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Vince Smith
Collections for the 21st Century, Florida
5-6 May 2014
No specimen left behind:
Collections digitisation at the
NHM, London*
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Some history…
“the rate of progress by the UK taxonomic institutions in digitising and making collections information available is disappointingly low… there is a significant risk of damage to the international reputation of major institutions such as The Natural History Museum”
House of Lords Science and Technology Committee Report on Taxonomy and Systematics, 2009
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Digitisation rates at the NHM (circa 2009)
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The prevailing attitude collections digitisation
Biodiversity Informatics
2010, 7: 120 – 129
2010 GBIF Task Group:
Global Strategy and Action Plan for the Digitisation of Natural History Collections
“Digitizing all specimens is not an achievable aim at present”
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More technology, more automation, more speed
Whole drawer scanning
Herbarium sheet scanning
Microscope slide scanning
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European collections rising to the challenge
Large-scale data capture & digitisation in France, Netherlands & Finland
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NHM London Science Strategy 2013-17
A New Voyage of Discovery
Three Focal Areas
1. Scientific discovery
2. Scientific Infrastructure
3. Scientific engagement
Five Challenges
1. The Digital NHM
2. Origins, evolution & futures
3. Biodiversity discovery
4. Natural resources & hazards
5. Science, society & skills
Resources & funding
Measuring success
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data.nhm.ac.uk/globe/
Digitisation target
20M specimens available by 2017
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A long way to go, practically, technically & culturally… NHM collections comprise c.80m objects Physical register: c.5m Digital data: 2.8m Images: 350k
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NHM Digital Collections Programme
A 2, 5 and 10 year plan...
To collate, organise and make available one of the world’s most important natural history collections as digital resource, delivering:
an online specimen / lot-level database to manage all holdings
core meta-data and / or images for key parts of the collection
flexible informatics tools
?750,000 for first 2 years
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Outline
Why
Internal objectives & benefits
Research opportunity - the iCollections example
What
How much data to digitise
Linking digitisation effort to project benefits
How
Digi-street pilots, quick wins (herbarium, drawer & slide scanning)
Crowdsourcing pilots & options
Where
NHM Data Portal
External Portals (E.g. GBIF, Europeana)
Links
Crowdfunding
H2020 projects (COST, SYNTHESYS, LOD, VRE, Dig. Inf.)
Other museums, herbaria & partners (e.g. CETAF & publishers)
When
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1. Why: Objectives
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1. Why: Research opportunity & the iCollections pilot
Using the NHM collections to track long-term seasonal response of butterflies to climate change
Digitisation of British and Irish Lepidoptera collection
Species poor, specimen rich
~500,000 specimens, 5,000 drawers
Re-curation, imaging, label data, georeferenced
~25% complete (started Jan.’13)
About 50% specimens ‘useable’
Many specimens in most years (late - 19th century to 1970)
Provide longer time perspective than most observational records (BMS post-1976)
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1. Why: Research opportunity & the iCollections pilot
Relationship between 10th percentile collection date of Anthocharis cardamines (Orange tip) and mean Mar. – May temp.
(N.B. temp. axis reversed)
1900-2000, strong correlation between initial collection dates & temperature
Critical marker on phenological response prior to recent rapid climate change
Longer time perspective than most observational records (BMS post-1976)
Museum data available for rare or hard to record species
An example of unique biological and ecological data from collections
Brooks, Self, Toloni & Sparks, 2014, Int. J. Biometeorol.
DOI 10.1007/s00484-013-0780-6
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2. What: Linking data capture effort to research benefits
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3. How: Digi-street pilots (Herbarium Sheets)
PROCESS
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3. How: Digi-street pilots (Herbarium Sheets)
33k Specimens per day, 3 shifts (6am-10pm), Netherlands collection complete in 1.5 years
€1.29 Euros per specimen image (if outsourced), transcription at similar cost
Video of Herbarium Sheet Digitisation
(Not available on SlideShare Version of this presentation)
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3. How: Digi-street pilots (Drawer scanning & segmentation)
SatScan whole drawer scanning
30 Million specimens, 130k drawers
Fast, high res. multi-specimen drawer images (5 mins. each)
No specimen handling
Limited drawer / unit tray metadata, plus identifiers
Specimen segmentation problem
Digital and physical collection gets out of sync
Need to automate specimen segmentation
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3. How: Digi-street pilots (Drawer scanning & segmentation)
Starting image
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3. How: Digi-street pilots (Slide scanning)
1. Slides cleaned & barcoded
2. Loaded into hopper
(50-100)
3. High resolution scan
4. Images stored & databased
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3. How: Crowdsourcing pilot
1 user with 32,629 transcriptions!
92 users with 100+ transcriptions
363 users with 1 transcription
Ranked users
Log no. of records transcribed
NHM Bird registers
No advertising
Hard to transcribe
Challenging starting project
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3. How: Crowdsourcing options
Zooniverse Projects
Smithsonian Digital Volunteers
Wikisource transcription (WiR)
[email protected]
Next steps: Survey and review of natural history transcription projects cf. paying transcribers
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4. Where: NHM Data Portal
A focus for deposition and discovery of NHM research & collections data
Stable, citable identifiers on datasets & specimen / lot records
Transparent data quality (un-reviewed, reviewed, reviewed & updated)
Download (DwCA), web-services & Linked Open Data
Build using CKAN, with enhanced mapping functionality
Search
Datasets matching criteria
Individual dataset
Results
Browse & search
criteria
Mapping, table & statistical views
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4. Where: External Portals
Flickr
GBIF
Europeana
e.g. NHM Coleoptera
NHM almost getting data to GBIF!
Submitting to Europeana portal (via Open-Up)
Niche collections on Flickr
Robust API services
Gateway to image analysis projects (e.g. species recognition & trait extraction tools)
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5. Links
Crowdfunding
Personalizes donation
Scales well
Requires lots of data
Most crowdsourcing platforms unsuitable
Potential for a data visualization to support our needs
H2020 Projects
EU Research & Innovation funding Programme
€80 Billion from 2014-2020
Strong record (EDIT, ViBRANT, SYNTHESYS1/2/3)
5 proposals in development for 2014/15
Better alignment with Digital Collections Programme
Partners
Major museums & herbaria (Kew, Smithsonian, & Euro.6)
Umbrella organisations & projects (GBIF, CETAF, iDigBio)
Universities (e.g. on Image analysis)
Data publishers (engagement on data & systems)
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6. When
Herbarium scanning
Pilot – TBC (starting late-2014)
Drawer scanning
Segmentation Software (Aug. 2014)
Pilots (Ongoing)
Slide scanner
Testing 6 systems (Complete)
Procurement / purchase (July 2014)
Pilot projects & system integration (From Sept. 2014)
Crowdsourcing pilots
Draft review paper (Aug. 2014)
Additional Notes from Nature Project (early 2015)
NHM Data Portal
Internal release (June 2014)
Public release (Jan. 2015
Funding
H2020 projects (submitted, Sept. 14 & Jan. 15)
Key dates over next 2 years
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Acknowledgements
Digital Collections Programme
Planning: Ian Owens, Ben Atkinson, Dave Thomas, Andy Purvis, Emilie Smith & Vince Smith.
iCollections
Project team: Gordon Paterson, Geoff Martin, Martin Honey, Blanca Huertas, Darrell Siebert, Vladimir Blagoderov , Steve Cafferty, Adrian Hine, Chris Sleep, Mike Sadka, Elisa Cane, Lyndsey Douglas, Joanna Durant, Gerardo Mazzetta, Flavia Toloni, Peter Wing, Malcolm Penn & Liz Duffle.
Research: Steve Brooks, Angela Self, Flavia Toloni & Tim Sparks.
Drawer scanning
NHM Satscan development: Vladimir Blagoderov, Laurence Livermore & Vince Smith.
Software: Pieter Holtzhausen & Stefan van der Walt (Stellenbosch University).
Slide scanner
Testing: Vladimir Blagoderov & Alex Ball.
Crowdsourcing
Pilots (NHM Team): Tim Conyers, Lawrence Brooks & Adrian Hine.
Review paper: Laurence Livermore & Vince Smith.
NHM Data Portal
Project team: Vince Smith, Darrell Siebert, Dave Thomas & Adrian Hine.
Development: Ben Scott & Alice Heaton.
Apologies to anyone I have missed!
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