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[bioontology-support] FMA plasma membrane

Michael Dorf mdorf at stanford.edu
Thu Mar 17 17:30:38 PDT 2016


Hi Maxwell,

This should now be resolved. I've tried your search for "plasma" and the results now include the term "Plasma membrane".

Please let me know if you run into any further issues. Thank you again for bearing with us while we were resolving this problem!

Michael


On Mar 16, 2016, at 16:36, Maxwell Neal <maxneal at gmail.com<mailto:maxneal at gmail.com>> wrote:

Great. Many thanks for the update!

M


On Wed, Mar 16, 2016 at 7:23 PM, Michael Dorf <mdorf at stanford.edu<mailto:mdorf at stanford.edu>> wrote:
Hi Maxwell,

I've tried re-parsing FMA ontology last Friday after updating the prefLabel, synonym, and definition property names for the ontology. Unfortunately, the processing had not completed successfully. I am taking another go at it today. This time, instead of re-processing the existing FMA submission, I've created a new one, which points to the original OWL file. At the moment it is still being parsed. I'll let you know once it's completed.

Thank you for your patience on this!

Michael


On Mar 16, 2016, at 13:48, Maxwell Neal <maxneal at gmail.com<mailto:maxneal at gmail.com>> wrote:

Hi Michael,

I wanted to check in and see how things were going with re-processing the FMA. On my end, I still can't retrieve the "Plasma membrane" term using the REST API. I also checked whether the term appears in the BioPortal class browser but I get the "We're sorry but something has gone wrong..." message when I click on the BioPortal PURL link on the main FMA page, and I get a blank page when I click on the "Classes" link at the top of that page. So I haven't been able to browse the FMA classes.

Any help is appreciated! Many thanks,

M


On Fri, Mar 11, 2016 at 2:13 PM, Michael Dorf <mdorf at stanford.edu<mailto:mdorf at stanford.edu>> wrote:
Maxwell, hi!

I've looked into this, and it turned out to be a tricky one. It appears that the term corresponding to "Plasma membrane" doesn't have the prefLabel or synonym properties set, which is what we use when we index an ontology for search. There are properties that define both, but they are not set as the "go-to" properties for determining prefLabel and synonyms:

http://data.bioontology.org/ontologies/FMA/classes/http%3A%2F%2Fpurl.org%2Fsig%2Font%2Ffma%2Ffma63841?display=all<http://data.bioontology.org/ontologies/FMA/classes/http://purl.org/sig/ont/fma/fma63841?display=all>

Note that prefLabel=null and synonym=[].

I looked at a different term that has the prefLabel set:

http://data.bioontology.org/ontologies/FMA/classes/http%3A%2F%2Fpurl.org%2Fsig%2Font%2Ffma%2Ffma86454/?display=all<http://data.bioontology.org/ontologies/FMA/classes/http://purl.org/sig/ont/fma/fma86454/?display=all>

As you can see, it appears to have some additional entries in the "properties: {}" block, one of which is used to define the prefLabel for this term.

I am going to set the ontology metadata to use the following properties for prefLabel, synonym and definition respectively, since they appear to be common across my sample pool of terms:

http://purl.org/sig/ont/fma/preferred_name
http://purl.org/sig/ont/fma/synonym
http://purl.org/sig/ont/fma/definition

I'll need to re-process the ontology once I make that change, which will take anywhere from an hour to six, depending on the size of the ontology. Hopefully, this will fix the problem. I'll keep you posted.

Thanks for reporting this!

Michael



On Mar 10, 2016, at 10:52, Maxwell Neal <maxneal at gmail.com<mailto:maxneal at gmail.com>> wrote:

Hello,

I wanted to check if you received my note from last week about the FMA term "Plasma membrane" not being returned by searches using the BioPortal REST API. My research team and I are conducting formal evaluations of our annotation software and unfortunately FMA:Plasma membrane is one of the terms that participants in our study are very likely to search for. So, for our research purposes, it's quite important that the term is returned via the BioPortal REST service. Below is my original note. Many thanks!

-Max

***
I have an application that uses the BioPortal REST API to allow users to search and retrieve classes from several ontologies on BioPortal.

My development team recently noticed that the FMA term "Plasma membrane" is not being returned when users search for "plasma", "membrane", or "plasma membrane." We can, however, retrieve many other FMA classes that contain the phrase "plasma membrane" (such as "Plasma membrane of biophil").

Here is an example of a REST call sent from our application to BioPortal that fails to retrieve the class:

http://data.bioontology.org/search?q=plasma&ontologies=FMA&format=xml&exact_match=false&apikey=c4192e4b-88a8-4002-ad08-b4636c88df1a

We also noticed that the name of the plasma membrane class is not visible in the FMA class tree browser on BioPortal. Instead, there is a blank node. You can actually click on the node and see the info for the plasma membrane class

Any help is appreciated!

***

On Fri, Mar 4, 2016 at 5:30 PM, Maxwell Neal <maxneal at gmail.com<mailto:maxneal at gmail.com>> wrote:
Hi BioPortal support team,

I have an application that uses the BioPortal REST API to allow users to search and retrieve classes from several ontologies on BioPortal.

My development team recently noticed that the FMA term "Plasma membrane" is not being returned when users search for "plasma", "membrane", or "plasma membrane." We can, however, retrieve many other FMA classes that contain the phrase "plasma membrane" (such as "Plasma membrane of biophil").

Here is an example of a REST call sent from our application to BioPortal that fails to retrieve the class:

http://data.bioontology.org/search?q=plasma&ontologies=FMA&format=xml&exact_match=false&apikey=c4192e4b-88a8-4002-ad08-b4636c88df1a

We also noticed that the name of the plasma membrane class is not visible in the FMA class tree browser on BioPortal. Instead, there is a blank node. You can actually click on the node and see the info for the plasma membrane class.

Any help is appreciated!

Many thanks,

M

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