Difference between revisions of "SpeciesTMPlugin"
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Revision as of 18:00, 14 December 2012
Species TM Plugin is a plugin of the Tree Manager service that defines and maintains tree views of biodiversity data sources exposed by the Species Manager services. Species TM Plugin provides an uniform model to access and storage data from SPD Service. Each Taxon generated via SPD Service is trasformed in a edge-labelled tree by Species TM Plugin.
Tree model
A tree generated by SpeciesTMPlugin has three subtrees:
- DwC: each data from SPD Service is mapped to Darwin Core concepts. A detailed description of the Darwin Core fields is listed here: https://gcube.wiki.gcube-system.org/gcube/index.php/Checklist_DwC.
- Properties: additional data elements from SPD Service are stored in this subtree.
- Provenance: information about provenance (wasDerivedFrom, wasGeneratedBy).
Generic model
<?xml version="1.0" ?> <t:root xmlns:t="http://gcube-system.org/namespaces/data/trees" SpeciesServiceId="PluginName:ID" t:id="PluginName:ID"> <DwC t:id="ID"> <nameAccordingTo> </nameAccordingTo> <scientificNameAuthorship> </scientificNameAuthorship> <taxonRank> </taxonRank> <parentNameUsageID> </parentNameUsageID> <scientificName> </scientificName> <acceptedNameUsageID> </acceptedNameUsageID> <taxonomicStatus> </taxonomicStatus> <taxonRemarks> </taxonRemarks> <bibliographicCitation> </bibliographicCitation> <scientificNameID> </scientificNameID> <modified> </modified> <kingdom> </kingdom> <phylum> </phylum> <class> </class> <order> </order> <family> </family> <genus> </genus> <subgenus> </subgenus> <specificEpithet> </specificEpithet> <infraspecificEpithet> </infraspecificEpithet> <verbatimTaxonRank> </verbatimTaxonRank> <vernacularNames> <language> </language> <locality> </locality> <vernacularName> </vernacularName> </vernacularNames> ......... <vernacularNames> <language> </language> <locality> </locality> <vernacularName> </vernacularName> </vernacularNames> </DwC> <Properties> <property> <key> </key> <value> </value> </property> ......... <property> <key> </key> <value> </value> </property> <Properties> <provenance> <wasDerivedFrom> </wasDerivedFrom> <wasGeneratedBy> </wasGeneratedBy> </provenance> </t:root>
Example
A taxon generated by SPD Service and mapped in a tree looks like this:
XXX
Bind request
An Activation Record allows the creation of collections. Using an Activation Record the user selects scientific names and data sources to create the collection.
A bind request has this form:
List<ScientificName> as ScientificName in List<DataSource> return Taxon
If List<DataSource> is empty, Species TM Plugin will retrieve data from all Data Sources.
Examples:
'Carcharodon carcharias' , 'Rosa' in ITIS, CatalogueOfLife return Taxon
'Carcharodon carcharias' , 'Rosa' return Taxon
'Carcharodon carcharias' return Taxon
Maven coordinates
<groupId>org.gcube.data.access</groupId> <artifactId>species-tree-plugin</artifactId> <version>1.0.0</version>
