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soilfoodwebontology / sfwo

The Soil Food Web Ontology is a formal conceptual model of soil trophic ecology.
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Aligning the SFWO with Crawford (1992) #80

Open Archilegt opened 1 year ago

Archilegt commented 1 year ago

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Terms in Crawford (1992) should be added to the SFWO and linked to that source. Information in Crawford (1992) can also be used to enrich the SFWO with examples and additional sources. Originally an invited lecture at the 8th International Congress of Myriapodology, Innsbruck, Austria, July 15 - 20, 1990, Crawford's (1992) paper was later published in the congress Proceedings.

Terms to add: macrodetritivore: a member of the macrofauna which typically consumes dead organic matter. Source: Crawford (1992: 277, 278). Remark: It should be a children of detritivore in the SFWO, and a children of macrofauna in an ontology including that term. Note that the SFWO already includes macroalgae and therefore it could also include macrofauna. Components: apterygote insects such as thysanurans, some termites, most land molluscs, amphipods, isopods, earthworms and millipedes, detritivorous orthopteroid insects such as cockroaches and crickets, some ants, larvae of dipterans (e.g. tipulids) and larvae as well as adults of many coleopterans such as scarabaeids and tenebrionids. Source: Crawford (1992: 278). plant organic matter: Source: Crawford (1992: 277). Remark 1: Millipedes aid in its breakdown. Remark 2: The term implicitly refers to and should be a children of dead organic mater. Linked to #17 and #44. macrodetritivore guild: macrodetritivores are considered to be a guild because they use the same class of environmental resources in the same general way. This term was first proposed by Crawford (1992: 277, 278) based on Hawkins & MacMahon (1989). Consider if it can be included in the SFWO. dead organic matter: Term mentioned by Crawford (1992: 277). Remark: The animals that consume it are "relatively omnivorous". litter: commonly applies to the uppermost layer of decaying organic matter in terrestrial ecosystems. Source: Ricklefs (1990) cited by Crawford (1992: 277). detritus: a more general term [than litter] that describes freshly dead or partly decomposed organic material. Source: Ricklefs (1990) cited by Crawford (1992: 277). Remark: litter should be a children of detritus. detritivore: an animal that feeds on detritus. Source: Begon et al. (1986) cited by Crawford (1992: 277). Synonyms: saprovore, saprotroph. Source: Crawford (1992: 277). Remark: It should be the parent of macrodetritivore, but see also macrofauna. Example: millipedes (Diplopoda). sapro: a prefix referring to decay. Source: Crawford (1992: 277) [based on Swift et al. (1979)?]. troph: a suffix implying no particular method of food utilization. Source: Crawford (1992: 277) [based on Swift et al. (1979)?]. vore: a suffix referring to food ingestion by animals. Source: Swift et al. (1979) cited by Crawford (1992: 277). Linked to #73. saprophage: an animal that mainly feeds on surface material. Source: Lamotte (1989) cited by Crawford (1992: 277). Linked to #84. geophage: an animal that mainly feeds on soil. Source: Lamotte (1989) cited by Crawford (1992: 277). Linked to #61.

microfauna: Sources: Wallwork (1970), Swift et al. (1979), and Anderson (1987), all cited by Crawford (1992: 278). Remark: Note that the SFWO already includes microalgae. mesofauna: Sources: Wallwork (1970), Swift et al. (1979), and Anderson (1987), all cited by Crawford (1992: 278). macrofauna: invertebrate fauna associated with soil, whose adult lengths exceed 10 mm and whose widths range between 2 mm and 20 mm. Sources: Wallwork (1970), Swift et al. (1979), and Anderson (1987), all cited by Crawford (1992: 278). Remark 1: It should be the parent of macrodetritivore, but see also detritivore. Remark 2: Note that the SFWO already includes macroalgae.

resource: a term refering specifically to food and habitat. Remark: Sometimes food (e.g. leaf litter) constitutes most or all of the habitat of a detritivore. Source: Crawford (1992: 280). Linked to #77. fungivore: Actions: Add millipedes (Diplopoda) as examples. Add supporting statements and sources. "Diplopods in Amazonia are exclusively fungivorous." according to Beck [year missing, reference missing] cited by Crawford (1992: 280). "A North American spirostreptid millipede exhibits preferential feeding on fungi." according to Taylor (1982) cited by Crawford (1992: 280-281).

References: Anderson, J.M. (1987): Interactions between invertebrates and microorganisms: noise or necessity for soil processes? - In: Fletcher, M., T.R.G. Gray & J.G. Jones (eds.), Ecology of microbial communities, 440 pp., Cambridge University Press, Cambridge: 125 - 145. ? Beck, L. (1983): Soil zoology of the Amazonian inundation forests. [in German] Amazoniana, 8 (1): 91-99. [see fungivore] ? Beck, L. (1983): Zur Bodenbiologie des Laubwaldes. Verhandlungen der Deutschen Zoologischen Gesellschaft, 76: 37-54. [see fungivore] Begon, M., J.L. Harper & C.R. Townsend (1986): Ecology: individuals, populations and communities. - Sinauer Associates, Inc., Sunderland, Massachusetts, 876 pp. Crawford, C.S. (1992): Millipedes as model detritivores. Pp. 277-288. In: Meyer, E., Thaler, K., and W. Schedl (Eds.): Advances in Myriapodology. Proceedings of the 8th International Congress of Myriapodology. Innsbruck, 15-20 July 1990. Berichte des naturwissenschaftlich-medizinischen Vereins in Innsbruck Supplementum, 10: XIII + 465 pp. Universitätsverlag Wagner, Innsbruck. http://www.literature.at/alo?objid=10407 Hawkins, C.P. & J.A. MacMahon (1989): Guilds: the multiple meanings of a concept. Ann. Rev. Entomol., 34: 423-451. Lamotte, M. (1989): Place des animaux detritivores et des microorganismes décomposeurs dans les flux d'énergie de savanes africaines. Pedobiologia, 33: 17 - 35. Ricklefs, R.E. (1990): Ecology. Third edition. - W.H. Freeman and Co., New York: 896 pp. Swift, M.J., O.W. Heal & J.M. Anderson (1979): Decomposition in terrestrial ecosystems. - Univ. California Press, Berkeley: 372 pp. Taylor, E.C. (1982): Fungal preference by a desert millipede Orthoporus ornatus (Spirostreptidae). Pedobiologia, 23: 329 - 334. Wallwork, J.A. (1970): Ecology of soil animals. - McGraw-Hill, London: 283 pp.

AntonCollembola commented 1 year ago

I generally support the idea of inclusion existing classifications in the ontology. But I would be careful about what to include. Here because of the three main reasons: 1) Old resources (30 years ago) can be non-compatible with the current state of the knowledge (e.g. protozoa=protists=animals) 2) Terminology developed for one specific group may be not generic enough 3) Most of these terminologies were developed by a single person and are far from ideal. There is no good rason to follow them if they do not match our needs

Specific comments: macrodetritivore - may work. In generally I like the idea of dividing all trophic guilds into 'macro' and 'micro': macrodetritivores, macropredators, macroherbivores etc. We used them partly here: https://doi.org/10.7554/eLife.75428 But this may need to be discussed.

plant organic matter - does not make any sense as a child of dead organic matter. Plant organicmatter can be living.

macrodetritivore guild - I think that creation of groups is a huge separate topic. In any case, I would follow the recent paper by Mike and co https://www.sciencedirect.com/science/article/pii/S0016706122003809

dead organic matter - add as a synonym of detritus?

litter, detritus, detritivore, saprophage, geophage - all included in the ontology as suggested saprovore, saprotroph - relation to detritivore is not clarified = useless

troph and vore - agree, would be cool to add, see a separate issue discussion

micro- meso- macrofauna - could be included because they are widely used and will be needed e.g. for the text mining in perspective

resource - excludes bacteria and fungi. I'm not sure.

Archilegt commented 1 year ago
  1. "Old resources" with reference to "protozoa=protists=animals". Not because of that the resource is old. It all depends on what is defined as "animal". The ZooCode 4, for example, rules over the formation and usage of names of animals, it is current, and includes protists.
  2. "Terminology developed for one specific group may be not generic enough". Generalizations are made from specializations. We need to record the specializations and align them with the generalizations. That's what alignment means in this context.
  3. "Most of these terminologies were developed by a single person". Not really. As mentioned above, Crawford gave an invited lecture, collated from multiple sources, which are mentioned in the list of references above. As an expert, he also proposed terms of its own. Many of the terms above are from books, which takes us back to what we discussed in EUdaphobase meetings: broad diffusion, adoption, and usage of many terms in the scientific literature happened because they were in textbooks. If we record those terms, we made ontologies more useful for data mining purposes.
  4. "plant organic matter - does not make any sense..." It does make sense if you read "Remark 2: The term implicitly refers to and should be a children of dead organic mater." That the term is ambiguous is a different thing. You can propose the longer, unambiguous term "dead plant organic matter" but that doesn't change that we need to record "plant organic matter" as a synonym and that data mining will retrieve true and false positives for the implicit meaning.
  5. "dead organic matter - add as a synonym of detritus?" Detritus is "freshly dead or partly decomposed organic material" (see above). Dead organic matter is not defined in Crawford (1992). For discussion on synonymization of those two terms I suggest opening a different issue and adding concepts of dead organic matter taken from different sources.
  6. "saprovore, saprotroph - relation to detritivore is not clarified = useless" The relation to detritivore is clarified. Read above in the entry for detritivore where it says "Synonyms: saprovore, saprotroph." That is useful, at least for discussion, as there is an expert source that unambiguously considers three terms as exact synonyms.
  7. "resource - excludes bacteria and fungi." Nothing has been excluded. From my point of view it is actually overly inclusive, as it is "food and habitat". As long as bacteria and fungi are food for other organisms, they are resources and therefore are not excluded.
nleguillarme commented 1 year ago

Some questions:

  1. 'macro' and 'micro' guilds: do you think it is possible to axiomatize the definition of these concepts? Are they relevant for all classes of diets or for a few? Could they be narrow synonyms of the corresponding guild?
  2. Could 'dead plant organic matter' be a synonym of plant litter? Then, maybe 'plant organic matter' could be related synonym for text mining purpose?
  3. What should be the parent class of micro, macro, mesofauna? Organism or group of organism? Is it possible to axiomatize these concepts based on the size of the organisms?