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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.

ICE 2016 Orlando Symposium proposal – Building the Biodiversity Knowledge Graph for Insects

Calls are going out currently to submit Symposium proposals for the XXV International Congress of Entomology (ICE 2016) in Orlando. Here is the summary for one such proposal led by Nico Franz and Katja Seltmann and intended for the category: Biodiversity, Biogeography and Conservation Biology. If you would like to contribute as potential speaker to this Symposium proposal, please contact Nico Franz (s0on).

Title: Building the Biodiversity Knowledge Graph for Insects – Components, Progress, Challenges.
Presentation Type: Combination Oral and Poster Presentations.

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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.

Accessioning a Donation: Part 2

Continuing from Part 1, this post documents the ongoing process of accessioning a large donation corresponding to the Ira Nadborne insect collection. Having frozen all donated material for an entire week, we can now safely sort through the specimens and curate them into our main collection. The first part of this journey is to determine which specimens we are keeping, and to move them out of their dermestid frass-filled boxes.

ira_nadborne_scarabs

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Weekly reading: NGS technology and inference challenges in review

Summary of Weekly Discussion papers read last semester (Fall 2014) on Next-Generation Sequencing methods and related phylogenomic inference challenges. With a few diversions in between. In chronological sequence.

  1. Barker. 2014. Philosophy of statistical phylogenetic methods.
  2. Witteveen. 2014. Naming and contingency: the type method of biological taxonomy.
  3. Lemmon & Lemmon. 2013. High-throughput genomic data in systematics and phylogenetics.
  4. Mardis. 2013. Next-Generation Sequencing platforms.
  5. Bybee et al. 2011. Targeted Amplicon Sequencing.
  6. Lemmon et al. 2012. Anchored Hybrid Enrichment.
  7. Kumar et al. 2012. Statistics and truth in phylogenomics.
  8. Wright & Hillis. 2014. Bayesian analysis outperforms parsimony for morphological data.
  9. Nguyen et al. 2012. Intermittent evolution and robustness of phylogenetic models.
  10. Schwartz et al. 2014. SISRS – Site Identification from Short Read Sequences.
  11. Narechania et al. 2012. RADICAL – Random Addition Concatenation Analysis.
  12. Philippe et al. 2011. Why more sequences are not enough.

We had some fun discussions. Topic for Spring 2015: Phenotype Ontologies.

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.

Systematics today: Why study comparative (insect) morphology

A New Year’s post whose motivation derives in part from an engaging discussion of a paper by Wright & Hillis 2014 we had during the past Fall semester. As I recall, we concurred that the paper was adequately executed in terms of running from premises to methods to conclusions. But we also thought (well, at least some of us) that it is yet another part of an unfortunate legacy in our field that tends to separate issues of ‘generating good evidence’ from issues of ‘identifying the right method of inference’. Lots of simulations were carried out when the matrix and characters in question were taken as is and essentially invisible.

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