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Posts tagged ‘phenotype’

Thoughts: Bio-ontologies with only minimal predetermined relations

Time for some reflection on this (2015) Spring’s Weekly Discussion on Phenotype ontologies – origins, theory, applications, prospects, and challenges. It gets to be a little (and intentionally) provocative (as opposed to very carefully thought out) towards the end.

We started off three months ago with Daduhl et al. 2010, who provide an inspiring vision on the subject (page 370):

“The application of ontologies to systematics has the potential to force clarification and improve communication about morphological character diversity across taxonomic domains. As a result, ontologies could extend the applicability and level of universality of characters for phylogenetic analysis and improve the knowledge of evolutionary transformations. These computable vocabularies could enable efficient computer processing of vast amounts of data and allow the exploration and aggregation of data across studies that is currently difficult to do in morphology-based phylogenetics.”

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What might we (systematists) want out of phenotype ontologies

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.”

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Weekly reading: Ramirez et al. on structural complexity in ancestral ontologies (again)

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.

Weekly reading: Balhoff et al. on a semantic model for wasp species description

Following Daduhl et al. and Vogt et al., our third paper in the phenotype ontologies Weekly Discussion series will dive into an applied example by Balhoff and co-authors (mainly of the Deans Lab) with a clear taxonomic emphasis. Already we have seen that different scientific orientations draw on phenotype ontologies with the expectation of reframing and solving specific problem complexes.

Daduhl et al.‘s focus was firmly within the bounds of evolutionary and phylogenetic analyses of phenotypes across broader and deeper taxonomic scales. Implementation challenges notwithstanding, there was an underlying agreement that the legacy of phenotype-centric systematic work could be appropriated towards the outlined representation and inference goals.

Vogt et al., in turn, emphasized a need for consistent, machine-processable standards with regards to phenotype syntactics, semantics, etc.; including a separation of descriptive and evolutionary/explanatory elements in our morphological terminology. This has the makings of a potentially divergent paradigm in relation to Daduhl et al.‘s program and perspective.

Another interesting development is the Phenoscape team’s exploration of homology relations in ontologies, outlined here: http://phenoscape.org/wiki/Reasoning_over_homology_statements.

In light of these different lines of research, we set ourselves two immediate questions to address:

1. What are actual applications that utilize phenotype ontologies and (optionally) reasoning for (a) multi-taxon studies with (b) an evolutionary/systematic orientation?

2. Suppose we had the “awesome ontology & reasoning” infrastructure on hand, where current technological limits no longer apply. What kinds of questions would  we ask this infrastructure to solve for us (that cannot be addressed otherwise)?

The paper for next week applies directly to these questions.

Balhoff, J.P., I. Mikó, M.J. Yoder, P.L. Mullins & A.R. Deans. 2013. A semantic model for species description applied to the ensign wasps (Hymenoptera: Evaniidae) of New Caledonia. Systematic Biology 62: 639–659. Available on-line here.

New publication: Finding our way through phenotypes

Three members of the taxonbytes lab (Sal Anzaldo, Nico Franz, and former postdoc Aaron Smith) are co-authors of a new paper published in PLoS Biology: Finding Our Way through Phenotypes. Lead authors (in a large community effort) are Andrew Deans, Paula Mabee, and members of the Phenotype Research Coordination Network.

Deans, A.R. et al. (73 co-authors, including S.S. Anzaldo, N.M. Franz & A.D. Smith). 2015. Finding our way through phenotypes. PLoS Biol 13(1): e1002033. Link to publication

Abstract. Despite a large and multifaceted effort to understand the vast landscape of phenotypic data, their current form inhibits productive data analysis. The lack of a community-wide, consensus-based, human- and machine-interpretable language for describing phenotypes and their genomic and environmental contexts is perhaps the most pressing scientific bottleneck to integration across many key fields in biology, including genomics, systems biology, development, medicine, evolution, ecology, and systematics. Here we survey the current phenomics landscape, including data resources and handling, and the progress that has been made to accurately capture relevant data descriptions for phenotypes. We present an example of the kind of integration across domains that computable phenotypes would enable, and we call upon the broader biology community, publishers, and relevant funding agencies to support efforts to surmount today’s data barriers and facilitate analytical reproducibility.

Weekly reading: Daduhl et al. on the Teleost Anatomy Ontology

Last semester’s Weekly Discussion series dealt with Next Generation Sequencing technologies and related informatics challenges and advances. A review of what we read and discussed remains pending. Meanwhile we have selected a topic for the coming Spring 2014 semester:

Phenotype ontologies – origins, theory, applications, prospects, and challenges.

As usual we will place an emphasis on the utility of ontology-centered approaches for systematics – phylogenetics, taxonomy – in particular. The series starts off with a helpful paper that covers a lot of ground and is closely aligned with the OBO Foundry community.

Dahdul, W.M., J.G. Lundberg, P.E. Midford, J.P. Balhoff, H. Lapp, T.J. Vision, M.A. Haendel, M. Westerfield & P.M. Mabee. 2010. The teleost anatomy ontology: anatomical representation for the genomics age. Systematic Biology 59: 369-383. Available on-line here.

Knowledge Representation in Systematic Biology – Edited book proposal seeking comments, contributions

I have an opportunity to edit a new book in the series “Species and Systematics” (originally UC Press; now CRC Press). The draft outline is below, but is subject to change and expansion as deemed appropriate.

I am looking for suggestions, and for potential contributors (naturally, while reserving standard/common sense rights to kindly accept or decline). The book will to collect a number of strong, diverse chapters on various projects and directions in this still very young field. Lead authors of chapters will coordinate with co-authors as preferred. I also intend to give authors much freedom to do and say things they maybe could not express using different publication outlets (while keeping things fair and high-minded).

Another key issue is (of course) – who may have time and motivation to contribute an original and impactful chapter in the coming six months? Either way, I am open to suggestions, contact me on- or off-line.

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