Open pbuttigieg opened 5 years ago
Is there a link to download the skos?
Looks like I could query it via sparql https://www.bodc.ac.uk/resources/products/web_services/vocab/ but slightly more convenient if there is a download link (preferably stable URLs for different versions)
@gwemon?
I know your collections are here, but what's the right way to get the SKOS?
Hi @pbuttigieg if you click this: view-source:http://vocab.nerc.ac.uk/collection/S27/current/ it will give you the skos. Or if you set your browser/software to receive rdf/xml. Is this what you want?
@pbuttigieg @cmungall You could start with the following: Matrix domain entities: http://vocab.nerc.ac.uk/collection/S21/current/ Matrix phase entities: http://vocab.nerc.ac.uk/collection/S23/current/ The one mentioned by Alex above is our chemical substance vocab: http://vocab.nerc.ac.uk/collection/S27/current/ The physical entity name and its subgroups: http://vocab.nerc.ac.uk/collection/S18/current/ and http://vocab.nerc.ac.uk/collection/S19/current/ The datum vocab: http://vocab.nerc.ac.uk/collection/S20/current/ The one for organs and various body parts is: http://vocab.nerc.ac.uk/collection/S12/current/ Any questions pls let us know.
Thanks @alko-k @gwemon! I think that will work, we'll ping you here if there are any issues
Ah, I see, conneg is used so I can just download the SKOS RDF easily, this is v clear, thanks!
On Thu, Mar 21, 2019 at 10:30 AM Gwen Moncoiffé notifications@github.com wrote:
@pbuttigieg https://github.com/pbuttigieg @cmungall https://github.com/cmungall You could start with the following: Matrix domain entities: http://vocab.nerc.ac.uk/collection/S21/current/ Matrix phase entities: http://vocab.nerc.ac.uk/collection/S23/current/ The one mentioned by Alex above is our chemical substance vocab: http://vocab.nerc.ac.uk/collection/S27/current/ The physical entity name and its subgroups: http://vocab.nerc.ac.uk/collection/S18/current/ and http://vocab.nerc.ac.uk/collection/S19/current/ The datum vocab: http://vocab.nerc.ac.uk/collection/S20/current/ The one for organs and various body parts is: http://vocab.nerc.ac.uk/collection/S12/current/ Any questions pls let us know.
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hi all, I would like to draw your attention to the Interoperability of observable properties description group at RDA. We are aiming to get endorsed as a WG. @gwemon is co-chairing this group, but I really like @adamml, @adamshepherd and @cmungall to look at this: https://rd-alliance.org/groups/harmonizing-fair-descriptions-observational-data-wg and eventually subscribe. Right now we are deciding about meeting days here: we will meet twice a month (first and third week of the month), first week: European/American friendly (18.00 CEST, Vienna/9:00 PDT, San Francisco). Please check doodle: https://doodle.com/poll/6u7469nr5sf3agsu to choose the week day third week: European/Australian friendly (9:00 CEST. Vienna/18:00 AEDT, Melbourne). Please check doodle: https://doodle.com/poll/gb45cmsy74pnwmsg to choose the week day !! Would be great to have Adam Leadbetter involved as we are thinking to reuse the Complex Property Model here... thanks barbara (barbara.magagna@umweltbundesamt.at)
thanks @mabablue for drawing this to our attention. we were sorry to miss the BoF, but i've joined the RDA group
@mabablue thanks for flagging this.
I'll take a look at the teleco times and see if I can join. It'll probably only be one a month due to other "real-life" commitments.
On Wed, 10 Apr 2019, 20:51 Adam Shepherd, notifications@github.com wrote:
thanks @mabablue https://github.com/mabablue for drawing this to our attention. we were sorry to miss the BoF, but i've joined the RDA group
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Thanks @mabablue - the mapping we're doing here can be an example of hard-wiring interoperability across terminology resources. Let's see if we can make this a common practice and a precursor to co-development as standard!
Work in Progress! This comment will be edited.
The idea of "spheres" in general seems a bit alchemical, and is not likely to be maintained in the ENVO architecture. Further, many of the definitions do not actually describe phases, but portions of physical bodies themselves (e.g. "gaseous" is actually referring to the gas parts of the atmosphere). The semantics should be stable, however, as I'm aligning by the definitions.
The notes below clarify why S23 terms may be aligned to ENVO terms with somewhat different labels. In all cases, the semantics reflect the S23 definitions, rather than their label.
Note to self: shell fragment
was a straggler from the previous S23 mapping, be sure to catch now that UBERON shell
is imported.
Great work @pbuttigieg! I will have a look at your comments. Note I could not access the ENVO links. It returns term not found.
Great work @pbuttigieg! I will have a look at your comments. Note I could not access the ENVO links. It returns term not found.
Hi @gwemon the PURLs are not live yet - they will be activated shortly after the release. Right now, they are "reserved" for the classes.
If you want to view the classes, you can open the envo-edit.owl
file in our src/envo/
directory. That's our pre-release dev space.
How will these mappings be packaged? Will it be in a separate graph? Is there an RDF representation of the mappings?
Hi @dr-shorthair
For the moment, I'm adding them as dbxrefs on the respective ENVO classes and will then request NERC to do the same.
I favour this over an external file as this is a "hard mapping" done by curators and it should be advertised with the classes themselves.
xref https://github.com/ESIPFed/sweet/issues/126
We certainly can release an additional RDF file, however.
Partially dependent on https://github.com/ontodev/robot/issues/312
@pbuttigieg Regarding "dissolved plus reactive particulate" , this is effectively "dissolved" i.e. the "liquid phase". However this is the theory and in practice the "purity" of the liquid phase will be dependent on the method used to separate the liquid from the solid phases. When I was at uni the accepted cut-off in oceanography text books was 0.45um. But some people used 0.4um filters and in the field GF/F (nominal pore size of 0.7um) or even sometimes GF/C (even coarser) was used . Still anything measured in the filtrate would be labelled "dissolved". So this is why we also define the filter size/type in a separate vocab (http://vocab.nerc.ac.uk/collection/S24/current/) as part of our semantic model.
Regarding "pigment" and "non-algal particle" I need to double-check the facts behind these with Roy Lowry. The terms were used to build P01 parameter codes for the light absorbance at various wavelength of material filtered and treated with various chemical to try and separate the pigmented from non-pigmented particles. I think they can be ignored for the time being.
Also SPM stands for suspended particulate material (we'll need to tidy those definitions at some stage!).
Finally for "shell and shell fragment", I am pretty sure that this is a misplaced term. It should not be in S23 bus in http://vocab.nerc.ac.uk/collection/S18/current/.
In https://github.com/EnvironmentOntology/envo/pull/728, created during a BODC / NERC-VS, BCO-DMO, and ENVO meeting at the Marine Institute in Dublin, we demonstrated how we would map ontology terms to the SKOS resources in the NERC VS.
We'd like to do this en masse as has been done for the SWEET-ENVO mapping by @cmungall: https://github.com/cmungall/sweet-obo-alignment
Indeed, the NERC Vocabs can be mapped to UBERON and several other OBO resources too.
@gwemon could you suggest which vocabs we should target first? Things that deal with environmental entities (geographic features, materials, etc) and anatomy would be a good place to start.
Ping: @gwemon @ashepherd @adamml