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[bioontology-support] mappingType

Madani,Sina AHMadani at
Tue May 22 08:07:58 PDT 2012

I just saw the announcement of Bioportal 3.8. This is really exciting!

Does the new release address mapping concerns that we had previously (mentioned below) ? If we purchase a third party terminology with mappings to CUIs and import it into our local Bioportal appliance, would it possible to expand the mapping to all other terminologies in the Bioportal appliance based on the CUIs?


From: Trish Whetzel [mailto:whetzel at]
Sent: Monday, February 06, 2012 3:41 PM
To: Madani,Sina
Cc: Paul R Alexander; Ray Fergerson; support at
Subject: Re: [bioontology-support] mappingType

Hi Sina,

I have a few ideas to help you populate the mapping table to use this data to expand results from the Annotator. Can you send information on what ontologies you are using that you would like mapping data for and what mapping data you would like? For example, are you interested in mapping data from UMLS for SNOMED and RxNorm?


On Feb 6, 2012, at 11:52 AM, Madani,Sina wrote:

Thank you Paul.
So I guess for the time being the only component that I can use in service calls for "extended/expanded" annotation is to use  "is-a relationship" feature by setting up maxlevel parameter.

Thanks again for clarification


From: Paul R Alexander [mailto:palexander at]
Sent: Monday, February 06, 2012 1:45 PM
To: Ray Fergerson
Cc: Madani,Sina; support at<mailto:support at>
Subject: Re: [bioontology-support] mappingType


Ray is correct with one exception, putting mappings into the mappings REST service will not make them available in the Annotator. There is a table, obs_map, that needs to be populated in order for the data to be available. There is no automated process for this. If you do populate the table, then whatever value you put for the "mapping_type" column is what will be available for use on your system.

Paul R Alexander
Web / UI Developer
NCBO BioPortal
Stanford Center for Biomedical Informatics Research

On 1/31/12 3:06 PM, Ray Fergerson wrote:

Unfortunately our mappings expert is out this week. He can provide a more definitive answer when he returns. My belief though is that, at some point in the past some process was run to generate lots mappings but that this process was not "productionized". I suspect that it was a one-time effort, probably done by a graduate student. I don't think that there is anything that we can give you that will generate these mappings. We are currently working on "productionizing" the LOOM (Lexical) mapping generation process. Eventually other automated mapping generators will be "productionized" and available with the VM. For now though I suspect that you will have to generate any mappings you want. There is a process (REST API) for getting the mapping into the system. There just is not a process to decide what should be mapped to what.


From: Madani,Sina [mailto:AHMadani at]
Sent: Tuesday, January 31, 2012 2:47 PM
To: Ray Fergerson; support at<mailto:support at>
Subject: RE: [bioontology-support] mappingType

not that I know of. There is a manual mapping available through the UI but I never used it.
Is there a way to post process loaded terminologies in our local instance to generate such mapping so that I can use the inter-cui option? Because the cui-s are there in the attributes.....
I guess my confusion comes from the annotator guide where it mentioned 4 different types of mapping: inter-cui, from-mrrel, automatic, and manual.

From: Ray Fergerson [mailto:ray.fergerson at]
Sent: Tuesday, January 31, 2012 4:40 PM
To: Madani,Sina; support at<mailto:support at>
Subject: RE: [bioontology-support] mappingType


Does your local installation have any mappings at all? I would be surprised. I thought that the VM came with essentially no ontologies and no mappings. If you haven't generated them then they probably aren't there.


From: bioontology-support-bounces at<mailto:bioontology-support-bounces at>[mailto:bioontology-support-bounces at] On Behalf OfMadani,Sina
Sent: Tuesday, January 31, 2012 1:52 PM
To: support at<mailto:support at>
Subject: [bioontology-support] mappingType

If I want to use mappingTypes parameter, like with inter-cui option, in our local Bioportal instance, do I need to perform any pre processing on the loaded terminologies?
I set the type to inter-cui but it doesn't seem to return any mapping for a given term "melanoma"



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Trish Whetzel, PhD
Outreach Coordinator
The National Center for Biomedical Ontology
Ph: 650-721-2378

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