Pilot 3

From pro-iBiosphere Wiki
Jump to: navigation, search

Interoperability model between PLAZI and the EDIT Platform for Cybertaxonomy based on transformations between XML-repositories and CDM-stores.

Persons leading the pilot: Donat Agosti - Plazi and Anton Güntsch - FUB-BGBM

Institutions involved in the pilot:

  • BGBM

Main focus of the pilot is to create a pipeline between Plazi and CDM.

Current workflow and tools to import marked-up data are:

  • CDM. At present no automated workflow is available. pro-iBiosphere WP3 & WP4 aims to streamline that process. FUB-BGBM (Patricia Kelbert) will be responsible for the imports of all the data that will be marked-up by the partners.
  • Plazi. Treatments are uploaded automatically.
  • Species ID. Link is already functional.

Synergies with other projects/initiatives in order to facilitate pipelines with BioVel, GIBIF, EoL, CoL, etc. will be explored.

Project integration activities lead by the FUB-BGBM are: PESI, ViBRANT, Synthesys,BioVEL, LifeWatch, GIBIF, i4Life
  • GBIF-CDM. Not a problem because marked up locality data is Darwin Core compliant.
Plazi-CDM. A TAPIR service is operational to transfer locality data to GIBIF.
  • EoL XXX.

Start of interoperability activities will depend on the mark-up results of the pilot taxa (see below) and on the availability of new species.

At present, a tool to link data on a taxon coming from different online platforms such as GBIF, EOL, PLAZI, Wikis, CDM, Scratchpads, etc. is lacking. Available tools like uBio and Pensoft's Taxon Profile are not enough. A mechanism based on persistent identifiers (topic October workshop) needs to be created (used for one and the same taxon in the different databases). pro-iBiosphere will provide the rationale for the development of such a tool including a time estimate.

Status October 2013:
PLAZI delivers a list of treatments, based on the original document id or on a taxonomic name. Treatments are available for each pilot group in the PLAZI repository [Plazi].

Currently a communication circuit between the cdm-developer, plazi and the mark-up user is going on, in order to improve the quality of the marked-up treatments. The manual checking of the data by the cdm-dev is time consuming and should therefore be replaced by an automatic (machine) checker before the submission to the PLAZI server. Integrity and quality check were discussed further at meeting 4 (October 2013, Berlin). The received feedback is evaluated right now.
Further commitment was established for a consistent space of stable identifiers for collection objects across European taxonomic institutions and a central registry for biodiversity-related services.
The poster made for the BIH conference (Sept.2013) represents an overview of the pipeline between PLAZI-CDM (see http://figshare.com/articles/Interoperability_model_between_PLAZI_and_the_CDM_Platform/784945)