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Slides prepared for the 6th European GBIF nodes meeting in Brussels. At the meeting these slides was replaced by a live online demo of these tools. Topics include citizen science transcription of specimen labels, persistent identifiers and custom collection portals. All slides are CC-by.
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European GBIF Nodes mee2ng in Brussels 8 to 10 April 2014
Slides prepared for the
Transcrip2on of label informa2on
Taking Notes from Nature
9 %
29%
45%
8%
9%
Museum specimens
Vertebrater
Planter
insekter
Invertebrater
Sopp
11 %
47%
26%
6% 10%
Digi-zed specimens
Vertebrater
Planter
insekter
Invertebrater
Sopp
2%
15%
44%
20%
19%
Number of species in Norway (≈42k)
Vertebrater
Planter
insekter
Invertebrater
Sopp
4%
69%
13%
0% 14%
GBIF (from the museum collec-ons)
Vertebrater
Planter
insekter
Invertebrater
Sopp
Slide by Eirik Rindal (NHM-‐UiO)
≈ 8,5 mill specimens in Norwegian collec2ons of natural history
Fungi: 640 000
Vascular plants: 2,2 mill
Vertebrates: 670 000
Invertebrates: 600 000
Insects: 3,4 mill
Photos: Karsten Sund; slide by Eirik Rindal (NHM-‐UiO)
Paleontology: 900 000
Digi2zed specimens Fungi: 640 000
Vascular plants: 2,2 mill
Vertebrates: 670 000
Invertebrates: 600 000
Insects: 3,4 mill
Photos: Karsten Sund; slide by Eirik Rindal (NHM-‐UiO)
Paleontology: 900 000 ?
Mass-‐digi2za2on at NHM-‐UiO
• 3-‐year project – Start in 2012 (dura2on 2013 to 2015) – 3 mill NOK each year (≈365 000 € / year)
• NHM-‐UiO vascular plants (240k – 280k) – Photo-‐imaging (high resolu2on) – QR-‐barcoded with hdp-‐PURL-‐UUID keys – Registra2on of taxon name and country – Imported to MUSIT DB and published to GBIF
Vascular plant
herbarium (175 k
specimens)
Transcrip2on at:
Imaging at:
8 8
Foto: Digitarium
Foto: NHM-‐UiO
Packing of the herbarium in Oslo, Norway
Un-‐packing of the herbarium in Joensuu, Finland
9
Status in March 2014: • Cost for each specimen:
– Tradi2onal ca 40-‐80 NOK – Mass-‐dig. 17,5 NOK
• NHM-‐UiO vascular plants (240k – 280k)
• The first 175k specimens are now ready
• Images: ca 15 terra byte • 50k specimens are transcribed (30%) – Taxon and country
Catalog number: O-‐L-‐000014, hdp://purl.org/nhmuio/id/41d9cbb4-‐4590-‐4265-‐8079-‐ca44d46d27c3
11
hdp://purl.org/nhmuio/id/d91e8253-‐0ac1-‐4681-‐ac69-‐e50070af86a2
12
Notes from Nature
• Find the label and drag a box around it.
• Fill in label informa2on using the provided drop-‐down menu or free text input.
• Each label is transcribed by three different ci2zen scien2sts to evaluate accuracy.
• NHM UiO has launched a prototype Norwegian transcrip2on portal, based on the NfN.
hdp://nh
m2.uio.no
/dugnad/transcrib
e
hdp://nh
m2.uio.no
/dugnad/transcrib
e
hdp://nh
m2.uio.no
/dugnad/transcrib
e
The purpose of iden2fiers …is to name things,
making it possible to refer to them.
What is an iden2fier: “Each iden2fier refers to one and only one thing” (Coyle 2006). “An associa&on between a string and a thing” (Kunze 2003). “A stated associa&on between a symbol and a thing; that the symbol may be used to unambiguously refer to the thing within a given context” (Campbell 2007).
19
UUID QR codes for museum objects at NHM-‐UiO provides: • Machine-‐readable iden-fiers. • Allows for new and efficient
workflows for collec2on management.
• Deployment for stable iden-fiers appropriate for data-‐basing.
20
hdp – PURL – UUID
hdp://purl.org/nhmuio/id/41d9cbb4-‐4590-‐4265-‐8079-‐ca44d46d27c3
hdp://purl.org/nhmuio/id/UUID à hdp://gbif.no/resolver/UUID
Custom collec2on portals
Slide by David Remsen (2011)
Artskart
UiT
UiB
S&L
Darwin Core Archive
Collec2ons and data sets published from the data owner as one single Darwin Core archive (DwC-‐A). Different data types from the same DwC-‐A can be included to different data portals.
GBIF Portal
Opportunities with Darwin Core:
Data portal for institute, region, or theme?
25
GBIF portal:
13,3 million occurrences are located in Norway. Published from 30 countries worldwide.
GBIF portal:
12,5 million occurrences published form Norwegian ins2tutes. Covering 180 countries worldwide.
Danmark Finland
Norway Sweden
Iceland
Oct 2013 Data set Occurences Denmark 45 9 311 741 Finland 57 14 666 474 Iceland 4 458 705 Norway 85 12 531 207 Sweden 47 43 374 550
Status Nordic GBIF data sets (data hosted by…)
33
Node Personnel Dag Endresen, Node Manager Chris2an Svindseth, Database manager Fridtjof Mehlum, Research Director Einar Timdal, Associate Professor Vegar Bakkestuen, Senior Scien2st Geir Søli, Associate Professor Wouter Koch, Artsdatabanken Nils Valland, Artsdatabanken
34