An Ontology-Based System for Querying Life in a Post-Taxonomic Age

<p>Grant proposal (project description and references cited) to the US National Science Foundation, Advances in Biological Informatics (ABI) program as Collaborative Research. Funded in 2015. Files include public abstract as submitted to NSF.  </p

Nuclear gene trees - reduced_8_taxa

Single .tre file containing all 130 nuclear gene trees reduced to 8 major lineages. Inferred using RAxML

Nuclear_alignments_130genes_paralogs_remov_rogue_remov

Concatenated alignment (.phy format) of 130 orthologous nuclear genes. Rogue taxa removed

Mesquite file

Nexus file with the list of 1018 species native to LVV and their occurrence coded on a standard matrix. Both MP and ML trees included, both Stochastic and MP mappings activated accordingly

trouble_w_triples-master

A zip file containing the scripts used to analyze a large dataset of identifiers from different systems - VertNet, BOLD and Genbank. The identifiers are also provided

A schematic representation showing proportional numbers of Darwin Core Triplets – represented as different sized ellipses - across repositories and the overlap between them.

<p>The inset shows the overlap regions in more detail. The numbers associated with each repository and areas of overlap are for all types of matches, not just triplet-to-triplet matches. The percentages represent the number of matches between two (or three repositories) divided by shared triples in the smallest of the two (or three) polygons.</p

Summary of DwC Triplets per repository.

<p>A canonical DwC Triplet is a triplet that is complete and conforms to standard representation. A “Coerced” DwC Triplet is one that is either missing a part of the triplet (e.g., a collection code) or in a non-standard syntax.</p><p>Summary of DwC Triplets per repository.</p

RAxML_bestTrees_genetrees

Single .fasta file containing all 518 nuclear gene trees inferred using RAxML

Nuclear_alignments_518genes

Concatenated alignment (.phy format) of 518 orthologous nuclear genes

Molecular module.

<p>Data can be entered in each tab or through the matrix view. Each cell is interactive and linked to GenBank if a number is provided or when sequences are directly imported from GenBank. Data is exported into fasta files. Alignments and primer information can be stored for sharing and future repurposing.</p