SpeciesTMPlugin

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 a uniform model to access and storage data from SPD Service.

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

Tree model

A tree created 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.

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.

Example:

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

        'Carcharodon carcharias' , 'Rosa' return Taxon

        'Carcharodon carcharias' return Taxon