TerraCoreValueSets
type: Ontology
imports: core#
imports: CL subset
imports: UBERON subset
version info: Created with TopBraid Composer

Amniotic fluid

Amniotic fluid
type: Class
subclass of: Body fluid
equivalent class: UBERON_0000173

Assembly

Assembly
type: Class
subclass of: Genomic

B cell

B cell
type: Class
subclass of: PrimaryCell
equivalent class: CL_0000236

BioSampleType
type: Class
subclass of: SampleType
definition: A classification of samples taken from organisms based on the type of material collected and grouped into primary, cell line and derived type.

Blood
type: Class
subclass of: Body fluid
equivalent class: UBERON_0000178

Body fluid
type: Class
subclass of: PrimaryType

Breast milk

Breast milk
type: Class
comment: Should this be simply Milk with hasAnatomicalSite of Mammary Glands? See https://biology.stackexchange.com/questions/39291/are-there-any-non-mammalian-species-known-that-lactate and http://purl.obolibrary.org/obo/UBERON_0001913
subclass of: Body fluid
equivalent class: Resource

BuffyCoat
type: Buffy coat

Buffy coat
type: Class
subclass of: Blood

CT scan
type: Class
subclass of: Medical Imaging

Cell free DNA
type: Cell-free DNA

Cell-free DNA
type: Class
subclass of: PrimaryType

Cell line
type: Cell Line

Cell Line
type: Class
comment: Will likely create instances for specific cell lines, but no concrete use case available yet. Also this should map to "cell line" in the Cell Line Ontology.
subclass of: BioSampleType

Cerebrospinal fluid

Cerebrospinal fluid
type: Class
subclass of: Body fluid
equivalent class: UBERON_0001359

DNA Chromatin Accessibility
type: Class
subclass of: Epigenomic

3D Contact Maps

3D Contact Maps
type: Class
subclass of: Epigenomic

DNA Binding

DNA Binding
type: Class
subclass of: Epigenomic

DNA Chromatin Accessibility

DNA Methylation

DNA Methylation
type: Class
subclass of: Epigenomic

Data Modality
type: Class
comment: This term attempts to characterize entities in terms of its channel of biological investigation. For example, activities that produce such results include assays, analysis pipelines, lab tests, and imaging -- x-ray, CT-scan, or microscopy as well as the data these activities generate.
subclass of: IAO_0000030
alternative label: Biological Data Type
alternative label: Data Category
definition: Data modality describes the biological nature of the information gathered as the result of an Activity, independent of the technology or methods used to produce the information.

DerivedType
type: Class
subclass of: BioSampleType

Electrocardiogram
alternative label: ECG
alternative label: EKG

Electrocardiogram
type: Class
comment: Is this an Imaging technology or should we have a category for lab tests and consider this a Lab Test or is it a type of assay?
subclass of: Medical Imaging

Electrophysiology

Electrophysiology
type: Class
subclass of: Imaging

Epigenomic

Epigenomic
type: Class
subclass of: Data Modality
definition: A property that indicates this entity is related to the biological investigation of the epigenome.

Erythrocyte

Erythrocyte
type: Class
subclass of: Blood
alternative label: RBC
alternative label: Red blood cell

Exome
alternative label: WES

Exome
type: Class
subclass of: Genomic
alternative label: WES

Genomic

Genomic
type: Class
subclass of: Data Modality
definition: A property that indicates this entity is related to the biological investigation of the genome.

Genotyping

Genotyping
type: Class
comment: Definition from Genotyping (operation_3196) in edamontology.org. Need to add this as an equivalent class. Note that this is often performed by calling SNPs from assays. It it intended to differentiate from larger scale genomic sequencing -- exome, genome.
subclass of: Genomic
definition: Analyse DNA sequence data to identify differences between the genetic composition (genotype) of an individual compared to other individual's or a reference sequence.

Histone Modification Location

Histone Modification Location
type: Class
subclass of: DNA Binding

Imaging

Imaging
type: Class
subclass of: Data Modality

Induced pluripotent stem cells
type: Class
subclass of: DerivedType

In vitro differentiated cells
type: Class
subclass of: DerivedType

Leukocyte

Leukocyte
type: Class
subclass of: Blood
alternative label: White blood cell

Lymphocyte

Lymphocyte
type: Class
subclass of: PrimaryCell
equivalent class: CL_0000542

MRI
alternative label: Magnetic resonance imaging

MRI
type: Class
subclass of: Medical Imaging

Medical Imaging

Medical Imaging
type: Class
subclass of: Imaging

Metabolomic
type: Class
subclass of: Data Modality
definition: A property that indicates this entity is related to the biological investigation of the metabolome.

Metagenomic
type: Class
subclass of: Data Modality

microRNA Counts
type: Transcriptomic Targeted
alternative label: miRNA counts

Microbiome
type: Class
subclass of: Data Modality
definition: A property that indicates this entity is related to the biological investigation of the microbiome.

Microscopy

Microscopy
type: Class
subclass of: Imaging

MolecularSample
type: MolecularSampleType

MolecularSampleType
type: Class
subclass of: SampleType
definition: A classification of molecular sample types.

Monocyte

Monocyte
type: Class
subclass of: PrimaryCell
equivalent class: CL_0000576

Organoid
type: Class
subclass of: DerivedType

PeripheralBloodMononuclearCell
type: Peripheral blood mononuclear cell

Peripheral blood mononuclear cell
type: Class
subclass of: Blood
alternative label: PBMC

Plasma

Plasma
type: Class
subclass of: Blood
equivalent class: UBERON_0001969

Platelet

Platelet
type: Class
subclass of: Blood
equivalent class: CL_0000233

Primary cell
type: PrimaryCell

PrimaryCell
type: Class
subclass of: PrimaryType

Primary culture

Primary culture
type: Class
subclass of: PrimaryType
equivalent class: CL_0000001

PrimaryType
type: Class
subclass of: BioSampleType

Proteomic
type: Class
subclass of: Data Modality
definition: A property that indicates this entity is related to the biological investigation of the proteome.

RNA Binding

RNA Binding
type: Class
subclass of: Epigenomic

RNASeq
type: Transcriptomic NonTargeted

Saliva

Saliva
type: Class
subclass of: Body fluid
equivalent class: UBERON_0001836

SampleType
type: Class
subclass of: IAO_0000030
definition: A classification of samples based on the type of material collected and grouped by subclass.

Semen

Semen
type: Class
subclass of: Body fluid
equivalent class: UBERON_0001968

Serum

Serum
type: Class
subclass of: Blood
equivalent class: UBERON_0001977

Spatial Transcriptomics
type: Class
subclass of: Transcriptomic

Stool

Stool
type: Class
subclass of: PrimaryType
equivalent class: UBERON_0001988

Synovial fluid

Synovial fluid
type: Class
subclass of: Body fluid
equivalent class: UBERON_0001090

T cell

T cell
type: Class
subclass of: PrimaryCell
equivalent class: CL_0000084

Tissue

Tissue
type: Class
subclass of: PrimaryType

Transcription Factor Location

Transcription Factor Location
type: Class
subclass of: DNA Binding

Transcriptomic
type: Class
subclass of: Data Modality
definition: A property that indicates this entity is related to the biological investigation of the transcriptome.

Transcriptomic NonTargeted
type: Class
subclass of: Transcriptomic

Transcriptomic Targeted
type: Class
subclass of: Transcriptomic

Urine

Urine
type: Class
subclass of: Body fluid
equivalent class: UBERON_0001088

Vaginal fluid

Vaginal fluid
type: Class
subclass of: Body fluid
equivalent class: UBERON_0036243
alternative label: Vaginal swab

Whole blood

Whole blood
type: Class
subclass of: Blood
equivalent class: UBERON_0000178

Whole Genome
type: Whole genome
alternative label: WGS

Whole genome
type: Class
subclass of: Genomic
alternative label: WGS

XRay
type: X ray

X ray
type: Class
subclass of: Medical Imaging
alternative label: X-ray