Added enzymatic tissue dissociation fields #1599
There are no files selected for viewing
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| Original file line number | Diff line number | Diff line change |
|---|---|---|
|
|
@@ -54,7 +54,56 @@ | |
| "type": "object", | ||
| "$ref": "module/process/purchased_reagents.json" | ||
| }, | ||
| "user_friendly": "Purchased reagents" | ||
| }, | ||
| "digestion_time": { | ||
| "description": "Time of digestion of the specimen.", | ||
| "type": "integer", | ||
| "example": "2; 5; 10", | ||
| "user_friendly": "Digestion time" | ||
| }, | ||
| "digestion_time_unit": { | ||
| "description": "The unit in which the digestion time is expressed.", | ||
| "type": "object", | ||
| "$ref": "module/ontology/time_unit_ontology.json", | ||
| "user_friendly": "Digestion time unit" | ||
| }, | ||
| "digestion_temperature": { | ||
| "description": "Temperature of digestion in Celsius or in general terms (i.e. cold, warm, room temperature).", | ||
| "pattern": "^(\\d+(\\.\\d+)?|frozen|cold|room temperature|warm)$", | ||
| "type": "string", | ||
| "example": "4; 37; cold", | ||
| "user_friendly": "Digestion temperature" | ||
| }, | ||
| "digestion_solution": { | ||
| "description": "Enzyme(s) or reagent(s) of the solution that was used for the digestion of the specimen.", | ||
| "type": "array", | ||
| "items": { | ||
| "type": "string", | ||
| "enum": [ | ||
| "Citric-acid based", | ||
| "Detergent-based", | ||
| "Lysis buffer", | ||
| "Accutase", | ||
| "Collagenase", | ||
| "Collagenase A", | ||
| "Collagenase D", | ||
| "Collagenase I", | ||
| "Collagenase II", | ||
| "Collagenase IV", | ||
| "Dispase", | ||
| "Dispase II", | ||
| "DNAse I", | ||
| "Elastase", | ||
| "Hyaluronidase", | ||
| "Liberase", | ||
| "Papain", | ||
| "Protease", | ||
| "TrypLE", | ||
| "Trypsin" | ||
| ] | ||
|
There was a problem hiding this comment. This bracket seems misaligned. There was a problem hiding this comment. Thanks for pointing that out, fixed in 0944f6e |
||
| }, | ||
| "user_friendly": "Digestion solution" | ||
| } | ||
| } | ||
| } | ||
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1 +1,6 @@ | ||
| Schema,Change type,Change message,Version,Date | ||
| type/protocol/biomaterial_collection/dissociation_protocol,minor,Changed user_friendly name of reagent field,, | ||
| type/protocol/biomaterial_collection/dissociation_protocol,minor,Added optional digestion_time field,, | ||
| type/protocol/biomaterial_collection/dissociation_protocol,minor,Added optional digestion_time_unit field,, | ||
| type/protocol/biomaterial_collection/dissociation_protocol,minor,Added optional digestion_temperature field,, | ||
| type/protocol/biomaterial_collection/dissociation_protocol,minor,Added optional digestion_solution field,, |
Oops, something went wrong.
Add this suggestion to a batch that can be applied as a single commit.
This suggestion is invalid because no changes were made to the code.
Suggestions cannot be applied while the pull request is closed.
Suggestions cannot be applied while viewing a subset of changes.
Only one suggestion per line can be applied in a batch.
Add this suggestion to a batch that can be applied as a single commit.
Applying suggestions on deleted lines is not supported.
You must change the existing code in this line in order to create a valid suggestion.
Outdated suggestions cannot be applied.
This suggestion has been applied or marked resolved.
Suggestions cannot be applied from pending reviews.
Suggestions cannot be applied on multi-line comments.
Suggestions cannot be applied while the pull request is queued to merge.
Suggestion cannot be applied right now. Please check back later.
There was a problem hiding this comment.
Choose a reason for hiding this comment
The reason will be displayed to describe this comment to others. Learn more.
The number pattern matches non-sensical strings such as 00000000021.210000000000. Consider a union (
anyOf) ofnumberandenum.Then again, instead of allowing the subjective English terms, you could just allow for a range. That might be more elegant and easier to process for consumers.
There was a problem hiding this comment.
Choose a reason for hiding this comment
The reason will be displayed to describe this comment to others. Learn more.
Thank you for your comment, I agree on using range instead of words however, the Lung bionetwork insisted on using words to record this, as they used in the published version 1 of their atlas.
I've added the solution with the union of types in 0944f6e .