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

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

support

Name: Emma Vos

Email: [hidden email]

Location: https%3A%2F%2Fbioportal.bioontology.org%2Fannotator


Feedback:

Dear BioPortal support,

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"

Would you be able to help me out with these issues? I have been comparing multiple annotator tools, and Annotator fits best with all of my requirements, so it would be really helpful.

Thank you in advance!

Kind regards,
Emma Vos


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

jvendetti
Hello Emma,


On Jul 15, 2020, at 10:57 AM, [hidden email] 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




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

jvendetti
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 <[hidden email]> 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 <[hidden email]> 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 <[hidden email]> wrote:
Hello Emma,


On Jul 15, 2020, at 10:57 AM, [hidden email] 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.   [hidden email]

T.   +31(0)30 700 9713

W.  www.thehyve.nl



--

Emma Vos | Data Engineer


E.   [hidden email]

T.   +31(0)30 700 9713

W.  www.thehyve.nl



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

Emma Vos
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 <[hidden email]> 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 <[hidden email]> 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 <[hidden email]> 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 <[hidden email]> wrote:
Hello Emma,


On Jul 15, 2020, at 10:57 AM, [hidden email] 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.   [hidden email]

T.   +31(0)30 700 9713

W.  www.thehyve.nl



--

Emma Vos | Data Engineer


E.   [hidden email]

T.   +31(0)30 700 9713

W.  www.thehyve.nl




--

Emma Vos | Data Engineer


E.   [hidden email]

T.   +31(0)30 700 9713

W.  www.thehyve.nl


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

jvendetti
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:


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


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



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






On Aug 11, 2020, at 11:53 PM, Emma Vos <[hidden email]> 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 <[hidden email]> 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 <[hidden email]> 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 <[hidden email]> 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 <[hidden email]> wrote:
Hello Emma,


On Jul 15, 2020, at 10:57 AM, [hidden email] 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.   [hidden email]

T.   +31(0)30 700 9713

W.  www.thehyve.nl



--

Emma Vos | Data Engineer


E.   [hidden email]

T.   +31(0)30 700 9713

W.  www.thehyve.nl




--

Emma Vos | Data Engineer


E.   [hidden email]

T.   +31(0)30 700 9713

W.  www.thehyve.nl



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

Samson Tu
Hi,

On Aug 12, 2020, at 10:29 AM, Jennifer Leigh Vendetti <[hidden email]> wrote:

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.


Actually, I think the difference is not between asserted vs inferred hierarchies, but between the kinds links displayed in the Bioportal and EBI hierarchies.The Bioportal hierarchy is a strict is-a hierarchy, whereas the EBI hierarchy is a mixed is-a/part-of hierarchy. Note the P icon in the EBI hierarchy, indicating that blood is part of hematopoietic system, whereas venous blood is a kind of blood. Bioportal correctly shows that hematopoietic system has no is-a child. 



With best regards,
Samson


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

John Graybeal-2
This seems possible. I believe BioPortal *can* display part-of hierarchies, if the ontology is configured to do so. But it is a "choose one" situation, so BioPortal can't support both views.

john

On Aug 12, 2020, at 4:17 PM, Samson Tu <[hidden email]> wrote:

Hi,

On Aug 12, 2020, at 10:29 AM, Jennifer Leigh Vendetti <[hidden email]> wrote:

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.


Actually, I think the difference is not between asserted vs inferred hierarchies, but between the kinds links displayed in the Bioportal and EBI hierarchies.The Bioportal hierarchy is a strict is-a hierarchy, whereas the EBI hierarchy is a mixed is-a/part-of hierarchy. Note the P icon in the EBI hierarchy, indicating that blood is part of hematopoietic system, whereas venous blood is a kind of blood. Bioportal correctly shows that hematopoietic system has no is-a child. 

<PastedGraphic-1.png>


With best regards,
Samson

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========================
John Graybeal
Technical Program Manager
Center for Expanded Data Annotation and Retrieval /+/ NCBO BioPortal
Stanford Center for Biomedical Informatics Research
650-736-1632  | ORCID  0000-0001-6875-5360




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

jvendetti
In reply to this post by Samson Tu
Thanks for that correction Samson, and apologies to all that I navigated down the wrong path in my last response.

Jennifer



On Aug 12, 2020, at 4:17 PM, Samson Tu <[hidden email]> wrote:

Hi,

On Aug 12, 2020, at 10:29 AM, Jennifer Leigh Vendetti <[hidden email]> wrote:

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.


Actually, I think the difference is not between asserted vs inferred hierarchies, but between the kinds links displayed in the Bioportal and EBI hierarchies.The Bioportal hierarchy is a strict is-a hierarchy, whereas the EBI hierarchy is a mixed is-a/part-of hierarchy. Note the P icon in the EBI hierarchy, indicating that blood is part of hematopoietic system, whereas venous blood is a kind of blood. Bioportal correctly shows that hematopoietic system has no is-a child. 

<PastedGraphic-1.png>


With best regards,
Samson



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

frans

Hi Jennifer and Eva et al,

With great interest I’ve been following this discussion from a professional point of interest.

The UBERON classification is based on anatomical properties.

In this respect the ‘hematopoietic system’ is most likely to be classified as part of ‘bone marrow’, because this is the place where most of the stem cells  resides.

The ‘blood’ class as we know it in daily practice is distinct from bone marrow because it flows around between in all compartments like ‘vascular system’ and ‘bone marrow’ system . 

‘Venous blood’ could anatomically be considered as the ‘venous part of’ the ‘vascular system’ (UBERON: distinct class); because this system in general can be divided into arterial, venous and capillary blood compartment; On the other hand the properties of biomarkers in venous blood are distinct from those in capillary and arterial  blood samples and  for this reason we report the lab results in conjunction with the type of sample. So from a propetrt point of view venous blood is a subclass of blood as a substance.  

So I conclude that the inferred classification that ‘venous blood’ isa/partof  ‘blood’ isa/partof ‘hematopoietic system’ might be misleading or even incorrect.  Or did I misinterpret the basics of this discussion?

 

Best regards

Frans van der Horst 

 

 

Van: bioontology-support <[hidden email]> Namens Jennifer Leigh Vendetti
Verzonden: donderdag 13 augustus 2020 02:57
Aan: Samson Tu <[hidden email]>
CC: [hidden email]; Emma Vos <[hidden email]>
Onderwerp: Re: [bioontology-support] [BioPortal] Feedback from Emma Vos

 

Thanks for that correction Samson, and apologies to all that I navigated down the wrong path in my last response.

 

Jennifer

 

 



On Aug 12, 2020, at 4:17 PM, Samson Tu <[hidden email]> wrote:

 

Hi,



On Aug 12, 2020, at 10:29 AM, Jennifer Leigh Vendetti <[hidden email]> wrote:

 

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.

 

 

Actually, I think the difference is not between asserted vs inferred hierarchies, but between the kinds links displayed in the Bioportal and EBI hierarchies.The Bioportal hierarchy is a strict is-a hierarchy, whereas the EBI hierarchy is a mixed is-a/part-of hierarchy. Note the P icon in the EBI hierarchy, indicating that blood is part of hematopoietic system, whereas venous blood is a kind of blood. Bioportal correctly shows that hematopoietic system has no is-a child. 

 

<PastedGraphic-1.png>

 

 

With best regards,

Samson

 

 


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

John Graybeal-2
Hello Frans,

I think you have slightly misinterpreted the basis of the discussion, in that almost all of us are semantic engineers, not medically trained. So we were only using the medical terms in question as a means of understanding what these three tools are displaying to users, given the UBERON model that has been defined and their own semantic approaches.

I think the inferred classification that is displayed in Protege might be a bit more precisely described than using the blended terms in your final paragraph, but I'd leave it to someone more semantically expert than myself to get it exactly right. (Samson?) 

But in regard to the medical understanding, we must send you to the builders of the UBERON ontology.

John



On Aug 13, 2020, at 12:15 AM, [hidden email] wrote:

Hi Jennifer and Eva et al,
With great interest I’ve been following this discussion from a professional point of interest.
The UBERON classification is based on anatomical properties. 
In this respect the ‘hematopoietic system’ is most likely to be classified as part of ‘bone marrow’, because this is the place where most of the stem cells  resides. 
The ‘blood’ class as we know it in daily practice is distinct from bone marrow because it flows around between in all compartments like ‘vascular system’ and ‘bone marrow’ system .  
‘Venous blood’ could anatomically be considered as the ‘venous part of’ the ‘vascular system’ (UBERON: distinct class); because this system in general can be divided into arterial, venous and capillary blood compartment; On the other hand the properties of biomarkers in venous blood are distinct from those in capillary and arterial  blood samples and  for this reason we report the lab results in conjunction with the type of sample. So from a propetrt point of view venous blood is a subclass of blood as a substance.   
So I conclude that the inferred classification that ‘venous blood’ isa/partof  ‘blood’ isa/partof ‘hematopoietic system’ might be misleading or even incorrect.  Or did I misinterpret the basics of this discussion? 
 
Best regards
Frans van der Horst  
 
 
Van: bioontology-support <[hidden email]> Namens Jennifer Leigh Vendetti
Verzonden: donderdag 13 augustus 2020 02:57
Aan: Samson Tu <[hidden email]>
CC: [hidden email]; Emma Vos <[hidden email]>
Onderwerp: Re: [bioontology-support] [BioPortal] Feedback from Emma Vos
 
Thanks for that correction Samson, and apologies to all that I navigated down the wrong path in my last response. 
 
Jennifer
 
 


On Aug 12, 2020, at 4:17 PM, Samson Tu <[hidden email]> wrote:
 
Hi,


On Aug 12, 2020, at 10:29 AM, Jennifer Leigh Vendetti <[hidden email]> wrote:
 
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.
 
 
Actually, I think the difference is not between asserted vs inferred hierarchies, but between the kinds links displayed in the Bioportal and EBI hierarchies.The Bioportal hierarchy is a strict is-a hierarchy, whereas the EBI hierarchy is a mixed is-a/part-of hierarchy. Note the P icon in the EBI hierarchy, indicating that blood is part of hematopoietic system, whereas venous blood is a kind of blood. Bioportal correctly shows that hematopoietic system has no is-a child. 
 
<PastedGraphic-1.png>
 
 
With best regards,
Samson
 
 
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Center for Expanded Data Annotation and Retrieval /+/ NCBO BioPortal
Stanford Center for Biomedical Informatics Research
650-736-1632  | ORCID  0000-0001-6875-5360




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

Samson Tu
There may be some inferencing involved for EBI hierarchy to display blood as a a part of hematopoietic system. However, that’s not the issue.  The issue is that Bioportal hierarchy is a pure is-a hierarchy, so it doesn’t display the part-of relation as a link in the hierarchy. The EBI hierarchy is a mixed is-a/part-of hierarchy, so you see these part-of descendants.

Once Bioportal correctly processed the ontology, it shouldn’t have any missing terms. It’s just that you are not going to find ‘blood’ as a (part-of) child of "hematopoietic system” in Bioportal’s display hierarchy, but only an “is-a” child of "haemolymphatic fluid”.

With best regards,
Samson


On Aug 13, 2020, at 7:57 AM, John Graybeal <[hidden email]> wrote:

Hello Frans,

I think you have slightly misinterpreted the basis of the discussion, in that almost all of us are semantic engineers, not medically trained. So we were only using the medical terms in question as a means of understanding what these three tools are displaying to users, given the UBERON model that has been defined and their own semantic approaches.

I think the inferred classification that is displayed in Protege might be a bit more precisely described than using the blended terms in your final paragraph, but I'd leave it to someone more semantically expert than myself to get it exactly right. (Samson?) 

But in regard to the medical understanding, we must send you to the builders of the UBERON ontology.

John



On Aug 13, 2020, at 12:15 AM, [hidden email] wrote:

Hi Jennifer and Eva et al,
With great interest I’ve been following this discussion from a professional point of interest.
The UBERON classification is based on anatomical properties. 
In this respect the ‘hematopoietic system’ is most likely to be classified as part of ‘bone marrow’, because this is the place where most of the stem cells  resides. 
The ‘blood’ class as we know it in daily practice is distinct from bone marrow because it flows around between in all compartments like ‘vascular system’ and ‘bone marrow’ system .  
‘Venous blood’ could anatomically be considered as the ‘venous part of’ the ‘vascular system’ (UBERON: distinct class); because this system in general can be divided into arterial, venous and capillary blood compartment; On the other hand the properties of biomarkers in venous blood are distinct from those in capillary and arterial  blood samples and  for this reason we report the lab results in conjunction with the type of sample. So from a propetrt point of view venous blood is a subclass of blood as a substance.   
So I conclude that the inferred classification that ‘venous blood’ isa/partof  ‘blood’ isa/partof ‘hematopoietic system’ might be misleading or even incorrect.  Or did I misinterpret the basics of this discussion? 
 
Best regards
Frans van der Horst  
 
 
Van: bioontology-support <[hidden email]> Namens Jennifer Leigh Vendetti
Verzonden: donderdag 13 augustus 2020 02:57
Aan: Samson Tu <[hidden email]>
CC: [hidden email]; Emma Vos <[hidden email]>
Onderwerp: Re: [bioontology-support] [BioPortal] Feedback from Emma Vos
 
Thanks for that correction Samson, and apologies to all that I navigated down the wrong path in my last response. 
 
Jennifer
 
 


On Aug 12, 2020, at 4:17 PM, Samson Tu <[hidden email]> wrote:
 
Hi,


On Aug 12, 2020, at 10:29 AM, Jennifer Leigh Vendetti <[hidden email]> wrote:
 
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.
 
 
Actually, I think the difference is not between asserted vs inferred hierarchies, but between the kinds links displayed in the Bioportal and EBI hierarchies.The Bioportal hierarchy is a strict is-a hierarchy, whereas the EBI hierarchy is a mixed is-a/part-of hierarchy. Note the P icon in the EBI hierarchy, indicating that blood is part of hematopoietic system, whereas venous blood is a kind of blood. Bioportal correctly shows that hematopoietic system has no is-a child. 
 
<PastedGraphic-1.png>
 
 
With best regards,
Samson
 
 
_______________________________________________
bioontology-support mailing list
[hidden email]
https://mailman.stanford.edu/mailman/listinfo/bioontology-support

========================
John Graybeal
Technical Program Manager
Center for Expanded Data Annotation and Retrieval /+/ NCBO BioPortal
Stanford Center for Biomedical Informatics Research
650-736-1632  | ORCID  0000-0001-6875-5360





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