OntologyDBWiki/MAGEOMDiscussion - Revision history

Alu: /* Use Case */

2011-10-28T13:28:54Z

Use Case

← Older revision		Revision as of 15:28, 28 October 2011
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	Please correct me if I misunderstood the concept of the object model. Any other comments/suggestions are of course appreciated!		Please correct me if I misunderstood the concept of the object model. Any other comments/suggestions are of course appreciated!

	~~Author: [http://www.cebitec.uni-bielefeld.de/~krunte Kai Runte]~~

Admin: 19 revisions

2011-10-26T06:13:40Z

19 revisions

← Older revision	Revision as of 08:13, 26 October 2011
(No difference)

imported>KaiRunte at 14:22, 13 December 2004

2004-12-13T14:22:35Z

← Older revision		Revision as of 16:22, 13 December 2004
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	Please correct me if I misunderstood the concept of the object model. Any other comments/suggestions are of course appreciated!		Please correct me if I misunderstood the concept of the object model. Any other comments/suggestions are of course appreciated!

			Author: [http://www.cebitec.uni-bielefeld.de/~krunte Kai Runte]

imported>KaiRunte at 14:21, 13 December 2004

2004-12-13T14:21:51Z

← Older revision		Revision as of 16:21, 13 December 2004
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	I will now describe how the data from the MGED ontology can be stored in the object model mentioned above. This alone should show that the object model make handling and querying an ontology awkward and time-consuming.		I will now describe how the data from the MGED ontology can be stored in the object model mentioned above. This alone should show that the object model make handling and querying an ontology awkward and time-consuming.

	First of all, the object model has no distinction between a class and an instance. As a workaround I define a class as an OntologyEntry with empty value attribute. For example, to define the term "disease state design", which is an instance of the PerturbationalDesign class, I create an object OntologyEntry with value="disease state design" and category="[[PerturbationalDesign]]"		First of all, the object model has no distinction between a class and an instance. As a workaround I define a class as an OntologyEntry with empty value attribute. For example, to define the term "disease state design", which is an instance of the PerturbationalDesign class, I create an object OntologyEntry with value="disease state design" and category="PerturbationalDesign". To define it as a sub-class of "ExperimentDesignType", I add as associations attribute a reference to another OntologyEntry object with empty value and category="ExperimentDesignType".
			To be able to search for all instances of ExperimentDesignType, we would need to add all "instance" OntologyEntry objects to the "ExperimentDesignType" object. As such this is not a problem, but very error-prone.

			Please correct me if I misunderstood the concept of the object model. Any other comments/suggestions are of course appreciated!

imported>KaiRunte at 14:14, 13 December 2004

2004-12-13T14:14:03Z

← Older revision		Revision as of 16:14, 13 December 2004
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	I will now describe how the data from the MGED ontology can be stored in the object model mentioned above. This alone should show that the object model make handling and querying an ontology awkward and time-consuming.		I will now describe how the data from the MGED ontology can be stored in the object model mentioned above. This alone should show that the object model make handling and querying an ontology awkward and time-consuming.

			First of all, the object model has no distinction between a class and an instance. As a workaround I define a class as an OntologyEntry with empty value attribute. For example, to define the term "disease state design", which is an instance of the PerturbationalDesign class, I create an object OntologyEntry with value="disease state design" and category="[[PerturbationalDesign]]"

imported>KaiRunte at 14:07, 13 December 2004

2004-12-13T14:07:55Z

← Older revision		Revision as of 16:07, 13 December 2004
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	== Use Case ==		== Use Case ==

	I want to extract information from the MGED ontology for the experiment design type while keeping the structure as it is defined in this ontology. In detail, the MGED ontology has a class [[ExperimentDesignType]] with several sub-classes (e.g. [[PerturbationalDesign]]). Each of these sub-classes has in turn instances that define the actual terms to use as values for an experiment design type. Of course, when these terms are stored in the ontology, they should be easily extractable, that is if I ask "Give me all values for [[ExperimentDesignType]]", I should receive all '''instances''' of [[ExperimentDesignType]] ''including'' its sub-classes.		I want to extract information from the MGED ontology for the experiment design type while keeping the structure as it is defined in this ontology. In detail, the MGED ontology has a class ExperimentDesignType with several sub-classes (e.g. PerturbationalDesign). Each of these sub-classes has in turn instances that define the actual terms to use as values for an experiment design type. Of course, when these terms are stored in the ontology, they should be easily extractable, that is if I ask "Give me all values for ExperimentDesignType", I should receive all '''instances''' of ExperimentDesignType ''including'' its sub-classes.

	I will now describe how the data from the MGED ontology can be stored in the object model mentioned above. This alone should show that the object model make handling and querying an ontology awkward and time-consuming.		I will now describe how the data from the MGED ontology can be stored in the object model mentioned above. This alone should show that the object model make handling and querying an ontology awkward and time-consuming.

imported>KaiRunte at 14:07, 13 December 2004

2004-12-13T14:07:08Z

← Older revision		Revision as of 16:07, 13 December 2004
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	== Use Case ==		== Use Case ==

			I want to extract information from the MGED ontology for the experiment design type while keeping the structure as it is defined in this ontology. In detail, the MGED ontology has a class [[ExperimentDesignType]] with several sub-classes (e.g. [[PerturbationalDesign]]). Each of these sub-classes has in turn instances that define the actual terms to use as values for an experiment design type. Of course, when these terms are stored in the ontology, they should be easily extractable, that is if I ask "Give me all values for [[ExperimentDesignType]]", I should receive all '''instances''' of [[ExperimentDesignType]] ''including'' its sub-classes.

			I will now describe how the data from the MGED ontology can be stored in the object model mentioned above. This alone should show that the object model make handling and querying an ontology awkward and time-consuming.

imported>KaiRunte at 13:55, 13 December 2004

2004-12-13T13:55:25Z

← Older revision		Revision as of 15:55, 13 December 2004
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	__NOTOC__		__NOTOC__
	= Discussion of the MAGE object model (MAGE-OM) ontology classes =		= Discussion of the MAGE object model (MAGE-OM) ontology classes =

			== Introduction ==

			In the section "overview" I introduce the classes as they were defined by Michi in O2DBI. I also highlight differences to the "official" documentation at the EBI: [http://www.ebi.ac.uk/arrayexpress/Schema/MAGE/MAGE.htm]. In the next section, "use case", I create a simple use case to show why it is not such a good idea to try to store a complex ontology like the MGED in this object model.

	== Overview ==		== Overview ==
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	*** description: String [?]		*** description: String [?]
	*** name: String [from Identifiable?]		*** name: String [from Identifiable?]
	*** db_ref: External BRIDGE reference		*** db_ref: External BRIDGE reference [?]
	*** alt_URI: List of Strings [?]		*** alt_URI: List of Strings [?]
	*** type: OntologyEntry [?]		*** type: OntologyEntry [?]
	*** maintainer_email: String [?]		*** maintainer_email: String [?]

	== Comments/Questions ==		=== Comments/Questions ===
	* all the attributes marked with [?] were not found in the [http://www.ebi.ac.uk/arrayexpress/Schema/MAGE/MAGE.htm array express object model documentation]. Where do these come from?		* all the attributes marked with [?] were not found in the [http://www.ebi.ac.uk/arrayexpress/Schema/MAGE/MAGE.htm array express object model documentation]. Where do these come from?

			== Use Case ==

imported>KaiRunte at 13:49, 13 December 2004

2004-12-13T13:49:17Z

← Older revision		Revision as of 15:49, 13 December 2004
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	*** version: String		*** version: String
	*** URI: String		*** URI: String
			*** description: String [?]
			*** name: String [from Identifiable?]
			*** db_ref: External BRIDGE reference
			*** alt_URI: List of Strings [?]
			*** type: OntologyEntry [?]
			*** maintainer_email: String [?]

	== Comments/Questions ==		== Comments/Questions ==
	* the attributes ~~owner and creator in OntologyEntry~~ were not found in the [http://www.ebi.ac.uk/arrayexpress/Schema/MAGE/MAGE.htm array express object model documentation]. Where do these come from?		* all the attributes marked with [?] were not found in the [http://www.ebi.ac.uk/arrayexpress/Schema/MAGE/MAGE.htm array express object model documentation]. Where do these come from?

imported>KaiRunte at 13:44, 13 December 2004

2004-12-13T13:44:27Z

← Older revision		Revision as of 15:44, 13 December 2004
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	*** URI: String		*** URI: String
	*** database: Reference to Database		*** database: Reference to Database
	* Class Database		* Class Database [http://www.ebi.ac.uk/arrayexpress/Schema/MAGE/cat3ac6541d0324/cat3b04193300ad/class3b04176c032a.htm EBI Documentation]
	** Attributes:		** Attributes:
	*** version: String		*** version: String