Multiplex Fluorescence Based Experiment (MxFBE)

Cell DIVE

Related files:

Metadata schema

Version 2 (use this one)
Version 1

Shared by all types

version

Version of the schema to use when validating this metadata.

constraint value
enum 1
required True

description

Free-text description of this assay.

constraint value
required True

donor_id

HuBMAP Display ID of the donor of the assayed tissue. Example: ABC123.

constraint value
pattern (regular expression) [A-Z]+[0-9]+
required True

tissue_id

HuBMAP Display ID of the assayed tissue. Example: ABC123-BL-1-2-3_456.

constraint value
pattern (regular expression) (([A-Z]+[0-9]+)-[A-Z]{2}\d*(-\d+)+(_\d+)?)(,([A-Z]+[0-9]+)-[A-Z]{2}\d*(-\d+)+(_\d+)?)*
required True

execution_datetime

Start date and time of assay, typically a date-time stamped folder generated by the acquisition instrument. YYYY-MM-DD hh:mm, where YYYY is the year, MM is the month with leading 0s, and DD is the day with leading 0s, hh is the hour with leading zeros, mm are the minutes with leading zeros.

constraint value
type datetime
format %Y-%m-%d %H:%M
required True

protocols_io_doi

DOI for protocols.io referring to the protocol for this assay.

constraint value
required True
pattern (regular expression) 10\.17504/.*
url prefix: https://dx.doi.org/

operator

Name of the person responsible for executing the assay.

constraint value
required True

operator_email

Email address for the operator.

constraint value
format email
required True

pi

Name of the principal investigator responsible for the data.

constraint value
required True

pi_email

Email address for the principal investigator.

constraint value
format email
required True

assay_category

Each assay is placed into one of the following 4 general categories: generation of images of microscopic entities, identification & quantitation of molecules by mass spectrometry, imaging mass spectrometry, and determination of nucleotide sequence.

constraint value
enum imaging
required True

assay_type

The specific type of assay being executed.

constraint value
enum Cell DIVE or cell-dive
required True

analyte_class

Analytes are the target molecules being measured with the assay.

constraint value
enum protein
required True

is_targeted

Specifies whether or not a specific molecule(s) is/are targeted for detection/measurement by the assay.

constraint value
type boolean
required True

acquisition_instrument_vendor

An acquisition instrument is the device that contains the signal detection hardware and signal processing software. Assays generate signals such as light of various intensities or color or signals representing the molecular mass.

constraint value
required True

acquisition_instrument_model

Manufacturers of an acquisition instrument may offer various versions (models) of that instrument with different features or sensitivities. Differences in features or sensitivities may be relevant to processing or interpretation of the data.

constraint value
required True

Unique to this type

number_of_antibodies

Number of antibodies.

constraint value
type integer
required True

number_of_channels

Number of fluorescent channels imaged during each cycle.

constraint value
type integer
required True

number_of_cycles

Number of cycles of 1. oligo application, 2. fluor application, 3. dye inactivation.

constraint value
type integer
required True

number_of_imaging_rounds

the total number of acquisitions performed on microscope to collect autofluorescence/background or stained signal.

constraint value
type integer
required True

resolution_x_value

The width of a pixel.

constraint value
type number
required True

resolution_x_unit

The unit of measurement of the width of a pixel. Leave blank if not applicable.

constraint value
enum nm or um
required False
required if resolution_x_value present

resolution_y_value

The height of a pixel.

constraint value
type number
required True

resolution_y_unit

The unit of measurement of the height of a pixel. Leave blank if not applicable.

constraint value
enum nm or um
required False
required if resolution_y_value present

processing_protocols_io_doi

DOI for analysis protocols.io for this assay. Leave blank if not applicable.

constraint value
required False
pattern (regular expression) 10\.17504/.*
url prefix: https://dx.doi.org/

overall_protocols_io_doi

DOI for protocols.io for the overall process.

constraint value
required True
pattern (regular expression) 10\.17504/.*
url prefix: https://dx.doi.org/

antibodies_path

Relative path to file with antibody information for this dataset.

constraint value
required True

contributors_path

Relative path to file with ORCID IDs for contributors for this dataset.

constraint value
required True

data_path

Relative path to file or directory with instrument data. Downstream processing will depend on filename extension conventions.

constraint value
required True
Version 0

Shared by all types

donor_id

HuBMAP Display ID of the donor of the assayed tissue. Example: ABC123.

constraint value
pattern (regular expression) [A-Z]+[0-9]+
required True

tissue_id

HuBMAP Display ID of the assayed tissue. Example: ABC123-BL-1-2-3_456.

constraint value
pattern (regular expression) ([A-Z]+[0-9]+)-[A-Z]{2}\d*(-\d+)+(_\d+)?
required True

execution_datetime

Start date and time of assay, typically a date-time stamped folder generated by the acquisition instrument. YYYY-MM-DD hh:mm, where YYYY is the year, MM is the month with leading 0s, and DD is the day with leading 0s, hh is the hour with leading zeros, mm are the minutes with leading zeros.

constraint value
type datetime
format %Y-%m-%d %H:%M
required True

protocols_io_doi

DOI for protocols.io referring to the protocol for this assay.

constraint value
required True
pattern (regular expression) 10\.17504/.*
url prefix: https://dx.doi.org/

operator

Name of the person responsible for executing the assay.

constraint value
required True

operator_email

Email address for the operator.

constraint value
format email
required True

pi

Name of the principal investigator responsible for the data.

constraint value
required True

pi_email

Email address for the principal investigator.

constraint value
format email
required True

assay_category

Each assay is placed into one of the following 4 general categories: generation of images of microscopic entities, identification & quantitation of molecules by mass spectrometry, imaging mass spectrometry, and determination of nucleotide sequence.

constraint value
enum imaging
required True

assay_type

The specific type of assay being executed.

constraint value
enum Cell DIVE
required True

analyte_class

Analytes are the target molecules being measured with the assay.

constraint value
enum protein
required True

is_targeted

Specifies whether or not a specific molecule(s) is/are targeted for detection/measurement by the assay.

constraint value
type boolean
required True

acquisition_instrument_vendor

An acquisition instrument is the device that contains the signal detection hardware and signal processing software. Assays generate signals such as light of various intensities or color or signals representing the molecular mass.

constraint value
required True

acquisition_instrument_model

Manufacturers of an acquisition instrument may offer various versions (models) of that instrument with different features or sensitivities. Differences in features or sensitivities may be relevant to processing or interpretation of the data.

constraint value
required True

Unique to this type

number_of_antibodies

Number of antibodies.

constraint value
type integer
required True

number_of_channels

Number of fluorescent channels imaged during each cycle.

constraint value
type integer
required True

number_of_cycles

Number of cycles of 1. oligo application, 2. fluor application, 3. dye inactivation.

constraint value
type integer
required True

number_of_imaging_rounds

the total number of acquisitions performed on microscope to collect autofluorescence/background or stained signal.

constraint value
type integer
required True

resolution_x_value

The width of a pixel.

constraint value
type number
required True

resolution_x_unit

The unit of measurement of the width of a pixel. Leave blank if not applicable.

constraint value
enum nm or um
required False
required if resolution_x_value present

resolution_y_value

The height of a pixel.

constraint value
type number
required True

resolution_y_unit

The unit of measurement of the height of a pixel. Leave blank if not applicable.

constraint value
enum nm or um
required False
required if resolution_y_value present

processing_protocols_io_doi

DOI for analysis protocols.io for this assay. Leave blank if not applicable.

constraint value
required False
pattern (regular expression) 10\.17504/.*
url prefix: https://dx.doi.org/

overall_protocols_io_doi

DOI for protocols.io for the overall process.

constraint value
required True
pattern (regular expression) 10\.17504/.*
url prefix: https://dx.doi.org/

antibodies_path

Relative path to file with antibody information for this dataset.

constraint value
required True

contributors_path

Relative path to file with ORCID IDs for contributors for this dataset.

constraint value
required True

data_path

Relative path to file or directory with instrument data. Downstream processing will depend on filename extension conventions.

constraint value
required True


Directory schemas

Version 2 (use this one) (draft - submission of data prepared using this schema will be supported by Sept. 30) Version 0
pattern required? description
channel_list\.txt Information about the capture channels and tags (comma separated)
slide_list\.txt Information about the slides used by the experiment- each line corresponds to a slide name (begins with S - e.g. S20030077) - used in filenames
HuBMAP_OME/region_\d+/S\d+_region_\d+\.ome\.tif (example: HuBMAP_OME/region_011/S20030092_region_011.ome.tif) OME TIFF Files for the corresponding region (e.g. region_001) by slide (e.g S20030077)
HuBMAP_rounds/round_info_\d+\.dat (example: HuBMAP_rounds/round_info_002.dat) Metadata file for the capture item-value tab separated format
extras\/.*   Folder for general lab-specific files related to the dataset. [Exists in all assays]