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Version 0.10
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@quirinmanz quirinmanz released this 20 Sep 12:52
· 31 commits to main since this release
V0.10
d89aa91

The CSV for the metadata can be found at openrefine/v0.10/IHEC_metadata_harmonization.v0.10.csv

The overall diff between v0.9 and v0.10 can be found at openrefine/v0.10/diff_v0.9_v0.10.json

The table below describes the columns included in the metadata table.

For explanations concerning the extended version, please see version 0.9.

Please always keep in mind that we try to stay as close to the IHEC Metadata Standard as possible.

Column Examples Explanation
EpiRR IHECRE00000001.4 EpiRR identifier. The number behind the dot (.) is the version.
EpiRR_status Complete Partial Whether this epigenome is Complete or Partial.
project CEEHRC BLUEPRINT The project from which the epigenome originated.
biomaterial_type cell line primary cell primary cell culture primary tissue One of primary cell,primary cell culture, cell line, primary tissue.
cell_type myeloid cell effector memory CD8-positive, alpha-beta T cell The cell type and main sample ontology classification for entries where biomaterial_type is primary cell or primary cell culture.
line MCF 10A The cell line and main sample ontology classification for entries where biomaterial_type is cell line.
tissue_type skeletal muscle tissue amygdala The cell line and main sample ontology classification for entries where biomaterial_type is primary tissue.
sample_ontology_curie CL:0000990 UBERON:0001876 EFO:0001200 The CURIE identifying the sample ontology term.
Different ontologies are used, depending on the biomaterial_type:
'CL' for primary cell or primary cell culture, 'EFO' for cell line and 'UBERON' for primary tissue.
sample_ontology_term_high_order_manual other T cell A manually refined higher level annotation describing the samples using ancestors in the ontology.
markers CD3+ CD4+ CD45RA+ CD3- CD19- CD56- Markers used to isolate and identify the cell type, when applicable.
disease Breast Carcinoma Acute Promyelocytic Leukemia with PML-RARA This attribute reflects the disease for this particular sample, not the donor health condition.
disease_ontology_curie NCIM:C0678222 NCIM:C0023487 The CURIE identifying the NCIM disease ontology term.
disease_high_order_manual Healthy/None Cancer Disease A manually refined higher level annotation describing the diseases using only three categories: Healthy/None, Cancer, Disease.
disease_intermediate_order_manual Carcinoma Leukemia A manually refined higher level annotation describing the disease for this particular sample using ancestors in the NCIT ontology.
NCIM CURIEs were mapped to NCIT CURIES, see version 0.9 for explanation.
donor_id CEMT0007 C07015 Identifier for donors within their projects.
donor_age 60-65 unknown 46 Age of donor. Can be an interval.
donor_age_unit year day Age unit of donor.
donor_life_stage embryonic adult Life stage of donor.
sex female male Sex of donor.
donor_health_status Breast Carcinoma Acute Promyelocytic Leukemia with PML-RARA Links to the health status of the donor that provided the sample. Does not describe the disease for this particular sample.
donor_health_status_ontology_curie NCIM:C0023487 NCIM:C0678222 The CURIE identifying the NCIM donor health status ontology term.
health_state dead alive Health state of donor: dead or alive.
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