Informatics and data products
Developments and plans
Tim Robertson, Andrea Hahn GBIF Secretariat

GB27
Photo of Aplysina fistularis by Mike G. Rutherford, via iNaturalist (CC BY-NC 4.0)

GROWTH AND DATA PUBLISHINGGROWTH IN USE

status: Aug 2020

Users of GBIF.org per week

~ 170k per month now (+20k over 2019)

Publications citing use of GBIF-mediated data

IPT (INTEGRATED PUBLISHING TOOLKIT)

not showing: 2385 datasets from UMS PatriNat (2020)

Datasets published through IPT installations,
cumulative
https://tinyurl.com/tdwg-2020-IPT-BPS-reportstatus: Sept 2020

newly mobilized IPT datasets per year
circles: number of countries involved

NAMES INFRASTRUCTURE
In partnership with the Catalogue of Life

MODERNIZING THE CATALOGUE OF LIFE
Complete and completing (Nov 2020)• New infrastructure deployed to manage data publication and assembly of the taxonomy
•
•
•
•
•

A new data exchange standard (COL Data Package)An evolution of GBIF ChecklistBank -> COL ChecklistBank
A workbench for editors to review and assemble
A new suite of APIs and R-based library (rOpenSci)
Developed in collaboration, hosted by GBIF

• Deployment of public interfaces• New COL website (November)• Migration of historical annual checklists (2006-2019)

Upcoming• Expand the taxonomy with content necessary for GBIF
• Automate reports on gaps

• Semi-automate assembly (with review)• Integrate with GBIF.org• New backbone end 2020

New website: https://www.catalogue.life/ (temporary URL)
COL ChecklistBank: https://data.catalogue.life/ (temporary URL)

Communities

Data Publishing

ChecklistBank

Workbench

Users

Prepare and curate
checklists

COL Repository or other web
repositories

Storage and access tochecklists

Construct and publish
integrated checklist

Web and machine
accessAPI

1

Primary
datasets

COLDP

Standardised
datasets
API

2a

4

API

SectorPublish directly
API
Sector3

DwC-A
Intermediate
Repository
Primary datasets

API
SectorAPI

ACEF

Sector2b• COL Checklist• Sector source
mappings• Two views:• Reviewed(contributed
sectors)• Comprehensive(incl. unreviewed)• API for both views• Links to data sources

5aAPI
Spreadsheet

Register

5b

APIStandardised accessto any checklist
Text Tree

Secondary copies

GBIF.ORG INFRASTRUCTURE

NEW GBIF.ORG FILTERS
Presence / Absence filter•

All records declared as present orabsent•14,7 million records of absence

Search by person identifiers•

Recorded by or identified by•

Variety of identifier schemas (e.g.
from ORCiD, WikiData)•

Working for TDWG Attribution
group

Search by Administrative Areas•

Uses 3 levels from the GADM.org
database e.g. country / state /county•Using the API can report counts
by e.g. county level

https://www.gbif.org/occurrence/search

DATA QUALITY - OUTLIER DETECTION
species – distance-based

datasets – distance-based
species - environmental
https://data-blog.gbif.org/post/outlier-detection-using-dbscan/Clustering• Example shows a specimen record (1), a taxonomic revision (2), a
DNA sequence (3)1• Grouped using location, identification, date, local identifiers andtype status (so far) and fuzzy matching• Stored as annotations against the records
2• Interface allows easy comparison of the fields on the record(details)• Purpose3

https://www.gbif.org/occurrence/865079977/cluster• Richer model of related information for researchers• Transferring information between institutional databases (images,
sequences, new identifications) which may reduce effort spent• Aid in deduplicating data
• Known to contribute towards data quality improvements• Contibution towards the Extended Digital Specimen / Open Digitalspecime concept (US and DiSSCo initiatives)

USING GBIF IN CLOUD ENVIRONMENTS
Growing interest in big data tools•

Google Big Query increasingly being used•

Google / Amazon / Microsoft etc clouds being used by several partners•

Opportunities with science computing clouds like the European Open Science Cloud•

Simplify research, ease integrations with other datasets

New download formats•

Apache Avro format•

Bionomia-specific format to reduce computation on client side•

Services to easily move GBIF downloads onto cloud environments (underway)

GBIF data as public datasets•

Strong interest expressed on the GBIF community forum•

Requires new citation service (underway)•

Exploring possibilities during 2021

https://discourse.gbif.org/t/gbif-exports-as-public-datasets-in-cloud-environments/1835

COLLECTIONS CATALOGUECOLLECTIONSCATALOGUE
GLOBALCONSULTATION

Trinidad National Herbarium, photo 2019 by Maheva Bagard Laursen (CC BY 2.0)•

Part of the EU Synthesys+ project and run as an initiative under the Alliance•

A virtual workshop held over 2 weeks•

Two two-hour preparatory webinars to introduce the Ideas Paper
https://doi.org/10.35035/p93g-te47•

Available in English, French, Spanish and simplified Chinese•

GBIF community forum https://discourse.gbif.org/g/Collections-catalog•

Daily summaries, in multiple languages•

Outcomes document to be draftedSOME OUTCOMES•

Many communities need information on collections•

Interest in a core set of common data elements•

Each community has specific needs; may document collections at different levels of granularity•

GBIF can:••••bring together complementary information
promote a consistent approach to the common elements
help national nodes showcase their collections and the value they offer
Use the DOI-based citation and usage tracking to add value to nodes and to individual collection institutions.

•

The catalogue may serve as a mechanism to attract funding; global partnerships to maintainbiodiversity collections•

The GRSciColl Catalogue••

Holds a basic core suitable to act as a stub for any collection
Can act as a first step towards better linking

Global Registry of Scientific Collections (GRSciColl)
https://www.gbif.org/grscicoll

ENHANCING THE GRSCICOLLCOLLECTIONS CATALOGUE• Monthly synchronisation with Index Herbariorum• Collaboration with iDigBio•••

Data imported from iDigBio catalogue
GRSciColl powering the iDigBio collections catalogue
Collaborative editing responsibility• Early exploration of synchronisation with NCBI BioCollections*• Linking ~170M specimen-related occurrences to GRSciColl
2021• Mature the processes around collaborative editing• Deploy an enhanced collections catalogue portal• Aim to broaden integrations (Australia)• Explore a sample profile of the TDWG collections description
standard• NCBI https://www.ncbi.nlm.nih.gov/biocollections• Visual concept of collection catalogue https://labs.gbif.org/visual-concepts/• iDigBio collections powered by GBIF infrastructure http://beta.idigbio.org/portal/collections (beta version)

HOSTED PORTALS•Introduced at GB26 as part of work to lower technical threshold forparticipation in GBIF•

Raised interest from many GBIF Participants and partners•

Development work ongoing this year•••

Reworking our APIs (GraphQL-based)
Developing the first modules of user interfaces (ReactJS-based)

Represents the next phase of infrastructure for GBIF••Will be consistent with GBIFWill contribute to the envisaged collections catalogue

THANK YOU!
trobertson@gbif.org
ahahn@gbif.org

Capacity and Engagement during lockdown
Maheva Bagard Laursen, Laura Russell, Mélianie RaymondImage by Maheva Bagard Laursen

UPDATE ON GBIF-LED PROGRAMMESCAPACITY ENHANCEMENT SUPPORT PROGRAMME - CESP
19 Concept Notes from17 GBIF participantsRequesting a total of€317,588
10 proposals invited tosubmit a full proposals
5 projects selected (total funding: €102,860):

Capacity Building through Regional Cooperation for Data
Mobilization in Belarus, Latvia and Lithuania
Enhancing capacity for biodiversity data mobilization and use insupport of sustainable development in West Africa

National Portals Workshop: taxonomic databases,
species data information and visualization

https://www.gbif.org/programme/82219/capacity-enhancement-support-programme

Mobilising endemic and economically useful species data for
agro-ecological policy, National Red List and KBA assessments

NORTHERN EURASIA
Coordinated by:• Natural History
Museum of Oslo
• GBIF Norway
Support from:• GBIF Secretariat

Support for capacity development & Call fordata papers from European Russia:
Funded by: €30,000
Key activities:• Training events• Call for data papers: an incentive for data
mobilization
www.gbif.org/programme/3ilFFs3JdY2SqmyCuac0uc/northern-eurasia

Objective:
Biodiversity data
management skills forstudents through:• Training courses• Translation• Capacity building

BIODIVERSITY INFORMATION FOR DEVELOPMENT (BID)
3 calls for proposals:• Sub-Saharan Africa(closed)• Caribbean (Open)• Pacific (Open)
4 grant types:• Institution-level• National• Regional• Data use

Early results from theBID call for proposal in
Sub-Saharan Africa:• 215 concept notes• From 39 countries in
the region
Concept notes received under the BID call in Sub-Saharan Africa

https://www.gbif.org/programme/82243/bid-biodiversity-information-for-development

TIMELINE

June 2020:
Africa Call

April 2021 – March
2023
Projects from Africa

Sept. 2020:
Caribbean Call
Pacific Call

July 2021 – June
2023:
Projects from the
Caribbean & Pacific

BID calls

Project implementation

Second quarter2021
BID workshop in
AfricaJuly 2023 – August2023
Impact studies andmetrics

Third quarter 2021
BID workshop in
Caribbean & PacificSeptember 2023
Report on BID
impactCapacity enhancement

Impact analysis

September 2023
End eventEnd eventBIODIVERSITY INFORMATION FUND FOR ASIA (BIFA)
32 Concept Notes from
13 countries in Asia
Requesting a total of€340,214
13 proposals invited tosubmit a full proposals

Cleaning and digitizing plant specimen records
from Helongjiang Province
Digitization of mycological collection in Nepal
Enriching the Bhutan Biodiversity Portal through digitizationand mobilization of specimen collections
Digitizing and Databasing of bee specimens in Thailand

Supporting conservation through mobilizing ecological data from
Kalimantan, Indonesia
https://www.gbif.org/programme/82629/bifa-biodiversity-information-fund-for-asia

9 projects selected (total funding: € 117,829):
Mobilizing invertebrate monitoring data in South-East Asia
Using citizen science to study whales and dolphins in
Vietnamese waters
Digitization of specimens at the University of the Philippines
Los Baños Museum of Natural History
Mobilizing Indonesian butterfly collections at theMuseum Zoologi Bogor (II)

CESP
BIFA

09 December 201915 June 2020

June 2020

October 2020

31 December 2021

Two stage selection
process:

Notification sent toprojects selected to
be fundedStart of the project

Webinar on Project
implementation

End of the project Concept note
 Full proposal

Call for proposals

Contract procedure

25 November 201914 May 2020

July 2020

Two stage selection
process:

Notification sent toprojects selected to
be fundedStart of the project Concept note

Project implementation (12 to 18 months)

 Full proposal

BID Final report

Call for proposals

Contract procedure

10 June 2020

07 September 2020

Sub-Saharan Africa

Pacific & Caribbean

Two stage selection
process:

Two stage selection
process: Concept note Concept note

 Full proposal Full proposal

Call for proposals

July 2020(virtual) Datamobilization
workshop
October 2020
Webinar on Progress
reporting

31 December 2021
End of the project Final report

Project implementation (12 to 18 months)
March 2021
Selected projects
from Africa
June 2021
Selected projects
from the Caribbean
and PacificContract procedure

April 2021 – March
2023
Projects from Africa

Second quarter 2021

July 2021 – June
2023:
Projects from the
Caribbean & PacificThird quarter 2021

BID workshop in
AfricaBID workshop in
Caribbean & PacificProject implementation (24 months)

Activities related to GBIF led-programme in 2020 - 2021

STREAMLINING PROCESSES TO INCREASE EFFICIENCY Grant review process

IMPORTANCE OF
THE GBIF
COMMUNITY Selection panel
 Project mentor Capacity enhancement workshop (Mentors & Trainers)
 Translations

UNEXPECTED CIRCUMSTANCES

Image by Maheva Bagard Laursen

DOCUMENTATION• OpenRefine guide:
https://doi.org/10.15468/doc-gzjg-af18• Sensitive species guide:
https://doi.org/10.15468/doc-5jp4-5g10• Georeferencing best practices guide:
https://doi.org/10.15468/doc-gg7h-s853• Georeferencing quick reference guide:
https://doi.org/10.35035/e09p-h128• Georeferencing calculator manual:https://doi.org/10.35035/gdwq-3v93• Publishing DNA-derived data guide:
https://doi.org/10.35035/doc-vf1a-nr22

https://www.gbif.org/news/4FjYcRwvbEnM5wPuc1JrXQ/georeferencing-documents-released-for-gbif-community-review

LEARNINGRESOURCES

https://bit.ly/GBIFGrantsAndFundingVideos

COURSEVIDEOShttps://bit.ly/GBIFDM-VimeoVideos

E-LEARNING PLATFORM

https://elearning.gbif.es/

VIRTUAL
WORKSHOP
Data Mobilization
for Asia 2020
6 July – 31 Aug

COURSEAGENDACOMMENTS FROM COURSE PARTICIPANTS

LESSONS LEARNED• Ability to teach more participants• Planning across disparate time zones is difficult• Continue to design online courses with options
for virtual or in-person activities.
• Find ways to virtually replicate networking
between individuals

WORKSHOP MENTORS AND TRAINERS

1.
2.
3.

Ahmad Taufiq, Oliver Griffin,
Dieta Sudarma, Abdulla Ghazal
Melissa Liu, Saunak Pal,
Arman Pili, Wei Song Hwang
Sharon Grant, Sophie Pamerlon,
David BloomREGIONAL
MEETINGS IN
2020
Support regional coordination
Facilitate regional
collaboration
Provide feedback to theSecretariat and NSG
Develop stronger regional
engagement

https://www.gbif.org/event/1fP9076vVBQUhjBohWJjEL/gbif-community-webinar-framing-the-2020-virtual-regional-meetings

VIRTUAL REGIONAL NODES MEETINGS
Latin America &Caribbean
18 & 20 May 2020

AfricaAsia

5-6 May 2020

Europe & CentralAsia
11-12 May 2020

10 & 12 June

17 July 2020

39 attendees

39 attendees

38 attendees

42 attendees

14 attendees

North America

Yellow Pitcher Plant (Sarracenia flava) by Erin Faulkner, Nevada Grayling (Pseudochazara hippolyte) by Shamal Murza, Tapirus terrestris(Tapirus terrestris) by pfaucher, Impala (Aepyceros melampus) by jordivanoort , Eastern Golden Frog (Pelophylax plancyi) by wynfee

BID REGIONAL ENGAGEMENT WEBINARS
Latin America &Caribbean

AfricaPacific

19 May 2020

11 June 2020

7 September 2020

101 attendees

94 attendees

29 attendees

Toco Tucan (Ramphastos toco) by João Vitor Andriola, Southern and Eastern African Cheetah (Acinonyx jubatus) by pma, Humboldt's
Araucaria (Araucaria humboldtensis) by Vtanguy | The Biodiversity Information for Development programme is funded by the European
Union

GBIF ASIA VIRTUAL SUMMIT
Asia
20 July 2020
144 attendees

Panel discussion to discuss theissues raised by the 20 year
review, including therecommendation to build
Eastern participation (R5)Black Nightshade (Solanum nigrum) by keitawatanabe
Biodiversity Information Fund for Asia (BIFA) is funded by the Ministry of the Environment, Government of JapanCHALLENGES OF VIRTUAL MEETINGS FOR OUR COMMUNITY ENGAGEMENT• More difficult tomanage large group
discussions andconsensus forming• Not easy to allow for
informaldiscussions, coffee
break
conversations,personal
connections• Complications ofworking across timezones

• At least as muchtime (or more time)spent onpreparation as for inperson meetings

ADVANTAGES OF VIRTUAL MEETINGS FOR OUR COMMUNITY ENGAGEMENT• Ability to invite more
people to our events• Easy to record
meetings for thosethat can’t attend at
the specified time

• Saving of travel
costs and travel
time (emissions andjet lag)• Some community
building effect,
especially in small
groups• Good for sharing
information andupdatesSTRONGCOMMUNITY
Thanks to thecommunity for theflexibility anddedication to
supporting the capacityand engagement work
this year

THANK YOU
mblaursen@gbif.org
larussell@gbif.org
mraymond@gbif.org

Linckia laevigata – Mélianie Raymnond – CCBY - https://www.inaturalist.org/photos/8403155

Private Sector Engagement
Andrew Rodrigues | Programme Officer

European Bee-Eater Merops apiaster observed in Karakiran, Turkey by ahmet_basoglan. Photo via iNaturalist (CC BY-NC
4.0)

BUSINESS AND BIODIVERSITY DATA• Business uses biodiversity data to mitigate
the impacts of their operations throughenvironmental and social impact
assessments• Companies want to build their social licenceto operate and demonstrate theircommitment to international development
goals• Data sharing represents a low cost
opportunity with high impact potential

Photo from flickr by Max Phillips (Jeremy Buckingham MLC) CC BY 2.0

DATA FROM BUSINESS AND GBIF

• 27 private sector companies are publishingdata through GBIF have published 1,419,240
records in GBIF• Private companies are willing to share datawhen there is pro-active engagement• Other engagement activities in past
• Eye on Earth• International Association for Impact
Assessments

Company

Activity sector

Country

DatasetsOccurrence
recordsAïgos SAS

Consulting

Colombia

3

2,404

Anadarko Colombia Company

EnergyColombia

3282

Arctic Research and Consulting DA

Consulting

Norway1

8,914

Asplan Viak AS
Biofokus

Engineering
Consulting

NorwayNorway14
1

3,779
508,993

Biolog J.B. Jordal AS

Consulting

Norway1

177,814

CelsiaEnergyColombia

1

35

Chevron Australia

EnergyAustralia

1

2,048

Ecofact

Consulting

Norway1

11,273

EDP - Energias de Portugal

EnergyPortugal

73

601,636

Faun Naturforvaltning AS

Consulting

Norway1

3,788

Federación Nacional de Cafeteros

Agriculture

Colombia

6

26,840

Hatovial SAS
INERCO
IsagenLafargeHolcim
Moam SAS
Multiconsult

Engineering
Consulting
EnergyMiningConsulting
Consulting

Colombia
Colombia
Colombia
Spain
Colombia
Norway

1
1
8
2
1
1

1,898
1,090
19,352
35
1,781
308

Naturrestaurering AS

Consulting

Norway

2

515

NNI

Consulting

Norway23,116Oleoducto Bicentenario

EnergyColombia

3

2,074Rådgivende Biologer

Consulting

Norway515,214

Stratos
SUEZ
SWECO Norge AS
Terrasos
Total

Consulting
EnergyEngineering
Consulting
EnergyColombia
Spain
NorwayColombia
France

1
1
1
4
1

849
56,847
1,139
9,781
324

SHIFT TOWARDS PUBLICATION
THROUGH GBIF

Move towards making biodiversity data openly
and freely available• New legislation e.g. Western Australia"I welcome agreement to progress digital environmental impact assessment.
Ensuring WA and the country has efficient and effective environmental
regulation systems is vital to protect our environment for future generations
and providing certainty to industry.”- Hon Stephen Da ws on MLC, Minis ter for Environment; Dis a bility Services ;Electora l Affa irs – Government of Wes tern Aus tra lia• Open da ta orga nis a tiona l policies

Media statement: https://www.mediastatements.wa.gov.au/Pages/McGowan/2019/11/Calls-for-Federal-action-on-critical-environmental-issues.aspx
https://wabsi.org.au/wp-content/uploads/2019/10/Digitally-Transforming-Environmental-Assessment_Working-Group-Report.pdf

Regions

SHIFT TOWARDS PUBLICATION
THROUGH GBIF

Financial institutions are also demandingtransparency and open data in the projects theyfinance-Equator Principles“The EPFI will encourage the client to share commerciallynon-sensitive Project-specific biodiversity data with the
Global Biodiversity Information Facility (GBIF) andrelevant national and global data repositories, using
formats and conditions to enable such data to beaccessed and re-used in future decisions and research
applications.”

Southern Africa
East Africa
North Africa
West and Central Africa
Total for Africa

No. of projects% of all GBIF% of non-bird,withmediated data
GBIF-mediatedenvironmental
generated by AFD data generated by
impactfinancing
AFD financing
assessments
8
0,07
2
25
1,17
23,8
21
5,04
157,2
74
12,15
23,4
128
0,85
15,5

Central America (onlyMexico)South America
The Antilles
Total for Latin America
and the Caribbean
Central Asia (onlyUzbekistan)
East Asia (only China)West Asia
South Asia
South-east Asia
Total for Asia

2

0,03

0,3

15
2

0,07
1,17

1,4
21,5

19

0,07

1,16

1

4,87

60

13
19
18
12
63

1,91
2,26
0,12
1,39
0,37

60,7
127,9
20,4
36
39,4

• Development Banks – Data4Nature
Media statement: https://www.mediastatements.wa.gov.au/Pages/McGowan/2019/11/Calls-for-Federal-action-on-critical-environmental-issues.aspx

NEXT STEPS•

Consolidating existing guidance and expertise
•
•
•

•

Capacity building for data publishing•••

OpenPSD Project
IAIA-GBIF
Equator Principles
Training materials
Helpdesk services

Continued promotion of biodiversity data sharing
by business••••Supporting campaigns such as Data4Nature
Engaging in sustainable business fora
Developing the GBIF business caseEngaging with sectoral associations and bodies

THANK YOU
Andrew Rodrigues
Programme Office for Participation and Engagement
arodrigues@gbif.org

www.gbif.org

2018

2020

981,464,491

1,602,089,347

DNA-DERIVED DATA IN GBIFGUIDANCE AND TRAINING
Dmitry Schigel | Scientific officer

October 2020

A WINDOW ON EVIDENCE ABOUT WHERE SPECIES HAVE LIVED, AND WHEN
Observations

Digitized specimens

Data publishing andindexing

Literature

Common standards(DwC)

Remote-sensing
Data discovery and use
Environmental DNA
https://www.gbif.org/zh/occurrence/searchTroudet et al. Nature Scientific Reports 2017

Image: FL Fawcett in Wheller Ann. Entomol. Soc. Am. 1990

GLOBAL BIODIVERSITY VS. DIGITALLY AVAILABLE DATADATA STREAMS IN GBIF

DNA-based evidence

Sequence names“taxon hypotheses”, OTUs
UNITE: SH

BOLD: BINs

SILVA

…

Indexing
dark taxa

natural history collections

DNA occurrences

Indexing
described taxa

human observations etc.

Latin names

DATA STREAMS IN GBIF

DNA-based evidence

Indexing
dark taxa

Sequence names“taxon hypotheses”, OTUs
UNITE: SH

BOLD: BINs

SILVA

natural history collections

DNA occurrences

species mixes (samples)

individuals / isolates

one or moremarker genes

Amplicon
Genomic Transcriptomic(metabarcoding)shotgunshotgunone or moreDNARNA
marker genes

INSDC / ENA
BOLD
occurrences

UNITE

Latin names

sequencing…

Amplicon(barcoding)Indexing
described taxa

human observations etc.

…

UNITE

Metagenomic

Metatranscriptomic

shotgunDNA

shotgunRNA

MGnifyMGnifyBIOWIDE…

DATA STREAMS IN GBIF

DNA-based evidence

Indexing
dark taxa

Sequence names“taxon hypotheses”, OTUs
BOLD: BINs

UNITE: SH

SILVA

natural history collections

DNA occurrences

Norway?

Amplicon(barcoding)one or moremarker genes

species mixes (samples)

Amplicon
Genomic Transcriptomic(metabarcoding)shotgunshotgunone or moreDNARNA
marker genes

INSDC / ENA
BOLD
occurrences

UNITE

Latin names

sequencing…
individuals / isolates

Targeted detection
qPCR

Indexing
described taxa

human observations etc.

…

UNITE

Metagenomic

Metatranscriptomic

shotgunDNA

shotgunRNA

MGnifyMGnifyBIOWIDE…

DNA-based evidence

Indexing
dark taxa

Sequence names“taxon hypotheses”, OTUs
BOLD: BINs

UNITE: SH

SILVA

natural history collections

DNA occurrences

Norway?

Amplicon(barcoding)one or moremarker genes

species mixes (samples)

Amplicon
Genomic Transcriptomic(metabarcoding)shotgunshotgunone or moreDNARNA
marker genes

INSDC / ENA
BOLD
occurrences

UNITE

Latin names

sequencing…
individuals / isolates

Targeted detection
qPCR

Indexing
described taxa

human observations etc.

…

OCCURRENCE DATASETSCHECKLISTSCHECKLISTSDATA STREAMS IN GBIFUNITE

Metagenomic

Metatranscriptomic

shotgunDNA

shotgunRNA

MGnifyMGnifyBIOWIDE…

SAMPLING EVENT DATASETSOPERATIONALTAXONOMICUNITSOTU = SH,Species hypothesis

SH ABC0001
GBIF
backbone taxonomy

OTU = BIN,
Barcodeidentification number

BIN DEF0002

INDIVIUDUAL SEQUENCES WITH COORDINATES
European Nucleotide Archive: 4.8M records

24 June 2020

International Barcode of Life: 6.8M records

METABARCODING: MGNIFY AND MORE

https://www.gbif.org/publisher/ab733144-7043-4e88-bd4f-fca7bf858880

920 datasets: 20.1M new records
14.8M Bacteria
2.3M Chromista

NEW GUIDE: PUBLISHING DNADERIVED DATA THROUGHBIODIVERSITY DISCOVERY
PLATFORMS

Mapping and data publishing
Cross-platform
About 40 pages long ”cookbook”
 Introduction
 Categorization
 Mapping* Visuals
 Future prospects
 Resources*Darwin Core and MIxS based

https://docs.gbif-uat.org/publishing-sequence-derived-data/1.0/en

PUBLISHING SEQUENCE-DERIVED DATA: THE “LEARN” SECTION

Introduction
 Rationale Audiences DNA derived occurrence data Biodiversity data
 Processing workflows
 Taxonomy of sequences

https://docs.gbif-uat.org/publishing-sequence-derived-data/1.0/en

PUBLISHING SEQUENCE-DERIVED DATA: THE “DO” SECTION

Data packaging and mapping
Categorisation of data
I
Sequence-based occurrences
II Enriched occurrences
III Targeted species detection (qPCR)IV Name references
V Metadata-only
Mapping
Examples
https://docs.gbif-uat.org/publishing-sequence-derived-data/1.0/en

NEW TRAINING COURSE ON GBIF AND BOLD SKILLS – WITH BIODATA /GBIF NORWAY
Accelerating biodiversity research through DNA barcodes,
collection and observation data
Work in progress
Why publish in GBIF?
KEY FACTS
Barcoding, data and biodiversity
Biodiversity databases in Georgia
Open data as a first-class research citizen• New GBIF course
Databases as a research tool
• Tbilisi, Georgia
Why do we need to identify species• 2021, 4 days
Concept of DNA barcoding
Data in and data out: recognize and understand your data
• needs
Onsite or virtual
Principles of data organization and personal data management• GBIF and BOLD
Data structure: standards
Data citation• publish and use
Data exposure: why and when
• DNA-derived FAIR data
Data papers
Barcode reference repositories• Learn and practice
Quality control
Use case Bombus and legumes: uncovering pollination mysteries

https://www.nhm.uio.no/english/research/projects/biodata/activities/202007-tbilisi.html

THANK YOU
Dmitry Schigel
dschigel@gbif.org

Data integration enables biodiversity synthesis
A literature review of GBIF-enabled studies

Mason Heberling1, Joe Miller2, Daniel Noesgaard2, Scott Weingart3, Dmitry Schigel2
1Carnegie Museum of Natural History Pittsburgh, PA

USA; heberlingm@carnegiemnh.org

2Global Biodiversity Information Facility Secretariat, Copenhagen, Denmark
3Carnegie Mellon University, Pittsburgh, PA USA

GB27 Meeting, October 2020gbif.org

gbif.org

gbif.org

gbif.org

The real value of biodiversity data is not in its volume, but in its use.

The Big Questions
1. How are GBIF-mediated data used? (the what)
2. Have uses changed through time? (the when)
3. Where are GBIF-mediated studies used? (the where and who)
4. How does GBIF-mediated papers compare to potential use? (the future)

Growth of GBIF data matched by growth of GBIF use.
Rapid growth in data.
+1,150% since 2007!

Rapid growth in data use.
2019 alone = 723 studies
Datasets are being used.
26,046 GBIF-mediateddatasets have >1 citation!
*median citations per dataset = 11

Thanks to John Waller for data help

Growth of GBIF data matched by growth of GBIF use.
Rapid growth in data.
+1,150% since 2007!

Rapid growth in data use.
2019 alone = 723 studies
Datasets are being used.
26,046 GBIF-mediateddatasets have >1 citation!
*median citations per dataset = 11

Thanks to John Waller for data help

The what
How are GBIF-mediated data used in scientific papers?

Approach:
Computational text analysis of 4,035 studies using GBIF.

Topics emerge from computation of word associations.

Results:
24 topics across a range of content areas
Species distribution modeling, a clear major use.

The when
Have major uses of GBIF data changed through time?

Approach:
Compare pre-2016 to recent (2016-19)
Color = growth (red) or decline (blue).

Results:

Temporal change(pre-2016 to recent)
growthIncreasing topics +:Species distribution models (applications), conservation,disease, species interactions, climate futures

Decreasing topics - :Species distribution models (tools), Biodiversity
informatics, invasion management, taxonomic treatments**NOTE: relative change between time periods.
E.g., ‘decreasing’ topics can remain common!

no change
declineThe who and where
GBIF data use includes a global authorship, though not evenly distributed.

The future: The GBIF Map of Science
GBIF research use spans many disciplines

Map generated via Sci2 Tool

GBIF-mediated data enables:-Connection of disparate data types and sources-Diverse topic areas and cross-disciplinary research use-Increasingly global network of research

Evidence for:-Areas to prioritize and foster-Continued data digitization and publishing-Creating, connecting and improving biodiversity data

Thanks!
Mason Heberlingheberlingm@carnegiemnh.org

Data integration enables biodiversity synthesis
A literature review of GBIF-enabled studies
Mason Heberling1, Joe Miller2, Daniel Noesgaard2, Scott Weingart3, Dmitry Schigel2
1Carnegie Museum of Natural History Pittsburgh, PA

USA

2Global Biodiversity Information Facility Secretariat, Copenhagen, Denmark
3Carnegie Mellon University, Pittsburgh, PA USA

GB27 Meeting, October 2020

Citations and use of GBIF-mediated data
Daniel Noesgaard | Science Comms Officer

TEN YEARS OF GROWTH
Peer-reviewed papers using GBIF-mediated data per year
1000
900
800
700
600
500
400
300
200
100
0
2011

2012

2013

2014

30 per cent annual growth on average—almost 1,000 citations in 2020 predicted

2015

2016

2017

2018

2019

2020 (proj.)USE OF DOIS IN CITATIONS
Citation types
1000
900
800
700
600
500
400
300
200
100
0
2018

2019
Generic

DOIs are now used in nearly a third of papers using GBIF-mediated data

DOI

2020 (proj.)NEW SOURCES/LANGUAGES OF LITERATURE

ChineseJapanese

Russian

400 papers added

Thanks to Dr Luo Maofang (IB-CAS): Bulk import of ~400 papers in Chinese via CNKI (China National Knowledge Infrastructure)

Others?

NEW CITATION SERVICE
Cloud environment
exports

Simple service• DOI of original “download” (e.g. a monthly snapshot)• A list of dataset identifiers/DOI preferably with record counts• A URL for the filtered dataset

Return• A new DOI presenting the cleaned data
• Linked to the specific contributing datasets with counts(attribution)• Provides access to the filtered dataset (reproducibility)

Search API derived
datasets (rgbif, etc.)

#CITETHEDOIDaniel Noesgaard
GBIF Secretariat

Positioning GBIF for the the post-2020
Global Biodiversity Framework
Tim Hirsch | Deputy Director

GB27 Day 2 | 20 October 2020

5TH GLOBAL BIODIVERSITY OUTLOOK

https://www.cbd.int/gbo5

GBIF SUPPORTING BIODIVERSITY INDICATORS- Trend in invasive
alien species
introductions (throughGlobal Register ofIntroduced andInvasive Species)-

Species Protection
Index

-

Protected Area
Representativeness
Index

-

-

https://www.bipindicators.net/

Comprehensivenessof conservation ofsocioeconomically/cu
lturally valuablespecies
Agrobiodiversity
Index
Crop Wild Relative
Index

-

Growth in species
occurrence records
accessible throughGBIF-

Species Status
Information Index

DELAYED TIMETABLE FOR NEW GLOBAL BIODIVERSITY FRAMEWORK• Subsidiary body meetings (SBSTTA 24, SBI3) - Canada | March 2021
• Final meeting of Open-ended Working Group - Cali, Colombia | ? 2021
• COP 15 (UN Biodiversity Conference) - Kunming, China | ? 2021

OPPORTUNITIES FOR GBIF
• Strong role for data and monitoring within new targets (draft new
Target 19)• Implementation support mechanisms (Knowledge generation,
management and sharing; capacity development)• Critical role of primary data for monitoring and reporting

https://www.cbd.int/conferences/post2020

ANALYSING DATA NEEDS FOR GLOBAL BIODIVERSITY FRAMEWORK• Competitive call for analysis of post-2020 data needs• Entries evaluated by panel including external experts• Contract awarded to VertNet consortium (Rob Guralnick,David Bloom, Paula Zermoglio)• Work timeline adjusted due to changes in CBD timetable• Project under way from September 2020, publication 2ndquarter 2021

https://www.gbif.org/news/1TMjgXqZ3LRynaCICIQr09/call-for-proposals-analysis-of-biodiversity-data-needs-in-the-post-2020-framework

PROJECT PLAN

1.

Historic inputs of primary biodiversity data (PBD) into CBD processes

2.

Projects and products that use PBD to support the post-2020 Framework

3.

PBD sources used in EBVs, Indicators, and other products

4.

Dependencies on PBD within the post-2020 Framework

5.

Conclusions and next steps

Research

Analysis

ReportHARMONIZING NATIONAL PLATFORMS• Project funded under Capacity Enhancement
Support Programme (CESP)• Developing plugin for incorporating GBIFpublished data in national Clearing-House
Mechanism (CHM) sites via Bioland tool
• Encouraging data-sharing from national CBD
platforms via GBIF Integrated Publishing Toolkit(IPT)• Starting with 8 francophone African countries, aim
for wider adoption

https://www.gbif.org/project/79ZRBGx5dNXYpR2ijHKebK/using-the-cbd-clearing-house-mechanism-to-strengthen-biodiversity-dataacquisition-and-data-sharing

RELEVANT 2021 WORK PROGRAMME ITEMS
Activity 1e (Expand national participation):• Actively seek new Voting Participant countries, and return of former Voting Participants, to broaden
the funding base ahead of the 2023-2027 financial period; in particular highlighting to governments
the value of GBIF in meeting data and capacity needs for national implementation of the post-2020
global biodiversity framework under the Convention on Biological Diversty (CBD)

Activity 5c (Support biodiversity assessment):• Publish outcomes of the analysis of primary data needs for the post-2020 Global Biodiversity
Framework, promote at relevant fora including the COP15 meeting of the CBD in Kunming, China

THANK YOU
thirsch@gbif.org

www.gbif.org