Diversity Collection

BioCASE

To publish your data on portals like GBIF data can be provided in the ABCD standard using BioCASe for mapping your data (see below). Use the ABCD package to convert the data into a format prepared for BioCASe. Configure the database and map the fields according to the examples.

For details about the BioCASe software please see the provided documentation. DiversityCollection transfers the data for every project in a separate schema. As BioCASe so far is unable to handle schemata in Postgres additional views for the package ABCD are created in the schema public and you need to provide a single database for every project.

 

Step by Step

To provide the data for BioCASe you need to transfer the data from DiversityCollection together with all auxiliary sources (Taxa, References, Gazetteer) depending on your data from the SQL-Server database to the SQL-Server cache database and from there to the Postgres cache database. In the Postgres database you need the package ABCD for mapping your data to BioCASe.

 

Metadata

The metadata for ABCD are taken from the project data in the module DiversityProjects to which the data in DiversityCollection are linked to. The metadata include links to DiversityAgents within DiversityProjects. That means that to receive all needed data in the project you must ensure that the agent data used within the project have been transferred to the Cache database as well. If addresses of the agents are needed, these must be unlocked. For further information see the manuals within DiversityProjects and DiversityAgents. The table below shows the source for several ABCD nodes.

Database Table Column ABCD Node
DiversityAgents Agent
DiversityAgents AgentContactInformation Email  
DiversityAgents AgentContactInformation Address  
DiversityProjects Project

These metadata are defined as Settings as shown below as children of the setting ABCD. The following ABCD topics are taken from the settings in DiversityProjects:

  • TaxonomicGroup
  • Dataset including GUID, Coverage, Version, Creators, Icon, Dates etc.
  • TechnicalContact
  • ContentContact
  • OtherProvider
  • Source
  • Owner
  • IPR
  • Copyright
  • TermsOfUse
  • Disclaimers
  • Acknowledgements
  • Citations (if Reference is missing - see below)
  • RecordBasis
  • RecordURI
  • KindOfUnit
  • HigherTaxonRank

For further information about the configuration of the settings in DiversityProjects, please see the manual for this module.

 

Metadata - Stable identifier = DatasetGUID

The DatasetGUID in ABCD is taken from the stable identifier defined in the module DiversityProjects for the database in combination with the ID of the project. To set the stable identifier choose Administration - Stable identifier from the menu in DiversityProjects and enter the basic path (e.g. see below). This stable identifier can only be set once. After it is set you will get a message as shown below.

Metadata - License

The license information for ABCD are taken from the first entry in the IPR & Licenses section in DiversityProjects (see below) where the first entry is the one entered first.

Metadata - Citation text

The citation for the project follows the form [<Authors>].] [<Title>][. [Dataset]. Data Publisher:] [<Data_center_name>]. [<URI>].

The Authors are taken from the Agents section (see below) where all agents with the role Author are included according to their sequence in the list and separated by ;.

The [<Publication_year>] is the year of the publication i.e.the current year. The [ <Title>] corresponds to the[Title] of the project. The [<Data_center_name>] istaken from the Agents section. Here the first agent with the role Publisher is used. The [<URI>] is taken from the field URI of the citation with the type BioCASe (GFBio) in the Citations & References section (see below).

 

Gathering - IsoCode

The IsoType for a country is taken from corresponding information in the module DiversityGazetteer. To ensure these information is available in the cache database, insert a source for a gazetteer project containing this information (see below).

 

Identification

The ABCD schema provided with this software is NOT including information from the module DiversityTaxonNames, so sources for Taxa are not needed by default. If for your own needs you decide to add additional data for the identifications from the module DivesityTaxonNames, ensure that the data corresponding to the names in your identifications are transferred from DiversityTaxonNames (see below).

 

Postgres database

The package ABCD providing the objects for mapping your data for BioCASE contains objects in the schema public. Therefore you need one database for every project you want to provide for BioCASE and the sources mentioned above have to be transferred in each of these databases.

 

Transfer

To provide the data for BioCASE you need to transfer all auxiliary sources as described above (Taxa, References, Gazetteer) depending on your data and the project data themselves from the SQL-Server databases to the SQL-Server cache database and from there to the Postgres cache database . The package itself needs a further transfer step if data have been changed after the creation of the package as the parts of the data in the Postgres database are imported into tables or materialized views according to the specifications of ABCD.