Metadata Types

In the HCA metadata schema, types represent the different parts of an experiment. The schema currently defines five core types (Biomaterial, Process, Protocol, Project, File). These core types are extended and refined by one or more subtypes.

For example, a biomaterial (e.g. a tissue sample) can undergo a process (e.g. dissociation) to produce another biomaterial (e.g. a sample of dissociated cells) or a set of data files (e.g. 10X fastq files). The process that was actually executed follows a specific protocol (e.g. a 10X protocol). All of these parts together make up the overall project (e.g. Understanding cell types in the human heart).

An overview of each of current HCA metadata schema types is given below. Please see the metadata structure or metadata design documentation for additional details and examples of how the schema is structured.

Biomaterials

Biomaterial types represent information about any biological material that was generated/used in the project including everything from a whole organism to subcellular components.

Cell lineInformation about the cell line or cell culture biomaterial.Cell suspensionInformation about the suspension of cells or nuclei derived from the collected or cultured specimen.Donor organismInformation about the donor from which a specimen was collected.Imaged specimenInformation about a tissue specimen after it has been sectioned and prepared for imaging.OrganoidInformation about an organoid biomaterial.Specimen from organismInformation about the specimen that was collected from the donor organism.

Processes

Process types represent information relevant to how a biomaterial or file was converted into another biomaterial or file.

Analysis processInformation about the analysis process.ProcessInformation about a process completed in the experiment.

Protocols

Protocol types represent information about an intended protocol that was followed in a process.

Analysis protocolInformation about the analysis protocol.Aggregate generation protocolInformation about how cultured cells are developed into cell aggregates.Collection protocolInformation about the biomaterial collection protocol.Differentiation protocolInformation about how a cell is differentiated to a desired cell type or organoid.Dissociation protocolInformation about the dissociation protocol used to separate individual cells or nuclei.Enrichment protocolInformation about how a biomaterial is enriched for a feature or characteristic of interest.iPSC induction protocolInformation about how a biomaterial is treated to become an induced pluripotent stem cell.Treatment protocolInformation about how cells are subjected to a treatment or stimulus, such as an immune activator or a drug.Imaging preparation protocolInformation about the preparation protocol of the imaged specimen used in an imaging experiment.Imaging ProtocolInformation about the imaging protocol.ProtocolInformation about the protocol.Library preparation protocolInformation about how a sequencing library was prepared.Sequencing protocolInformation about the sequencing protocol.

Files

File types represent information about files produced from any process.

Analysis fileA file analysis results produced by a secondary analysis pipeline.Image fileInformation about an image file generated by an imaging experiment.Reference fileA reference file used by a secondary reference pipeline.Sequence fileA file of read sequences generated by a sequencing experiment.Supplementary fileSupplementary files belonging to a project.

Projects

The project type specifies information about a project that contributes to the HCA Data Portal.

ProjectA project entity contains information about the overall project.

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