02-biospecimen.yaml

Biospecimen ID:
  description: Identifier for the Biospecimen
  type: string
  significance: required
Parent ID:
  description: Parent Identifier from which the biospecimen was obtained. The parent
    could be another biospecimen or a research participant.
  type: string
  significance: required
Adjacent Biospecimen ID:
  description: List of Identifiers (separated by commas) of adjacent biospecimens
    cut from the same sample
  type: string
  significance: required
Biospecimen Type:
  description: Biospecimen Type
  type: string
  valid-values:
  - Tissue
  - Bone Marrow
  - Cell Block
  - Blood
  - Fluids
  significance: required
Analyte Type:
  description: Text term that represents the kind of molecular specimen analyte.
  type: string
  significance: required
Protocol Link:
  description: Identifier that describes the protocol by which the sample was obtained
    or generated. E.g. Protocols.io
  category: Collection and Processing
  type: doi
  significance: required
Timepoint Label:
  description: Label to identify the time point at which the biospecimen was obtained.
  category: Collection and Processing
  type: string
  valid-values:
  - Baseline
  - End of Treatment
  - Overall survival
  - Final
  significance: required
Collection Days From Index:
  description: Number of days from the research participant's index date that the
    biospecimen was obtained.
  category: Collection and Processing
  type: float
  significance: required
Acquisition Method Type:
  description: Records the method of acquisition or source for the specimen under
    consideration.
  category: Collection and Processing
  type: string
  valid-values:
  - Autopsy
  - Biopsy
  - Fine needle aspirate
  - Surgical Resection
  - Punch biopsy
  - Shave biopsy
  - Excision
  - Re-excision
  - Sentinel node biopsy
  - Lymphadenectomy
  significance: required
Post-mortem Interval:
  description: Number of days from the research participant's date of death that the
    biospecimen was obtained
  category: Collection and Processing
  type: float
  significance: required
Tumor tissue type:
  description: Text that describes the kind of disease present in the tumor specimen
    as related to a specific time point.
  category: Collection and Processing
  type: string
  valid-values:
  - Primary Tumor
  - Local Tumor Recurrence
  - Distant Tumor Recurrence
  - Metastatic
  - Premalignant
  significance: required
Preservation method:
  description: Text term that represents the method used to preserve the sample.
  category: Collection and Processing
  type: string
  valid-values:
  - Formaldehyde fixed paraffin embedded (FFPE)
  - Frozen
  significance: required
Fixative Type:
  description: The field to identify the type of fixative used to preserve a tissue
    specimen
  category: Collection and Processing
  type: string
  significance: required
Fixation Duration:
  description: The length of time, from beginning to end, required to process or preserve
    biospecimens in fixative (measured in minutes)
  category: Collection and Processing
  type: integer
  significance: required
Slide Charge Type:
  description: A description of the charge on the glass slide.
  category: Collection and Processing
  type: string
  valid-values:
  - Uncharged
  - Charged
  - Coverslip
  - Coated
  - Not applicable
  significance: required
Section Thickness Value:
  description: Numeric value to describe the thickness of a slice to tissue taken
    from a biospecimen, measured in microns (um).
  category: Collection and Processing
  type: float
  significance: required
Days to sectioning:
  description: Number of days between the date of sample acquisition and the date
    that the specimen was sectioned
  category: Collection and Processing
  type: float
  significance: required
Storage Method:
  description: The method by which a biomaterial was stored after preservation or
    before another protocol was used.
  category: Collection and Processing
  type: string
  valid-values:
  - Ambient temperature
  - 4C
  - -20C
  - -80C
  significance: required
Days to processing:
  description: Number of days between the date of sample acquisition and the date
    that the biospecimen was processed
  category: Collection and Processing
  type: float
  significance: required
Shipping Conditions:
  description: Text descriptor of the shipping environment of a biospecimen.
  category: Collection and Processing
  type: string
  valid-values:
  - Ambient Pack
  - Cold Pack
  - Dry Ice
  - Ice Pack
  - Liquid Nitrogen
  - Other Shipping Environment
  - Specimen at Room Temperature
  - Not shipped
  significance: required
Histology Assessments By:
  description: Text term describing who made the histological assessments of the sample
  category: Histologic Assessment
  type: string
  valid-values:
  - Pathologist
  - Research Scientist
  - Other
  - Unknown
  significance: required
Histology Assessment Medium:
  description: The method of assessment used to characterize histology
  category: Histologic Assessment
  type: string
  valid-values:
  - Digital
  - Microscope
  significance: recommended
Tumor infiltrating lymphocytes:
  description: Number of tumor-infiltrating lymphocytes
  category: Histologic Assessment
  type: integer
  significance: recommended
Degree of dysplasia:
  description: Information related to the presence of cells that look abnormal under
    a microscope but are not cancer. Records the degree of dysplasia for the cyst
    or lesion under consideration.
  category: Histologic Assessment
  type: string
  valid-values:
  - Normal
  - basal cell hyperplasia
  - or metaplasia Mild dysplasia
  - Moderate dysplasia
  - Severe dysplasia
  - Carcinoma in Situ
  significance: recommended
Dysplasia fraction:
  description: Information related to the presence of cells that look abnormal under
    a microscope but are not cancer. Records the degree of dysplasia for the cyst
    or lesion under consideration.
  category: Histologic Assessment
  type: float
  significance: recommended
Number proliferating cells:
  description: Numeric value that represents the count of proliferating cells determined
    during pathologic review of the sample slide(s).
  category: Histologic Assessment
  type: integer
  significance: recommended
Percent Necrosis:
  description: Numeric value to represent the percentage of cell death in a malignant
    tumor sample or specimen.
  category: Histologic Assessment
  type: float
  significance: recommended
Percent Normal Cells:
  description: Numeric value to represent the percentage of normal cell content in
    a malignant tumor sample or specimen.
  category: Histologic Assessment
  type: float
  significance: recommended
Percent Stromal Cells:
  description: Numeric value to represent the percentage of reactive cells that are
    present in a malignant tumor sample or specimen but are not malignant such as
    fibroblasts, vascular structures, etc.
  category: Histologic Assessment
  type: float
  significance: recommended
Percent Tumor Cells:
  description: Numeric value to represent the percentage of infiltration by tumor
    cells in a sample.
  category: Histologic Assessment
  type: float
  significance: recommended
Percent Tumor Nuclei:
  description: Numeric value to represent the percentage of tumor nuclei in a malignant
    neoplasm sample or specimen.
  category: Histologic Assessment
  type: float
  significance: recommended
Fiducial marker:
  description: Fiducial markers for the alignment of images taken across multiple
    rounds of imaging.
  category: Imaging
  type: string
  valid-values:
  - Nuclear Stain (DAPI)
  - Fluorescent beads
  - Grid slides (hemocytometer)
  - Adhesive markers
  significance: required  (unless n/a)
Mounting medium:
  description: The solution in which the specimen is embedded, generally under a cover
    glass. It may be liquid, gum or resinous, soluble in water, alcohol or other solvents
    and be sealed from the external atmosphere by non-soluble ringing media.
  category: Imaging
  type: string
  valid-values:
  - Aqueous (water based) medium
  - Non-Aqueous (Solvent) based
  - Xylene
  - Toluene
  - Antifade with DAPI
  - Antifade without DAPI
  - PBS
  significance: recommended
Slicing method:
  description: The method by which the tissue was sliced.
  category: Imaging
  type: string
  valid-values:
  - Vibratome
  - Cryosectioning
  - Tissue molds
  - Sliding microtome
  - Sectioning
  significance: recommended
Control:
  description: Control tissue / area
  category: Imaging
  type: string
  valid-values:
  - Cell line
  - tissue
  - mutation
  - matrix
  - metal coating
  - fiducials
  significance: recommended