Last updated on 2023-09-15
This page is intended to describe describes the workflow required to build, edit, and update the data model for MODEL-AD.
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Guide to Developing Data Models in JSON-LD
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https://sagebio.shinyapps.io/amp-ad-metadata-dictionary/
Data Curator App
http://dca.app.sagebionetworks.org
https://dca-dev.app.sagebionetworks.org
https://github.com/adknowledgeportal/data_curator
https://github.com/adknowledgeportal/data-models
Projects
Folder Structure
Code Block |
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.
├── 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
Second Test
AD Portal DCA Test ProjectFileview AD Portal DCA Test Project - Table
https://github.com/adknowledgeportal/test-data-model/blob/main/model-ad/model-ad.data.model.jsonld
https://github.com/adknowledgeportal/data_curator
https://github.com/adknowledgeportal/test-data-model AD Portal DCA Test Project - Table -models/blob/main/README.md#editing-data-models
AD data model → modular
repo:
branch: test-split-csvs
folders:
modules/
..biosopecimen/
..mouse/
Jira Legacy | ||||||
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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:syn51753858/tables/
https://github.com/Sage-Bionetworks/data_curator_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 | ||
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