Please cite The Broad Institute of Harvard and MIT, Data Sciences Platform.
An activity occurs over a period of time, generates an entity, and may include consuming, processing, transforming, modifying, relocating, or using entities. This subclass of prov:Activity restricts members to those with a DataModality relevant to biomedical research.
A physical address for a Person or Organization.
An activity that aligns the output of a Sequencing Activity (a genetic sequence) to produce an aligned sequence.
An electronic record of the alignment of a genetic sequence for a particular Sample compared with a reference sequence generated by an AlignmentActivity.
An activity that records the output of a specific analysis method. Software version, components, arguments are described in prov:SoftwareAgent.
A reference to the antibody/antibodies used in this Activity.
An activity that generates an electronic record documenting the result of the Assay performed.
Data about a physical sample consisting of one or more cells taken from an organism (living or deceased) or derived from such a Sample.
Activity which results in the separation of a BioSample into individual cells or a cell suspension.
A quality of an organism indicating physical sexual characteristics. Equivalent of PATO's phenotypic sex but pseudohermaphrodite is not relevant to existing data and is not recommended.
A country represented by the ISO-3166 Alpha-2 code and name (as a label). https://www.iso.org/obp/ui/#search
Result of a medical investigation that often identies a disease or condition.
An organism from which a sample or test result is available
Activities or processes undertaken with the expectation of therapeutic value to the Donor.
An operation or procedure carried out under controlled conditions to make a discovery or to test or establish a hypothesis. In the context of this data model, an experiment is a collection of related activities, possibly including sample preparation, sequencing, assays and/or downstream analysis.
Family member has biological relationship to a Donor. Limited health information. A family member for whom samples, imaging studies, lab tests or other healthcare information is available may be considered a Donor.
Used definition from http://semanticscience.org/resource/SIO_000396 but equivalence to http://www.w3.org/ns/dcat#Distribution doesn't make sense in this context; thus we have our own class. Also added electronic.
A file is an information-bearing electronic object that contains a physical embodiment of some information using a particular character encoding.
Instance of Homo sapiens organism to define organism type.
Activity which results in the creation of a library from fragments of genomic material in preparation for further analysis.
The record of the size, quantity or outcome of a clinical or laboratory test.
Data about a physical sample consisting of one or more molecular entities, either purified from a Sample or synthesized.
Instance of Mus musculus organism to define organism type.
Activity to separate the nucleus or nuclei from the cell.
The principal or lead person who carries out an investigation assigned by a sponsor or authorizing agent.
A collective effort with an objective related to biomedical research.
Instances should include either a cross reference to the reference sequence or an official GRCName from the Genome Reference Consortium, or both.
DNA sequence data identified as representative of specific organism's DNA.
Data about a physical material collected for the purpose of research.
Activity which transforms a BioSample into another BioSample. Typically the sample treatment activity involves adding something to cells or tissue, for example, treatment with chemicals, drugs, biological infection, irradiation, exposures, or other non-genetic modifications. This treatment excludes mechanical separation of a BioSample into single cells (covered by BioSampleDissociation), and is not needed for genetic modifications to cells (covered by hasGeneticModification).
An electronic record of the genetic sequence for a particular Sample generated by a SequencingActivity.
The location of a sequence feature defined by its start and end position based on a reference coordinate system.
An activity that produces an electronic record of a genetic sequence from a Sample
Data about a physical sample consisting of a single cell or nucleus taken from an organism (living or deceased) or derived from such a Sample.
An activity that infers a cell type based on analysis.
Activity to separate individual cells or nuclei.
A variation in genetic sequence for a particular Sample and VariantCallingActivity.
An electronic record of a collection of variations in genetic sequence for a particular Sample that have been generated by a VariantCallingActivity.
An activity that identifies genetic sequence alterations in a Sample when compared to a reference.
A property that identifies a disease or condition has been confirmed through diagnosis. Contrast with hasDisease.
A reference to the type of activity, preferably using an identifier in a recommended standard ontology.
A reference to the Age of the Donor at the point in time that data was collected or that the BioSample was obtained.
A reference to the Age of the Donor at time of death.
A reference to the Age of the Donor at the point in time that diagnosis was made.
A reference to the Age of the Donor at the onset of the disease associated with the diagnosis.
A reference to the unit of time during which an entity has existed.
Consider replacing with a measurement ontology
A property that identifies the numerical quantity of an entity.
A property that captures the units of an entity. The units may be an amount such as moles or grams; or a concentration, such as g/mL or molarity. Other units may include enzyme activity, the specific activity of a radionucleotide, or the titer of an antibody
Many groups are convening to define Common Coordinate Frameworks for specific organs/species. This will be a rapidly evolving area in the near future. Thus allowing text or URI as we wait for the field to mature allows us to support what we hope will at a minimum be controlled vocabulary under discussion of these groups.
A reference to the physical location within the AnatomicalSite from which the BioSample was taken.
May want to consider restricting this to UBERON terms but currently any URI is allowed. This is useful for imaging and other whole body samples as UBERON does not have "whole body". Use NCIT:C13041 for this.
A reference to the site within the organism from which the BioSample was taken.
A subproperty of usedBy which indicates that an AssayActivity was performed using this entity.
A reference to the type of assay, preferably using an identifier in the Ontology for Biomedical Investigations assay entity (http://purl.obolibrary.org/obo/OBI_0000070).
This property references the BioSample donated by the Donor.
A property that describes the stage of the cell cycle at the time the sample was obtained.
A property that describes the cell’s metabolic or electrophysiological state.
A property that identifies genetic children.
Reference to the entity in another electronic system. The data stored about the entity may vary from system to system, but this relationship asserts that the reference represents the same entity.
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.
Date the BioSample was originally collected from its Donor.
A reference to the data of birth of the Donor or Family Member.
A property that identifies a Diagnosis including provenance and the disease or condition diagnosed.
A property that identifies a disease or condition has been reported in this entity.
This property references the Donor organism from which the BioSample was acquired.
A reference to the Age of the Donor at the point in time that the BioSample was obtained or other representative entity (test, diagnosis, treatment...) was created.
A reference to the Age of the Donor at the point in time that the event or administration occured.
A reference to the dosage information relevant to this Donor Treatment or Medication.
A property identifies the family with whom this Donor is affiliated.
The definition of this field follows the convention used by the Human Cell Atlas.
An indication of the format of an electronic file; include the full file extension including compression extensions.
Property that describes the approximate size of a file in megabytes.
Name of the Reference Assembly in Genome Reference Consortium format (ncbi.nlm.nih.gov/grc. Still draft.
A specific gene identified that applies to this variant.
A property that characterizes the gene expression patterns at work in the cell.
Recommend using HANCESTRO ancestry category subclasses as options here.
A property that relects a HumanDonor's reported major contributing ancestral origins based on genetic/genomic data.
A reference to a genetic modification of a BioSample.
The method of a GeneticModification, see ValueSets.
An external reference to a genetic modification method.
Add equivalence to http://purl.obolibrary.org/obo/PATO_0020000
A biological sex quality inhering in an individual based upon genotypic composition of sex chromosomes. [PATO]
A property that identifies genetic half siblings.
Target is a string for now but will ultimately be a class. CHEBI term CHEBI:60816
An indicator of whether the referenced library was prepared for paired or single end sequencing.
A subproperty of usedBy which indicates that LibraryPreparation was performed using this entity.
A serial or lot number that was manufactured together. Added for Antibodies but domain can expand.
Text form of the address, including country and postal code.
A reference to a Measurement related to this Donor.
Recommend term or URL from MEDDRA or RxNORM. Note that this model of a medication is subject to change.
A reference to the medication information relevant to this entity.
The reason choices are taken from the International Nucleotide Sequencing Data Collaborative (INSDC); see https://www.insdc.org/missing-value-reporting#.
For example: Homo sapiens from NCBITaxon or http://purl.obolibrary.org/obo/NCBITaxon_9606
A property that identifies genetic parents.
The part number is for reordering. Added for Antibodies but domain can expand.
The part number or catalogue number (e.g. Stock Keeping Unit) of an entity.
A reference to the phenotype, preferably from the Human Phenotype Ontology. Phenopackets handled separately.
Phenotype term or free text description for additional phenotype information.
A reference to the BiologicalSex of the Donor organism. "An organismal quality inhering in a bearer by virtue of the bearer's physical expression of sexual characteristics. [PATO]"
A reference to the instrument or platform type used to conduct this activity.
Method used to preserve the BioSample, if relevant, or Fresh for BioSamples that were not preserved.
Considering using HANCESTRO ancestry category subclasses as options here. In the meantime, capturing a text string. Also consider whether we need to track reported and genetic as determined by genetic analysis.
A property that relects a HumanDonor's reported race.
Domain will change from File to SequencingOutputFile or SequenceActivity in future.
See also https://vrs.ga4gh.org/en/stable/terms_and_model.html#allele for a more comprehensive model.
The state of a molecule at a identified location.
Recommend using HANCESTRO ancestry category subclasses but a text string is also acceptable.
A property that relects a HumanDonor's reported ethnic origins.
A subproperty of prov:usedBy which indicates that a SampleTreatmentActivity was performed using this entity.
The method of a SampleTreatmentActivity.
The type of a BioSample treatment type, see valuesets for examples.
See https://vrs.ga4gh.org/en/stable/terms_and_model.html#sequence-expression and https://vrsatile.readthedocs.io/en/latest/value_object_descriptor/index.html#expression.
An expression describing a Sequence, for example HGVS or ISCN.
Location of variation on a sequence. For example, for human genome: chr7:140753336-140753337
A subproperty of usedBy which indicates that a SequencingActivity was performed using this entity.
A reference to the organization performing this activity.
A reference to the BiologicalSex assigned to the donor organism at birth by a medical professional.
A property that identifies full genetic siblings.
The source is a string but will ultimately be a Vendor class. Added for Antibodies but domain can expand.
A reference to the start position on the chromosome identified.
A sequence variant that changes one or more structural features. (Sequence Ontology)
Target is a string for now but will ultimately be a class, and this will change to an ObjectProperty.
A reference to the therapeutic treatment undertaken for this Donor.
Should the model define a preferred vocabulary? e.g. positive, negative, no effect? The specific outcome may need to be more specific, reduced tumor size by .. but the categories listed are useful.
A reference to the outcome of this Treatment.
A property that provides a measurement of the mass of a material entity.
A reference to the measurement unit for mass.
A relationship defining the funding source. The range is expected to include grants, organizations, or a string indicating the funding source.
Can be used as an ObjectProperty with the Antibody class or as a DataType property, depending on need. Antibody should be linked to OBI in future. Note this could link to nonassay activities like CHiP
May be a reference to an antibody used for a SampleTreatmentActivity or another Activity.
A reference to a Sequencing Library used in this activity.
A reference to the collection of sequences taken as the standard for a given organism. May be defined by https://www.ncbi.nlm.nih.gov/grc.
BioSample and MolecularSample both inherit range from Sample
A reference to the sample used by this activity.
A reference to a software tool or command line