[July - Sep] Dataset Curation Workflow Tracking

[aditigopalan]

This ticket tracks curation workflow progression.

Note: It is possible for work to take place simultaneously in the three sections with overlapping periods, allowing curation workflows for different months to coincide.

1. Curation and Annotation

• Run Pubmed crawler to generate PublicationView manifest [205 publications generated, long sprint anticipated]
• Send Amber and Jineta a copy of the PublicationView manifest from latest crawl to review for MC2 Center Newsletter publication highlights
• Send Amber "News from CCKP" for MC2 Center Newsletter
• Annotate publications in PublicationView manifest [In progress]
• Generate ToolView and DatasetView manifests based on PublicationView manifest
• Run the automated curation workflow to upload publications, datasets and tools [This includes splitting manifests, processing and validating manifests, generating target synapse IDs for upload, schema updates, upload to synapse and (in progress) a validation check for uploads)
• Generate UNION tables
• QC of staging tables
• Performing automate portal sync to CCKP
• Validate data on the CCKP

Status check [Plan to report numbers for each category following pubmed crawl]:

• Publication upload [ ]
• Tool upload [ ]
• Data set upload [ ]

2. Data model

• Update valid values in the data model and build
• Generate templates from new model
• Release new model version [no changes, no release]
• Update DCA config [no changes, no update]

3. Contributor Engagement

• Emails to contributors (by grant) with info on newly added manifests, link to project, DCA, and instructions on review, annotation, validation, and submission, as applicable
• Jira Help Desk ticket tracking, review, triage, with data model updates, as needed (TBD)
• Annotation gap-filling of DatasetView and ToolView manifests