to find clades on phylogenetic trees? ✤ Could we design a system flexible enough to match many different kinds of phyloreferences? ✤ Could we create a test set of phyloreferences and their expected matches for testing our software and others?
classes based on definitions. ✤ e.g. A Maharashtrian is a Person who was born in the Indian state of Maharashtra. ✤ Uses OWL Reasoners to infer unknown facts from known facts.
of a Node that: ✤ :has_Descendant :Campanula_latifolia Descendants of the ancestors of Campanula latifolia that exclude the ancestors of Lobelia cardinalis
of a Node that: ✤ :has_Descendant :Campanula_latifolia ✤ :excludes_lineage_to :Lobelia_cardinalis Descendants of the ancestors of Campanula latifolia that exclude the ancestors of Lobelia cardinalis
of a Node that: ✤ :has_Descendant :Campanula_latifolia ✤ :has_Child :Campanula_latifolia ✤ :excludes_lineage_to :Lobelia_cardinalis Descendants of the ancestors of Campanula latifolia that exclude the ancestors of Lobelia cardinalis
of a Node that: ✤ :has_Descendant :Campanula_latifolia ✤ :has_Child :Campanula_latifolia ✤ :has_Child [:has_Child :Campanula_latifolia] ✤ :excludes_lineage_to :Lobelia_cardinalis Descendants of the ancestors of Campanula latifolia that exclude the ancestors of Lobelia cardinalis
of a Node that: ✤ :has_Descendant :Campanula_latifolia ✤ :has_Child :Campanula_latifolia ✤ :has_Child [:has_Child :Campanula_latifolia] ✤ :has_Child [:has_Child [:has_Child :Campanula_latifolia]] ✤ :excludes_lineage_to :Lobelia_cardinalis Descendants of the ancestors of Campanula latifolia that exclude the ancestors of Lobelia cardinalis
of a Node that: ✤ :has_Descendant :Campanula_latifolia ✤ :has_Child :Campanula_latifolia ✤ :has_Child [:has_Child :Campanula_latifolia] ✤ :has_Child [:has_Child [:has_Child :Campanula_latifolia]] ✤ … ✤ :excludes_lineage_to :Lobelia_cardinalis Descendants of the ancestors of Campanula latifolia that exclude the ancestors of Lobelia cardinalis
of a Node that: ✤ :has_Descendant :Campanula_latifolia ✤ :excludes_lineage_to :Lobelia_cardinalis ✤ Either :has_Sibling :Lobelia_cardinalis Descendants of the ancestors of Campanula latifolia that exclude the ancestors of Lobelia cardinalis
of a Node that: ✤ :has_Descendant :Campanula_latifolia ✤ :excludes_lineage_to :Lobelia_cardinalis ✤ Either :has_Sibling :Lobelia_cardinalis ✤ Or :has_Sibling that :has_Descendent :Lobelia_cardinalis Descendants of the ancestors of Campanula latifolia that exclude the ancestors of Lobelia cardinalis
of a Node that: ✤ :has_Descendant :Campanula_latifolia ✤ :excludes_lineage_to :Lobelia_cardinalis Descendants of the ancestors of Campanula latifolia that exclude the ancestors of Lobelia cardinalis
converting phylogenies to logical statements. ✤ Ontologies to make these relationships simple and clear. ✤ Defining terms like excludes_lineage_to so you don’t have to.
converting phylogenies to logical statements. ✤ Ontologies to make these relationships simple and clear. ✤ Defining terms like excludes_lineage_to so you don’t have to. ✤ Web application and web service to make phyloreferences quick and easy to use.
converting phylogenies to logical statements. ✤ Ontologies to make these relationships simple and clear. ✤ Defining terms like excludes_lineage_to so you don’t have to. ✤ Web application and web service to make phyloreferences quick and easy to use. ✤ Testing to ensure that phyloreferences match the correct nodes on the tree.
tree based on phyloreferences expressed in OWL. ✤ But can we make them work fast, through easy-to-use websites and over web services? ✤ Continuous testing will make sure that all existing phyloreferences continue to work in the future.
tree based on phyloreferences expressed in OWL. ✤ But can we make them work fast, through easy-to-use websites and over web services? ✤ Continuous testing will make sure that all existing phyloreferences continue to work in the future. ✤ We need you to submit useful phyloreferences and tricky phylogenies, to complain about phyloreferences that don’t make sense to you, and to use our infrastructure to identify clades in your datasets.
other projects funded by NSF’s GoLife program to obtain large phylogenies, gather sources for meaningful phyloreferences, and develop phyloreferencing proof-of-concept applications for these. These applications will include aggregating trait and other domain-relevant data.” ✤ “Strong background in Systematic Biology required. You should be well versed in all aspects of theoretical phylogenetics and related topics.” ✤ http://www.phyloref.org/blog/2016/10/postdoc2-ad/
originating with the most recent common ancestor of Campanula latifolia Linnaeus 1753 and all extant organisms or species that share a more recent common ancestor with Campanula latifolia than with Roussea simplex J. E. Smith 1789, Pentaphragma ellipticum Poulsen 1903, or Stylidium graminifolium Swartz ex Willdenow 1805. Campanuloideae The clade originating with the most recent common ancestor of Campanula latifolia Linnaeus 1753, Wahlenbergia linifolia A. de Candolle 1830, and Platycodon grandiflorus (Jacquin) A. de Candolle 1830.
B B C C C Last common ancestor of B and C X Last ancestor of B that is not an ancestor of A Last ancestor of B that exhibits apomorphy X The clade originating with:
gaurav
bob3bob3
sshimizu2006
nagano
gully
andreamrau
genomethica
thomaselove
sansan_randd
siddroid
fr0gger
mprove
afnizarnur
roundedbygravity
matthewcrist
chrisshort
keithpitt
tammielis
chriscoyier
tmm1
samlambert
dougneiner
colly
sonatard
