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Minimum Information About a Phylogenetic Analysis (MIAPA) vocabularies and tools
http://www.evoio.org/wiki/MIAPA
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How to express that a tree is ultrametric, and how it was made ultrametric? #19

Open hlapp opened 10 years ago

hlapp commented 10 years ago

There more context on the underlying use-case in ropensci/RNeXML#26. The relevant excerpt from the thread, quoting @cboettig:

Many of the phylogenetic methods in R that I am familiar with require ultrametric trees. Some of these are time-calibrated using fossils, others just using heuristic methods. It would be most valuable to annotate that a tree has been time-calibrated and what the units (and possible uncertainty, which may be a branch-level annotation) are on the branch lengths. It would also be useful to annotate the method in which a tree has been time-calibrated, as well as the method with which it has been generated. (Imagine a user wants to select from a library of nexml files only those trees produced by MrBayes, or exclude trees generated by phylomatic, or access only truly time calibrated trees). In some cases the mechanism of the calibration might be documented -- e.g. if tree was made ultrametric with the R function 'chronopl', and what parameter value was used for that calibration).

I haven't been able to stumble across the ontological vocabulary for any of this, e.g. one might hope to express this as:

<meta property="phylogeny-from", content="MrBayes", datatype = "xsd:string" xsi:type="LiteralMeta">
<meta href="path/to/Script/for/MrBayes/run" rel="script" xsi:type="ResourceMeta">
<meta property="ultrametric" content="true" datatype = "xsd:boolean" xsi:type="LiteralMeta">
<meta property="calibration-method" content="ape::chronopl", datatype = "xsd:string" xsi:type="LiteralMeta">    
<meta property="calibration-method-parameter" content="lambda" datatype = "xsd:string" xsi:type="LiteralMeta">
<meta property="calibration-method-parameter-value", content="1.2" datatype = "xsd:long" xsi:type="LiteralMeta">

etc etc. Clearly these triples could be much more logically constructed ; but I'm not trying to propose an onotology, just looking for existing terms. Just haven't found them.