Invited Presentation given at the University of Illinois Urbana Champaign iSchool, Center for Informatics Research in Science and Scholarship, CIRSS Seminar, Friday, February 17, 2017.

1. Non-unitary syntheses
of systematic knowledge
Please
@taxonbytes
Nico Franz
School of Life Sciences, Arizona State University
CIRSS Seminar – Center for Informatics Research in Science and Scholarship
February 17, 2017 – iSchool, University of Illinois Urbana-Champaign
@ http://www.slideshare.net/taxonbytes/franz-2017-uiuc-cirss-non-unitary-syntheses-of-systematic-knowledge

2. • Why are phylogenies and classifications (so) unstable?
• How (well) can taxonomic names and relationships – the "Linnaean system" –
manage the taxonomic similarities and differences across versions?
• Introducing the Euler/X alignment tool
• The primate use case (classifications)
• The avian use case (phylogenies)
• Biodiversity data aggregation
• Implications of achieving synthesis (CSCW..)
Overview

3. • Why are phylogenies and classifications (so) unstable?
• How (well) can taxonomic names and relationships – the "Linnaean system" –
manage the taxonomic similarities and differences across versions?
• Introducing the Euler/X alignment tool
• The primate use case (classifications)
• The avian use case (phylogenies)
• Biodiversity data aggregation
• Implications of achieving synthesis (CSCW..)
Overview

4. doi:10.1038/nature.2016.20567

6. "Here, we use new genomic data from over
1,000 uncultivated and little known organisms,
together with published sequences, to infer a
dramatically expanded version of the tree of
life, with Bacteria, Archaea and Eukarya
included."
doi:10.1038/nmicrobiol.2016.48

7. The pluralistic domain of human taxonomy making
Source: Rylands & Mittermeyer. 2014. Primate taxonomy: species and conservation. doi:10.1002/evan.21387
"100 years
of primate
taxonomies"

8. The pluralistic domain of human taxonomy making
• Taxonomies are endorsed by us (humans); more or less democratically.
• They consist of sets of labels, data, and theories about the natural world.
Source: Rylands & Mittermeyer. 2014. Primate taxonomy: species and conservation. doi:10.1002/evan.21387
"100 years
of primate
taxonomies"

9. The pluralistic domain of human taxonomy making
• Taxonomies are endorsed by us (humans); more or less democratically.
• They consist of sets of labels, data, and theories about the natural world.
• Over time, these theories change – converge or conflict (often in parallel).
Source: Rylands & Mittermeyer. 2014. Primate taxonomy: species and conservation. doi:10.1002/evan.21387
"100 years
of primate
taxonomies"

10. A model to separate the human-made versus natural domains
• While human taxonomy making unfolds (e.g. 1758 onwards), natural taxa –
which 'took' millions of years to realize – tend to not change much.
Domain of human
taxonomy making
("mimic")

11. • While human taxonomy making unfolds (e.g. 1758 onwards), natural taxa –
which 'took' millions of years to realize – tend to not change much.
Natural domain
("model")
A model to separate the human-made versus natural domains
Domain of human
taxonomy making
("mimic")

12. • While human taxonomy making unfolds (e.g. 1758 onwards), natural taxa –
which 'took' millions of years to realize – tend to not change much.
• At any time, our labels and theories (concepts) aim to stand for taxa; yet the
correspondence may be approximate.
Reliable?
Reliable?
Reliable?
A model to separate the human-made versus natural domains
Natural domain
("model")
Domain of human
taxonomy making
("mimic")

13. Remsen: Using names, we're lucky when revisions are infrequent
"In biology, there are many taxa that are so under-studied that
they are only known from their original description and
none or very few subsequent references […].
The name alone, so long as it is a unique name,
is sufficient to locate all related material."
– David Remsen 2016: 213
Source: Remsen. 2016. The use and limits of scientific names in biological informatics. doi:10.3897/zookeys.550.9546

14. • Why are phylogenies and classifications (so) unstable?
• How (well) can taxonomic names and relationships – the "Linnaean system"
– manage the taxonomic similarities and differences across versions?
• Introducing the Euler/X alignment tool
• The primate use case (classifications)
• The avian use case (phylogenies)
• Biodiversity data aggregation
• Implications of achieving synthesis (CSCW..)
Overview

15. http://taxonbytes.org/wp-content/uploads/2014/10/Peet-BIGCB-2014-Changing-Perspectives-on-Plant-Distributions.pdf

16. The challenge: names refer to non-type specimens contingently
Source: Dubois. 2005. Zoosystema 27: 365-426. http://sciencepress.mnhn.fr/sites/default/files/articles/pdf/z2005n2a8.pdf
Names
Non-
types

17. doi:10.1017/S1477200003001063

18. 4: Amauris (Amaura) (damocles) hyalites makuyuensis Carcasson (1964) sec. Vane-Wright (2003)
genus superspecies subspecies
subgenus semispecies

19. Oscillating meanings of the species epithet hyalites – 1911 to 2003
Phenotypicdiversity
Type-anchorednameidentityrelations
Narrowest holotype "region"

20. Connecting to the occurrence level.

21. Holdings, May 2015
• 27 herbarium collections
• 607,300 occurrences
• 17,300 species-level units
sernecportal.org
Introducing the SERNEC portal (sustained by Symbiota)

22. Andropogon glomeratus
- Bushy bluestem
Photo by Max Licher (ASU Herbarium); Cottonwood, Arizona.
http://swbiodiversity.org/seinet/imagelib/imgdetails.php?imgid=43175
5
Ok. SERNEC search!

23. Search for "Andropogon glomeratus" returns 255 occurrences1
Source herbaria: 9
Year collected: 1885-2013
Year identified: 1973-2010
Identifier named: 161 occ.
1 SERNEC portal, May 15, 2015; with synonyms, raw taxonomy.

24. Isn't that one similar to virginicus?

25. Source herbaria: 13
Year collected: 1873-2013
Year identified: 1973-2015
Identifier named: 200 occ.
Search for "Andropogon virginicus" returns 442 occurrences1
1 SERNEC portal, May 15, 2015; with synonyms, raw taxonomy.

26. What about the nominal subspecies?

27. Source herbaria: 6
Year collected: 1920-2013
Year identified: 2003
Identifier named: 66 occ.
Search for "A. virginicus var. virginicus" returns 101 occurrences1
1 SERNEC portal, May 15, 2015; with synonyms, raw taxonomy.

28. I believe some Floras recognize capillipes.

29. Source herbaria: 5
Year collected: 1940-2006
Year identified: 1986
Identifier named: 1 occ.
Search for "Andropogon capillipes" returns 72 occurrences1
1 SERNEC portal, May 15, 2015; with synonyms, raw taxonomy.

30. Show four-in-one occurrence-based maps.

31. Combined four-in-one search returns 769 occurrences1
Source herbaria: 13
Year collected: 1873-2013
Year identified: 1973-2015
Identifier named: 407
1 SERNEC portal, May 15, 2015; with synonyms, raw taxonomy.

32. Ready to do science?
Maybe. There are some issues.

33. Taxonomic concept alignment, Andropogon glomeratus-virginicus
complex, spanning across 11 classifications authored 1889-2015
• 36 unique taxonomic names
• 88 taxonomic concept labels
name sec. author strings
• Alignment by A.S. Weakley
row position = congruence
• 1/36 names with unique 1 : 1
name : meaning cardinality
across all classifications
• Andropogon virginicus
• Source: Franz et al. 20161
1 Franz et al. 2016. Names are not good enough: reasoning over taxonomic change in the Andropogon complex.
Semantic Web Journal (IOS). doi:10.3233/SW-160220

34. Also: This is how we built this.
(provenance tracking)

35. "When I first came here, this was all swamp.
Everyone said I was daft to build a castle on a
swamp, but I built it all the same, just to show
them."

36. "It sank into the swamp."

37. "So I built a second one."

38. "That sank into the swamp."

39. "So I built a third."

40. "That burned down, fell over, then sank into the swamp."

41. "But the fourth one stayed up. And that's what you're
going to get, Lad, the strongest castle in all of England."

42. • Why are phylogenies and classifications (so) unstable?
• How (well) can taxonomic names and relationships – the "Linnaean system" –
manage the taxonomic similarities and differences across versions?
• Introducing the Euler/X alignment tool
• The primate use case (classifications)
• The avian use case (phylogenies)
• Biodiversity data aggregation
• Implications of achieving synthesis (CSCW..)
Overview

43. Why Euler/X?

44. Concepts: tracking progress and conflict in the human domain
• Taxonomic names and nomenclatural relationships are only so-so in terms of
tracking congruent and incongruent taxonomic perspectives.

45. • Taxonomic names and nomenclatural relationships are only so-so in terms of
tracking congruent and incongruent taxonomic perspectives.
• Logic-based multi-taxonomic alignments require better contextualization of
labels and relationships, and better specification of "taxonomic sameness".
1912 vs. 1967
Logically
reconcilable?
Δ = ?
Δ
Δ
Δ
Concepts: tracking progress and conflict in the human domain

46. Querying systematic advancement – premises & questions
• The term "tree of life" characterizes a goal that we strive to reach
eventually, more so than where we are now (for many perceived groups).

47. • The term "tree of life" characterizes a goal that we strive to reach
eventually, more so than where we are now (for many perceived groups).
• Therefore it would be useful to have a "systematic knowledge advancement
service". The service satisfies queries such as:
Querying systematic advancement – premises & questions

48. • The term "tree of life" characterizes a goal that we strive to reach
eventually, more so than where we are now (for many perceived groups).
• Therefore it would be useful to have a "systematic knowledge advancement
service". The service satisfies queries such as:
1. "Does this sequence of related systematic inferences
have a stabilizing or destabilizing trend?"
Querying systematic advancement – premises & questions

49. • The term "tree of life" characterizes a goal that we strive to reach
eventually, more so than where we are now (for many perceived groups).
• Therefore it would be useful to have a "systematic knowledge advancement
service". The service satisfies queries such as:
1. "Does this sequence of related systematic inferences
have a stabilizing or destabilizing trend?"
2. "Are two or more tree hierarchies – each differentially sub-sampled
at lower levels – in congruence or in conflict?"
Querying systematic advancement – premises & questions

50. • The term "tree of life" characterizes a goal that we strive to reach
eventually, more so than where we are now (for many perceived groups).
• Therefore it would be useful to have a "systematic knowledge advancement
service". The service satisfies queries such as:
1. "Does this sequence of related systematic inferences
have a stabilizing or destabilizing trend?"
2. "Are two or more tree hierarchies – each differentially sub-sampled
at lower levels – in congruence or in conflict?"
3. "How can an applied comparative study tied to one (earlier) hierarchy
be "updated" (integrated) with another (later) hierarchy?"
Querying systematic advancement – premises & questions

51. • The term "tree of life" characterizes a goal that we strive to reach
eventually, more so than where we are now (for many perceived groups).
• Therefore it would be useful to have a "systematic knowledge advancement
service". The service satisfies queries such as:
1. "Does this sequence of related systematic inferences
have a stabilizing or destabilizing trend?"
2. "Are two or more tree hierarchies – each differentially sub-sampled
at lower levels – in congruence or in conflict?"
3. "How can an applied comparative study tied to one (earlier) hierarchy
be "updated" (integrated) with another (later) hierarchy?"
Service  We can prioritize research agendas accordingly.
Service  Sampling an issue? Or are signals complementary?
Service  Effects of "systematic variable" on conclusions can be controlled for.
Querying systematic advancement – premises & questions

52. An update on Euler/X:
Logic, use cases, and novel services

53. Euler/X – logically consistent RCC–5 alignments
• Input: multiple taxonomies and/or phylogenies; expert-provided articulations.
• Output: logic consistency checking; Maximally Informative Relations (MIR);
alignment visualizations.

54. Products – concept taxonomy in theory and in practice
ZooKeys. doi:10.3897/zookeys.528.6001
Semantic Web. doi:10.3233/SW-160220
Biological Theory. doi:10.1007/s13752-017-0259-5
PloS ONE. doi:10.1371/journal.pone.0118247
Systematics Biodiv. doi:10.1080/14772000.2013.806371
Systematic Biology. doi:10.1093/sysbio/syw023
Biodiversity Data Journal. doi:10.3897/BDJ.5.e10469 Research Ideas and Outcomes. doi: 10.3897/rio.2.e10610

55. Source: Thau, D.M. 2010. Reasoning about taxonomies. Thesis, UC Davis. http://gradworks.proquest.com/3422778.pdf
Region Connection Calculus (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)

56. Source: Thau, D.M. 2010. Reasoning about taxonomies. Thesis, UC Davis. http://gradworks.proquest.com/3422778.pdf
Region Connection Calculus (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.

57. Use cases – primate classifications & avian phylogenies
1. Primate classifications sec. MSW2 (1993) versus MSW3 (2005)
a. Microcebus + Mirza sec. MSW3 (2005)
 with coverage constraint
b. Quantifying name (identifier) reliability
c. Reasoning achieves scalability (matrix)
2. Avian phylogenies sec. Prum et al. (2015) versus Jarvis et al. (2014)
a. Psittaciformes with & without coverage
b. Alignment of the "Neoavian explosion"

58. Use case 1:
Two primate classifications –
MSW2 (1993) versus MSW3 (2005)
Starts with a live demo.

59. Use case 1.a. Aligning Microcebus + Mirza sec. MSW3 (2005)
"Taxonomic concept labels"
identify input concept regions
RCC–5 articulations provided
for each species-level concept
• Input visualization: MSW3 (2005) versus MSW2 (1993)
Source: Franz et al. 2016. Two influential primate classifications logical aligned. doi:10.1093/sysbio/syw023

60. • Alignment visualization: "grey means taxonomically congruent"
Use case 1.a. Aligning Microcebus + Mirza sec. MSW3 (2005)

61. One name &
congruent region
Use case 1.a. Aligning Microcebus + Mirza sec. MSW3 (2005)
• Alignment visualization: "grey means taxonomically congruent"

62. One name &
congruent region
Many names &
congruent region
Use case 1.a. Aligning Microcebus + Mirza sec. MSW3 (2005)
• Alignment visualization: "grey means taxonomically congruent"

63. One name &
congruent region
Many names &
congruent region
One name &
non-congruent regions
Use case 1.a. Aligning Microcebus + Mirza sec. MSW3 (2005)
• Alignment visualization: "grey means taxonomically congruent"

64. One name &
congruent region
Many names &
congruent region
One name &
non-congruent regions
Many names &
non-congruent regions
Use case 1.a. Aligning Microcebus + Mirza sec. MSW3 (2005)
• Alignment visualization: "grey means taxonomically congruent"

65. One name &
congruent region
Many names &
congruent region
One name &
non-congruent regions
Many names &
non-congruent regions
New names &
exclusive regions
Use case 1.a. Aligning Microcebus + Mirza sec. MSW3 (2005)
• Alignment visualization: "grey means taxonomically congruent"

66. One name &
congruent region
Many names &
congruent region
One name &
non-congruent regions
Many names &
non-congruent regions
New names &
exclusive regions
• Application of coverage constraint: parent-to-parent articulations (><) are
fully defined by alignment signal propagated from their respective children.
 Sensible when complete sampling of children is intended.
Use case 1.a. Aligning Microcebus + Mirza sec. MSW3 (2005)
• Alignment visualization: "grey means taxonomically congruent"

67. Use case 1.b.: Quantifying name (identifier) reliability
One name &
congruent region
• Alignment visualization: RCC–5 as an identifier assessment tool [good / not]
Many names &
congruent region
One name &
non-congruent regions
Many names &
non-congruent regions
New names &
exclusive regions

68. One name &
congruent region
• Alignment visualization: RCC–5 as an identifier assessment tool [good / not]
Many names &
congruent region
One name &
non-congruent regions
Many names &
non-congruent regions
New names &
exclusive regions
• Query services rendered: (1) MSW3 destabilizes MSW2; (2) non-congruence
is not only caused by differential low-level sampling; (3) alignment constitutes
a taxonomic meaning integration map to navigate across MSW3 & MSW2.
Use case 1.b.: Quantifying name (identifier) reliability

69. 1 in 3 names is unreliable across MSW2/MSW3 classifications
Source: Franz et al. 2016. Two influential primate classifications logical aligned. doi:10.1093/sysbio/syw023

70. Use case 1.c.: Reasoning achieves scalability (MIR matrix)
Source: Dang et al. 2015. ProvenanceMatrix: a visualization tool for multi-taxonomy alignments. CEUR Workshop
Proceedings 1456: 13–24. http://ceur-ws.org/Vol-1456/paper2.pdf
• Input: 402 articulations. Output: 153,111 Maximally Informative Relations
Salmon cells
↔ reasoning

71. Use case 2:
Avian phylogenies sec. Prum et al. (2015)
versus Jarvis et al. (2014)

72. Source: Thomas, G.H. 2015. An avian explosion. Nature 526: 516–517. doi:10.1038/nature15638
2015 2014
Phylogenetic inferences
can vary over time.

73. Use case 2: Aves sec. Prum et al. (2015) versus Jarvis et al. (2014)
• Sampling is highly differential: 198 versus 48 species-level entities
• Only 12 species-level concept pairs are congruent [green cells]

74. Use case 2.a.: Psittaciformes with & without coverage constraint
• Psittaciformes sec. 2015 – with global coverage constraint
Input visualization
 Only disjoint articulations

75. • Psittaciformes sec. 2015 – with global coverage constraint
• No low-level congruence ↔ no congruent alignment regions
Input visualization
 Only disjoint articulations
Alignment visualization
 108 MIR; all disjoint
Use case 2.a.: Psittaciformes with & without coverage constraint

76. • Psittaciformes sec. 2015 – with coverage locally relaxed
Input visualization
Use case 2.a.: Psittaciformes with & without coverage constraint

77. • Psittaciformes sec. 2015 – with coverage locally relaxed
• "No coverage" constraint for 2014/2015.[Psittacidae, Nestor]
Input visualization
Use case 2.a.: Psittaciformes with & without coverage constraint

78. • Psittaciformes sec. 2015 – with coverage locally relaxed
• "No coverage" constraint for 2014/2015.[Psittacidae, Nestor]
• Allows for 3 congruent & 7 inclusive RCC–5 articulations
Input visualization
Use case 2.a.: Psittaciformes with & without coverage constraint

79. • Psittaciformes sec. 2015 – with coverage locally relaxed
• Higher-level congruence despite low-level non-congruence
• 160 MIR: 10 congruent; 65 (inversely) properly inclusive
Alignment visualization
Use case 2.a.: Psittaciformes with & without coverage constraint

80. • Psittaciformes sec. 2015 – with coverage locally relaxed
• Higher-level congruence despite low-level non-congruence
• 160 MIR: 10 congruent; 65 (inversely) properly inclusive
Alignment visualization
 Additional 2015 low-level sampling
Use case 2.a.: Psittaciformes with & without coverage constraint

81. Use case 2.b.: Alignment of the "Neoavian explosion"
• Aves sec. 2015/2014, down to ordinal level – with coverage locally relaxed

82. • Aves sec. 2015/2014, down to ordinal level – with coverage locally relaxed
Non-congruence within
2015.Paleognathae Non-congruence within
2014.Pelecanimorphae
Use case 2.b.: Alignment of the "Neoavian explosion"

83. • Aves sec. 2015/2014, down to ordinal level – with coverage locally relaxed
Non-congruence within
2015/2014.Neoaves
(see next slide)
Use case 2.b.: Precise semiotics for the "avian explosion"

84. • Neoaves sec. 2015/2014, and 3–4 less inclusive levels
 26 overlapping articulations in the sub-
Neoavian alignment region cannot be
assigned to differential sampling
 'Genuine' phylogenetic conflict
Use case 2.b.: Precise semiotics for the "avian explosion"

85. • Why are phylogenies and classifications (so) unstable?
• How (well) can taxonomic names and relationships – the "Linnaean system" –
manage the taxonomic similarities and differences across versions?
• Introducing the Euler/X alignment tool
• The primate use case (classifications)
• The avian use case (phylogenies)
• Biodiversity data aggregation
• Implications of achieving synthesis (CSCW..)
Overview

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

87. Thesis: Unitary hierarchies create mistrust in aggregated data
91dd0ee1-8a37-4efc-85b7-8176874cf5be
• Many aggregators are designed to impose a single taxonomic hierarchy –
one at a time – onto all taxonomically annotated records.

88. 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: Unitary hierarchies create mistrust in aggregated data

89. 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: Unitary hierarchies create mistrust in aggregated data

90. 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: Unitary hierarchies create mistrust in aggregated data

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

92. 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")

93. 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

94. 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

95. 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

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

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

98. 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

99. 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

100. 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

101. 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

102. 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

103. 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

104. 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

105. 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

106. 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

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

108. 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

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

110. # 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]

111. # 6: Generate comprehensive, consistent RCC–5 alignments
• Euler/X is a toolkit that infers logically consistent RCC–5 alignments

112. # 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

113. # 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

114. 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

115. • 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

116. • 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

117. # 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.)

118. • Why are phylogenies and classifications (so) unstable?
• How (well) can taxonomic names and relationships – the "Linnaean system" –
manage the taxonomic similarities and differences across versions?
• Introducing the Euler/X alignment tool
• The primate use case (classifications)
• The avian use case (phylogenies)
• Biodiversity data aggregation
• Implications of achieving synthesis (CSCW..)
Overview

119. "As the ongoing efforts to integrate prokaryote phylogeny
into universal phylogeny demonstrate, integration does not always
mean greater inclusiveness of data, methods or explanation […].
Integration may involve considerable exclusiveness
to achieve the desired integrative aim.
– Maureen O'Malley 2013: 559
Source: O'Malley. 2013. When integration fails. Stud. Hist. Philos. Biol. Biomed. Sci. doi:10.1016/j.shpsc.2012.10.003
Rethinking systematic synthesis as an agreed-upon conflict alignment

120. Acknowledgements & links to products and references
• CIRSS hosts: Bertram L. & Janet Eke!
• Euler/X & ETC teams (extended): Shawn Bowers, Mingmin Chen, Hong Cui,
Parisa Kianmajd, James Macklin, Timothy McPhillips, Robert Morris, Thomas
Rodenhausen, and Shizhuo Yu.
• ProvenanceMatrix: Tuan Nhon Dang.
• NSF DEB–1155984, DBI–1342595 (PI Franz).
• NSF IIS–118088, DBI–1147273 (PI Ludäscher).
• Information @ http://taxonbytes.org/tag/concept-taxonomy/
• Euler/X code @ https://github.com/EulerProject/EulerX

121. Interested in exploring
multi-taxonomy & -
phylogeny alignments?
Please contact us.
nico.franz@asu.edu
@taxonbytes
https://biokic.asu.edu/