Duplicate ontology terms

[Jon-bioinfo]

I've come across these ontology terms which have the same samples:

"DOID:285 ! hairy cell leukemia": [ "lymphoma, malignant, hairy B-cell cell line:MLMA.CNhs11935.10775-110G1", "hairy cell leukemia cell line:Mo.CNhs11843.10712-109I1" ],
and
"DOID:1040 ! chronic lymphocytic leukemia": [ "lymphoma, malignant, hairy B-cell cell line:MLMA.CNhs11935.10775-110G1", "hairy cell leukemia cell line:Mo.CNhs11843.10712-109I1" ],

This seems to mean that the avg annotation column in the results is being given both terms separated by a comma e.g.
ACTGAGTAGATAGCAT-1,"DOID:1040 ! chronic lymphocytic leukemia, DOID:285 ! hairy cell leukemia",0.342386323

This is a bit annoying to parse when the ontology names themselves are often comma separated e.g. CL:0002397 ! CD14-positive, CD16-positive monocyte

I've not checked if there are other cases like this of duplicate ontology terms. Is this intended?

Best,

[asrhou]

Hi there,

Yes, it is intended. A sample is usually associated with mulitple ontology terms. But your suggestion is great, I will use semi colon instead of comma to separate these terms in the next version.

Cheers,
Rui

[Jon-bioinfo]

Sure, a sample is usually associated with multiple ontology terms. My point here was that these ontology terms have exactly the same set of samples. So the scores for DOID:285 and DOID:1040 are always equal.

[Jon-bioinfo]

Didn't mean to close

[asrhou]

Hi Jon,

Sorry for the late reply!

Yes, for the current reference dataset, the scores for DOID:285 and DOID:1040 are always equal. We intend to expand the reference dataset and provide each ontology term a unique set of reference samples in the future.

Best,
Rui