Re: [bioontology-support] trying to use rootpath service.

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Re: [bioontology-support] trying to use rootpath service.

Ray Fergerson

Lori,

 

First let me admit up front that this is terribly confusing. I will try to explain, but I will have to give you more information that you would expect to have to know.

 

This functionality (get all paths to root) is implemented on top of the annotator database rather than on top of the BioPortal ontology store directly. The result is that it behaves quite differently from other BioPortal methods. In particular:

(1)    Only one version of the ontology is in the annotator db so only one version is available to query.

(2)    The version available to query is the one that was current when the annotator db was created. Ideally this would be a week ago. Currently though the difference is several months.

(3)    You can make the rest call with the version id rather than the virtual id but you may not get anything back because that ontology version is not in the db. The virtual id will always give you access to whatever is in the db.  That is why this call is recommended in the docs.

 

You don’t have to tell me that this is terrible behavior. We know. It will eventually get fixed.

 

The only way to get all paths to root for a particular version is to calculate it directly from the BioPortal get term calls. The “get single path to root” API does use the BioPortal ontology store. It only returns a random path to root though an not all of them.

 

Ray

 

 

From: Phillips, Lori C. [mailto:[hidden email]]
Sent: Wednesday, April 06, 2011 10:27 AM
To: Ray Fergerson
Subject: trying to use rootpath service.

 

Hi Ray,

 

I have been told that I can use rootpath to get all delimited paths to root for a term:  e.g.

<a href="http://rest.bioontology.org/bioportal/virtual/rootpath/1353/9932004?delim=\&amp;email=example@example.org"> http://rest.bioontology.org/bioportal/virtual/rootpath/1353/9932004?delim=\&email=example@... 

 

1. Does it only work with virtual ids?

2. Does it not work for views?   2021 is the id for the SNOMED Organism view.

     

  Following  returns error that ontology id is not found

 

<a href="http://rest.bioontology.org/bioportal/virtual/rootpath/1353/9932004?delim=\&amp;email=example@example.org"> http://rest.bioontology.org/bioportal/virtual/rootpath/2021/9932004?delim=\&email=example@... 

 

Thanks

Lori



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Re: [bioontology-support] trying to use rootpath service.

Ray Fergerson

Lori,

 

You are correct. If you need get all paths to root for any version of an ontology other than the one used for annotation then currently you have to calculate it yourself.

 

Ray

 

From: Phillips, Lori C. [mailto:[hidden email]]
Sent: Wednesday, April 06, 2011 1:44 PM
To: Ray Fergerson
Subject: RE: trying to use rootpath service.

 

Trying to make sure I understand, but let me give you my situation...

 

The biggest issue I have in the NCBO extraction tool for i2b2 is building the i2b2 fullname (paths to root) for each term.

I originally did this by making successive getTerm calls, but as you may remember, this was discouraged because I was causing too much traffic on your network. I was also encouraged to use views (especially in the case of SNOMED) because it would break down the problem of trying to get all of SNOMED at once.  Nigam suggested that I use the 'all' rest service to page through and get all the concepts in a view and then go back and do a 'get all paths to root'  for each term.  This latter part (get all paths to root) is what I am attempting to do now.

 

But you are saying (I think) that this information (get all paths to root) is not necessarily available...

 

Sounds like the only option I have that is dependable is to compute the path myself...

Yes? No?

 

Thanks

Lori

 


From: Ray Fergerson [mailto:[hidden email]]
Sent: Wednesday, April 06, 2011 4:21 PM
To: Phillips, Lori C.
Cc: [hidden email]
Subject: RE: trying to use rootpath service.

Lori,

 

First let me admit up front that this is terribly confusing. I will try to explain, but I will have to give you more information that you would expect to have to know.

 

This functionality (get all paths to root) is implemented on top of the annotator database rather than on top of the BioPortal ontology store directly. The result is that it behaves quite differently from other BioPortal methods. In particular:

(1)    Only one version of the ontology is in the annotator db so only one version is available to query.

(2)    The version available to query is the one that was current when the annotator db was created. Ideally this would be a week ago. Currently though the difference is several months.

(3)    You can make the rest call with the version id rather than the virtual id but you may not get anything back because that ontology version is not in the db. The virtual id will always give you access to whatever is in the db.  That is why this call is recommended in the docs.

 

You don’t have to tell me that this is terrible behavior. We know. It will eventually get fixed.

 

The only way to get all paths to root for a particular version is to calculate it directly from the BioPortal get term calls. The “get single path to root” API does use the BioPortal ontology store. It only returns a random path to root though an not all of them.

 

Ray

 

 

From: Phillips, Lori C. [mailto:[hidden email]]
Sent: Wednesday, April 06, 2011 10:27 AM
To: Ray Fergerson
Subject: trying to use rootpath service.

 

Hi Ray,

 

I have been told that I can use rootpath to get all delimited paths to root for a term:  e.g.

<a href="http://rest.bioontology.org/bioportal/virtual/rootpath/1353/9932004?delim=\&amp;email=example@example.org"> http://rest.bioontology.org/bioportal/virtual/rootpath/1353/9932004?delim=\&email=example@... 

 

1. Does it only work with virtual ids?

2. Does it not work for views?   2021 is the id for the SNOMED Organism view.

     

  Following  returns error that ontology id is not found

 

<a href="http://rest.bioontology.org/bioportal/virtual/rootpath/1353/9932004?delim=\&amp;email=example@example.org"> http://rest.bioontology.org/bioportal/virtual/rootpath/2021/9932004?delim=\&email=example@... 

 

Thanks

Lori



The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.


_______________________________________________
bioontology-support mailing list
[hidden email]
https://mailman.stanford.edu/mailman/listinfo/bioontology-support