Annotation templates are spreadsheet templates that allow contributors to annotate resources uploaded to the repository. See interactive use of these templates at our NF Data Curator App. Templates implement “minimum metadata” standards specific to the type of data/resource (hence variants exist for assay types and “raw” vs “processed” data). Templates also contain common components, e.g. many will collect core sample info associated with the data.
Unless the template field is free-text, it is meant to be filled by the contributor using the ontology terms/controlled vocabulary defined here. For example, the “assay” property allows the contributor to use terms under Assay.
Raw or processed data files from a genomics assay should be annotated using one of these templates.
These are standard terms available to NF resource contributors for annotation of their resource. Terms are grouped into modules. When using these terms, contributors are helping to label and classify resources using standard semantics for improved interoperability and findability.
This partial graph view logically relates assays to
metadata templates available at the NF Data
Curator App. For example, assays under the classification of
Imaging_Assay currently uses a generic
Imaging_Assay_Template for annotation. More specialized
templates may be made available as needed for specific assays.
Sample typically refers to a biosample, but on some rare occasions can refer to an inorganic sample from which data are generated. For biosamples, there is a distinction between individual-level and specimen-level data. Data can be linked to individual-level sample information such as sex, species, diagnosis, and genotype. Data can be linked to specimen-level information such as sample site (the organ or body part), specimen type or cell type, tumor class (if specimen is a tumor), and specimen state.
Terminology to help characterize experiment.
Reserved annotation properties also describe the resource in some way, but they are not expected to be edited directly by contributors. They are computed/automated annotations set by the data platform and DCC activities.