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 further processed the output of an Alignment Activity on a genetic sequence.
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.
The location of a sequence feature defined by its start and end position on a chromosome in a reference coordinate system.
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
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.
Placeholder for medical record information. Likely a series of visits/encounters with results. Need to connect to the BioSample.
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.
An activity that records the output of a specific software pipeline. Pipeline version, components, arguments are described in prov:SoftwareAgent.
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.
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 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.
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.
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.
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.
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 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 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.
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.
A subproperty of usedBy which indicates that LibraryPreparation was performed using this entity.
Location of variation on a sequence. For example, for human genome: chr7:140753336-140753337
Text form of the address, including country and postal code.
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 obo:NCBITaxon_9606
A property that identifies genetic parents.
Domain will change from File to SequencingOutputFile or SequenceActivity in future.
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]"
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.
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 usedBy which indicates that a SequencingActivity was performed using this entity.
A reference to the BiologicalSex assigned to the donor organism at birth by a medical professional.
A property that identifies full genetic siblings.
Text string to represent the strain of the donor organism.
Target is a string for now but will ultimately be a class.
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.
Antibody should be linked to OBI in future.