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New particle formation event #602
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we should name the classes using terms used by the research community. So far ENVO hasn't really recognized any distinction between events and processes at the ontological level. A process is simply something that happens. Connections between smaller units and larger units would be achieved using relations like part-of. But we'd be open to other ways of modeling, especially if this fits better with other ways of modeling. We also try to represent the underlying process rather than it's observation. A crucial point for the ontology is the level of granularity we're talking about. Does a single instance of particle formation generate a single particle? Or are we talking about assemblages of these? We have somewhat fudged this in analogous biological process ontologies, with the formal definition of metabolic or signaling processes being in terms of individual molecules, but with the classes used to represent statistical aggregates of these. |
An instance of a new particle formation event generates a polydisperse aerosol, so multiple particles of different diameter sizes. During the event (which lasts several hours), the aerosol changes, overall the particles get bigger in size. What scientists describe are events, e.g. the duration, particle growth rate. I fully agree we need to model this how the research community conceptualizes. I hope to get some involved here. |
I would prefer to have separately "new particle formation", where one can describe the process, which can be clearly defined. The "new particle formation event" is not only an occasion of a formation of particles, but it stands for a period of regionally and continuously (e.g. close to or over an hour) elevated atmospheric new particle formation rate. And the threshold for the formation rate to be classified as an event is not very exact, it is basically our capability of detecting elevated rate out of noise. |
Thanks @PauliPaasonen and @mazaidan for joining in and your comment. Are you suggesting to have two separate concepts, one for process and one for event? To my understanding of your (particle size distribution) data analysis workflow, you do describe individual new particle formation events, those occasions of a formation of particles. This is what I understand as "secondary data" generated in analysis (also visually) of particle size distribution data (the "primary data", in this context). The attempt here with ENVO is to provide a "guideline" for how to describe such events, their type, spatio-temporal location, and other attributes such as formation rate. I guess there is uncertainty in all these values (strictly speaking even in spatio-temporal location but also the assessed type (Ia, Ib, II, etc.)). This is another matter, and we may need to think how to capture uncertainty. First, though, we need to develop a scheme to capture the actual values in a coherent data object. Agreed? From your comment I am unclear how the event relates to the process. I think this needs to be clarified but I wonder if it can be done in a second step? |
I think that would be good, to have 2 separate entries. Wasn't it possible to have one under another? My point with the definition of the term new particle formation event (NPF event) is that it stands for regional atmospheric burst of new particles. E.g. new particle formation in the tale-pipe or exhaust plume of a car or industry stack is not a NPF event, at least I have never heard NPF event referring to these kinds of situations of new particle formation. |
Excellent. I conclude that we need a concept named "New Particle Formation Event" and I understand this is a kind of New Particle Formation (a subclass), one that does not include things like new particle formation in tale-pipe or exhaust plume. Now, ENVO currently includes the concept "formation of particles in an atmosphere" with two special kinds, "formation of liquid droplets" and "formation of solid particles", and more specific kinds, e.g. "formation of solid particles from gaseous material in an atmosphere". @PauliPaasonen: is it accurate to say that a "New Particle Formation Event" (in the context discussed here) is a "formation of solid particles from gaseous material in an atmosphere"? If positive, is "New Particle Formation Event" equivalent to "formation of solid particles from gaseous material in an atmosphere" or, rather, a more specific type (subclass)? Depending on the answers, @pbuttigieg can we adopt "New Particle Formation Event" into ENVO? This implies a classification of the Event as a Process. I believe there is disagreement on this matter (in the literature). Some consider Event and Process as ontologically distinct. But I leave this to @pbuttigieg and @cmungall and their understanding of ENVO and its alignment with BFO. To my understanding, for the science community it is important to have the term "New Particle Formation Event" appearing in the ontology, because this is how these events a called. If we are lucky, we can simply align "New Particle Formation Event" to the current class hierarchy. Possible subclassing of "formation of solid particles from gaseous material in an atmosphere" relies on the correctness of the current description, namely that a "New Particle Formation Event" is a formation of particles that occurs in some atmosphere and has solid aerosol as output (but I suppose this should be correct). We should then be able to further constrain the concept "New Particle Formation Event". |
Event vs process naming: I'm happy to use whatever terminology the community uses. Event v process ontologically: BFO doesn't have a distinction between event and process. This doesn't mean we can't introduce logical distinctions where they are important. So far I haven't seen a use case, simplistic treatment of everything as processes in the bfo sense seems to work. Ontologically there are not many commitments here. Each instance of a process has a start and an end (which may be fiat, and may be unknown to us). A process has participants. In our design patterns these participants can be subdivided into inputs, outputs. To me its more important to fit each process/event into a design pattern that to worry about upper level classification. |
Agree with @cmungall here, though I find the label 'Process' a bit non-intuitive because of the English verb with the same name. I try to remind myself to filter it to 'the BFO meaning of Process'. By now this is history and isn't going to change. |
@markusstocker: "New Particle Formation Event" cannot be only "formation of solid particles from gaseous material in an atmosphere". But "new particle formation", if we want to put it in very simple way, can be "formation of solid or liquid particles from gas-phase molecules". To be more exact, it could be "process, in which gas-phase molecules form solid or liquid particles, which are stable enough to continue growing by condensation of other gas-phase molecules more probably than to evaporate back to gas-phase". "New particle formation event" is an atmospheric phenomenon, in which the new particle formation (from well dispersed gas-phase molecules) is intense enough in large enough area and for long enough time for us to observe the formed particle population. This non-exact definition comes from the history and is related to the detection limits of the instruments and stationary nature of the measurements sites. This would need more time to be well explained. Anyhow, there is no exact thresholds for the intensity, area and duration of the enhanced new particle formation, which could be used for determining whether there is a new particle formation event or not. If elevated new particle formation rate is observed in the atmosphere (away from direct sources of the related gas-phase molecules) for a period of time, it can be called an event. Note that at least the last statement is not objective, even though I tried to make it such. |
Many thanks all for the great discussion here! In response to #602 (comment)
We can move the existing label to an alternative label field to preserve common usage. As long as the definition is the same the semantics work. If there are any other synonyms, please let us know. See below for the specifics of how we suggest handling this case.
Again, I don't really see the difference here (as processes can have other processes as parts). As noted above, the idea of this being that part of a process which is observed can be used as a valid differentiae in BFO aligned systems. I do think that the rate differentia suggest by @PauliPaasonen is more clear.
Great! From #602 (comment)
Okay, we can adjust the outputs accordingly and update the aerosol hierarchy. From #602 (comment)
We could do this by having the event as a subclass of the process differentiated by its increased rate. The semantics to do so exist in PATO and are similar to what we use for storms and other entities that feature processes with increased rates. From #602 (comment)
I think we're aligned here. We can axiomatise with some of our "natural" differentia to make sure this is understood as a process without a technological source and that occurs in an atmosphere.
See below.
I think it's much clearer now. In this case, as long as we have a good definition (which was provided by @PauliPaasonen) we don't mind the label text. I'll include an editors' note to indicate that this is the common usage and the label should be retained as discussed here.
Yes. See below.
Yes, much easier now to move forward. As long as we have a good consensus definition, we can worry about handling the upper level stuff while making sure user requirements are met. I'm with @cmungall in :
As said above, if the def is clear enough, we can make sure it works. From #602 (comment)
Indeed, but we can insulate the userbase from this and make sure their terminology and synonyms are reproduced faithfully. This will help any NLP or text-mining efforts immensely. From #602 (comment)
I suggest that we include a comment on the class indicating these concerns, but avoid over axiomatising it with observation semantics imported from OBI or BCO where we would define what kind of observational thresholds need to be passed. I don't think that's necessary yet, but we can make sure the comment sketches out this route as a potential extension. The class is currently in the editors' version as:
Naturally, this class is tied to the aerosol outputs by the inclusion of the other classes as parts. @markusstocker @PauliPaasonen if you'd like to be credited for this content (and help us trace where the knowledge came from), please add your ORCIDs or equivalent to this thread. Many thanks! |
The class has a reserved (not released yet) PURL of: http://purl.obolibrary.org/obo/ENVO_01001359 |
Hi,
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Thanks @PauliPaasonen
I'll then cast the event as a special case of the formation process. Would this work? And then... And ...
The alternative term is attempting to phrase this in more BFO-compliant ways for future work / disentangling. |
Yes, that is correct to have the "event" as a special feature of new particle formation (NPF). However, I find the higher level terms a bit complicated to understand, since the term "particle formation" (or "formation of particles") means, at least for me, the exactly same thing, new particle formation. Additionally, new particle formation can occur also elsewhere than in the atmosphere, e.g. in a car tale pipe. |
As it is currently modeled and shown by @pbuttigieg, "new particle formation event" is a "special case" (a sub category/set/class) of "new particle formation" (and "particle formation process" more abstractly). Concretely, this means that every instance of "new particle formation event" is a "particle formation process". I am not sure this is semantically equivalent to an event being "a special feature of new particle formation". @pbuttigieg: Does something speak against the proposal of harmonizing "particle formation" and "formation of particles" to "new particle formation"? Also, it seems that classifying "new particle formation" as "formation of particles in an atmosphere" is incorrect. Here is a more formal version of what @PauliPaasonen suggested above:
Since "new particle formation" can occur also elsewhere than in the atmosphere, we need to specialize "new particle formation" for formation that occurs in the atmosphere and a sensible label may be "atmospheric new particle formation", thus:
Now, even if we accept this structure, one remaining question is how it relates to "new particle formation event", the event. Considering what @PauliPaasonen said above:
This seems to suggest that "new particle formation event" is indeed a special case of "new particle formation", namely the case in which the observed formation rate is elevated for a period of time:
Updated to reflect @PauliPaasonen's comments below |
@markusstocker: This formalization of my suggestion looks very good! Two minor suggestions: 1) comment for "secondary aerosol formation" could be "Formation of solid or liquid particulate matter from gas phase molecules". This because "formation of particles" sounds like "formation of new particles", but "secondary aerosol formation" can also be "condensation of vapours on pre-existing particles", as you have in the next line. 2) "new particle formation event" should be sub-class of "atmospheric new particle formation", since the word "event" is typically applied only for atmospheric events. |
Thanks @PauliPaasonen, I updated the comment above to reflect your suggestions. |
Rearranging the points in #602 (comment) to respond to @PauliPaasonen
This is much clearer - I'll use this to refactor the surrounding hierarchy. We can fit in multiple processes and events in here while offering more clarity. The only thing that's ambiguous now is that secondary formation can include simple mass-increases (i.e. no actual formation at all). Is there a source that's well known in your field I can reference for this?
I think the aerosol formation hierarchy can help us here. I'll add "new particle formation" (the process and the event) as a broad synonym of an aerosol formation event, which seems to be the most likely thing being observed.
The higher level terms were defined only by their output (some particulate matter) and not by where they occur or their rates. Thus they were more general. The aerosol hierarchy you provided will likely be less confusing. |
@markusstocker our thinking on @PauliPaasonen's comment was quite similar; I'll fold in your suggestions to the current hierarchy. |
A good reference for aerosol formation (and all other aerosol pehnomena) is "Atmospheric Chemistry and Physics: From Air Pollution to Climate Change, 3rd Edition", by John H. Seinfeld and Spyros N. Pandis, Wiley, ISBN: 978-1-118-94740-1. @pbuttigieg , I understand your comment "secondary formation can include simple mass-increases (i.e. no actual formation at all)", but aerosol formation is in this analogous to "ice formation" or "cloud formation" in which both it is not required that a new piece of ice or a new cloud is formed, but increase in the volume or mass of ice or cloud is enough. |
Hi @pbuttigieg, when you are ready, can you post a screenshot as above so that we can review the current classification, before you publish the update? I think it is good if @PauliPaasonen has a chance to check it again and approve it. Once we have the classification of the concept "new particle formation event" right, the actual fun begins, namely how to integrate the attributes and data about events we need/should/want to capture, for instance spatio-temporal locations but also the event class (according to some scheme, e.g. Class Ia, Ib, II according to dal Maso et al. or similar following another scheme) but also growth rate, etc. I think this part will need some f2f time (seems a bit challenging via GitHub and I am not sure to what extent it is strictly within the scope of ENVO). Once we have the concept for "new particle formation event" accept and published I will draft a proposal for the attributes and post it somewhere for review. Perhaps we can organize some f2f time in Hyytiälä this August. Thanks everyone so far for all your input! Knowledge engineering and ontology is tough. |
Indeed, it takes some doing; however, as we've shown here, there are quite a few subtleties out there that can confuse data integration at a later stage unless hammered out. A little trouble here can save a great deal of trouble later.
@PauliPaasonen this is a great example of how ontologies can help clarify terminology. I'll create classes for both processes (the mass increase and the actual formation) and then a union class for the term that you use in your field. I'll add your instructive note about cloud formation and ice formation as a comment.
The continuous formation of aerosols would be the process. Following our discussion above, the event is indeed a period of increased rate in the process (intensive formation). I don't see an issue here, am I missing something?
Yes. Will do.
Yes, this sounds like a more involved discussion best done in a teleconference. OBO resources can provide semantics for spatiotemporal entities fairly easily. ENVO can offer subclasses of the event if their are clear differentiae between them.
We can keep it on our tracker, cross-referencing this issue. |
The problem is that for a big part of the aerosol community "aerosol formation" = "condensation growth of particles" or "primary emissions". As especially in health and legislation issues only the aerosol mass has been considered, this is logical: "new particle formation event" increases the number of particles, but the mass is not impacted before the particles have grown (due to condensation) to larger sizes. For this reason, "new particle formation" is a good term to use always when discussing the formation of new aerosol particles. Thus also the event, if meaning the period of intensive formation of new particles from vapours, should be referred to as "new particle formation event", not "aerosol formation event" or "formation of aerosols". |
It's a little painful, but this is the right place to figure out a way to expose this ambiguity coherently. Thank you for your engagement. We're unlikely to get this in a perfect state, but we can get close to communicating what's going on in the heads of scientists working with these phenomena. |
Updates pushed to editors' version, release in a few days. |
I had a meeting with the research community in Helsinki, including @mazaidan. It was pointed out that "formation of particles in an atmosphere" really should be called "new particle formation event". The researchers felt very strongly about having new and event in the concept. It was also pointed out that a process is not observed, rather the event is observed. To my understanding, the event consists of many processes. The point is, the correct naming of these terms isn't settled and I like to open this issue to try getting this straight, and I like to directly involve the research community (also Pauli et al. but not sure if they are on GitHub, @mazaidan can you check?).
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