new classes: phase transition process & relevant subclasses

[kaiiam]

Hey @pbuttigieg ENVO needs some more basic physical processes: Here a few we should add:

phase transition process ref

A process during which a portion of matter is converted from one phase to another.

freezing ref

A phase transition process whereby a portion of environmental material transitions from a liquid to a solid phase.

melting ref

A phase transition process whereby a portion of environmental material transitions from a solid to a liquid phase.

depositional phase change ref

A phase transition process whereby a portion of environmental material transitions from a gas to a solid phase.

vaporisation ref

A phase transition process whereby a portion of environmental material transitions from a liquid to a gas phase

condensation ref

A phase transition process whereby a portion of environmental material transitions from a gas to a liquid phase.

sublimation ref

A phase transition process whereby a portion of environmental material transitions from a solid to a gas phase.

compaction or compaction process

A physical process which forces molecules of a material entity closer together.

material accumulation process

A process whereby the mass of one or more materials increases at the same site.
as a comment for this we'd say:
A material accumulation process ends a material movement process.

material transport process

A process whereby material is displaced from it's original location and transported either to a new location or back to the original location.

[pbuttigieg]

Do these not exist in a chemical or reaction ontology? If you can't find satisfactory classes elsewhere, please start drafting the classes.

…

On 27 Mar 2017 16:25, "Kai Blumberg" ***@***.***> wrote: Hey @pbuttigieg <https://github.com/pbuttigieg> ENVO needs some more basic physical processes: Here a few we should add: phase transition process source <https://www.britannica.com/science/phase-state-of-matter>: A process during which a portion of matter is converted from one phase to another. freezing source <http://www.kentchemistry.com/links/Matter/PhaseChanges.htm>: A phase transition process whereby a portion of environmental material transitions from a liquid to a solid phase. melting source <http://www.kentchemistry.com/links/Matter/PhaseChanges.htm>: A phase transition process whereby a portion of environmental material transitions from a solid to a liquid phase. depositional phase change source <http://www.kentchemistry.com/links/Matter/PhaseChanges.htm>: A phase transition process whereby a portion of environmental material transitions from a gas to a solid phase. vaporisation source <http://www.kentchemistry.com/links/Matter/PhaseChanges.htm>: A phase transition process whereby a portion of environmental material transitions from a liquid to a gas phase condensation source <http://www.kentchemistry.com/links/Matter/PhaseChanges.htm>: A phase transition process whereby a portion of environmental material transitions from a gas to a liquid phase. sublimation source <http://www.kentchemistry.com/links/Matter/PhaseChanges.htm>: A phase transition process whereby a portion of environmental material transitions from a solid to a gas phase. compaction or compaction process A physical process which forces molecules of a material entity closer together. material accumulation process A process whereby the mass of one or more materials increases at the same site. as a comment for this we'd say: A material accumulation process ends a material movement process. material movement process A process whereby material is displaced from it's original location and transported either to a new location or back to the original location. — You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub <#474>, or mute the thread <https://github.com/notifications/unsubscribe-auth/ACK7MhzYPPKSOglbkS84VGfT32VRwudlks5rp8bTgaJpZM4MqV1n> .

[pbuttigieg]

I like the way this article discusses phase transitions as it's a little more clear on what's going on in the material. I would prefer a little more depth in at least the top level defs.

[cmungall]

[REX:0000171](http://purl.obolibrary.org/obo/REX_0000171) ! phase transition The ontology is abandoned AFAICT, if it looks like we'll need to make modifications to it we can discuss with the wider OBO community

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On 27 Mar 2017, at 7:34, Pier Luigi Buttigieg wrote: Do these not exist in a chemical or reaction ontology? If you can't find satisfactory classes elsewhere, please start drafting the classes. On 27 Mar 2017 16:25, "Kai Blumberg" ***@***.***> wrote: > Hey @pbuttigieg <https://github.com/pbuttigieg> ENVO needs some more > basic physical processes: Here a few we should add: > > phase transition process source > <https://www.britannica.com/science/phase-state-of-matter>: > > A process during which a portion of matter is converted from one > phase to > another. > > freezing source > <http://www.kentchemistry.com/links/Matter/PhaseChanges.htm>: > > A phase transition process whereby a portion of environmental > material > transitions from a liquid to a solid phase. > > melting source > <http://www.kentchemistry.com/links/Matter/PhaseChanges.htm>: > > A phase transition process whereby a portion of environmental > material > transitions from a solid to a liquid phase. > > depositional phase change source > <http://www.kentchemistry.com/links/Matter/PhaseChanges.htm>: > > A phase transition process whereby a portion of environmental > material > transitions from a gas to a solid phase. > > vaporisation source > <http://www.kentchemistry.com/links/Matter/PhaseChanges.htm>: > > A phase transition process whereby a portion of environmental > material > transitions from a liquid to a gas phase > > condensation source > <http://www.kentchemistry.com/links/Matter/PhaseChanges.htm>: > > A phase transition process whereby a portion of environmental > material > transitions from a gas to a liquid phase. > > sublimation source > <http://www.kentchemistry.com/links/Matter/PhaseChanges.htm>: > > A phase transition process whereby a portion of environmental > material > transitions from a solid to a gas phase. > > compaction or compaction process > > A physical process which forces molecules of a material entity closer > together. > > material accumulation process > > A process whereby the mass of one or more materials increases at the > same > site. > as a comment for this we'd say: > A material accumulation process ends a material movement process. > > material movement process > > A process whereby material is displaced from it's original location > and > transported either to a new location or back to the original > location. > > — > You are receiving this because you were mentioned. > Reply to this email directly, view it on GitHub > <#474>, or mute the > thread > <https://github.com/notifications/unsubscribe-auth/ACK7MhzYPPKSOglbkS84VGfT32VRwudlks5rp8bTgaJpZM4MqV1n> > . > -- You are receiving this because you are subscribed to this thread. Reply to this email directly or view it on GitHub: #474 (comment)

[pbuttigieg]

Thanks for the link @cmungall, I think we should ask the community if we can edit REX - it would be a real asset for ENVO and many others.

[kaiiam]

Thank you @cmungall for chiming in. @pbuttigieg I assume it would be best if we were to hold off on adding the phase transition terms until we know if REX is the right place to put them and if we get edit permissions.

I would, however, like to add the compaction process, material accumulation process, material transport process terms to ENVO. Would it be ok to do so as I currently have them defined?

[pbuttigieg]

@pbuttigieg I assume it would be best if we were to hold off on adding the phase transition terms until we know if REX is the right place to put them and if we get edit permissions.

Agreed.

I would, however, like to add the compaction process, material accumulation process, material transport process terms to ENVO. Would it be ok to do so as I currently have them defined?

Generally yes (switch the wherbys to 'during which's. We may do some minor edits to the defs later, but they're okay for now.

@cmungall is there a procedure for approaching the community regarding REX? Should we try to contact the lead developer first? Jana Hastings is still listed as the contact, but she's no longer with the EBI.

[kaiiam]

I'd also like to add material transformation process

A process during which material is transformed from one state to another.

@pbuttigieg is that ok for now?

[cmungall]

On 28 Mar 2017, at 7:03, Pier Luigi Buttigieg wrote: > ***@***.***(<https://github.com/pbuttigieg>) I assume it would be > best if we were to hold off on adding the phase transition terms > until we know if REX is the right place to put them and if we get > edit permissions. Agreed.

I wonder if there is a split analogous to the mixture-molecular entity split in CHEBI, with basic physical processes at the level of atoms and sub-atomic particles in REX, and mixture-level processes like freezing at a higher level of granularity (with ENVO being a natural home for the latter). If so, these would ultimately be linked by something like has_part, but you could certainly defer on linking to the lower level of granularity for now.

[pbuttigieg]

@kaiiam for compaction, see #426, we may be able to do something quite general

@cmungall I agree with the process part approach between REX and ENVO. I can also imagine that the "pure" freezing/melting/... processes could live in REX and that their environmental manifestations could reside in ENVO; however, this sounds too Platonic and, remembering my chemistry days, we know that there is no pure substance to freeze/melt/etc. (supporting ENVO as the home for bulk processes like these)