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[bioontology-support] FMA plasma membrane

John Graybeal jbgmeta1 at stanford.edu
Fri Mar 11 10:03:48 PST 2016


Hi Maxwell,

I’m not sure if there was a response already, but wanted to let you know we have started to take a look at this. It seems a bit odd, but I’m sure we’ll get it tracked down.

John

On Mar 10, 2016, at 10:52 AM, 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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========================
John Graybeal
Technical Program Manager
Center for Expanded Data Annotation and Retrieval /+/ NCBO BioPortal
Stanford Center for Biomedical Informatics Research
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