View a video recording here: https://vimeo.com/195024485 Franz & Sterner @ #TDWG16 - "A new power balance is needed for trustworthy biodiversity data". Talk # 1134, Friday, December 09, 2016, 11:30 am. Session Contributed Papers 05: Data Gaps, Trust, Knowledge Acquisition. See https://mbgserv18.mobot.org/ocs/index.php/tdwg/tdwg2016/schedConf/program

1. A new power balance is needed
for trustworthy biodiversity data
Please
@taxonbytes
Nico Franz1 & Beckett W. Sterner1
With contributions by Edward Gilbert1, Andrew Johnston1,
Guanyang Zhang1, Bertram Ludäscher2 & Alan Weakley3
1 School of Life Sciences, Arizona State University
2 iSchool, University of Illinois at Urbana-Champaign
3 Herbarium, University of North Carolina at Chapel Hill
TDWG 2016 – Biodiversity Information Standards
December 09, 2016 – Instituto Tecnológico de Costa Rica (#TDWG16)
@ http://www.slideshare.net/taxonbytes/franz-sterner-tdwg-2016-new-power-balance-needed-for-trustworthy-biodiversity-data

2. Largely derived from doi:10.3897/rio.2.e10610
91dd0ee1-8a37-4efc-85b7-8176874cf5be

3. Premise: We agree that there are significant data quality issues
91dd0ee1-8a37-4efc-85b7-8176874cf5be
Aggregated Australian millipede data 'taken to the cleaners'

4. Premise: We agree that there are significant data quality issues
91dd0ee1-8a37-4efc-85b7-8176874cf5be
Aggregated Australian millipede data 'taken to the cleaners'
Aggregators respond to the charges

5. Premise: We agree that there are significant data quality issues
91dd0ee1-8a37-4efc-85b7-8176874cf5be
Aggregated Australian millipede data 'taken to the cleaners'
Aggregators respond to the charges
But this leaves open the question(s):
Who (exactly) is responsible for
how much of each particular issue?

6. We seem to disagree on the question of responsibility assignment(s)
91dd0ee1-8a37-4efc-85b7-8176874cf5be
Source: Belbin et al. 2013. A specialist's audit […]: An 'aggregator's' perspective. doi:10.3897/zookeys.305.5438
Page 73

7. Often enough, aggregators respond by:
• Acknowledging the general issues and their relevance.
• Pointing to many issues that effectively reside "with the sources".
• Calling for more collaboration across all levels; as well as new tools and
annotation options that "motivate and empower" the research community.
91dd0ee1-8a37-4efc-85b7-8176874cf5be
Source: Belbin et al. 2013. A specialist's audit […]: An 'aggregator's' perspective. doi:10.3897/zookeys.305.5438
Page 74

8. Thesis: For taxonomy integration, this both wrong and self-defeating
91dd0ee1-8a37-4efc-85b7-8176874cf5be
• Many aggregators are designed to impose a single taxonomic hierarchy –
one at a time – onto all taxonomically annotated records.

9. 91dd0ee1-8a37-4efc-85b7-8176874cf5be
• Many aggregators are designed to impose a single taxonomic hierarchy –
one at a time – onto all taxonomically annotated records.
• By design, these "backbones" are rarely attributable to individual (expert)
authors, but instead are newly created systematic theories that only appear
at the system level.
Thesis: For taxonomy integration, this both wrong and self-defeating

10. 91dd0ee1-8a37-4efc-85b7-8176874cf5be
• Many aggregators are designed to impose a single taxonomic hierarchy –
one at a time – onto all taxonomically annotated records.
• By design, these "backbones" are rarely attributable to individual (expert)
authors, but instead are newly created systematic theories that only appear
at the system level.
• Data are aggregated accordingly; yet backbone-driven modifications may
newly disrupt the original integrity of submitted data packages.
Thesis: For taxonomy integration, this both wrong and self-defeating

11. 91dd0ee1-8a37-4efc-85b7-8176874cf5be
• Many aggregators are designed to impose a single taxonomic hierarchy –
one at a time – onto all taxonomically annotated records.
• By design, these "backbones" are rarely attributable to individual (expert)
authors, but instead are newly created systematic theories that only appear
at the system level.
• Data are aggregated accordingly; yet backbone-driven modifications may
newly disrupt the original integrity of submitted data packages.
• By deflecting on responsibilities, aggregators may cause additional self-harm.
Ultimately, the power balance – as presently built in – must shift to bring
experts back into the process of licensing succinct, trustworthy data packages.
Thesis: For taxonomy integration, this both wrong and self-defeating

12. Let's re-diagnose:
What happens in dynamic,
open systems?
Charly Lewisw, CC BY-SA 3.0

13. Taxonomic views of a frequently revised organismal lineage
Source: Franz et al. 2016. Controlling the taxonomic variable: […]. RIO Journal. doi:10.3897/rio.2.e10610
• 9 schemata for the NA Cleistes/Cleistesiopsis complex (orchids, "pogonias")

14. Snapshot of a more frequently revised organismal lineage
• 9 schemata for the NA Cleistes/Cleistesiopsis complex (orchids, "pogonias")
• Vertical sections identify taxonomic concept regions
Source: Franz et al. 2016. Controlling the taxonomic variable: […]. RIO Journal. doi:10.3897/rio.2.e10610

15. Snapshot of a more frequently revised organismal lineage
• 9 schemata for the NA Cleistes/Cleistesiopsis complex (orchids, "pogonias")
• Vertical sections identify taxonomic concept regions
• Colors identify lineages of taxonomic names (epithets) in use
Source: Franz et al. 2016. Controlling the taxonomic variable: […]. RIO Journal. doi:10.3897/rio.2.e10610

16. Snapshot of a more frequently revised organismal lineage
• 9 schemata for the NA Cleistes/Cleistesiopsis complex (orchids)
• Vertical sections identify taxonomic concept regions
• Colors identify lineages of taxonomic names (epithets) in use
• There is no consensus! Five incongruent schemata are used concurrently
Source: Franz et al. 2016. Controlling the taxonomic variable: […]. RIO Journal. doi:10.3897/rio.2.e10610

17. Further diagnosis:
If incongruent taxonomies are endorsed
– locally, provisionally, and democratically –
then what is the impact for
aggregated biodiversity data?

18. Further diagnosis:
 Taxonomy becomes a variable
that we need to represent,
and thereby control for
(at the system level)

19. The 'consensus'
• Query: "Where do these orchid
species occur?"
• Same set of 250 orchid specimens,
according to 4 taxonomies.
"Controllingthetaxonomicvariable" Example: the Cleistes use case
Source: Franz et al. 2016. Controlling the taxonomic variable: […]. RIO Journal. doi:10.3897/rio.2.e10610

20. The 'consensus' The 'bible'
"Controllingthetaxonomicvariable"
• Query: "Where do these orchid
species occur?"
• Same set of 250 orchid specimens,
according to 4 taxonomies.
Example: the Cleistes use case
Source: Franz et al. 2016. Controlling the taxonomic variable: […]. RIO Journal. doi:10.3897/rio.2.e10610

21. The 'consensus' The 'bible'
The (formerly)
federal 'standard'
"Controllingthetaxonomicvariable"
Source: Franz et al. 2016. Controlling the taxonomic variable: […]. RIO Journal. doi:10.3897/rio.2.e10610

22. The 'consensus' The 'bible'
The (formerly)
federal 'standard'
The 'best', latest
regional flora
"Controllingthetaxonomicvariable"
Source: Franz et al. 2016. Controlling the taxonomic variable: […]. RIO Journal. doi:10.3897/rio.2.e10610

23. The 'consensus' The 'bible'
The (formerly)
federal 'standard'
The 'best', latest
regional flora
"Controllingthetaxonomicvariable"
Expert views
are in conflict
Source: Franz et al. 2016. Controlling the taxonomic variable: […]. RIO Journal. doi:10.3897/rio.2.e10610

24. The 'consensus' The 'bible'
The (formerly)
federal 'standard'
The 'best', latest
regional flora
"Controllingthetaxonomicvariable"
Expert views
are in conflict
"Just bad"
Source: Franz et al. 2016. Controlling the taxonomic variable: […]. RIO Journal. doi:10.3897/rio.2.e10610

25. The 'consensus' The 'bible'
The (formerly)
federal 'standard'
The 'best', latest
regional flora
Impact:
Name-based aggregation has created
a novel synthesis that nobody believes in
"Controllingthetaxonomicvariable"
"Just bad"
Source: Franz et al. 2016. Controlling the taxonomic variable: […]. RIO Journal. doi:10.3897/rio.2.e10610

26. The 'consensus' The 'bible'
The (formerly)
federal 'standard'
The 'best', latest
regional flora
"Controllingthetaxonomicvariable"
"Just
bad"
Expert views
are in conflict
Solution:
Instead of aggregating
an artificial 'consensus',
…
Source: Franz et al. 2016. Controlling the taxonomic variable: […]. RIO Journal. doi:10.3897/rio.2.e10610

27. The 'consensus' The 'bible'
The (formerly)
federal 'standard'
The 'best', latest
regional flora
"Controllingthetaxonomicvariable"
"Just
bad"
Expert views
are reconciled
Solution:
Instead of aggregating
an artificial 'consensus',
build translation services
Source: Franz et al. 2016. Controlling the taxonomic variable: […]. RIO Journal. doi:10.3897/rio.2.e10610

28. Challenges:
How can we redesign aggregation to yield
high-quality biodiversity data packages?

29. Challenges:
How can we redesign aggregation to yield
high-quality biodiversity data packages?
What does this mean for Darwin Core1
and how we use this aggregation standard?
1 Wieczorek et al. 2012. Darwin Core: an evolving […]. PLoS ONE 7(1): e29715. doi:10.1371/journal.pone.0029715

30. Preview of solution with eight steps
• DwC is insufficient, and part of the problem

31. # 1: Represent only taxonomic concept labels (TCLs) 1
• Syntax (TCL): taxonomic name [author, year, page] sec. source
1 Multi-taxonomy input/alignment visualizations generated with Euler/X toolkit: https://github.com/EulerProject/EulerX
Cleistes divaricata
sec. Gregg & Catling 1993
Pogonia
sec. Brown & Wunderlin 1997

32. # 1: DwC score keeping  TCLs are optional; < 1% realized?
• TCL ~ DwC: nameAccordingTo
• SCAN: 19,722 of nearly 9 million records have TCLs (0.2%)
• Lack of enforcement to use TCLs makes standard less big data-ready
"Who authors GBIF's Backbone?"
https://storify.com/taxonbytes/who-authors-gbif-s-backbone

33. # 2: Represent each source coherently (Parent-Child relationships)
• Syntax (PC): TCL1 is a child/parent of TCL2 [where TCL1/2 = same source]
Cleistesiopsis bifaria sec. Pans. & de Barr. 2008
is a child of
Cleistesiopsis sec. Pans. & de Barr. 2008

34. # 2: DwC score keeping  Not (adequately) represented
• PC ~ DwC: genus, family, order (etc.; higherClassification)
• However, higher-level names in DwC are not modeled as TCLs
• Taxonomic coherence of sources cannot be preserved with DwC alone
DwC record with higherClassification
(BDJ)

35. # 3: Do not force a single hierarchy onto all tip-level TCLs
• Syntax (PC): Tip-level TCL1 , TCL2 , etc. [where TCL1/2 = different sources]

36. # 3: DwC score keeping  Optional Not (ever?) practiced
• No PC ~ DwC: infra-/specificEpithet only
• Typically, a single, 'unitary' higher-level classification is represented
• Combinations of algorithmic and social practices achieve the single hierarchy
"Who authors GBIF's Backbone?"
https://storify.com/taxonbytes/who-authors-gbif-s-backbone

37. # 4: Link TCLs via expert-provided RCC–5 articulations
• Syntax (RCC–5): TCL1 {==, >, <, ><, !} TCL2 [where TCL1/2 = diff. sources]
• RCC–5 = Region Connection Calculus
• 14 articulations provided by: http://tinyurl.com/Weakley-Flora-2015
Cleistes bifaria "Coastal Populations" sec. Smith et al. 2004
== (is congruent with)
Cleistesiopsis oricamporum sec. Brown & Pans. 2009
==

38. Source: Thau, D.M. 2010. Reasoning about taxonomies. Thesis, UC Davis. http://gradworks.proquest.com/3422778.pdf
Region Connection Calculus (semantics: set constraints)
== < > >< !
• Two regions N, M are either:
• congruent (N == M)
• properly inclusive (N < M)
• inversely properly inclusive (N > M)
• overlapping (N >< M)
• exclusive of each other (N ! M)
• RCC–5 articulations answer the query: "can we join regions N and M?"
• Taxonomies have multiple RCC–5 alignable components: nodes (parents,
children), node-associated traits, even node-anchoring specimens

39. # 4: DwC score keeping  Not (adequately) represented
• RCC–5 ~ DwC: accepted(Scientific)Name(Usage), relationshipOfResource,
taxonomicStatus (etc.; nomenclatural relationships)
• Nomenclatural relationships are type-focused, not region-focused
• "Taxonomic Concept Schema"  yes! (however: http://www.tdwg.org/standards/117)
Source: Vane-Wright. 2003. Indifferent philosophy versus […]. Syst. Biodiv. 1: 3–11. doi:10.1017/S1477200003001063
Example:
Milkweed butterflies

40. Oscillating meanings of the epithet hyalites – 1911 to 2003
Phenotypicdiversity
Type-anchorednameidentityrelations
Source: Vane-Wright. 2003. Indifferent philosophy versus […]. Syst. Biodiv. 1: 3–11. doi:10.1017/S1477200003001063

41. # 5: Identify occurrence records only to TCLs
Records:
EKY39235
MTSU003611
NCSC00040204
…
Records:
BOON8098
CLEMS0061133
WILLI39399
…
Records:
GMUF-0039355
IBE006808
USCH58399
…
Records:
CONV0006268
MDKY00006482
NCU00038930
…
Records:
BRYV0023582, BRYV0023584
KHD00032030, MISS0016604
MMNS000227, NCSC00040206
USMS_000002923, USMS_000002924
VSC0053223, VSC0065528
…
Records:
ARIZ393087
DBG39049
USCH51217
…
Records:
NCU00040710
USCH96248
VSC0053218
…
Records:
CLEMS0012881
FUGR0003293
GA023130
…
Records:
BOON8100
NCSC00040210
SJNM45487
…
Records:
GA023144
LSU00012494
MISS0016608
…
Records:
IBE006810, IND-0012374, MMNS000227
Records:
NY8654
• Syntax (ID): Occurrence / organism is identified to TCL
"CLEMS0012881"
is identified to
Cleistes divaricata sec. Smith et al. 2004
[additional ID metadata]

42. DwC record with Identification metadata
(BDJ)
# 5: DwC score keeping  ID metadata optional; > 50% realized
• ID ~ DwC: Identification, (date)identified(By), identificationReference
• SCAN: 4,715,277 of nearly 9 million records have ID metadata (52.5%)
• Enforcement…still also require use of TCLs

43. # 6: Generate comprehensive, consistent RCC–5 alignments
• Euler/X is a toolkit that infers logically consistent RCC–5 alignments

44. # 6: Generate comprehensive, consistent RCC–5 alignments
• Valued-added: MIR – set of Maximally Informative Relations containing
the RCC–5 articulation for every possible TCL pair  scalability
Reasonerinference

45. # 7: Joining occurrence-to-TCL identifications & RCC–5 alignments
Records:
BOON8098, CLEMS0061133, CONV0006268, EKY39235
GMUF-0039355, IBE006808, IBE006810, IND-0012374
MDKY00006482, MMNS000227, MTSU003611, NCSC00040204
NCU00038930, NY8654, USCH58399, WILLI39399
…
Records:
ARIZ393087, BRYV0023582, BRYV0023584, DBG39049
KHD00032030, MISS0016604, MMNS00022, NCSC00040206
USMS_000002923, USMS_000002924, VSC0053223, VSC0065528
…
Records:
BOON8100, CLEMS0012881, FUGR0003293
GA023130, GA023144, LSU00012494
MISS0016608, NCSC00040210, NCU00040710
SJNM45487, USCH96248, VSC0053218
…
• Specimen integration is fully driven by TCL-to-TCL RCC–5 signals

46. The 'consensus' The 'bible'
The (formerly)
federal 'standard'
The 'best', latest
regional flora
"Controllingthetaxonomicvariable"
Impact:
"Please select your preference (A – D);
we can perform all translations"
Source: Franz et al. 2016. Controlling the taxonomic variable: […]. RIO Journal. doi:10.3897/rio.2.e10610

47. • We can now respond to queries such as:
• "Show all specimens identified to the taxonomic name Cleistes divaricata"
• Returns many records  resolves incongruent lineage of name usages
# 8: "Do you trust us now?" Aggregation as a translational service

48. • We can now respond to queries such as:
• "Show all specimens identified to the taxonomic name Cleistes divaricata"
• Returns many records  resolves incongruent lineage of name usages
• "Now show specimens with the TCL Cleistesiopsis divaricata sec. Weakley 2015"
• Returns record subset  resolving only one narrowly circumscribed concept
# 8: "Do you trust us now?" Aggregation as a translational service

49. # 8: "Do you trust us now?" Aggregation as a translational service
• We can now respond to queries such as:
• "Show all specimens identified to the taxonomic name Cleistes divaricata"
• Returns many records  resolves incongruent lineage of name usages
• "Now show specimens with the TCL Cleistesiopsis divaricata sec. Weakley 2015"
• Returns record subset  resolving only one narrowly circumscribed concept
• "Now show specimens identified to the TCL Cleistes divaricata sec. RAB 1968,
yet translated into the more granular TCLs sec. Weakley 2015"
• Returns (again) many records, yet represents and contrasts two treatments,
as opposed to providing the ambiguous lineage view (above)
• "Show all specimens with ambiguous 2010/2015 TCL identifications…" (etc.)

50. Conclusion – designing trusted biodiversity data services
• The Darwin Core standard for aggregating biodiversity data:
(1) Has under-utilized options for better representing taxonomic expertise
(2) Is part of a design paradigm that undermines the plurality of expertise

51. • The Darwin Core standard for aggregating biodiversity data:
(1) Has under-utilized options for better representing taxonomic expertise
(2) Is part of a design paradigm that undermines the plurality of expertise
• Solutions are in development that realize data aggregation via translational
services – not as disenfranchising "backbones" – and without disrupting the
formation of expert-licensed, high-quality biodiversity data packages
Conclusion – designing trusted biodiversity data services

52. • The Darwin Core standard for aggregating biodiversity data:
(1) Has under-utilized options for better representing taxonomic expertise
(2) Is part of a design paradigm that undermines the plurality of expertise
• Solutions are in development that realize data aggregation via translational
services – not as disenfranchising "backbones" – and without disrupting the
formation of expert-licensed, high-quality biodiversity data packages
• All of us – not just aggregators – "own" the responsibility of designing
systems where the plurality of taxonomic expertise is fairly accommodated
Conclusion – designing trusted biodiversity data services

53. Acknowledgments & links to products
• Cleistes use case: Alan Weakley (UNC)
• Euler/X toolkit: Shizhuo Yu (UC Davis)
• Other data issues, discussions: Andrew Johnston, Guanyang Zhang
• NSF DEB–1155984, DBI–1342595 (PI Franz)
• NSF IIS–118088, DBI–1147273 (PI Ludäscher)
• Euler/X code @ https://github.com/EulerProject/EulerX
• Franz et al. 2016. Two influential primate classifications logically aligned.
Systematic Biology 65(4): 561–582. Link

54. Interested in exploring
multi-taxonomy and/or
-phylogeny alignments?
Please contact me.
nico.franz@asu.edu
@taxonbytes
https://biokic.asu.edu/