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Merge pull request #2 from JULIELab/cdbm-1.1.0
Cdbm 1.0.0
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,23 +1,25 @@ | ||
| <project xmlns="http://maven.apache.org/POM/4.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/xsd/maven-4.0.0.xsd"> | ||
| <modelVersion>4.0.0</modelVersion> | ||
| <parent> | ||
| <groupId>de.julielab</groupId> | ||
| <artifactId>julielab-concept-db-manager</artifactId> | ||
| <version>1.0.0-SNAPSHOT</version> | ||
| </parent> | ||
| <artifactId>julielab-concept-creation-bioportal</artifactId> | ||
| <name>JULIE Lab Concept Creation for BioPortal</name> | ||
| <description>This project uses the JULIE Lab BioPortal Tools to create database concepts for ontology classes.</description> | ||
| <dependencies> | ||
| <dependency> | ||
| <groupId>de.julielab</groupId> | ||
| <artifactId>julielab-concept-db-manager-core</artifactId> | ||
| <version>${project.parent.version}</version> | ||
| </dependency> | ||
| <dependency> | ||
| <groupId>de.julielab</groupId> | ||
| <artifactId>julielab-bioportal-ontology-tools</artifactId> | ||
| <version>1.0.3</version> | ||
| </dependency> | ||
| </dependencies> | ||
| <project xmlns="http://maven.apache.org/POM/4.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" | ||
| xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/xsd/maven-4.0.0.xsd"> | ||
| <modelVersion>4.0.0</modelVersion> | ||
| <parent> | ||
| <groupId>de.julielab</groupId> | ||
| <artifactId>julielab-concept-db-manager</artifactId> | ||
| <version>1.0.0</version> | ||
| </parent> | ||
| <artifactId>julielab-concept-creation-bioportal</artifactId> | ||
| <name>JULIE Lab Concept Creation for BioPortal</name> | ||
| <description>This project uses the JULIE Lab BioPortal Tools to create database concepts for ontology classes. | ||
| </description> | ||
| <dependencies> | ||
| <dependency> | ||
| <groupId>de.julielab</groupId> | ||
| <artifactId>julielab-concept-db-manager-core</artifactId> | ||
| <version>${project.parent.version}</version> | ||
| </dependency> | ||
| <dependency> | ||
| <groupId>de.julielab</groupId> | ||
| <artifactId>julielab-bioportal-ontology-tools</artifactId> | ||
| <version>1.0.4</version> | ||
| </dependency> | ||
| </dependencies> | ||
| </project> |
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47 changes: 47 additions & 0 deletions
47
julielab-concept-creation-bioportal/src/main/resources/bioportalconcepts.xsd
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| <xs:schema xmlns:xs="http://www.w3.org/2001/XMLSchema" | ||
| xmlns="http://www.julielab.de/conceptdb/concepts/bioportal" | ||
| targetNamespace="http://www.julielab.de/conceptdb/concepts/bioportal" | ||
| version="1.0.0" | ||
| elementFormDefault="qualified"> | ||
|
|
||
| <!-- The name of the BioPortal Concept Creator provider. Only names determining the respective class are allowed. --> | ||
| <xs:element name="name"> | ||
| <xs:simpleType> | ||
| <xs:restriction base="xs:string"> | ||
| <xs:enumeration value="JulielabBioPortalToolsConceptCreator"/> | ||
| <xs:enumeration value="de.julielab.concepts.db.creators.JulielabBioPortalToolsConceptCreator"/> | ||
| </xs:restriction> | ||
| </xs:simpleType> | ||
| </xs:element> | ||
|
|
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| <xs:element name="path" type="xs:string"> | ||
| <xs:annotation> | ||
| <xs:documentation xml:lang="en"> | ||
| The path to a single JSON ontology names file or a directory of such files. The files may be compressed | ||
| using GZIP. The JSON format is the one used by the | ||
| <a href="https://github.com/JULIELab/julielab-bioportal-ontology-tools">JULIE Lab BioPortal Tools</a> | ||
| which can also be used to download ontologies and extract ontology classes, their names and their | ||
| hierarchy for concept database import. | ||
| </xs:documentation> | ||
| </xs:annotation> | ||
| </xs:element> | ||
|
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||
| <!-- The provider configuration --> | ||
| <xs:element name="configuration"> | ||
| <xs:complexType> | ||
| <xs:all> | ||
| <xs:element ref="path"/> | ||
| </xs:all> | ||
| </xs:complexType> | ||
| </xs:element> | ||
|
|
||
| <!-- The root concept creator element --> | ||
| <xs:element name="creator"> | ||
| <xs:complexType> | ||
| <xs:sequence> | ||
| <xs:element ref="name"/> | ||
| <xs:element ref="configuration"/> | ||
| </xs:sequence> | ||
| </xs:complexType> | ||
| </xs:element> | ||
| </xs:schema> |
67 changes: 67 additions & 0 deletions
67
julielab-concept-creation-bioportal/src/main/resources/bioportalfacet.xsd
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| <?xml version="1.0" encoding="UTF-8" ?> | ||
| <xs:schema xmlns:xs="http://www.w3.org/2001/XMLSchema" | ||
| targetNamespace="http://www.julielab.de/conceptdb/facets/bioportal" | ||
| version="1.0.0" | ||
| xmlns="http://www.julielab.de/conceptdb/facets/bioportal" | ||
| elementFormDefault="qualified"> | ||
|
|
||
|
|
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| <xs:element name="labels"> | ||
| <xs:annotation> | ||
| <xs:documentation xml:lang="en"> | ||
| A set of labels that will be added as Neo4j node labels in the database. | ||
| </xs:documentation> | ||
| </xs:annotation> | ||
| <xs:complexType> | ||
| <xs:sequence> | ||
| <xs:element name="label" type="xs:string" maxOccurs="unbounded"/> | ||
| </xs:sequence> | ||
| </xs:complexType> | ||
| </xs:element> | ||
| <xs:element name="nofacet" type="xs:boolean" default="false"> | ||
| <xs:annotation> | ||
| <xs:documentation xml:lang="en"> | ||
| Indicates that the facet node should not be placed under the <em>facets</em> top node but under the <em>nofacets</em> top node in the database. "No-facet" facets are still meant to contribute concepts to an application but should be handled as second-class citizens and not be displayed on the application frontend, for example. | ||
| </xs:documentation> | ||
| </xs:annotation> | ||
| </xs:element> | ||
|
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| <xs:element name="facetgroup"> | ||
| <xs:annotation> | ||
| <xs:documentation xml:lang="en"> | ||
| All facets are assembled in facet groups. Facet groups are just nodes in the database that collect multiple facets, creating an additional hierarchical layer. They are uniquely identified via their name. | ||
| </xs:documentation> | ||
| </xs:annotation> | ||
| <xs:complexType> | ||
| <xs:sequence> | ||
| <xs:element name="name" type="xs:string"/> | ||
| </xs:sequence> | ||
| </xs:complexType> | ||
| </xs:element> | ||
|
|
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| <xs:element name="configuration"> | ||
| <xs:complexType> | ||
| <xs:sequence> | ||
| <xs:element ref="labels" minOccurs="0"/> | ||
| <xs:element ref="nofacet" minOccurs="0"/> | ||
| <xs:element ref="facetgroup"/> | ||
| </xs:sequence> | ||
| </xs:complexType> | ||
| </xs:element> | ||
|
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| <xs:element name="creator"> | ||
| <xs:annotation> | ||
| <xs:documentation xml:lang="en"> | ||
| BioPortal facets are directly derived from the respective ontologies. Each ontology is transformed into a | ||
| facet. The facet name and ID is the BioPortal ontology acronym. The source type is always hierarchic. | ||
| Labels can be specified that would be added to all BioPortal facets and the facet group name. | ||
| </xs:documentation> | ||
| </xs:annotation> | ||
| <xs:complexType> | ||
| <xs:sequence> | ||
| <xs:element ref="configuration"/> | ||
| </xs:sequence> | ||
| </xs:complexType> | ||
| </xs:element> | ||
|
|
||
| </xs:schema> |
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