JGI Scientific Data Management Metadata

Scientific Data Management (SDM) metadata database for JGI. Manages analysis workflows, file metadata, NCBI submissions, and data publishing. DATABASE: sdm dev mongo.sdm_metadata_dev TABLES: 33 KEY FUNCTIONALITY: - Analysis workflow management - File and data store tracking - NCBI/SRA submission management - Metadata templates and macros - Publishing flag management

URI: https://w3id.org/jgi/sdm_metadata

Name: sdm_metadata

Classes

Class	Description
Analysis	Analysis workflow or pipeline run
AnalysisCallerWarnings	Warnings from analysis callers/tools
AnalysisMacro	Macro definitions for analysis workflows
AnalysisPlocations	Physical locations for analysis data
AnalysisPublishingFlags	Publishing status flags for analyses
AnalysisTagTemplate	Tag template for analysis categorization
AnalysisTemplate	Template defining an analysis workflow
DataStore	Data storage location
DeletedAnalysis	Record of deleted analyses
DeletedFile	Record of deleted files
Email	Email notification record
File	File metadata record
FileIngest	File ingestion record
Macro	Reusable macro for workflows
Metadata	Generic metadata record
MetadataRefresh	Metadata refresh/update record
NcbiSubmission	NCBI submission record
NcbiTaxon	NCBI taxonomy reference
NcbiWorker	NCBI submission worker process
ProcessService	Process service configuration
Publication	Publication linked to data
Query	Saved query
Service	SDM service definition
SraSubmission	SRA (Sequence Read Archive) submission
SraUnsubmittable	Records that cannot be submitted to SRA
Subscription	Data subscription
SubscriptionJira	Jira ticket linked to subscription
Template	Generic template
User	SDM user

Slots

Slot	Description
analysis_id
checksum
data_store_id
definition
deleted_time
description
doi
email
file_id
id	Analysis identifier
ingest_time
is_public
jira_id
key
location
macro_id
name
original_analysis_id
original_file_id
path
pmid
published_date
query_text
reason
recipient
refresh_time
sent_time
service_id
size
sra_id
status
subject
submission_id
taxon_id
template_id
user_id
username
value
warning_message

Enumerations

Enumeration	Description

Types

Type	Description
Boolean	A binary (true or false) value
Curie	a compact URI
Date	a date (year, month and day) in an idealized calendar
DateOrDatetime	Either a date or a datetime
Datetime	The combination of a date and time
Decimal	A real number with arbitrary precision that conforms to the xsd:decimal speci...
Double	A real number that conforms to the xsd:double specification
Float	A real number that conforms to the xsd:float specification
Integer	An integer
Jsonpath	A string encoding a JSON Path
Jsonpointer	A string encoding a JSON Pointer
Ncname	Prefix part of CURIE
Nodeidentifier	A URI, CURIE or BNODE that represents a node in a model
Objectidentifier	A URI or CURIE that represents an object in the model
Sparqlpath	A string encoding a SPARQL Property Path
String	A character string
Time	A time object represents a (local) time of day, independent of any particular...
Uri	a complete URI
Uriorcurie	a URI or a CURIE

Subsets

Subset	Description