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[bioontology-support] FMA plasma membrane

Maxwell Neal maxneal at gmail.com
Fri Mar 18 06:11:58 PDT 2016


Hi Michael,

Yep, it's working on my end. Many thanks for following through with the fix!

M


On Thu, Mar 17, 2016 at 8:30 PM, Michael Dorf <mdorf at stanford.edu> wrote:

> 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> wrote:
>
> Great. Many thanks for the update!
>
> M
>
>
> On Wed, Mar 16, 2016 at 7:23 PM, Michael Dorf <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> 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> 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> 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> 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
>>>>
>>>
>>> _______________________________________________
>>> bioontology-support mailing list
>>> bioontology-support at lists.stanford.edu
>>> https://mailman.stanford.edu/mailman/listinfo/bioontology-support
>>>
>>>
>>>
>>
>>
>
>
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