Data Schema for Liver OmixAtlas

All types of data on Polly goes through Polly Curation process and are stored as tabular files or H5AD files (for single cell data) as described here. All data on Liver Omix Atlas have the metadata curated and harmonized using controlled vocabularies. There is data from various sources in the Liver OmixAtlas as follows :

  1. GEO
  2. TCGA
  3. GTEx
  4. MetaboLights
  5. Metabolomics Workbench
  6. Human Protein Atlas
  7. CCLE
  8. Depmap
  9. LINCS
  10. CPTAC

Here is the list of different data types available in the Liver OmixAtlas :

  1. Transcriptomics
  2. Single Cell
  3. Mutation
  4. Metabolomics
  5. Proteomics
  6. Drug Screens
  7. Gene Dependency
  8. Gene Effect
  9. Methylation
  10. miRNA

Some metadata fields are common across all data types and sources whereas others are data type or source specific. The structure of data and metadata for each source and data type is described below:

1 Common Metadata Fields Across Data Types

All the common metadata fields are curated in a consistent manner regardless of the source of the data. All the data in the Omix Atlas can be queried using these curated fields.

1.1 Dataset Level Fields

All the datasets in the liver omix atlas has been annotated for unique id, description, organism, disease, tissue, experimental conditions, source, publication and curated for datatype, drug, cell line, cell type. These annotations helps in defining and mapping the characteristics of each data. These values has been standardized across all the datasets and are aligned with the FAIR guidelines. The dataset level mapping helps in narrowing down a dataset of interest.

Field Type Description Example values Exception
dataset_id String A unique id for dataset/study/project to represent a group of samples ST000915_AN001489, GSE100155_GPL6884, LIHC_Proteomics_TCGA
description String Brief text description providing details of the samples/experiment MiRNA profile of liver cell lines, Liver hepatocellular carcinoma methylation data
kw_data_type String Identifies the type of measurement present in the dataset. For example Transcriptomics data_type contains gene expression values, metabolomics contains intensity measurement from mass spec instruments etc. Transcriptomics,Drug screens,Mutation
organism String/List The organism over which the experiment for the dataset was conducted Homo sapiens,Mus musculus
disease List The name of the studied disease and associated effects Fatty Liver, Inflammation, Obesity, Diabetes Mellitus
tissue List The tissue on which the experiment was conducted for the said dataset Liver, Adipose Tissue, Kidney, Brain
kw_drug List A database for drugs, chemical entity, natural and synthetic compounds which has been used as a treatment during the experiment in different samples Troglitazone, Berberine, Clofibrate, Rosiglitazone Studies with no drug perturbations will have this field as "None"
kw_cell_line List List of population of modified cells used for the study in quest Hep-G2, MCF-7, HeLa, A549, TFK-1 All TCGA datasets have this field as "None"
kw_cell_type List A list of differentitated cells which can be identified at morphological, structural and physiological level Liver cells, Kidney Cells, Brain Cells
dataset_source String The name of the repository from where data has been originally deposited GEO, TCGA, LINCS
publication String If the dataset has an associated publication, this field contains a link to the publication; in other cases, it contains a link to the data source providing more information regarding the dataset
total_num_samples Int The total number of samples present in the dataset 22, 84, 267
total_num_cells Int Number of cells in the experiment 100 This curated field is available only for Single cell studies

1.2 Sample Level Fields

Sample level annotations directly defines the biological characteristics of each sample. All the samples in the liver omix atlas has been curated for disease, cell line, drug, cell type, genetic modifications, modified gene and tissue. The datasets can be queried using these fields as well.

Field Type Description Example values Exception
kw_column String A unique id for a sample GSM173533, GSM4454526, HEP3B217_LIVER
kw_doc_id String Path to the dataset file discover-prod-datalake-v1@@@liver_atlas@@data@@Transcriptomics@@GSE10409_GPL1355.gct
kw_curated_disease String Name of the disease condition for that particular sample Normal, Liver Cirrhosis
kw_curated_cell_line String Population of modified cells used for the sample SMMC-7721, Hep-G2, none All TCGA samples have this field as "none"
kw_curated_drug String A database for drugs, chemical entity, natural and synthetic compounds which has been used as a treatment in the sample Troglitazone, Berberine, Clofibrate, Rosiglitazone, All the samples without drug perturbation will have this field as "none"
kw_curated_cell_type String Differentiated cells which can be identified at morphological, structural and physiological level hepatocyte, endothelial cell of lymphatic vessel
kw_curated_genetic_mod_type String The type of genetic modification done on the sample wildtype, knockout, knockin, knockdown
kw_curated_modified_gene String A gene or list of genes modified in the sample TP53, COL18A1, PRKAA2 All the wildtype samples will have this field as "none"
kw_curated_tissue String A tissue or a list of tissues from which the sample has been obtained Liver, Kidney, Brain, Colon

1.3 Feature Level Fields

The datasets has also been annotated for features of each sample which provides description about the gene being studied, unique identifier, path to the doc.

1.3.1 All Datatypes Except Single Cell

Field Type Description Example values Exception
kw_index List Symbol for the molecule (gene, metabolite, protein etc) studied in the experiment Epas1, Tpgs1,Cxcl12
kw_column.kw_column List Unique ID for each sample GSM3034529, GSM2928029
kw_column.kw_expression List Feature intensity of a sample. For genomics this will be expression value and for proteomics, lipidomics this will be metabolite intensity. 0.7943000197410583, 0.3294999897480011, 0.6687999963760376
kw_doc_id List Path to the dataset file. discover-prod-datalake-v1@@@liver_atlas@@data@@Transcriptomics@@GSE10409_GPL1355.gct

1.3.2 Single Cell

Field Type Description Example values Exception
feature_name List Symbol for the gene studied in the experiment Ntm
celltype List Unique ID for each sample geneexp_cluster_7, geneexp_cluster_16, geneexp_cluster_4
Value List Feature intensity of a sample 0.000243683270913317, 0.000549465175768581
Dataset List Path to the dataset discover-prod-datalake-v1@@@liver_atlas@@data@@SingleCell@@GSE124395_GPL16791.h5ad

2 Specific metadata fields from various sources

All the source specific fields which are mentioned in the following section are not curated by Polly and are present as they are in the source. Data in the Atlas can be queried using these fields as well. These fields may not be present in all the data on the source and hence as a result may not be present for all the data on Liver Omix Atlas as well.

2.1 CCLE (Sample level fields)

Field Type Description Example values Exception
ccle_id List This ID helps in mapping the cell line in CCLE database HEP3B217_LIVER, SNU886_LIVER
depmapid List This is a unique ID which helps in finding the data in DepMap(Dependency Map) portal ACH-000625, ACH-000739
histology List This column provides the relevant information about the type of disease being studied carcinoma, adenocarcinoma
name List Unique name for cell line HEL9217, MCF7, 253JBV, SNU-878
gender List Gender identity of the patient from whom the cell line has been obtained Male, Female
age List Age of the patient from whom the cell line has been obtained 8, 52, 56,43,28
year List Year in which the sample was deposited 2015, 2018

2.2 DepMap (Sample level fields)

Field Type Description Example values Exception
ccle_name List This list provides the detail about cell line and associated disease HL60_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE, LS513_LARGE_INTESTINE, MCF7_BREAST
cas9_activity List Percentage value for the efficiency of crispr cas 9 nuclease activity in the mammalian cell system 65.2, 76.9, 92, 86.6, 52.4, 65.2
sex List Gender identity of the patient from whom the cell line has been obtained Male, Female
primary_disease List Original disease for which the cell line is model system Kidney Cancer, Liver Cancer, Colon/Colorectal Cancer, Skin Cancer
subtype List A dictionary for smaller classes of cancer that a cancer can be grouped on the basis of physiological characteristics of cancer cell line Melanoma, Adenocarcinoma, Rhabdomyosarcoma, Glioblastoma
age List Age of the patient from whom the cell line has been obtained 8, 52, 56,43,28
primary_tissue List Source tissue of cell line Liver, Colon, Breast, Kidney

2.3 LINCS (Sample level fields)

Field Type Description Example values Exception
pert_time List Depicts the numerical value of time of treatment of drugs during the experiment 6, 12, 24, 48, 1
pert_time_unit List Depicts the unit of time of treatment of drugs during the experiment h, min, sec, week
pert_type List Column describing the experimental conditions eg: control/treated/untreated ctl_vehicle, trt_cp, ctl_untrt
cell_id List Unique LINCS cell id for each cell line which acts as internal identifier in the LINCS database A375.311, CL34
pert_iname List Describes the condition of samples treated/untreated UnTrt, Trt, DMSO
pert_dose List This column denotes the numerical value for the dose of chemical used during the experiment 2, 25, 6
pert_dose_unit List Provides information about the unit of the dose of the drug uL, mL, mg
curated_is_control List Depicts information the sample is a control or a perturbation for a particular experiment 1
curated_cohort_id List The cohort of the sample 2
curated_cohort_name List Name of the group of samples trt_cp - Gsk-429286a, ctl_vehicle - none

2.4 MetaboLights (Sample level fields)

Field Type Description Example values Exception
sample_source_name List Provides information about original condition/place/organization/laboratory from where the sample has been acquired. BIIE Treatment Control, NPY Treatment, Moin Saleem, Bristol UK, IMTEK , S0_1_4_LAq, T5_2_9_MAq, plant
assay_ms_assay_name List Unique id which helps in mapping the samples origin/date of indexing/type of ms assay performed. 0018_LC_20180917_sample_87, 0018_LC_20180917_sample_103, 0018_LC_20180917_sample_107
subject id List Unique ID for sample factor value DDO142, DDO93, DDO233
factors_gender List Gender identity of the patient Male, Female
factors_genotype List Contains information wild type genotype, Hi-MYC
factors_strain List Name of the strain of mice used during the experiment. C57BL/6, B6
factors_smoking status List Describes the smoking condition of the donor. Never Smoker, Smoker
factors_cohort List Group of samples at a particular stage/in a particular experimental condition validation, 1, 2
factors_cell_type List Population of cells in which has been studied during the experiment. control lung fibroblast, IPF lung fibroblast, Human peripheral blood mononuclear cells, non small cell lung cancer cell (NSCLC)
factors_plasma List Depicts the experimental condition of the samples which has been treated with plasma in a specific disease condition. Non-thermal plasma sham, biological rep3, Time point 4 h after Non-thermal plasma treated 1 min, biological rep1, Cells Incubated with ACS-pre Patient Plasma, Cells Incubated with Normal Patient Plasma
factors_drug List Drugs used as a treatment. WCB001_Mock_1d_RNA_4, DER, Tamoxifen, Deoxynivalenol, Solvent, Solvent+Spike
factors_injury List Provides information about type of injury of the donor. alveolar cell injury, respiratory failure, AEC sham control, AEC mechanical injury 0 hr SW_N14, AEC cyclic stretch 8 hr SW_N25
additional sample data_height cm List Height of the donor 180.34, 164.084, 177.8
additional sample data_weight kg List Weight of the donor 102.965468, 80.73944186, 90.31024087
additional sample data_tumor_type List Type of cancer donor is suffering from. adenocarcinoma, lung adenocarcinoma, non-small cell lung cancer
factors_obesity List Type of obesity related disease donor is suffering from. insulin-sensitive (HOMA-IR<3) obese individual, liver dysfunction in obesity

2.5 Metabolomics Workbench (Sample level fields)

Field Type Description Example values Exception
sample_id List Unique Identity for each sample obtained from Metabolomics Workbench NASH001, NASH013, NASH029, T26-6, T30-2
Subject ID List Unique ID for the subject SU0004318, SU0004310
Factors.Diagnosis List List of disease which was diagnosed in the donor Normal, Cirrhosis, Steatosis
Additional sample data.BMI List Body Mass Index of the patient 43.3, 27, 34
Additional sample data.AGE List Age of the patient 45,72,83,34

2.6 GEO - Single Cell (Sample level fields)

Field Type Description Example values Exception
umi_counts Int Unique Molecular Identifier count per cell. It represents absolute number of observed transcripts. The number should be higher than 500 in a cell. 500-1000
gene_counts Int Number of reads that align to each gene using different programs. 74.5446 fpkm, 30.6890 fpkm
sample String Unique Identifier for the sample. GSM2787809, GSM3396732
characteristics_ch1 List Depicts the information about tissue/developmental stage/sample type/strain. tissue: Pancreatic islets, developmental stage: adult, sample type: Single Cell
cell_type List This column lists the population of cells used during the experiment. Dendritic cells, Basophils, CD4+ Cells, Progenitors, mesenchymal cells
age List Age of the patient from whom the cell line has been obtained 8, 52, 56,43,28
donor List The organism from which the cells has been extracted Homo sapiens, Mus musculus
location List Origin place of the donor New York, USA, Bristol, UK
genes_detected List number of genes detected per sample (defined as genes with cpm > 1); cpm=counts per million
donor_organism_sex List Gender identity of the donor organism Male, Female
cell_subtype List Population of cells which has been studied during the experiment. CD45+, GR1-, SSClow, CD11c+, MHCII+, CD11b+, CD24+, differentiated non lung cancer stem like cells (OSK-A549-SN)
cell type clust List Cluster of cell type which has been studied during the experiment. C01_CD8-LEF1, C05_CD8-GZMK
gender List Gender identity of the donor organism Male, Female

2.7 GEO - Transcriptomics (Sample level fields)

Field Type Description Example values Exception
geo_accession List Unique ID for each sample GSM2699628, GSM2699632
source_name_ch1 List Name of the source from which the sample has been obtained liver cancer cells
curated_is_control List Depicts information the sample is a control or a perturbation for a particular experiment. 1,2
curated_cohort_id List The cohort of the sample. For one cohort the values will remain same. 0,1
curated_cohort_name List Name of the group of samples providing information about experimental condition/tissue/cell line/treatment. Noodle diet; WAT_N-group; WAT_Noodle diet, hepatocellular carcinoma; liver cancer cells; hepg2_0µg/ml_H
title List Description about the type/genotype/origin/experimental condition of the sample hepg2_0µg/ml_H1

2.8 GTEX (Sample level fields)

Field Type Description Example values Exception
SAMPID List Unique ID for each sample GTEX-ZTPG-1426-SM-51MT3, GTEX-ZPU1-0826-SM-57WG2
SMPTHNTS List Description about the treatment condition of the tissue 2 pieces, diffuse macro and microvesucular steatosis, nodular regenerative
SMTS List Source Tissue Liver
SMNABTCH List Batch ID BP-43375, BP-43529
DTHHRDY List List the cause of death of the patient Fast death of natural causes, Ventilator Case, Intermediate death

2.9 TCGA (Sample level fields)

Field Type Description Example values Exception
sample_id List Unique ID for each sample TCGA-2Y-A9GU-01A, TCGA-2V-A95S-01A
sample_type List The type of disease from which the sample has been extracted Primary Tumor
primary_diagnosis List Type and cause of disease the patient has suffered from Hepatocellular carcinoma-- NOS
primary_site List Primary site of tumor Liver and intrahepatic bile ducts
disease_type List Type of disease the donor patient suffered from. Adenomas and Adenocarcinomas
vital_status List Status of the donor patient. Alive, Dead
bcr_patient_barcode List First four fields of the barcode. TCGA-2Y-A9GU-01A, TCGA-2V-A95S-01A
barcode List Unique indexed identifier for each donor patient. TCGA-2Y-A9GU-01A-11R-A38B-07, TCGA-2V-A95S-01A-11R-A37K-07
patient_id List Unique ID of the donor. Contains first three fields of barcode. TCGA-2Y-A9GU, TCGA-2V-A95S
gender List Gender of the donor patient. Male, Female
age_at_diagnosis List Age of the patient during diagnosis. 20187, 21318, 28387
age_at_index List Age of the patient while indexing the data. 55
race List Racial classification of the donor patient. white, caucasian, hispanic, latino
Ethnicity List Cultural origin of the donor patient. not hispanic or latino, African American, Caucasian American
primary site List Primary site of the tumor. Liver and intrahepatic bile ducts
Ajcc pathologic tumor stage List Stage of cancer Stage I, Stage II, Stage III, Stage IIIA
days_to_death List Number of days the donor patient died after indexing the sample. 724, 819
subtype List Distinct molecular subtypes of tumor. COC3, COC2, COC1
tumor_status List Description of the sample for tumor status. TUMOR FREE, WITH TUMOR
tumor_stage List Depicts the stage of tumor of the donor patient. Adverse, Intermediate
tumor_grade List Description of a tumor on the basis of characteristics of tumor tissue and cells under the microscope. not reported, G2, G3
classification_of_tumor List Types of tumor classified on the basis of genomic, proteomic and other molecular analysis. not reported, Uveal Melanoma, acute myeloid leukemia
progression_or_recurrence List History of cancer spread or recurrent tumor. not reported
days_to_last_follow_up List Number of days after the last follow up with the donor patient. 1939, 947
history_other_malignancy List History of the patient suffering from other cancer type. [Not Available]
history_neoadjuvant_treatment List History of patient undergoing neoadjuvant therapy No, Yes
new_tumor_event_dx_indicator List New tumor after initial treatment. YES, No
treatment_outcome_first_course List Definition of the disease state on the basis of recurrence of tumor. [Unknown], Complete, Remission/Response

3 Molecular Identifiers

Molecular identifiers have been standardized for identifying molecules of interest from various sources. The following are the molecular identifiers used for the data in Omix Atlas.

3.1 CCLE

Field Type
Mutation HUGO Gene Symbol
Transcriptomics HUGO Gene Symbol
miRNA miRBase ids
Metabolomics Refmet
Proteomics RPPA Antibody ids

3.2 DepMap

Field Type
Mutation HUGO Gene Symbol
Transcriptomics HUGO Gene Symbol
miRNA miRBase ids
Metabolomics Refmet
Proteomics RPPA Antibody ids

3.3 LINCS, GTEX & GEO

Field Type
Transcriptomics HUGO Gene Symbol

3.4 TCGA

Field Type
Mutation HUGO Gene Symbol
Transcriptomics HUGO Gene Symbol
miRNA miRBase ids
Copy Number HUGO Gene Symbol
Proteomics RPPA Antibody ids
Methylation CPG island Ids