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Schematic + Data Curator App Workflow Notes

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Repository

https://github.com/Sage-Bionetworks/schematic

Install

Schematic will run on Python 3.10. We must control the Pytheon Environment. PyEnv is one option., https://fathomtech.io/blog/python-environments-with-pyenv-and-vitualenv/ 

pyenv install 3.10.11
pyenv virtualenv 3.10.11 schematic_3_10_11
pyenv activate schematic_3_10_11
pyenv -m pip install schematic_3_10_11
pip install schematicpy

Create a data model formatted as a CSV

Where is the reference to how data model needs to be formatted?

Convert data model from CSV to JSONLD

schematic schema convert input.csv output.jsonld

AD Data Models https://github.com/adknowledgeportal/data-models
DCA app development version

https://dca-dev.app.sagebionetworks.org/
Abby's request for testing

https://sagebionetworks.slack.com/archives/C02A2FBN3G8/p1682116574295509

https://github.com/adknowledgeportal/test-data-model/blob/main/model-ad/model-ad.data.model.jsonld

https://sagebio.shinyapps.io/adknowledgeportal-data-curator/
https://www.synapse.org/#!Synapse:syn33582398/wiki/619343
https://github.com/adknowledgeportal/data_curator
https://github.com/adknowledgeportal/test-data-model

Annotate study folder with contentType = 'dataset'

https://www.synapse.org/#!Synapse:syn36759435/tables/
Add CSV + JSONLD to github – test-data-model

https://github.com/adknowledgeportal/test-data-model
https://github.com/adknowledgeportal/data_curator/blob/18dc00723f2e95a98525ff695401ac67e7785475/schematic_config.yml#L31
Data Model Validation Rules

/wiki/spaces/SCHEM/pages/2645262364


RegEx - extract individual and specimen ID from filenames

Data Model

  • https://github.com/Sage-Bionetworks/1kD-model

  • /wiki/spaces/SCHEM/pages/2473623559

  • OWL Tutorial

  • https://schema.org/

  • https://linkml.io/linkml/

  • https://learnxinyminutes.com/docs/yaml/

  • https://json-ld.org/

  • http://vowl.visualdataweb.org/webvowl.html

  • https://medium.com/wallscope/understanding-linked-data-formats-rdf-xml-vs-turtle-vs-n-triples-eb931dbe9827

  • https://webprotege.stanford.edu/#projects/cb219a51-dd90-4921-bec4-c836bd96f680/edit/Properties?selection=ObjectProperty(%3Chttp://example.com/BallpointPenOntology/hasCharacteristic%3E)

  • https://sagebionetworks.jira.com/wiki/spaces/CDC

ELITE

Upload Data

https://dca-docs.scrollhelp.site/DCA/Working-version/Project-Agnostic/organize-your-data-upload#OrganizeyourDataUpload-FlattenedDataLayoutExample

https://dca-docs.scrollhelp.site/DCA/Working-version/Project-Agnostic/uploading-data

https://dca-docs.scrollhelp.site/DCA/Working-version/ELITE/validate-and-submit-your-metadata

ELITE

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