Franz 2017 sols cbs seminar the limits of synthesis for integrative biology

The limits of synthesis

for integrative biology

Nico Franz

School of Life Sciences, Arizona State University

Center of Biology + Society Conversation Series

October 11, 2017 – School of Life Sciences, ASU

@ http://www.slideshare.net/taxonbytes/franz-2017-sols-cbs-seminar-the-limits-of-synthesis-for-integrative-biology

http://www.slideshare.net/taxonbytes/franz-2017-sols-cbs-seminar-the-limits-of-synthesis-for-integrative-biology

Premise: The notion of synthesis is appealing

doi:10.1371/journal.pbio.1001468

Premise: The notion of synthesis is appealing

https://www.nsf.gov/funding/index.jsp

https://www.nsf.gov/funding/index.jsp

Implementation (in systematics): Synthesis = one view (at a time)

• Example: The Open Tree of Life project

doi:10.1073/pnas.1423041112


• Example: The Global Biodiversity Information Facility (GBIF)

https://www.slideshare.net/mdoering/gbif-checklist-bank-and-the-backbone

https://www.slideshare.net/mdoering/gbif-checklist-bank-and-the-backbone


• Example: The Global Biodiversity Information Facility (GBIF)

• "It is updated regularly through an automated process in which the Catalogue of Life acts as a

starting point also providing the complete higher classification above families. The following 54

sources have been used to assemble the GBIF backbone: …"

doi:10.5072/hufs9m

Initial questions – How to integrate biological data?

• Does synthesis necessarily mean one view?



⇒ No. Most generally: "The combination of components or elements

to form a connected whole" (~ Oxford).





• Is equating synthesis with one hierarchy empirically and socially adequate,

or desirable?






or desirable?

⇒ Likely not if novel or conflicting views are thereby somehow suppressed.






or desirable?


• What are the consequences of synthesis = one view?

• What are the remedies?

• What are the incentives to conceive of synthesis differently?

• What are the obstacles to doing so?






or desirable?


• What are the consequences of synthesis = one view?

• What are the remedies?

• What are the incentives to conceive of synthesis differently?

• What are the obstacles to doing so?

⇒ To be explored for the use case of biological systematics / biodiversity data.

Language

Types

Background: Linnaean names refer to "non-types" contingently

Dubois. 2005. http://sciencepress.mnhn.fr/sites/default/files/articles/pdf/z2005n2a8.pdf

Non-types

http://sciencepress.mnhn.fr/sites/default/files/articles/pdf/z2005n2a8.pdf

Language



Non-types

Cleistes bifaria

acc. to author 1


Language



Non-types

Cleistes bifaria

acc. to author 2


Language



Non-types

Cleistes bifaria

acc. to author 3


The Cleistes/Cleistesiopsis use case

⇒ 20 orchid occurrence records, 3 taxonomies, 1 synthesis

⇒ Let's map them!

Charly Lewis, CC BY-SA 3.0doi:10.1101/157214

https://commons.wikimedia.org/wiki/File:Cleistesiopsis_divaricata.jpg

A. sec. Radford, Ahles & Bell 1968 – The Bible

Source: Radford, Ahles & Bell. 1968. Manual of the vascular flora of the Carolinas. UNC Press, Chapel Hill.

B. sec. Kartesz 2010 – The Federal Standard

Source: Kartesz. 2010. Floristic synthesis of North America, version 9-15-2010. Biota of North America Program, Chapel Hill.

C. sec. Weakley 2015 – The "Best" New Regional Flora

Source: Weakley. 2015. Flora of the Southern and Mid-Atlantic States. UNC Herbarium, Chapel Hill.

Expert views are in conflict.

One aggregate may distort any/all views!

D. sec. SERNEC Raw – Mid-Level Herbarium Aggregator

Source: SERNEC Data Portal. 2017. Available from http://sernecportal.org. Accessed 01 June 2017.

http://sernecportal.org/

E. sec. SERNEC Synthesis – Mid-Level Herbarium Aggregator

Source: SERNEC Data Portal. 2017. Available from http://sernecportal.org. Accessed 01 June 2017.

http://sernecportal.org/

What are the implications of "synthesis"?

⇒ The orchids are variously rare and red-listed

Charly Lewis, CC BY-SA 3.0


Individual expert views are in conflict; however...

doi:10.1101/157214

...the synthesis merges the conflicts "unevenly".

doi:10.1101/157214

One view yields novel inferences, with no expert provenance.

doi:10.1101/157214

How to remedy?

⇒ Synthesis as a conflict exposition and alignment service

Charly Lewis, CC BY-SA 3.0


Remedy: Representing taxonomic concepts and alignments

• 9 schemata for the Cleistes/Cleistesiopsis complex

doi:10.3897/rio.2.e10610


• Vertical sections identify congruent taxonomic concept regions


doi:10.3897/rio.2.e10610



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


doi:10.3897/rio.2.e10610



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

• There is no consensus! Five incongruent schemata are used concurrently


doi:10.3897/rio.2.e10610

Further diagnosis:

If incongruent taxonomies are endorsed

– locally, provisionally, and democratically –

then what is the impact for

aggregated biodiversity data?

Further diagnosis:

⇒ Taxonomy becomes a variable

that we need to represent,

and thereby control for

(at the system level).

The 'consensus' The 'bible'

The (formerly)

federal 'standard'

The 'best', latest

regional flora

"Controlling the taxonomic variable"

"Just

bad"

Expert views

are in conflict

Solution:

Instead of aggregating

an artificial 'consensus',

…

doi:10.3897/rio.2.e10610


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

doi:10.3897/rio.2.e10610

Challenge:

How can we redesign aggregation to yield

high-quality biodiversity data packages?

(very abbreviated version)

Step 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

https://github.com/EulerProject/EulerX

Step 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

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

== < > >< !

• 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)

Step 3⇒ Align concepts with Region Connection Calculus (RCC–5)

http://gradworks.proquest.com/3422778.pdf

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

== < > >< !

• 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.

Step 3⇒ Align concepts with Region Connection Calculus (RCC–5)

http://gradworks.proquest.com/3422778.pdf

Step 4⇒ 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]

Step 5⇒ Generate logically consistent RCC–5 alignments

• Euler/X is a toolkit that infers logically consistent RCC–5 alignments

• Valued-added: MIR – set of Maximally Informative Relations containing

the RCC–5 articulation for every possible TCL pair ⇒ Scalability

Reasoner inference

Step 5⇒ Generate logically consistent RCC–5 alignments

Step 6⇒ Integrate occurrence-to-TCL identifications & 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"

doi:10.3897/rio.2.e10610

• 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

Remedy: Aggregation as a translational service




• "Now show specimens with the TCL Cleistesiopsis divaricata sec. Weakley 2015"

• Returns record subset ⇒ Resolves only one narrowly circumscribed concept





• "Now show specimens with the TCL Cleistesiopsis divaricata sec. Weakley 2015"

• Returns record subset ⇒ Resolves 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.)


Synthesis, conflict,

and integrative biology:

Incentives and obstacles

Understanding the attraction of synthesis = one view

• Ok, so we have diagnosed an issue. How prevalent does it need to be for

aggregation designs to actually change?




• Complication: Under the one-view design, we cannot measure the extent of the

phenomenon very well.






• Is the threshold (of the prevalence of the phenomenon) shared universally

between contributors and users? [⇒ Fitness for use]








• Are unitary aggregation systems designed to foster distrust particularly among

career-advancing experts (e.g. graduate students, postdocs, early-career

researchers) who tend to produce novel, "groundbreaking" views?











• Is the "sweeping under the rug" of conflict an expectation grounded in the long

history of taxonomy? It's 2017 for crying out load, shouldn't we have figured

out orchids already? Why can't we have one unified "webpage" for every

species? Or: We're so close, fund us once more and we'll promise to "get there".











• Is the "sweeping under the rug" of conflict an expectation grounded in the long

history of taxonomy? It's 2017 for crying out load, shouldn't we have figured

out orchids already? Why can't we have one unified "webpage" for every

species? Or: We're so close, fund us once more and we'll promise to "get there".

• Is the quieting of conflict an increasingly acceptable design feature of big data?


• Better integration – that accounts for past/present/future conflict – requires a

kind of cognitive readjustment. "I need to ready my data now so that a

dissenting view is more easily/scalably linkable to them". That may be asking

for too much…





for too much…

• Better integration will likely also force contributors and users to be more

transparent upfront regarding the aims of integration, i.e., to make stronger and

more transparent commitments about fitness for use. Again, asking a lot.





for too much…




• It does seem that we are in the process of giving something up for the sake of

big data integration. To some extent the integration designs are still too driven

by technical feasibility constraints (which are a moving target, however).





for too much…







• Dealing with ambiguity and conflict in the ways we humans are accustomed to

in integrative biology, is not something that we have translated well enough

into the machine processing realm yet.





for too much…







• Dealing with ambiguity and conflict in the ways we humans are accustomed to

in integrative biology, is not something that we have translated well enough

into the machine processing realm yet.

• Personal issue: At what point should my advocacy "stop"?

Acknowledgments

• CBS hosts: Kelle Dhein, Andrea Cottrell & Beckett Sterner – Thank you!

• Euler/X team: Bertram Ludäscher, Shizhuo Yu, Jessica Cheng, Ed Gilbert.

• NSF DEB–1155984 (PI Franz); IIS–118088, DBI–1147273 (PI Ludäscher).

• If you have to read one paper: https://doi.org/10.1093/sysbio/syw023

https://doi.org/10.1093/sysbio/syw023

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

Franz 2017 sols cbs seminar the limits of synthesis for integrative biology

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