Schema revision v2 for BCDC project inventory #35
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| @startuml | ||
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| hide empty members | ||
| 'hide circle | ||
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| 'Enums | ||
| enum WebResourceType { | ||
| Download | ||
| Information | ||
| Explore | ||
| View | ||
| } | ||
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| enum AccessControl { | ||
| Open | ||
| Embargoed | ||
| Controlled | ||
| } | ||
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| enum CompletionState { | ||
| Complete | ||
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There was a problem hiding this comment. 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. 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. |
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| InProgress | ||
| } | ||
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| enum AgentType { | ||
| Person | ||
| Organization | ||
| } | ||
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| 'Entity-like | ||
| class Agent { | ||
| * id: String! | ||
| agent_id: String! | ||
| agentType: AgentType | ||
| organization: Organization | ||
| person: Person | ||
| type: AgentType! | ||
| } | ||
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| class Modality { | ||
| * id: String! | ||
| name: String! | ||
| handle: String | ||
| } | ||
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| class SpecimenType { | ||
| * id: String! | ||
| name: String! | ||
| handle: String | ||
| } | ||
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| class WebResource { | ||
| * id: String! | ||
| handle: String! | ||
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There was a problem hiding this comment. what is handle? This doesn't seem like a typical field name. Should be webresource "name" maybe? There was a problem hiding this comment. Changed handle to name |
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| title: String! | ||
| shortTitle: String! | ||
| url: String! | ||
| rrid: String | ||
| } | ||
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| class Project { | ||
| * id: String! | ||
| doi: String | ||
| handle: String! | ||
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There was a problem hiding this comment. Changed handle to name |
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| title: String! | ||
| shortTitle: String! | ||
| description: String! | ||
| bkpWebResource: WebResource! | ||
| informationWebResource: WebResource | ||
| subprogram: [Subprogram]! | ||
| technique: [Technique]! | ||
| collection: [Collection]! | ||
| specimenType: [SpecimenType]! | ||
| contact: Contact | ||
| creator: [Agent]! | ||
| fundingSource: [Award]! | ||
| contributor: [Agent] | ||
| highlightedWebResource: [WebResource] | ||
| protocol: [Protocol] | ||
| dataArchive: [Organization] | ||
| externalId: String | ||
| species: [Species]! | ||
| modality: [Modality]! | ||
| publication: [Publication] | ||
| dateModified: Date | ||
| dateCreated: Date! | ||
| } | ||
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| class Collection { | ||
| * id: String! | ||
| handle: String! | ||
| title: String! | ||
| shortTitle: String! | ||
| description: String! | ||
| doi: String | ||
| rrid: String | ||
| citation: String | ||
| externalId: String | ||
| dataArchive: Organization | ||
| bkpWebResource: [WebResource]! | ||
| dataArchive: [Organization]! | ||
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| species: [Species]! | ||
| specimenCount: [SpecimenCount]! | ||
| license: License! | ||
| accessControl: AccessControl! | ||
| completionState: CompletionState! | ||
| modality: [Modality]! | ||
| technique: [Technique]! | ||
| webResource: [WebResource] | ||
| dateModified: Date | ||
| dateCreated: Date! | ||
| } | ||
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| class Subprogram { | ||
| * id: String! | ||
| doi: String | ||
| handle: String! | ||
| title: String! | ||
| shortTitle: String! | ||
| description: String! | ||
| bkpWebResource: WebResource | ||
| program: Program! | ||
| informationWebResource: WebResource | ||
| } | ||
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| class Program { | ||
| * id: String! | ||
| doi: String | ||
| handle: String! | ||
| title: String! | ||
| shortTitle: String! | ||
| description: String! | ||
| bkpWebResource: WebResource | ||
| informationWebResource: WebResource | ||
| } | ||
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| class Protocol { | ||
| * id: String! | ||
| handle: String | ||
| title: String! | ||
| shortTitle: String! | ||
| webResource: WebResource! | ||
| } | ||
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| class Person { | ||
| * id: String! | ||
| name: String! | ||
| givenName: String! | ||
| familyName: String! | ||
| handle: String | ||
| orcid: String | ||
| } | ||
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| class Organization { | ||
| * id: String | ||
| name: String! | ||
| handle: String! | ||
| ror: String | ||
| webResource: WebResource | ||
| contact: Contact | ||
| } | ||
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| class License { | ||
| * id: String! | ||
| handle: String | ||
| name: String! | ||
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There was a problem hiding this comment. what is the name vs the handle here? |
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| title: String! | ||
| shortTitle: String! | ||
| webResource: WebResource! | ||
| } | ||
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| class Award { | ||
| * id: String | ||
| name: String! | ||
| title: String! | ||
| identifier: String! | ||
| reportSymbol: String | ||
| funder: Agent! | ||
| awardee: [Agent]! | ||
| } | ||
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| class Technique { | ||
| * id: String! | ||
| handle: String | ||
| name: String! | ||
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There was a problem hiding this comment. would like to begin adding on a field to link to ontology There was a problem hiding this comment. Added ontology id field to technique, modality and specimenType |
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| } | ||
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| class Species { | ||
| * id: String! | ||
| name: String! | ||
| common_name: String! | ||
| scientific_name: String | ||
| ncbi_taxonomy_id: String! | ||
| rrid: String | ||
| } | ||
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| class SpecimenCount { | ||
| * id: String! | ||
| count: Int | ||
| specimenType: SpecimenType! | ||
| } | ||
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| class Contact { | ||
| * id: String! | ||
| name: String! | ||
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There was a problem hiding this comment. how does this interact with person? There was a problem hiding this comment. 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. |
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| email: String | ||
| } | ||
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| class Publication { | ||
| * id: String! | ||
| TBD | ||
| } | ||
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| circle webResource | ||
| webResource --> WebResource | ||
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| circle bkpWebResource | ||
| bkpWebResource --> WebResource | ||
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| circle informationWebResource | ||
| informationWebResource --> WebResource | ||
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| circle highlightedWebResource | ||
| highlightedWebResource --> WebResource | ||
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| circle contact | ||
| contact --> Contact | ||
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| circle dataArchive | ||
| dataArchive --> Organization | ||
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| circle specimenType | ||
| specimenType --> SpecimenType | ||
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| circle species | ||
| species --> Species | ||
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| circle technique | ||
| technique --> Technique | ||
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| circle modality | ||
| modality --> Modality | ||
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| 'Organization --o| Contact : contact | ||
| Organization --o| contact | ||
| Organization --o| webResource | ||
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| 'Relationships | ||
| Agent --o| Person : person | ||
| Agent --o| Organization : organization | ||
| Agent --|| AgentType : type | ||
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| 'SpecimenCount --|| SpecimenType : specimenType | ||
| SpecimenCount --|| specimenType | ||
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| WebResource --|| WebResourceType : type | ||
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| 'Technique --o{ Protocol : protocol | ||
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| Collection --|{ modality | ||
| Collection --|{ species | ||
| Collection --|{ SpecimenCount : specimenCount | ||
| Collection --|{ technique | ||
| Collection --|| AccessControl : accessControl | ||
| Collection --|| CompletionState : completionState | ||
| Collection --|| License : license | ||
| Collection --|{ bkpWebResource | ||
| 'Collection --|{ Organization : dataArchive | ||
| Collection --|{ dataArchive | ||
| Collection --o{ webResource | ||
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| Award --|| Agent : funder | ||
| Award --|{ Agent : awardee | ||
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| Contact --o| Agent: agent | ||
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| Project --|{ Collection : collection | ||
| Project --|{ Award : fundingSource | ||
| 'Project --o{ WebResource : highlightedWebResource | ||
| Project ---o{ highlightedWebResource | ||
| Project --|{ Agent : creator | ||
| Project --o{ Agent : contributor | ||
| 'Project --o{ Contact : contact | ||
| Project --o{ contact | ||
| 'Project --|{ SpecimenType : specimenType | ||
| Project --|{ specimenType | ||
| Project --|{ technique | ||
| Project --|{ Subprogram : subprogram | ||
| 'Project --o| webResource | ||
| Project --|| bkpWebResource | ||
| Project --o| informationWebResource | ||
| 'Project --|| webResource : bkpWebResource | ||
| 'Project --|> Program | ||
| Project --o{ Protocol : protocol | ||
| Project --|{ dataArchive | ||
| Project --|{ species | ||
| Project --|{ modality | ||
| Project --o{ Publication : publication | ||
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| Program --o| informationWebResource | ||
| Program --o| bkpWebResource | ||
| 'Program --o| webResource : bkpWebResource | ||
| 'Program --|| webResource : informationWebResource | ||
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| Subprogram --o| informationWebResource | ||
| Subprogram --|| Program : program | ||
| Subprogram --o| bkpWebResource | ||
| 'Subprogram --|> Program: program | ||
| 'Subprogram --o| webResource : bkpWebResource | ||
| 'Subprogram --|| webResource: informationWebResource | ||
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| Protocol --|| webResource | ||
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| License --|| webResource | ||
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| @enduml | ||
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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.
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Added an 'accessControlCode' class linked to data collections, and a free text field 'accessControlDescription' to data collection.