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[bioontology-support] FMA plasma membrane

Michael Dorf mdorf at stanford.edu
Fri Mar 11 11:13:18 PST 2016


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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