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Posts tagged ‘analysis’

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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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.

Weekly reading: RADICAL – Random Addition Concatenation Analysis

An interesting paper and powerful tool that cuts empirically through the longstanding and somewhat dispiriting total evidence ‘versus’ partitions discussion thread in our field.

Narechania, A., R.H. Baker, R. Sit, S.O. Kolokotronis, R. DeSalle & P.J. Planet. 2012. Random Addition Concatenation Analysis: A novel approach to the exploration of phylogenomic signal reveals strong agreement between core and shell genomic partitions in the Cyanobacteria. Genome Biology and Evolution 4(1): 30-43. Available on-line here.