Factors affecting ontology development in ecology
Few ontologies in the ecological domain exist, but their development can take advantage of gained experience in other domains and from existing modeling practices in ecology. Taxonomies do not suffice because more expressive modeling techniques are already available in ecology, and the perspective of flow with its centrality of events and processes cannot be represented adequately in a taxonomy. Therefore, formal ontologies are required for sufficient expressivity and to be of benefit to ecologists, which also enables future reuse. We have created a formal mapping between the software-supported ecological modeling method and software tool STELLA and ontology elements, which simplifies bottom-up ontology development considerably and has excellent potential for semi-automated ontology development. However, the conducted experiments also revealed that ontology development for ecology is close to being part of ecological research that through the formalized representation of the knowledge more clearly points to lacunas and suggestions for further research in ecology.
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This supplementary material contains the four tables corresponding to the different STELLA elements and their mappings to ontology elements for the Microbial Loop model . Some explaining notes for each element are included in the third column of each table.
- Table 1. From Stock to Endurant
- Table 2. From Flow to Perdurant
- Table 3. From Converter to Quality or State
- Table 4. From Action Connector to Relationship type
The MicrobialLoop ontology and the experimental Pollution ontology are available online as OWL file.
A colour screenshot of a section of the MicrobialLoop using ezOWL is included in this supplementary material after the tables (here).
Table 1. From Stock to Endurant
|Phyto C||Yes - NAPO*||Phyto C = phytoplankton organic carbon. The phytoplankton is definitely an APO, but the 'phyto C' is part of the APO: it concerns itself only with the organic carbon of the phytoplankton, not the organism as an active agent as such|
|Phyto N||Yes - NAPO||Phyto N = phytoplankton nitrogen|
|Proto C||Yes - NAPO||Proto C = Protozoa organic carbon|
|Proto N||Yes - NAPO||Proto N = Protozoa nitrogen|
|DOC||Yes - NAPO||DOC = detrital organic carbon. Detritus is an endurant with no unity, and as such an amount of matter (M), but here, like with the organisms, there is focus on only a part of the NAPO|
|DON||Yes - NAPO||DON = detrital organic nitrogen|
|Bact C||Yes - NAPO||Bact C = bacterial organic carbon|
|Bact N||Yes - NAPO||Bact N = bacterial nitrogen|
|Nitrate||Yes - NAPO||Dissolved nitrate. Molecules are non agentive and, however small, still physical objects.|
|Ammonium||Yes - NAPO||Dissolved ammonium|
|Zoo N||Yes - NAPO||Zoo N = zooplankton nitrogen|
Table 2. From Flow to Perdurant
|Flow||(Type of) Perdurant||Comments|
|Photosynthesis||Yes - PRO||To phytoplankton N|
|Respiration||Yes - PRO||From phytoplankton N|
|Excr||Yes - ACC||C excretion from phytoplankton C to detrital organic carbon|
|Uptake||Yes - ACC||Of Nitrate by phytoplankton N. Each Nitrate is taken up, which has completion of that process but is not a continuous flow into the phytoplankton|
|N excr||Yes - PRO||By phytoplankton N into the detrital organic nitrogen|
|Bact assim C||Yes - PRO||Assimilation of C by Bacteria C from the detrital organic carbon|
|Bact assim N||Yes - PRO||Assimilation of N by Bacteria N from the detrital organic nitrogen|
|Uptake||Yes - ACC||Of Ammonium by phytoplankton N. Each Ammonium is taken up, which has completion of that process but not a continuous flow into the phytoplankton|
|Ammonium oxidation||Yes - ACH||From Ammonium to Nitrate. This is not a continuous process: each Ammonium gets oxidized into nitrate, which has completion of that process|
|Prot grazing phyto||Yes - PRO||Presumably carbon grazing, of the protozoa C on the phytoplankton C|
|Prot grazing phyto N||Yes - PRO||Nitrogen grazing by the protozoa N by eating the phytoplankton for N|
|Proto respiration||Yes - PRO||From protozoa C|
|Prot grazing bac||Yes - PRO||Protozoa that are grazing on the Bacterial C|
|Zoo grazing phyto||Yes - PRO||Mesozooplankton grazing on the phytoplankton C|
|Zoo grazing protozoa||Yes - PRO||Mesozooplankton grazing on the protozoa (the C)|
|Zoo grazing phyto N||Yes - PRO||Mesozooplankton grazing on the phytoplankton N|
|Proto grazing bact N||Yes - PRO||Protozoa grazing on the bacterial N|
|Bact resp||Yes - PRO||Bacterial respiration|
|Zoo grazing proto N||Yes - PRO||Mesozooplankton grazing on the protozoa N|
|Zoo excretion||Yes - ACC||The mesozooplankton N excrete ammonium|
|Bact ass amm||Yes - PRO||Bacteria N assimilating ammonia|
Table 3. From Converter to Quality or State.
|Converter||State or Quality||Comments|
|Grazing pressure "1"||ST||The top one is meant here, which is drawn outside the Microplankton window. Because it acts on a process (see Table 2), it is a 'parameter' affecting the process of grazing, hence may be a quality, because it is specifically constantly dependent on the entity it inheres in (grazing): at any time, a quality can't be present unless the entity it inheres in is also present. However, if there is no plankton the grazer may be grazing on something else, if there are no grazers, then the grazing pressure simply reaches zero. Thus 'grazing pressure' is always there, hence a state.|
|Grazing pressure "2"||ST||Duplication of the converter symbol and attached name in the diagram.|
Table 4. From Action Connector to Relationship type.
|Action connector||Relationship type||Comments|
|"1"||Yes||See the two converter entries in Table 3: Acts on the mesozooplankton grazing on the protozoa, and acts on the mesozooplankton grazing on the phytoplankton. This would translate as a relationship of e.g. suffersGrazingPressure or hasGrazingPressure|
|"2"||Yes||See the two converter entries in Table 3: The grazing pressure acts also on mesozooplankton grazing on protozoa N and on mesozooplankton grazing on phytoplankton N.|
Figure 1. Section of the MicrobialLoop ontology; graphical representation with ezOWL.