Biodiversity Data Publishing:...

Biodiversity Data Publishing: Overview Fhatani Ranwashe

Biodiversity Data Publishing: Overview

INDEX

• Background

• Data publishing landscape

• Biodiversity data publishing

o Data types

o Data standards

o Data quality

o Data publishing methods

• Data publishing in South Africa

Background

“Free and open access to primary biodiversity data is

essential for informed decision-making to achieve

conservation of biodiversity and sustainable development.

However, primary biodiversity data are neither easily

accessible nor discoverable. “ (Chavan and Penev, 2011)

Biodiversity data publishing refers to making biodiversity

data available to the public in a standard form via the

internet.


Data publishing landscape

Publishing and discovery of biodiversity data: the constraints and challenges

• the lack of sustainable practices for data publishing;

• the lack of easy-to-use tools and related guidelines for authoring metadata

documents;

• the difficulty of dealing with heterogeneity and diversity of standards;

• the cost of creation and maintenance of infrastructure by small- and medium-scale

data publishers; and

• the lack of professional reward structures or incentives.

Chavan and Penev, BMC Bioinformatics 2011, 12(Suppl 15):S2



“Currently the GBIF facilitates discovery of over 10,000 data resources,

providing access to over 267 million primary biodiversity data records.” (Chavan

and Penev, 2011)

Partnerships with other international organisations such as the Catalogue of

Life, Biodiversity Information Standards (TDWG), the Consortium for the

Barcode of Life (CBOL), the Encyclopaedia of Life (EoL), and Integrated

Taxonomic Information System (ITIS).


2008 2009 2010 2011 2012

The data publishing area is in continuous evolution and expansion.

2014

Idea for simple,

compressed text-based file for publishing introduced at

TDWG

DiGIR/TAPIR in high use to

publish biodiversity

data

GBIF introduces

IPT 1.0

Darwin Core

standards established by TDWG

GBIF redevelops

IPT

GBIF introduces

IPT 2.0

Data Publishing taught at Nodes

training.

Nodes and aggregators

begin to install and use IPTs

Occurrence and checklist type datasets show

continued growth

GBIF introduces

IPT 3.0 with Digital

Object Identifier

(DOI)

Data Types

• Occurrences (observations, specimens etc)

o 'collection event'

o an observation in the field, vouchered (labeled) specimen in a museum or

herbarium, or other evidence.

Data Types

• Checklists (names)

o lists of scientific names of organisms grouped into taxonomic hierarchies,

o provide taxonomic 'backbones' around which species information can be

organized.

Data Types

• Metadata (data about data)

o structured descriptions of datasets

o help to give context to datasets and enable users to assess whether data are

fit for use in a particular research project or application

Data Types

http://www.gbif.org/publishing-data/summary#datatypes

• Sampling-event (quantitative information )

o records from thousands of different kinds of environmental, ecological, and

natural resource monitoring and assessment investigations


Data Standards

ABCD Access to Biological Collection Data (2005)

DwC Darwin Core (2009)

AC Audubon Core Multimedia Resources Metadata Schema (2013)

NCD Natural Collection Descriptions (Draft)

http://www.tdwg.org


Darwin Core

Mapping cores

• Taxon Core – Species information

The category of information pertaining to taxonomic names, taxon

name usages, or taxon concepts. 43 terms.

• Occurrence Core – Collection event information

The category of information pertaining to evidence of an

occurrence in nature, in a collection, or in a dataset (specimen,

observation, etc.). 169 terms.

• Event – Sampling information

The category of information pertaining to a sampling event. Issued

29 May 2015. 95 terms


Extensions

• Darwin Core does not provide terms for every possible type of data.

– 22 registered

– 25 under development

• Examples

– Audubon Media Description (aka Audubon Core)

– Darwin Core Identification History

– Darwin Core Measurement or Facts


Darwin Core Archive

• A Darwin Core Archive (DwCA) is the text

representation of data formatted to Darwin

Core.

• A DwCA is a compressed file containing a

minimum of three files.


Star schema

Literature

Taxon

Core

Descriptio

n

Occurrences

meta.xml

EML.xml

+

DwC Archive

Checklist

Vernacula

r

Distributio

n

Type

s


Simple Darwin Core

• SIMPLEDWC - flat file

structure showing how to

use taxa & occurrence

Darwin Core terms.

• Use if someone suggests

to "Format your data

according to the Darwin

Core"


Data quality

“Data quality and error in data are often neglected issues with environmental

databases, modelling systems, GIS, decision support systems, etc. Too often, data are

used uncritically without consideration of the error contained within, and this can lead

to erroneous results, misleading information, unwise environmental decisions

and increased costs.” (Chapman, 2005)

• Data capture and recording at the time of gathering,

• Data manipulation prior to digitisation (label preparation, copying of data to a

ledger, etc.),

• Identification of the collection (specimen, observation) and its recording,

• Digitisation of the data,

• Documentation of the data (capturing and recording the metadata),

• Data storage and archiving,

• Data presentation and dissemination (paper and electronic publications, web-

enabled databases, etc.),

• Using the data (analysis and manipulation).


Data publishing methods

Data publishing in South Africa

South Africa is a country node for GBIF

• SANBI IPT:

o http://197.189.235.147:8080/iptsanbi/

o 2737451 records published

• ADU IPT

o http://aduipt.uct.ac.za:8080/ipt-2.3.2/


• SAIAB IPT

o http://ipt.saiab.ac.za


• ICLEI IPT

o http://197.189.235.147:8080/ipticlei/

• KwaZulu-Natal Museum IPT

• Endangered Wildlife Trust IPT

2.1m

SANBI and Data Partners by numbers

649k

105k

78k

8.5m

5k

51k (Nematodes)

SANBI-IPT (Trusted Data Hosting Centre)

18k (Algae)

17k

91k

Thank You!

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