New terms for refineries and reactors #1184
Merged
Conversation
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
http://purl.obolibrary.org/obo/ENVO_02000139 used for transport of http://purl.obolibrary.org/obo/ENVO_02000145 used for processing of http://purl.obolibrary.org/obo/ENVO_02000137 nuclear power reactor http://purl.obolibrary.org/obo/ENVO_02000138 mangrove biome soil http://purl.obolibrary.org/obo/ENVO_02000141 refinery http://purl.obolibrary.org/obo/ENVO_02000142 petroleum oil refinery http://purl.obolibrary.org/obo/ENVO_02000143 sugar refinery http://purl.obolibrary.org/obo/ENVO_02000144 natural gas processing plant
pbuttigieg
requested changes
Jun 17, 2021
src/envo/envo-edit.owl
Outdated
| @@ -4115,6 +4127,23 @@ AnnotationAssertion(<http://purl.obolibrary.org/obo/IAO_0000115> <http://purl.ob | |||
| AnnotationAssertion(rdfs:comment <http://purl.obolibrary.org/obo/ENVO_01001307> "Definition modified from 'surrounded by'.") | |||
| AnnotationAssertion(rdfs:label <http://purl.obolibrary.org/obo/ENVO_01001307> "partially_surrounded_by") | |||
|
|
|||
| # Object Property: <http://purl.obolibrary.org/obo/ENVO_02000139> (used for transport of) | |||
|
|
|||
| AnnotationAssertion(<http://purl.obolibrary.org/obo/IAO_0000115> <http://purl.obolibrary.org/obo/ENVO_02000139> "A relation between a material entity and a material where the function of the material entity is realized as a process that results in the movement of the material.") | |||
There was a problem hiding this comment.
A relation between a material entity and a material where the function of the material entity is realized as a process that results in the movement of the material
Comments:
- I don't think functions can be realised "as" processes
- many non-utilitarian relations can result in the movement of a material
Questions:
- This appears to be shorthand to avoid creating the function class and linking to the transport process itself correct? Is there documentation on how to formulate these shorthand relations?
- Are you keeping this broad enough to allow it to be used for things like "xylem used_for_transport_of water" ? Or does this have to be intentional usage?
I'd rather have the actual functions and processes, especially if there's no convention or documentation on how these shorthand relations should be understood (is there?).
src/envo/envo-edit.owl
Outdated
|
|
||
| # Object Property: <http://purl.obolibrary.org/obo/ENVO_02000145> (used for processing of) | ||
|
|
||
| AnnotationAssertion(<http://purl.obolibrary.org/obo/IAO_0000115> <http://purl.obolibrary.org/obo/ENVO_02000145> "A relation between a two material entities where the function of the first is realized as a process that has the second as input.") |
There was a problem hiding this comment.
As above. Also, as above, the phrasing of the definition is unclear - how can a function be realised as a processes?
|
|
||
| # Class: <http://purl.obolibrary.org/obo/ENVO_02000137> (nuclear power reactor) | ||
|
|
||
| AnnotationAssertion(Annotation(<http://www.geneontology.org/formats/oboInOwl#hasDbXref> "https://en.wikipedia.org/wiki/Nuclear_reactor") <http://purl.obolibrary.org/obo/IAO_0000115> <http://purl.obolibrary.org/obo/ENVO_02000137> "A nuclear reactor which is used as a source of power.") |
There was a problem hiding this comment.
Seems circular, but we do have the power plant branch - could that be used / cross-axiomatised here? Like a power plant that has part some nuclear reactor?
There was a problem hiding this comment.
it sounds circular but it's not, as the differentia is in the intended use/function, to produce power (as opposed to say producing radioisotopes for imaging). We do have a logical axiom connecting the plane to the reactor.
I do think it's worth doing an overall review of design patterns for the existing terms for power plant - do you mind if we do this as a separate ticket/PR?
There was a problem hiding this comment.
it sounds circular but it's not, as the differentia is in the intended use/function, to produce power (as opposed to say producing radioisotopes for imaging). We do have a logical axiom connecting the plane to the reactor.
Okay, clarified.
I do think it's worth doing an overall review of design patterns for the existing terms for power plant - do you mind if we do this as a separate ticket/PR?
Yes, that should be separate to stay focused.
|
|
||
| # Class: <http://purl.obolibrary.org/obo/ENVO_02000143> (sugar refinery) | ||
|
|
||
| AnnotationAssertion(Annotation(<http://www.geneontology.org/formats/oboInOwl#hasDbXref> "https://en.wikipedia.org/wiki/Sugar_refinery") <http://purl.obolibrary.org/obo/IAO_0000115> <http://purl.obolibrary.org/obo/ENVO_02000143> "a refinery which is used for processing raw sugar. Raw sugar is processed from cane or beets into white refined sugar.") |
There was a problem hiding this comment.
Capitalisation and gloss extraction as above. Also, there's something off about these definitions - one doesn't "use" the whole refinery for this, and some which are inactive are still refineries.
Perhaps a pattern like:
A refinery which is capable of processing raw sugar.
There was a problem hiding this comment.
Gloss extraction to comment on:
Raw sugar is processed from cane or beets into white refined sugar.
|
On Thu, Jun 17, 2021 at 8:45 AM Pier Luigi Buttigieg < ***@***.***> wrote:
***@***.**** requested changes on this pull request.
Thanks for the additions, interesting stuff - minor comments in general
but there's something a bit off about the definitional pattern to me (as
noted in sugar refinery)
------------------------------
In src/envo/envo-edit.owl
<#1184 (comment)>
:
> @@ -4115,6 +4127,23 @@ AnnotationAssertion(<http://purl.obolibrary.org/obo/IAO_0000115> <http://purl.ob
AnnotationAssertion(rdfs:comment <http://purl.obolibrary.org/obo/ENVO_01001307> "Definition modified from 'surrounded by'.")
AnnotationAssertion(rdfs:label <http://purl.obolibrary.org/obo/ENVO_01001307> "partially_surrounded_by")
+# Object Property: <http://purl.obolibrary.org/obo/ENVO_02000139> (used for transport of)
+
+AnnotationAssertion(<http://purl.obolibrary.org/obo/IAO_0000115> <http://purl.obolibrary.org/obo/ENVO_02000139> "A relation between a material entity and a material where the function of the material entity is realized as a process that results in the movement of the material.")
A relation between a material entity and a material where the function of
the material entity is realized as a process that results in the movement
of the material
Comments:
- I don't think functions can be realised "as" processes
- many non-utilitarian relations can result in the movement of a
material
Questions:
- This appears to be shorthand to avoid creating the function class
and linking to the transport process itself correct? Is there documentation
on how to formulate these shorthand relations?
- Are you keeping this broad enough to allow it to be used for things
like "xylem used_for_transport_of water" ? Or does this have to be
intentional usage?
I'd rather have the actual functions and processes, especially if there's
no convention or documentation on how these shorthand relations should be
understood (is there?).
Concerns understood. Working on shortcut docs. There are challenges here
due to limitations of OWL.
What I suggest is that I amend the PR to create process classes (not
function classes). The general pattern would be
{SubjectMaterialEntity} sub capable-of some ({Process} and
{process-to-ME-relation} some {ObjectMaterialEntity}
This fits in well with ENVO as we have a good set of process classes there
already, and we are using various RO process-to-ME-relations anyway. There
is definitely room for improvement in these, but this would apply to our
whole process hierarchy
So for example
oil-pipeline sub capable-of some ('material transport' and has-input some
oil)
I would create a new process class for refining (potentially with
sub-processes)
[oh, I see you say something equivalent below]
------------------------------
In src/envo/envo-edit.owl
<#1184 (comment)>
:
> @@ -4115,6 +4127,23 @@ AnnotationAssertion(<http://purl.obolibrary.org/obo/IAO_0000115> <http://purl.ob
AnnotationAssertion(rdfs:comment <http://purl.obolibrary.org/obo/ENVO_01001307> "Definition modified from 'surrounded by'.")
AnnotationAssertion(rdfs:label <http://purl.obolibrary.org/obo/ENVO_01001307> "partially_surrounded_by")
+# Object Property: <http://purl.obolibrary.org/obo/ENVO_02000139> (used for transport of)
+
+AnnotationAssertion(<http://purl.obolibrary.org/obo/IAO_0000115> <http://purl.obolibrary.org/obo/ENVO_02000139> "A relation between a material entity and a material where the function of the material entity is realized as a process that results in the movement of the material.")
+AnnotationAssertion(<http://purl.obolibrary.org/obo/IAO_0000232> <http://purl.obolibrary.org/obo/ENVO_02000139> "This may be later moved to RO")
+AnnotationAssertion(<http://purl.org/dc/elements/1.1/creator> <http://purl.obolibrary.org/obo/ENVO_02000139> "cjm"^^xsd:string)
+AnnotationAssertion(rdfs:label <http://purl.obolibrary.org/obo/ENVO_02000139> "used for transport ***@***.***)
+ObjectPropertyDomain(<http://purl.obolibrary.org/obo/ENVO_02000139> <http://purl.obolibrary.org/obo/BFO_0000040>)
+ObjectPropertyRange(<http://purl.obolibrary.org/obo/ENVO_02000139> <http://purl.obolibrary.org/obo/BFO_0000040>)
+
+# Object Property: <http://purl.obolibrary.org/obo/ENVO_02000145> (used for processing of)
+
+AnnotationAssertion(<http://purl.obolibrary.org/obo/IAO_0000115> <http://purl.obolibrary.org/obo/ENVO_02000145> "A relation between a two material entities where the function of the first is realized as a process that has the second as input.")
As above. Also, as above, the phrasing of the definition is unclear - how
can a function be realised as a processes?
should be realizes, but as per above, I can simply remove this relation
------------------------------
In src/envo/envo-edit.owl
<#1184 (comment)>
:
> @@ -37272,6 +37302,57 @@ AnnotationAssertion(<http://www.geneontology.org/formats/oboInOwl#hasDbXref> <ht
AnnotationAssertion(rdfs:label <http://purl.obolibrary.org/obo/ENVO_02000131> "flue gas desulfurization ***@***.***)
SubClassOf(<http://purl.obolibrary.org/obo/ENVO_02000131> <http://purl.obolibrary.org/obo/ENVO_02000127>)
+# Class: <http://purl.obolibrary.org/obo/ENVO_02000133> (nuclear reactor)
+
+AnnotationAssertion(Annotation(<http://www.geneontology.org/formats/oboInOwl#hasDbXref> "https://en.wikipedia.org/wiki/Nuclear_reactor") <http://purl.obolibrary.org/obo/IAO_0000115> <http://purl.obolibrary.org/obo/ENVO_02000133> "a human construction which is used to initiate and control a fission nuclear chain reaction or nuclear fusion reactions.")
Capitalisation needed on first word.
will do
------------------------------
In src/envo/envo-edit.owl
<#1184 (comment)>
:
> @@ -37272,6 +37302,57 @@ AnnotationAssertion(<http://www.geneontology.org/formats/oboInOwl#hasDbXref> <ht
AnnotationAssertion(rdfs:label <http://purl.obolibrary.org/obo/ENVO_02000131> "flue gas desulfurization ***@***.***)
SubClassOf(<http://purl.obolibrary.org/obo/ENVO_02000131> <http://purl.obolibrary.org/obo/ENVO_02000127>)
+# Class: <http://purl.obolibrary.org/obo/ENVO_02000133> (nuclear reactor)
+
+AnnotationAssertion(Annotation(<http://www.geneontology.org/formats/oboInOwl#hasDbXref> "https://en.wikipedia.org/wiki/Nuclear_reactor") <http://purl.obolibrary.org/obo/IAO_0000115> <http://purl.obolibrary.org/obo/ENVO_02000133> "a human construction which is used to initiate and control a fission nuclear chain reaction or nuclear fusion reactions.")
+AnnotationAssertion(<http://purl.org/dc/elements/1.1/creator> <http://purl.obolibrary.org/obo/ENVO_02000133> <https://orcid.org/0000-0002-6601-2165>)
+AnnotationAssertion(rdfs:label <http://purl.obolibrary.org/obo/ENVO_02000133> "nuclear ***@***.***)
+SubClassOf(<http://purl.obolibrary.org/obo/ENVO_02000133> <http://purl.obolibrary.org/obo/ENVO_00000070>)
+SubClassOf(<http://purl.obolibrary.org/obo/ENVO_02000133> ObjectSomeValuesFrom(<http://purl.obolibrary.org/obo/RO_0002215> ObjectIntersectionOf(<http://purl.obolibrary.org/obo/ENVO_2000012> ObjectSomeValuesFrom(<http://purl.obolibrary.org/obo/BFO_0000055> <http://purl.obolibrary.org/obo/ENVO_2000025>))))
+
+# Class: <http://purl.obolibrary.org/obo/ENVO_02000134> (thermal nuclear reactor)
+
+AnnotationAssertion(Annotation(<http://www.geneontology.org/formats/oboInOwl#hasDbXref> "https://en.wikipedia.org/wiki/Thermal-neutron_reactor") <http://purl.obolibrary.org/obo/IAO_0000115> <http://purl.obolibrary.org/obo/ENVO_02000134> "a nuclear reactor which uses slow or thermal neutrons.")
Capitalisation. Further, this definition seems insufficient - what are
slow neutrons?
how about
A nuclear reactor which uses a nuclear moderator to reduce the speed of
fast neutrons. A fast neutron is a free neutron with a kinetic energy level
close to 1 MeV (100 TJ/kg), hence a speed of 14,000 km/s, or higher.
from
https://en.wikipedia.org/wiki/Thermal-neutron_reactor
https://en.wikipedia.org/wiki/Neutron_moderator
We could keep going unwinding terms in differentia but before we know it we
have rewritten CHEBI and created a complete nuclear power plant ontology.
My general strategy here is to unwind to a reasonable level leaving hooks
that can be expanded later. In this case we may introduce a new class for
nuclear moderator but we wouldn't go any further, and we wouldn't try and
capture the nuances of the necessary and sufficient conditions in an
equivalence axiom, but capture what we can of the necessary conditions with
subclass axioms
------------------------------
In src/envo/envo-edit.owl
<#1184 (comment)>
:
> +
+AnnotationAssertion(Annotation(<http://www.geneontology.org/formats/oboInOwl#hasDbXref> "https://en.wikipedia.org/wiki/Nuclear_reactor") <http://purl.obolibrary.org/obo/IAO_0000115> <http://purl.obolibrary.org/obo/ENVO_02000133> "a human construction which is used to initiate and control a fission nuclear chain reaction or nuclear fusion reactions.")
+AnnotationAssertion(<http://purl.org/dc/elements/1.1/creator> <http://purl.obolibrary.org/obo/ENVO_02000133> <https://orcid.org/0000-0002-6601-2165>)
+AnnotationAssertion(rdfs:label <http://purl.obolibrary.org/obo/ENVO_02000133> "nuclear ***@***.***)
+SubClassOf(<http://purl.obolibrary.org/obo/ENVO_02000133> <http://purl.obolibrary.org/obo/ENVO_00000070>)
+SubClassOf(<http://purl.obolibrary.org/obo/ENVO_02000133> ObjectSomeValuesFrom(<http://purl.obolibrary.org/obo/RO_0002215> ObjectIntersectionOf(<http://purl.obolibrary.org/obo/ENVO_2000012> ObjectSomeValuesFrom(<http://purl.obolibrary.org/obo/BFO_0000055> <http://purl.obolibrary.org/obo/ENVO_2000025>))))
+
+# Class: <http://purl.obolibrary.org/obo/ENVO_02000134> (thermal nuclear reactor)
+
+AnnotationAssertion(Annotation(<http://www.geneontology.org/formats/oboInOwl#hasDbXref> "https://en.wikipedia.org/wiki/Thermal-neutron_reactor") <http://purl.obolibrary.org/obo/IAO_0000115> <http://purl.obolibrary.org/obo/ENVO_02000134> "a nuclear reactor which uses slow or thermal neutrons.")
+AnnotationAssertion(<http://purl.org/dc/elements/1.1/creator> <http://purl.obolibrary.org/obo/ENVO_02000134> <https://orcid.org/0000-0002-6601-2165>)
+AnnotationAssertion(<http://www.geneontology.org/formats/oboInOwl#hasExactSynonym> <http://purl.obolibrary.org/obo/ENVO_02000134> "thermal reactor")
+AnnotationAssertion(rdfs:label <http://purl.obolibrary.org/obo/ENVO_02000134> "thermal nuclear ***@***.***)
+SubClassOf(<http://purl.obolibrary.org/obo/ENVO_02000134> <http://purl.obolibrary.org/obo/ENVO_02000137>)
+
+# Class: <http://purl.obolibrary.org/obo/ENVO_02000135> (fast neutron reactor)
As above.
ok
------------------------------
In src/envo/envo-edit.owl
<#1184 (comment)>
:
> +AnnotationAssertion(<http://purl.org/dc/elements/1.1/creator> <http://purl.obolibrary.org/obo/ENVO_02000134> <https://orcid.org/0000-0002-6601-2165>)
+AnnotationAssertion(<http://www.geneontology.org/formats/oboInOwl#hasExactSynonym> <http://purl.obolibrary.org/obo/ENVO_02000134> "thermal reactor")
+AnnotationAssertion(rdfs:label <http://purl.obolibrary.org/obo/ENVO_02000134> "thermal nuclear ***@***.***)
+SubClassOf(<http://purl.obolibrary.org/obo/ENVO_02000134> <http://purl.obolibrary.org/obo/ENVO_02000137>)
+
+# Class: <http://purl.obolibrary.org/obo/ENVO_02000135> (fast neutron reactor)
+
+AnnotationAssertion(Annotation(<http://www.geneontology.org/formats/oboInOwl#hasDbXref> "https://en.wikipedia.org/wiki/Fast-neutron_reactor") <http://purl.obolibrary.org/obo/IAO_0000115> <http://purl.obolibrary.org/obo/ENVO_02000135> "A nuclear reactor in which the fission chain reaction is sustained by fast neutrons.")
+AnnotationAssertion(<http://purl.org/dc/elements/1.1/creator> <http://purl.obolibrary.org/obo/ENVO_02000135> <https://orcid.org/0000-0002-6601-2165>)
+AnnotationAssertion(<http://www.geneontology.org/formats/oboInOwl#hasExactSynonym> <http://purl.obolibrary.org/obo/ENVO_02000135> "fast reactor")
+AnnotationAssertion(rdfs:label <http://purl.obolibrary.org/obo/ENVO_02000135> "fast neutron ***@***.***)
+SubClassOf(<http://purl.obolibrary.org/obo/ENVO_02000135> <http://purl.obolibrary.org/obo/ENVO_02000137>)
+
+# Class: <http://purl.obolibrary.org/obo/ENVO_02000136> (research nuclear reactor)
+
+AnnotationAssertion(Annotation(<http://www.geneontology.org/formats/oboInOwl#hasDbXref> "https://en.wikipedia.org/wiki/Research_reactor") <http://purl.obolibrary.org/obo/IAO_0000115> <http://purl.obolibrary.org/obo/ENVO_02000136> "A nuclear reactor which serves primarily as a neutron source.")
The definition doesn't match the label. There are more uses for neutron
sources than simply research.
It does sound odd I agree. Do we have any domain experts we can reach out
to here?
------------------------------
In src/envo/envo-edit.owl
<#1184 (comment)>
:
> +AnnotationAssertion(rdfs:label <http://purl.obolibrary.org/obo/ENVO_02000135> "fast neutron ***@***.***)
+SubClassOf(<http://purl.obolibrary.org/obo/ENVO_02000135> <http://purl.obolibrary.org/obo/ENVO_02000137>)
+
+# Class: <http://purl.obolibrary.org/obo/ENVO_02000136> (research nuclear reactor)
+
+AnnotationAssertion(Annotation(<http://www.geneontology.org/formats/oboInOwl#hasDbXref> "https://en.wikipedia.org/wiki/Research_reactor") <http://purl.obolibrary.org/obo/IAO_0000115> <http://purl.obolibrary.org/obo/ENVO_02000136> "A nuclear reactor which serves primarily as a neutron source.")
+AnnotationAssertion(<http://purl.org/dc/elements/1.1/creator> <http://purl.obolibrary.org/obo/ENVO_02000136> <https://orcid.org/0000-0002-6601-2165>)
+AnnotationAssertion(<http://www.geneontology.org/formats/oboInOwl#hasExactSynonym> <http://purl.obolibrary.org/obo/ENVO_02000136> "non-power reactor")
+AnnotationAssertion(<http://www.geneontology.org/formats/oboInOwl#hasExactSynonym> <http://purl.obolibrary.org/obo/ENVO_02000136> "nuclear test reactor")
+AnnotationAssertion(rdfs:label <http://purl.obolibrary.org/obo/ENVO_02000136> "research nuclear ***@***.***)
+SubClassOf(<http://purl.obolibrary.org/obo/ENVO_02000136> <http://purl.obolibrary.org/obo/ENVO_02000133>)
+DisjointClasses(<http://purl.obolibrary.org/obo/ENVO_02000136> <http://purl.obolibrary.org/obo/ENVO_02000137>)
+
+# Class: <http://purl.obolibrary.org/obo/ENVO_02000137> (nuclear power reactor)
+
+AnnotationAssertion(Annotation(<http://www.geneontology.org/formats/oboInOwl#hasDbXref> "https://en.wikipedia.org/wiki/Nuclear_reactor") <http://purl.obolibrary.org/obo/IAO_0000115> <http://purl.obolibrary.org/obo/ENVO_02000137> "A nuclear reactor which is used as a source of power.")
Seems circular, but we do have the power plant branch - could that be used
/ cross-axiomatised here? Like a power plant that has part some nuclear
reactor?
good idea. There is some cross-linking already but I like the has-part
based definition, with the functional aspect pushed down to the functional
subcomponent
------------------------------
In src/envo/envo-edit.owl
<#1184 (comment)>
:
> +AnnotationAssertion(<http://www.geneontology.org/formats/oboInOwl#hasExactSynonym> <http://purl.obolibrary.org/obo/ENVO_02000136> "nuclear test reactor")
+AnnotationAssertion(rdfs:label <http://purl.obolibrary.org/obo/ENVO_02000136> "research nuclear ***@***.***)
+SubClassOf(<http://purl.obolibrary.org/obo/ENVO_02000136> <http://purl.obolibrary.org/obo/ENVO_02000133>)
+DisjointClasses(<http://purl.obolibrary.org/obo/ENVO_02000136> <http://purl.obolibrary.org/obo/ENVO_02000137>)
+
+# Class: <http://purl.obolibrary.org/obo/ENVO_02000137> (nuclear power reactor)
+
+AnnotationAssertion(Annotation(<http://www.geneontology.org/formats/oboInOwl#hasDbXref> "https://en.wikipedia.org/wiki/Nuclear_reactor") <http://purl.obolibrary.org/obo/IAO_0000115> <http://purl.obolibrary.org/obo/ENVO_02000137> "A nuclear reactor which is used as a source of power.")
+AnnotationAssertion(<http://purl.org/dc/elements/1.1/creator> <http://purl.obolibrary.org/obo/ENVO_02000137> <https://orcid.org/0000-0002-6601-2165>)
+AnnotationAssertion(<http://www.geneontology.org/formats/oboInOwl#hasExactSynonym> <http://purl.obolibrary.org/obo/ENVO_02000137> "power reactor")
+AnnotationAssertion(rdfs:label <http://purl.obolibrary.org/obo/ENVO_02000137> "nuclear power ***@***.***)
+SubClassOf(<http://purl.obolibrary.org/obo/ENVO_02000137> <http://purl.obolibrary.org/obo/ENVO_02000133>)
+
+# Class: <http://purl.obolibrary.org/obo/ENVO_02000138> (mangrove biome soil)
+
+AnnotationAssertion(Annotation(<http://www.geneontology.org/formats/oboInOwl#hasDbXref> "https://doi.org/10.1093/treephys/tpq048") <http://purl.obolibrary.org/obo/IAO_0000115> <http://purl.obolibrary.org/obo/ENVO_02000138> "Soil which is located in a mangrove biome. Mangrove soils are typically saline, anoxic, acidic and frequently waterlogged.")
Please move the gloss to a comment.
OK. Can this be updated to make this policy clearer?
https://github.com/EnvironmentOntology/envo/wiki/Creating-good-definitions
My own views on gloss are here:
https://douroucouli.wordpress.com/2019/07/08/ontotip-write-simple-concise-clear-operational-textual-definitions/
```
If you need to include discursive text, *use either the definition gloss or
a separate description field*. The ‘gloss’ is the part of the text
definition that comes after the first period/full-stop. A common practice
in the GO is to recapitulate the definition of the differentia in the
gloss. For example, the definition for ‘ectoderm development’ is
“*The process whose specific outcome is the progression of the ectoderm
over time, from its formation to the mature structure. **In animal embryos,
the ectoderm is the outer germ layer of the embryo, formed during
gastrulation*.”.
(embedded ‘ectoderm’ definition underlined)
This suffers some problems as it violates DRY
<https://en.wikipedia.org/wiki/Don%27t_repeat_yourself> (if the wording of
the definition of *ectoderm* changes, then the wording of the definition of
‘*ectoderm development*’ changes). However, it provides utility as users do
not have to traverse the elements of the OWL definition to achieve the
bigger picture. It is marginally easier to semi-automatically update the
gloss, compared to the situation where the redundant information permeates
the core text definition.
When the conventions for a particular ontology allow for gloss, it is
important to be consistent about how this is used, and to include only
necessary and sufficient conditions *before* the period.
```
When curveying GO curators, their opinions often differed from formal
ontologists. They often found the gloss to be the most important part of
the definition, and did not want to see it detached into a separate field.
I would be great to better standardize this across OBO, but for now I will
follow ENVO conventions
------------------------------
In src/envo/envo-edit.owl
<#1184 (comment)>
:
> @@ -37280,6 +37361,38 @@ AnnotationAssertion(rdfs:label <http://purl.obolibrary.org/obo/ENVO_02000140> "f
EquivalentClasses(<http://purl.obolibrary.org/obo/ENVO_02000140> ObjectUnionOf(<http://purl.obolibrary.org/obo/ENVO_01000797> <http://purl.obolibrary.org/obo/ENVO_01000798> <http://purl.obolibrary.org/obo/ENVO_01000815>))
SubClassOf(<http://purl.obolibrary.org/obo/ENVO_02000140> <http://purl.obolibrary.org/obo/ENVO_00010483>)
+# Class: <http://purl.obolibrary.org/obo/ENVO_02000141> (refinery)
+
+AnnotationAssertion(<http://purl.obolibrary.org/obo/IAO_0000115> <http://purl.obolibrary.org/obo/ENVO_02000141> "a human construction which is used to refine certain materials or converting raw material into products of value.")
a human construction which is used to refine certain materials or
converting raw material into products of value
Change to something like:
A human construction which is used to process materials into forms that
have increased value or utility in downstream processes.
will do
------------------------------
In src/envo/envo-edit.owl
<#1184 (comment)>
:
> @@ -37280,6 +37361,38 @@ AnnotationAssertion(rdfs:label <http://purl.obolibrary.org/obo/ENVO_02000140> "f
EquivalentClasses(<http://purl.obolibrary.org/obo/ENVO_02000140> ObjectUnionOf(<http://purl.obolibrary.org/obo/ENVO_01000797> <http://purl.obolibrary.org/obo/ENVO_01000798> <http://purl.obolibrary.org/obo/ENVO_01000815>))
SubClassOf(<http://purl.obolibrary.org/obo/ENVO_02000140> <http://purl.obolibrary.org/obo/ENVO_00010483>)
+# Class: <http://purl.obolibrary.org/obo/ENVO_02000141> (refinery)
+
+AnnotationAssertion(<http://purl.obolibrary.org/obo/IAO_0000115> <http://purl.obolibrary.org/obo/ENVO_02000141> "a human construction which is used to refine certain materials or converting raw material into products of value.")
+AnnotationAssertion(<http://purl.org/dc/elements/1.1/creator> <http://purl.obolibrary.org/obo/ENVO_02000141> <https://orcid.org/0000-0002-6601-2165>)
+AnnotationAssertion(rdfs:label <http://purl.obolibrary.org/obo/ENVO_02000141> ***@***.***)
+SubClassOf(<http://purl.obolibrary.org/obo/ENVO_02000141> <http://purl.obolibrary.org/obo/ENVO_00000070>)
+
+# Class: <http://purl.obolibrary.org/obo/ENVO_02000142> (petroleum oil refinery)
+
+AnnotationAssertion(Annotation(<http://www.geneontology.org/formats/oboInOwl#hasDbXref> "https://en.wikipedia.org/wiki/Oil_refinery") <http://purl.obolibrary.org/obo/IAO_0000115> <http://purl.obolibrary.org/obo/ENVO_02000142> "A refinery which is used for processing petroleum oil. Petroleum processing is an industrial process in which crude oil is transformed and refined into useful products such as petroleum naphtha, gasoline, diesel fuel, asphalt base, heating oil, kerosene, liquefied petroleum gas, jet fuel and fuel oils.")
Please move the gloss to a comment.
yep
------------------------------
In src/envo/envo-edit.owl
<#1184 (comment)>
:
> +AnnotationAssertion(<http://purl.org/dc/elements/1.1/creator> <http://purl.obolibrary.org/obo/ENVO_02000141> <https://orcid.org/0000-0002-6601-2165>)
+AnnotationAssertion(rdfs:label <http://purl.obolibrary.org/obo/ENVO_02000141> ***@***.***)
+SubClassOf(<http://purl.obolibrary.org/obo/ENVO_02000141> <http://purl.obolibrary.org/obo/ENVO_00000070>)
+
+# Class: <http://purl.obolibrary.org/obo/ENVO_02000142> (petroleum oil refinery)
+
+AnnotationAssertion(Annotation(<http://www.geneontology.org/formats/oboInOwl#hasDbXref> "https://en.wikipedia.org/wiki/Oil_refinery") <http://purl.obolibrary.org/obo/IAO_0000115> <http://purl.obolibrary.org/obo/ENVO_02000142> "A refinery which is used for processing petroleum oil. Petroleum processing is an industrial process in which crude oil is transformed and refined into useful products such as petroleum naphtha, gasoline, diesel fuel, asphalt base, heating oil, kerosene, liquefied petroleum gas, jet fuel and fuel oils.")
+AnnotationAssertion(<http://purl.org/dc/elements/1.1/creator> <http://purl.obolibrary.org/obo/ENVO_02000142> <https://orcid.org/0000-0002-6601-2165>)
+AnnotationAssertion(<http://www.geneontology.org/formats/oboInOwl#hasExactSynonym> <http://purl.obolibrary.org/obo/ENVO_02000142> "oil refinery")
+AnnotationAssertion(rdfs:label <http://purl.obolibrary.org/obo/ENVO_02000142> "petroleum oil ***@***.***)
+EquivalentClasses(<http://purl.obolibrary.org/obo/ENVO_02000142> ObjectIntersectionOf(<http://purl.obolibrary.org/obo/ENVO_02000141> ObjectSomeValuesFrom(<http://purl.obolibrary.org/obo/ENVO_02000145> <http://purl.obolibrary.org/obo/ENVO_00002984>)))
+SubClassOf(<http://purl.obolibrary.org/obo/ENVO_02000142> <http://purl.obolibrary.org/obo/ENVO_02000141>)
+
+# Class: <http://purl.obolibrary.org/obo/ENVO_02000143> (sugar refinery)
+
+AnnotationAssertion(Annotation(<http://www.geneontology.org/formats/oboInOwl#hasDbXref> "https://en.wikipedia.org/wiki/Sugar_refinery") <http://purl.obolibrary.org/obo/IAO_0000115> <http://purl.obolibrary.org/obo/ENVO_02000143> "a refinery which is used for processing raw sugar. Raw sugar is processed from cane or beets into white refined sugar.")
Capitalisation and gloss extraction as above. Also, there's something off
about these definitions - one doesn't "use" the whole refinery for this,
and some which are inactive are still refineries.
Perhaps a pattern like:
A refinery which is capable of processing raw sugar.
agreed
… —
You are receiving this because you authored the thread.
Reply to this email directly, view it on GitHub
<#1184 (review)>,
or unsubscribe
<https://github.com/notifications/unsubscribe-auth/AAAMMOK5B3K2YQSLNHJP2K3TTIKBRANCNFSM462NR4BA>
.
|
cmungall
commented
Jun 24, 2021
|
@pbuttigieg - I believe all comments addressed |
pbuttigieg
requested changes
Jun 25, 2021
Comment on lines
+37327
to
+37328
| AnnotationAssertion(rdfs:comment <http://purl.obolibrary.org/obo/ENVO_02000136> "An example use of a research nucelar reactor is the production of radioisotopes for medicine and industry") | ||
| AnnotationAssertion(rdfs:comment <http://purl.obolibrary.org/obo/ENVO_02000136> "Research reactors are simpler than power reactors and operate at lower temperatures. They need far less fuel, and far less fission products build up as the fuel is used") |
|
|
||
| # Class: <http://purl.obolibrary.org/obo/ENVO_02000137> (nuclear power reactor) | ||
|
|
||
| AnnotationAssertion(Annotation(<http://www.geneontology.org/formats/oboInOwl#hasDbXref> "https://en.wikipedia.org/wiki/Nuclear_reactor") <http://purl.obolibrary.org/obo/IAO_0000115> <http://purl.obolibrary.org/obo/ENVO_02000137> "A nuclear reactor which is used as a source of power.") |
There was a problem hiding this comment.
it sounds circular but it's not, as the differentia is in the intended use/function, to produce power (as opposed to say producing radioisotopes for imaging). We do have a logical axiom connecting the plane to the reactor.
Okay, clarified.
I do think it's worth doing an overall review of design patterns for the existing terms for power plant - do you mind if we do this as a separate ticket/PR?
Yes, that should be separate to stay focused.
|
|
||
| AnnotationAssertion(Annotation(<http://www.geneontology.org/formats/oboInOwl#hasDbXref> "https://en.wikipedia.org/wiki/Nuclear_reactor") <http://purl.obolibrary.org/obo/IAO_0000115> <http://purl.obolibrary.org/obo/ENVO_02000137> "A nuclear reactor which is used as a source of power.") | ||
| AnnotationAssertion(<http://purl.org/dc/elements/1.1/creator> <http://purl.obolibrary.org/obo/ENVO_02000137> <https://orcid.org/0000-0002-6601-2165>) | ||
| AnnotationAssertion(<http://www.geneontology.org/formats/oboInOwl#hasExactSynonym> <http://purl.obolibrary.org/obo/ENVO_02000137> "power reactor") |
There was a problem hiding this comment.
This would be a broad synonym
|
|
||
| # Class: <http://purl.obolibrary.org/obo/ENVO_02000143> (sugar refinery) | ||
|
|
||
| AnnotationAssertion(Annotation(<http://www.geneontology.org/formats/oboInOwl#hasDbXref> "https://en.wikipedia.org/wiki/Sugar_refinery") <http://purl.obolibrary.org/obo/IAO_0000115> <http://purl.obolibrary.org/obo/ENVO_02000143> "a refinery which is used for processing raw sugar. Raw sugar is processed from cane or beets into white refined sugar.") |
There was a problem hiding this comment.
Gloss extraction to comment on:
Raw sugar is processed from cane or beets into white refined sugar.
|
|
||
| # Class: <http://purl.obolibrary.org/obo/ENVO_02000144> (natural gas processing plant) | ||
|
|
||
| AnnotationAssertion(Annotation(<http://www.geneontology.org/formats/oboInOwl#hasDbXref> "https://en.wikipedia.org/wiki/Natural-gas_processing") <http://purl.obolibrary.org/obo/IAO_0000115> <http://purl.obolibrary.org/obo/ENVO_02000144> "A refinery which is capable of processing natural gas. Natural-gas processing encompasses a range of industrial processes designed to purify raw natural gas by removing impurities, contaminants and higher molecular mass hydrocarbons to produce what is known as pipeline quality dry natural gas") |
|
|
||
| # Class: <http://purl.obolibrary.org/obo/ENVO_02000147> (refinement process) | ||
|
|
||
| AnnotationAssertion(Annotation(<http://www.geneontology.org/formats/oboInOwl#hasDbXref> "https://en.wikipedia.org/wiki/Refining") <http://purl.obolibrary.org/obo/IAO_0000115> <http://purl.obolibrary.org/obo/ENVO_02000147> "A planned material transformation process which takes as input a material and removes impurities.") |
There was a problem hiding this comment.
A planned material transformation process which takes as input a material and removes impurities
Do we define impurities anywhere? If not, something showing an active designation would be useful:
A planned material transformation process during which material designated as impurities are removed from an material taken as input.
| # Class: <http://purl.obolibrary.org/obo/ENVO_02000148> (Haber-Bosch process) | ||
|
|
||
| AnnotationAssertion(<http://purl.obolibrary.org/obo/IAO_0000115> <http://purl.obolibrary.org/obo/ENVO_02000148> "A chemical engineering process that produces ammonia en masse via artificial nitrogen fixation.") | ||
| AnnotationAssertion(<http://purl.org/dc/elements/1.1/creator> <http://purl.obolibrary.org/obo/ENVO_02000148> "cjm"^^xsd:string) |
There was a problem hiding this comment.
cjm
You replaced these with ORCIDs below
|
|
||
| # Class: <http://purl.obolibrary.org/obo/ENVO_02000148> (Haber-Bosch process) | ||
|
|
||
| AnnotationAssertion(<http://purl.obolibrary.org/obo/IAO_0000115> <http://purl.obolibrary.org/obo/ENVO_02000148> "A chemical engineering process that produces ammonia en masse via artificial nitrogen fixation.") |
There was a problem hiding this comment.
I think "en masse" is extraneous, but not a blocker
| # Class: <http://purl.obolibrary.org/obo/ENVO_02000149> (hydrogen production process) | ||
|
|
||
| AnnotationAssertion(Annotation(<http://www.geneontology.org/formats/oboInOwl#hasDbXref> "https://en.wikipedia.org/wiki/Hydrogen_production") <http://purl.obolibrary.org/obo/IAO_0000115> <http://purl.obolibrary.org/obo/ENVO_02000149> "A chemical engineering process which generates hydrogen gas.") | ||
| AnnotationAssertion(<http://purl.org/dc/elements/1.1/creator> <http://purl.obolibrary.org/obo/ENVO_02000149> "cjm"^^xsd:string) |
pbuttigieg
approved these changes
Aug 9, 2022
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
Add this suggestion to a batch that can be applied as a single commit.
This suggestion is invalid because no changes were made to the code.
Suggestions cannot be applied while the pull request is closed.
Suggestions cannot be applied while viewing a subset of changes.
Only one suggestion per line can be applied in a batch.
Add this suggestion to a batch that can be applied as a single commit.
Applying suggestions on deleted lines is not supported.
You must change the existing code in this line in order to create a valid suggestion.
Outdated suggestions cannot be applied.
This suggestion has been applied or marked resolved.
Suggestions cannot be applied from pending reviews.
Suggestions cannot be applied on multi-line comments.
Suggestions cannot be applied while the pull request is queued to merge.
Suggestion cannot be applied right now. Please check back later.
New terms for refineries and reactors:
http://purl.obolibrary.org/obo/ENVO_02000137 nuclear power reactor
http://purl.obolibrary.org/obo/ENVO_02000138 mangrove biome soil
http://purl.obolibrary.org/obo/ENVO_02000141 refinery
http://purl.obolibrary.org/obo/ENVO_02000142 petroleum oil refinery
http://purl.obolibrary.org/obo/ENVO_02000143 sugar refinery
http://purl.obolibrary.org/obo/ENVO_02000144 natural gas processing plant
some of these are used for gold mapping
for axiomatization this includes two new OPs:
http://purl.obolibrary.org/obo/ENVO_02000139 used for transport of
http://purl.obolibrary.org/obo/ENVO_02000145 used for processing of
These may be later added to RO