Template:All modeling issues

The logistics of carrying out metabolism set limits on cell size.

"A device/sensor/software application produces a piece of data (e.g., a measure for a sensor, a computation for an application).

Also, the editor should be flexible enough to represent taxonomies based on new types of relationships and specific features, proposed by the user.

- "gross income" calculatedBy ("yield" multipliedBy "price")

For instance, if I ask a question like "Where did this emergency occur?" I could simply represent it as a string. However, the question contains a lot of information, so in some cases one might want to represent it formally, and possibly reason on the question itself. For instance, we may want to derive that the answer should be of type "location" from the fact that the question uses the keyword "where".

We have identified two main aspects of this modeling issue:

1. How can we refer to the detailed description of the question?
2. How can we model the semantics of the question itself?

The first issue concerns the case when we would like to include both the question as a string, i.e., the human readable version of the question, and the question as a formal model. In this case we may have a class "Question", with a string property containing its representation in natural language. How do we now link also a formal description of this question, i.e., a set of triples, to the question class?

The second issue concerns how to represent the semantics of the question itself, i.e., an ontology for modeling those triples we wanted to refer to above. We would like to model things such as, the variable of the question, the expected answer type, any other constraints set in the question etc. For instance, in order to be able to ask questions such as: What is the expected answer type of this question? Is this answer correct with respect to the constraints of this question?

The problem is how to best represent ordered lists in RDF/OWL. In the decision representation domain the problem arises when modeling options, where one of the options will be selected, i.e., it will be the decision.

For example if the pattern was (this is informally written): "replace each two equivalent classes with a single one". We will search in A for each match(i.e. two equivalent classes) and replace them with one class in B. patterns are expressed using SPARQL. I need this pattern for the following reason: I was wondering if cardinalities in ontology can be included in a pattern. Actually I'm on an issue that uses ontology as conceptual formalization of relational data sources and I want to apply some transformations to handle some situations (e.g transform many-to-many to another type) on the conceptual model, which needs handling the cardinalities in the ontology. Is this topic covered somewhere in some design pattern?

The ingredients are substances in a concrete dosage. The ingredients are divided in one main ingredient (mainly an active ingredient) and a set of excipients (other substances) The drugs are uniques based on their concrete composition.

The Golgi apparatus consists of stacks of flattened sacs, or cisternae, which, unlike ER cisternae, are not physically connected.

The centrioles are not essential for cell division.

The usual replication machinery provides no way to complete the 5' ends of daughter DNA strands.

Temomeres do not contain genes.

The special base triplets UAA, UAG, and UGA do not code for amino acids but instead act as signals to stop translation.

Both nucleoli and ribosomes, unlike most other organelles, are not enclosed in membrane.

Prokaryotes do not have mitotic spindle.

Because bacteria lack nuclei, their DNA is not segregated from ribosomes and the other protein-synthesizing equipment.

The leader and trailer are not translated, nor is the poly(A) tail.

This means that most eukaryotic genes and their RNA transcripts have long noncoding stretches of nucleotides, regions that are not translated.

Molecules of tRNA are not all identical.

However, there are many requirements in domain modelling which require to talk about both the problem and solution spaces within a same universe of discourse. This is the case of legal knowledge (factual knowledge and legal cases vs. normative knowledge), services, planning and control knowledge (actual facts vs. expected facts), diagnostic knowledge and situational awareness (e.g. bare facts vs. typically unwanted facts), etc. All those cases fit into the abstract task of "classifying a situation" according to possibly incomplete, alternative or loose constraints, where those constraints must be explicit and explicitly linked to the representation of a situation. There are content patterns for representing situation classification, such as descriptionandsituation.owl, which relies on reification of conepts and relations. These patterns can represent situations and descriptions, and their given links (e.g. entities of a situation that play roles from a description, values of a situation that fit parameters from a description, etc.). But it's very hard to represent in general (not based on locally defined axioms, e.g. owl:equivalentClass axioms for a particular situation/description pair) how to:

1) make a situation emerge out of scattered facts 2) decide if a situation (or a set of facts) can be (partly or fully) classified under a description 3) evaluate which description fits best a certain set of facts etc.

Classical approaches represent situation classification within some algorithm or in the semantics of some appropriate meta-model. The modeling issue here is: