EDRN Data Model

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Biomarker Data Models

Biomarker Data Models

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- 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.
    
    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.
      
      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.
        
        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.
    
    identifier Item_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.
      
      identifier Item_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.
    
    identifier Institution_Name_Abbrev EDRN_Funding_Date_Start EDRN_Funding_Date_Finish Identifier 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.
      
      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.
      
      identifier 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
    - 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.
      
      Volume Year SiteID identifier Item_Title Description Issue Journal PMID Publication_URL
Cancer Biomarker Data Commons

Cancer Biomarker Data Commons

The Biomarker Data Commons (powered by the Laboratory Catalog and Archive System (LabCAS)) has a set of objects and common data elements relating to capture, search, and retrieval of scientific data. The Resource Description Format (RDF) knowledge produced from LabCAS describes the collections of scientific data.

Stewardship

Version 1.0 maintained by Heather Kincaid. Last updated 2023-09-01.
- 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.
  
  identifier Collection Name Collection Description LeadPIID LeadPIName DataCustodian DataCustodianEmail InstitutionID InstitutionName ProtocolID ProtocolName ProtcolAbbreviatedName Discipline DataCategory Organ EDRNCollaborativeGroup ResultsAndConclusionSummary PubMedID ReferenceURL Consortium Species OwnerPrincipal DOI DOIURL CollectionVersion CollectionID
  - 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.
    
    DatasetName DatasetDescription InvestigatorID InvestigatorName Institution InstitutionName BlindedSiteID MethodDetails Instrument SpecimenType Discipline DataCategory AssayType ProcessingSoftware ContentType DOI DOI URL DateDatasetFrozen DatasetVersion DatasetID
    - 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.
      
      FileName DateFileGenerated SubmittingSiteID SubmittingPersonID ProcessingLevel ContentType AssayType Processing software Processing software version Instrument md5sum DOI DOI URL FileSubmissionDate SubmissionVersion FileType FileSize

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: Collection Name
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: Collection Description
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: The lead prinicipal investigators or co-investigators person id
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: The lead prinicipal investigators or co-investigators name
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

PersonName from eSIS (DMCC)

Element text: DataCustodian
Definition: The person responsible for this data 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: DataCustodianEmail
Definition: Data custodian's email address
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: InstitutionID
Definition: The institutionID(s)that collected this 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 from dataset level

Permissible Values

SiteID from eSIS (DMCC)

Element text: InstitutionName
Definition: The institution name(s) that collected this data
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 protocol title that describes the study this data was captured under. This is 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 Title from eSIS (DMCC)

Element text: ProtcolAbbreviatedName
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: 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: This attribute does not inherit values from other objects.
Data Type: (Type information not available.)
Explanatory Note: can populate from dataset level

Permissible Values

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

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: EDRNCollaborativeGroup
Definition: The EDRN Collaborative group.
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

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

Element text: ResultsAndConclusionSummary
Definition: The results and conclusions from this data collection.
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: PubMedID
Definition: The 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: (Type information not available.)
Explanatory Note: (No notes were given for this element.)

Element text: ReferenceURL
Definition: A 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: (Type information not available.)
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: 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. Deaults 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: The 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: The 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: 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: 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: DatasetName
Definition: A short name for 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: 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 prinicipal 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 prinicipal investigators or co-investigators name
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

PersonName from eSIS (DMCC)

Element text: Institution
Definition: If data is blinded create an anonomized ID created. 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: 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: 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: (No definition provided.)
Requirement: Optional
Inheritance: This attribute does not inherit values from other objects.
Data Type: (Type information not available.)
Explanatory Note: This generally comes from the specific extension dictionaries

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 from dataset level

Permissible Values

Sequencing
RNA Sequencing
DNA Methylation Sequencing
DNA Microarray Analysis
Mass Spectrometry
Whole Slide Imaging
Tissue Micro Array
Immunohistochemestry
CT
MRI
Mammography
Fluoroscopy
PET
Documentation
Biospecimen
Clinical
Immunoassay
ELISA
Luminex
LabMAP
Protein Microarray
Single Slide Image
Multiplex-Immunoflourescent 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
mIHC
RNA-Seq
RNA-Seq (SMART-3SEQ)
DNA-Seq
Single-cell Seq
WES

Element text: ProcessingSoftware
Definition: (No definition provided.)
Requirement: Optional
Inheritance: If no values are specified, this attribute inherits values from other objects.
Data Type: Free-text
Explanatory Note: (No notes were given for this element.)

Element text: ContentType
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: (No notes were given for this element.)

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: DOI URL
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: (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: 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: 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: 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: SubmittingPersonID
Definition: The lead person submitting the 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

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: (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

Clinical
Biospecimen
SOP
Documentation
Instrument Output
Metadata
Ancillary Data
Summary

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: Processing software
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: Processing software version
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: Instrument
Definition: (No definition provided.)
Requirement: Optional
Inheritance: This attribute does not inherit values from other objects.
Data Type: (Type information not available.)
Explanatory Note: Can populate up

Element text: md5sum
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: 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: DOI URL
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: 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: 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 panel's 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 quality analysis of this 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 the 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 prdicate 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, these are strictly digits in the inclusive range of 1..5.

Permissible Values

Element text: referencedInPublication
Definition: Publications in the context of the 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 PubMed IDs.

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: 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: Identifier
Definition: DMCC-assigned number of the site
Requirement: Optional
Inheritance: This attribute does not inherit values from other objects.
Data Type: string
Explanatory Note: Although a string, it's typically a base-10 positive integer; note that this is "Identifier" with a capital I, which differentiates it from the RDF subject URI "identifier" with a lowercase "i"

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: URL
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 mere 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 even more lowly 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: identifier
Definition: RDF subject URI of the protocl
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 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: string
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: string
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 protcol
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 the EDRN portal 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". The portal does not display this.

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". The portal does not display this.

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". The portal does not display this.

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: Categorizes 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: 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: 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: 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: string
Explanatory Note: Not used since the PubMed ID provides an ideal way to reference the publication.

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: 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: Name of file containing a portrait of the person
Requirement: Optional
Inheritance: This attribute does not inherit values from other objects.
Data Type: string
Explanatory Note: In practice, this contains a name of a file of a GIF image taken approximately 15+ years ago of the person; only five are currently set as of 2023-07-27. The original set of images are available at https://edrn.jpl.nasa.gov/cancerdataexpo/staff-photographs. Note that the portal will use this image if it is given, but will fall back to the Gravatar service to find an image of the individual.

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: string
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 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: Item_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: Item_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.

EDRN Data Model

Biomarker Data Models

Biomarker Database

Stewardship

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

Cancer Biomarker Data Commons

Stewardship

Collection

Attributes

Dataset

Attributes

File

Attributes

identifier

Collection Name

Collection Description

LeadPIID

Permissible Values

LeadPIName

Permissible Values

DataCustodian

DataCustodianEmail

InstitutionID

Permissible Values

InstitutionName

Permissible Values

ProtocolID

Permissible Values

ProtocolName

Permissible Values

ProtcolAbbreviatedName

Permissible Values

Discipline

Permissible Values

DataCategory

Permissible Values

Organ

Permissible Values

EDRNCollaborativeGroup

Permissible Values

ResultsAndConclusionSummary

PubMedID

ReferenceURL

Consortium

Permissible Values

Species

Permissible Values

OwnerPrincipal

Permissible Values

DOI

DOIURL

CollectionVersion

CollectionID

DatasetName

DatasetDescription

InvestigatorID

Permissible Values

InvestigatorName

Permissible Values

Institution

Permissible Values