Data publication meeting at the Department of Ecology and Natural Resource Management, Norwegian University of Life Sciences (NMBU), GBIF Norway and the Norwegian Biodiversity Information Centre (Artsdatabanken).

1. NMBU,
Ås,
January
2015

2. Status
27.
January
2015
GBIF
enables
free
and
open
access
to
biodiversity
data
online.
We
are
an
interna>onal
government-­‐ini>ated
and
-­‐funded
ini>a>ve
focused
on
making
biodiversity
data
available
to
all
and
anyone,
for
scien>fic
research,
conserva>on
and
sustainable
development.
2

3. GBIF
provides
a
data
discovery
system
global
registry
data
portal
that
is
dependent
on
resolvable
stable
iden<fiers
for
efficient
func<onality
3

4. 1. Informa*on
infrastructure
–
an
Internet-­‐
based
index
of
a
globally
distributed
network
of
interoperable
databases
that
contain
primary
biodiversity
data.
2. Community-­‐developed
tools,
standards
and
protocols
–
the
tools
data
providers
need
to
format
and
share
their
data.
3. Capacity-­‐building
and
training
–
and
access
to
a
global
expert
community.

5. Map of GBIF Country Participants
31
DEC
2014
participation
NB!
The
low
membership
coverage
in
Asia
and
Africa
is
an
important
gap!
GBIF
Secretariat
in
Copenhagen
with
20
staff
members
[link]

6. Node
team
at
UiO
NHM:
Dag
Endresen,
Node
Manager
Chris>an
Svindseth,
Database
manager
Fridtjof
Mehlum,
Research
Director
Einar
Timdal,
Associate
Professor
Geir
Søli,
Associate
Professor
Artsdatabanken
Trondheim:
Wouter
Koch,
Advisor
Nils
Valland,
Senior
advisor
The
Research
Council
of
Norway:
Per
Backe-­‐Hansen,
Head
of
delega>on
6

7.
Artskart
provides
the
Norwegian
portal
for
species
occurrences.
a
subset
of
the
same
data
as
in
GBIF

8. Why GBIF?

9. OECD
Global
Science
Forum
(1999):
“establish
and
support
a
distributed
system
of
interlinked
and
interoperable
modules
(databases,
soCware
and
networking
tools,
search
engines,
analy<cal
algorithms,
etc.)
that
together
will
form
a
Global
Biodiversity
Informa<on
Facility
(GBIF)”.
[First
global
GBIF
mee<ng
in
2001;
Secretariat
in
Copenhagen
2003]

10.
The
Millennium
Ecosystem
Assessment
showed
that
human
ac>ons
ogen
lead
to
irreversible
losses
in
the
diversity
of
life,
and
these
losses
have
been
more
rapid
in
the
past
50
years
than
ever
before
in
human
history.
Biological
diversity
is
key
to
resilience
–
the
ability
of
natural
and
social
systems
to
adapt
to
change,
and
is
essen>al
for
nearly
every
aspect
of
human
well-­‐
being.
Because
human
threats
to
biodiversity
occur
across
large
spa>al
and
temporal
scales,
biodiversity
and
ecosystem
monitoring,
forecas>ng,
and
risk
assessments
require
data
to
be
organized
in
a
globally-­‐accessible,
integrated
infrastructure.
GBIF
provides
this
infrastructure.
(Wilson,
2002;
Worm
et
al.,
2006;
Duke
et
al.,
2007)

11. GBIF and GEO
Intergovernmental group on earth observations
Data Integration & Interoperability
GBIF provides the infrastructure delivering species occurrence data in GEO.
GEO
BON
Biodiversity
observa>on
network

12. GIASIP
Global
Invasive
Alien
Species
Informa>on
Partnership
GBIF provides the infrastructure delivering species occurrence data in GIASIP.

13. GBIF and IPBES
(Naturpanelet)
Intergovernmental Science-Policy Platform on
Biodiversity and Ecosystem Services (IPBES)
IPBES
provides
a
plalorm
to
support
policy
decisions
based
on
biodiversity
research
results.
GBIF
provides
the
infrastructure
delivering
species
occurrence
data
in
IPBES.
Science
Policy
Biodiversity
Data,
informa>on
and
knowledge
IPBES
GBIF

14. Data publication

15. Data distribution in GBIF
Density of georeferenced species occurrence records published through GBIF
(see http://www.gbif.org/occurrence)Last
updated:
2014-­‐07-­‐09

16. Data published through GBIF.org
hnp://www.gbif.org
|
16
JAN
2015
Trend in primary biodiversity records (millions)
datapublishing
100
150
200
250
300
350
400
450
500
550

18. Data published — by GBIF participant
NOTE:
Datasets
are
assigned
to
countries
according
to
the
loca<on
of
the
publishing
ins<tu<on,
including
aggregated
datasets
with
contributors
from
many
other
countries.
hnp://www.gbif.org
|
16
JAN
2015
datapublishing
1. United States 67,332,382 6. Sweden 5,165,053
2. Netherlands 15,659,739 7. Norway 4,845,994
3. Germany 6,988,553 8. Finland 2,506,681
4. United Kingdom 5,564,923 9. Belgium 2,492,458
5. Australia 5,351,016 10. Canada 1,512,676
1. United States 209,492,282 6. Germany 18,733,051
2. Sweden 49,346,620 7. Finland 18,511,977
3. United Kingdom 47,237,309 8. France 17,503,770
4. Australia 36,653,791 9. Norway 17,338,833
5. Netherlands 21,268,595 10. Spain 10,194,958
Number of new records published—Top 10 participant Countries
(1 Jan to 31 Dec 2014)
Total number of records published—Top 10 Participant Countries
(as of 31 Dec 2014)

19. GBIF
portal:
18,0
million
occurrences
are
located
in
Norway.
Published
from
31
countries
worldwide.

20. GBIF
portal:
17,2
million
occurrences
published
form
Norwegian
ins>tutes.
Covering
201
countries
worldwide.

21. Danmark
Finland
Norway
Sweden
Iceland
Jan
2015
Datasets
Occurrences
Denmark
53
9
384
792
Finland
57
18
514
033
Iceland
4
458
705
Norway
93
17
188
892
Sweden
35
50
083
140
Status
for
Nordic
GBIF
nodes
(data
hosted
by…)
hnp://www.gbif.org/country/NO

22. Download data

24. GBIF
Portal
–
download
data
• Before
downloading
species
occurrence
data
from
GBIF,
please
take
the
>me
to
register.
– hnp://www.gbif.org/user/register
• Downloads
from
the
GBIF
portal
are
packaged
as
a
Darwin
Core
Archive
(DwC-­‐A).
– hnp://www.gbif.org/faq/datause
• The
species
occurrence
data
are
found
in
the
“occurrence.txt”
data
file.
• This
tab-­‐delimited
text
file
can
e.g.
be
imported
to
a
spreadsheet
such
as
Excel
or
to
a
database.
• NOTE:
the
data
files
can
become
very
large!
So
look
at
the
file
size
before
you
open
them
in
MS
Excel.

26. Data download requests, by country
Requests
for
download
do
not
necessarily
result
in
data
actually
being
downloaded.
Based
on
country
indicated
by
user
login
|
16
JAN
2015
useofgbif.org
1. United States 22,539 6. China 2,886
2. Mexico 11,354 7. United Kingdom 2,873
3. Spain 6,229 8. Costa Rica 2,869
4. Denmark 5,432 9. Colombia 2,685
5. Brazil 4,132 10. Australia 2,635
Total of
84,951 requests
from users in
106 countries, islands
and territories
1 Jan 2014 – 31 Dec 2014

27. Data use in research

28. Use citations, by country of authors
15
JAN
2015
researchuse
1. United States 114 6. Italy 22
2. Spain 41 7. Mexico 20
3. United Kingdom 40 8. Brazil 19
4. Germany 36 9. France 18
5. Australia 32 10. South Africa 17
Total 2014
Number of research publications from January to December 2014 citing use of
GBIF-mediated data, ranked by country according to affiliation of author. Top 10
countries shown.
Relationship line represents collaboration between authors affiliated in different countries.
Dec 2014
1. United States 22 4. South Africa 5
2. United Kingdom 9 7. Switzerland 4
3. Spain 8 7. China 4
4. Germany 5 7. Mexico 4
4. Italy 5
Dec 2014
Number of research publications in December 2014 citing use of GBIF-mediated
data, ranked by country according to affiliation of author.
Top 9 countries shown.

29. GBIF citation in research 2008-2014
Last
updated:
2014-­‐09-­‐02
57
43
61
66
90
76
80
17
35
48
66
63
33
29
52
89
148
169
229
249
194
0
50
100
150
200
250
300
2008
2009
2010
2011
2012
2013
2014
(Jan-­‐Aug)
No.
of
peer-­‐reviewed
publica>ons
GBIF
men>oned
GBIF
discussed
GBIF-­‐mediated
data
used

30. Scien>sts
from
Norwegian
ins>tutes
are
using
GBIF-­‐mediated
data:

31. Darwin Core

32. Unifying
species
data
Integrated
access
for
records
of
the
occurrence
of
any
species:
• What?
• When?
• Where?
• What
evidence?
• Data
owner?
• Link
to
full
record
Presence
only
data
Collec*ons
Ecological
Monitoring
Genomics
Darwin
Core
2015:
Survey
data
compa>ble
with
exis>ng
Darwin
Core
data,
plus:
• Which
species
were
recorded
together?
• Which
sets
of
data
are
directly
comparable?
• Which
species
were
most
abundant
in
each
sample?
Presence/absence
Darwin
Core
+
Core
Survey
Fields
Sample
Id
Method
Id
Rela>ve
abundance
...
Slide
by
Donald
Hobern,
2012

33. Darwin Core – a vocabulary of terms
Wieczorek
J,
Bloom
D,
Guralnick
R,
Blum
S,
Döring
M,
De
Giovanni
R,
Robertson
T,
and
Vieglais
D
(2012)
Darwin
Core:
An
Evolving
Community-­‐Developed
Biodiversity
Data
Standard.
PLoS
ONE
7(1):
e29715.
(doi:10.1371/journal.pone.0029715)

34. hnp://rs.tdwg.org/dwc/terms/

35. Darwin Core Archive (DwC-A)
v DwC-A publish DwC records including terms
from DwC-A extensions.
v Simple text based format.
v Zipped single file archive.
Germplasm.txt

36. Survey & plot data
GBIF priority in 2015

37. Wiser
SK,
Spencer
N,
De
Caceres
M,
Kleikamp
M,
Boyle
B
&
Peet
RK
(2011).
Veg-­‐X
–
an
exchange
standard
for
plot-­‐based
vegeta>on
data.
Journal
of
Vegeta>on
Science
22
(2011)
598–609.
DOI:10.1111/j.
1654-­‐1103.2010.01245.x
“A
primary
technical
impediment
to
large-­‐scale
sharing
of
vegeta<on
data
is
the
lack
of
a
recognized
interna<onal
exchange
standard
for
linking
the
panoply
of
tools
and
database
implementa<ons
that
exist”
(…)
The
specimen-­‐based
standards
cited
above
[Darwin
Core
and
ABCD],
however,
are
not
adequate
for
community
sampling
because
the
informa<on
required
goes
beyond
specimen
and
occurrence
data”
(Wiser
et
al.
2011).
hnp://terms.tdwg.org/wiki/Vegeta>on_Survey
Survey
&
plot
data
(priority
in
2015)

38. Vegeta>on
plot
data
Image
credit:
Onar
Michelsen,
Norwegian
University
of
Science
and
Technology

40. Identifiers

41. Record-­‐level
Terms
dcterms:type
|
dcterms:modified
|
dcterms:language
|
dcterms:rights
|
dcterms:rightsHolder
|
dcterms:accessRights
|
dcterms:bibliographicCita>on
|
dcterms:references
|
ins*tu*onID
|
collec*onID
|
datasetID
|
ins*tu*onCode
|
collec*onCode
|
datasetName
|
ownerIns>tu>onCode
|
basisOfRecord
|
informa>onWithheld
|
dataGeneraliza>ons
|
dynamicProper>es
Occurrence
occurrenceID
|
catalogNumber
|
occurrenceRemarks
|
recordNumber
|
recordedBy
|
individualID
|
individualCount
|
sex
|
lifeStage
|
reproduc>veCondi>on
|
behavior
|
establishmentMeans
|
occurrenceStatus
|
prepara>ons
|
disposi>on
|
otherCatalogNumbers
|
previousIden>fica>ons
|
associatedMedia
|
associatedReferences
|
associatedOccurrences
|
associatedSequences
|
associatedTaxa
MaterialSample
materialSampleID
Event
eventID
|
samplingProtocol
|
samplingEffort
|
eventDate
|
eventTime
|
startDayOfYear
|
endDayOfYear
|
year
|
month
|
day
|
verba>mEventDate
|
habitat
|
fieldNumber
|
fieldNotes
|
eventRemarks
dcterms:Loca*on
loca*onID
|
higherGeographyID
|
higherGeography
|
con>nent
|
waterBody
|
islandGroup
|
island
|
country
|
countryCode
|
stateProvince
|
county
|
municipality
|
locality
|
verba>mLocality
|
verba>mEleva>on
|
minimumEleva>onInMeters
|
maximumEleva>onInMeters
|
verba>mDepth
|
minimumDepthInMeters
|
maximumDepthInMeters
|
minimumDistanceAboveSurfaceInMeters
|
maximumDistanceAboveSurfaceInMeters
|
loca>onAccordingTo
|
loca>onRemarks
|
verba>mCoordinates
|
verba>mLa>tude
|
verba>mLongitude
|
verba>mCoordinateSystem
|
verba>mSRS
|
decimalLa>tude
|
decimalLongitude
|
geode>cDatum
|
coordinateUncertaintyInMeters
|
coordinatePrecision
|
pointRadiusSpa>alFit
|
footprintWKT
|
footprintSRS
|
footprintSpa>alFit
|
georeferencedBy
|
georeferencedDate
|
georeferenceProtocol
|
georeferenceSources
|
georeferenceVerifica>onStatus
|
georeferenceRemarks
GeologicalContext
geologicalContextID
|
earliestEonOrLowestEonothem
|
latestEonOrHighestEonothem
|
earliestEraOrLowestErathem
|
latestEraOrHighestErathem
|
earliestPeriodOrLowestSystem
|
latestPeriodOrHighestSystem
|
earliestEpochOrLowestSeries
|
latestEpochOrHighestSeries
|
earliestAgeOrLowestStage
|
latestAgeOrHighestStage
|
lowestBiostra>graphicZone
|
highestBiostra>graphicZone
|
lithostra>graphicTerms
|
group
|
forma>on
|
member
|
bed
Iden*fica*on
iden*fica*onID
|
iden>fiedBy
|
dateIden>fied
|
iden>fica>onReferences
|
iden>fica>onVerifica>onStatus
|
iden>fica>onRemarks
|
iden>fica>onQualifier
|
typeStatus
Taxon
taxonID
|
scien*ficNameID
|
acceptedNameUsageID
|
parentNameUsageID
|
originalNameUsageID
|
nameAccordingToID
|
namePublishedInID
|
taxonConceptID
|
scien>ficName
|
acceptedNameUsage
|
parentNameUsage
|
originalNameUsage
|
nameAccordingTo
|
namePublishedIn
|
namePublishedInYear
|
higherClassifica>on
|
kingdom
|
phylum
|
class
|
order
|
family
|
genus
|
subgenus
|
specificEpithet
|
infraspecificEpithet
|
taxonRank
|
verba>mTaxonRank
|
scien>ficNameAuthorship
|
vernacularName
|
nomenclaturalCode
|
taxonomicStatus
|
nomenclaturalStatus
|
taxonRemarks
ResourceRela*onship
(Auxiliary
Terms)
resourceRela*onshipID
|
resourceID
|
relatedResourceID
|
rela>onshipOfResource
|
rela>onshipAccordingTo
|
rela>onshipEstablishedDate
|
rela>onshipRemarks
MeasurementOrFact
(Auxiliary
Terms)
measurementID
|
measurementType
|
measurementValue
|
measurementAccuracy
|
measurementUnit
|
measurementDeterminedDate
|
measurementDeterminedBy
|
measurementMethod
|
measurementRemarks

42. The
purpose
of
iden*fiers
…is
to
name
things,
making
it
possible
to
refer
to
them.

43. hnp
–
PURL
–
UUID
hnp://purl.org/nhmuio/id/41d9cbb4-­‐4590-­‐4265-­‐8079-­‐ca44d46d27c3

44. Including
machine
readable
formats

45. Citizen science
Transcription

46. hnp://gbif.no/dugnad/

47. Custom data portals

51. Data paper

52. • Peer
review
op>on
for
biodiversity
datasets.
• Authors
get
scien>fic
credit
for
data
publica>on.
• Mee>ng
concerns
over
data
quality.
• Mee>ng
concerns
over
data
cita*on
mechanism.
hnp://www.gbif.org/publishingdata/datapapers

53. Metadata
requirements
• Dataset
descrip>on
• Project
descrip>on
• People
and
Organiza>ons
(including
roles)
• Coverage
– Taxonomic
coverage
– Geographic
coverage
– Temporal
coverage
• Methods
• Intellectual
property
rights,
licensing
• Keywords

54. Data
paper
workshop
• The
first
Norwegian
data
paper
wri>ng
workshop,
in
Oslo
2nd
to
3rd
December
2014
with
11
par>cipants
hnp://goo.gl/GtW1Vx
• A
second
data
paper
workshop
will
be
organized
in
Trondheim,
24th
to
25th
March
2015
with
20-­‐25
par>cipants
hnp://goo.gl/Ef1ZAy
Dimitri
Brosens,
GBIF
Belgium

55. Publish your own data!

56. Many
species
occurrence
data
are
“hidden”
in
reports
and
documents
produced
by
universi*es,
research
ins*tutes,
public
agencies
and
the
university
museums.
Publish
your
biodiversity
data!
Photo
by:
Niklas
Bildhauer

57. Publish
and
archive
your
own
species
occurrence
data
• You
can
always
publish
your
species
occurrence
data
by
sending
an
email
to
gbif-­‐drig@nhm.uio.no
• The
GBIF
Norway
helpdesk
will
assist
with
data
publishing
(to
GBIF
and
Artskart)!
• You
can
install
a
data
publishing
sogware
such
as
the
GBIF
Integrated
Publishing
Toolkit
(IPT).
• Ci*zen
Science
portals
such
as
Artsobservasjoner,
iNaturalist,
Anymals
+
Plants,
…
• You
can
also
use
a
data
archiving
pla_orm
such
as
B2SHARE
(EUDAT)
or
NorStore
(Norwegian
research
data,
EUDAT).

59. hnp://artsobservasjoner.no/
CC-­‐BY
Dag
Endresen

60. Published
to
GBIF

63. Archive your own
data!

64. Work
in
progress…!

65. Grants for biodiversity
data preparation

66. Small
grant
to
support
data
prepara=on
• GBIF
Norway
has
some
funds
for
suppor>ng
new
data
providers
with
prepara>on
of
exis>ng
biodiversity
datasets.
• To
assist
data
owners
to
start
publishing
data.
• The
applica>on
form
and
condi>ons
can
be
requested
by
email
from
gbif-­‐drig@nhm.uio.no

67. Thanks
for
listening!
Dag
Endresen
dag.endresen@nhm.uio.no
Chris>an
Svindseth
chris>an.svindseth@nhm.uio.no
gbif-­‐drig@nhm.uio.no