12-25 Curation Workflow Tracking

[aditya-nath-sage]

This ticket tracks curation workflow progression.

Curation and Annotation

• Run Pubmed crawler to generate PublicationView manifest

• 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]

• Work through a number of the backlog of old restricted access pubs that have become open access (and list how many have been done out of how many remaining)

• 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

• Dataset Upload

• Tool Upload

[aditya-nath-sage]

New publication manifests generated for curation (for these two months and backlog):

Nov-Dec: https://docs.google.com/spreadsheets/d/1XNA7iitIx6Mbh-lDA90wMoF0DANUXbuiabXLFyn8uCU/edit?usp=drive_link (total of 31 new pubs)

Backlog: https://docs.google.com/spreadsheets/d/1VaCPESb5mWN_ipGXIw9kIyjrrEpKwN8iURrs5_Lucx8/edit?usp=drive_link (total of 238)

[aclayton555]

@aditya-nath-sage please update. thanks!

[aditya-nath-sage]

Publication, Dataset, and Tools manifest for this month manually curated!

Pubs: https://docs.google.com/spreadsheets/d/1XNA7iitIx6Mbh-lDA90wMoF0DANUXbuiabXLFyn8uCU/edit?usp=sharing
Datasets: https://docs.google.com/spreadsheets/d/1rKjp6lriW4gTCvlR8FSkdtoApa8ibb-v98-vovxFkiU/edit?usp=sharing
Tools: https://docs.google.com/spreadsheets/d/1TdnV02oXWLzmhQS3hkfjqb8cDF94RsDkyKOkE_m3f08/edit?usp=sharing