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[bioontology-support] [BioPortal] Feedback from Venkat

John Graybeal jgraybeal at
Thu Aug 9 11:27:50 PDT 2018


We do not have an example in R in our repository (examples are at that I am aware of.

However, the thread in the support list archives at has quite a bit more information that may be useful.

In addition, OntoCat (described in "ontoCAT: an R package for ontology traversal and search", is written in R and accesses BIoPortal. So you may find some useful code in that source as well.


On Aug 9, 2018, at 8:49 AM, support at<mailto:support at> wrote:

Name: Venkat

Email: gadepallivs at<mailto:gadepallivs at>



I am an R user, do you have an example of downloading data using R?
I am interested in the complete lineage of Microorganism/Prokaryote/bacteria lineage ...
Trying to convert each branch into a row, however because of cyclic network I am failing to do so.

Wondering if there is an easier way to download the network into a table format?

appreciate your inputs

bioontology-support mailing list
bioontology-support at<mailto:bioontology-support at>

John Graybeal
Technical Program Manager
Center for Expanded Data Annotation and Retrieval /+/ NCBO BioPortal
Stanford Center for Biomedical Informatics Research

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