Concepts and Tools Needed to Increase

Bottom-Up Taxonomic Expert Participation

in a Global Names-Based Infrastructure

Nico Franz, David Patterson, Sudhir Kumar & Edward Gilbert

School of Life Sciences, Arizona State University

TDWD 2013 Annual Conference, Florence, Italy

Developing a Names-Based Architecture for Linking Biodiversity Data

October 31, 2013

Slides @ http://taxonbytes.org/tdwg-2013-concepts-and-tools-needed-for-taxonomic-expert-participation-in-a-global-names-based-infrastructure/

Arizona State University's current GN involvement

Biodiversity Informatics @ ASUhttp://taxonbytes.org/informatics

http://globalnames.fulton.asu.edu

http://www.globalnames.org/

http://pinkava.asu.edu/starcentral/custar/portal.php

Biodiversity Informatics @ ASUhttp://taxonbytes.org/informatics

http://globalnames.fulton.asu.edu

http://www.globalnames.org/

http://pinkava.asu.edu/starcentral/custar/portal.php

Arizona State University's current GN involvement

Concept/proposal of a GN

Taxonomic Clearing House (TCH)

• "My belief is that the taxonomic community feels *disenfranchised* – in various ways – and we MUST change that, in a tangible manner. [The Commissioners] do whatever we can to interact with the broader community […] to help demystify the Code and improve the perception of the Commission."

• "My own personal vision is far more than that, however: I am convinced that we have a culture of taxonomists many of whom do not understand the Code, or outright oppose it (or parts thereof, such as gender agreement), and that the BEST way to get them to care about the Code is to give them an actual voice. In effect, we need to deputize them – offer a role in which every taxonomist is given a measure of authority, of control."

• "Not replacing ALL of the functions and duties of the Commission, but redesigning the process so each and every taxonomist has a direct, personal stake in the enterprise (to the extent that they choose to exercise that privilege)."

– ICZN Commissioner, 2013 (to D. Patterson)

TCH concept supposes that one can:• Replace Code with major aggregator project or perspective (such as CoL), and• Replace Commission with project leadership,

and retain a sense of truth. Hence – empower individual experts.

Two motivating quotes – 1. Counteract disenfranchisement

Two motivating quotes – 2. Build for the taxonomic process

• "There is a shared awareness among taxonomists that "outside communities" would like usable, precise classifications to apply to their research challenges. However this reasonable demand is not the same as asking for a single, semi-arbitrarily flattened view that does not actually represent the underlying complexities."

• "Many taxonomy users are aware that their current system in use is ephemeral. There are valid pressures to improve long-term data integration, and *that* is what many users will value over having a single system."

• "Mandating a single view should never work as something that can fairly represent and attract taxonomic research and progress. […] These are in my view worthwhile challenges that address the demands for representing taxonomic discourse and progress as well as serving the user communities with better integrated and less ephemeral products."

– NMF, Aug. 2013, on Taxacom ("Global Species Lists and Taxonomy" thread)

TCH concept includes a taxonomic editing layer ("GNITE") that supports:• Multiple, partial, alternative classifications and phylogenies (a.k.a. "the process");• Concepts, relationships, and visualizations of given/inferred concept provenance.

Hence – prepare for concept-level semantics, services.

Two hurdles to a GN concept-level platform1

1 Not exhaustive, or even very fair to people and projects who have dealt with these "hurdles" and have overcome them.

• "What is a concept? Nobody really understands this."

• "What about concept inflation? This is not scalable."

A way to address: promote semantic, social practices that minimize pitfalls.

DOI:10.1080/14772000.2013.806371 (link)

What is a concept? – shallow, technical

Source: http://code.google.com/p/darwin-sw/

• Name /Authority works as a most context-neutral

(or -vacuous) definition.

• Practical situations facilitate different inference abilities once context is given.

• "The soundest motivation for using taxonomic concepts in biology is not

merely to improve data management (Berendsohn, 1995) but to increase the

semantic precision of taxonomic names (Franz et al., 2008)."

• "We suggest that this approach should be pursued if and where the (not

inconsiderable) cost of doing so is offset by yielding better integration of

taxonomically labeled biological information, and therefore better biological

inferences."

– Franz & Cardona-Duque, 2013

Deeper issues – why bother?

• "Whenever a name appears in subsequent paragraphs, we transparently signal either:

(1) that this usage refers to a single and specific previous or current concept of that name (sec.); or

Think: intended ability to contribute to SW-type reasoning

Perelleschus O'Brien & Wibmer sec. Franz & O'Brien 2001

• "Whenever a name appears in subsequent paragraphs, we transparently signal either:

(1) that this usage refers to a single and specific previous or current concept of that name (sec.); or

(2) that it refers more vaguely to the cumulative history of concepts associated with that name (no additional labeling); or

Think: intended ability to contribute to SW-type reasoning

Perelleschus O'Brien & Wibmer sec. Franz & O'Brien 2001

Perelleschus O'Brien & Wibmer

• "Whenever a name appears in subsequent paragraphs, we transparently signal either:

(1) that this usage refers to a single and specific previous or current concept of that name (sec.); or

(2) that it refers more vaguely to the cumulative history of concepts associated with that name (no additional labeling); or

(3) that we utilize this name in an even more non-committal sense (non-focal), typically as a semantic crutch to help contextualize names whose meanings we actually intend to focus on.

Think: intended ability to contribute to SW-type reasoning

Perelleschus O'Brien & Wibmer sec. Franz & O'Brien 2001

Perelleschus O'Brien & Wibmer

Ganglionus O'Brien & Wibmer [non-focal]

• "Whenever a name appears in subsequent paragraphs, we transparently signal either:

(1) that this usage refers to a single and specific previous or current concept of that name (sec.); or

(2) that it refers more vaguely to the cumulative history of concepts associated with that name (no additional labeling); or

(3) that we utilize this name in an even more non-committal sense (non-focal), typically as a semantic crutch to help contextualize names whose meanings we actually intend to focus on.

• By consistently specifying the nomenclatural and/or taxonomic context in which names are used (or the inverse), and what expectations towards our readership are implied, we are a step closer to achieving a machine-interpretable annotation of these usages.

– Franz & Cardona-Duque, 2013

Think: intended ability to contribute to SW-type reasoning

Perelleschus O'Brien & Wibmer sec. Franz & O'Brien 2001

Perelleschus O'Brien & Wibmer

Ganglionus O'Brien & Wibmer [non-focal]

• "Whenever a name appears in subsequent paragraphs, we transparently signal either:

(1) that this usage refers to a single and specific previous or current concept of that name (sec.); or

(2) that it refers more vaguely to the cumulative history of concepts associated with that name (no additional labeling); or

(3) that we utilize this name in an even more non-committal sense (non-focal), typically as a semantic crutch to help contextualize names whose meanings we actually intend to focus on.

• By consistently specifying the nomenclatural and/or taxonomic context in which names are used (or the inverse), and what expectations towards our readership are implied, we are a step closer to achieving a machine-interpretable annotation of these usages.

– Franz & Cardona-Duque, 2013

What are speakers expecting from their (machine, KRR) audience?

Perelleschus O'Brien & Wibmer sec. Franz & O'Brien 2001

Perelleschus O'Brien & Wibmer

Ganglionus O'Brien & Wibmer [non-focal]

Heavy duty semantic reasoning, precise

Some reasoning, gets worse as time increases

More limited to no reasoning expectation

Putting concepts, names, [non-focal]to use in a new classification

With conventions in place, we can compartmentalize & innovate

• Perelleschus (2013) revision combines name/concept taxonomy organically

(1) Concept

(2) Name

(3) Non-focal

• Concept taxonomy "cuts through" any separation of classification vs. phylogeny; though outgroups may be viewed as [non-focal].

Consistency – maximize concepts when possible, minimize names

Key to species-level concepts, old & new names

Distributionmap

Figureshowing

specimens,traits

New species, diagnosis

Consistency – maximize concepts when possible, minimize names

Key to species-level concepts, old & new names

Distributionmap

Figureshowing

specimens,traits

New species, diagnosis

Names are essentially restricted to Introduction/Discussion, i.e.when the entire taxonomic history related to a name is referred to.

As an expert aware of context at all times, I can almost omit them.(not so with [non-focal] cases which are needed).

Concepts for ranked Linnaean names, focal & non-focal clades

Phylogenetic characters,concepts for clades

Phylogenetic character matrix

Phylogenetic tree

Historically endorsed concepts are readily flagged as such

• Revision includes complete circumscriptions for 54 related concepts, 1936-2013

1986 2001

Represent all pertinent prior & current classifications & phylogenies

1936 1954

2006 2013

= "carludovicae" (name), cumulative history

Reasoning over concept evolution

Get ready for taxonomic KRR, I: identifying individual concepts

• Name Perelleschus contributes to 5 concepts; sec. 1954, 1986, 2001, 2006, 2013

Get ready for taxonomic KRR, II: assemble classifications (P/C)

Get ready for taxonomic KRR, III: express concept articulations

• Articulations use Franz & Peet (2009)1 terms which significantly improve upon TDWG-TCS

1 Franz & Peet. 2009. Towards a language for mapping relationships among taxonomic concepts. Systematics and Biodiversity 7: 5-20. Link

Concept resolution and merge taxonomy visualization via Euler/X

2013 higher-level concepts

2001 higher-level concepts

2013/2001 species concepts

Euler/X uses ASP reasoning, RCC• Reads in 3 concept tables• Logic / consistency check• Inconsistency explanation• Provence, repair options• Max. inform. relations (mir)• Merge taxonomy visualization

• More in SfB – Formal Models

Euler project URL: https://sites.google.com/site/eulerdi/home

Interim conclusions – concepts provide valuable TCH services

• The core semantics and prototype tools are in place to:

1. Handle both novel nomenclatural and taxonomic/phylogenetic data via

small (to large), incremental expert submissions to a suitable TCH.

Interim conclusions – concepts provide valuable TCH services

• The core semantics and prototype tools are in place to:

1. Handle both novel nomenclatural and taxonomic/phylogenetic data via

small (to large), incremental expert submissions to a suitable TCH.

2. Concepts allow the new submissions of taxonomic effort and progress to:

1. Be identified as such (as are their individual authors).

2. By delimited from imprecise, or existing information.

3. Be semantically represented (parent/child hierarchies).

4. Be logically integrated with relevant previous concepts (Euler/X).

5. Be visualized in merge taxonomies that resolve provenance.

Interim conclusions – concepts provide valuable TCH services

• The core semantics and prototype tools are in place to:

1. Handle both novel nomenclatural and taxonomic/phylogenetic data via

small (to large), incremental expert submissions to a suitable TCH.

2. Concepts allow the new submissions of taxonomic effort and progress to:

1. Be identified as such (as are their individual authors).

2. By delimited from imprecise, or existing information.

3. Be semantically represented (parent/child hierarchies).

4. Be logically integrated with relevant previous concepts (Euler/X).

5. Be visualized in merge taxonomies that resolve provenance.

• Jointly these services are needed to (1) counter disenfranchisement, (2) build

for the taxonomic process, and (3) facilitate better inferences in biology.

How might this work in a TCH?

Focus new development on the GN Interface for Taxonomic Editing

• Prototyped for GN1 (U.S.) by Mozzherin, Patterson & Shorthouse at MBL.

• In need of adding new functionality, interoperability, user community.

Upgrades to a native GN taxonomy editing layer are just one part of a grander TCH infrastructure

and service package.

TCH infrastructure

TCH infrastructure "Run" by experts,individually, in groups.

TCH infrastructure Taxonomists, phylogeneticists work within "native" platforms.

TCH infrastructure Strategy: initial establishment with select expert communities.

TCH infrastructure Capitalizing on existing, diversified

GN1 infrastructure and services.

TCH infrastructure

Expand GNITE into 3 powerful layers for single classification assembly, nomen-

clatural editing, and concept taxonomy

TCH infrastructure

Build a FP "Lite" system to track all TCH submissions, edits, assignments of authorship, track expert credit profiles

TCH infrastructure

GN "Union" = endorsed classification, although multiple alternatives are an essential part of TCH output service;

"intelligent alerts" notify experts

Conclusions – unless we build for the process, products will suffer

• "TCH embodies the view that improving existing classification repositories and

services is very much a matter of improving their ability to accommodate the

systematic research and publication process."

Conclusions – unless we build for the process, products will suffer

• "TCH embodies the view that improving existing classification repositories and

services is very much a matter of improving their ability to accommodate the

systematic research and publication process."

• "It is not just a matter of gathering more classifications into static structures

with limited options for expert access, editing, and classification provenance

tracking."

Conclusions – unless we build for the process, products will suffer

• "TCH embodies the view that improving existing classification repositories and

services is very much a matter of improving their ability to accommodate the

systematic research and publication process."

• "It is not just a matter of gathering more classifications into static structures

with limited options for expert access, editing, and classification provenance

tracking."

• "Rather, it is about bottom-up collaboration that allows merger, critical input,

refinement, and due recognition of, and respect for, a diversity of views that

will lead to evolving authoritative taxonomic compilations."

• TDWG 2013 Symposium organizers – Yde de Jong & Richard L. Pyle

• GN1 team – Dmitry Mozzherin, Richard Pyle, David Shorthouse, Robert Whitton

• Euler team, UC Davis – Bertram Ludäscher, Mingmin Chen, Shizhuo Yu, Shawn Bowers

• Juliana Cardona-Duque – Universidad de Antioquia, Medellín, Colombia

• Steven Baskauf (concept/occurrence graph) – Vanderbilt University

Acknowledgments

http://taxonbytes.org https://sols.asu.edu