Plazi

Summary
Type of tool	Suite of taxonomic bibliographic tools
Function	Text mining and bibliographic service
Online / Desktop	Online data server and desktop taxonomic editor
Computer infrastructure	Windows editor
Development status	New, active and developing
Time of use	Before data is sent to ALA; while data is with ALA; as a post-process
Licence	Free

Plazi is an association supporting and promoting the development of persistent and openly accessible digital taxonomic literature.1 Plazi hosts a web based service that offers access to descriptions of species and an archive to store marked-up documents.2

 

Description

3

Plazi aims to:4

• Maintain a digital taxonomic literature repository to enable archiving of taxonomic treatments.
• Enhance submitted taxonomic treatments by creating TaxonX-XML versions.
• Participate in the development of new models for publishing taxonomic treatments in order to maximize interoperability with other relevant cyber infrastructure components (e.g., name servers, biodiversity resources, etc...)

 

GoldenGATE Editor5

The GoldenGATE Document Editor is a visual editor for marking up documents in XML. It is designed to do most of the mark-up automatically; manual work is reduced to correcting the output of automated components.

 

The automated mark-up for taxonomic documents includes finding taxonomic names, figuring out their genus, species, etc., and obtaining an LSID for them. In addition, there are functions for marking up taxonomic treatments and their inner structure, i.e. which part of the treatment provides a morphological description of a taxon, which one lists materials examined, etc.

 

TaxonX Schema6

TaxonX is a lightweight and flexible schema which may be applied to the wide variety of formatting present in both legacy documents and new publications. It permits, and sometimes relies on, the use of external schema. It has a loose content requirement and allows for instances to be encoded over time and at many levels of granularity.

 

The schema can be readily converted to or expressed as an extension of the NLM/NCBI Journal Archiving DTD.

 

TaxonX is used for encoding taxonomic literature in order to:

• Create open, stable, persistent, full text digital surrogates of taxonomic treatments
• Identify taxonomic treatments and their major structural components to enable networked reference and citation
• Identify lower level textual data such scientific names, localities, morphological characters, and bibliographic citations to facilitate their extraction by, and integration with, external applications and resources
• Study and describe the structure of systematics publications by creating specific bodies of literature, such as an entire journal (eg AMNH Novitates), across taxa (e.g all ant systematics papers post 1995), or faunistic (e.g. all ant systematics papers covering Madagascar ranging from 1758 to 2006)

 

Search and Retrieval Server

This facility allows archive searching through the taxonomic name index, the collection location index and the document metadata index.

 

Function

• Taxonomy
  • literature
• Non-electronic data
  • literature
  • digitisation
• User interface
  • Personal and institutional use
  • Raw data and visual presentation

 

Why use this tool?

• Improved access to the content of  taxonomic literature enhanced by refining the granularity of:7
  • species names
  • specimens (geographic names and collecting events)
  • bibliographic references
  • images
  • gene sequences
• For access to stable and persistent locations of species descriptions through identifiers for publications and treatments8
• Text mining

 

Who will use this tool?

• Data creation
• Data providers
  • Institutions
• Data users
  • Expert
• ALA infrastructure

 

How will the tool be used?

Plazi provides access to the content of taxonomic literature in a variety of formats.

Whenever possible a PDF version of the original publication is made available in the DSpace based Digital Archive.

 

An increasing number of publications also have been encoded in the TaxonX-XML schema which identifies and delineates the significant “atoms” of information which comprise taxonomic descriptions in order to facilitate retrieval, analysis, and integration with other e-science resources.

 

During the mark up process, the documents are enhanced with links to name servers, digital bibliographies, or specimen databases.

The Search and Retrieval Server (SRS) provides a search interface to the marked up descriptions allowing for mining of rich source of taxonomic data. 9

 

• Online: Digital Archive and Search and Retrieval Server
• Desktop: GoldenGATE Editor
• TaxonX-XML schema: http://taxonx.org/schema/v1/taxonx1.xsd
• Editor requires Windows, Java Runtime Environment
• User input is required with GoldenGATE Editor

 

Where in the data chain could this tool be used?

• ALA central
• User’s machine

 

When could this tool be used?

• Before data is made available to ALA: GoldenGATE Editor
• While data is stored with ALA: TaxonX schema, Search and Retrieval Server (SRS)
• As a post process, after data is with the user: Search and Retrieval Server (SRS)

 

Availability

• PLAZI: http://plazi.org/
• Contact: Guido Sautter - sautter@ipd.uka.de

  Donat Agosti - agosti@plazi.org

• Download GoldenGATE Editor: http://idaho.ipd.uka.de/GoldenGATE/GoldenGATE.zip
• GoldenGATE User Manual: http://plazi.org/files/GoldenGATE_end_user_manual2.pdf
• GoldenGATE FAQ: http://plazi.org/?q=node/16
• TaxonX Schema: http://plazi.org/?q=node/10
• Licence: GoldenGATE Editor freeware10

 

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