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Schematic

Glossary

Manifest - metadata table submitted for datasets

Summary

This page describes the workflow required to build, edit, and update the data model for MODEL-AD.

Table of Contents
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Schematic

Summary

Data Modeling at Sage requires using two in-house tools: Schematic and the Data Curator App (DCA). SCHEMATIC is an acronym for Schema Engine for Manifest Ingress and Curation. The Python based infrastructure provides tool is a novel schema-based, metadata ingress ecosystem, that is meant intended to streamline the process of biomedical dataset annotation, metadata validation and submission to a data repository for various data contributors.

Documentation

/wiki/spaces/SCHEM/pages/2967568387

Code in Github

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

Installation

https://pypi.org/project/schematicpy/

Install for data curator app:

Code Block
python3 -m venv .venv
source .venv/bin/activate
python3 -m pip install schematicpy

Setup Python Environment

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

Code Block
pyenv install 3.10.1110
pyenv virtualenv 3.10.1110 schematicpy_3_10_1110
pyenv activate schematicpy_3_10_11
pyenv -m pip install schematic_3_10_11
pip install schematicpy

Edit Configuration

The following parameters need to be set in the config.yml

https://github.com/Sage-Bionetworks/schematic/blob/develop/config.yml

Using Schematic

Command Line Reference

https://sage-schematic.readthedocs.io/en/develop/cli_reference.html

Need to run commands from ~/schematic

Data Model

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Development

A data model defines attributes (i.e. data elements) describing metadata associated with any given dataset type. The data model also describes relationships between these attributes.

Documentation

/wiki/spaces/SCHEM/pages/2473623559

Build a Data Model

The data model is defined in a table, then stored (i.e. serialized) in a JSON-LD schema.

The JSON-LD schema follows the specifications from Schema.org for attributes.

https://sagebionetworks.jira.com/wiki/spaces/SCHEM/pages/2473623559/The+Data+Model+Schema#A.-Schema-properties-and-relationships

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Create Data Model

https://sagebionetworks.jira.com/wiki/spaces/SCHEM/pages/

...

2967568387/Guide+How+to+use+Schematic+for+Data+Model+

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Development#Create-

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a-

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Data-

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Schematic DB is a package used to ingress the manifests created by Schematic into a database.

  • Schematic DB will use any of these validation rules:

    • str

    • float

    • num

    • int

    • date

    • If the attribute has none of the above rules it use a string type

    • the attribute datatype will be determined based on the rule

Build a Data Model

Model

The data model is defined in a table, then stored (i.e. serialized) in a JSON-LD schema which specifies attributes as suggested by Schema.org.

/wiki/spaces/SCHEM/pages/2473623559

https://docs.google.com/presentation/d/129pSx58qDm7Y1OQmSSHKDq6tsoD3pW_gDRNXiX2rd0w/edit#slide=id.g13aaf3b8358_0_0

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Documentationhttps:/wiki/spacesgithub.com/SCHEM/pages/2473623559

Recommendations

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Draw a diagram for data model

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Lucid.app - can use templates like ERD example

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Start small - skeleton --> schema

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Schema visualization tools?

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Useful reference when building

adknowledgeportal/data-models

Sage Data Models for Reference

Recommendations

  • Draw a diagram. A diagram is a useful reference when developing the model.

  • Start small with a basic skeleton and then build.

  • Use schematic in dev mode to convert model to JSON-LD regularly to check for errors

...

Requirements

The data model requires these columns:

  1. Attribute

  2. Description

  3. ValidValues

  4. DependsOn

  5. required

  6. source

  7. parent

  8. properties

  9. dependsOnComponent

Data Model Validation

/wiki/spaces/SCHEM/pages/2645262364

Example Model

This model does NOT validate as provided.

Schematic DB

https://

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sagebionetworks.

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Namespace collisions - should use "Biothings" schema

graph modeling requires unique names. some protected names too. no underscores.

Schematic dev mode helps find and deal with erors by iteratively checking JSON-LD

Generate JSON-LDF 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

command line reference

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

/jira.com/wiki/spaces/SCHEM/pages/2473623559/The+Data+Model+Schema#Schemas-and-Schematic-DB

Schematic DB is a package used to ingress the manifests created by Schematic into a database.

  • Schematic DB will use any of these validation rules:

    • str, float, num, int, date

    • If no rule provided, defaults to a string type

    • the attribute datatype is based on the rule

Data Model Validation

/wiki/spaces/SCHEM/pages/2645262364

Data Model Visualization

Convert Data Model from CSV to JSON-LD

https://sagebionetworks.jira.com/wiki/spaces/SCHEM/pages/

...

/wiki/spaces/SCHEM/pages/2458419217

JSON for Linking Data JSON-LD

...

2967568387/Guide+How+to+use+Schematic+for+Data+Model+Development#Convert-Data-Model

schematic schema convert model.csv

What is JSON-LD?

Data models are formatted in JavaScript Object Notation-LinkedData. JSON-LD in schematic is its support by http://schema.orgdataset discoverability in search engines like: ​Dataset Search

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Error Troubleshooting

SchemaHub Documentation on Confluence. This includes definitions of data model like validation rules

Github Tickets Sage-Bionetworks/schematic

Add ticket workflow

Click on Issue
Issue: Feature Request
Add title
Describe problem and a potential solution
Importance
Timeline
Additional Context
Attach any needed documents or screenshots

  • blah: [e.g. chrome, safari]

  • ca

http://regex101.com

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

Guide to Developing Data Models in JSON-LD

JSON-LD, or JavaScript Object Notation for Linked Data, is a JSON-based format for serializing Linked Data. It extends JSON with additional functionality to represent linked data structures, such as contexts, @id, and @type. JSON-LD is a lightweight and flexible format that can be used to represent a variety of data models.This guide provides an introduction to developing data models in JSON-LD. It covers the following topics:

JSON-LD

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JSON-LD contexts

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Modeling entities and relationships

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Using vocabularies

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Best practices for developing JSON-LD data models

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Syntax

JSON-LD documents are valid JSON documents. They consist of key-value pairs, where the keys are strings and the values can be strings, numbers, objects, arrays, or booleans. JSON-LD documents can also contain additional keywords that provide additional information about the data.

...

  • @context: The context URI specifies the vocabulary that is used to interpret the data. In this case, the vocabulary is http://Schema.org .

  • @id: The @id property uniquely identifies the resource. In this case, the resource is a book.

  • type: The type property specifies the type of the resource. In this case, the resource is a book.

  • name: The name property specifies the name of the book.

  • author: The author property specifies the author of the book.

JSON-LD Contexts

JSON-LD contexts are used to map IRIs (Internationalized Resource Identifiers) to human-readable names. Contexts can also be used to define prefixes for IRIs. This can make JSON-LD documents easier to read and write.

...

The type property is now prefixed with schema:. This makes the document easier to read and understand.

Modeling Entities and Relationships

Entities in a JSON-LD data model are represented by objects. Relationships between entities are represented by properties. For example, the following JSON-LD document describes a book and a person:

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The author property in the book object refers to the person object. This indicates that Douglas Adams is the author of The Hitchhiker's Guide to the Galaxy.

Using Vocabularies

Vocabularies are collections of terms and definitions that are used to describe data. JSON-LD data models can use vocabularies to provide a common understanding of the data.

...

  • http://Schema.org

  • Dublin CoreFriend of a Friend (FOAF)

  • GoodRelations

  • GeoNames

  • MusicBrainz

When developing a JSON-LD data model, it is important to choose the appropriate vocabulary. The vocabulary should be relevant to the type of data that you are modeling.

**Best Practices

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Ontology Resources

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Metadata Dictionary

AD Knowledge Portal Metadata Dictionary

https://sagebio.shinyapps.io/amp-ad-metadata-dictionary/

Data Curator App

http://dca.app.sagebionetworks.org

https://dca-docs.scrollhelp.site/DCA/Working-version/Project-Agnostic/uploading-datadev.app.sagebionetworks.org

https://github.com/adknowledgeportal/data_curator

https://github.com/adknowledgeportal/data-models

https://sagebionetworks.jira.com/wiki/spaces/SCHEM/pages/2458648589/Setting+up+a+DCC+Asset+Store#How-do-I-Structure-My-DCC-Synapse-Project-to-Work-with-the-Data-Curator-App%3F

Projects

Folder Structure

https://dca-docs.scrollhelp.site/DCA/Working-version/ELITEProject-Agnostic/validateorganize-andyour-submitdata-your-metadata

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 upload#OrganizeyourDataUpload-FlattenedDataLayoutExample

Code Block
.
├── biospecimen_experiment_1
    ├── manifest1.csv
├── biospecimen_experiment_2
    ├── manifestA.csv
├── single_cell_RNAseq_batch_1
    ├── manifestX.csv
    ├── fileA.txt
    ├── fileB.txt
    ├── fileC.txt
    └── fileD.txt
└── single_cell_RNAseq_batch_2
    ├── manifestY.csv
    └── file1.txt

Study Content

/wiki/spaces/AKP/pages/1057882353

  • Study Description in wiki

  • Methods description in each data folder

/wiki/spaces/EPD1/pages/2900819969

AMP-AD

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

https://sagebiogithub.shinyapps.iocom/adknowledgeportal-/data-curatormodels/
https:blob/main/www.synapse.org/#!Synapse:syn33582398/wiki/619343
https://github.com/adknowledgeportal/data_curator
https://github.com/adknowledgeportal/test-data-model README.md#editing-data-models

AD data model → modular

repo:

branch: test-split-csvs

folders:

modules/

..biosopecimen/

..mouse/

Jira Legacy
serverSystem JIRA
serverIdba6fb084-9827-3160-8067-8ac7470f78b2
keyADM-836

Term = Attribute in the data model where Parent = DataProperty

test-split0csvs branch

MODEL-AD

ELITE

Annotate study folder with contentType = 'dataset'

Flattened file structure

Create Project

Maintain File permission access easily

Top level: assay folders

All data files of one type in assay folder

These assay folder names will be displayed

data_folder/

Schematic Configuration needed config.yml

master_file view ‘synID’

which refers to this:

Fileview - Files and Folders https://www.synapse.org/#!Synapse:syn36759435syn51753858/tables/Add CSV + JSONLD to github – test-data-model

...

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

/wiki/spaces/SCHEM/pages/2645262364

...

_config

needs to point to this fileview and the data model

fork repo

edit dca-template-config.json

add MODEL-AD folder and edit configuration as needed send a pull request

ADKP example

Fileview DCA Asset View that DCA uses

folder contentType = ‘dataset’

One project for all of AD

Templates

Lref gdrive file
urlhttps://

...

drive.google.com/

...

drive/

...

folders/

...

1M90FJX2seyb1s-QzKIHRrSCDuLC97NJO

https://

...

/wiki/spaces/SCHEM/pages/2473623559

...

OWL Tutorial

...

https://schema.org/

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


Resources

https://linkml.io/

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schemasheets/#examples

https://

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linkml.

...

io/

...

linkml/

...

intro/tutorial.html

Lref gdrive file
urlhttps://

...

docs.google.com/document/d/1nZGLRKW5LXpY-LBrtrgs4MyO-fb0kDDeouEOvW36xo0/edit#heading=h.o7ihd22lafi

https://

...

learnxinyminutes.com/docs/

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yaml/

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

ELITE

...

Glossary

Template

Manifest - metadata table submitted for dataset