During the weekend of Feb 21 & 22, Joe Hunter, an undergraduate research student, and I attended a Software Carpentry workshop at University of Arizona hosted by the iPlant Collaborative. The workshop was intended to teach scientists to analyze and manage data (beyond just using Excel and storing data in a laptop). Read more
Hi everyone! For this week’s discussion, we will be reading a paper by Nikolov et al. (found here) discussing the mechanical properties of lobster cuticle as described using a set of nested, hierarchical equations. There are two papers that discuss this topic, of which, this is the less-technical. The other paper can be found here, and has some neat figures outlining the structure of the cuticle. Come ready to discuss how this model might be connected to and incorporated within an anatomy ontology, and how this might (or not) be useful in a phylogenetic context. There a few terms/concepts I really recommend looking up on Wikipedia before reading the paper, simply because they get used frequently (they are easy):
1.) Isotropic vs. Anisotropic
2.) Stress & Strain
3.) Young’s Modulus of Elasticity
4.) Poisson’s Ratio
Held at the Southwestern Research Station (SWRS) in the Chiricahua Mountains in SE Arizona (a 2.5 hour drive from Tucson), the focus of the Lep Course 2015 (August 16-25, 2015) is to train graduate students, postdocs, faculty, state and federal employees, and citizen-scientists in the classification and identification of adult Lepidoptera and their larvae. Topics to be covered include the biology and systematics of major families of Lepidoptera, an introduction to adult and larval morphology with a focus on taxonomically important traits, extensive field work that concentrates on both collecting and photographing adults and larvae, collecting and curatorial techniques, genitalic dissection, larval classification, use (and abuse) of DNA barcoding, and general topics in Lepidoptera systematics, ecology, and evolution.
With its extensive series of Sky Island mountain ranges, SE Arizona has the highest Lepidoptera diversity in the United States. With low desert scrub, oak and mixed oak-pine woodland, lush riparian, juniper, Douglas fir, and mountain meadow habitats – all within a 40 minute drive from the station – the SWRS is an ideal location from which to sample this diversity of both habitats and species.
If you want to interact with other Lepidoptera enthusiasts, see a spectacular Dysschema, identify the Organ of vom Rath, sort through trap samples with hundreds of species, learn about diversity of Lepidoptera, and enjoy the vistas of the SE Arizona, then this course will provide a unique experience.
Partial list of invited instructors (subject to change):
- Richard Brown (Mississippi Entomological Museum)
- Jennifer Bundy (RD4AG)
- Chris Grinter (Illinois Natural History Survey)
- Don Harvey (Smithsonian Institution)
- Sangmi Lee (Arizona State University Hasbrouck Insect Collection)
- Chris Schmidt (Canadian National Collection)
- Bruce Walsh (University of Arizona)
For more information, see http://research.amnh.org/swrs/education/lepidoptera-course or www.lepcourse.org or contact Bruce Walsh at email@example.com. You can also see photos and comments from students in the 2011 course at their facebook site, “2011 Lep Course, SWRS SEAZ”.
Quick note ahead of the main entry: New paper by István Mikó et al. 2015. Generating semantic phenotypes. Worth a careful read.
The innovative paper by Ramírez & Michalik (2014) made for (another) lively discussion last week. The paper is rich with ideas and densely presented, which motivated an attempt by us to enumerate the sequence of data production and analytical steps. Another interesting question is to what extent (and why!) the authors’ approach moves away from the prevalent multi-taxon phenotype ontology approach. For instance, statements like the following (page 642) depart from the prevalent OBO language:
“As the Spider Ontology arose to manage the morphological concepts used in phylogenetic datasets, it is natural that it incorporated much of the pre-processed homology correspondences on its structure and definitions, to make room for the variety of form and function that the same organ may have in different organisms. In this way, the ontology accommodates the vast majority of homology statements currently accepted in spider systematics.”
Yesterday the ASU Natural History Collections, Informatics & Outreach Group was represented at the “IUCN – CBO Partnership Workshop”, held on February 25-26, 2014, Arizona State University, Tempe. The workshop was sponsored by the Center for Biodiversity Outcomes. Below is a collection of broad themes, keywords, and links that are relevant to the workshop.
1. ASU Natural History Collections – http://taxonbytes.org/impressions-alameda-grand-opening/
2. Searching SEINet
- Go to http://swbiodiversity.org/seinet/index.php
- Search Collections = ASU.
- Taxa: Physalis crassifolia, Physalis hederifolia.
- Region: Arizona.
- Observe abundantly vouchered, largely disjunct taxon distributions.
3. Via Dr. Les Landrum
- Here is a demo that shows what one can do with georeferenced specimens. Go to http://pinkava.asu.edu/PlantMap/
- We have a fairly rare species of plant – Fremontodendron californicum. Map that species and then use the Biotic communities map (one of 3 options) to see where it grows.
- Infer community identity, occurrence correlations “from the bottom up”.
- Can create analytical models with different kinds of question- and data-driven themes on top of this evidential biodiversity information layer.
4. Via Ed Gilbert
- Symbiota software package – building biodiversity data communities.
- Networked Symbiota Plant Portals: 3.9 million record, and growing.
- From 125 institutions, and growing.
- It is a portal network of 7 regional plant portals, also growing; see http://symbiota.org/docs/symbiota-introduction/active-symbiota-projects/
- A tool for creating and managing inventories (floras).
- Vouchers are linked in directly from collections.
- A tool for identification.
- Shared development environment.
- Regions with funding support other regions with lean funding times.
- All projects benefit from new tools developed by funded projects.
- All data can be managed online as a community effort.
- Lots of support and future looks promising.
- Many other options are possible.
5. Arthropod collections and “research readiness” – Cobb, Seltmann & Franz. 2014.
Last week we read and appreciated Seltmann et al.’s (2012) effort to carefully describe the benefits, use, and user community roll-out of the spectacularly well annotated Hymenoptera Anatomy Ontology Portal. We clearly need and want something like this for Coleoptera. That said, we continue to explore options to maybe do things a little differently. Looking for inspiration, we are reading once more what is to my mind one of the best demonstrations of how phenotype ontologies can be used to address research questions – by phylogenetic systematists, for phylogenetic systematists.
Ramírez, M.J. & P. Michalik. 2014. Calculating structural complexity in phylogenies using ancestral ontologies. Cladistics (Early View). Available here.
We are also starting, based on this semester’s cumulative readings, to formulate some interests of our own. Hence the following homework for all; due by next Wednesday’s discussion.
Formulate three research themes or questions that are comparative/phylogenetic in nature and could possibly make use of phenotype ontologies. Be very specific; ideally starting with the taxonomic group and character system that you are most intimately acquainted with. (in my case, e.g., that might be acalyptine weevil mouthparts). Best to work outward from the current core of your taxonomic expertise. Research ideas might take into account (yet are clearly not limited to):
- Evolution of phenotype complexity, reduction.
- Correlations across character systems.
- Presence/absence of traits across larger phylogenetic groups and within/among subgroups.
- Relationships of traits to non-organismal variables (e.g., environment).
- Annotations and inferences targeting the specimen level versus or higher taxon entities.
- Evolutionary rates, timing.
- Associations, coevolutionary themes.
- Information availability, completeness, suitability for analysis.
- … [insert your favored domain of phenomena or inquiry here]
The idea is to engage in a bit of a reverse engineering exercise. We know that the earliest phenotype ontologies came out of the model organism community – what Nelson & Platnick (1981) might refer to as “general biology” (pages 4-5). Yet systematists tend to ask comparative questions. What (if any) general structures, entities, and relationships do these comparative/phylogenetic questions entail? Which kinds of inferences are we (most) interested in? How would the components needed to accommodate the inferences be fruitfully translated into a logic framework?
In other words, let’s pretend we are well advised to engage in some conceptual modeling for the future design of a Coleoptera Anatomy Ontology (which may not carry such a name in the end). Start with nailing down our most highly domain-specific questions. Abstract overarching design needs from these. Pretend that solutions will follow.
The first, fleshed out use case of the Euler/X project was published yesterday in PLoS ONE. This paper is a companion to the phylogenetic revision of the acalyptine weevil genus Perelleschus sec. Franz & Cardona-Duque (2013), and translates the 54 taxonomic concepts and 75 RCC-5 articulations provided in that paper into 13 logically consistent alignments and visualizations, with additional inferred articulations.
Franz, N.M., M. Chen, S. Yu, P. Kianmajd, S. Bowers & B. Ludäscher. 2015. Reasoning over taxonomic change: exploring alignments for the Perelleschus use case. PLoS ONE 10(2): e0118247. doi:10.1371/journal.pone.0118247. Available on-line here.
Very glad to see this one published; at the same time there are other use case papers in the pipeline (Andropogon, Primates). The particular motivation for this paper was to resolve sets of several small-scale yet taxonomically and phylogenetically complex input trees with the RCC-5 concept alignment approach and Euler/X toolkit. The paper is written in a “how to?” style, successively exploring and explaining the connections between the user-provided input constraints and the over-, under-, or well-specified reasoning outcomes. It deals with issues of logical consistency, input sufficiency, ambiguity, and alternative ways to align (parent) concepts in reference to either (1) their intensionally circumscribed properties (which may include synapomorphies) or (2) the ostensively indicated members. This corresponds to the program outlined in Franz & Thau (2010).
One reviewer wrote: “With an exceptionally suited use case, the complexity of taxonomic reasoning and its translation to machine processing are depicted in unprecedented form.” Our ultimate goal is to develop a widely applicable reference and linkage system for taxonomic products that human users create but which is actually optimized for computational processing – without compromising the Linnaean system whose services to humans are profoundly valuable.
If it were that kind of semester, maybe it would be neat to summarize our thoughts on all the ways in which last week’s paper – one of the theoretical foundations of the OBO Foundry approach – was puzzling to us. But, so far it isn’t (that kind of semester). Just three thoughts then.
1. Many of us seem to want to be realists.
2. Whatever the merits of the theory, implementation matters too. The two need not always be entirely and reciprocally consistent. (that is putting things mildly)
3. Consider this statement by Smith (2004), top of page 79 in the publisher paper.
“Good ontologies are reality representations, and the fact that such representations are possible is shown by the fact that, as is documented in our scientific textbooks, very many of them have already been achieved, though of course always only at some specific level of granularity and to some specific degree of precision, detail and completeness.”
I think it is fair to say that this statement leaves room for both the empiricist and the realist acknowledging the importance of theories and concepts in science while not elevating them a priori to a level where they are either unassailably reliable or misguided. It is a sensible enough statement to make. Strangely, to my thinking at least, Smith takes this statement to work as something of a wedge between reality- and concept-based ontology design maxims. But the statement itself speaks more to the notion of reality (which by the way remains under-defined) and concepts being intertwined in scientific advancement. Whatever else may be said here, we concluded that following his outlined path does require ‘a strong ontological commitment’. I doubt that this message has been received and ratified by most practitioners.
Anyway, onto to more practical issues; up this week:
Seltmann, K., M. Yoder, I. Miko, M. Forshage, M. Bertone, D. Agosti, A. Austin, J. Balhoff, M. Borowiec, S. Brady, G. Broad, D. Brothers, R. Burks, M. Buffington, H. Campbell, K. Dew, A. Ernst, J. Fernandez-Triana, M. Gates, G. Gibson, J. Jennings, N. Johnson, D. Karlsson, R. Kawada, L. Krogmann, R. Kula, M. Ohl, C. Rasmussen, F. Ronquist, S. Schulmeister, M. Sharkey, E. Talamas, E. Tucker, L. Vilhelmsen, P. Ward, R. Wharton & R. Deans. 2012. A hymenopterists’ guide to the Hymenoptera Anatomy Ontology: utility, clarification, and future directions. Journal of Hymenoptera Research 27: 67-88. Available on-line here.