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from MdH:

These samples are missing the annotation "animal cell" and "eukaryotic cell":
11274-116H5 Melanocyte - light, donor1
11351-117H1 Melanocyte - light, donor2
11423-118G1 Melanocyte - light, donor3
11281-116I3 Skeletal Muscle Cells, donor1
11358-117H8 Skeletal Muscle Cells, donor2
11430-118G8 Skeletal Muscle Cells, donor3
11240-116D7 Skeletal Muscle Satellite Cells, donor1
11321-117D7 Skeletal Muscle Satellite Cells, donor2
11397-118D2 Skeletal Muscle Satellite Cells, donor3

I am not sure at what level in the hierarchy "animal cell" should appear; maybe at "pigment cell" for melanocytes and "cell of skeletal muscle" for the skeletal muscle / satellite cells?

from MdH:

These samples are missing the annotation "somatic cell":
11510-119G7 Alveolar Epithelial Cells, donor1
11590-120G6 Alveolar Epithelial Cells, donor2
11671-122G6 Alveolar Epithelial Cells, donor3
11247-116E5 Mesothelial Cells, donor1
11402-118D7 Mesothelial Cells, donor3

https://fantom5-collaboration.gsc.riken.jp/files/data/shared/UPDATE_022

Reported by MdH

from MdH:

These samples are missing the annotation "in vivo cell sample":

11512-119G9 Smooth Muscle Cells - Bronchial, donor1
11239-116D6 Smooth Muscle Cells - Colonic, donor1
11320-117D6 Smooth Muscle Cells - Colonic, donor2
11396-118D1 Smooth Muscle Cells - Colonic, donor3
11212-116A6 Smooth Muscle Cells - Umbilical Artery, donor0
11367-117I8 Smooth Muscle Cells - Umbilical Artery, donor2
11439-118H8 Smooth Muscle Cells - Umbilical Artery, donor3

Hi Chris, Terry,

In the FANTOM5 sample ontology annotation, sample 11590-120G6 is listed as "Renal Glomerular Endothelial Cells, donor2"; this is the entry in ff-phase2-140729.obo.txt:

[Term]
id: FF:11590-120G6
name: Renal Glomerular Endothelial Cells, donor2
namespace: FANTOM5
comment: Previously: Alveolar Epithelial Cells, donor2
subset: phase1
subset: phase2
subset: update022
is_a: EFO:0002091 ! biological replicate
is_a: FF:0000153 ! human renal glomerular endothelial cell sample

However, the .bam file names still refer to "Alveolar Epithelial Cells, donor2":
...
Alveolar%20Epithelial%20Cells%2c%20donor2.CNhs12084.11590-120G6.hg19.ctss.bed.gz
Alveolar%20Epithelial%20Cells%2c%20donor2.CNhs12084.11590-120G6.hg19.nobarcode.bam
Alveolar%20Epithelial%20Cells%2c%20donor2.CNhs12084.11590-120G6.hg19.nobarcode.bam.bai
Alveolar%20Epithelial%20Cells%2c%20donor2.CNhs12084.11590-120G6.hg19.nobarcode.rdna.fa.gz
...
on the FANTOM5 website; and also in the sRNA data in UPDATE_023:
/analysisdata/mirrors/F5_file_current/UPDATE_023/f5pipeline/human.primary_cell.sRNA/Alveolar%20Epithelial%20Cells%2c%20donor2.SRhi10002.11590-120G6.hg19.CTTGTA.bam.bai
/analysisdata/mirrors/F5_file_current/UPDATE_023/f5pipeline/human.primary_cell.sRNA/Alveolar%20Epithelial%20Cells%2c%20donor2.SRhi10002.11590-120G6.hg19.CTTGTA.bam

Marina checked the expression for some genes to verify the expression patterns of the two samples below (Renal vs Aveolar cells), and based on that we think the .bam file names are correct. (Expression of sox7 is enriched in renal cells (zero in alveolar), vice versa expression of elf3 is high in alveolar cells and null in renal cells).

I am wondering, since the entry in the ontology file has the comment "Previously: Alveolar Epithelial Cells, donor2", if you know what happened to this sample, and should the ontology file be corrected?

Thanks in advance,
-Michiel

Need to check with @hkawaji - what are the criteria for being in the slim?

We don't have a tissue lineage for this sample. Check: should be placental villous?

From MdH:

The new bugs are these lines, in which NCBITaxon_2759 and NCBITaxon_10088 should be NCBITaxon:2759 and NCBITaxon:10088 :

id: NCBITaxon_2759
id: NCBITaxon_10088
is_a: NCBITaxon_2759 ! Eukaryota
is_a: NCBITaxon_10088 ! Mus

FF:11521-119H9 Hepatic Sinusoidal Endothelial Cells, donor1
FF:11601-120H8 Hepatic Sinusoidal Endothelial Cells, donor2
FF:11682-122H8 Hepatic Sinusoidal Endothelial Cells, donor3
have these three annotations:
is_a: FF:0000046 ! human endothelial cell sample
is_a: FF:0000076 ! hepatic sinusoidal endothelial cell sample
is_a: FF:0000078 ! human hepatocyte sample

Similar to #6 but for phase 2
cc @hkawaji

use list here:
https://fantom5-collaboration.gsc.riken.jp/files/data/shared/FREEZE_PHASE2/

https://fantom5-collaboration.gsc.riken.jp/files/data/shared/UPDATE_023/f5pipeline/human.stem_cell.sRNA/

Should these be added to the main ontology?

Reported by Michiel de Hoon