Merge pull request #123 from mc2-center/add-fileview

Add FileView, Study, and terms for light sheet microscopy dataset
mc2-center · Jul 22, 2024 · 48c38c0 · 48c38c0
2 parents a6594ec + 00bf092
commit 48c38c0
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Showing 21 changed files with 6,652 additions and 1,377 deletions.
diff --git a/all_valid_values.csv b/all_valid_values.csv
@@ -35,6 +35,7 @@ dataset_species,Unspecified,
 dataset_species,Worm,
 dataset_species,Yeast,
 dataset_species,Fruit Fly,Drosophila melanogaster
+dataset_species,Zebrafish,Danio rerio
 tumorType,Cutaneous Melanoma,"Melanoma of Skin, Malignant Melanoma of Skin, Skin Melanoma, Malignant Melanoma (of Skin), Stage Unspecified, Cutaneous (Skin) Melanoma, CM, Skin, Melanoma, Skin Cutaneous Melanoma, Melanoma of the Skin, Malignant Melanoma of Skin Stage Unspecified, Malignant Cutaneous Melanoma"
 tumorType,Acinar Cell Carcinoma,"Acinar Carcinoma, Acinar adenocarcinoma, Acinar Cell Adenocarcinoma, Acinar carcinoma, Acinic Cell Carcinoma, Acinic Cell Adenocarcinoma, Acinar Adenocarcinoma, Acinic cell adenocarcinoma"
 tumorType,Acute Lymphoblastic Leukemia,"Precursor Lymphoblasic Leukemia, Acute lymphatic leukemia, Precursor Lymphoblastic Leukemia, Acute Lymphoid Leukemia, Precursor Cell Lymphoblastic Leukemia, Acute Lymphoblastic Leukemia (ALL), Acute lymphoblastic leukemia (ALL), Acute lymphoblastic leukemia, precursor cell type, Lymphoblastic Leukemia, ALL, Acute Lymphogenous Leukemia, ALL - Acute Lymphocytic Leukemia, Acute lymphoid leukemia, Acute Lymphocytic Leukaemia, Acute Lymphocytic Leukemia, ALL_TYPE, Acute Lymphocytic Leukemias, Acute lymphocytic leukemia, acute lymphocytic leukemia"
@@ -400,6 +401,7 @@ dataset_file_format,CDS,
 dataset_file_format,CHP,
 dataset_file_format,COOL,
 dataset_file_format,CSV,
+dataset_file_format,DAE,
 dataset_file_format,DB,
 dataset_file_format,DS_Store,
 dataset_file_format,FASTA,
@@ -773,7 +775,6 @@ assay,MALDI-TOF Mass Spectrometry,"Matrix-Assisted Laser Desorption/Ionization T
 assay,MEMA Cell Growth Assay,"MEMA, Mema cell growth assay"
 assay,MNase-Seq,"Mnase-seq, MNase-seq"
 assay,MULTI-Seq,"multiplexing using lipid-tagged indices for single-cell and single-nucleus RNA sequencing, MULTI-seq, Multi-seq"
-assay,MULTI-seq,
 assay,Macrophage Polarization Assay,"macrophage polarization assay, Macrophage polarization assay"
 assay,Magnetic Resonance Imaging,"magnetic resonance imaging, NMRI, Magnetic Resonance, Medical Imaging, Magnetic Resonance / Nuclear Magnetic Resonance, MR Imaging, Magnetic resonance elastography, MRI Scan, MR, nuclear magnetic resonance imaging, Magnetic Resonance Imaging Scan, MRI, NMR Imaging, Nuclear Magnetic Resonance Imaging"
 assay,Magnetic Tweezers,"Magnetic Tweezers, Magnetic tweezers"
@@ -992,6 +993,7 @@ assay,Targeted Error Correction Sequencing,TEC-Seq
 assay,Tuba-Seq,
 assay,SDS-PAGE,
 assay,Cell Fractionation,
+assay,Multiscale Light Sheet Microscopy,
 processLevel,Level 1,
 processLevel,Level 2,
 processLevel,Level 3,

diff --git a/docs/model/file.md b/docs/model/file.md
@@ -0,0 +1,3 @@
+[⤓ Download template](https://github.com/mc2-center/data-models/raw/main/templates/FileView.csv)
+
+{{ read_csv('file/template.csv') }}
diff --git a/docs/model/study.md b/docs/model/study.md
@@ -0,0 +1,3 @@
+[⤓ Download template](https://github.com/mc2-center/data-models/raw/main/templates/Study.csv)
+
+{{ read_csv('study/template.csv') }}
diff --git a/docs/valid_values/file.md b/docs/valid_values/file.md
@@ -0,0 +1,63 @@
+List of standard terms for the [Dataset Sharing Plan Model](../model/file.md).
+
+## Attribute: `File Level`
+
+<div style="max-height:650px; overflow-x: hidden; overflow-y: auto;">
+
+{{ read_csv('shared/processLevel.csv', header=0, names=['Valid Value','Description'], usecols=['Valid Value','Description'], tablefmt='html') }}
+
+</div>
+
+
+## Attribute: `File Assay`
+
+<div style="max-height:650px; overflow-x: hidden; overflow-y: auto;">
+
+{{ read_csv('shared/assay.csv', header=0, names=['Valid Value','Description'], usecols=['Valid Value','Description'], tablefmt='html') }}
+
+</div>
+
+
+## Attribute: `File Species`
+
+<div style="max-height:650px; overflow-x: hidden; overflow-y: auto;">
+
+{{ read_csv('shared/dataset_species.csv', header=0, names=['Valid Value','Description'], usecols=['Valid Value','Description'], tablefmt='html') }}
+
+</div>
+
+
+## Attribute: `File Tumor Type`
+
+<div style="max-height:650px; overflow-x: hidden; overflow-y: auto;">
+
+{{ read_csv('shared/tumorType.csv', header=0, names=['Valid Value','Description'], usecols=['Valid Value','Description'], tablefmt='html') }}
+
+</div>
+
+
+## Attribute: `File Tissue`
+
+<div style="max-height:650px; overflow-x: hidden; overflow-y: auto;">
+
+{{ read_csv('shared/tissue.csv', header=0, names=['Valid Value','Description'], usecols=['Valid Value','Description'], tablefmt='html') }}
+
+</div>
+
+
+## Attribute: `File Format`
+
+<div style="max-height:650px; overflow-x: hidden; overflow-y: auto;">
+
+{{ read_csv('shared/dataset_file_format.csv', header=0, names=['Valid Value','Description'], usecols=['Valid Value','Description'], tablefmt='html') }}
+
+</div>
+
+
+## Attribute: `Data Use Codes`
+
+<div style="max-height:650px; overflow-x: hidden; overflow-y: auto;">
+
+{{ read_csv('shared/duo.csv', header=0, names=['Valid Value','Description'], usecols=['Valid Value','Description'], tablefmt='html') }}
+
+</div>