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Using the GBIF Infrastructure to Develop and Use a Thematic Species Checklist

The following is a example case of a user community utilising components of the GBIF infrastructure to integrate their domain-specific interests.

It starts with a small community interested in developing a thematically-organised species list. The initial objective is to create a checklist of cold-tolerant species. In this case, the species list is not defined by a monophyletic group or confined to a particular geographic region. It is primarily defined by a range of physiological characteristics. Nonetheless, a checklist defined in this way will aspire to be taxonomically up-to-date, ideally tied to explicitly referenced taxon concepts. The list itself would be taxonomically organised with terminal taxa organised into higher taxonomic groups, species names would be correctly spelled with proper authorship and publication year. Synonymy and vernacular name information might also be included. Our ambition is to facilitate the development of this list based on access to index taxonomic authority data.

This example was developed in concernt with Mélianie Raymond (GBIFS)

Phase 1: Use the Global Names Architecture to create a thematic checklist tied to a taxonomic authority file. Example a list of Cold-Tolerant species.

• A simple tool, perhaps a variation or expansion of the TaxonTagger refinement, allows a user to input a list of species or a publication containing a list of species.
• The tool allows the user to select a taxonomic authority from the registered list of taxonomic authority files in the Checklist Bank

• When a name is selected, either by being entered by the user or is identified in the source publication using Taxonomic Name Recognition, it is cross-referenced to the taxonomic publication using the general mapping method.
• The matching taxonomic information is imported to the tool which places the taxon name in the taxonomic hierarchy of the source and provides taxonomic status, spelling, synoyms, vernacular names, etc.
• The taxonomic data also includes a persistent link to the source database, for example a Catalogue of Life identifier (LSID).
• This functions to maintain a dynamic link to the record which will allow the derived list to stay in synch with any changes to the taxon
• This functions to allow users to instantly access the source authority file at the source
• The user repeats this exercise to create a complete taxonomic list

Phase 2: Publish the resultant thematic list to the GBIF network

This phase of the project would utilise the GBRDS to register the resultant checklist. It would allow the checklist to be identified as a species checklist, derived and linked to, a taxonomic authority. It would illustrate the use of GBRDS 'machine tagging' to present the semantic context of the list, allowing a domain-specific namespace to be created.

• The outcome of this phase would be the publication to the GBIF network of a thematically-scoped species list, identifiable by Globally Unique Identifiers and illustrating the capacity of the GBIF Registry.

Phase 3: Extend the thematic checklist with theme-specific data extensions.

This phase would allow the user-community to extend the Core GNA taxonomic data with a registered extension allowing them to define domain-specific data elements to be included with the thematic checklist.

1. user community would create a new extension on the GBIF Vocabulary and Extension Server
2. Would draft a list of extension terms and create controlled vocabularies for those terms as needed.

Outcome would be a communally derived extension that allows:

• the user community to now publish data relevant to their community through the GBIF network
• other participants to review the extension and provide new sources of data to the community from within their previously published data sources that include the new terms.

Phase 4: Using the thematic checklist to access biodiversity resources. RSS, publications, specimens, etc.

In this phase we would use the Checklist of Cold-tolerant species as a species profile to aggregate and organise biodiversity data. See uBioRSS as an example.

Phase 5: Accessing the thematic list for context from within other biodiversity data.

• An application like taxonTagger is used to load an Environmental Impact Assessment or other similar publication (a reference document).
• Taxon names in the document are automatically identified with Taxon Name Recognition Services
• A list of matching Checklist Resources is presented as an array, sort-able by various criteria.
• A match includes any checklist resource that references at least one taxon in the referent publication
• Selecting a Checklist resource provides metadata about the resource and presents a list of matching taxa
• Taxonomic annotations are provided such as if the name in the reference document is not an accepted name and the accepted name is provided

Phase 6: Additional demonstration within GeoSpatial applications

• Similar to 5 but in this case a geo-spatial representation of species data is illustrated as point or polygon occurrences
• A list of species is derived from the geo-spatial display
• A list of checklist resources is derived from the list of species
• Selecting a list has the effect of changing the display to reflect only the geospatial distribution of the members of the list.
• Additional services could be called to illustrate the integrative capacity of the network. For example, selecting a point or a taxon could display a list of recent publications tied to that taxon. Even better, if the registered resource has a publication profile created in our publication index it would limit publications to that profile, i.e., the list of publications would be limited to the set defined as relevant to Cold-Tolerant species

Links

Google Books Example Encyclopedia of the Antarctic

Supports strategic applications and campaigns (See 2009 Mid-Year report) on developing informatics tools and applications for lay audience illustrating integration of GBIF data with other content.