-
Notifications
You must be signed in to change notification settings - Fork 6
New issue
Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.
By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.
Already on GitHub? Sign in to your account
Schema revision v2 for BCDC project inventory #35
base: master
Are you sure you want to change the base?
Conversation
View | ||
} | ||
|
||
enum AccessControl { |
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.
In the omics data management meeting last week, scientists asked to have the listing of the conditions for accessing controlled access data available before they go to NDA. We don't have a field for this yet, would be good to add. There are codes for this, but also need free text fields to describe, such as "For the study of the Brain in Health and Disease" which is the requirement for data from one of our tissue providers.
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.
Added an 'accessControlCode' class linked to data collections, and a free text field 'accessControlDescription' to data collection.
} | ||
|
||
enum CompletionState { | ||
Complete |
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.
There are additional states for triple store ingest and validation, do we want yto incorporate them here as well?
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.
Triple store ingest/validation states apply to individual uploads, and we can have multiple uploads per data collection/multiple data collections per upload. We do have an association table for uploads/data collections, but that is outside of this schema.
design/schema/bcdc.puml
Outdated
|
||
class WebResource { | ||
* id: String! | ||
handle: String! |
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.
what is handle? This doesn't seem like a typical field name. Should be webresource "name" maybe?
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.
Changed handle to name
design/schema/bcdc.puml
Outdated
class Project { | ||
* id: String! | ||
doi: String | ||
handle: String! |
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.
change handle to name?
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.
Changed handle to name
class License { | ||
* id: String! | ||
handle: String | ||
name: String! |
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.
what is the name vs the handle here?
class Technique { | ||
* id: String! | ||
handle: String | ||
name: String! |
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.
would like to begin adding on a field to link to ontology
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.
Added ontology id field to technique, modality and specimenType
design/schema/bcdc.puml
Outdated
|
||
class Contact { | ||
* id: String! | ||
name: String! |
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.
how does this interact with person?
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.
This was polymorphic, with contact being either an organization or person. Updated to be a direct link to Person, with a circle for contact for readability.
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.
Thanks, @kasbaker!
@kasbaker - I'm comparing the BCDC model to DANDI. Many fields are pretty easy to compare, but there are some that I'm not completely sure if I understand correctly (e.g. |
|
externalId: String | ||
dataArchive: Organization | ||
bkpWebResource: [WebResource]! | ||
dataArchive: [Organization]! |
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.
repetition, see l.102
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.
I think generally looks good from a bossdb perpsective, highlighted a couple additional existing connections between the metadata of bossdb if helpful.
Project.handle,,,, | ||
Project.highlightedWebResource,,,,Project.Links | ||
Project.informationWebResource,,,, | ||
Project.modality,,,,Project.ImagingModalities/Specific |
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.
For bossdb, this is a possible link!
Collection.modality->project.imagingmodalities (a project could be multi-modal in bossdb)
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.
Added, thank you!
design/schema/mappings.csv
Outdated
Project.highlightedWebResource,,,,Project.Links | ||
Project.informationWebResource,,,, | ||
Project.modality,,,,Project.ImagingModalities/Specific | ||
Project.protocol,Dataset.Methods,Dandiset.protocol,BDBag.ProtocolID, |
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.
For bossdb, this is a possible link!
project.protocol->experiment.protocol
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.
Added, thank you!
Planned revisions version 2 for BCDC data model.
Changes: