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[bioontology-support] [BioPortal] Feedback from Emma Vos

Emma Vos emma at thehyve.nl
Tue Aug 11 23:53:26 PDT 2020


Dear Jennifer,

Thank you for your reply. Sorry for any confusion!
I can give one example:

I was looking at some UBERON classes, like "venous blood" (UBERON:0013756).
If I resolve the ID of this class (
http://purl.obolibrary.org/obo/UBERON_0013756),
I see that that "venous blood" is a descendant of "hematopoietic system"
(UBERON:0002390):
[image: image.png]
But "venous blood" doesn't show up as one of the descendants of the
"hematopoietic system" class in BioPortal.
The descendants page of the "hematopoietic system" class is even completely
empty:
http://data.bioontology.org/ontologies/UBERON/classes/http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FUBERON_0002390/descendants

Similar to when I look at ancestors of "venous blood", the "hematopoietic
system" class doesn't show up as ancestor:
http://data.bioontology.org/ontologies/UBERON/classes/http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FUBERON_0013756/ancestors


So both the classes "venous blood" and "hematopoietic system" are present
in BioPortal, but the hierarchy doesn't seem to be complete/correct.

I hope I made it a bit more clear. Thank you for your quick response and
help!

Kind regards,
Emma

On Wed, Aug 12, 2020 at 12:23 AM Jennifer Leigh Vendetti <
vendetti at stanford.edu> wrote:

> Hello Emma,
>
> I reprocessed the UBERON ontology in our system. However, the
> "hematopoietic system” class is still shown as a leaf node with no
> children. As a secondary step, I downloaded the ontology source file and
> double checked against different software, i.e., I loaded the ontology into
> the Protege ontology editor. Protege displays the same hierarchy with this
> particular class as a leaf node (screen shot below).
>
> Could you be more specific with regard to why you think there are classes
> missing from the ontology, and/or why the structure isn’t what you’re
> expecting?
>
> Kind regards,
> Jennifer
>
>
>
>
>
>
> On Aug 10, 2020, at 2:58 AM, Emma Vos <emma at thehyve.nl> wrote:
>
> Dear Jennifer,
>
> As I was querying terms in the UBERON ontology, I figured there is a
> similar issue as with the Cell Ontology.
> I was looking for children/descendants of the class "hematopoietic
> system", but these are missing in BioPortal.
> Other classes seem to be missing as well.
>
> Would you be able to help me out with this as well?
>
> Kind regards,
> Emma Vos
>
> On Mon, Jul 27, 2020 at 8:48 AM Emma Vos <emma at thehyve.nl> wrote:
>
>> Dear Jennifer,
>>
>> That's great, thank you very much!
>>
>> Kind regards,
>> Emma
>>
>> On Thu, Jul 16, 2020 at 11:40 PM Jennifer Leigh Vendetti <
>> vendetti at stanford.edu> wrote:
>>
>>> Hello Emma,
>>>
>>>
>>> On Jul 15, 2020, at 10:57 AM, support at bioontology.org wrote:
>>>
>>> I wanted to annotate some cell types (e.g. "monocyte") with Cell
>>> Ontology terms, using the Annotator tool. Unfortunately, this didn't work.
>>> When browsing through the Cell Ontology, I saw that part of the ontology is
>>> missing in BioPortal. For example, Cell Ontology contains a term for
>>> "monocyte": http://purl.obolibrary.org/obo/CL_0000576 . But this term
>>> is not included in the Cell Ontology on BioPortal. Hence why I couldn't
>>> annotate this "monocyte" properly using the Annotator tool.
>>>
>>> Another issue I had was with downloading the CSV file of Cell Ontology.
>>> I get the following error:
>>> "Cannot read latest submission upload file:
>>> /srv/ncbo/repository/CL/73/CL.csv.gz"
>>>
>>>
>>>
>>> Apologies for the inconvenience. It appears there was an error that
>>> occurred during the processing of the latest submission of the Cell
>>> Ontology. I reprocessed the ontology and the issues you reported are
>>> resolved - the CSV file is downloadable again, and the classes page appears
>>> normal.
>>>
>>> Kind regards,
>>> Jennifer
>>>
>>>
>>>
>>> <Screenshot 2020-07-16 14.36.38.png>
>>>
>>
>>
>> --
>>
>> Emma Vos | Data Engineer
>>
>>
>> E.   emma at thehyve.nl
>>
>> T.   +31(0)30 700 9713
>>
>> W.  www.thehyve.nl
>>
>
>
> --
>
> Emma Vos | Data Engineer
>
>
> E.   emma at thehyve.nl
>
> T.   +31(0)30 700 9713
>
> W.  www.thehyve.nl
>
>
>

-- 

Emma Vos | Data Engineer


E.   emma at thehyve.nl

T.   +31(0)30 700 9713

W.  www.thehyve.nl
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