- 1 Species interactions, vocabulary of concepts
- 1.1 Collection Terms
- 1.2 Concept Terms
- 1.3 Species interactions
- 1.4 Species interactions vocabulary of concepts
Species interactions, vocabulary of concepts
The taxon occurrence interactions vocabulary of concepts is described by the canonical URI http://rs.gbif.org/terms/tdwg/interaction (the vocabulary is of rdf:type = skos:ConceptScheme). The preferred namespace prefix is "spi" with namespace URI = http://rs.gbif.org/terms/tdwg/interaction#. Minting the interaction concepts here, each concept will have it's own Wiki page with a definition and further descriptions. Concepts are presented here organized alphabetical by their group (skos:Collection). The first step when setting up a new vocabulary (with external namespace URIs) is to import the concept identifier URIs to the Wiki. This is done using a special wiki page in the "MediaWiki" wiki-namespace and starting with "Smw_import_" followed by the local namespace prefix to be used by the Wiki. For the species interaction concepts we use: MediaWiki:Smw_import_interaction and MediaWiki:Smw_import_toi.
Controlled values for Controlled Value Vocabularies are recommended by the VoMaG task group (http://community.gbif.org/pg/groups/21382/) to be RE-USED from a SKOS RDF resource. The SKOS RDF resource is recommended to provide the definition of the concepts designed for maximal potential to be re-used. A new draft SKOS RDF resource for species interactions was developed and made available at http://rs.gbif.org/sandbox/terms/interaction.rdf. This new and draft SKOS vocabulary provides the definitions for the concepts re-used here in a controlled value vocabulary for species interactions. This model allows for multiple controlled value vocabularies to re-use concepts from the same SKOS vocabularies. And each Controlled Value Vocabulary may re-use concepts defined by different SKOS vocabularies.
This SKOS RDF vocabulary is based on the TDWG LSID Ontology model for taxon occurrence interactions, developed by Kevin Richards in 2007 (Richards, 2007) and aimed at describing the interactions between TaxonOccurrences, observations, specimens etc. Eg the Interaction class can be expressed a host/parasite relation between two TaxonOccurrences (Richards, 2007). The TDWG LSID Ontology is again based on earlier developments from 2007 (De Giovanni, Cartolano, Giannini, Saraiva and Pizzigatti, 2007) supported in part by the Pollinators Thematic Network of the Inter-American Biodiversity Information Network (IABIN) and by the Pollination Information Management System of the Food and Agriculture Organization of the United Nations (FAO).
This current update of the list of species interaction concepts was initiated in March 2012 to include concepts to describe species interactions for saproxylic organisms living on decaying wood. The new draft controlled value vocabulary for species interactions is available at: http://vocabularies.gbif.org/vocabularies/Interaction/
Would it be most appropriate to update the TDWG Interaction Ontology (http://rs.tdwg.org/ontology/voc/TaxonOccurrenceInteraction) to include new concepts and definitions for species interactions. The recommendation from the VoMaG task group is to establish a SKOS vocabulary of basic concepts and terms for re-use in Darwin Core extensions and controlled vocabularies as well as re-used when building ontologies. SKOS concepts provides greater potential for re-use because of they declare fewer semantic restrictions for their re-use. Here is proposed to establish a new and normative SKOS resource at: http://rs.gbif.org/terms/tdwg/interaction.rdf See also the discussion page at the GBIF Community Site at: http://community.gbif.org/pg/pages/view/22551/species-interactions
- De Giovanni, Renato; Etienne Cartolano; Tereza Giannini; Antonio Saraiva; and Pedro Pizzigatti (2007). Interaction Extension. TDWG Biodiversity Information Standards. Published online 16 May 2007. Available at http://wiki.tdwg.org/twiki/bin/view/DarwinCore/InteractionExtension
- Richards, Kevin (2007). TDWG Interaction LSID Ontology. TDWG Biodiversity Information Standards. Published online 08 July 2007. Available at http://rs.tdwg.org/ontology/voc/TaxonOccurrenceInteraction.rdf
Minting the groups for organizing the interaction concepts here (groups are of rdf:type = skos:Collection).
- spi:TaxonOccurrenceInteraction  (concepts from the TDWG Interaction Ontology)
- spi:SaproxylicInteraction  (saproxylic interactions)
- spi:ParasiteInteraction  (parasite interactions)
- spi:WoodDecayerInteraction  (wood decayer interactions)
Minting the individual interaction concepts here (concepts are of rdf:type = skos:Concept).
Concepts imported from the TDWG Interaction Ontology (spi:TaxonOccurrenceInteraction )
toi:HasHost | toi:HostOf | toi:PreysUpon | toi:PreyedUponBy | toi:ParasiteOf | toi:PathogenOf | toi:InfectedBy | toi:NestedIn | toi:UsedAsNestBy | toi:VisitedFlowerOf | toi:FlowerVisitedBy | toi:DispersedSeedOf | toi:SeedDispersedBy | toi:ExtractsResinFrom | toi:ResinExtractedBy |
Saproxylic interactions (spi:SaproxylicInteraction)
spi:SugarFungus | spi:WoodDecayer | spi:WoodDecayerBrownRot | spi:WoodDecayerWhiteRot | spi:WoodDecayerSoftRot | spi:WoodDecayerResidual | spi:OccursAsMycoparasite | spi:OccursAsMycodecomposer | spi:Detrivore | spi:OccursAsMicrobivore | spi:OccursAsAmbrosiaConsumer | spi:OccursAsFungivore | spi:OccursAsScavenger | spi:OccursAsOmnivor | spi:OccursAsPredator | spi:OccursAsParasite | spi:OccursAsParasitoid | spi:OccursAsHyperparasitoid | spi:OccursAsCleptoparasite | spi:AssociatedSpecies | spi:Epixylic | spi:WoodNester |
Parasite interactions (spi:ParasiteInteraction)
We might eg. choose list the parasite species interactions as a separate group or category...?
Species interactions vocabulary of concepts
|Label||Taxon occurrence interactions|
|Title||Species interactions vocabulary of concepts|
|Description||This SKOS vocabulary is based the TDWG LSID Ontology model for taxon occurrence interactions, developed by Kevin Richards in 2009 and aimed at describing the interactions between TaxonOccurrences, observations, specimens etc. Eg the Interaction class can be expressed a host/parasite relation between two TaxonOccurrences. The TDWG LSID Ontology is again based on earlier developments from 2007 supported in part by the Pollinators Thematic Network of the Inter-American Biodiversity Information Network (IABIN) and by the Pollination Information Management System of the Food and Agriculture Organization of the United Nations (FAO).|
|Creator||Global Biodiversity Information Facility (GBIF)|
|Rights holder||Biodiversity Information Standards (TDWG)|
|Note||Notice that the base URI of the Species Interaction Vocabulary is http://rs.gbif.org/terms/tdwg/Interaction# . Please make sure that you are only using element identifiers in this namespace, e.g. http://rs.gbif.org/terms/tdwg/Interaction#CONCEPT. There may be copies of the ontology file on the Web which can be retrieved from other locations, but those locations should not be used as the basis of identifiers. This is the first draft vocabulary scheduled to be deprecated and replaced.|