Franz et al ice 2016 addressing the name meaning drift challenge in open ended biodiversity information environments

Addressing the name:meaning drift
challenge in open biodiversity
information environments
Please
@taxonbytes
Nico M. Franz1 , Salvatore A. Anzaldo1, Edward E. Gilbert1,
M. Andrew Jansen1, M. Andrew Johnston1 & Bertram Ludäscher2
1 School of Life Sciences, Arizona State University
2 iSchool, University of Illinois at Urbana-Champaign
Symposium: Building the Biodiversity Knowledge Graph for Insects – Components, Progress, and Challenges
2016 XXV International Congress of Entomology, Orlando, FL – September 26, 2016 (#ICE2016)
Presentation available @ SlideShare: http://tinyurl.com/franz-et-al-ice-2016

Our biodiversity informatics research program, summarized
• We are no longer just putting articles and monographs on library shelves.
91dd0ee1-8a37-4efc-85b7-8176874cf5be

• This is more than 'just technology'; we must develop new systematic theory
to deal with inherently dynamic, open data systems.
91dd0ee1-8a37-4efc-85b7-8176874cf5be

• This is more than 'just technology'; we must develop new systematic theory
to deal with inherently dynamic, open data systems.
• The concept taxonomy approach has practical implications for strengthening
the roles that individual experts play in big biodiversity data environments.
91dd0ee1-8a37-4efc-85b7-8176874cf5be

Products – concept taxonomy in theory and in practice
ZooKeys. doi:10.3897/zookeys.528.6001
Semantic Web. doi:10.3233/SW-160220
Biological Theory (in review). doi:10.1101/022145
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 (in review). #6093
Research Ideas and Outcomes (in review). #6302

Premise: We're lucky that insect revisions are not so frequent
"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 […]. ZooKeys 550: 207–223. doi:10.3897/zookeys.550.9546

Diagnosis:
What happens in dynamic, open systems?

Snapshot of a more frequently revised organismal lineage
Source: Franz et al. 2016. Controlling the taxonomic variable […]. Research Ideas and Outcomes (RIO). (In Review)
• 9 schemata for the NA Cleistes/Cleistesiopsis complex (orchids)

• Vertical sections identify taxonomic concept regions

• Colors identify lineages of taxonomic names (epithets) in use

• Colors identify lineages of taxonomic names (epithets) in use
• There is no consensus! Five incongruent schemata are used concurrently

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

Conclusion:
 Taxonomy becomes a variable
that we need to represent,
and control for

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

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

The (formerly)
federal 'standard'

The (formerly)
federal 'standard'
The 'best', latest
regional flora

The (formerly)
federal 'standard'
The 'best', latest
regional flora
Expert views
are in conflict

The (formerly)
federal 'standard'
The 'best', latest
regional flora
Expert views
are in conflict
"Just bad"

The (formerly)
federal 'standard'
The 'best', latest
regional flora
Impact:
Name-based aggregation has created
a novel synthesis that nobody believes in
"Just bad"

The (formerly)
federal 'standard'
The 'best', latest
regional flora
"Just
bad"
Expert views
are in conflict
Solution:
Instead of aggregating
an artificial 'consensus',
…

The (formerly)
federal 'standard'
The 'best', latest
regional flora
"Just
bad"
Expert views
are reconciled
Solution:
Instead of aggregating
an artificial 'consensus',
build translation services

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

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

Preview of solution with 8 steps
• DwC is insufficient, and part of the problem
Step 7:

# 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

# 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
DwC record with nameAccordingTo (TCL)
(BDJ)
"Who authors GBIF's Backbone?"
https://storify.com/taxonbytes/who-authors-gbif-s-backbone

# 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

# 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)

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

# 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

# 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
==

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)

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

# 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

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

# 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]

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

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

# 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

# 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

The (formerly)
federal 'standard'
The 'best', latest
regional flora
Impact:
"Please select your preference (A – D);
we can perform all translations"

• 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

• "Now show specimens with the TCL Cleistesiopsis divaricata sec. Weakley 2015"
• Returns record subset  resolving only one narrowly circumscribed concept

• "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.)

Conclusions – 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

• We are developing new solutions – including TCLs, PC relations, RCC–5, and
scalable logic applications – that realize data aggregation via translational
services, without disrupting the formation of expert-licensed, high-quality
biodiversity data packages

• We are developing new solutions – including TCLs, PC relations, RCC–5, and
scalable logic applications – that realize data aggregation via translational
services, 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

Acknowledgments & links to products
• Cleistes use case: Alan Weakley (UNC)
• Euler/X toolkit: Shizhuo Yu (UC Davis)
• Data trajectories: Beckett Sterner (ASU)
• OBKMS design: Viktor Senderov (Pensoft)
• 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

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

Franz et al ice 2016 addressing the name meaning drift challenge in open ended biodiversity information environments

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