Architecture - Revision history

Palexand: /* The class mappings:Mapping_Metadata */

2010-09-09T19:53:29Z

The class mappings:Mapping_Metadata

Palexand: /* The class mappings:Mapping_Metadata */

2010-09-08T01:31:06Z

The class mappings:Mapping_Metadata

Palexand: /* The class mappings:Mapping_Metadata */

2010-09-08T01:29:50Z

The class mappings:Mapping_Metadata

Palexand: /* The class mappings:Mapping_Metadata */

2010-09-08T01:27:17Z

The class mappings:Mapping_Metadata

Noy: /* The class OMV:Ontology */

2010-05-03T17:22:25Z

The class OMV:Ontology

Noy: /* The class mappings:One_to_one_mapping */

2010-01-16T00:51:01Z

The class mappings:One_to_one_mapping

Noy: /* The class changes:Proposal */

2009-10-22T01:17:44Z

The class changes:Proposal

Noy: /* The class changes:Proposal */

2009-10-22T01:17:23Z

The class changes:Proposal

Noy: /* The class changes:Proposal */

2009-10-22T01:09:03Z

The class changes:Proposal

Noy: Added requirements for proposals

2009-10-22T01:03:08Z

Added requirements for proposals

@@ Line 235: / Line 235: @@
 A class <tt>'''mappings:Mapping_Metadata'''</tt> represents the metadata about each mapping:
 * <tt>applicationContext</tt> (range: String)
-* <tt>mappingSource</tt> (range: <tt>mappingSource</tt>, a class with three subclasses <tt>mappingAlgorithm</tt>, <tt>organization</tt> and <tt>application</tt>)
+* <tt>mappingSource</tt> (range: <tt>mappingSource</tt>, a class with three subclasses <tt>algorithm</tt>, <tt>organization</tt> and <tt>application</tt>)
-** <tt>mappingSource</tt> name, url, algorithm
+** <tt>algorithm</tt> name, url, algorithm
 ** <tt>organization</tt> name, url, contact info
 ** <tt>application</tt> name, url, contact info

@@ Line 239: / Line 239: @@
 ** <tt>organization</tt> name, url, contact info
 ** <tt>application</tt> name, url, contact info
-* <tt>mappingType</tt> How the mapping originated. <tt>automatic</tt> or <tt>manual</tt> (range: literal)
+* <tt>mappingType</tt> (range: <tt>automatic</tt> or <tt>manual</tt>)
 * <tt>comment</tt> (range: <tt>String</tt>)
 * <tt>date</tt> (range: <tt>date</tt>)

@@ Line 236: / Line 236: @@
 * <tt>applicationContext</tt> (range: String)
 * <tt>mappingSource</tt> (range: <tt>mappingSource</tt>, a class with three subclasses <tt>mappingAlgorithm</tt>, <tt>organization</tt> and <tt>application</tt>)
-** mappingSource: name, url, algorithm
+** <tt>mappingSource</tt> name, url, algorithm
-** organization: name, url, contact info
+** <tt>organization</tt> name, url, contact info
-** application: name, url, contact info
+** <tt>application</tt> name, url, contact info
 * <tt>comment</tt> (range: <tt>String</tt>)
 * <tt>date</tt> (range: <tt>date</tt>)

@@ Line 235: / Line 235: @@
 A class <tt>'''mappings:Mapping_Metadata'''</tt> represents the metadata about each mapping:
 * <tt>applicationContext</tt> (range: String)
-* <tt>authority</tt> (range: <tt>Authority</tt>, a class with two subclasses <tt>Authority_Algorithm</tt> and <tt>Authority_Manual</tt>; the former contains the details of the algorithm)
+* <tt>mappingSource</tt> (range: <tt>mappingSource</tt>, a class with three subclasses <tt>mappingAlgorithm</tt>, <tt>organization</tt> and <tt>application</tt>)
 * <tt>comment</tt> (range: <tt>String</tt>)
 * <tt>date</tt> (range: <tt>date</tt>)

← Older revision		Revision as of 17:22, 3 May 2010
Line 56:		Line 56:

	We also add some instances for ontology engineering tools and methodologies to account for OBO ontologies (OBO-Edit tool and the DAG ontology structure) and to include the OBO Foundry, caBIG, and others as endorsing organizations.		We also add some instances for ontology engineering tools and methodologies to account for OBO ontologies (OBO-Edit tool and the DAG ontology structure) and to include the OBO Foundry, caBIG, and others as endorsing organizations.
		+
		+
		+	==== Full list of properties for instances of <tt>OMV:Ontology</tt> ====
		+
		+	Here is the full list of properties for instances of the class <tt>OMV:Ontology</tt>. It includes the properties that are added in the BioPortal metadata ontology, in addition to the ones that were inherited from OMV.
		+
		+	* <tt>designedForOntologyTask</tt>: a textual description of the task for which the ontology was designed
		+	* <tt>endorsedBy</tt>: organizations that endorsed the ontology (e.g., caBIG, OBO Foundry, WHO, etc.)
		+	* <tt>hasContributor</tt>: names of contributors to the ontology
		+	* <tt>hasCreator</tt>: the creator of the ontology
		+	* <tt>hasDomain</tt>: a category that describes the ontology, from a pre-defined list of categories (e.g., Anatomy, names of specific organisms, Diseases, etc.)
		+	* <tt>hasFormalityLevel</tt>: is it a taxonomy, a formal ontology, etc.
		+	* <tt>hasLicense</tt>: license under which the ontology is distributed
		+	* <tt>hasOntologyLanguage</tt>: the language in which the ontology was developed
		+	* <tt>usedOntologyEngineeringTool</tt>: the tool that was used to develop the ontology
		+	* <tt>currentVersion</tt>: version number
		+	* <tt>URI</tt>: the URI of the ontology
		+	* <tt>acronym</tt>: the ontology acronym
		+	* <tt>creationDate</tt>, <tt>modificationDate</tt>
		+	* <tt>description</tt>: description of the ontology
		+	* <tt>keyClasses</tt>: the list of key classes in the ontology
		+	* <tt>keywords</tt>: the list of keywords describing the ontology
		+	* <tt>name</tt>: name of the ontology
		+	* <tt>status</tt>: alpha, pre-production. production, etc.
		+	* <tt>hasContactEmail</tt>, <tt>hasContactEmail</tt>: contact information for the ontology authors (can be a mailing list)
		+	* <tt>urlPublications</tt>: a link to the list of publications about the ontology
		+	* <tt>urlHomepage</tt>: the homepage for the ontology (different from URI; this is a page intended for humans_
		+	* <tt>synonymProperty</tt>: which property holds the synonyms for class names (default: <tt>[http://www.w3.org/2004/02/skos/core#altLabel skos:altLabel]</tt>
		+	* <tt>preferredNameProperty</tt>: which property holds the preferred names for classes (default: <tt>[http://www.w3.org/2000/01/rdf-schema#label rdfs:label]</tt>
		+	* <tt>documentationProperty</tt>: which property holds the class definitions (default: <tt>[http://www.w3.org/2004/02/skos/core#definition skos:definition]</tt>
		+	* <tt>authorProperty</tt>: which property holds the author of a class (default: <tt>[http://purl.org/dc/elements/1.1/creator dc:creator]</tt>
		+
		+	Administration and maintenance in BioPortal; database information for finding the ontology in BioPortal. These properties are specific to the BioPortal implementation
		+	* <tt>administeredBy</tt>: the BioPortal user who administers the ontology
		+	* <tt>codingScheme</tt>: used for UMLS terminologies
		+	* <tt>fileNames</tt>: the name of the file for downloading the ontology
		+	* <tt>filePath</tt>: the location of the file for downloading the ontology
		+	* <tt>isFoundry</tt>: is the ontology pulled from the OBO Foundry site?
		+	* <tt>oboFoundryID</tt>: the id of the ontology on the OBO Foundry site (used for OBO Pull)
		+	* <tt>isManual</tt>: is ontology uploaded directly to BioPortal or pulled from a different repository (such as OBO Foundry)
		+	* <tt>isRemote/tt>: is the ontology uploaded to BioPortal or did the authors provide only metadata, but not the ontology itself
		+	* <tt>uploadDate</tt>: the date when the ontology was uploaded to BioPortal
		+
		+
		+
		+	Properties for handling ontology versioning:
		+
		+	* <tt>hasPriorVersion</tt>: a pointer to the earlier version of the ontology
		+	* <tt>isVersionOfVirtualOntology</tt>: a pointer to the "virtual ontology" instance -- the container for all versions of the same ontology
		+	* <tt>id</tt>: BioPortal internal version number

	=== The class <tt>VirtualOntology</tt> ===		=== The class <tt>VirtualOntology</tt> ===

@@ Line 175: / Line 175: @@
 * <tt>relation</tt> (range: <tt>URL</tt>)
 * <tt>mapping_metadat</tt>a (range: <tt>Mapping_Metadata</tt>)
 === The class <tt>mappings:Mapping_Metadata</tt> ===

← Older revision		Revision as of 01:17, 22 October 2009
Line 143:		Line 143:

	* Merge this concept with another concept (class <tt>changes:MergeProposal</tt>): Merge the selected concept into another concept. The expected side-effect is that the current concept will be retired (Thus, <tt>changes:MergeProposal</tt> may need to be a subclass of <tt>changes:RetireProposal</tt>). The fields are:		* Merge this concept with another concept (class <tt>changes:MergeProposal</tt>): Merge the selected concept into another concept. The expected side-effect is that the current concept will be retired (Thus, <tt>changes:MergeProposal</tt> may need to be a subclass of <tt>changes:RetireProposal</tt>). The fields are:
−
	** Merge with (property <tt>changes:targetEntity</tt>): what to merge the current entity with.		** Merge with (property <tt>changes:targetEntity</tt>): what to merge the current entity with.

@@ Line 129: / Line 129: @@
 ** New parent (property <tt>changes:newParent</tt>): where the class should be moved
 ** Keep the old parent? (property <tt>changes:moveOrCopy</tt>): should the proposed new parent be added to the list of parents (copy) or should the old parent be removed and the class should be moved to the new parent (move)?
 == Representing reviews ==

@@ Line 121: / Line 121: @@
 ** Synonyms (property <tt>changes:synonyms</tt>): synonyms for the new term
 ** Definition (property <tt>changes:definition</tt>): proposed definition for the new term
-** Superclass (property <tt>changes:parent</tt>): proposed parents of the new term (the note is usually attached to the proposed parent; so, by default the value for <tt>changes:parent</tt> is the same as the value for <tt>changes:annotates</tt>
+** Superclass (property <tt>changes:parent</tt>): proposed parents of the new term (the note is usually attached to the proposed parent; so, by default the value for <tt>changes:parent</tt> is the same as the value for <tt>changes:annotates</tt>)
 ** Comment (property <tt>changes:reasonForChange</tt>): a free-text comment explaining the reason for the proposed change
 == Representing reviews ==

← Older revision		Revision as of 01:03, 22 October 2009
Line 108:		Line 108:


−	~~The only subclass~~ of the class <tt>Annotation</tt> ~~that we will currently use is~~ the class <tt>Review</tt> that represents the reviews of the ontologies (see below).	+	We will use two subclasses of the class <tt>Annotation</tt>:
		+	* the class <tt>Review</tt> that represents the reviews of the ontologies (see below).
		+	* the class <tt>Proposal</tt> (and its subclasses) to represent structured proposals
		+
		+	=== The class <tt>changes:Proposal</tt> ===
		+
		+	Many of the structured notes in BioPortal are '''proposals''' for ontology changes. We represent several types of change proposals:
		+
		+	* New term proposal (class <tt>changes:NewEntityProposal</tt>): a structured proposal to create a new term in an ontology. It contains the following fields:
		+	** Generated ID (property <tt>changes:entityID</tt>): an automatically generated id for the new term that the proposer can use while the ontology curators are adding the term to the ontology
		+	** Preferred name (property <tt>changes:preferredName</tt>): preferred name (label) for the new term
		+	** Synonyms (property <tt>changes:synonyms</tt>): synonyms for the new term
		+	** Definition (property <tt>changes:definition</tt>): proposed definition for the new term
		+	** Superclass (property <tt>changes:parent</tt>): proposed parents of the new term (the note is usually attached to the proposed parent; so, by default the value for <tt>changes:parent</tt> is the same as the value for <tt>changes:annotates</tt>
		+	** Comment (property <tt>changes:reasonForChange</tt>): a free-text comment explaining the reason for the proposed change

	== Representing reviews ==		== Representing reviews ==