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[bioontology-support] [BioPortal] Feedback from Venkat

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


Venkat,

We do not have an example in R in our repository (examples are at https://github.com/ncbo/ncbo_rest_sample_code) that I am aware of.

However, the thread in the support list archives at http://ncbo-support.2288202.n4.nabble.com/bioontology-support-API-Example-Code-in-R-td4655378.html has quite a bit more information that may be useful.

In addition, OntoCat (described in "ontoCAT: an R package for ontology traversal and search", https://academic.oup.com/bioinformatics/article/27/17/2468/223268) is written in R and accesses BIoPortal. So you may find some useful code in that source as well.

John


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


Name: Venkat

Email: gadepallivs at vcu.edu<mailto:gadepallivs at vcu.edu>

Location: http%3A%2F%2Fbioportal.bioontology.org<http://2Fbioportal.bioontology.org>%2F

Feedback:

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


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========================
John Graybeal
Technical Program Manager
Center for Expanded Data Annotation and Retrieval /+/ NCBO BioPortal
Stanford Center for Biomedical Informatics Research
650-736-1632


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