SpeciesTMPlugin

Species TM Plugin

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 stores and retrieves data from SPD Service.

Each Taxonomy Item generated via SPD Service is trasformed in a edge-labelled tree.

Tree model

A tree generated by SpeciesTMPlugin has three subtrees:

• DwC: each data from SPD Service is mapped to Darwin Core concepts. A more 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 saved in this subtree.
• Provenance: information about provenance.

Example

<?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>

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.

Example:

        'Carcharodon carcharias' , 'Rosa' in ITIS, CatalogueOfLife return Taxon

        'Carcharodon carcharias' , 'Rosa' return Taxon

        'Carcharodon carcharias' return Taxon