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

Jennifer Leigh Vendetti vendetti at stanford.edu
Wed Aug 12 10:29:35 PDT 2020


Hello Emma,

I assume the screen shots you provided are from the Ontology Lookup Service (https://www.ebi.ac.uk/ols/ontologies/uberon)?


One thing to note:

As far as I can tell, BioPortal and OLS serve different distributions of UBERON. We’re serving the distribution of UBERON available at this URL:

http://purl.obolibrary.org/obo/uberon/ext.owl

The OLS appears to be serving the distribution of UBERON from this URL:

http://purl.obolibrary.org/obo/uberon.owl

The OBO Foundry website describes the differences between the various distributions of UBERON:

http://www.obofoundry.org/ontology/uberon.html


Another thing to note:

With regard to the display of class hierarchies, there’s a distinct difference between an “asserted" hierarchy and an “inferred" hierarchy. BioPortal is displaying the asserted class hierarchy. If you open the uberon.owl file that OLS serves in the Protege ontology editor, you can see that the “venous blood” class is also show as a leaf term, i.e., in the position that it was manually defined in the asserted hierarchy (screen shot below). You can also see in the same screen shot that the “venous blood” class has a subClassOf axiom:

'part of' some 'hematopoietic system’

This means that "venous blood" will be shown as a subclass of "hematopoietic system” in any instance where an *inferred* hierarchy is displayed. In order to display an inferred hierarchy, you need to perform reasoning on an ontology. I don’t know the internal of the OLS software - however, I’m guessing that somewhere in their pipeline they perform a reasoning task that allows them to display terms in the context of an inferred hierarchy.

The hierarchy that BioPortal displays isn’t incomplete and/or incorrect. The differences you see between the two pieces of software have to do with asserted vs. inferred hierarchies.

Kind regards,
Jennifer


[cid:526E261A-F25A-4C02-A8A4-42D926EA593D at stanford.edu]




On Aug 11, 2020, at 11:53 PM, Emma Vos <emma at thehyve.nl<mailto:emma at thehyve.nl>> wrote:

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.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<mailto: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


<Screen Shot 2020-08-11 at 3.15.04 PM.png>




On Aug 10, 2020, at 2:58 AM, Emma Vos <emma at thehyve.nl<mailto: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<mailto: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<mailto:vendetti at stanford.edu>> wrote:
Hello Emma,


On Jul 15, 2020, at 10:57 AM, support at bioontology.org<mailto: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

[https://docs.google.com/uc?export=download&id=1p1QmNUCB4EKQ-qI0YTgYN0eZt8b_bV0M&revid=0B7YE47A_Oq-IT1gyUTNvMk96Wk16Vy9JRDZmcG8yd1dReWl3PQ]

E.   emma at thehyve.nl<mailto:emma at thehyve.nl>

T.   +31(0)30 700 9713

W.  www.thehyve.nl<http://www.thehyve.nl/>


--

Emma Vos | Data Engineer

[https://docs.google.com/uc?export=download&id=1p1QmNUCB4EKQ-qI0YTgYN0eZt8b_bV0M&revid=0B7YE47A_Oq-IT1gyUTNvMk96Wk16Vy9JRDZmcG8yd1dReWl3PQ]

E.   emma at thehyve.nl<mailto:emma at thehyve.nl>

T.   +31(0)30 700 9713

W.  www.thehyve.nl<http://www.thehyve.nl/>



--

Emma Vos | Data Engineer

[https://docs.google.com/uc?export=download&id=1p1QmNUCB4EKQ-qI0YTgYN0eZt8b_bV0M&revid=0B7YE47A_Oq-IT1gyUTNvMk96Wk16Vy9JRDZmcG8yd1dReWl3PQ]

E.   emma at thehyve.nl<mailto:emma at thehyve.nl>

T.   +31(0)30 700 9713

W.  www.thehyve.nl<http://www.thehyve.nl/>

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