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Example Model
https://github.com/Sage-Bionetworks/schematic/blob/develop/tests/data/example.model.csv
Formatted for readability:
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Schematic DB
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Documentation
/wiki/spaces/SCHEM/pages/2473623559
Recommendations.
Draw a diagram for data modelLucid. app - can Can use templates like ERD example in an app like Lucid
Start small - skeleton --> schema
Schema visualization tools?
with a basic skeleton and then build the schema
Diagram is a Useful reference when building
Start from single table
Use schematic in dev mode to convert model to JSON-LD regularly to check for errors
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Attribute
Description
ValidValues
DependsOn
required
source
parent
properties
dependsOnComponent
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Example Model
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https://github.com/Sage-Bionetworks/schematic/blob/develop/tests/data/example.model.csv
Formatted for readability:
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Schematic dev mode helps find and deal with erors by iteratively checking JSON-LD
Generate JSON-LDF LD from CSV:
schematic schema convert data_model.csv
`schematic model --config config.hyml submit --manifest_path manifest.csv --datset_id synId -- manifest_record_type table
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Data Model Validation
/wiki/spaces/SCHEM/pages/2645262364
Ontology
Data Model Visualization
https://linkml.io/linkml/intro/tutorial.html
https://docs.google.com/spreadsheets/d/1vDdcqt3Lgehyq1iCnlF1H9JZi63pLj-u/edit#gid=1939820452
https://portal.includedcc.org/dashboard
https://linkml.io/schemasheets/#examples
https://docs.google.com/spreadsheets/d/1w6zDfz3_yrCjjrqfpXBGNmd0LZL4B03gr1KfzJtk5Cs/edit#gid=674286209
https://docs.google.com/presentation/d/129pSx58qDm7Y1OQmSSHKDq6tsoD3pW_gDRNXiX2rd0w/edit#slide=id.g4d21a8c2ba_0_11
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Manifest - metadata table submitted for datasets
JSON for Linking Data
JSON-LD
Data models are defined in https://www.json.org/json-en.html . Specifically, JSON-LinkedDirectory (JSON-LD) files.
https://cambridgesemantics.com/blog/semantic-university/learn-rdf/rdf-nuts-bolts-2/
One reason we use JSON-LD in schematic is its support by http://schema.org : https://schema.org/
And a reason for http://schema.org is dataset discoverability: https://datasetsearch.research.google.com/
JSON-LD useful for search engines (http://schema.org )
for anyone who wants to learn more about "linked data”, reading about ideas related to "semantic web" can be a fun rabbit hole to go down…w3 stds
Error Troubleshooting
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SchemaHub Documentation on Confluence. This includes definitions of data model like validation rules
Github Tickets Sage-Bionetworks/schematic
Add ticket workflow
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blah: [e.g. chrome, safari]
ca
Create a data model formatted as a CSV
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/wiki/spaces/SCHEM/pages/2645262364 RegEx -
Regular Expression Search of Filenames
extract individual and specimen ID from filenames
Data Model
Lref gdrive file url https://docs.google.com/document/d/1nZGLRKW5LXpY-LBrtrgs4MyO-fb0kDDeouEOvW36xo0/edit#heading=h.o7ihd22lafi
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