Metadata
========

.. _measurement-info-metadata:

:doc:`METADATA </api_reference/api/phenotypic.schema.METADATA>`
---------------------------------------------------------------

.. list-table:: Category: **MetadataImage**
   :header-rows: 1

   * - Column label
     - Description
     - Type
   * - ``MetadataImage_UUID``
     - The unique identifier of the image.
     - :bdg-ref-muted:`Identity / design <measurement-classification>`
   * - ``MetadataImage_ImageName``
     - The name of the image.
     - :bdg-ref-muted:`Identity / design <measurement-classification>`
   * - ``MetadataImage_ParentImageName``
     - The name of the parent image.
     - :bdg-ref-muted:`Identity / design <measurement-classification>`
   * - ``MetadataImage_ParentUUID``
     - The UUID of the parent image.
     - :bdg-ref-muted:`Identity / design <measurement-classification>`
   * - ``MetadataImage_ImageFormat``
     - The format of the image.
     - :bdg-ref-muted:`Identity / design <measurement-classification>`
   * - ``MetadataImage_ImageType``
     - The type of the image.
     - :bdg-ref-muted:`Identity / design <measurement-classification>`
   * - ``MetadataImage_BitDepth``
     - The bit depth of the image.
     - :bdg-ref-muted:`Identity / design <measurement-classification>`
   * - ``MetadataImage_FileSuffix``
     - The file suffix of the original file the image was imported from
     - :bdg-ref-muted:`Identity / design <measurement-classification>`

.. _measurement-info-acquisition-metadata:

:doc:`ACQUISITION_METADATA </api_reference/api/phenotypic.schema.ACQUISITION_METADATA>`
---------------------------------------------------------------------------------------

.. list-table:: Category: **MetadataAcquisition**
   :header-rows: 1

   * - Column label
     - Description
     - Type
   * - ``MetadataAcquisition_ImagingDate``
     - Date the image was acquired.
     - :bdg-ref-muted:`Identity / design <measurement-classification>`
   * - ``MetadataAcquisition_Instrument``
     - Imaging instrument or scanner model.
     - :bdg-ref-muted:`Identity / design <measurement-classification>`
   * - ``MetadataAcquisition_Experimenter``
     - Person who acquired the image or ran the experiment.
     - :bdg-ref-muted:`Identity / design <measurement-classification>`
   * - ``MetadataAcquisition_Resolution``
     - Image resolution (e.g. DPI or pixels per mm).
     - :bdg-ref-muted:`Identity / design <measurement-classification>`
   * - ``MetadataAcquisition_ExposureTime``
     - Camera exposure time.
     - :bdg-ref-muted:`Identity / design <measurement-classification>`

.. _measurement-info-condition-metadata:

:doc:`CONDITION_METADATA </api_reference/api/phenotypic.schema.CONDITION_METADATA>`
-----------------------------------------------------------------------------------

.. list-table:: Category: **MetadataCondition**
   :header-rows: 1

   * - Column label
     - Description
     - Type
   * - ``MetadataCondition_Media``
     - Growth medium name (e.g. YPD, SC, LB).
     - :bdg-ref-muted:`Identity / design <measurement-classification>`
   * - ``MetadataCondition_CarbonSource``
     - Primary carbon source (e.g. glucose, galactose).
     - :bdg-ref-muted:`Identity / design <measurement-classification>`
   * - ``MetadataCondition_NitrogenSource``
     - Primary nitrogen source.
     - :bdg-ref-muted:`Identity / design <measurement-classification>`
   * - ``MetadataCondition_pH``
     - pH of the growth medium.
     - :bdg-ref-muted:`Identity / design <measurement-classification>`
   * - ``MetadataCondition_Supplement``
     - Medium supplement or additive.
     - :bdg-ref-muted:`Identity / design <measurement-classification>`
   * - ``MetadataCondition_Antibiotic``
     - Antibiotic added to the medium.
     - :bdg-ref-muted:`Identity / design <measurement-classification>`
   * - ``MetadataCondition_Inducer``
     - Inducing agent (e.g. galactose, IPTG, doxycycline).
     - :bdg-ref-muted:`Identity / design <measurement-classification>`
   * - ``MetadataCondition_Treatment``
     - Experimental treatment or perturbation.
     - :bdg-ref-muted:`Identity / design <measurement-classification>`
   * - ``MetadataCondition_Compound``
     - Chemical compound or drug applied.
     - :bdg-ref-muted:`Identity / design <measurement-classification>`
   * - ``MetadataCondition_Concentration``
     - Concentration of the compound or treatment.
     - :bdg-ref-muted:`Identity / design <measurement-classification>`
   * - ``MetadataCondition_Dose``
     - Dose applied to the sample.
     - :bdg-ref-muted:`Identity / design <measurement-classification>`
   * - ``MetadataCondition_Stress``
     - Applied stress condition (e.g. heat, osmotic, oxidative).
     - :bdg-ref-muted:`Identity / design <measurement-classification>`

.. _measurement-info-culture-metadata:

:doc:`CULTURE_METADATA </api_reference/api/phenotypic.schema.CULTURE_METADATA>`
-------------------------------------------------------------------------------

.. list-table:: Category: **MetadataCulture**
   :header-rows: 1

   * - Column label
     - Description
     - Type
   * - ``MetadataCulture_Temperature``
     - Culture temperature in degrees Celsius.
     - :bdg-ref-muted:`Identity / design <measurement-classification>`
   * - ``MetadataCulture_Time``
     - Elapsed growth time.
     - :bdg-ref-muted:`Identity / design <measurement-classification>`
   * - ``MetadataCulture_TimeUnit``
     - Unit for the Time value (e.g. hours, days).
     - :bdg-ref-muted:`Identity / design <measurement-classification>`
   * - ``MetadataCulture_Timepoint``
     - Human-readable label for a discrete timepoint in a time series (e.g. '24h', 'stationary'); may be non-numeric. For the integer capture ordinal, use FrameIndex.
     - :bdg-ref-muted:`Identity / design <measurement-classification>`
   * - ``MetadataCulture_FrameIndex``
     - 1-based ordinal index of the image within the time-course capture sequence; the monotonic-integer companion to the free-form Timepoint label.
     - :bdg-ref-muted:`Identity / design <measurement-classification>`
   * - ``MetadataCulture_Day``
     - Day index of the experiment.
     - :bdg-ref-muted:`Identity / design <measurement-classification>`
   * - ``MetadataCulture_Generation``
     - Generation or passage number.
     - :bdg-ref-muted:`Identity / design <measurement-classification>`
   * - ``MetadataCulture_Humidity``
     - Relative humidity during culture.
     - :bdg-ref-muted:`Identity / design <measurement-classification>`
   * - ``MetadataCulture_Atmosphere``
     - Atmospheric condition (e.g. aerobic, anaerobic).
     - :bdg-ref-muted:`Identity / design <measurement-classification>`

.. _measurement-info-experiment-metadata:

:doc:`EXPERIMENT_METADATA </api_reference/api/phenotypic.schema.EXPERIMENT_METADATA>`
-------------------------------------------------------------------------------------

.. list-table:: Category: **MetadataExperiment**
   :header-rows: 1

   * - Column label
     - Description
     - Type
   * - ``MetadataExperiment_ExperimentID``
     - Unique identifier for the experiment.
     - :bdg-ref-muted:`Identity / design <measurement-classification>`
   * - ``MetadataExperiment_Project``
     - Project name or identifier.
     - :bdg-ref-muted:`Identity / design <measurement-classification>`
   * - ``MetadataExperiment_Dataset``
     - Dataset name (matches the CLI-emitted MetadataExperiment_Dataset column).
     - :bdg-ref-muted:`Identity / design <measurement-classification>`
   * - ``MetadataExperiment_Protocol``
     - Protocol name or version followed.
     - :bdg-ref-muted:`Identity / design <measurement-classification>`
   * - ``MetadataExperiment_Notes``
     - Free-text notes or comments.
     - :bdg-ref-muted:`Identity / design <measurement-classification>`

.. _measurement-info-genetic-metadata:

:doc:`GENETIC_METADATA </api_reference/api/phenotypic.schema.GENETIC_METADATA>`
-------------------------------------------------------------------------------

.. list-table:: Category: **MetadataGenetic**
   :header-rows: 1

   * - Column label
     - Description
     - Type
   * - ``MetadataGenetic_Organism``
     - Species or organism name (e.g. Saccharomyces cerevisiae).
     - :bdg-ref-muted:`Identity / design <measurement-classification>`
   * - ``MetadataGenetic_Strain``
     - Strain name or identifier (e.g. BY4741).
     - :bdg-ref-muted:`Identity / design <measurement-classification>`
   * - ``MetadataGenetic_Genotype``
     - Genotype description of the strain.
     - :bdg-ref-muted:`Identity / design <measurement-classification>`
   * - ``MetadataGenetic_Background``
     - Genetic background or parent strain.
     - :bdg-ref-muted:`Identity / design <measurement-classification>`
   * - ``MetadataGenetic_Allele``
     - Specific allele or mutation under study.
     - :bdg-ref-muted:`Identity / design <measurement-classification>`
   * - ``MetadataGenetic_Plasmid``
     - Plasmid carried by the sample.
     - :bdg-ref-muted:`Identity / design <measurement-classification>`
   * - ``MetadataGenetic_SelectionMarker``
     - Selectable marker gene (e.g. URA3, KanMX).
     - :bdg-ref-muted:`Identity / design <measurement-classification>`
   * - ``MetadataGenetic_MatingType``
     - Mating type for yeast (e.g. MATa, MATalpha).
     - :bdg-ref-muted:`Identity / design <measurement-classification>`
   * - ``MetadataGenetic_Ploidy``
     - Ploidy of the organism (e.g. haploid, diploid).
     - :bdg-ref-muted:`Identity / design <measurement-classification>`

.. _measurement-info-plate-metadata:

:doc:`PLATE_METADATA </api_reference/api/phenotypic.schema.PLATE_METADATA>`
---------------------------------------------------------------------------

.. list-table:: Category: **MetadataPlate**
   :header-rows: 1

   * - Column label
     - Description
     - Type
   * - ``MetadataPlate_PlateID``
     - Identifier of the assay/imaging plate.
     - :bdg-ref-muted:`Identity / design <measurement-classification>`
   * - ``MetadataPlate_Batch``
     - Experimental batch grouping.
     - :bdg-ref-muted:`Identity / design <measurement-classification>`
   * - ``MetadataPlate_ArrayDensity``
     - Colony array density, i.e. wells per plate (e.g. 96, 384, 1536).
     - :bdg-ref-muted:`Identity / design <measurement-classification>`
   * - ``MetadataPlate_IncubatorPosition``
     - Physical position of the plate within the incubator.
     - :bdg-ref-muted:`Identity / design <measurement-classification>`

.. _measurement-info-sample-metadata:

:doc:`SAMPLE_METADATA </api_reference/api/phenotypic.schema.SAMPLE_METADATA>`
-----------------------------------------------------------------------------

.. list-table:: Category: **MetadataSample**
   :header-rows: 1

   * - Column label
     - Description
     - Type
   * - ``MetadataSample_SampleID``
     - Unique identifier for the biological sample.
     - :bdg-ref-muted:`Identity / design <measurement-classification>`
   * - ``MetadataSample_BioReplicate``
     - Biological replicate identifier. Biological replicates are parallel measurements of biologically distinct samples that capture random biological variation.
     - :bdg-ref-muted:`Identity / design <measurement-classification>`
   * - ``MetadataSample_CondReplicate``
     - Experimental Conditional replicate identifier. An example  of an experimental replicate would be a pinned colony of  the same strain on another plate being subjected to the same conditions.
     - :bdg-ref-muted:`Identity / design <measurement-classification>`
   * - ``MetadataSample_TechReplicate``
     - Technical replicate identifier.
     - :bdg-ref-muted:`Identity / design <measurement-classification>`
   * - ``MetadataSample_Clone``
     - Clone or isolate identifier.
     - :bdg-ref-muted:`Identity / design <measurement-classification>`
   * - ``MetadataSample_LibraryID``
     - Source library or collection identifier (e.g. a deletion collection).
     - :bdg-ref-muted:`Identity / design <measurement-classification>`
   * - ``MetadataSample_SourcePlate``
     - Identifier of the source plate the sample was pinned from.
     - :bdg-ref-muted:`Identity / design <measurement-classification>`
   * - ``MetadataSample_SourceWell``
     - Well position on the source plate (e.g. A1). This can potentially be distinct from `Grid` values when using irregular or sparse grid parameters.
     - :bdg-ref-muted:`Identity / design <measurement-classification>`
   * - ``MetadataSample_Barcode``
     - Molecular or sample barcode.
     - :bdg-ref-muted:`Identity / design <measurement-classification>`
   * - ``MetadataSample_Control``
     - Control designation (e.g. positive, negative, blank).
     - :bdg-ref-muted:`Identity / design <measurement-classification>`

.. _measurement-info-study-metadata:

:doc:`STUDY_METADATA </api_reference/api/phenotypic.schema.STUDY_METADATA>`
---------------------------------------------------------------------------

.. list-table:: Category: **MetadataStudy**
   :header-rows: 1

   * - Column label
     - Description
     - Type
   * - ``MetadataStudy_Title``
     - Study title.
     - :bdg-ref-muted:`Identity / design <measurement-classification>`
   * - ``MetadataStudy_Description``
     - Free-text study description.
     - :bdg-ref-muted:`Identity / design <measurement-classification>`
   * - ``MetadataStudy_PrivateUntilDate``
     - Embargo date until which the study stays private.
     - :bdg-ref-muted:`Identity / design <measurement-classification>`
   * - ``MetadataStudy_Keywords``
     - Keywords describing the study.
     - :bdg-ref-muted:`Identity / design <measurement-classification>`
   * - ``MetadataStudy_Author``
     - Study author(s); delimited string when multiple.
     - :bdg-ref-muted:`Identity / design <measurement-classification>`
   * - ``MetadataStudy_License``
     - Data license (e.g. CC0, CC-BY-4.0).
     - :bdg-ref-muted:`Identity / design <measurement-classification>`
   * - ``MetadataStudy_Funding``
     - Funding statement or grant reference(s).
     - :bdg-ref-muted:`Identity / design <measurement-classification>`
   * - ``MetadataStudy_Publications``
     - Associated publication(s) or DOI(s).
     - :bdg-ref-muted:`Identity / design <measurement-classification>`
   * - ``MetadataStudy_Links``
     - Related links or external resource URLs.
     - :bdg-ref-muted:`Identity / design <measurement-classification>`
   * - ``MetadataStudy_Acknowledgements``
     - Acknowledgements text.
     - :bdg-ref-muted:`Identity / design <measurement-classification>`