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Right now this is contained in nexml2cdao.xsl, which is less than desirable for several reasons:
1. It's in an obscure location not readily discovered from the normative documents of the standard.
2. …
hlapp updated
10 years ago
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Code to reproduce the bug with error log:
```R
> library("tidyverse")
> library("RNeXML")
Loading required package: ape
> library("treeio")
Attaching package: ‘treeio’ The following o…
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MIAPA has a clear annotation to indicate that a character matrix in a nexml file (`characters` element) contains an alignment that was used to generate the phylogeny. Character matrices are frequentl…
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As mentioned [in the wiki](https://github.com/TreeViz/metastyle/wiki/TreeSS-expressions) TSS is planned to support expressions that format elements of a tree depending on the values of annotations in …
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I understand that GEXF's design is mostly done around Gephi, nonetheless, it may be a good idea to try to keep track of other Graph XML formats providing similar support. This could bring ideas about …
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The `test_publish.R` code is wrapped in `if(0)`, i.e., it's never run. That's bad in multiple ways, one of which is that it's not even reported as a test that's being skipped even though effectively …
hlapp updated
5 years ago
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Thanks to @calliem's work, a curator will have the ability to pre-fill EQ annotations in Phenex from a named entity recognition service. Many times, these will need subsequent manual adjustment by the…
hlapp updated
8 years ago
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It would be useful to compute existential relation graphs for the core bio-ontologies. Some background is here: https://github.com/NCI-Thesaurus/thesaurus-obo-edition/wiki/NCIt-graph-queries
I have…
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`ami-phylo` will run from the commandline and should, as far as possible, manage options from there. Please list here the options that should be part of the commandline.