How to map ontology term to database field/entity name

[Public-Health-Bioinformatics]

This is more of a peer-peer project inquiry about how you are handling the relation between ontology datum fields and their use in non-ontology-driven apps. Now maybe APOLLO_SV is narrowly targeted at your Apollo app and therefore this is unnecessary; but since I was thinking of adopting some of your ontology terms ...

You have the AnnotationProperty APOLLO_SV_0000040, "Unique Apollo Label", UAL. "This annotation property gives the unique label of all Apollo_SV entities that are refered to in the schema. The UAL is the denotator for the Apollo_SV class in the schema. There can at all times only be ONE value of UAL for each class."

In GenEpiO I was planning on mapping terms to their database equivalents via the hasDbXref relation.

Just thinking that this is fairly multipurpose insofar as an ontology can use hasDbXref to map a field to any number of 3rd party database fields. Avoids having to introduce a relation for each of them. Thought that might be attractive?

[Public-Health-Bioinformatics]

An update on this. Your resource is much appreciated! GenEpiO is now importing over 30 APOLLO_SV terms! Glad to see it is in Ontofox too.

So to recap, you have annotations like

<apollo_sv:APOLLO_SV_0000040 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">commissions</apollo_sv:APOLLO_SV_0000040>

I had been thinking this could be accomplished by a more generic type of annotation that would enable systematic mapping to more than one 3rd party database or format without need for more annotation codes?

<oboInOwl:hasDbXref>Apollo: commissions</oboInOwl:hasDbXref>

We don't really need to lobby for this anymore. As the cross-database compatibility of many fields depends on the details of their formatting, variable type, etc, I've shifted our own approach in GenEpiO to reference 3rd party fields by establishing a '[name of 3rd party standard or database] data item' class, and making GenEpiO terms subclasses, with all the details of the 3rd party field name, datatype etc annotated on the subclass relation. This will facilitate automated data conversion in the future).

[hoganwr]

Damion, We'll look into doing that. By the way, I was just looking at two classes in GenEpiO to import into Apollo-SV! created date (http://purl.obolibrary.org/obo/GENEPIO_0001882) updated date (http://purl.obolibrary.org/obo/GENEPIO_0001874)

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On Fri, Apr 21, 2017 at 1:14 PM, Damion Dooley ***@***.***> wrote: An update on this. Your resource is much appreciated! GenEpiO is now importing over 30 APOLLO_SV terms! Glad to see it is in Ontofox too. So to recap, you have annotations like <apollo_sv:APOLLO_SV_0000040 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">commissions</apollo_sv:APOLLO_SV_0000040> I had been thinking this could be accomplished by a more generic type of annotation that would enable systematic mapping to more than one 3rd party database or format without need for more annotation codes? <oboInOwl:hasDbXref>Apollo: commissions</oboInOwl:hasDbXref> We don't really need to lobby for this anymore. As the cross-database compatibility of many fields depends on the details of their formatting, variable type, etc, I've shifted our own approach in GenEpiO to reference 3rd party fields by establishing a '[name of 3rd party standard or database] data item' class, and making GenEpiO terms subclasses, with all the details of the 3rd party field name, datatype etc annotated on the subclass relation. This will facilitate automated data conversion in the future). — You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub <#51 (comment)>, or mute the thread <https://github.com/notifications/unsubscribe-auth/ABMe9jildyBhMkye8jVcKMlOC-T_qXNOks5ryOPwgaJpZM4J5ihP> .