Karlburke/parameterized search

docs/search-indices/assay-type-schemas/af.md

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+---
+layout: page
+---
+# AF
+
+## Overview:
+This schema is for autofluorescence (AF). For an example of an AF dataset & directory, see this example autofluorescence dataset and click the Globus link.
+
+### Last Updated: 2023-04-25
+
+### Version 1 (current)
+
+## Metadata Schema
+
+| Attribute | Description | shared/unique | enum | required | format | required if | type | pattern (regular expression) | url |
+|-----------|-------------|---------------|------|----------|--------|-------------|------|------------------------------|-----|
+| version | Version of the schema to use when validating this metadata. | Shared by all types | 1 | True |   |   |   |   |   |
+| description | Free-text description of this assay. | Shared by all types |   | True |   |   |   |   |   |
+| donor_id | HuBMAP Display ID of the donor of the assayed tissue. Example: ABC123. | Shared by all types |   | True |   |   |   | [A-Z]+[0-9]+ |   |
+| tissue_id | HuBMAP Display ID of the assayed tissue. Example: ABC123-BL-1-2-3_456. | Shared by all types |   | True |   |   |   | (([A-Z]+[0-9]+)-[A-Z]{2}\d*(-\d+)+(_\d+)?)(,([A-Z]+[0-9]+)-[A-Z]{2}\d*(-\d+)+(_\d+)?)* |   |
+| 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. | Shared by all types |   | True | %Y-%m-%d %H:%M |   | datetime |   |   |
+| protocols_io_doi | DOI for protocols.io referring to the protocol for this assay. | Shared by all types |   | True |   |   |   | 10\.17504/.* | prefix: https://dx.doi.org/ |
+| operator | Name of the person responsible for executing the assay. | Shared by all types |   | True |   |   |   |   |   |
+| operator_email | Email address for the operator. | Shared by all types |   | True | email |   |   |   |   |
+| pi | Name of the principal investigator responsible for the data. | Shared by all types |   | True |   |   |   |   |   |
+| pi_email | Email address for the principal investigator. | Shared by all types |   | True | email |   |   |   |   |
+| 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. | Shared by all types | imaging | True |   |   |   |   |   |
+| assay_type | The specific type of assay being executed. | Shared by all types | AF | True |   |   |   |   |   |
+| analyte_class | Analytes are the target molecules being measured with the assay. Leave blank if not applicable. | Shared by all types |   | False |   |   |   |   |   |
+| is_targeted | Specifies whether or not a specific molecule(s) is/are targeted for detection/measurement by the assay. | Shared by all types |   | True |   |   | boolean |   |   |
+| 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. | Shared by all types |   | 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. | Shared by all types |   | True |   |   |   |   |   |
+| resolution_x_value | The width of a pixel. | Unique to this type |   | True |   |   | number |   |   |
+| resolution_x_unit | The unit of measurement of the width of a pixel. Leave blank if not applicable. | Unique to this type | nm or um | False |   | resolution_x_value present |   |   |   |
+| resolution_y_value | The height of a pixel. | Unique to this type |   | True |   |   | number |   |   |
+| resolution_y_unit | The unit of measurement of the height of a pixel. Leave blank if not applicable. | Unique to this type | nm or um | False |   | resolution_y_value present |   |   |   |
+| resolution_z_value | Optional if assay does not have multiple z-levels. Note that this is resolution within a given sample: z-pitch (resolution_z_value) is the increment distance between image slices, ie. the microscope stage is moved up or down in increments to capture images of several focal planes. | Unique to this type |   | True |   |   | number |   |   |
+| resolution_z_unit | The unit of incremental distance between image slices. Leave blank if not applicable. | Unique to this type | mm, um, or nm | False |   | resolution_z_value present |   |   |   |
+| number_of_channels | Number of channels capturing the emission spectrum from natural fluorophores in the sample. | Unique to this type |   | True |   |   | integer |   |   |
+| overall_protocols_io_doi | DOI for protocols.io referring to the overall protocol for the assay. | Unique to this type |   | True |   |   |   | 10\.17504/.* | prefix: https://dx.doi.org/ |
+| contributors_path | Relative path to file with ORCID IDs for contributors for this dataset. | Unique to this type |   | True |   |   |   |   |   |
+| data_path | Relative path to file or directory with instrument data. Downstream processing will depend on filename extension conventions. | Unique to this type |   | True |   |   |   |   |   |

docs/search-indices/assay-type-schemas/antibodies.md

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+---
+layout: page
+---
+# antibodies
+
+## Overview:
+Changes:
+
+### Last Updated: 2023-04-25
+
+### Version 2 (current)
+
+## Metadata Schema
+
+| Attribute | Description | shared/unique | enum | required | format | required if | type | pattern (regular expression) | url |
+|-----------|-------------|---------------|------|----------|--------|-------------|------|------------------------------|-----|

docs/search-indices/assay-type-schemas/bodyct.md

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+---
+layout: page
+---
+# Body CT
+
+## Overview:
+This schema is for clinical imaging using body computed tomography (Body CT).
+
+### Last Updated: 2023-04-25
+
+### Version 1 (current)
+
+## Metadata Schema
+
+| Attribute | Description | shared/unique | enum | required | format | required if | type | pattern (regular expression) | url |
+|-----------|-------------|---------------|------|----------|--------|-------------|------|------------------------------|-----|
+| version | Version of the schema to use when validating this metadata. | Shared by all types | 1 | True |   |   |   |   |   |
+| description | Free-text description of this assay. | Shared by all types |   | True |   |   |   |   |   |
+| donor_id | HuBMAP Display ID of the donor of the assayed tissue. Example: ABC123. | Shared by all types |   | True |   |   |   | [A-Z]+[0-9]+ |   |
+| tissue_id | HuBMAP Display ID of the assayed tissue. Example: ABC123-BL-1-2-3_456. | Shared by all types |   | True |   |   |   | (([A-Z]+[0-9]+)-[A-Z]{2}\d*(-\d+)+(_\d+)?)(,([A-Z]+[0-9]+)-[A-Z]{2}\d*(-\d+)+(_\d+)?)* |   |
+| 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. | Shared by all types |   | True | %Y-%m-%d %H:%M |   | datetime |   |   |
+| protocols_io_doi | DOI for protocols.io referring to the protocol for this assay. | Shared by all types |   | True |   |   |   | 10\.17504/.* | prefix: https://dx.doi.org/ |
+| operator | Name of the person responsible for executing the assay. | Shared by all types |   | True |   |   |   |   |   |
+| operator_email | Email address for the operator. | Shared by all types |   | True | email |   |   |   |   |
+| pi | Name of the principal investigator responsible for the data. | Shared by all types |   | True |   |   |   |   |   |
+| pi_email | Email address for the principal investigator. | Shared by all types |   | True | email |   |   |   |   |
+| 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. | Shared by all types | clinical_imaging | True |   |   |   |   |   |
+| assay_type | The specific type of assay being executed. | Shared by all types | Body CT | 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. | Shared by all types |   | 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. | Shared by all types |   | True |   |   |   |   |   |
+| single_file_export_format | The format in which each single imaging file will be exported. (Example: DICOM, tiff, avi, etc.) | Shared by all clinical imaging assays |   | True |   |   |   |   |   |
+| max_x_width_value | Image width value of the ROI acquisition. | Shared by all clinical imaging assays |   | True |   |   | number |   |   |
+| max_x_width_unit | Units of image width of the ROI acquisition. Leave blank if not applicable. | Shared by all clinical imaging assays | um or mm | False |   | max_x_width_value present |   |   |   |
+| max_y_height_value | Image height value of the ROI acquisition. | Shared by all clinical imaging assays |   | True |   |   | number |   |   |
+| max_y_height_unit | Units of image height of the ROI acquisition. Leave blank if not applicable. | Shared by all clinical imaging assays | um or mm | False |   | max_y_height_value present |   |   |   |
+| roi_description | A description of the region of interest (ROI) captured in the image. | Shared by all clinical imaging assays |   | True |   |   |   |   |   |
+| roi_id | Multiple images (1-n) are acquired from regions of interest (ROI1, ROI2, ROI3, etc) on a slide. The roi_id is a number from 1-n representing the ROI captured on a slide. Leave blank if not applicable. | Shared by all clinical imaging assays |   | False |   |   | integer |   |   |
+| resolution_x_value | The width of a pixel. | Shared by all clinical imaging assays |   | True |   |   | number |   |   |
+| resolution_x_unit | The unit of measurement of the width of a pixel. Leave blank if not applicable. | Shared by all clinical imaging assays | nm, um, or mm | False |   | resolution_x_value present |   |   |   |
+| resolution_y_value | The height of a pixel. | Shared by all clinical imaging assays |   | True |   |   | number |   |   |
+| resolution_y_unit | The unit of measurement of the height of a pixel. Leave blank if not applicable. | Shared by all clinical imaging assays | nm, um, or mm | False |   | resolution_y_value present |   |   |   |
+| resolution_z_value | Optional if assay does not have multiple z-levels. Note that this is resolution within a given sample: z-pitch (resolution_z_value) is the increment distance between image slices, ie. the microscope stage is moved up or down in increments to capture images of several focal planes. Leave blank if not applicable. | Shared by all clinical imaging assays |   | False |   |   | number |   |   |
+| resolution_z_unit | The unit of incremental distance between image slices.(um) Leave blank if not applicable. | Shared by all clinical imaging assays | nm, um, or mm | False |   | resolution_z_value present |   |   |   |
+| pixel_size_z_value | Depth value of the pixel or voxel measurement (distinct from the image resolution_z_value). Leave blank if not applicable. | Shared by all clinical imaging assays |   | False |   |   | number |   |   |
+| pixel_size_z_unit | Depth unit of the pixel or voxel measurement. Leave blank if not applicable. | Shared by all clinical imaging assays | nm, um, or mm | False |   | pixel_size_z_value present |   |   |   |
+| number_of_images | The total number of images in the dataset. | Shared by all clinical imaging assays |   | True |   |   | integer |   |   |
+| contributors_path | Relative path to file with ORCID IDs for contributors for this dataset. | Unique to this type |   | True |   |   |   |   |   |
+| data_path | Relative path to file or directory with instrument data. Downstream processing will depend on filename extension conventions. | Unique to this type |   | True |   |   |   |   |   |