Tree of life and data integration challenges at the first FuturePhy workshop

April 6, 2016

What are the challenges in building, visualizing and using the Tree of Life? How can we best utilize and build on existing phylogenetic knowledge and look ahead to address the challenges of data integration? Recently, fellow Phenoscaper Jim Balhoff and I attended the first FuturePhy workshop in Gainesville, Florida (February 20-22, 2016). The workshop brought together three taxonomically-defined working groups (catfish, beetles, barnacles) to build megatrees from existing phylogenetic studies, and identify and begin applying diverse data layers for their respective groups. Open Tree and Arbor personnel were on hand discuss and help solve issues in data integration.

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New article on the Teleost Anatomy Ontology published in Systematic Biology

March 30, 2010

We are pleased to announce the publication of the article “The Teleost Anatomy Ontology: Anatomical Representation for the Genomics Age” in Systematic Biology.  The paper describes how we developed this multispecies anatomy ontology for the annotation of systematic characters, and general solutions to various challenges in representing anatomical structures across a diverse clade of fishes.

Open access links to online versions of the paper are given below:

Wasila M. Dahdul; John G. Lundberg; Peter E. Midford; James P. Balhoff; Hilmar Lapp; Todd J. Vision; Melissa A. Haendel; Monte Westerfield; Paula M. Mabee.  2010.  The Teleost Anatomy Ontology: Anatomical Representation for the Genomics Age.  Systematic Biology.  View full text or download PDF.

New fossil tells how piranhas got their teeth

August 16, 2009

A recent publication on Megapiranha paranensis from Phenoscape curators Wasila Dahdul and John Lundberg is in the news!

click for full-zise image

DURHAM, N.C. — How did piranhas — the legendary freshwater fish with the razor bite — get their telltale teeth? Researchers from Argentina, the United States and Venezuela have uncovered the jawbone of a striking transitional fossil that sheds light on this question. Named Megapiranha paranensis, this previously unknown fossil fish bridges the evolutionary gap between flesh-eating piranhas and their plant-eating cousins. Read the rest of this entry »

Teleost Anatomy Ontology (TAO) working again on the NCBO Bioportal

May 18, 2008

Searching as well as visualizing the Teleost Anatomy Ontology (TAO) on the NCBO Bioportal was broken for more than a week but has been fixed since Friday.

The other good update from the Bioportal development is that terms can now be found by their synonyms as well. For example, try searching TAO for the ‘dermosphenotic’, which at present isn’t the name of a term in the ontology. Instead, you get the ‘infraorbital 5‘, for which dermosphenotic is a synonym.

Fish morphologists will note that this is actually problematic, since in reality the dermosphenotic is the synonym for the last infraorbital bone. In zebrafish, with which we seeded the TAO, this is indeed the 5th in the series of infraorbitals, but in other clades of teleosts it is the 6th or yet another one. But that’s another story, which we’ll highlight in a forthcoming post on building the TAO.

The Teleost Taxonomy Ontology

May 14, 2008

One of the two main ontologies developed and used by the Phenoscape project is the Teleost Taxonomy Ontology (TTO). Although the Phenoscape project is focused on the Ostariophysi, the TTO covers not just teleosts, but all the species listed in Bill Eschmeyer’s Catalog of Fish. This post will discuss how the current TTO was constructed and the work flow we use to update it. A later posting will discuss the effort to update the ontology to better represent current thinking about metaphysical status of species and other taxonomic terms.

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Teleost Anatomy and Taxonomy Ontologies on-line at the NCBO BioPortal

January 31, 2008

The Teleost Anatomy Ontology (TAO) and the Teleost Taxonomy Ontology (TTO) are finally on-line and searchable on the NCBO BioPortal.

The ontologies were deposited into the OBO versioning system already in November, but a database loading problem prevented their functioning in the BioPortal browser earlier.