[Esip-cor] [EXT]Re: [EXTERNAL] SWEET ENVO Cryosphere term mapping

[Mcgibbney, Lewis J (172B)]

Hi Kai,


From: Kai Blumberg <kblumberg at email.arizona.edu>
Date: Wednesday, June 17, 2020 at 12:21 PM
To: "Mcgibbney, Lewis J (172B)" <lewis.j.mcgibbney at jpl.nasa.gov>
Cc: "esip-semanticharmonization at lists.esipfed.org" <esip-semanticharmonization at lists.esipfed.org>, Ruth Duerr <ruth.duerr3 at gmail.com>, Anne Thessen <annethessen at gmail.com>, "Charlesl.lm8ms F. Vardeman II" <charles.vardeman at gmail.com>, Gary Berg-Cross <gbergcross at gmail.com>, Pier Buttigieg <pbuttigi at mpi-bremen.de>, Mark Schildhauer <schild at nceas.ucsb.edu>
Subject: Re: [EXT]Re: [EXTERNAL] SWEET ENVO Cryosphere term mapping

Yes I did, SWEET is small enough that I find working with it manually to be most efficient, especially for a task like this.

OK great.

Unfortunately as far as I can tell, SWEET terms still don’t have definitions at least the version shown on bioportal,

Progress on this issue can be seen at https://github.com/ESIPFed/sweet-tools/pull/5
I will go back to complete that item which will hopefully resolve a large part of this problem

and their id’s which should be URLS e.g., http://sweetontology.net/matrWater/Hydrate don’t seem to resolve.

Thanks for picking this up. I can replicate the behavior. Here is the issue… the pyLODE service (https://github.com/mmisw/orr-portal/wiki/Using-pyLODE-for-ontology-documentation) is servicing Brower-based traffic to SWEET HTTP URIs. For example, see http://sweetontology.net/matrWater. For what I can tell right now, the problem seems to be servicing embedded/nested content… which is strange. Maybe we have some sort of rule which needs to be corrected. I’m going to look into it right now.

There are some automated mappings for example this one made by Chris Mungall 5 years ago<https://github.com/EnvironmentOntology/envo/blob/master/mappings/sweetrealm-mapping.tsv>. Bioportal also has a feature that does automated mappings, see this one between SWEET and ENVO<https://bioportal.bioontology.org/mappings/show/SWEET?target=http://data.bioontology.org/ontologies/ENVO&height=600&width=800>.

I’ve seen these before and they are useful. I was unable to reproduce them myself and spoke to Chris Mungall about this ages ago. We didn’t get any further with it at the time.

Right now, I’m going to work on the COR issues you’ve highlighted. I’m tracking it through https://github.com/mmisw/orr-portal/issues/167
I’ll follow-up her once we fix this.

Lewis
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