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IHEC / epiATLAS-metadata-harmonization

IHEC metadata merging and cleanup
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missing information for some AMED-CREST entries #63

Closed quirinmanz closed 2 years ago

quirinmanz commented 2 years ago
Three entries do not have corresponding terms in the cell ontology: EpiRR Description origin_sample
IHECRE00001959 Epithelial cells were isolated from a secretory phase endometrium. placenta
IHECRE00001961 Epithelial cells were isolated from a follicula phase endometrium.
IHECRE00003715 Epithelial cells were isolated from a secretory phase endometrium. placenta

epithelial cell CL:0000066 may not be specific enough

mlist commented 2 years ago

Let's switch to biomaterial_type tissue and UBERON:0004811 (endometrium epithelial cells)

mlist commented 2 years ago

Remove placenta from origin sample since the cells do not originate from there.

quirinmanz commented 2 years ago

The biomaterial_type of these entries are reversed to primary cell and the sample_ontology_curie and cell_type is CL:0009084 and "epithelial cell of endometrial gland"