The goal is to broadly disseminate information to the larger scientific community regarding phenotype ontologies and their utility and involve new participants in the RCN.

Consider submitting an application. Any questions about opportunities offered by the Phenotype RCN should be directed to Paula Mabee (Paula.Mabee@usd.edu), Eva Huala (huala@acoma.stanford.edu), or Andy Deans (adeans@gmail.com).

The next NCBO Webinar will be presented by James Malone from the European Bioinformatics Institute on “Ontology Driven Annotation, Integration and Analysis of Gene Expression Data” at 10:00am PDT, Wednesday, May 15.

Archiving, integrating, and adding semantic value to high-throughput gene-expression data present major challenges in bioinformatics. The data are both diverse, covering many species, disease, and tissue types, and the annotations need to be detailed enough to capture complex experimental nuance relating to experimental process and biology. The main challenges in annotating such data lie in identification of suitable ontologies, consistent application of ontologies to the data in the context of annotation tools, provision of context specific views of existing ontologies for query, and development of automated annotation pipelines to support curators. We describe in this talk our progress in addressing these challenges, specifically: the development of tools to help build ontologies for applications, the development of a linked data repository of annotation knowledge and the publication of our gene expression database as RDF linked data, connecting our ontology annotations to the data. Finally, we outline our future work in developing an analysis package for use with this semantically rich expression data enabling the generation and analysis of gene lists of biological relevance. We highlight how we utilise NCBO tools and the drivers we have identified as a result of this work.

For information on how to join the online meeting via WebEx and accompanying teleconference, see:

http://www.bioontology.org/ontology-driven-analysis-of-gene-expression-data

For the full schedule of the NCBO Webinar presentations see: http://www.bioontology.org/webinar-series.

The next NCBO Webinar will be presented by Mike Kellen from Sage Bionetworks on “Accelerating Health Advances through Open Challenges” at 10:00am PDT, Wednesday, May 1.

In this seminar, Dr. Kellen will discuss the Synapse technology platform and data repository, and its potential to impact large-scale collaborative research. He is the Director of Technology Platform and Services for Sage Bionetworks, where he leads efforts to develop Synapse and other Sage technology initiatives.  Prior to joining Sage, Dr. Kellen worked in a commercial bioinformatics startup where he brought several technology products to market and held positions in engineering and product management.  He holds a PhD in Bioengineering from the University of Washington.

For information on how to join the online meeting via WebEx and accompanying teleconference, see:

http://www.bioontology.org/node/807

For the full schedule of the NCBO Webinar presentations see: http://www.bioontology.org/webinar-series.

https://academy.nescent.org/wiki/Ontologies_for_evolutionary_biology

Evolutionary research has been revolutionized by the explosion of genetic information available, and ontologies must play a central role in relating this knowledge to observable diversity. Ontologies provide scaffolding that interconnects many kinds of observations; across species, they provide evolutionary, developmental, and mechanistic insights. The theme for this year’s course is “enrichment”. We aim to help participants enrich their research through the use of ontologies, to enrich existing ontologies with new content, and to bring new domain expertise to the ontology community.

The next NCBO Webinar will be presented tomorrow by Erich Gombocz from IO Informatics, “On the road to production: Semantic integration cases indicate successful adoption to improve knowledge-based decisions in Pharma and healthcare” at 10:00am PDT, Wednesday, Apr. 17.

Dr. Gombocz has 35+ years experience in Life Science research, laboratory automation and data management in distributed environments, and 35+ years programming experience in instrument control, user interface, database design, scientific analysis, on-line laboratory automation, and innovative software architecture.

For information on how to join the online meeting via WebEx and accompanying teleconference, see:

http://www.bioontology.org/Production-ready%3Asuccessful-semantic-integration-stories

For the full schedule of the NCBO Webinar presentations see: http://www.bioontology.org/webinar-series.

 Postdoctoral fellow: Bioinformatics, Phenotypes

We are recruiting a postdoc with training in bioinformatics who is interested in studying phenotypic evolution by combining model organism genetic data with comparative anatomical data from throughout the vertebrates.  One of the biggest challenges in systems biology is the inclusion of whole organism phenotypes.  In the Phenoscape group, we have developed ontology-based methods for representing phenotypes of diverse species in order to integrate them with model organism developmental and genetic data. We have collected these data in a sophisticated Knowledgebase, which has an initial focus on the diversity of phenotypes in ostariophysan fish, including zebrafish (kb.phenoscape.org). We are currently scaling up our approach to the vertebrates as a whole, with a goal of allowing similarities to be identified between phenotypes from sources as diverse as dinosaur fossils and mouse knockout mutants.

We invite postdoctoral applicants to propose an independent project that uses the Phenoscape Knowledgebase as a research platform.  In particular, we are interested in projects that will leverage functional genomic data to study the evolution of whole-organism phenotype in nonmodel organisms.  Projects may range from primarily computational to primarily biological.

The postdoc will work under the direction of Paula Mabee (University of South Dakota) and Todd Vision (University of North Carolina), as part of a distributed, multidisciplinary team that includes evolutionary biologists, computer scientists, model organism experts, and bioinformaticists.   It will be based in South Dakota, with opportunities to travel to other sites, including the National Evolutionary Synthesis Center (NESCent), the University of Chicago, and the California Academy of Sciences.

Starting date: This two year postdoctoral position is available to be filled immediately.

Required qualifications:

• Ph.D. degree with strong background in bioinformatics;
• Preferred previous experience in one of the following: ontologies, functional genomics, developmental biology
• Demonstrated ability to work in a team setting
• Demonstrated communication and writing skills, in English

How to apply: Please contact Dr. Mabee (pmabee@usd.edu) for inquiries. Applications should be directed to Dr. Mabee and include a cover letter, CV, a brief statement detailing your research interests and career goals, and three letters of reference.  For more information, please see https://phenoscape.org and http://kb.phenoscape.org/.

• Developing anatomical reference ontologies.

• Aligning and synchronizing anatomy ontologies using homology and other similarity.

• Defining anatomy ontology development best practices and standards.

• Reaching out to ancillary phenotype groups to share with them common concepts and practices.

• Educating the community about the methods for developing ontologies and their importance and utility in research.

Already the RCN has contributed funding and support for collaborations relating to neural crest representation, head and neck musculo-skeletal anatomy ontology development, and the chick anatomy ontology.

Do you have a great idea for a research exchange? Consider submitting an application. Any questions about opportunities offered by the Phenotype RCN may be directed to Paula Mabee (Paula.Mabee@usd.edu), Eva Huala (huala@acoma.stanford.edu), or Andy Deans (adeans@gmail.com).

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.

Winner of a competition among participants to illustrate the essence of Phenoscape, from Paul Sereno

It’s easy to get caught up in the details when developing infrastructure. You know it will be useful – because the grant application said so!  But there’s so much engineering to do. And no matter how thoughtful and deliberate a process you follow to anticipate the needs of your future users, once they have a complicated thing in their hands who knows how they will actually use it.

Enter the Phenoscape Knowledgebase.  After a heroic data collection push this winter, our next release of the Knowledgebase will contain millions of evolutionary phenotypes from throughout the vertebrates, linked to genetic phenotypes from human, mouse, Xenopus, and zebrafish, and a particularly rich set of annotations for skeletal features of fins and limbs.  The Knowledgebase is far from comprehensive, and annotations do not capture the full richness of the original characters in the evolutionary literature, but we think it’s a pretty useful resource.

So, it’s time to see what capabilities our users are excited by and what limitations frustrate them. To that end, we brought a small group of experts who look at phenotypes in a variety of different ways (e.g. genetics, systematics, evo-devo, clinical biomedicine, paleontology, even zooarchaeology) to the California Academy of Sciences in February, and we asked them what questions they’d most like to address using the KB as it exists today.

To help us in tapping into the assembled brainpower, we enlisted KnowInnovation, facilitation pioneers that specialize in helping researchers self-organize into teams to tackle creative research challenges. This they did with amazing resourcefulness, milking ideas out of us that we wouldn’t have imagined we even had.  The workshop was no ordinary parade of PowerPoints. We did speed-dating to toss research ideas off of each other, generated a  staggering number of post-it notes, sculpted creatures and skeletal parts out of clay and engaged in a host of other seemingly contrived but strangely liberating activities.  We watched in amazement as Karl Gude took visual minutes.

And we came up with some great collaborative ideas for research that take leverage the Knowledgebase to ask questions that would have been difficult to impossible to answer without it, including questions about genetic convergence and parallelism, global comparisons of intra and interspecific phenotypic variation, and the evolution of phenotypes affected by duplicated genes. These projects will now serve as driving applications for Phenoscape so that we know better what our users really need the Knowledgebase to do for them.  We look forward to reporting on the outcome of those in due course.

A big thank you to David Blackburn and the Cal Academy for providing such an inspiring venue, being exquisite hosts, and for conveniently having an open museum night during our workshop.  Thanks also to a great group of participants and facilitators, and to to NSF for a supplemental award that helped to make the workshop a success.

The NSF funds Research Coordination Networks to ‘encourage and foster interactions among scientists to create new research directions or advance a field’. Now at the midway point in our five-year funding period, the Phenotype RCN is focused on inspiring research and proposals that use ontology-annotated data to address scientific questions – at the same time as we continue to support coordinated ontology and standards development.  The two primary themes for this meeting reflected these goals: the use of text mining for extracting computable phenotypes from text and the representation of behavior in ontologies, arguably one of the most difficult phenotypes to consider.

The focus on text mining methods to extract phenotypes from the voluminous legacy literature, as well as from current data, was instructive and led to research ideas involving large-scale phenotypes.  To foster communication between biologists (who know the literature in which the phenotypes are embedded) and methods folks (the Natural Language Processing (NLP) experts), we held a ‘Phenomixer’ on the first morning, where groups of 4-5 people rotated among experts who in 2-3 minutes presented their story, answered questions and discussed possible proposals and ideas.  This successful (but exhausting) exercise enabled participants to make personal connections and helped them find collaborators.  Excellent talks that introduced phenotype extraction methods and corresponding driving scientific problems, along with panel discussions, supported this goal.  Most of the participants in the behavior ontology workshop who met the preceding day (see blog post below) stayed for the annual summit meeting where they presented their work and continued their discussions and plans for collaboration.

We were especially pleased with the synergies from this meeting and are eager to support the early stages of collaborations as they form.  Please consider applying for collaboration funds from the RCN.  If you have any questions, please contact us (pmabee@usd.edu).

Paula