Search Mailing List Archives


Limit search to: Subject & Body Subject Author
Sort by: Reverse Sort
Limit to: All This Week Last Week This Month Last Month
Select Date Range     through    

[bioontology-support] FMA plasma membrane

Maxwell Neal maxneal at gmail.com
Thu Mar 10 10:52:00 PST 2016


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
>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://mailman.stanford.edu/pipermail/bioontology-support/attachments/20160310/0cf218d6/attachment.html>


More information about the bioontology-support mailing list