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Informatics

Overview

Our group is becoming increasingly invested into the field of biodiversity informatics research. To this end we strive to mobilize “legacy information”, in particular information related to natural history collection specimens. We furthermore aim to develop new concepts and practices to revise and produce new systematic information in ways that are more compatible with computational logic and knowledge representation and reasoning. Below is an overview of areas of data mobilization activity and development of new methods and tools in biodiversity informatics.


1. Symbiota Software Platform – Networking Collections

symbiotalogo

The Symbiota software platform, developed through a series of NSF projects related to the creation and expansion of SEINet, is ASU’s most prominent specimen/observation collections management and networking software. The Symbiota development team is led by Ed Gilbert and Ben Brandt. Symbiota is grounded in a social model of scientific collaboration that effectively leverages the identity and synergy of collection communities linked by specific taxonomic and/or regional interests, thereby improving the data digitization process and value for research and outreach.

Symbiota has established itself as a popular choice for creating Thematic Collection Networks sponsored through the NSF Advancing Digitization of Biological Collections (ADBC) program. In addition to maintaining SEINet, Symbiota is also the central platform sustaining SCAN.

 Areas of Active Research

  • Our lab is immediately involved in developing and popularizing a new Symbiota module for SCAN. This module allows imaged yet insufficiently identified arthropod specimens to be flagged as such and made available for remote identifications via annotations by interested experts within and outside of the network. For this purpose we are working with the Filtered Push (FP) team at Harvard University. The FP functionality is close to completion and will soon be tested; see this SCAN link for an introduction to the annotation process.
  • Within the context of an ASU-Smithsonian Partnership we have support to carry out a joint, Symbiota-based biodiversity informatics project with STRI collaborator Dr. Matthew Miller. The project aims to establish new collaborative portals for select STRI natural history and DNA tissue collections (vertebrates, insects, plants). We will also create new tools for identifying Panamanian arthropod species and understanding inter- and intra-specific (phylogeographic) occurrence patterns. The emerging portals are accessible here:

Two TDWG 2013 presentations with relevance to Symbiota are posted here and here.


2. mx – Revisionary Systematics and Anatomy Ontologies

mx-Minyomerus

Researchers in our lab use Matt Yoder’s mx content management system to assemble information for phylogenetic revisions of select insect groups such as entimine weevils and Eleodes darkling beetles. The creation of a Coleoptera Anatomy Ontology that would serve a  purpose similar to the innovative model/template for Hymenoptera is a longer term goal. mx is also the the platform for collaborator Aaron Smith’s tenebrioniDBase.


3. Concept Taxonomy – the Euler/X Toolkit Project

Euler-Workflow

In close collaboration with the research group led by Bertram Ludäscher at the University of California at Davis, we are developing a logic-based implementation for representing and integrating taxonomic concepts. Project members in the Ludäscher group include Ph.D. students Mingmin Chen and Shizhuo Yu. The development focuses on the Euler/X Toolkit which implements a workflow where two or more input taxonomies and their initial expert-made alignments are read in, then gradually checked for alignment consistency and minimal ambiguity, to produce a merge taxonomy.

This NSF-sponsored project has wide-ranging implications for the annotation of taxonomic insights, shown with the Perelleschus use case. It utilizes Answer Set Programming logic representation and implements taxonomy-specific tree constraints with Region Connection Calculus (RCC-5) relationships. The Euler/X code is available here. See also the Euler Project website.

A TDWG 2013 presentation with relevance to Euler/X is posted here.


4. Reasoning over Nomenclatural and Taxonomic Change

Tax9-1-TwoSpecies-Expanded-Case3-RevisedForWebThe group’s most recent informatics project involves a collaboration with ASU computer scientist Joohyung Lee and graduate student Chao Zhang. The goal is to utilize Answer Set Programming (ASP), in particular the F2LP encoding approach in combination with Potassco reasoners, in order to simulate use cases in which particular configurations of nomenclatural priority and typification in an original classification have varying name-changing effects given a single or multiple taxonomic rearrangements. ASP is particularly well suited for representing the complicated, exception-rich yet also logically specifiable rules of nomenclature. This novel approach to encode nomenclatural rules in logic and undertake reasoning can be utilized to optimize for nomenclatural stability given a set of necessary taxonomic changes, and can generally render the nomenclature/taxonomy interplay more computationally accessible.

A TDWG 2013 presentation with relevance to the ASP/Nomenclature project is posted here.


5. ASU and the Global Names Project

globalnames_dot_org_logo3bWe collaborate with David Patterson and other members of the North American section of the Global Names Architecture (GNA) to promote a comprehensive “Taxonomic Clearing House”  informatics solution that integrates scalable services related to nomenclature, evolving taxonomic classifications, and phylogenies while facilitating bottom-up expert involvement. Our group at ASU presently maintains several GNA related websites, including:

A TDWG 2013 presentation with relevance to the Global Names Architecture and Taxonomic Clearing House is posted here.


6. Other ASU Initiatives

Arizona State University is home to many innovative projects and initiatives related to the field of biodiversity informatics; including Ask A Biologist, The Embryo Project Encyclopedia, International Institute for Species Exploration, and TimeTree.