Scratchpads for community involvement for natural history collections

Fourth Annual Summit | Feb 21-23 2014 | Tucson, AZ

Scratchpads for community involvement for natural history collections

Dr Dimitris KoureasBiodiversity Informatics Group | Department of Life Sciences

Natural History Museum London

Fourth Annual Summit | Feb 21-23 | Tucson, AZ

Fourth Annual Summit | Feb 21-23 2014 | Tucson, AZ

Inaccessible | native format/private silos

Disconnected | not aggregated or discoverable

Redundant | overlapping efforts no coordination

Cluttered | small and dispersed datasets

20% 80%

The long tail of Biodiversity data

What is we try to tackle?

Typically produced by small communities

Fourth Annual Summit | Feb 21-23 2014 | Tucson, AZ

Virtual Research Environmentsefficient in incentivising and enabling researchers to mobilise their data

Online collaborative environments

“Our goal is to make every researcher digital”

Can VREs help?

Underlying technologies that help semantically enrich and aggregate data on a higher level

Provide efficient tools, simple interfaces and comprehensive documentation

Incentivise researchers to enter, share and finally mobilise their datasets

Fourth Annual Summit | Feb 21-23 2014 | Tucson, AZ

Enter – Structure – Curate – Link – PublishBiodiversity data online

7 years of continuing development | 3 major Grants | Industry leading platform

Fourth Annual Summit | Feb 21-23 2014 | Tucson, AZ

22%

78%

Content

Specimen records/Taxon descriptions

Other

65,000 unique visitors/month

Per month unique visitors to Scratchpads sites

660 Scratchpads Communities

by 7,100 active registered users

covering 90,000 taxa

in 615,000 pages.

In total more than

1,600,000 visitors

Fourth Annual Summit | Feb 21-23 2014 | Tucson, AZ

Taxa(Classifications, taxon profiles, specimens, literature, images, maps, phenotypic, genotypic

& morphometric datasets, keys, phylogenies)

ProjectsConservation Regions Societies

Fourth Annual Summit | Feb 21-23 2014 | Tucson, AZ

A Scratchpad is a gateway to big data

In-house data

External data & services

Biodiversity standards (TDWG, DwC, Audubon)

Fourth Annual Summit | Feb 21-23 2014 | Tucson, AZ

Mark-up / Data annotation

Atomisation

CollaborateCurate

Link

Source data

Aggregate

Publish

UnstructuredOverlappingDisconnectedNative formats & vocabularies

Controlled vocabularies are key for efficient data capture

Fourth Annual Summit | Feb 21-23 2014 | Tucson, AZ

In order to capture and annotate data we need

Fine grained pre-defined fields

and

Comprehensivecontrolled vocabularies

1.

2.

Fourth Annual Summit | Feb 21-23 2014 | Tucson, AZ

Capturing specimen record dataTaxonomic identificationDateCollectorLocation- Continent- Country- State/Province- GPS- Locality - Area/place - Habitat - Substrate (Environmental material) - biome

Usually transcribed from labelSome inferred by curatorsProvided in highly inconsistent way

EOL

IUCN

ISOweb service

DwC

What we currently use

Generating character/trait projectsMorphological/anatomical characters

Ecological traits

1. 2.

Fourth Annual Summit | Feb 21-23 2014 | Tucson, AZ

Users of Virtual Research Environments

consumers as well as contributors to ontologies

Biodiversitycommunities

Communitiesworking onontologies

Bottom-up approach

Top-down approach

Fourth Annual Summit | Feb 21-23 2014 | Tucson, AZ

Com

mun

ity in

volv

emen

t

Ontology granularity

Top-downapproach

Bottom-upapproach

High level approach

Deep hierarchy

End-user community involvement

Fourth Annual Summit | Feb 21-23 2014 | Tucson, AZ

Simple and intuitive end-user products

Controlled vocabularies over highly structured ontologies for data capture

Mechanisms for updating vocabularies based on user custom entries

1.

2.3.

Fourth Annual Summit | Feb 21-23 2014 | Tucson, AZ

Ontologies as Infrastructure

Communal / agreedPersistentEssential

Robust & reliable

Ontologies as Research

Concerns specific communities

Experimentation

Frequent changes

Before we can widely implement the use of ontologies we need to shift from one to another

Good forKnowledge representation

and reasoning

Good forData capturing

Fourth Annual Summit | Feb 21-23 2014 | Tucson, AZ

users

Products

Services

Infrastructure

Researchers & Research communities

VREs, online toolsWebservices, interoperable systems

Ontologies, Computing

Verti

cal a

ppro

ach

Horizontal approach

The e-infrastructures pyramid

Fourth Annual Summit | Feb 21-23 2014 | Tucson, AZ

Thank you

Comments/questions?

@DimitrisKoureasd.koureas@nhm.ac.uk