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Posts from the ‘Weekly Discussion’ Category

Weekly reading: Adding a little reality to building ontologies for biology

We are moving from practical designs and implementations of ontologies in systematics to design theory. One issue to understand, or least have an intuitive position on, is the strength of the interaction or interdependency between ontology design and functionality. And “design” could reach as far up the chain of representation as “why Description Logics and not another flavor of logic?” The term “Realism” plays a role. About five years ago there was a fairly spirited debate on this topic, reviewed here. We are reading one paper from the longer list.

Lord, P. & R. Stevens. 2010. Adding a little reality to building ontologies for biology. PLoS ONE 5(9): e12258. Available on-line here.

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:

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.

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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Weekly reading: Why more sequences are not enough

Momentarily the last item in our semester-long NGS and phylogenomic analyses reading sequence. Phenomics (and ontologies) will be on the continuing menu, soon enough.

Philippe, H., H. Brinkmann, D.V. Lavrov, D.T.J. Littlewood, M. Manuel, G. Wörheide & D. Baurain. 2011. Resolving difficult phylogenetic questions: Why more sequences are not enough. PLoS Biology 9(3): e1000602. Available on-line here.

New course – Spring 2015: Current topics in systematics

Short announcement – we will continue our now formally offered Weekly Discussion sessions during the Spring 2015 Semester, in the format of a 1-credit “Current Topics in Systematics” seminar/course with a double billing as either BIO 494 (undergraduate level) or EVO 598 (graduate level). Wednesdays, 12:00 – 1:00 pm, seminar room pending. Ontologies and reasoning are part of the envisioned themes to explore. Hoping for good turnout and discussions. ASU’s Course Catalogue is available on-line here.