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[bioontology-support] [BioPortal] Feedback from Marvin Martens

Jennifer Leigh Vendetti vendetti at stanford.edu
Wed Aug 2 17:40:23 PDT 2017


Hi Marvin,


On Jul 31, 2017, at 5:54 AM, support at bioontology.org<mailto:support at bioontology.org> wrote:


Name: Marvin Martens

Email: marvin.martens at maastrichtuniversity.nl<mailto:marvin.martens at maastrichtuniversity.nl>

Location: http%3A%2F%2Fbioportal.bioontology.org<http://2Fbioportal.bioontology.org>%2Fontologies%2FPW%3Fp%3Dclasses%26conceptid%3Dhttp%253A%252F%252Fpurl.obolibrary.org<http://252Fpurl.obolibrary.org>%252Fobo%252FPW_0000001

Feedback:

Dear BioPortal group,
I am working on pathways on WikiPathways, which uses your Pathway ontology. However, I work on a type of pathways that is not in there, and is different: Adverse Outcome Pathways. They are pathways that cover multiple cell types, multiple processes, and often multiple biological levels. I think it would be a great addition if we could work on an ontology for this kind of patway, as it is a growing concept and soon many more of these pathways will be made in wikipathways. Could you tell me what is the best thing to do? What are the possibilities?

I’m not sure I can offer you much in the way of assistance. This support list is focused around addressing questions / issues with the BioPortal software, and/or parsing issues that arise when ontologies are submitted. You might want to consider contacting the authors of the PW ontology (their contact information is listed on the ontology summary page [1]), as they may have ideas about how to extend their ontology, or create a related one.

Alternatively, if you’re looking for assistance with how to model the concepts in your domain, you could try posting a message on the support list for the Protege ontology editing environment [2]. Their list has a large number of subscribers, many of whom are familiar with best practices when building ontologies.

Kind regards,
Jennifer

[1] http://bioportal.bioontology.org/ontologies/PW
[2] http://protege.stanford.edu/support.php
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