Supplementary Material of the Data Integration in the Life Sciences 2005 (DILS2005) article:

Factors affecting ontology development in ecology


Abstract

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.
(article - back to publications)


Supplematary material

This supplementary material contains the four tables corresponding to the different STELLA elements and their mappings to ontology elements for the Microbial Loop model [3]. 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

Stock Endurant Comments
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
* Abbreviations in the second column are taken from the DOLCE categories [1].


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.