Issue 5557: Instances of OntologyEntries need a way to be further qualified (gene-expression-ftf) Source: Rosetta Biosoftware Business Unit (Mr. Michael D Miller, nobody) Nature: Uncategorized Issue Severity: Summary: Some ontologies, such as GeneOntology, don't have this concept but others, such as MGED's, do. Request from a number of sources to modify the model: * add a new class named "Slot" to the Description package with the following: - attribute: "name" of type String, required - parent base class: Extendable - association to Measurement named "Measurement" Slot end: - aggregates Measurement end - cardinality: 1..1 Measurement End: - name: "measurement" - cardinality: 0..1 - navigable - association to OntologyEntry named "SlotValue" Slot end: - aggregates OntologyEntry end - cardinality: 1..1 OntologyEntry end: - name: slotValue - cardinality: 0..1 - navigable - add rule that Slot has either measurement or ontologyEntry, exclusive * OntologyEntry has association to Slot named "Slots" OntologyEntry end: - aggregates Slot end - cardinality: 1..1 Slot end: - name: slots - cardinality: 0..N - navigable An simpler alternative would be an association from OntologyEntry to itself named "Associations": 1st OntologyEntry end: - aggregates 2nd OntologyEntry end - cardinality: 1..1 2nd OntologyEntry end: - name: associations - cardinality: 0..N - navigable (MAGE ISSUE 7) Resolution: see below Revised Text: Changes to the Specification: Section 2.1.3, Description Add to the QuantitationType Association documentation: Currently: " \bontologyReference\b : DatabaseEntry (0..1) Many ontology entries will not yet have formalized ontologies. In those cases, they will not have a database reference to the ontology. In the future it is highly encouraged that these ontologies be developed and ontologyEntry be subclassed from DatabaseReference." Becomes: " \bontologyReference\b : DatabaseEntry (0..1) Many ontology entries will not yet have formalized ontologies. In those cases, they will not have a database reference to the ontology. In the future it is highly encouraged that these ontologies be developed and ontologyEntry be subclassed from DatabaseReference. \bassociations\b : OntologyEntry (0..n) Allows an instance of an OntologyEntry to be further qualified." Replace Figure 2-4 MAGE-OM and the generated MAGE.xmi are updated, adding the association from OntologyEntry to itself. MAGE-ML.dtd Modify Element and Attlist declarations for OntologyEntry Currently: " ontologyReference: Many ontology entries will not yet have formalized ontologies. In those cases, they will not have a database reference to the ontology. In the future it is highly encouraged that these ontologies be developed and ontologyEntry be subclassed from DatabaseReference." Becomes: " ontologyReference: Many ontology entries will not yet have formalized ontologies. In those cases, they will not have a database reference to the ontology. In the future it is highly encouraged that these ontologies be developed and ontologyEntry be subclassed from DatabaseReference. associations: Allows an instance of an OntologyEntry to be further qualified." Currently: "<!ELEMENT Annotations_assnlist (OntologyEntry+) > <!ELEMENT Category_assn (OntologyEntry) >" Becomes: "<!ELEMENT Annotations_assnlist (OntologyEntry+) > <!ELEMENT Associations_assnlist (OntologyEntry+) > <!ELEMENT Category_assn (OntologyEntry) >" Currently: "<!ELEMENT OntologyEntry ((%Extendable_content;), OntologyReference_assn?) >" Becomes: "<!ELEMENT OntologyEntry ((%Extendable_content;), OntologyReference_assn?, Associations_assnlist?) >" Actions taken: July 29, 2002: received issue December 11, 2002: closed issue Discussion: Some ontologies, such as GeneOntology, don't have this concept but others, such as MGED's, do. There ws a lot of discussion on this issue and two proposed modifications. The alternative presented for a vote was the simpler of the two, which was to add a nested association to itself. End of Annotations:===== X-Server-Uuid: F7D3E4A3-3C15-41D2-AC5D-A7D3F094E28F From: "Miller, Michael (Rosetta)" To: "'Juergen Boldt'" cc: gene-expression-ftf@omg.org Subject: Gene Expression FTF issues Date: Mon, 29 Jul 2002 07:30:43 -0700 X-Mailer: Internet Mail Service (5.5.2653.19) X-WSS-ID: 115B8FEF18115-01-01 Hi Juergen, Here's the last batch. Officially, I guess I'm entering them but these are collated from the MGED efforts for which there is no clear consensus yet. thanks, as always, Michael Michael Miller Senior Application Developer Rosetta Biosoftware michael_miller@rosettabio.com www.rosettabio.com Instances of OntologyEntries need a way to be further qualified. Some ontologies, such as GeneOntology, don't have this concept but others, such as MGED's, do. Request from a number of sources to modify the model: * add a new class named "Slot" to the Description package with the following: - attribute: "name" of type String, required - parent base class: Extendable - association to Measurement named "Measurement" Slot end: - aggregates Measurement end - cardinality: 1..1 Measurement End: - name: "measurement" - cardinality: 0..1 - navigable - association to OntologyEntry named "SlotValue" Slot end: - aggregates OntologyEntry end - cardinality: 1..1 OntologyEntry end: - name: slotValue - cardinality: 0..1 - navigable - add rule that Slot has either measurement or ontologyEntry, exclusive * OntologyEntry has association to Slot named "Slots" OntologyEntry end: - aggregates Slot end - cardinality: 1..1 Slot end: - name: slots - cardinality: 0..N - navigable An simpler alternative would be an association from OntologyEntry to itself named "Associations": 1st OntologyEntry end: - aggregates 2nd OntologyEntry end - cardinality: 1..1 2nd OntologyEntry end: - name: associations - cardinality: 0..N - navigable (MAGE ISSUE 7)