scratchpads for community involvement for natural history collections
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Scratchpads for community involvement for natural history collections . Dr Dimitris Koureas Biodiversity Informatics Group | Department of Life Sciences Natural History Museum London. Fourth Annual Summit | Feb 21-23 | Tucson, AZ. What is we try to tackle?. - PowerPoint PPT PresentationTRANSCRIPT
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
