From 0279963e591d907f76c000ba27f319996979cfdf Mon Sep 17 00:00:00 2001 From: Marijan Mihaljev Date: Fri, 26 Dec 2025 18:03:40 +0200 Subject: [PATCH 1/3] ODM-12958: changed data classes: - renamed Nanopore to Long-read sequencing (Nanopore, PacBio) - added new data classes --- docs/tools/odm-sdk/terminal/study/uploading-study.md | 2 +- .../doc-odm-user-guide/import-data-in-odm.md | 11 ++++++++--- 2 files changed, 9 insertions(+), 4 deletions(-) diff --git a/docs/tools/odm-sdk/terminal/study/uploading-study.md b/docs/tools/odm-sdk/terminal/study/uploading-study.md index a7677d87..9e5eec79 100644 --- a/docs/tools/odm-sdk/terminal/study/uploading-study.md +++ b/docs/tools/odm-sdk/terminal/study/uploading-study.md @@ -67,7 +67,7 @@ Additional optional parameters: sample/library/preparation name from the measurement name in column headers: `-ms ':'` or `--measurement-separator ':'` - to specify the uploaded data as a data class `C`: `-dc 'C'` or `--data-class 'C'` - - The following options are available: `Bulk transcriptomics`, `Single cell transcriptomics`, `Differential abundance (FC, pval, etc.)`, `Pathway analysis`, `Proteomics`, `Single cell proteomics`, `Metabolomics`, `Lipidomics`, `Epigenomics`, `DNA methylation`, `Chemoinformatics`, `Imaging features`, `Gene panel data`, `Biomarker data`, `Physical measures`, `Blood counts`, `Other body fluid counts`, `Nanopore`, `Gene variant (VCF)`, `Flow Cytometry`, `Other` + - The following options are available: `Bulk transcriptomics`, `Single cell transcriptomics`, `Differential abundance (FC, pval, etc.)`, `Pathway analysis`, `Proteomics`, `Single cell proteomics`, `Metabolomics`, `Lipidomics`, `Epigenomics`, `DNA methylation`, `Chemoinformatics`, `Imaging features`, `Gene panel data`, `Biomarker data`, `Physical measures`, `Blood counts`, `Other body fluid counts`, `Long-read sequencing (Nanopore, PacBio)`, `Gene variant (VCF)`, `Flow Cytometry`, `Spatial transcriptomics`, `Phenomics`, `Copy number alterations`, `Microbiome / metagenomics`, `Genetic screens (CRISPR / RNAi)`, `Cell imaging`, `Document`, `Other` --- diff --git a/docs/user-guide/doc-odm-user-guide/import-data-in-odm.md b/docs/user-guide/doc-odm-user-guide/import-data-in-odm.md index 6fffe1b8..974dceea 100644 --- a/docs/user-guide/doc-odm-user-guide/import-data-in-odm.md +++ b/docs/user-guide/doc-odm-user-guide/import-data-in-odm.md @@ -100,12 +100,17 @@ In addition to the samples, libraries, and preparations metadata described above - Physical measures - Blood counts - Other body fluid counts -- Nanopore +- Long-read sequencing (Nanopore, PacBio) - Gene variant (VCF) - VCF format - Flow Cytometry - FACS format +- Spatial transcriptomics +- Phenomics +- Copy number alterations +- Microbiome / metagenomics +- Genetic screens (CRISPR / RNAi) +- Cell imaging - Document -- Other - +- Other To upload experimental data or attach files, navigate to the **Data Tab** From 57719bb351bc52d07ba923fefd6d346d51148029 Mon Sep 17 00:00:00 2001 From: Marijan Mihaljev Date: Mon, 29 Dec 2025 12:37:52 +0200 Subject: [PATCH 2/3] ODM-12958: fixed typo for Microbiome / Metagenomics --- docs/tools/odm-sdk/terminal/study/uploading-study.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/docs/tools/odm-sdk/terminal/study/uploading-study.md b/docs/tools/odm-sdk/terminal/study/uploading-study.md index 9e5eec79..66a9f2ac 100644 --- a/docs/tools/odm-sdk/terminal/study/uploading-study.md +++ b/docs/tools/odm-sdk/terminal/study/uploading-study.md @@ -67,7 +67,7 @@ Additional optional parameters: sample/library/preparation name from the measurement name in column headers: `-ms ':'` or `--measurement-separator ':'` - to specify the uploaded data as a data class `C`: `-dc 'C'` or `--data-class 'C'` - - The following options are available: `Bulk transcriptomics`, `Single cell transcriptomics`, `Differential abundance (FC, pval, etc.)`, `Pathway analysis`, `Proteomics`, `Single cell proteomics`, `Metabolomics`, `Lipidomics`, `Epigenomics`, `DNA methylation`, `Chemoinformatics`, `Imaging features`, `Gene panel data`, `Biomarker data`, `Physical measures`, `Blood counts`, `Other body fluid counts`, `Long-read sequencing (Nanopore, PacBio)`, `Gene variant (VCF)`, `Flow Cytometry`, `Spatial transcriptomics`, `Phenomics`, `Copy number alterations`, `Microbiome / metagenomics`, `Genetic screens (CRISPR / RNAi)`, `Cell imaging`, `Document`, `Other` + - The following options are available: `Bulk transcriptomics`, `Single cell transcriptomics`, `Differential abundance (FC, pval, etc.)`, `Pathway analysis`, `Proteomics`, `Single cell proteomics`, `Metabolomics`, `Lipidomics`, `Epigenomics`, `DNA methylation`, `Chemoinformatics`, `Imaging features`, `Gene panel data`, `Biomarker data`, `Physical measures`, `Blood counts`, `Other body fluid counts`, `Long-read sequencing (Nanopore, PacBio)`, `Gene variant (VCF)`, `Flow Cytometry`, `Spatial transcriptomics`, `Phenomics`, `Copy number alterations`, `Microbiome / Metagenomics`, `Genetic screens (CRISPR / RNAi)`, `Cell imaging`, `Document`, `Other` --- From 50286a5675caa57af902a47e7203a56ac5357d58 Mon Sep 17 00:00:00 2001 From: Marijan Mihaljev Date: Mon, 29 Dec 2025 12:38:47 +0200 Subject: [PATCH 3/3] ODM-12958: fixed typo for Microbiome / Metagenomics --- docs/user-guide/doc-odm-user-guide/import-data-in-odm.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/docs/user-guide/doc-odm-user-guide/import-data-in-odm.md b/docs/user-guide/doc-odm-user-guide/import-data-in-odm.md index 974dceea..0e146680 100644 --- a/docs/user-guide/doc-odm-user-guide/import-data-in-odm.md +++ b/docs/user-guide/doc-odm-user-guide/import-data-in-odm.md @@ -106,7 +106,7 @@ In addition to the samples, libraries, and preparations metadata described above - Spatial transcriptomics - Phenomics - Copy number alterations -- Microbiome / metagenomics +- Microbiome / Metagenomics - Genetic screens (CRISPR / RNAi) - Cell imaging - Document