From 9b68e449bc57185b8e2b36f52026bee50f92f27c Mon Sep 17 00:00:00 2001 From: Hilmar Lapp Date: Fri, 1 Feb 2013 11:11:40 -0700 Subject: [PATCH] Removed SILVA (#9), added parsimony algorithm (#7), created a class for a set of trees (and networks) (#10), and added operation for pruning and grafting (#11). --- ontology/miapa.owl | 101 +++++++++++++++++++++++++++++++--- ontology/miapa_no-imports.owl | 101 +++++++++++++++++++++++++++++++--- 2 files changed, 184 insertions(+), 18 deletions(-) diff --git a/ontology/miapa.owl b/ontology/miapa.owl index 7c56423..f633e9b 100644 --- a/ontology/miapa.owl +++ b/ontology/miapa.owl @@ -295,6 +295,15 @@ + + + + Phylogenetic tree construction (method centric) + + + + + @@ -518,15 +527,6 @@ Alternatively, we could model this as dc:isPartOf some prov:Plan. - - - - SILVA - - - - - @@ -599,6 +599,89 @@ Alternatively, we could model this as dc:isPartOf some prov:Plan. + + + + Parsimony method + + A method for finding the minimum transitions to account for a character given a phylogenetic tree, and by extension, a character-based phylogeny inference method in which the inferred phylogenetic tree (the "maximum parsimony tree") is the phylogenetic tree that minimizes evolutionary transitions over all characters. + Prosdocimi, Francisco, Brandon Chisham, Enrico Pontelli, J.D. Thompson, and Arlin Stoltzfus. 2009. “Initial Implementation of a Comparative Data Analysis Ontology.” Evolutionary Bioinformatics Online (5): 47–66. http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2747124/ + https://www.nescent.org/wg_evoinfo/Concept_Glossary#Parsimony_Method + + + + + + + + Phylogenetic tree construction (pruning and grafting) + + Phylogenetic tree construction that prunes and grafts a collection of one or more source trees to create the resulting tree. + Hilmar Lapp + + + + + + + + SetOfNetworks + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + SetOfTrees + + + + + + + + + + + + + + + + + + + + + + + + + + diff --git a/ontology/miapa_no-imports.owl b/ontology/miapa_no-imports.owl index 657d5c1..42787a8 100644 --- a/ontology/miapa_no-imports.owl +++ b/ontology/miapa_no-imports.owl @@ -293,6 +293,15 @@ + + + + Phylogenetic tree construction (method centric) + + + + + @@ -516,15 +525,6 @@ Alternatively, we could model this as dc:isPartOf some prov:Plan. - - - - SILVA - - - - - @@ -597,6 +597,89 @@ Alternatively, we could model this as dc:isPartOf some prov:Plan. + + + + Parsimony method + + A method for finding the minimum transitions to account for a character given a phylogenetic tree, and by extension, a character-based phylogeny inference method in which the inferred phylogenetic tree (the "maximum parsimony tree") is the phylogenetic tree that minimizes evolutionary transitions over all characters. + Prosdocimi, Francisco, Brandon Chisham, Enrico Pontelli, J.D. Thompson, and Arlin Stoltzfus. 2009. “Initial Implementation of a Comparative Data Analysis Ontology.” Evolutionary Bioinformatics Online (5): 47–66. http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2747124/ + https://www.nescent.org/wg_evoinfo/Concept_Glossary#Parsimony_Method + + + + + + + + Phylogenetic tree construction (pruning and grafting) + + Phylogenetic tree construction that prunes and grafts a collection of one or more source trees to create the resulting tree. + Hilmar Lapp + + + + + + + + SetOfNetworks + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + SetOfTrees + + + + + + + + + + + + + + + + + + + + + + + + + +