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OHDSI / OMOP-Standardized-Vocabularies

This repository is not longer active. It used to have the only purpose of creating releases of the Standardized Vocabularies, i.e. the content, not those of the Pallas Vocabulary Build System itself. As of 17-July-2018, vocabulary releases are also processed by Pallas. Please visit https://github.com/OHDSI/Vocabulary-v5.0/releases.
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MeSH-to-standard concept mapping #39

Closed kp14 closed 5 years ago

kp14 commented 5 years ago

Hi,

In Athena, the MeSH concept 'Zika Virus Infection' (concept ID 28543) is listed as mapping to the the standard concept ID 4214984 in the section 'term connections' (see here). Based on this, when I downloaded the MeSH vocabulary data from Athena, I expected to find a 'Maps to' relationship from 28543 -> 4214984 in the file CONCEPT_RELATIONSHIP.csv. It is not there though.

Is there a way to explore mappings of the non-standard MeSH concepts to the standard concepts apart from looking at individual terms in Athena?

Note: I have only just started exploring Athena so it might well be that I am not seeing the obvious or lack understanding of the OMOP mappings.

Any pointers you might be able to give will be greatly appreciated.

Regards, Klemens

dimshitc commented 5 years ago

Did you include both MeSH and Snomed in a bunch? There are checkboxes near the vocabulary names.

On Fri, May 31, 2019 at 1:56 PM kp14 notifications@github.com wrote:

Hi,

In Athena, the MeSH concept 'Zika Virus Infection' (concept ID 28543) is listed as mapping to the the standard concept ID 4214984 in the section 'term connections' (see here http://athena.ohdsi.org/search-terms/terms/28543). Based on this, when I downloaded the MeSH vocabulary data from Athena, I expected to find a 'Maps to' relationship from 28543 -> 4214984 in the file CONCEPT_RELATIONSHIP.csv. It is not there though.

Is there a way to explore mappings of the non-standard MeSH concepts to the standard concepts apart from looking at individual terms in Athena?

Note: I have only just started exploring Athena so it might well be that I am not seeing the obvious or lack understanding of the OMOP mappings.

Any pointers you might be able to give will be greatly appreciated.

Regards, Klemens

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kp14 commented 5 years ago

No, I downloaded them separately. Aha, so the preparation process that takes place before a download is ready takes care of linking the selected vocabularies? I will try that. Thanks for the hint!

kp14 commented 5 years ago

Yes, that was it. Now I have the expected mapping.

Thank you very much for your help!