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[bioontology-support] [BioPortal] Feedback from Karen Yook

Jennifer Leigh Vendetti vendetti at stanford.edu
Wed Aug 15 15:55:16 PDT 2018


Hi Karen,

I made a mistake in my replies to you. There is apparently a difference between OBO Foundry and OBO library ontologies. There’s a set of 10 OBO Foundry ontologies, which can be seen on the OBO Foundry website (http://www.obofoundry.org/) shaded in blue:

[cid:98E254C6-BF21-4F66-BA0E-AD5348CDFD8E at stanford.edu]



All other ontologies on their website (shaded in white) are OBO library ontologies. BioPortal’s OBO_Foundry group is only supposed to contain the set of 10 OBO Foundry ontologies, so I will need to undo the addition of WB-PHENOTYPE to that group. When you’re using the Ontology Browser page and looking for an OBO ontology that’s not one of the 10 OBO Foundry ontologies, please instead use the “OBO” filter in the Format box:

[cid:EE3F89DC-9FDA-4B5C-9F01-28D210928E5C at stanford.edu]

Apologies for the confusion.

Jennifer





On Aug 15, 2018, at 1:56 PM, Jennifer Leigh Vendetti <vendetti at stanford.edu<mailto:vendetti at stanford.edu>> wrote:

I added the ontology to the OBO_Foundry group, so you should be able to use that filter now on the Ontology Browser page.

You mentioned that you think some of the ontology metadata like the name is out of date? We could ping the contact person and ask them to update this information. Do you know if Gary Schindelman is still the maintainer?

Jennifer



<Screenshot 2018-08-15 13.55.51.png>



On Aug 15, 2018, at 1:15 PM, Karen Yook <karen at wormbase.org<mailto:karen at wormbase.org>> wrote:

Ah, that must be it.  Also I was searching for the original name of the ontology, that being Worm Phenotype Ontology, which is not found. I do not know when the name changed or if that ever gets used anymore.
Thanks for your reply.

Karen


~~~~
Karen Yook

Curator
WormBase Caltech
Tel: 415.306.4150
e-mail: kyook at caltech.edu<mailto:kyook at caltech.edu>
e-mail: karen at wormbase.org<mailto:karen at wormbase.org>
skype name: wbkaren


On Wed, Aug 15, 2018 at 1:10 PM, Jennifer Leigh Vendetti <vendetti at stanford.edu<mailto:vendetti at stanford.edu>> wrote:
Hi Karen,

I don’t follow exactly what you’re asking. The ontology is listed in our Ontology Browser page (screen shot below). Do you mean that it should also be designated as part of the “OBO_Foundry” group?

Jennifer



<Screenshot 2018-08-15 13.08.10.png>



On Aug 15, 2018, at 1:02 PM, support at bioontology.org<mailto:support at bioontology.org> wrote:


Name: Karen Yook

Email: karen at wormbase.org<mailto:karen at wormbase.org>

Location: https%3A%2F%2Fbioportal.bioontology.org<http://2fbioportal.bioontology.org/>%2Fontologies%3Ffilter%3DOBO_Foundry

Feedback:

I'm wondering why the C. elegans phenotype ontology isn't listed in the library of ontologies. It seems like it should be. Is this a matter of file naming?

https://bioportal.bioontology.org/ontologies/WB-PHENOTYPE/?p=summary

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<Screen Shot 2018-08-15 at 1.13.31 PM.png>

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