highlighting fitness-for-use of published biodiversity data

HIGHLIGHTING FITNESS-FOR-USE OF PUBLISHED BIODIVERSITY DATA

Javier Otegui, Arturo H. AriñoUniversity of Navarra

JAVIER OTEGUI & ARTURO H. ARIÑO: HIGHLIGHTING FITNESS-FOR-USE OF PUBLISHED BIODIVERSITY DATA. TDWG2012, BEIJING, 22-X-2012

PUBLISHING DATA

• Data published in papers• Data papers published• Data published


WHAT, WHERE, WHEN

OUR TARGET DATA

Primary Biodiversity Data RecordPBR


WHAT, WHERE, WHEN

PBR

Megaptera novaehollandiaeAdult female, live

Off North Truro, MA, USA42.101 N, 70.169 W

2010.09.29 21:47 GMT

Arturo H. AriñoAboard Dolphin VICanon Eos 450D, 200 mm lens

un


GBIF GEOREFERENCED DATA

237.348.923 animal data records by Oct. 2012 (total georeferenced records: 327.048.532)


THE CASE FOR DIRECT DATA PUBLICATION

• Access to massive data increasingly commonalized: GBIF

• Spectrum of possible uses increasing: new science, new paradigms

• Data-Intensive Science– Reliance on good data: Opportunity for discovery– Reliance on bad data: Risk of “undiscoveries”


WHAT, WHERE, WHEN

PBR

Nautilus pompilus4 specimens

Off Palau Islands

1921

Legit :unknownDet.: J.A. SalinasCollection: JDR at MZNA

un


BARRIERS TO DIRECT DATA PUBLICATION

• Data availability• Data sharing mechanisms• Data publication incentives• Data quality


DATA AVAILABILITY INCREASE

DATA AVAILABILITY INCREASE

GBIF, October 2012


Ariño, 2010. Biodiv. Informat. 7: 15-26


ESTIMATED DATA IN MISSING COLLECTIONS

BCI

GBIF

GSAP –DNHC survey

unknown

est. CI

Cexp = 8.37K

Nexp = 2.01G


WHAT, WHERE, WHEN

PBR

Saccharomyces cerevisaeTCP1-beta

Cask in wreck of ARGO2 km E of Akta Képhalos

Stratum 2000 BC

Legit : Homer S.Det.: LoScanSQ-XCollection: Museum of Beer History (MBH)

un??


THE TRUST PARADOX

• Papers are generally more trusted than raw/downloadable data– Papers have gone through peer review

• Published data have common sources:– Experiments,– Observations,– Digitizations

• Raw data in published papers can go unreviewed– Review focuses on soundness, methods, conclusions– Data assumed to be true & correct

• Direct publication of data, in fact, should facilitate revision– Enforcing rules– Filtering– Pattern detection


FITNESS-FOR-USE

• FFU defines whether data can be used for a specific purpose

• Useful compromise for publishing data• FFU not equal to data quality

Quality Fitness-for-useIntrinsic to data Depends on intended use

Conceptual PragmaticalGood quality predicting good FFU Good FFU not predict good quality


FFU ASSESSMENT

• In 2006 AHA started analyzing our own DB for FFU, creating pattern-detection visualizations– First reported in TDWG-2006 (St. Louis)

• In 2008 we started to analyze raw & processed GBIF data (2.4G records by 2012) (JOT’s thesis)– Building on works by Chapman, Yesson, Wieckzorek, etc.,

changing scope and perspective• Started producing reports in 2009, 2010• Teamed up with GBIF-Sec, 2011• Created BIDDSAT, 2012


Latitude Longitude

30.37, -87.176548.5584, -123.46342.3487, -123.7841.7866, -100.061-73.9071, 42.702838.8749, -104.8844.3964, -75.666842.1927, -89.10632.693, -79.960644.2124, -88.4241.6637, -81.378239.6992, -121.77846.13, -72.719638.7231, -77.067427.7349, -82.647936.0852, -121.61639.0901, -77.5203-83.1662, 43.062241.2956, -74.595645.5146, -73.813142.0755, -122.75941.1047, -81.494442.4792, -89.033340.6956, -74.8913...

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+

Otegui & Ariño, 2009. Proceedings of the TDWG 2009 Annual Conference, Montpellier, FR


DATA INDEXING

ProviderB

ProviderA

ProviderC

ProviderD

GBIF index

?


DATA QUERYING

ProviderB

ProviderA

ProviderC

ProviderD

GBIF index

?


Análisis detallado de GBIFDetailed assessment of GBIF

Bad data Good data


Otegui , Ariño, Gaiji & Chavan, in press


CONTROL AND FFU TOOLS AT INDEXING

Gaiji et al., 22011-2012 – EMBARGOED DECEMBER 2012


CORRECTING MECHANISMS: EXAMPLES

• GBIF has implemented many georeferencing correction algorithms, such as e.g. coordinate/country match

• This removes many bogus data points, for example redressing reversed lat/long when serving data

• Still, original data need to be corrected: GBIF cannot alter original data (only tag them)

David Remsen, TDWG-2011. In ViBRANT, http://vbrant.eu/content/gbif-integration

http://vbrant.eu/content/gbif-integration


2010.04.28

2011.14.09 ErrCode: 10

10: Fields “month” and “day” probably swapped

FILTER MECHANISMS: EXAMPLE

• Original data unchanged• Index entry corrected• Error entry generated in issue log


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+

Otegui et al., 2012

FILTERS CANNOT GET ALL


Otegui , Ariño, Gaiji & Chavan, in press

FILTERS CANNOT SOLVE ALL


Modified from Otegui et al. In press

All GBIF data

Some date element wrong

Some date element missing

All date elements missing


BIDDSAT

• Tool to detect space-time and other patterns• Applicable to data publishers sharing data

through GBIF• Uses tailored visualizations• http://www.unav.es/unzyec/mzna/biddsat/• Open source: https://github.com/jotegui/BIDDSAT• Bioinformatics, DOI: 10.1093/bioinformatics/BTS359

http://www.unav.es/unzyec/mzna/biddsat/


https://github.com/jotegui/BIDDSAT

https://github.com/jotegui/BIDDSAT


0 100Percentage of completeness

Num

ber o

f col

lecti

ons

0

15

30

45

60

Source: BIDDSAT

DATA COMPLETNESS


0 100Percentage of completeness

Num

ber o

f col

lecti

ons

0

15

30

45

60

• Wrong implementation of exchange standards (DwC) – solvable

• Data loss – not solvable

• Limited room for improvement

Fuente: BIDDSAT

DATA COMPLETNESS


Data Provider LEONIDAS, Resource SHIELDGBIF 2008/05 Version


Data Provider LEONIDAS, Resource SHIELDGBIF 2009/09 Version


1/Jan31/Dec

1/Mar

1/Feb

1/Apr

1/May

1/Jun

1/Jul

1/Aug

1/Sep

1/Oct

1/Nov

1/Dec

Fall

Winter

SpringSummer

1750 Year 2012

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Cronhorogram. Introduced by Ariño & Otegui, 2008, TDWG


Source: BIDDSAT


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Hebdogram. Iintroduced by Ariño & Otegui, 2008. Proceedings of TDWG


Ariño, Otegui & Robles, 2009

Provider 180All datasets


2008/05

Data ProviderCodename:BORODIN


Data Provider Codename: BORODIN2009/092008/05


ActinopterigiiChordata

AnimaliaCell surface:

• Number of species• Number of records (PBR)

Treemap by Google Charts API on authors’ data


Anim

alia

PlantaeFungi

INDEX TAXONOMY

Gaiji et al. in press


• Patchy data publishing… also in papers

• Opportunistic behavior: “Low-hanging fruit”

• Data can (and will) evolve

• The human factor still counts

PATTERNS OF PATTERNS


0

5

10

15

20

25

0 5 10 15

Clase de distancia

Cla

se d

e im

pre

cisi

ón

0 10000 20000 30000 40000

Chordata

Orthoptera

Lepidoptera

Hymenoptera

Diptera

Coleoptera

Thysanoptera

Collembola

Acari

Polychaeta

Oligochaeta

Nematoda

Georreferenciado

Localidad sincoordenadas

Sin localidad

PAPER WOES: PBR FROM LITERATURE


Publisher: Swedish

Publisher: German

Publisher: French

Publisher: British

Publisher: Norwegian

A MATTER OF CONVENIENCE

Otegui, Robles & Ariño, 2009. eBiosphere, London, UK.

Publisher: Parisien

Publisher: Spanish


CLASSIFICATIONACCORDING TO:

Ariño, Otegui & Robles, 2009

PROVIDERSP2K

GBIF RECORDSSAMPLE

EVOLUTIONARY DATA

T H E E N D

THANK YOU

T H E E N D

THANK YOU

WITH SPECIAL THANKS TO:

VISHWAS CHAVAN, SAMY GAIJI, ANDREA HAHN, TIM ROBERTSON, ANDTHE DIGIT SCIENCE SUBCOMITEE AND THE GSAP-NHC AND CNA TASK GROUPS

THE GBIF SECRETARIAT (COPENHAGUEN) ANDTHE SPANISH COORDINATION NODE (GBIF.ES)

ESTRELLA ROBLES AND THE PEOPLE AT THE DEPARTMENT OFZOOLOGY AND ECOLOGY (UNZYEC),

THE UNIVERSITY OF NAVARRA

No bytes were seriously harmed while preparing this PPTX.(And copies exist of those who actullay were anyway).

This file used 328 watt-hours, offset by forfeiting Cantonese roast duck for far too long.

All images, plots and analyses by the authors except where otherwise noted

PPTX © 2012 A.H. Ariño, University of Navarra

www.unav.es/unzyec

WITH SPECIAL THANKS TO:

VISHWAS CHAVAN, SAMY GAIJI, ANDREA HAHN, TIM ROBERTSON, ANDTHE DIGIT SCIENCE SUBCOMITEE AND THE GSAP-NHC AND CNA TASK GROUPS

THE GBIF SECRETARIAT (COPENHAGUEN) ANDTHE SPANISH COORDINATION NODE (GBIF.ES)

ESTRELLA ROBLES AND THE PEOPLE AT THE DEPARTMENT OFZOOLOGY AND ECOLOGY (UNZYEC),

THE UNIVERSITY OF NAVARRA

No bytes were seriously harmed while preparing this PPTX.(And copies exist of those who actullay were anyway).

This file used 328 watt-hours, offset by forfeiting Cantonese roast duck for far too long.

All images, plots and analyses by the authors except where otherwise noted

PPTX © 2012 A.H. Ariño, University of Navarra

www.unav.es/unzyec

BIDDSAT, WWW.UNAV.ES/UNZYEC/MZNA/BIDDSAT/, WWW.NCBI.NLM.NIH.GOV/PUBMED/22730433. SOON IN A PDF NEAR YOU.


http://www.ncbi.nlm.nih.gov/pubmed/22730433

highlighting fitness-for-use of published biodiversity data

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