Data Model Viewer

To use the data models:

Click/tap on the triangle icon to the left of each section to expand and view its contents.
Click/tap on the text within a section to access detailed information about the model, including its specific attributes and details.

Biomarker Data Models

View as a spreadsheet

Biomarker Ontology

Biomarker Ontology

Models related specifically to the research and development of biomarkers

Stewardship

Version 1.0 of these models are maintained by Heather Kincaid.
- Biomarker Database
  
  Biomarker Database
  
  The EDRN Focus Biomarker Database (BMDB) is a tool that captures and curates biomarkers (indicators for diseases). It produces Resource Description Format (RDF) knowledge about those biomarkers, and the organs for which they indicate disease. Within the context of the Biomarker Database, the term "Study" is used frequently in place of "Protocol" and the word "Organ" is often preferred to "Body System".
  
  Stewardship
  
  Version 1.0 maintained by Maureen Ryan and Kristen Anton. Last updated 2023-09-01
  - Biomarker
    
    Biomarker
    
    An indicator for disease.
    
    Attributes
    
    Attributes shown with are required, while those with inherit values from other objects.
    
    Click/tap on an attribute text box below to view details about that attribute.
    
    identifier Alias HgncName Title URN Description QAState Security Type ShortName IsPanel hasBiomarker memberOfPanel AccessGrantedTo AssociatedDataset referencedInPublication referencesResource indicatorForOrgan hasBiomarkerStudyDatas
    - Biomarker-Organ
      
      Biomarker-Organ
      
      Indicator for disease on a specific body system (organ)
      
      Attributes
      
      Attributes shown with are required, while those with inherit values from other objects.
      
      Click/tap on an attribute text box below to view details about that attribute.
      
      identifier URN Biomarker Description PerformanceComment Organ Phase QAState Certification AccessGrantedTo referencedInPublication referencesResource hasBiomarkerOrganStudyDatas
      - Biomarker-Organ-Study
        
        Biomarker-Organ-Study
        
        Protocol-specifics for a biomarker's indication for diseases on a specific body system (organ)
        
        Attributes
        
        Attributes shown with are required, while those with inherit values from other objects.
        
        Click/tap on an attribute text box below to view details about that attribute.
        
        identifier referencesStudy DecisionRule Phase referencedInPublication referencesResource
- Biomarker Study Data
  
  Biomarker Study Data
  
  The Data Management and Coordinating Center (DMCC) has the EDRN Study Information System (eSIS) and related databases that are converted to the open Resource Description Format (RDF) by the CancerDataExpo.
  
  Stewardship
  
  Version 1.0 maintained by the Data Management and Coordinating Center. Last updated 2023-09-01
  - Body System
    
    Body System
    
    A body system is an organ or a related system of organs in the human body
    
    Attributes
    
    Attributes shown with are required, while those with inherit values from other objects.
    
    Click/tap on an attribute text box below to view details about that attribute.
    
    identifier title description
    - Disease
      
      Disease
      
      A disease is an ailment affecting body systems
      
      Attributes
      
      Attributes shown with are required, while those with inherit values from other objects.
      
      Click/tap on an attribute text box below to view details about that attribute.
      
      identifier title description icd9 icd10 body_system
  - Site
    
    Site
    
    A principal investigator at an institution constitutes a "site" which receives funding to do reserach for EDRN
    
    Attributes
    
    Attributes shown with are required, while those with inherit values from other objects.
    
    Click/tap on an attribute text box below to view details about that attribute.
    
    identifier Institution_Name_Abbrev EDRN_Funding_Date_Start EDRN_Funding_Date_Finish Member_Type Institution_URL Associate_Members_Sponsor ID_for_Principal_Investigator IDs_for_CoPrincipalInvestigators IDs_for_CoInvestigators IDs_for_Investigators IDs_for_Staff specialty proposal
    - Person
      
      Person
      
      A person is a human member of EDRN that belongs to a Site and is typically an investigator or other staff
      
      Attributes
      
      Attributes shown with are required, while those with inherit values from other objects.
      
      Click/tap on an attribute text box below to view details about that attribute.
      
      identifier Name_First Name_Middle Name_Last Phone Email Fax Specialty Photo_file_name EDRN_title userID Role_Secure_Site Salutation Site_id Degree1 Degree2 Degree3 Staff_Status
    - Protocol
      
      Protocol
      
      A protocol is a kind of action plan document describing how a clinical trial is conducted
      
      Attributes
      
      Attributes shown with are required, while those with inherit values from other objects.
      
      Click/tap on an attribute text box below to view details about that attribute.
      
      Title Eligibility_criteria Protocol_Abstract Protocol_Publications Coordinating_Investigator_Site_ID Lead_Investigator_Site_ID Protocol_Field_of_Research Protocol_Cancer_Type BiomarkerName Protocol_5_Phase_Status Protocol_Aims Protocol_Analytic_Method Protocol_Blinding Protocol_Collaborative_Group Protocol_Comments Protocol_Data_Sharing_Plan Protocol_Data_Sharing_Plan_In_Place Protocol_Date_Finish Protocol_Date_Finish_Estimate Protocol_Date_Start Protocol_Name_Abbrev Protocol_Objective Protocol_or_Project_Flag Protocol_Results_Outcome Protocol_Results_Outcome_Secure_Site Protocol_Type Sample_Size_Final Sample_Size_Planned identifier
    - Publication
      
      Publication
      
      An article, paper, column, book, or other published scientific research
      
      Attributes
      
      Attributes shown with are required, while those with inherit values from other objects.
      
      Click/tap on an attribute text box below to view details about that attribute.
      
      identifier Volume Year SiteID Item_Title Description Issue Journal PMID Publication_URL

Element text: identifier
Definition: RDF subject URI of the biomarker
Requirement: Required
Inheritance: This attribute does not inherit values from other objects.
Data Type: URI
Explanatory Note: Uniform resource identifiers uniquely identify any kind of resource; subject URIs are the subjects in statements made about resources

Element text: Alias
Definition: Alternative names for the biomarker
Requirement: Optional
Inheritance: This attribute does not inherit values from other objects.
Data Type: string
Explanatory Note: May appear multiple times in RDF statements

Element text: HgncName
Definition: HUGO Gene Nomenclature Committee's name
Requirement: Optional
Inheritance: This attribute does not inherit values from other objects.
Data Type: string
Explanatory Note: May still appear in RDF but as an empty string

Element text: Title
Definition: The "primary" name of the biomarker
Requirement: Required
Inheritance: This attribute does not inherit values from other objects.
Data Type: string
Explanatory Note: (No notes were given for this element.)

Element text: URN
Definition: Uniform resource name of the biomarker
Requirement: Required
Inheritance: This attribute does not inherit values from other objects.
Data Type: string
Explanatory Note: This value could (and perhaps should) be used as the RDF subject "identifier"

Element text: Description
Definition: A short summary of the biomarker
Requirement: Optional
Inheritance: This attribute does not inherit values from other objects.
Data Type: string
Explanatory Note: (No notes were given for this element.)

Element text: QAState
Definition: The state of the quality analysis of the biomarker
Requirement: Optional
Inheritance: This attribute does not inherit values from other objects.
Data Type: string
Explanatory Note: (No notes were given for this element.)

Permissible Values

Accepted
Curated
New
Under Review

Element text: Security
Definition: Whether the biomarker is private or not
Requirement: Optional
Inheritance: This attribute does not inherit values from other objects.
Data Type: string
Explanatory Note: Note that this is determined solely by cheking the QAState; if it's "Accepted" it's "Public", otherwise it's "Private"

Permissible Values

Private
Public

Element text: Type
Definition: What kind of biomarker it is
Requirement: Optional
Inheritance: This attribute does not inherit values from other objects.
Data Type: string
Explanatory Note: While this value is optional, it can appear in RDF with an empty string literal value

Permissible Values

Epigenetic
Gene
Genetic
Genomic
Glycomic
Metabolomic
Protein
Proteomic

Element text: ShortName
Definition: Unused
Requirement: Optional
Inheritance: This attribute does not inherit values from other objects.
Data Type: string
Explanatory Note: While this value is optional, it can appear in RDF with an empty string literal value. Also, it is not used.

Element text: IsPanel
Definition: Whether the biomarker is a panel comprised of other biomarkers
Requirement: Optional
Inheritance: This attribute does not inherit values from other objects.
Data Type: string
Explanatory Note: A string of "1" indicates that the biomarker is a panel

Permissible Values

Element text: hasBiomarker
Definition: For biomarker panels only, the RDF subject URIs of those biomarkers that are part of the panel
Requirement: Optional
Inheritance: This attribute does not inherit values from other objects.
Data Type: URI
Explanatory Note: This statement appears once for each biomarker that's part of a biomarker's panel membership

Element text: memberOfPanel
Definition: For biomarkers that belong to panels, the RDF subject URIs of those panels
Requirement: Optional
Inheritance: This attribute does not inherit values from other objects.
Data Type: URI
Explanatory Note: The statement appears once for each biomarker panel that a biomarker is a member of. This is often just one biomarker panel, but a single biomarker can (and in practice does, see "Annexin 1") belong to multiple panels.

Element text: AccessGrantedTo
Definition: Names of LDAP groups allowed to view this biomarker
Requirement: Optional
Inheritance: This attribute does not inherit values from other objects.
Data Type: string
Explanatory Note: Note that these are the common names of the groups, not full distinguished names (DNs); this contrasts with the Data Commons' notion of "OwnerPrincipal", which does use full DNs

Element text: AssociatedDataset
Definition: URI of the scientific data collection referenced with this biomarker
Requirement: Optional
Inheritance: This attribute does not inherit values from other objects.
Data Type: URI
Explanatory Note: Note that while the text of this data element reads "AssociatedDataset", it's actually the Collections—not the Datasets—associated with the biomarker

Element text: referencedInPublication
Definition: URI of the publication associated with this biomarker
Requirement: Optional
Inheritance: This attribute does not inherit values from other objects.
Data Type: URI
Explanatory Note: It would be better to use a PubMed ID

Element text: referencesResource
Definition: URI of additional resources associated with this biomarker
Requirement: Optional
Inheritance: This attribute does not inherit values from other objects.
Data Type: URI
Explanatory Note: Although URIs are allowed here, in practice they are all URLs

Element text: indicatorForOrgan
Definition: URI of the body system (organ) for which this biomarker can indicate disease
Requirement: Optional
Inheritance: This attribute does not inherit values from other objects.
Data Type: URI
Explanatory Note: (No notes were given for this element.)

Element text: hasBiomarkerStudyDatas
Definition: Bag of URIs to biomarker-study statements
Requirement: Optional
Inheritance: This attribute does not inherit values from other objects.
Data Type: b-node
Explanatory Note: Each resource in the bag identifies a BiomarkerStudyData object that references a single protocol by URI. In retrospect it would'be been much simpler to simply reference the protocol URIs directly.

Element text: identifier
Definition: RDF subject URI of the biomarker-organ
Requirement: Required
Inheritance: This attribute does not inherit values from other objects.
Data Type: URI
Explanatory Note: Uniform resource identifiers uniquely identify any kind of resource; subject URIs are the subjects in statements made about resources. Note that these are unused by the EDRN portal

Element text: URN
Definition: Unused
Requirement: Required
Inheritance: This attribute does not inherit values from other objects.
Data Type: string
Explanatory Note: Note that although this is a literal string, it should be an RDF resource URI. But that doesn't really matter as nothing uses this anyway

Element text: Biomarker
Definition: RDF subject URI of the biomarker
Requirement: Required
Inheritance: This attribute does not inherit values from other objects.
Data Type: URI
Explanatory Note: This "connects" organ-specific data to its biomarker object

Element text: Description
Definition: A brief summary of how the biomarker indicates for the given organ
Requirement: Optional
Inheritance: This attribute does not inherit values from other objects.
Data Type: string
Explanatory Note: (No notes were given for this element.)

Element text: PerformanceComment
Definition: A remark on how well the biomarker indicates disease for the organ
Requirement: Optional
Inheritance: This attribute does not inherit values from other objects.
Data Type: string
Explanatory Note: (No notes were given for this element.)

Element text: Organ
Definition: The name of the body system (organ) for which the biomarker indicates disease
Requirement: Required
Inheritance: This attribute does not inherit values from other objects.
Data Type: string
Explanatory Note: This should be a URI to the Body System object, but alas is a string from a semi-controlled vocabulary

Element text: Phase
Definition: The phase of research completed for this biomarker-organ plan
Requirement: Required
Inheritance: This attribute does not inherit values from other objects.
Data Type: string
Explanatory Note: Although a string, this should be a single digit in the range 1–5

Permissible Values

Element text: QAState
Definition: The state of the quality analysis of the biomarker with regard to the diseases for which it indicates for the organ
Requirement: Optional
Inheritance: This attribute does not inherit values from other objects.
Data Type: string
Explanatory Note: Although optional, sometimes there are blank predicates in RDF statements

Permissible Values

Accepted
Curated
New
Under Review

Element text: Certification
Definition: URI to clinical translation certification
Requirement: Optional
Inheritance: This attribute does not inherit values from other objects.
Data Type: URI
Explanatory Note: In current practice, when statements involving this predicate appear, the URI referenced is either "http://www.cms.gov/Regulations-and-Guidance/Legislation/CLIA/index.html" to indicate CLIA certification or "http://www.fda.gov/regulatoryinformation/guidances/ucm125335.htm" for FDA certification. It's possible for both to appear for a single biomarker-organ.

Element text: AccessGrantedTo
Definition: Names of LDAP groups allowed to view this biomarker-organ
Requirement: Optional
Inheritance: This attribute does not inherit values from other objects.
Data Type: string
Explanatory Note: Note that these are the common names of the groups, not full distinguished names (DNs); this contrasts with the Data Commons' notion of "OwnerPrincipal", which does use full DNs

Element text: referencedInPublication
Definition: URI of the publication associated with this biomarker-organ
Requirement: Optional
Inheritance: This attribute does not inherit values from other objects.
Data Type: URI
Explanatory Note: It would be better to use a PubMed ID

Element text: referencesResource
Definition: URI of additional resources associated with this biomarker-organ
Requirement: Optional
Inheritance: This attribute does not inherit values from other objects.
Data Type: URI
Explanatory Note: Although URIs are allowed here, in practice they are all URLs

Element text: hasBiomarkerOrganStudyDatas
Definition: Bag of URIs to biomarker-organ-study statements
Requirement: Optional
Inheritance: This attribute does not inherit values from other objects.
Data Type: b-node
Explanatory Note: Each resource in the bag identifies BiomarkerOrganStudyData objects that each tell more about how a specific protocol (study) refines the knowledge about a biomarker-organ-protocol relationship and includes a URI to the actual protocol (study).

Element text: identifier
Definition: RDF subject URI of the biomarker-organ-study
Requirement: Required
Inheritance: This attribute does not inherit values from other objects.
Data Type: URI
Explanatory Note: Uniform resource identifiers uniquely identify any kind of resource; subject URIs are the subjects in statements made about resources. Note that these are unused by the EDRN portal

Element text: referencesStudy
Definition: URI of the protocol (study) providing context for the biomarker-organ
Requirement: Required
Inheritance: This attribute does not inherit values from other objects.
Data Type: URI
Explanatory Note: Identifies a single protocol by its RDF subject URI

Element text: DecisionRule
Definition: Unknown
Requirement: Optional
Inheritance: This attribute does not inherit values from other objects.
Data Type: string
Explanatory Note: A variety of values appear here

Element text: Phase
Definition: Phase of research as to how far a single protocol (study) has progressed with regard to a biomarker's ability to indicate disease for a body system (organ)
Requirement: Optional
Inheritance: This attribute does not inherit values from other objects.
Data Type: string
Explanatory Note: Although a string, this should be a single digit in the range 1–5

Permissible Values

Element text: referencedInPublication
Definition: URI of the publication associated with this biomarker-organ-protocol (study)
Requirement: Optional
Inheritance: This attribute does not inherit values from other objects.
Data Type: URI
Explanatory Note: It would be better to use a PubMed ID

Element text: referencesResource
Definition: URI of additional resources associated with this biomarker-organ-study
Requirement: Optional
Inheritance: This attribute does not inherit values from other objects.
Data Type: URI
Explanatory Note: Although URIs are allowed here, in practice they are all URLs

Element text: identifier
Definition: RDF subject URI of the body system
Requirement: Required
Inheritance: This attribute does not inherit values from other objects.
Data Type: URI
Explanatory Note: Uniform resource identifiers uniquely identify any kind of resource; subject URIs are the subjects in statements made about resources

Element text: title
Definition: Name of the body system or organ
Requirement: Required
Inheritance: This attribute does not inherit values from other objects.
Data Type: string
Explanatory Note: Typical values are "Colon", "Lymph nodes", "Liver", etc

Permissible Values

Colon
Cervix
Breast
Brain
Bone
Bladder
Esophagus
Head and Neck
Kidney
Liver
Lung
Ovary
Pancreas
Prostate
Rectum
Stomack
Thyroid
Uterus
Skin
Testis
Lymph Node
Vagina

Element text: description
Definition: A short summary of the body system or organ
Requirement: Optional
Inheritance: This attribute does not inherit values from other objects.
Data Type: string
Explanatory Note: In practice, this is never set

Element text: identifier
Definition: RDF subject URI of the disease
Requirement: Required
Inheritance: This attribute does not inherit values from other objects.
Data Type: URI
Explanatory Note: Uniform resource identifiers uniquely identify any kind of resource; subject URIs are the subjects in statements made about resources

Element text: title
Definition: The name of the disease
Requirement: Required
Inheritance: This attribute does not inherit values from other objects.
Data Type: string
Explanatory Note: Typical values are "Liver cell carcinoma" or "Malignant neoplasm of colon"

Element text: description
Definition: A short summary of the disease
Requirement: Optional
Inheritance: This attribute does not inherit values from other objects.
Data Type: string
Explanatory Note: So long as the DMCC curated this data, the only description to ever appear was for disease №14, "Lymphoid leukaemia", with the descriptive text "43 different diseases"

Element text: icd9
Definition: International Classification of Disease code, 9th edition
Requirement: Optional
Inheritance: This attribute does not inherit values from other objects.
Data Type: string
Explanatory Note: Although optional, every disease the DMCC curates has a value for ICD9

Element text: icd10
Definition: International Classification of Disease code, 10th edition
Requirement: Optional
Inheritance: This attribute does not inherit values from other objects.
Data Type: string
Explanatory Note: Although optional, every disease the DMCC curates has a value for ICD10

Element text: body_system
Definition: URIs of the body systems affected by this disease
Requirement: Optional
Inheritance: This attribute does not inherit values from other objects.
Data Type: URI
Explanatory Note: As produced by the DMCC SOAP API, this is a comma-separated list of base-10 codes matching the "Body_System" endpoint. The CancerDataExpo turns these into a series of URI references.

Element text: identifier
Definition: RDF subject URI of the site
Requirement: Required
Inheritance: This attribute does not inherit values from other objects.
Data Type: URI
Explanatory Note: Uniform resource identifiers uniquely identify any kind of resource; subject URIs are the subjects in statements made about resources

Element text: Institution_Name_Abbrev
Definition: A short name for the site
Requirement: Optional
Inheritance: This attribute does not inherit values from other objects.
Data Type: string
Explanatory Note: Could be an acronym, an initialism, a shortening, a contraction, or other kind of abbreviation

Element text: EDRN_Funding_Date_Start
Definition: When money was first given
Requirement: Optional
Inheritance: This attribute does not inherit values from other objects.
Data Type: string
Explanatory Note: A string field, but typically a date; format is not enforced, but the DMCC tends to use US-centric date formats

Element text: EDRN_Funding_Date_Finish
Definition: When the money stopped flowing
Requirement: Optional
Inheritance: This attribute does not inherit values from other objects.
Data Type: string
Explanatory Note: A string field, but typically a date; format is not enforced, but the DMCC tends to use US-centric date formats

Element text: Member_Type
Definition: The kind of site it is
Requirement: Optional
Inheritance: This attribute does not inherit values from other objects.
Data Type: string
Explanatory Note: The "kind" determines certain affordances based on the structure of the Early Detection Research Network

Permissible Values

Associate Member A - EDRN Funded
Associate Member B
Associate Member C
Biomarker Characterization Center
Biomarker Developmental Laboratories
Biomarker Reference Laboratories
Clinical Validation Center
Data Management and Coordinating Center
Informatics Center
National Cancer Institute
Non-EDRN Site
SPOREs

Element text: Institution_URL
Definition: URL to the site's home page
Requirement: Optional
Inheritance: This attribute does not inherit values from other objects.
Data Type: string
Explanatory Note: A uniform resource locator, as oppsoed to a uniform resrouce identifier

Element text: Associate_Members_Sponsor
Definition: For associate member sites, RDF subject URI of the site's sponsor
Requirement: Optional
Inheritance: This attribute does not inherit values from other objects.
Data Type: URI
Explanatory Note: Associate members (see "Member_Type") are sponsored by other EDRN sites

Element text: ID_for_Principal_Investigator
Definition: RDF subject URI of the Person who is the site's principal investigator
Requirement: Optional
Inheritance: This attribute does not inherit values from other objects.
Data Type: URI
Explanatory Note: Although officially optional, in practice it is essential to associate a site with a PI

Element text: IDs_for_CoPrincipalInvestigators
Definition: RDF subject URIs of the Persons who are the co-principal investigators
Requirement: Optional
Inheritance: This attribute does not inherit values from other objects.
Data Type: URI
Explanatory Note: In textual form, this is a comma-separated list; extra spaces are to be trimmed

Element text: IDs_for_CoInvestigators
Definition: RDF subject URIs of the Persons who are co-investigators
Requirement: Optional
Inheritance: This attribute does not inherit values from other objects.
Data Type: URI
Explanatory Note: In textual form, this is a comma-separated list; extra spaces are to be trimmed

Element text: IDs_for_Investigators
Definition: RDF subject URIs of the Persons who are no more than investigators
Requirement: Optional
Inheritance: This attribute does not inherit values from other objects.
Data Type: URI
Explanatory Note: In textual form, this is a comma-separated list; extra spaces are to be trimmed

Element text: IDs_for_Staff
Definition: RDF subject URIs of the Persons who are just staff members
Requirement: Optional
Inheritance: This attribute does not inherit values from other objects.
Data Type: URI
Explanatory Note: In textual form, this is a comma-separated list; extra spaces are to be trimmed

Element text: specialty
Definition: What the site's really good at
Requirement: Optional
Inheritance: This attribute does not inherit values from other objects.
Data Type: string
Explanatory Note: This is often a long'ish abstract

Element text: proposal
Definition: Title of the propsal that produced this site
Requirement: Optional
Inheritance: This attribute does not inherit values from other objects.
Data Type: string
Explanatory Note: This applies only to Biomarker Development Laboratories; it may be blank for all other kinds of sites

Element text: Title
Definition: The name of the protocol
Requirement: Required
Inheritance: This attribute does not inherit values from other objects.
Data Type: string
Explanatory Note: Essentially the Dublin Core concept of title

Element text: Eligibility_criteria
Definition: The requirements for participation in the protocol
Requirement: Optional
Inheritance: This attribute does not inherit values from other objects.
Data Type: string
Explanatory Note: This can be a long form paragraph; although it should be plain text, some protocols incorrectly include HTML markup

Element text: Protocol_Abstract
Definition: A short summary of the protocol
Requirement: Optional
Inheritance: This attribute does not inherit values from other objects.
Data Type: string
Explanatory Note: Essentially the Dublin Core concept of description, however if not given the portal will use, in preference order, Protocol_Objective, Protocol_Aims, Protocol_Outcome. This field can be a long form paragraph; although it should be plain text, some protocols incorrectly include HTML markup

Element text: Protocol_Publications
Definition: URIs of the publications made with this protocol
Requirement: Optional
Inheritance: This attribute does not inherit values from other objects.
Data Type: URI
Explanatory Note: In the SOAP API this is a comma-separated list, which the CancerDataExpo converts into a sequence of URI references to Publication objects

Element text: Coordinating_Investigator_Site_ID
Definition: URI of the site that coordinates this protocol
Requirement: Optional
Inheritance: This attribute does not inherit values from other objects.
Data Type: URI
Explanatory Note: In the SOAP API this is a singe site number, which the CancerDataExpo converts into a URI reference to another Site object

Element text: Lead_Investigator_Site_ID
Definition: URI of the site that leads this protocol
Requirement: Optional
Inheritance: This attribute does not inherit values from other objects.
Data Type: URI
Explanatory Note: In the SOAP API this is a singe site number, which the CancerDataExpo converts into a URI reference to another Site object

Element text: Protocol_Field_of_Research
Definition: Areas studied by this protocol
Requirement: Optional
Inheritance: This attribute does not inherit values from other objects.
Data Type: string
Explanatory Note: In the SOAP API, this is a comma-separated list of topics such as "Genomics" or "Proteomics" which the CancerDataExpo translates into a sequence of predicates

Element text: Protocol_Cancer_Type
Definition: Types of diseases studied by this protocol
Requirement: Optional
Inheritance: This attribute does not inherit values from other objects.
Data Type: URI
Explanatory Note: In the SOAP API, this is a comma-separated list of numeric IDs to Diseases, which the CancerDataExpo translates into a sequence of URI references to Disease objects

Element text: BiomarkerName
Definition: Names of biomarkers studied by this protocol
Requirement: Optional
Inheritance: This attribute does not inherit values from other objects.
Data Type: string
Explanatory Note: This is a single string consisting of comma-separated namees of biomarkers. Unforuntately, they do not necessarily correspond to the names of biomarkers in the Biomarker Database. An improvement would be to use RDF reference URIs to those biomarkers

Element text: Protocol_5_Phase_Status
Definition: Uncertain
Requirement: Optional
Inheritance: This attribute does not inherit values from other objects.
Data Type: string
Explanatory Note: In the SOAP API, this contains either "1" or "2" or "3" or "4"; no more is known at this time

Element text: Protocol_Aims
Definition: The long term goals of this protocol
Requirement: Optional
Inheritance: This attribute does not inherit values from other objects.
Data Type: string
Explanatory Note: This can be a long form paragraph; although it should be plain text, some protocols incorrectly include HTML markup

Element text: Protocol_Analytic_Method
Definition: How things in this protocol are analyzed
Requirement: Optional
Inheritance: This attribute does not inherit values from other objects.
Data Type: string
Explanatory Note: This can be a long form paragraph; although it should be plain text, some protocols incorrectly include HTML markup

Element text: Protocol_Blinding
Definition: How subjects were blinded by this protocol
Requirement: Optional
Inheritance: This attribute does not inherit values from other objects.
Data Type: string
Explanatory Note: There is not a controlled vocabulary for this, however this is not used in any RDF-consuming application at this time in any case

Element text: Protocol_Collaborative_Group
Definition: Names of EDRN collaborative groups involved in this protocol
Requirement: Optional
Inheritance: This attribute does not inherit values from other objects.
Data Type: string
Explanatory Note: Although there should be a controlled vocabulary for this, there are a number of aliases, truncations, and abbreviations emitted by the DMCC. As a result, the EDRN portal treats this as a simple single-valued string field.

Element text: Protocol_Comments
Definition: Various remarks, observations, statements, pronouncements, and reflections about the protocol
Requirement: Optional
Inheritance: This attribute does not inherit values from other objects.
Data Type: string
Explanatory Note: This can be a long form paragraph; although it should be plain text, some protocols incorrectly include HTML markup

Element text: Protocol_Data_Sharing_Plan
Definition: The plan on sharing data
Requirement: Optional
Inheritance: This attribute does not inherit values from other objects.
Data Type: string
Explanatory Note: This can be anything from "Follow EDRN guidelines" to long-form paragraphs. The EDRN portal does not store or display this information.

Element text: Protocol_Data_Sharing_Plan_In_Place
Definition: Is there an "in situ" plan on sharing data, yes or no
Requirement: Optional
Inheritance: This attribute does not inherit values from other objects.
Data Type: string
Explanatory Note: The EDRN portal does not display this

Permissible Values

Element text: Protocol_Date_Finish
Definition: When this protocol ceased
Requirement: Optional
Inheritance: This attribute does not inherit values from other objects.
Data Type: string
Explanatory Note: The format of the string is always: "Mon D Year 12:00AM" where "Mon" is a capitalized three-letter abbreviation of the month (Jan, Feb, …), D is a left-space padded day of the month ("01", "02", … "11", "12", … "30", "31"), and Year is a full 4-digit year. This is always followed by a space and the literal string "12:00AM". (Note: the portal consumes this but displays only the month, day, and year.)

Element text: Protocol_Date_Finish_Estimate
Definition: When this protocol is estimated to cease
Requirement: Optional
Inheritance: This attribute does not inherit values from other objects.
Data Type: string
Explanatory Note: The format of the string is always: "Mon D Year 12:00AM" where "Mon" is a capitalized three-letter abbreviation of the month (Jan, Feb, …), D is a left-space padded day of the month ("01", "02", … "11", "12", … "30", "31"), and Year is a full 4-digit year. This is always followed by a space and the literal string "12:00AM". (Note: the portal consumes this but displays only the month, day, and year.)

Element text: Protocol_Date_Start
Definition: When this protocol will start or was started
Requirement: Optional
Inheritance: This attribute does not inherit values from other objects.
Data Type: string
Explanatory Note: The format of the string is always: "Mon D Year 12:00AM" where "Mon" is a capitalized three-letter abbreviation of the month (Jan, Feb, …), D is a left-space padded day of the month ("01", "02", … "11", "12", … "30", "31"), and Year is a full 4-digit year. This is always followed by a space and the literal string "12:00AM". (Note: the portal consumes this but displays only the month, day, and year.)

Element text: Protocol_Name_Abbrev
Definition: An abbreviated name for this protocol
Requirement: Required
Inheritance: This attribute does not inherit values from other objects.
Data Type: string
Explanatory Note: This could be an initialism, an acronym, a shortening, a contraction, or other kind of abbreviation

Element text: Protocol_Objective
Definition: The objectives of this protocol
Requirement: Optional
Inheritance: This attribute does not inherit values from other objects.
Data Type: string
Explanatory Note: This can be a long form paragraph; although it should be plain text, some protocols incorrectly include HTML markup

Element text: Protocol_or_Project_Flag
Definition: Is this protocol actually a project or is it really a protocol?
Requirement: Optional
Inheritance: This attribute does not inherit values from other objects.
Data Type: string
Explanatory Note: Rather than being a flag (true or false), this is either "Project" or "Protocol". Those protocols that are in fact projects get a special badge in the EDRN portal.

Permissible Values

Project
Protocol

Element text: Protocol_Results_Outcome
Definition: What came out of this protocol
Requirement: Optional
Inheritance: This attribute does not inherit values from other objects.
Data Type: string
Explanatory Note: This can be a long form paragraph; although it should be plain text, some protocols incorrectly include HTML markup

Element text: Protocol_Results_Outcome_Secure_Site
Definition: A more secret outcome of this protocol
Requirement: Optional
Inheritance: This attribute does not inherit values from other objects.
Data Type: string
Explanatory Note: This can be a long form paragraph; although it should be plain text, some protocols incorrectly include HTML markup

Element text: Protocol_Type
Definition: What kind of protocol this is
Requirement: Required
Inheritance: This attribute does not inherit values from other objects.
Data Type: string
Explanatory Note: Categorized protocols (and projects)

Permissible Values

Clinical Utility Trial
Collaboration
Other specify
Reference Set
Single
Validation

Element text: Sample_Size_Final
Definition: At the conclusion of the protocol, the size of the sample set
Requirement: Optional
Inheritance: This attribute does not inherit values from other objects.
Data Type: string
Explanatory Note: Essentially free text

Element text: Sample_Size_Planned
Definition: At the beginning of the protocol, the planned size of the sample set
Requirement: Optional
Inheritance: This attribute does not inherit values from other objects.
Data Type: string
Explanatory Note: Essentially free text

Element text: identifier
Definition: RDF subject URI of the protocol
Requirement: Required
Inheritance: This attribute does not inherit values from other objects.
Data Type: URI
Explanatory Note: Uniform resource identifiers uniquely identify any kind of resource; subject URIs are the subjects in statements made about resources

Element text: identifier
Definition: RDF subject URI of the person
Requirement: Required
Inheritance: This attribute does not inherit values from other objects.
Data Type: URI
Explanatory Note: Uniform resource identifiers uniquely identify any kind of resource; subject URIs are the subjects in statements made about resources

Element text: Name_First
Definition: First name
Requirement: Optional
Inheritance: This attribute does not inherit values from other objects.
Data Type: string
Explanatory Note: The first name of a person, although not necessarily the given name—and, in some cultures, there may not be a first name at all

Element text: Name_Middle
Definition: Middle name
Requirement: Optional
Inheritance: This attribute does not inherit values from other objects.
Data Type: string
Explanatory Note: The person's "middle" name—although in some cultures, there is no notion of a middle name

Element text: Name_Last
Definition: Last name
Requirement: Required
Inheritance: This attribute does not inherit values from other objects.
Data Type: string
Explanatory Note: The last name of a person; be aware that this is not always a family name, and in some cultures there is not a "last" name

Element text: Phone
Definition: Telephone number
Requirement: Optional
Inheritance: This attribute does not inherit values from other objects.
Data Type: string
Explanatory Note: This is essentially free-form; the data in the DMCC often is US-centric in format (no initial + symbol) and lacks country codes, but sometimes there are hyphens or parentheses or spaces—and sometimes even just completely blank spaces. The EDRN portal staunchly refuses to record phone numbers at all for privacy purposes, although the phone numbers are clearly visible in the RDF for registered persons.

Element text: Email
Definition: Email address
Requirement: Optional
Inheritance: This attribute does not inherit values from other objects.
Data Type: string
Explanatory Note: Prior to generation of RDF, invalid email addresses like "n/a" or email addresses for invalid domains are filtered out

Element text: Fax
Definition: Facsimilie telephone number
Requirement: Optional
Inheritance: This attribute does not inherit values from other objects.
Data Type: string
Explanatory Note: This suffers from the same data quality issues as Phone; please see the explanatory note for the Phone element

Element text: Specialty
Definition: Forte, strong point, strength, etc.
Requirement: Optional
Inheritance: This attribute does not inherit values from other objects.
Data Type: string
Explanatory Note: This can be anything from "Molecular Biology" to "OCN" to "BS in Anatomy" to "Registered Nurse", etc. Note the portal does not record or display this information.

Element text: Photo_file_name
Definition: URL of a portrait of the person
Requirement: Optional
Inheritance: This attribute does not inherit values from other objects.
Data Type: URI
Explanatory Note: The portal will fall back to the Gravatar service to find an image of an individual if this is not given

Element text: EDRN_title
Definition: Job title for the person in regards to EDRN
Requirement: Optional
Inheritance: This attribute does not inherit values from other objects.
Data Type: string
Explanatory Note: (No notes were given for this element.)

Permissible Values

Co-Investigator
Co-Principal Investigator
DMCC
EDRN Associate Member
EDRN Principal Investigator
Investigator
Other Admin Staff
Other Lab Staff
Other Site Staff
Primary Admin Staff
Primary Lab Staff
Principal Investigator
Staff

Element text: userID
Definition: Login account name for the person
Requirement: Optional
Inheritance: This attribute does not inherit values from other objects.
Data Type: string
Explanatory Note: This, along with a password, affords logins for the person to the EDRN "secure" site, the EDRN portal, EDRN LabCAS, Biomarker Database, and other EDRN applications

Element text: Role_Secure_Site
Definition: Role the user has when logged into the "secure" site
Requirement: Optional
Inheritance: This attribute does not inherit values from other objects.
Data Type: string
Explanatory Note: This is used solely by the EDRN "secure" site and no other EDRN application

Element text: Salutation
Definition: A gesture or utterance made as a greeting or acknowledgement of the person
Requirement: Optional
Inheritance: This attribute does not inherit values from other objects.
Data Type: string
Explanatory Note: Used for greetings, addressings, hails, welcomes, toastings, tributes, homages, and obeisances

Permissible Values

Dr.
Miss
Mr.
Mrs.
Ms.

Element text: Site_id
Definition: RDF subject URI of the site
Requirement: Required
Inheritance: This attribute does not inherit values from other objects.
Data Type: URI
Explanatory Note: In the DMCC data, this exists as a simple string of base-10 digits; in RDF it's translated into a uniform resource identifier of the site to which the user belongs

Element text: Degree1
Definition: The first academic degree bestowed upon the person
Requirement: Optional
Inheritance: This attribute does not inherit values from other objects.
Data Type: string
Explanatory Note: (No notes were given for this element.)

Element text: Degree2
Definition: The second academic degree bestowed upon the person
Requirement: Optional
Inheritance: This attribute does not inherit values from other objects.
Data Type: string
Explanatory Note: (No notes were given for this element.)

Element text: Degree3
Definition: The third academic degree bestowed upon the person
Requirement: Optional
Inheritance: This attribute does not inherit values from other objects.
Data Type: string
Explanatory Note: (No notes were given for this element.)

Element text: Staff_Status
Definition: Whether the person is a current or former member of EDRN
Requirement: Optional
Inheritance: This attribute does not inherit values from other objects.
Data Type: string
Explanatory Note: While this element name and its permissible values implies the EDRN employs people directly, it should be considered as a flag. If the value is "Current employee", the person is active in EDRN. Otherwise the person was formerly active with EDRN and is no more.

Permissible Values

Current employee
Former employee

Element text: identifier
Definition: RDF subject URI of the publication
Requirement: Required
Inheritance: This attribute does not inherit values from other objects.
Data Type: URI
Explanatory Note: Uniform resource identifiers uniquely identify any kind of resource; subject URIs are the subjects in statements made about resources

Element text: Volume
Definition: The singular collection in a printed series of a periodical in which the publication appears
Requirement: Optional
Inheritance: This attribute does not inherit values from other objects.
Data Type: string
Explanatory Note: Not used since the PubMed ID provides an ideal way to reference the publication

Element text: Year
Definition: The year in which the publication was published
Requirement: Optional
Inheritance: This attribute does not inherit values from other objects.
Data Type: string
Explanatory Note: Not used since the PubMed ID provides an ideal way to reference the publication

Element text: SiteID
Definition: The URI of the site that produced the publication
Requirement: Optional
Inheritance: This attribute does not inherit values from other objects.
Data Type: URI
Explanatory Note: The site ID as published by the DMCC is a string consisiting of base-10 digits indicating the producing site; this is converted into an RDF subject URI by the CancerDataExpo

Element text: Item_Title
Definition: Title of the publication
Requirement: Optional
Inheritance: This attribute does not inherit values from other objects.
Data Type: string
Explanatory Note: Not used since the PubMed ID provides an ideal way to reference the publication

Element text: Description
Definition: A short summary of the publication
Requirement: Optional
Inheritance: This attribute does not inherit values from other objects.
Data Type: string
Explanatory Note: Not used since the PubMed ID provides an ideal way to reference the publication

Element text: Issue
Definition: In which issue of a periodical the publication appears
Requirement: Optional
Inheritance: This attribute does not inherit values from other objects.
Data Type: string
Explanatory Note: Not used since the PubMed ID provides an ideal way to reference the publication

Element text: Journal
Definition: The name of the periodical that published the publication
Requirement: Optional
Inheritance: This attribute does not inherit values from other objects.
Data Type: string
Explanatory Note: Not used since the PubMed ID provides an ideal way to reference the publication

Element text: PMID
Definition: National Library of Medicine's unique identifier for the publication in MEDLINE
Requirement: Required
Inheritance: This attribute does not inherit values from other objects.
Data Type: string
Explanatory Note: A string of base 10 digits that uniquely identifies the publication in the National Library of Medicine's MEDLINE database

Element text: Publication_URL
Definition: An optional resource locator for the publication
Requirement: Optional
Inheritance: This attribute does not inherit values from other objects.
Data Type: URL
Explanatory Note: Not used since the PubMed ID provides an ideal way to reference the publication

Cancer Biomarker Data Commons (LabCAS) Data Model

View as a spreadsheet

Collection

Collection

A collection is the highest-level structural element for organizing data in LabCAS. Collections contain datasets.

Attributes

Attributes shown with are required, while those with inherit values from other objects.

Click/tap on an attribute text box below to view details about that attribute.

identifier CollectionName CollectionDescription LeadPIId LeadPIName DataCustodian DataCustodianEmail InstitutionID InstitutionName ProtocolId ProtocolName ProtocolAbbreviatedName Discipline DataCategory Organ OrganId CollaborativeGroup De-identificationMethod ResultsAndConclusionSummary MethodDetails PubMedID ReferenceURLLink ReferenceURLDescription Consortium Instrument InstrumentManufacturer InstrumentModel InstrumentSoftwareVersion Species OwnerPrincipal DOI DOIURL CollectionVersion CollectionID DataDisclaimer UUID DeliveryStatus DataStructureDescription AdditionalInvolvedResearchers ProtocolStartDate ProtocolEndDate DataCaptureStartDate DataCaptureEndDate FAIRAlignmentStatus ProtocolLeadInvestigatorName ProtocolLeadInvestigatorID
- Dataset
  
  Dataset
  
  A dataset contains a set of data files but can also contain other datasets, forming a nested composition. Datasets containing files cannot contain other datasets. Attributes that are not specified for a dataset inherit their values from their parent datasets or parent collection
  
  Attributes
  
  Attributes shown with are required, while those with inherit values from other objects.
  
  Click/tap on an attribute text box below to view details about that attribute.
  
  DatasetName DatasetDescription InvestigatorID InvestigatorName InstitutionId InstitutionName BlindedSiteID MethodDetails Instrument InstrumentDetails SpecimenType Discipline DataCategory AssayType ProcessingSoftware ContentType DOI DOIURL DateDatasetFrozen DatasetVersion DatasetId SubmittingSiteID SubmittingPersonID DataStructureDescription AnnotationStatus InstrumentManufacturer InstrumentModel InstrumentSoftwareVersion
  - AnnotationsExtension
    
    AnnotationsExtension
    
    Extension used when a Dataset contains annotation objects, labels, regions, contours, segmentations, measurements, classification outputs, or reviewer-generated findings.
    
    Attributes
    
    Attributes shown with are required, while those with inherit values from other objects.
    
    Click/tap on an attribute text box below to view details about that attribute.
    
    AnnotationType AnnotationFormat AnnotationSource AnnotationReviewStatus AnnotationTargetLevel SourceImageFileID SourceSeriesID AnnotationLabel AnnotationDescription AnnotationMethod AnnotationDate AnnotationCoordinateSystem
  - File
    
    File
    
    Core files are the actual computer files of data that comprise the scientific instrument output of observations, experiments, and so forth. Attributes that are not specified for a core file inherit their values from their parent datasets or parent collection
    
    Attributes
    
    Attributes shown with are required, while those with inherit values from other objects.
    
    Click/tap on an attribute text box below to view details about that attribute.
    
    Instrument InstrumentManufacturer InstrumentModel InstrumentSoftwareVersion SpecimenType Discipline AssayType ProcessingSoftware DOI DOIURL FileName DateFileGenerated SubmittingSiteID SubmittingPersonID ProcessingLevel ContentType ProcessingSoftwareVersion md5sum ChecksumType Checksum FileSubmissionDate SubmissionVersion FileType FileSize
  - PathologyImagingExtension
    
    PathologyImagingExtension
    
    Extension for pathology image-specific metadata, including stain type, staining date, scan type, nominal magnification, pixel spacing, and related slide/image acquisition metadata.
    
    Attributes
    
    Attributes shown with are required, while those with inherit values from other objects.
    
    Click/tap on an attribute text box below to view details about that attribute.
    
    StainType StainingDate ScanType NominalMagnification PixelSpacing PixelSpacingUnit

Element text: identifier
Definition: RDF subject URI of the collection
Requirement: Required
Inheritance: This attribute does not inherit values from other objects.
Data Type: URI
Explanatory Note: Uniform resource identifiers uniquely identify any kind of resource; subject URIs are the subjects in statements made about resources

Element text: CollectionName
Definition: A short name for high level data collection
Requirement: Required
Inheritance: This attribute does not inherit values from other objects.
Data Type: Free-text
Explanatory Note: (No notes were given for this element.)

Element text: CollectionDescription
Definition: A description of the data captured in this data collection
Requirement: Required
Inheritance: This attribute does not inherit values from other objects.
Data Type: Free-text
Explanatory Note: (No notes were given for this element.)

Element text: LeadPIId
Definition: DMCC/eSIS person identifier for the PI or data producer responsible for the LabCAS data collection.
Requirement: Required
Inheritance: If no values are specified, this attribute inherits values from other objects.
Data Type: (Type information not available.)
Explanatory Note: Can populate from dataset level

Permissible Values

PersonID from eSIS (DMCC)

Element text: LeadPIName
Definition: Name of the PI or data producer responsible for the LabCAS data collection. This is populated from the LeadPI ID.
Requirement: populate from PersonID
Inheritance: This attribute does not inherit values from other objects.
Data Type: (Type information not available.)
Explanatory Note: (No notes were given for this element.)

Permissible Values

PersonID from eSIS (DMCC)

Element text: DataCustodian
Definition: The person responsible for this data collection
Requirement: Required
Inheritance: This attribute does not inherit values from other objects.
Data Type: (Type information not available.)
Explanatory Note: (No notes were given for this element.)

Element text: DataCustodianEmail
Definition: Data custodian's email address
Requirement: Required
Inheritance: This attribute does not inherit values from other objects.
Data Type: (Type information not available.)
Explanatory Note: (No notes were given for this element.)

Element text: InstitutionID
Definition: The institutionID(s) that collected this data
Requirement: Required
Inheritance: This attribute does not inherit values from other objects.
Data Type: (Type information not available.)
Explanatory Note: (No notes were given for this element.)

Permissible Values

SiteID from eSIS (DMCC)

Element text: InstitutionName
Definition: The institution name(s) that collected this data. This is populated from the Site ID.
Requirement: populate from SiteID
Inheritance: This attribute does not inherit values from other objects.
Data Type: (Type information not available.)
Explanatory Note: (No notes were given for this element.)

Permissible Values

SiteName from eSIS (DMCC)

Element text: ProtocolId
Definition: The protocol ID assigned by the DMCC
Requirement: Required
Inheritance: This attribute does not inherit values from other objects.
Data Type: (Type information not available.)
Explanatory Note: (No notes were given for this element.)

Permissible Values

Protocol ID from eSIS (DMCC)

Element text: ProtocolName
Definition: The protocol title that describes the study this data was captured under. This is assigned by the DMCC. This is populated from the Protocol ID.
Requirement: populate from ProtocolID
Inheritance: This attribute does not inherit values from other objects.
Data Type: (Type information not available.)
Explanatory Note: (No notes were given for this element.)

Permissible Values

Protocol Title from eSIS (DMCC)

Element text: ProtocolAbbreviatedName
Definition: The abbreviated protocol title assigned by the DMCC
Requirement: populate from ProtocolID
Inheritance: This attribute does not inherit values from other objects.
Data Type: (Type information not available.)
Explanatory Note: (No notes were given for this element.)

Permissible Values

Protocol abreviated name from eSIS (DMCC)

Element text: Discipline
Definition: A domain or grouping of medical science technologies
Requirement: Required
Inheritance: This attribute does not inherit values from other objects.
Data Type: (Type information not available.)
Explanatory Note: can populate up from dataset level

Permissible Values

Genomics
Immunology
Metabolomics
Pathology
Pathology Images
Proteomics
Radiology
Other

Element text: DataCategory
Definition: A subgroup of discipline
Requirement: Required
Inheritance: This attribute does not inherit values from other objects.
Data Type: (Type information not available.)
Explanatory Note: can populate from dataset level

Permissible Values

Antibody Microarray
Biospecimen
CT
Clinical
DNA Methylation Sequencing
DNA Microarray Analysis
Documentation
ELISA
Fluoroscopy
Immunoassay
Immunohistochemistry
LabMAP
Luminex
MRI
Mammography
Mass Spectrometry
Multiplex-Immunofluorescent Staining
PET
Protein Microarray
RNA Sequencing
Radiomics
Sequencing
Single Slide Image
Tissue Micro Array
Whole Slide Imaging
Other

Element text: Organ
Definition: A unique macroscopic (gross) anatomic structure that performs specific functions. It is composed of various tissues. An organ is part of an anatomic system or a body region. Representative examples include the heart, lung, liver, spleen, and uterus
Requirement: Required
Inheritance: This attribute does not inherit values from other objects.
Data Type: (Type information not available.)
Explanatory Note: can populate from dataset level

Permissible Values

Organ from eSIS (DMCC)

Element text: OrganId
Definition: The specific DMCC/Cancer Data Expo identifier assigned to the organ or anatomical structure that is the focus of the data collection.
Requirement: Required
Inheritance: This attribute does not inherit values from other objects.
Data Type: String
Explanatory Note: Populated from the controlled organ/body system source.

Permissible Values

Cancer Data Expo Body Systems

Element text: CollaborativeGroup
Definition: The EDRN Collaborative group
Requirement: Required
Inheritance: This attribute does not inherit values from other objects.
Data Type: String
Explanatory Note: (No notes were given for this element.)

Permissible Values

Lung and Upper Areodigestive
G.I. and Other Associated
Breast and Gynecological
Prostate and Urologic

Element text: De-identificationMethod
Definition: The HIPAA Privacy Rule de-identification method. Please refer to Health and Human Services - Methods for De-identification of PHI for more information. Expert Determination: A qualified expert certifies that the risk of re-identification is very small, documents the methods used, and justifies the determination. Safe Harbor: Specific identifiers (e.g., names, addresses) are removed as per the Privacy Rule (see full list on HHS website).
Requirement: (Information not provided.)
Inheritance: This attribute does not inherit values from other objects.
Data Type: (Type information not available.)
Explanatory Note: (No notes were given for this element.)

Permissible Values

Safe Harbor
Expert Determination

Element text: ResultsAndConclusionSummary
Definition: The results and conclusions from this data collection
Requirement: Required
Inheritance: This attribute does not inherit values from other objects.
Data Type: Free-text
Explanatory Note: (No notes were given for this element.)

Element text: MethodDetails
Definition: A comprehensive description of the methodologies and procedures used in the collection and processing of the data collection. This includes information on the experimental design, data collection techniques, equipment used, protocols followed, and any specific conditions or settings applied during the data acquisition process. Additionally, it captures details about any tools, software, or algorithms utilized in data processing and analysis, ensuring transparency and reproducibility of the research.
Requirement: Required
Inheritance: This attribute does not inherit values from other objects.
Data Type: Free-text
Explanatory Note: (No notes were given for this element.)

Element text: PubMedID
Definition: NIH PubMed identifier that links to the publication produced by this data collection
Requirement: Optional
Inheritance: This attribute does not inherit values from other objects.
Data Type: String
Explanatory Note: (No notes were given for this element.)

Element text: ReferenceURLLink
Definition: URL used to reference additional information or point to data in external repositories
Requirement: Optional
Inheritance: This attribute does not inherit values from other objects.
Data Type: String
Explanatory Note: (No notes were given for this element.)

Element text: ReferenceURLDescription
Definition: Description of the URL used to reference additional information or point to data in external repositories.
Requirement: Optional
Inheritance: This attribute does not inherit values from other objects.
Data Type: String
Explanatory Note: (No notes were given for this element.)

Element text: Consortium
Definition: (No definition provided.)
Requirement: Required
Inheritance: This attribute does not inherit values from other objects.
Data Type: (Type information not available.)
Explanatory Note: (No notes were given for this element.)

Permissible Values

EDRN

Element text: Instrument
Definition: A human-readable description of the equipment, instrument, scanner, platform, or system used to collect, acquire, or generate the data. At the collection level, this may summarize instruments used across sites or datasets. Specific instrument details should be captured in structured instrument metadata fields when available.
Requirement: Optional
Inheritance: If no values are specified, this attribute inherits values from other objects.
Data Type: Free-text
Explanatory Note: Retained as a human-readable summary field for display, legacy compatibility, and collections where instrument details vary across datasets. Use structured instrument metadata fields for normalized search, filtering, and downstream reuse when available. For the example, I’d update it to include both a specific example and a multi-site example: Example: “Hologic Selenia FFDM 2D units and Hologic Dimensions digital breast tomosynthesis units operating in 2D mode.” Example for multi-site imaging collections: “Site-specific clinical CT and PET/CT scanners used to acquire submitted DICOM images. Scanner manufacturer and model may vary by contributing site, with specific details captured at the dataset level and/or in DICOM metadata.” This may also be obtained from the specific extension dictionaries

Element text: InstrumentManufacturer
Definition: Manufacturer of the instrument
Requirement: Required
Inheritance: This attribute does not inherit values from other objects.
Data Type: String
Explanatory Note: (No notes were given for this element.)

Element text: InstrumentModel
Definition: Model of the Instrument
Requirement: Optional
Inheritance: This attribute does not inherit values from other objects.
Data Type: String
Explanatory Note: (No notes were given for this element.)

Element text: InstrumentSoftwareVersion
Definition: Software or firmware version associated with the instrument, when available.
Requirement: Optional
Inheritance: This attribute does not inherit values from other objects.
Data Type: String
Explanatory Note: (No notes were given for this element.)

Element text: Species
Definition: (No definition provided.)
Requirement: Required
Inheritance: This attribute does not inherit values from other objects.
Data Type: (Type information not available.)
Explanatory Note: (No notes were given for this element.)

Permissible Values

Homo sapiens
Mus musculus
Bos taurus
Escherichia coli
Rattus norvegicus
Caenorhabditis elegans
Cricetulus griseus
Saccharomyces cerevisiae

Element text: OwnerPrincipal
Definition: List of LDAP groups within EDRN or LDAP user names of specific people that would be allowed to access this data. Defaults to all the groups that the LeadPI belongs to. Can be set to the special DN=public string to enable unrestricted access
Requirement: Required
Inheritance: This attribute does not inherit values from other objects.
Data Type: (Type information not available.)
Explanatory Note: (No notes were given for this element.)

Permissible Values

LDAP groups

Element text: DOI
Definition: Digital Object Identifier created for this collection
Requirement: Optional
Inheritance: This attribute does not inherit values from other objects.
Data Type: (Type information not available.)
Explanatory Note: can be generated by JPL

Element text: DOIURL
Definition: Digital Object Identifier URL that points to this collection
Requirement: Optional
Inheritance: This attribute does not inherit values from other objects.
Data Type: (Type information not available.)
Explanatory Note: (No notes were given for this element.)

Element text: CollectionVersion
Definition: (No definition provided.)
Requirement: Required
Inheritance: This attribute does not inherit values from other objects.
Data Type: (Type information not available.)
Explanatory Note: (No notes were given for this element.)

Element text: CollectionID
Definition: (No definition provided.)
Requirement: System generated
Inheritance: This attribute does not inherit values from other objects.
Data Type: (Type information not available.)
Explanatory Note: (No notes were given for this element.)

Element text: DataDisclaimer
Definition: Approved disclaimer text associated with the data collection.
Requirement: Required
Inheritance: This attribute does not inherit values from other objects.
Data Type: (Type information not available.)
Explanatory Note: Approved text entered at creation of collection "Data and information released from the National Cancer Institute (NCI) are provided on an "AS IS" basis, without warranty of any kind, including without limitation the warranties of merchantability, fitness for a particular purpose and non-infringement. Availability of this data and information does not constitute scientific publication. Data and/or information may contain errors or be incomplete. NCI and its employees make no representation or warranty, express or implied, including without limitation any warranties of merchantability or fitness for a particular purpose or warranties as to the identity or ownership of data or information, the quality, accuracy or completeness of data or information, or that the use of such data or information will not infringe any patent, intellectual property or proprietary rights of any party. NCI shall not be liable for any claim for any loss, harm, illness or other damage or injury arising from access to or use of data or information, including without limitation any direct, indirect, incidental, exemplary, special or consequential damages, even if advised of the possibility of such damages. In accordance with scientific standards, appropriate acknowledgment of NCI should be made in any publications or other disclosures concerning data or information made available by NCI. "

Element text: UUID
Definition: System-generated universally unique identifier for the collection.
Requirement: System Generated
Inheritance: This attribute does not inherit values from other objects.
Data Type: (Type information not available.)
Explanatory Note: Generated by LabCAS or supporting system logic.

Element text: DeliveryStatus
Definition: Status of data capture and delivery for the LabCAS data collection.
Requirement: Required
Inheritance: This attribute does not inherit values from other objects.
Data Type: String
Explanatory Note: Maintained by LabCAS/JPL curators to indicate whether data are planned, actively being delivered, updated, or complete.

Permissible Values

Planning – Actively working with Site(s) and DMCC to develop timeline, identify resources and ensure data aligns with FAIR principles.
New Delivery: The data delivery process is underway, with new data actively being transferred and ingested according to the established delivery plan.
Data Update: Data delivery underway with data being updated to ensure data aligns with FAIR principles.
Complete: The data delivery process has been successfully finished, and all intended data has been transferred and verified as required.
Reached Out: Initial communication has been initiated to explore or discuss the possibility of delivering data.

Element text: DataStructureDescription
Definition: A detailed description of the organization of the data collection, including the relationships between components, the rationale behind the structure, and any relevant terminology. This includes explanations of naming conventions, hierarchical organization, and meanings of data elements to facilitate understanding and reuse of the data.
Requirement: Required
Inheritance: This attribute does not inherit values from other objects.
Data Type: String
Explanatory Note: Data collections that are complicated should use a Readme file.

Element text: AdditionalInvolvedResearchers
Definition: Name of additional involved researcher, separated by commas, in priority order.
Requirement: Optional
Inheritance: This attribute does not inherit values from other objects.
Data Type: Free Text
Explanatory Note: (No notes were given for this element.)

Element text: ProtocolStartDate
Definition: Start date of the EDRN protocol associated with the collection, as provided by DMCC/eSIS.
Requirement: System Populated
Inheritance: This attribute does not inherit values from other objects.
Data Type: Date
Explanatory Note: (No notes were given for this element.)

Element text: ProtocolEndDate
Definition: End date of the EDRN protocol associated with the collection, as provided by DMCC/eSIS.
Requirement: System Populated
Inheritance: This attribute does not inherit values from other objects.
Data Type: Date
Explanatory Note: Populated from the DMCC/eSIS SOAP API when available. This describes the protocol, not the LabCAS collection completion date.

Element text: DataCaptureStartDate
Definition: The date when the data included in the collection began to be collected, generated, acquired, or recorded.
Requirement: Optional
Inheritance: This attribute does not inherit values from other objects.
Data Type: Date
Explanatory Note: (No notes were given for this element.)

Element text: DataCaptureEndDate
Definition: The date when the data included in the collection stopped being collected, generated, acquired, or recorded. Leave blank if data capture is ongoing or the end date has not yet been confirmed.
Requirement: Optional
Inheritance: This attribute does not inherit values from other objects.
Data Type: Date
Explanatory Note: (No notes were given for this element.)

Element text: FAIRAlignmentStatus
Definition: Current FAIR alignment and usability review status of the data collection.
Requirement: Required
Inheritance: This attribute does not inherit values from other objects.
Data Type: String
Explanatory Note: Maintained by LabCAS/JPL curators. This is not submitted by sites.

Permissible Values

Data Ready – Indicates that the dataset is complete, validated, and ready for use.
Under Review - Indicates the data collection is being reviewed for completeness and compliance, and if it can be made public.

Element text: ProtocolLeadInvestigatorName
Definition: Name of the lead investigator for the overall EDRN protocol/study, as provided by DMCC/eSIS.
Requirement: System Populated
Inheritance: This attribute does not inherit values from other objects.
Data Type: String
Explanatory Note: This may be different from LeadPIName, which identifies the PI or data producer responsible for the LabCAS data collection.

Element text: ProtocolLeadInvestigatorID
Definition: DMCC/eSIS person identifier for the protocol-level lead investigator.
Requirement: Required
Inheritance: This attribute does not inherit values from other objects.
Data Type: String
Explanatory Note: This may be different from LeadPIID, which identifies the PI or data producer responsible for the LabCAS data collection.

Permissible Values

PersonID from eSIS (DMCC)

Element text: DatasetName
Definition: A short name for the dataset
Requirement: Required
Inheritance: This attribute does not inherit values from other objects.
Data Type: Free-text
Explanatory Note: (No notes were given for this element.)

Element text: DatasetDescription
Definition: A description of the data captured in this dataset
Requirement: Required
Inheritance: This attribute does not inherit values from other objects.
Data Type: Free-text
Explanatory Note: (No notes were given for this element.)

Element text: InvestigatorID
Definition: The principal investigators or co-investigators person id. If data is blinded this can be "undisclosed
Requirement: Optional
Inheritance: If no values are specified, this attribute inherits values from other objects.
Data Type: (Type information not available.)
Explanatory Note: can populate down from collection or up from dataset to collection

Permissible Values

PersonID from eSIS (DMCC)

Element text: InvestigatorName
Definition: The principal investigators or co-investigators name
Requirement: populate from personID
Inheritance: If no values are specified, this attribute inherits values from other objects.
Data Type: (Type information not available.)
Explanatory Note: can populate down from collection or up from dataset to collection

Permissible Values

PersonName from eSIS (DMCC)

Element text: InstitutionId
Definition: If data is blinded create an anonomized ID. The Site Name is set to 'undisclosed'
Requirement: Optional
Inheritance: If no values are specified, this attribute inherits values from other objects.
Data Type: (Type information not available.)
Explanatory Note: can populate down or up

Permissible Values

SiteID from eSIS (DMCC)

Element text: InstitutionName
Definition: (No definition provided.)
Requirement: populate from SiteID
Inheritance: If no values are specified, this attribute inherits values from other objects.
Data Type: (Type information not available.)
Explanatory Note: can populate down or up

Permissible Values

SiteName from eSIS (DMCC)

Element text: BlindedSiteID
Definition: Randomly generated id that is assigned by the IC Center to blind LabCAS users from the actual Site
Requirement: Optional
Inheritance: This attribute does not inherit values from other objects.
Data Type: (Type information not available.)
Explanatory Note: (No notes were given for this element.)

Element text: MethodDetails
Definition: The rules and procedures followed for research and evaluating results
Requirement: Optional
Inheritance: This attribute does not inherit values from other objects.
Data Type: Free-text
Explanatory Note: (No notes were given for this element.)

Element text: Instrument
Definition: A human-readable description of the equipment, instrument, scanner, platform, or system used to collect, acquire, or generate the data in the dataset. At the dataset level, this should describe the instrument used for that dataset when known, especially when instrument details vary across datasets within a collection.
Requirement: Optional
Inheritance: If no values are specified, this attribute inherits values from other objects.
Data Type: (Type information not available.)
Explanatory Note: Retained as an active human-readable summary field for display, legacy compatibility, and dataset-level context. Use structured instrument metadata fields such as InstrumentManufacturer, InstrumentModel, and InstrumentSoftwareVersion for normalized search, filtering, and downstream reuse when available.This may come from the specific extension dictionaries.

Element text: InstrumentDetails
Definition: (No definition provided.)
Requirement: (Information not provided.)
Inheritance: This attribute does not inherit values from other objects.
Data Type: (Type information not available.)
Explanatory Note: (No notes were given for this element.)

Element text: SpecimenType
Definition: (No definition provided.)
Requirement: Optional
Inheritance: This attribute does not inherit values from other objects.
Data Type: (Type information not available.)
Explanatory Note: (No notes were given for this element.)

Permissible Values

From KSDB List

Element text: Discipline
Definition: A domain or grouping of medical science technologies
Requirement: Optional
Inheritance: If no values are specified, this attribute inherits values from other objects.
Data Type: (Type information not available.)
Explanatory Note: can populate up from dataset level

Permissible Values

Genomics
Proteomics
Pathology Images
Radiology
Immunology
Pathology
Undefined

Element text: DataCategory
Definition: A subgroup of discipline
Requirement: Optional
Inheritance: If no values are specified, this attribute inherits values from other objects.
Data Type: (Type information not available.)
Explanatory Note: can populate up from dataset level

Permissible Values

Sequencing
RNA Sequencing
DNA Methylation Sequencing
DNA Microarray Analysis
Mass Spectrometry
Whole Slide Imaging
Tissue Micro Array
Immunohistochemistry
CT
MRI
Mammography
Fluoroscopy
PET
Documentation
Biospecimen
Clinical
Immunoassay
ELISA
Luminex
LabMAP
Protein Microarray
Single Slide Image
Multiplex-Immunofluorescent Staining
Radiomics
Antibody Microarray

Element text: AssayType
Definition: (No definition provided.)
Requirement: Optional
Inheritance: This attribute does not inherit values from other objects.
Data Type: (Type information not available.)
Explanatory Note: (No notes were given for this element.)

Permissible Values

"H&E
IHC
mIF
RNA-Seq
RNA-Seq (SMART-3SEQ)
DNA-Seq
Single-cell Seq
WES"

Element text: ProcessingSoftware
Definition: Software used to process, transform, analyze, convert, or generate the dataset, when applicable.
Requirement: Optional
Inheritance: If no values are specified, this attribute inherits values from other objects.
Data Type: Free-text
Explanatory Note: May populate from file-level metadata or be summarized at the dataset level when processing software applies across files in the dataset.

Element text: ContentType
Definition: A high-level classification of the type of content included in the dataset, used to describe the general nature or role of the dataset contents.
Requirement: Optional
Inheritance: If no values are specified, this attribute inherits values from other objects.
Data Type: (Type information not available.)
Explanatory Note: May populate from file-level metadata or be summarized at the dataset level when the dataset contains a consistent content type.

Permissible Values

Clinical
Biospecimen
SOP
Documentation
Instrument Output
Metadata
Ancillary Data
Summary

Element text: DOI
Definition: (No definition provided.)
Requirement: Optional
Inheritance: This attribute does not inherit values from other objects.
Data Type: (Type information not available.)
Explanatory Note: (No notes were given for this element.)

Element text: DOIURL
Definition: (No definition provided.)
Requirement: Optional
Inheritance: This attribute does not inherit values from other objects.
Data Type: (Type information not available.)
Explanatory Note: (No notes were given for this element.)

Element text: DateDatasetFrozen
Definition: (No definition provided.)
Requirement: Optional
Inheritance: This attribute does not inherit values from other objects.
Data Type: (Type information not available.)
Explanatory Note: (No notes were given for this element.)

Element text: DatasetVersion
Definition: The version identifier for the Dataset, used to track updates or releases of the Dataset over time.
Requirement: System generated
Inheritance: This attribute does not inherit values from other objects.
Data Type: (Type information not available.)
Explanatory Note: (No notes were given for this element.)

Element text: DatasetId
Definition: (No definition provided.)
Requirement: System generated
Inheritance: This attribute does not inherit values from other objects.
Data Type: (Type information not available.)
Explanatory Note: (No notes were given for this element.)

Element text: SubmittingSiteID
Definition: The DMCC/eSIS site identifier for the institution submitting the dataset.
Requirement: Required
Inheritance: If no values are specified, this attribute inherits values from other objects.
Data Type: String
Explanatory Note: SubmittingSiteID and SubmittingPersonID identify the DMCC/eSIS site and individual associated with the data submission. These values may be populated from dataset-level or file-level metadata when available and may differ from the investigator, originating institution, or collection-level institution.

Permissible Values

SiteID from eSIS (DMCC)

Element text: SubmittingPersonID
Definition: The DMCC/eSIS person identifier for the individual submitting the dataset.
Requirement: Required
Inheritance: If no values are specified, this attribute inherits values from other objects.
Data Type: String
Explanatory Note: SubmittingSiteID and SubmittingPersonID identify the DMCC/eSIS site and individual associated with the data submission. These values may be populated from dataset-level or file-level metadata when available and may differ from the investigator, originating institution, or collection-level institution.

Permissible Values

PersonID from eSIS (DMCC)

Element text: DataStructureDescription
Definition: A detailed description of the organization of the data collection, including the relationships between components, the rationale behind the structure, and any relevant terminology. This includes explanations of naming conventions, hierarchical organization, and meanings of data elements to facilitate understanding and reuse of the data.
Requirement: Required
Inheritance: This attribute does not inherit values from other objects.
Data Type: String
Explanatory Note: For complex datasets, a README or supplemental documentation may also be used.

Element text: AnnotationStatus
Definition: Indicates whether the dataset contains annotation data.
Requirement: Optional
Inheritance: This attribute does not inherit values from other objects.
Data Type: String
Explanatory Note: Use Annotated when annotation files, ROIs, contours, segmentations, labels, or similar annotation objects are included.

Permissible Values

Not Annotated; Annotated; Unknown

Element text: InstrumentManufacturer
Definition: Manufacturer of the instrument used to collect or generate the dataset.
Requirement: Optional
Inheritance: This attribute does not inherit values from other objects.
Data Type: String
Explanatory Note: Use when available. For DICOM images, this may map to Manufacturer (0008,0070).

Element text: InstrumentModel
Definition: Model of the instrument used to collect or generate the dataset.
Requirement: Optional
Inheritance: This attribute does not inherit values from other objects.
Data Type: String
Explanatory Note: For DICOM images, this may map to Manufacturer’s Model Name (0008,1090).

Element text: InstrumentSoftwareVersion
Definition: Software or firmware version associated with the instrument, when available.
Requirement: Optional
Inheritance: This attribute does not inherit values from other objects.
Data Type: String
Explanatory Note: For DICOM images, this may map to Software Versions (0018,1020).

Element text: Instrument
Definition: A human-readable description of the equipment, instrument, scanner, platform, or system used to collect, acquire, or generate the file, when known.
Requirement: Optional
Inheritance: If no values are specified, this attribute inherits values from other objects.
Data Type: (Type information not available.)
Explanatory Note: Retained as an active human-readable summary field for display, legacy compatibility, and file-level context. This value may populate up to the Dataset or Collection level when files share a consistent instrument. Use structured instrument metadata fields from relevant extensions when normalized instrument details are available.

Element text: InstrumentManufacturer
Definition: Manufacturer of the instrument
Requirement: Optional
Inheritance: This attribute does not inherit values from other objects.
Data Type: String
Explanatory Note: (No notes were given for this element.)

Permissible Values

Instrument Manufacturer

Element text: InstrumentModel
Definition: Model of the Instrument
Requirement: Optional
Inheritance: This attribute does not inherit values from other objects.
Data Type: String
Explanatory Note: (No notes were given for this element.)

Permissible Values

Instrument Model

Element text: InstrumentSoftwareVersion
Definition: Software or firmware version associated with the instrument, when available.
Requirement: Optional
Inheritance: This attribute does not inherit values from other objects.
Data Type: String
Explanatory Note: Use for software or firmware associated with the instrument itself, such as scanner software or acquisition software. This is different from ProcessingSoftwareVersion, which describes downstream processing, transformation, or analysis software.

Permissible Values

Instrument Software Version

Element text: SpecimenType
Definition: (No definition provided.)
Requirement: Optional
Inheritance: If no values are specified, this attribute inherits values from other objects.
Data Type: (Type information not available.)
Explanatory Note: Can populate up

Permissible Values

From KSDB List

Element text: Discipline
Definition: A domain or grouping of medical science technologies
Requirement: Optional
Inheritance: If no values are specified, this attribute inherits values from other objects.
Data Type: (Type information not available.)
Explanatory Note: Can populate up

Permissible Values

Genomics
Proteomics
Pathology Images
Radiology
Immunology
Pathology
Undefined

Element text: AssayType
Definition: (No definition provided.)
Requirement: Optional
Inheritance: If no values are specified, this attribute inherits values from other objects.
Data Type: (Type information not available.)
Explanatory Note: Can populate up

Permissible Values

H&E
IHC
mIF
RNA-Seq
RNA-Seq (SMART-3SEQ)
DNA-Seq
Single-cell Seq
WES

Element text: ProcessingSoftware
Definition: Software used to process, transform, analyze, convert, or generate the file, when applicable.
Requirement: Optional
Inheritance: If no values are specified, this attribute inherits values from other objects.
Data Type: Free-text
Explanatory Note: May populate up to the Dataset or Collection level when the same processing software applies across multiple files.

Element text: DOI
Definition: (No definition provided.)
Requirement: Optional
Inheritance: If no values are specified, this attribute inherits values from other objects.
Data Type: (Type information not available.)
Explanatory Note: Can populate up

Element text: DOIURL
Definition: (No definition provided.)
Requirement: Optional
Inheritance: If no values are specified, this attribute inherits values from other objects.
Data Type: (Type information not available.)
Explanatory Note: Can populate up

Element text: FileName
Definition: The name of the file being uploaded
Requirement: Required
Inheritance: This attribute does not inherit values from other objects.
Data Type: (Type information not available.)
Explanatory Note: (No notes were given for this element.)

Element text: DateFileGenerated
Definition: The date the file being uploaded was generated
Requirement: Optional
Inheritance: This attribute does not inherit values from other objects.
Data Type: (Type information not available.)
Explanatory Note: (No notes were given for this element.)

Element text: SubmittingSiteID
Definition: The institutionID(s)that is submitting the data
Requirement: Required
Inheritance: If no values are specified, this attribute inherits values from other objects.
Data Type: (Type information not available.)
Explanatory Note: Can populate up

Permissible Values

SiteID from eSIS (DMCC)

Element text: SubmittingPersonID
Definition: The lead person submitting the data
Requirement: Required
Inheritance: If no values are specified, this attribute inherits values from other objects.
Data Type: (Type information not available.)
Explanatory Note: Can populate up

Permissible Values

PersonID from eSIS (DMCC)

Element text: ProcessingLevel
Definition: (No definition provided.)
Requirement: Required
Inheritance: This attribute does not inherit values from other objects.
Data Type: (Type information not available.)
Explanatory Note: (No notes were given for this element.)

Permissible Values

Raw
Intermediate
Processed

Element text: ContentType
Definition: A high-level classification of the primary content contained in the file, used to describe the file’s role within the dataset or collection.
Requirement: Required
Inheritance: If no values are specified, this attribute inherits values from other objects.
Data Type: (Type information not available.)
Explanatory Note: At the file level, ContentType describes the type of information contained in an individual file. This value may populate up to the Dataset or Collection level when files share a consistent content type, or may populate down when all files in a dataset or collection share the same content type.

Permissible Values

Clinical
Biospecimen
SOP
Documentation
Instrument Output
Metadata
Ancillary Data
Summary

Element text: ProcessingSoftwareVersion
Definition: Version of the software used to process, transform, analyze, convert, or generate the file, when applicable.
Requirement: Optional
Inheritance: This attribute does not inherit values from other objects.
Data Type: (Type information not available.)
Explanatory Note: Use with ProcessingSoftware when the software version is known. This is different from InstrumentSoftwareVersion, which describes software or firmware associated with the acquisition instrument.

Element text: md5sum
Definition: Deprecated legacy field containing an MD5 checksum value for the file.
Requirement: Optional
Inheritance: This attribute does not inherit values from other objects.
Data Type: (Type information not available.)
Explanatory Note: (No notes were given for this element.)

Element text: ChecksumType
Definition: The algorithm used to generate the checksum value for the file.
Requirement: Optional
Inheritance: This attribute does not inherit values from other objects.
Data Type: (Type information not available.)
Explanatory Note: (No notes were given for this element.)

Permissible Values

MD5
SHA-1
SHA-256
SHA-512

Element text: Checksum
Definition: Hash value generated for the file using the algorithm specified in ChecksumType, used for file integrity verification.
Requirement: Optional
Inheritance: This attribute does not inherit values from other objects.
Data Type: String
Explanatory Note: (No notes were given for this element.)

Element text: FileSubmissionDate
Definition: (No definition provided.)
Requirement: System generated
Inheritance: This attribute does not inherit values from other objects.
Data Type: (Type information not available.)
Explanatory Note: (No notes were given for this element.)

Element text: SubmissionVersion
Definition: (No definition provided.)
Requirement: System generated
Inheritance: This attribute does not inherit values from other objects.
Data Type: (Type information not available.)
Explanatory Note: (No notes were given for this element.)

Element text: FileType
Definition: (No definition provided.)
Requirement: System generated
Inheritance: This attribute does not inherit values from other objects.
Data Type: (Type information not available.)
Explanatory Note: (No notes were given for this element.)

Element text: FileSize
Definition: (No definition provided.)
Requirement: System generated
Inheritance: This attribute does not inherit values from other objects.
Data Type: (Type information not available.)
Explanatory Note: (No notes were given for this element.)

Element text: StainType
Definition: Broad category of stain or staining method used to prepare the slide or image.
Requirement: Required
Inheritance: If no values are specified, this attribute inherits values from other objects.
Data Type: String
Explanatory Note: Broad stain category. For IHC, ISH, CISH, FISH, or related assays, use this extension together with the PathologySlideScan-IHC-ISH Extension for antibody, probe, reagent, and assay details. CISH and FISH do not need to be separate high-level values for v1.0.0 unless they need to be searchable independently. Use Not Applicable when the image is not based on a stained slide. Use Unknown when staining status is not documented.

Permissible Values

H&E; IHC; In situ hybridization; mIHC; Other; Unknown; Not Applicable

Element text: StainingDate
Definition: Date the staining was performed, when available.
Requirement: Optional
Inheritance: This attribute does not inherit values from other objects.
Data Type: Date
Explanatory Note: Use when the staining date is known and can be shared. This should not be required because dates may be unavailable, sensitive, or transformed for de-identification. Must not include PHI. If dates are shifted or transformed for de-identification, document the date handling approach at the collection or dataset level.

Element text: ScanType
Definition: Type of pathology image scan or image capture performed.
Requirement: Required
Inheritance: If no values are specified, this attribute inherits values from other objects.
Data Type: String
Explanatory Note: Describes whether the image represents a full slide scan or a more limited scanned region, field of view, tile, or image capture.

Permissible Values

Whole Slide Image; Region of Interest; Single Field of View; Tile; Other; Unknown

Element text: NominalMagnification
Definition: Reported optical or nominal magnification used during image acquisition.
Requirement: Optional
Inheritance: If no values are specified, this attribute inherits values from other objects.
Data Type: String
Explanatory Note: Reported scan magnification used to digitize the slide. Examples: 20X, 40X. Use the value reported by the scanner, image metadata, or submitting site when available.

Element text: PixelSpacing
Definition: Physical size represented by each pixel in the pathology image.
Requirement: Optional
Inheritance: If no values are specified, this attribute inherits values from other objects.
Data Type: Decimal / Number
Explanatory Note: Numeric value only. Unit should be recorded separately in PixelSpacingUnit. For pathology images, this commonly represents microns per pixel.

Element text: PixelSpacingUnit
Definition: Unit used to describe pixel spacing.
Requirement: Required if PixelSpacing is provided
Inheritance: If no values are specified, this attribute inherits values from other objects.
Data Type: String
Explanatory Note: Use with PixelSpacing. Default expected value for pathology imaging is µm/pixel when pixel spacing is expressed as microns per pixel. Use Unknown only when the unit cannot be determined.

Permissible Values

µm/pixel; Unknown

Element text: AnnotationType
Definition: The type or category of annotation represented by the file or metadata record.
Requirement: Required
Inheritance: This attribute does not inherit values from other objects.
Data Type: String
Explanatory Note: May be system-populated when the annotation type can be reliably inferred from the file format, DICOM SOP Class UID, or known collection workflow. When not inferable, this should be supplied by the submitter.

Permissible Values

RT Structure Set; Segmentation Mask; ROI; Classification Label; Bounding Box; Point Annotation; Measurement; Review Finding; Other; Unknown

Element text: AnnotationFormat
Definition: The format or standard used to encode the annotation.
Requirement: Required
Inheritance: This attribute does not inherit values from other objects.
Data Type: String
Explanatory Note: May be system-populated from file format, file extension, MIME type, DICOM SOP Class UID, or other file-level metadata when available. When not inferable, this should be supplied by the submitter.

Permissible Values

DICOM RTSTRUCT; DICOM SEG; JSON; XML; GeoJSON; CSV; TSV; NIfTI; TIFF Mask; OME-TIFF; Other; Unknown

Element text: AnnotationSource
Definition: The person, role, system, or process that generated the annotation.
Requirement: Optional
Inheritance: This attribute does not inherit values from other objects.
Data Type: String
Explanatory Note: Use when the source of the annotation is known. This may identify a role, organization, system, or process rather than a named individual. Use Unknown when the source is not documented.

Permissible Values

Radiologist; Pathologist; Researcher; Algorithm; Instrument; Site; DMCC; JPL; Other; Unknown

Element text: AnnotationReviewStatus
Definition: Indicates whether the annotation has been reviewed or validated.
Requirement: Optional
Inheritance: This attribute does not inherit values from other objects.
Data Type: String
Explanatory Note: Use Reviewed when the annotation has been evaluated by an appropriate reviewer. Use Adjudicated when review discrepancies have been resolved through consensus or final review. Use Unknown when review status is not documented.

Permissible Values

Reviewed; Not Reviewed; Pending Review; Adjudicated; Rejected; Unknown

Element text: AnnotationTargetLevel
Definition: The level or granularity of the data that the annotation describes.
Requirement: Required
Inheritance: This attribute does not inherit values from other objects.
Data Type: String
Explanatory Note: May be system-populated when the target level is clear from the annotation format or file references. For custom, tabular, or non-DICOM annotations, this should be supplied by the submitter.

Permissible Values

File; Series; Study; Dataset; Slide; Region; Pixel/Voxel; Object; Frame; Other; Unknown

Element text: SourceImageFileID
Definition: Identifier for the source image file that the annotation references.
Requirement: Required if annotation targets a specific file
Inheritance: This attribute does not inherit values from other objects.
Data Type: String
Explanatory Note: May be extracted or mapped when the annotation file references specific source image files. For annotations that target one or more individual files, provide the relevant source file identifier(s) when available.

Element text: SourceSeriesID
Definition: Identifier for the source image series that the annotation references.
Requirement: Required if annotation targets a series
Inheritance: This attribute does not inherit values from other objects.
Data Type: String
Explanatory Note: May be extracted from DICOM-referenced series information when available. For non-DICOM annotations, provide when the annotation targets an image series or equivalent grouped image object.

Element text: AnnotationLabel
Definition: Human-readable label, class name, ROI name, structure name, or finding represented by the annotation.
Requirement: Optional
Inheritance: This attribute does not inherit values from other objects.
Data Type: String
Explanatory Note: May be extracted from annotation metadata when available, such as DICOM ROI names, structure names, class labels, or region labels. When not extractable, this may be supplied by the submitter.

Element text: AnnotationDescription
Definition: A short description of the annotation content, purpose, or interpretation.
Requirement: Optional
Inheritance: This attribute does not inherit values from other objects.
Data Type: String
Explanatory Note: Use to provide additional human-readable context about the annotation, especially when the label, type, or source does not fully describe the annotation content or purpose.

Element text: AnnotationMethod
Definition: The method used to create the annotation.
Requirement: Optional
Inheritance: This attribute does not inherit values from other objects.
Data Type: String
Explanatory Note: Use Manual for human-created annotations, Semi-automated when human interaction or correction was involved, Automated for algorithm-generated annotations, and Derived when the annotation was generated from another annotation or data product.

Permissible Values

Manual; Semi-automated; Automated; Imported; Derived; Unknown

Element text: AnnotationDate
Definition: Date the annotation was created, reviewed, or finalized.
Requirement: Optional
Inheritance: This attribute does not inherit values from other objects.
Data Type: Date
Explanatory Note: Use when the annotation creation, review, or finalization date is known. If multiple dates are available, prioritize the finalized or reviewed date and document additional dates in AnnotationDescription if needed.

Element text: AnnotationCoordinateSystem
Definition: Coordinate system used to define the annotation location or geometry.
Requirement: Optional
Inheritance: This attribute does not inherit values from other objects.
Data Type: String
Explanatory Note: May be system-populated for formats with known spatial reference conventions, such as DICOM RTSTRUCT or DICOM SEG. For custom annotations, this should be supplied when needed to support spatial alignment with the source image.

Permissible Values

Image Pixel; Slide Coordinate; DICOM Patient Coordinate; DICOM Frame of Reference; Normalized Coordinate; Other; Unknown

For questions about the data models, email the Informatics Center.

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Biomarker

Attributes

Biomarker-Organ

Attributes

Biomarker-Organ-Study

Attributes

Biomarker Study Data

Stewardship

Body System

Attributes

Disease

Attributes

Site

Attributes

Person

Attributes

Protocol

Attributes

Publication

Attributes

identifier

Alias

HgncName

Title

URN

Description

QAState

Permissible Values

Security

Permissible Values

Type

Permissible Values

ShortName

IsPanel

Permissible Values

hasBiomarker

memberOfPanel

AccessGrantedTo

AssociatedDataset

referencedInPublication

referencesResource

indicatorForOrgan

hasBiomarkerStudyDatas

identifier

URN

Biomarker

Description

PerformanceComment

Organ

Phase

Permissible Values

QAState

Permissible Values

Certification

AccessGrantedTo

referencedInPublication

referencesResource

hasBiomarkerOrganStudyDatas

identifier

referencesStudy

DecisionRule

Phase

Permissible Values

referencedInPublication

referencesResource

identifier

title

Permissible Values

description

identifier

title

description

icd9

icd10