care. 1988;12:207-211. Washington DC, November 6-9, 1988.

10. Dr. Floyd's notes: 
 specimen anatomic site
	organ
	site within organ
                
 specimen collection
	how collected: surgical, aspiration, etc.
	time from collection to fixation or processing
                     
 frozen section
                   
 fixation
	primary fixative
		duration
	secondary fixative
		duration
                      
 processing
	standard paraffin
	other protocol
		microwave
                    
 section thickness
                  
 staining
	stain type
		stain reagent(s) variant and source
	pre-treatments (hierarchy for immunostainss, mordants for traditional)
                 
 specials or experimentals
	specific protocols (where can be found)


11. Large Resection Checklists for CAP/AJCC/UICC:

College of American Pathologists (CAP): http://www.cap.org

Click on REFERENCE RESOURCES AND PUBLICATIONS (top of screen). Under PRACTICE RESOURCES, click on CANCER PROTOCOLS AND CHECKLISTS.
Breast: http://www.cap.org/apps/docs/cancer_protocols/2005/breast05_ckw.doc
Anus: http://www.cap.org/apps/docs/cancer_protocols/2005/anus05_ckw.doc
Colon and Rectum: http://www.cap.org/apps/docs/cancer_protocols/2005/colonrectum05_ckw.doc
Esophagus: http://www.cap.org/apps/docs/cancer_protocols/2005/esophagus05_ckw.doc
Liver: http://www.cap.org/apps/docs/cancer_protocols/2005/liver05_ckw.doc
Gallbladder: http://www.cap.org/apps/docs/cancer_protocols/2005/gallbladder05_ckw.doc
Pancreas, endocrine: http://www.cap.org/apps/docs/cancer_protocols/2005/pancreasendo05_ckw.doc
Pancreas, exocrine: http://www.cap.org/apps/docs/cancer_protocols/2005/pancreasexo05_ckw.doc
Small intestine: http://www.cap.org/apps/docs/cancer_protocols/2005/smintestine05_ckw.doc
Stomach: http://www.cap.org/apps/docs/cancer_protocols/2005/stomach05_ckw.doc
Kidney: http://www.cap.org/apps/docs/cancer_protocols/2005/kidney05_ckw.doc
Prostate: http://www.cap.org/apps/docs/cancer_protocols/2005/prostate05_ckw.doc
Testis: http://www.cap.org/apps/docs/cancer_protocols/2005/testis05_ckw.doc
Urinary bladder: http://www.cap.org/apps/docs/cancer_protocols/2005/urbladder05_ckw.doc
Endometrium: http://www.cap.org/apps/docs/cancer_protocols/2005/endometrium05_ckw.doc
Fallopian tube: http://www.cap.org/apps/docs/cancer_protocols/2005/fallopian05_ckw.doc
Ovary: http://www.cap.org/apps/docs/cancer_protocols/2005/ovary05_ckw.doc
Trophoblastic tumor: http://www.cap.org/apps/docs/cancer_protocols/2005/trophoblast05_ckw.doc
Uterine cervix: http://www.cap.org/apps/docs/cancer_protocols/2005/uterinecervix05_ckw.doc
Vagina: http://www.cap.org/apps/docs/cancer_protocols/2005/vagina05_ckw.doc
Vulva: http://www.cap.org/apps/docs/cancer_protocols/2005/vulva05_ckw.doc
Thyroid: http://www.cap.org/apps/docs/cancer_protocols/2005/thyroid05_ckw.doc
Upper aerodigestive tract: http://www.cap.org/apps/docs/cancer_protocols/2005/upperaero05_ckw.doc
Bone marrow: http://www.cap.org/apps/docs/cancer_protocols/2005/bonemarrow05_ckw.doc
Gastrointestinal lymphoma: http://www.cap.org/apps/docs/cancer_protocols/2005/lymphGI05_ckw.doc
Hodgkin's lymphoma: http://www.cap.org/apps/docs/cancer_protocols/2005/lymphhodgkin05_ckw.doc
Non-Hodgkin's lymphoma: http://www.cap.org/apps/docs/cancer_protocols/2005/lymphnonhodg05_ckw.doc
Skin Carcinoma: http://www.cap.org/apps/docs/cancer_protocols/2005/skincarcinoma05_ckw.doc
Lung: http://www.cap.org/apps/docs/cancer_protocols/2005/lung05_ckw.doc
Peripheral Neurectodermal Tumor / Ewing Sarcoma: http://www.cap.org/apps/docs/cancer_protocols/2005/pnetewing05_ckw.doc


12. American Joint Committee on Cancer (AJCC): http://www.cancerstaging.org

13. Unio Internationalis Contra Cancrum (UICC): http://www.uicc.org


14. International Anatomical Nomenclature Committee.
Nomina anatomica. Fifth Edition.
Baltimore: Williams and Wilkins. 1983;:.
ISBN 0-683-06550-5.

15. Maung RTA.
What is the best indicator to determine anatomic pathology workload? Canadian experience.
Am J Clin Pathol. 2005;123:45-55.

16. Upstate Medicare Division.
Sample CPT® Fee Schedule: Upstate Medicare Division, 2004 Fee Schedule.
http://www.umd.nycpic.com/2005_80000-89999.html
Accessed March 10, 2006.
From:
http://www.umd.nycpic.com/
Note: CPT® NUMBER and CPT® DESCRIPTOR are copyrighted products of the American Medical Association.

17. Department of Veterans Affairs.
VistA® LABORATORY ANATOMIC PATHOLOGY (AP). ELECTRONIC SIGNATURE USER MANUAL/INSTALLATION GUIDE. PATCH LR*5.2*259. Version 5.2.
2004 May;:. Department of Veterans Affairs. VistA® Health Systems Design & Development.


18. Description of VistA® Filemanager.
http://www.hardhats.org
Includes instructions for obtaining at-cost copies of the complete, public-domain system, through the Freedom of Information Act.

19. Berman JJ.
LDIP correspondence. 3/21/2006. Criteria for CDE "consistency".
1. CDEs should not be redundant.
2. If something belongs to a class, a closely-related CDE should be in the same class.
3. The classes shouldn't be their own ancestors, i.e., if A is father of B, B should not be grandfather of A.
4. Consistency can be achieved by careful proof-reading.
GWM response: As a practical matter, point 4 is probably correct. However, the process should be formalizable, and thus all interested parties could perform their own "consistency" tests. Points 1 and 3 have a formal definition, as I shall develop below.

In point 2, "closely-related CDE" is unclear to me, unless there is a list of "closely-related CDEs".

The basic idea of a CDE hierarchy, i.e., CDEH, is PARENTHOOD. Conventionally, parenthood is represented as carriage-return followed by indentation. SIBSHIP is represented as carriage-return-no-indentation. Thus, for example:
Abraham..
.Ishmael.
.Isaac.
..Esau
..Jacob
For convenience, one may also represent parenthood with colon (:) and sibship with comma (,). Thus:
Abraham:Ishmael,Isaac.
and
Isaac:Esau,Jacob.
Then, point 3, i.e., a class shouldn't be its own ancestor, means that there should exist no X, Y in the CDEH such that X:Y:...:X.

The obvious interpretation of point 1, i.e., CDE branches should not be redundant, is that there should exist no X:W,V,U,... at more than one place in the CDEH. This idea can be usefully extended to state that if X:W1,V1,U1,... and X:W2,V2,U2,... exist in two different places in the CDEH, and if X:W1,V1,U1,... IMPLIES X:W2,V2,U2,... then X:W2,V2,U2,... is redundant. Since any branch on the CDEH implies itself, then my extended definition includes the obvious definition of redundancy.

The reason for using my extended definition of redundancy is to catch instances where there is an unintended omission/deficiency or redundancy. For example, suppose that one part of the CDEH gives the layers of the epidermis as:
Epidermis.
.Stratum corneum.
.Stratum granulosum.
.Stratum spinosum.
.Stratum basale.
whereas another part of the CDEH gives the layers of the epidermis as:
Epidermis.
.Stratum corneum.
.Stratum lucidum.
.Stratum granulosum.
.Stratum spinosum.
.Stratum basale.
Then either the second classification is redundant (since the first implies the second); or the first classification is deficient. Determining which is the correct table is the job of the human classifier.

I could envision an interactive process in which the human classifier tunes up an initial, proposed classification by repeatedly running these redundancy/ancestry tests by computer until the computer program finds no errors in the classification.

In colon/comma notation, using 0 to denote origin, the primary classification may be summarized as:
0:patient,tissue_orientation,histologic_stain,tissue_fixative.
patient:image,pathology_report:specimen:specimen_container:specimen_container_tissue_block:specimen_container_tissue_block_slide:specimen_container_tissue_block_slide_stain:specimen_container_tissue_block_slide_stain_image.
histologic_stain:histologic_stain_name,histologic_stain_class,histologic_stain_method,histologic_stain_manufacturer.
The proposed Perl program would work as follows. The fundamental operation of Aristotelian/Boolean logic is NAND (logical-not-and). A transistor in computer science is a NAND-gate. We say that X NAND Y NAND Z... if and only if X, Y, Z... cannot mutually coexist; and we denote the set {X, Y, Z...} as a NANDSET. We may combine two nandsets using MODUS PONENS where {+X, +Y} MP {-Y, +Z} = {+X, +Z}. Exhaustive application of SUBSET and MODUS PONENS finds all and only the true nandsets for a collection of nandsets.

The connection to CDEHs is as follows: A:B,C,D,... in colon/comma notation is equivalent to the nandset, {+A,-B,-C,-D,...}.

For point 1, CDEs should not be redundant, nandset X is redundant for nandset Y if and only if Y SUBSET X.

For point 3, a class shouldn't be its own ancestor, there should exist no elements X, Y in the CDEH such that {+X,-Y} and {-X,+Y} are true nandsets.

20. Elder DE, Lever WF, eds.
Lever's Histopathology of the Skin. Ninth Edition.
Philadelphia: Lippincott Williams & Wilkins. 2004;:.
ISBN: 0781737427, 1200 pages.

14. GLOSSARY.



ACS: American College of Surgeons. http://www.facs.org In order to be certified by the American College of Surgeons as a Cancer Center, the pathology department must sign out all large cancer resections according to CAP/AJCC/UICC standard protocols.

AJCC: American Joint Committee on Cancer. http://www.cancerstaging.org

ARISTOTELIAN (384-322 BCE) LOGIC: Logic of syllogisms. The foundation of Western logical philosophy. For example: All Greeks are mortal; Socrates is a Greek; therefore, Socrates is mortal. This inferential method is an example of MODUS PONENS, i.e., X implies Y, Y implies Z, therefore X implies Z. The two bedrock principles of Aristotelian logic are: LAW OF CONTRADICTION and LAW OF EXCLUDED MIDDLE. See:
http://en.wikipedia.org/wiki/Aristotle


Boolean (1815-1864) logic: Algebraicized form of Aristotelian logic. For example, Greek implies mortal; Socrates implies Greek; Socrates implies mortal. Using algebraic symbols: G ⇒ M; S ⇒ G; S ⇒ M (modus ponens). In Boolean notation, ⇒ in logic behaves somewhat like > in algebra. Likewise, ∨ in logic behaves somewhat like + in algebra; ∧ in logic behaves somewhat like × in algebra.
http://en.wikipedia.org/wiki/George_Boole


Boolean search: Database search employing ∨ and (logical-inclusive-or) ∧ (logical-and).

CAP: College of American Pathologists: http://www.cap.org

CUI: Concept Unique Identifier, from UMLS.

LAW OF CONTRADICTION: Also known as Reductio ad absurdum (reduction to absurdity) and Ex falso quod libet (from contradiction, anything that one wishes). See:
http://en.wikipedia.org/wiki/Reductio_ad_absurdum


LAW OF EXCLUDED MIDDLE.
http://en.wikipedia.org/wiki/Law_of_excluded_middle


SYMBOLIC LOGIC:

NOMINA ANATOMICA: Anatomic names (Latin). See:
Sack WO, Habel RE, eds.
Nomina Anatomica Veterinaria / Nomina Anatomica Veterinaria / Nomina Histologica / Nomina Embryologica Veterinaria.
ISBN: 0960044477.


STOP WORD: Name given to high-frequency words in a document, such as prepositions, auxiliary verbs, conjunctions, etc., which because of their low information content, do not contribute to an index. The historical basis for stopwords is the 47 UNIMPORANT WORDS designated by Prof. James Strong [1822-1894], Professor of Exegeteal Theology at Drew University, in his comprehensive index of the King James Version of the Holy Bible.
http://en.wikipedia.org/wiki/Strong%27s_Concordance
Strong identified 8674 distinct Hebrew words, over half of them proper nouns, in the Old Testament, and 5523 distinct Greek words, likewise over half of them proper nouns, in the New Testament.

UICC: Unio Internationalis Contra Cancrum. (International Union against Cancer): http://www.uicc.org

UMLS: Unified Medical Language System of USNLM.

USNLM: U. S. National Library of Medicine. Founded by John Shaw Billings, MD, a U. S. Civil War surgeon, based initially upon his own private medical library.

METADATA; Images themselves are called DATA (Latin: things given), and the text-descriptions of these images, used for filing and retrieval, are called METADATA (Greek: μετα = after or beyond). There are two levels of metadata: LOW-LEVEL METADATA (features such as color, brightness, contrast, etc.) and HIGH-LEVEL METADATA, clinicopathologic features.

WORLDWIDE WEB: The worldwide web is largely responsible for the popularity of the Internet over the past decade. The Internet had been in existence, in one form or another, since the late 1960s. (The original internet, according to legend, was a connection between the Laboratory of Artificial Intelligence at MIT to the Pepsi machine on a different floor, which included a thermocouple to verify that the Pepsis were cold.) The typical Internet connection in those days was a dedicated line, which tied up the attention of the server-computer even while the slow human typist is entering a command-line from the client-computer. On the worldwide web, the server-computer sends a webpage to the client-computer, and then "takes a nap" until the client-computer sends back a page. The server-computer then serves other client-computers in the meantime. This simple trick allows the fast server-computer to serve many client-computers almost simultaneously, due to the enormous difference in processing speeds between the server-computer and human-typists.

HYPERTEXT WEB: Historically, a hypertext webpage shows only positioned, formatted information, consisting of texts, images, canned audio or video clips, etc., in various colors, fonts, placements on the page, etc. In a web dialog between the server-computer and a human client, the human-client sends a command to the server-computer; and the server-computer sends back a new hypertext webpage, based upon information supplied by the human-client. The language for presenting such positioned, formatted information is HYPERTEXT MARKUP LANGUAGE (HTML), which consists of text and MARKUP (i.e., the formatting commands). On the SEMANTIC WEB, the contents of the webpage have a MEANING (semantic content), as well as a position and appearance on the webpage. The language for presenting semantic information is EXTENDED MARKUP LANGUAGE (XML). The semantic web is in its infancy, because there is currently no widespread agreement on the vocabulary for various domains of expertise.

SEMANTIC WEB: Historically, a hypertext webpage shows only positioned, formatted information on a webpage. On the SEMANTIC WEB, the contents of the webpage have a MEANING (semantic content), as well as a position and appearance on the webpage. The language for presenting semantic information is EXTENDED MARKUP LANGUAGE (XML). The semantic web is in its infancy, because there is currently no widespread agreement on the vocabulary for various domains of expertise.

WORLDWIDE WEB CONSORTIUM (W3C): Godfathers of the worldwide web. See:

ANNOTATION: Synonym for metadata.

OWL

RDF

PARENT:

CHILD:

ORIGIN:

INTERNATIONAL STANDARDS ORGANIZATION (ISO):

VistA®: Veterans Health Information Systems & Technology Architecture, formerly DHCP (Decentralized Hospital Computer Program). Product of the United States Department of Veterans Affairs, which includes data-definitions for all the non-billing processes performed in an automatic hospital system. (There is a rudimentary billing system, which has not been widely implemented.) VistA® is used on a routine basis in various forms since the 1970s by the Veterans Hospital Administration (VHA), which includes 172 medical centers, 85,000 full-time-equivalent workers of varying levels of training, and cares for five million veteran patients.

ZULU: Name given to Greenwich Mean Time, located in Greenwich, UK, which is the commonly used world standard for time.

Perl: Computer scripting language, widely used on the Internet, and available cost-free from numerous sources.

CONSISTENCY: The mathematical property that a binary statement cannot be both true AND false.

COMPLETENESS: The mathematical property that every true binary statement is provable or computable.

REDUNDANCY: The mathematical property that equivalent statements do not appear more than once in the CDEH.

MODUS PONENS:

ALTERNATION:

CONJUNCTION:

NAND:

INCLUSIVE_OR (IOR):

EXCLUSIVE_OR (XOR):

IMPLIES:

IMPLIED BY:

EQUALS:

GÖDEL:

SYMBOLIC LOGIC:

WILLARD VAN ORMAN QUINE: Late Harvard Professor of Philosophy, member of the Vienna Circle of Exact Philosophy, who contributed ground-breaking studies to understanding and solution of logic systems.

LOTFI A. ZADEH: So-called Pope of Fuzzy Logic, whose classic publication:


Zadeh LA.
Fuzzy Algorithms.
Inform Control. 1968;12:94-102.
has been cited in over 11,000 peer-reviewed articles.


Last updated: 4/27/2006, by G. William Moore, MD, PhD.