GBIF-GNA feeds

Text available for public review: The digitisation of biological nomenclatural and taxonomic information by Richard Pankhurst

Fri, 11 Nov 2011 11:10:04 +0000

Dear members of the GNA group,

I am happy to announce that there's a new text available for public review: 'The digitisation of biological nomenclatural and taxonomic information' by Richard Pankhurst.

The document guides the reader through the process of digitazing information about taxonomic names and relationships. It explains the nature of the taxonomic data with many examples and gives advice on how to proceed in the digitization process in each case, independently of the software used. After the digitization process, the data can be published on the internet through networks such as GBIF.

The public review period ends the 9th December 2011. The author will consider all comments received and a final version will be released soon afterwards.

Please send your comments through the community site or to training@gbif.org.

Thanks for your participation!

http://community.gbif.org/pg/file/read/18107/

PUBLIC REVIEW: The digitisation of biological nomenclatural and taxonomic information by Richard Pankhurst

Fri, 11 Nov 2011 10:13:58 +0000

This document guides the reader through the process of digitazing information about taxonomic names and relationships. It explains the nature of the taxonomic data with many examples and gives advice on how to proceed in the digitization process in each case, independently of the software used. After the digitization process, the data can be published on the internet through networks such as GBIF.

THIS DOCUMENT IS AVAILABLE FOR PUBLIC TILL THE 9TH DECEMBER 2011. Please add your comments to this Community Site item, or send them to training@gbif.org.

Abstract: "This text explains and advises how best to set up and populate a database for the taxonomy and biodiversity documentation of a group of organisms. Examples will be taken from experience gained while creating the Rosaceae (Rose family) global taxonomic database, and will therefore relate to flowering plants (Angiospermae), and in particular to the International Code of Botanical Nomenclature (ICBN, McNeill 2006) which states the rules for wild plant nomenclature. There is a separate and different code for the naming of cultivated plants, and again separate from the codes for zoology and for bacteria. For organisms covered by these other codes the approach will necessarily be somewhat different."

GBIF Call for Proposals: National Checklist Building Best Practices

Wed, 07 Sep 2011 12:26:17 +0000

The GBIF Secretariat invites proposals to develop a document entitled Best Practice Guidelines in the Development and Maintenance of National Species Checklists. We seek to identify individuals or groups who have been directly involved in the compilation, maintenance and dissemination of a national species checklist to develop these guidelines in order to compile a set of practices that may serve as a guide for future efforts to build and maintain national species lists.

See http://www.gbif.org/communications/news-and-events/showsingle/article/call-for-proposals-to-draft-best-practices-in-the-development-and-maintenance-of-national-species-c/ for more information.

Google Docs Taxonomic Name Service

Fri, 03 Jun 2011 09:35:59 +0000

Mike Giddens of SilverBiology, has experimented with Google Docs scripting services to create a very nice name-mapping tool using Google Spreadsheets.

A user can paste a list of names into a spreadsheet, and then have each name looked up in GBIFs name services, and the classification, taxonomic status, and links to more information can be embedded into the spreadsheet.

To try out this service:

1. Log in to your google account (you must be logged in)

2. Go to https://spreadsheets0.google.com/spreadsheet/pub?hl=en_US&hl=en_US&key=0AhdYOHWBUlw_dF83RVRtQjdiQ2dwZXJCRERlUWR0SkE&output=html

3. Paste your own list of names into column A or if there are existing names, you can use them.

4. If there is already classification information in columns B-H you can select and delete these to clear them

5. Select a series of names in column B.

6. Go to the "GBIF" option in the menu. Select one of the two options.

You can add a link to this script in your own docs by calling

http://labs.silverbiology.com/gbifclblookup/code.js

Google Docs Taxonomic Name Service

Fri, 03 Jun 2011 09:35:54 +0000

Mike Giddens of SilverBiology, has experimented with Google Docs scripting services to create a very nice name-mapping tool using Google Spreadsheets.

To try out this service:

1. Log in to your google account (you must be logged in)

2. Go to https://spreadsheets0.google.com/spreadsheet/pub?hl=en_US&hl=en_US&key=0AhdYOHWBUlw_dF83RVRtQjdiQ2dwZXJCRERlUWR0SkE&output=html

3. Paste your own list of names into column A or if there are existing names, you can use them.

4. If there is already classification information in columns B-H you can select and delete these to clear them

5. Select a series of names in column B.

6. Go to the "GBIF" option in the menu. Select one of the two options.

Publishing Species Checklists, A Step by Step Guide

Fri, 15 Apr 2011 07:04:49 +0000

A new GBIF user guide has been released today. "Publishing Species Checklists, A Step by Step Guide" provides a high-level guide to a suite of tools, reference guide, and best practices for publishing annotated species checklists through the GBIF network. http://links.gbif.org/checklist_how_to

Screencast available for using the Darwin Core Archive Assistant

Wed, 13 Apr 2011 07:28:43 +0000

Publishing biodiversity data using Darwin Core Archives (DwC-A) is simple enough that it can be done with no dedicated software installed on your servers. There is one XML file, called the metafile, that is required in a DwC-A. The Darwin Core Archive Assistant is a service that builds this file for you. See a 10 minute screencast that demonstrates this service at http://www.youtube.com/watch?v=_hF0sslw-B4

GBIF becomes member of Species 2000

Tue, 05 Apr 2011 05:56:29 +0000

On 14 March, GBIF, joined the Species 2000 consortium as a new member.

GBIF TaxonFinder service and the new TIKA document service

Mon, 20 Dec 2010 11:43:15 +0000

The GBIF TaxonFinder service, a web service for extracting scientific names from documents, now has the means to extract names from PDF files, word documents, even powerpoint, using the new GBIF TIKA service. An illustration of the 3 steps to using this service to extract names from documents is as follows:

Identify a source document URL. For example, this URL provides a PDF publication listing the biodiversity of earthworms in Taiwan http://tai2.ntu.edu.tw/taiwania/pdf/tai.2006.51.3.226.pdf.
Append the document URL to the url parameter of the GBIF TIKA service. http://ecat-dev.gbif.org/ws-tika/?url=http://tai2.ntu.edu.tw/taiwania/pdf/tai.2006.51.3.226.pdf The output of this service is an XML document containing the full text of the PDF.
Use the URL from 2 as an input parameter to the GBIF TaxonFinder Service or any other name-finding service that supports the GNA Name-Finder API. For the GBIF TaxonFinder Service use the base service call:
1. http://tools.gbif.org/ws/taxonfinder?
2. input a type=url and a input of the URL as in 2

See the XML output here.

Taxonomic Name Processing

Fri, 17 Dec 2010 13:09:15 +0000

Processing scientific names is often a necessary component of working with biodiversity information. A number of focal areas have emerged and been the subject of work within GNA Nomina meetings. These areas of focus include:

Name recognition tools that can recognize known scientific names in free-text
Name discovery algorithms extend recognition to include novel taxon names.
Name reconciliation or de-aliasing methods that group spelling-variations of names and reconcile them to correctly-spelled names.
Atomizers and canonizers that can break a name into identified component parts (Genus, Species, Authorship, etc.) and into a normalized form.
Services and applications that use the tools described in this list.

This site provides forums for discussion, documentation, files and links to source repositories containing dictionaries, source code and development support.