diff --git a/docs/assets/data_model.svg b/docs/assets/data_model.svg new file mode 100644 index 00000000..57c7f7ee --- /dev/null +++ b/docs/assets/data_model.svg @@ -0,0 +1,1257 @@ + + + + + + + + + + + + + + + + + + + + + +Metadata stored in relational database + + + + + + + +Study + + + + + + + +Samples + + + + + + + +Libraries/Preparations + + + + + + + +Measurements + + + + + + + +Omics Metadata + + + + + + + +Measurementsmetadata + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +Indexed data stored in columnar database + + + + + + + +Files copied to ODM S3 bucket + + + + + + + +Non-​indexed experiment data and its descriptione.g. supplementary files, reports, images, h5 filesDiseaseAgeSample IDSample_1Sample_25054diabetescancerAssay TypeRINmRNALibrary IDLibrary_1Library_29.28.5mRNA + + + + + + + +Context of experimente.g. aim, experimental design + + + + + + + +Biological attributese.g. tissue, disease, treatment + + + + + + + +(Optional) Sample preparation libraries + + + + + + + +Processed omics datae.g. tabular data or vcf, and its description e.g. assay type, normalisation, instrument + + + + + + + +Attachment + + + + + + + +Attachment + + + + + + + +Omics Metadata + + + + + + + +Attachmentmetadata + + + + + + + + + + + + + + + +Cells + + + + + + + + + + + + + + + +(Optional) For single-​cell data percent_mitoCell TypeCell IDCell_1Cell_2adipocyteNK0.3544981010.655132133Cell_1Cell_2Gene ID-1.7888Gene NamePRSS1SPINK1ENSG00000204983ENSG00000164266-0.5665-0.11810.3693 diff --git a/docs/tools/odm-sdk/terminal/study/uploading-study.md b/docs/tools/odm-sdk/terminal/study/uploading-study.md index 2066c20d..0ad51ea3 100644 --- a/docs/tools/odm-sdk/terminal/study/uploading-study.md +++ b/docs/tools/odm-sdk/terminal/study/uploading-study.md @@ -75,7 +75,7 @@ Additional optional parameters: ## Data model The script supports several data models: -![Data Model](uploading-study/data-model.png) +![Data Model](../../../../assets/data_model.svg) - Study - Samples - Omics data: - the script uses this data model if no parameters are specified for libraries or preparations loading; diff --git a/docs/tools/odm-sdk/terminal/study/uploading-study/data-model.png b/docs/tools/odm-sdk/terminal/study/uploading-study/data-model.png deleted file mode 100644 index c6f66249..00000000 Binary files a/docs/tools/odm-sdk/terminal/study/uploading-study/data-model.png and /dev/null differ diff --git a/docs/user-guide/doc-odm-user-guide/doc-odm-user-guide/images/data-model.png b/docs/user-guide/doc-odm-user-guide/doc-odm-user-guide/images/data-model.png deleted file mode 100644 index c6f66249..00000000 Binary files a/docs/user-guide/doc-odm-user-guide/doc-odm-user-guide/images/data-model.png and /dev/null differ diff --git a/docs/user-guide/doc-odm-user-guide/import-data-using-api.md b/docs/user-guide/doc-odm-user-guide/import-data-using-api.md index a8ca1678..ce3c0c71 100644 --- a/docs/user-guide/doc-odm-user-guide/import-data-using-api.md +++ b/docs/user-guide/doc-odm-user-guide/import-data-using-api.md @@ -47,7 +47,7 @@ The correct order of linking follows the system logic and available endpoints: - **Attached files** are linked directly to a **Study** -![image](doc-odm-user-guide/images/data-model.png) +![image](../../assets/data_model.svg) ## Data Loading via APIs To load the data via APIs each entity is created via a separate endpoint specific for this data type. Then they are sequentially linked in the Integration layer.