add Protocol-definition.yml #8
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| description: Whether a viral vector was removed after induction | ||
| type: boolean | ||
| format: boolean | ||
| options: |
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@ishitasati11 Use enum instead of options to specify list of possible values.
https://swagger.io/docs/specification/data-models/enums/
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Also values should be without quotes
| description: Whether tiles were collected with overlap | ||
| type: boolean | ||
| format: boolean | ||
| options: |
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@ishitasati11 Use enum
| minimum_size: | ||
| description: Minimum cell or organelle size passing selection, in microns | ||
| type: integer | ||
| format: "\xB5m" |
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@ishitasati11 If a given attribute is encoded please specify the type in an additional encoding property.
https://metacpan.org/pod/Unicode::String#$us-%3Eutf8(-$newval-).
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@ishitasati11 What i understand is that if you are using the format property then it should specify the format of the value it stores and not the unit of measurement. Generally, for this you can store it in a property simply called uom and then specify the encoding.
minimum_size:
description: Minimum cell or organelle size passing selection, in microns
type: integer
format: numeric
units:
description: Unit is a quantity of constant magnitude which is used to measure the magnitudes of
other quantities of the same manner
uom: "\xB5m"
encoding: UTF-8
| maximum_size: | ||
| description: Maximum cell or organelle size passing selection, in microns | ||
| type: integer | ||
| format: "\xB5m" |
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@ishitasati11 Same as above
| pixel_size: | ||
| description: Pixel size in nanometers | ||
| type: integer | ||
| format: nm |
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@ishitasati11 Let's separate format from unit of measurement wherever applicable
| description: Information about each channel used in the imaging protocol | ||
| type: array | ||
| format: text | ||
| ontology_link: https://bioportal.bioontology.org/ontologies/BAO?p=classes&conceptid=http%3A%2F%2Fwww.bioassayontology.org%2Fbao%23BAO_0000459 |
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This ontology link redirects to the label scanning probe microscopy. Not sure how is this relevant to channel attribute
| type: integer | ||
| format: number | ||
| tile_size_y: | ||
| description: ' Y size of the tile in micrometers' |
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@ishitasati11 Remove single quotes
| computational_method: | ||
| description: A URL to a versioned workflow and versioned execution environment | ||
| type: string | ||
| format: text |
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@ishitasati11 format for storing a URL
format: alphanumeric
| description: Core protocol-level information | ||
| type: string | ||
| format: text | ||
| computational_method: |
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@ishitasati11 Are we only storing URL here?
A suggestion would be to store the URL as a subproperty of this attribute in url.
| format: text | ||
| ontology_link: https://bioportal.bioontology.org/ontologies/ATOM?p=classes&conceptid=http%3A%2F%2Furi.interlex.org%2Ftgbugs%2Furis%2Freadable%2Fatlas%2FTransformationMatrix | ||
| bioinformatics_software: | ||
| description: Name of software used |
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@ishitasati11 This property stores the description of the attribute and not the value it stores. So the description could be something like
A wide array of computer programs and tools designed to manage, analyze, and interpret biological data.
| format: text | ||
| ontology_link: https://bioportal.bioontology.org/ontologies/NGBO?p=classes&conceptid=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FNGBO_6000410 | ||
| bioinformatics_software_version: | ||
| description: Version of software used |
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@ishitasati11 Same as above
|
@ishitasati11 Please revisit the |
| expansion_factor: | ||
| description: Factor by which the imaged tissue was expanded in one dimension | ||
| type: integer | ||
| format: number |
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@ishitasati11 format: numeric
Please change wherever applicable
Added new YAML for Protocol