Machine Annotation Service Resources

This page contains an assortment of resources to help explain the structure and relationship of the Machine Annotation object.

Latimer Core Resources

This page contains an assortment of resources to help facilitate activities associated with the Latimer Core standard.

SSSOM

SKOS Mappings metadata elements based on Simple Standard for Sharing Ontological Mappings (SSSOM)

DiSSCo has developed three SSSOM mappings to other data standards: DwC-A, ABCD(EFG), DwC-DP. For each of these there is a tsv available for the 0.4.0 version of the Digital Specimen and Digital Media object. The basis for this mapping is the logic developed in the DiSSCo Translator.

Darwin Core Archive: https://schemas.dissco.tech/schemas/data-mapping/0.4.0/sssom_dwca.tsv
Access to Biological Collection Data (ABCD) + Extension for Geosciences (EFG) : https://schemas.dissco.tech/schemas/data-mapping/0.4.0/sssom_abcdefg.tsv
Darwin Core Data Package: https://schemas.dissco.tech/schemas/data-mapping/0.4.0/sssom_dwc_dp.tsv

More information on the SSSOM standard can be found here:

Specification: https://mapping-commons.github.io/sssom/
Repository: https://github.com/mapping-commons/sssom
Citation: Nicolas Matentzoglu, James P Balhoff, Susan M Bello, Chris Bizon, Matthew Brush, Tiffany J Callahan, Christopher G Chute, William D Duncan, Chris T Evelo, Davera Gabriel, John Graybeal, Alasdair Gray, Benjamin M Gyori, Melissa Haendel, Henriette Harmse, Nomi L Harris, Ian Harrow, Harshad B Hegde, Amelia L Hoyt, Charles T Hoyt, Dazhi Jiao, Ernesto Jiménez-Ruiz, Simon Jupp, Hyeongsik Kim, Sebastian Koehler, Thomas Liener, Qinqin Long, James Malone, James A McLaughlin, Julie A McMurry, Sierra Moxon, Monica C Munoz-Torres, David Osumi-Sutherland, James A Overton, Bjoern Peters, Tim Putman, Núria Queralt-Rosinach, Kent Shefchek, Harold Solbrig, Anne Thessen, Tania Tudorache, Nicole Vasilevsky, Alex H Wagner, Christopher J Mungall, A Simple Standard for Sharing Ontological Mappings (SSSOM), Database, Volume 2022, 2022, baac035, https://doi.org/10.1093/database/baac035

Diagrams

Class Diagrams

                            classDiagram
 class MachineAnnotationService { 
   schema:identifier : string 
   ods:fdoType : string 
   ods:status : string 
   schema:version : integer 
   schema:name : string 
   schema:description : string 
   schema:dateCreated : string 
   schema:dateModified : string 
   schema:creator : object 
   ods:containerImage : string 
   ods:containerTag : string 
   ods:hasTargetDigitalObjectFilter : object 
   schema:creativeWorkStatus : string 
   schema:codeRepository : string 
   schema:programmingLanguage : string 
   ods:serviceAvailability : string 
   schema:maintainer : object 
   schema:license : string 
   ods:slaDocumentation : string 
   ods:topicName : string 
   ods:maxReplicas : integer 
   ods:batchingPermitted : boolean 
   ods:timeToLive : integer 
   ods:hasTombstoneMetadata : object 
   ods:hasEnvironmentalVariables : array<ods:EnvironmentalVariable> 
   ods:hasSecretVariables : array<ods:SecretVariable> 
   ods:isIngestionCompatible : boolean 
 }
 class schema:ContactPoint { 
   schema:description : string 
   schema:email : string 
   schema:url : string 
   schema:telephone : string 
 }
 class TombstoneMetadata { 
   ods:tombstoneDate : string 
   ods:tombstoneText : string 
   ods:hasAgents : array<ods:Agent> 
   ods:hasRelatedPIDs : array<ods:RelatedPID> 
 }
 class RelatedPID { 
   dcterms:identifier : string 
   schema:identifier : string 
   ods:relationshipType : string 
 }
 class Agent { 
   schema:identifier : string 
   schema:name : string 
   ods:hasRoles : array<ods:Role> 
   schema:email : string 
   schema:url : string 
   ods:hasIdentifiers : array<ods:Identifier> 
 }
 class Role { 
   schema:roleName : string 
   schema:startDate : string 
   schema:endDate : string 
   schema:position : integer 
 }
 class SecretVariable { 
   schema:name : string 
   ods:secretKeyRef : string 
 }
 class EnvironmentalVariable { 
   schema:name : string 
   schema:value : ['string', 'integer', 'boolean'] 
 }
 class Identifier { 
   dcterms:title : string 
   dcterms:type : string 
   dcterms:identifier : string 
   dcterms:format : array<string> 
   dcterms:subject : array<string> 
   ods:isPartOfLabel : boolean 
   ods:gupriLevel : string 
   ods:identifierStatus : string 
 }
MachineAnnotationService -- ContactPoint
MachineAnnotationService -- TombstoneMetadata
TombstoneMetadata -- RelatedPID
MachineAnnotationService -- Agent
Agent -- Role
TombstoneMetadata -- Agent
MachineAnnotationService -- SecretVariable
MachineAnnotationService -- EnvironmentalVariable

Entity-Relationship Diagrams

                            erDiagram
    MachineAnnotationService ||--o{ ContactPoint : Has
    MachineAnnotationService ||--o| TombstoneMetadata : Has
    TombstoneMetadata ||--o{ RelatedPID : Has
    MachineAnnotationService ||--|{ Agent : Has
    Agent ||--|{ Role : Has
    TombstoneMetadata ||--|{ Agent : Has
    MachineAnnotationService ||--o{ SecretVariable : Has
    MachineAnnotationService ||--o{ EnvironmentalVariable : Has

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