Computable evolutionary phenotype knowledge: a hands-on workshop

September 29, 2017

Call for Participation:

Computable evolutionary phenotype knowledge: a hands-on workshop

The Phenoscape project is hosting a hands-on workshop on Dec 11-14, 2017, at Duke University in Durham, North Carolina.

Evolutionary phenotype data that is amenable to computational data science, including computation-driven discovery, remains relatively new to science. Therefore use-cases and applications that effectively exploit these new capabilities are only beginning to emerge. If you are interested in discovering, linking to, recombining, or computing with machine-interpretable evolutionary phenotypes, this is the workshop for you!

The event will bring together a diverse group of people to collaboratively design and work hands-on on targets of their interest that take advantage and promote reuse of Phenoscape’s online evolutionary data resources and services. The event is designed as a hands-on unconference-style workshop. Participants will break into subgroups to collaboratively tackle self-selected
work targets.

The full Call for Participation, including motivation and scope, is posted here:

To apply to participate in the event, please fill out the application form by Oct 9, 2017. Travel sponsorship is available but limited, as is space.

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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Phenoscape poster at Evolution 2014

August 27, 2014

I attended the Evolution 2014 meeting a few months ago in Raleigh, NC, and presented a poster on Phenoscape’s curation effort: “Moving the mountain: How to transform comparative anatomy into computable anatomy?”, with coauthors A. Dececchi, N. Ibrahim, H. Lapp, and P. Mabee. In this work, we assessed the efficiency of our workflow for the curation of evolutionary phenotypes from the matrix-based phylogenetic literature. We identified the bottlenecks and areas of improvement in data preparation, phenotype annotation, and ontology development. Gains in efficiency, such as through improved community data practices and development of text-mining tools, are critical if we are to translate evolutionary phenotypes from an ever-growing literature. The poster was well received and several researchers at the meeting were interested in learning more about open source tools for phenotype annotation.

Report from Tucson: from characters to annotations with text mining

March 30, 2013

There is a wealth of phenotypic information in the evolutionary literature that comes in the the form of semi-structured character state descriptions. To get that information into computable form is, right now, an awfully slow process. In Phenoscape I, we estimated that it took about five person-years in total to curate semantic phenotype anphenowordcloudnotations from 47 papers. If we are to get computable evolutionary phenotypes from a larger slice of the literature, we really need to figure out ways to speed this up.

One promising approach is to use text-mining.  This could contribute in a few different ways.  First, one could efficiently identify all the terms in the text that are not currently represented in ontologies and add them en masse, so that data curation does not have to stop and resume whenever such terms are encountered. Second, one could present a human curator with suggestions for what terms to use and what relations those terms have to one another, speeding the process of composing an annotation.

CharaParser, developed by Hong Cui at the University of Arizona, is an expert-based system that decomposes character descriptions into recognizable grammatical components, and it is now being used in several different biodiversity informatics projects. Baseline evaluation results from BioCreative III showed that a naive workflow combining CharaParser and Phenex, the software curators use to compose ontological annotations and relate them to character states, was capable of identifying candidate entity and quality phrases (it outperformed biocurators by 20% in recall on average) but had difficulty translating those into ontological annotations.  This first iteration workflow also was not yet reducing curation time.

In March, a small contingent from NESCent (Jim Balhoff, Hilmar Lapp and Todd Vision) visited Hong Cui’s group in Tucson. We talked through improvements to CharaParser and the curation workflow, brainstormed plans for a more thorough set of evaluation tests, began refactoring of the code so that it can be more easily shared across projects, and gained a better understanding of what features make a character difficult to curate for humans vs. text-mining.  We made substantial progress on all fronts, and are looking forward to seeing how much improvement in the accuracy and efficiency of curation will be achieved in the next round of testing.

We are also pleased to report that the CharaParser codebase will now be available from GitHub under an open source (MIT) license.

Phenex 1.6 released

October 10, 2012

Phenex 1.6 has been released. Updates:

  • Support for entry of polymorphic values in matrix cells (documentation).
  • Improvements to the tab-delimited export format.

Download for Mac, Windows, or Unix.

DILS 2012

August 28, 2012

In June I had the opportunity to attend DILS 2012 (Data Integration in the Life Sciences), at the University of Maryland in College Park. I presented a poster on Phenoscape, “The Phenoscape Knowledgebase: Integrating phenotypic data across taxonomy, from biodiversity to developmental genetics”. The poster highlighted some of the new directions the Phenoscape project is heading, such as broadening taxonomic coverage and adoption of semantic web technologies. DILS was a small conference but had several talks discussing the applications of ontologies to biological data. I’m looking forward to DILS 2013 in Montreal, in conjunction with ICBO and the Canadian Semantic Web conference.

Phenex 1.4.2 released

August 16, 2012

A new bugfix release of Phenex is available. Phenex 1.4.2 addresses the following issues: