Oct 152014
 

Several members of the Plant Working Group got together at Phoenix Bioinformatics in lovely Redwood City California at the end of September to write up results of the long-running Plant Phenotype Pilot Project (or PPPP as the cognoscenti call it). The first draft is affectionately known as the Plant Phenotype Pilot Project Preliminary Paper (or PPPPPP).

Left: Wild type Arabidopsis and several adherent leaf mutants, from Voisin et al. 2009, PLoS Genetics 5(10):e1000703 Fig. 1.  Right: Zea mays adherent dwarf. From MaizeGDB (http://images.maizegdb.org/db_images/Variation/mgn/5207_1613_1042_29.jpg).

Figure 1   5207_1613_1042_29

Despite their obsession with the letter P, working group members Carolyn Lawrence, David Meinke, Ramona Walls, Lisa Harper and Eva Huala — with the help of Anika Oellrich, Laurel Cooper, Pankaj Jaiswal and George Gkoutos who were able to join via Skype — made good progress over the course of two and a half days on writing up sections describing the assembly and analysis of the phenotype dataset produced by the group, which includes 6361 Entity-Quality statements describing mutant phenotypes associated to 2744 genes across six well-studied plant species (Arabidopsis, rice, maize, soybean, Medicago, and tomato).

Other recent activities from the plant working group include submission of a grant proposal to NSF-ABI over the summer to fund the continuation of this work. The submission was made to “Advances in Biological Informatics” with funding sought from both the NSF and BBSRC under the “UK BBSRC-US NSF/BIO Lead Agency Pilot Opportunity” program.

IMG_2828   IMG_2832

The plant working group would like to thank the RCN for covering travel expenses for this and previous working group meetings; this funding has enabled the group to work together effectively despite being scattered over a wide range of institutions in the USA and UK.

IMG_2822

 

 Posted by on October 15, 2014 at 10:08 pm
Sep 262014
 

A team led by University of Chicago Phenoscapers Nizar Ibrahim and Paul Sereno have published new findings about the remarkable semiaquatic predatory dinosaur Spinosaurus aegyptiacus in the latest issue of Science.  It has been receiving some nice coverage at NPR and other news outlets.

Workers at the National Geographic Museum in Washington grind the rough edges off a life-size replica of a spinosaurus skeleton.  Credit: Mike Hettwer/National Geographic.

From the abstract:

We describe adaptations for a semiaquatic lifestyle in the dinosaur Spinosaurus aegyptiacus. These adaptations include retraction of the fleshy nostrils to a position near the mid-region of the skull and an elongate neck and trunk that shift the center of body mass anterior to the knee joint. Unlike terrestrial theropods, the pelvic girdle is downsized, the hindlimbs are short, and all of the limb bones are solid without an open medullary cavity, for buoyancy control in water. The short, robust femur with hypertrophied flexor attachment and the low, flat-bottomed pedal claws are consistent with aquatic foot-propelled locomotion. Surface striations and bone microstructure suggest that the dorsal “sail” may have been enveloped in skin that functioned primarily for display on land and in water.

Citation: Ibrahim N, Sereno PC, Dal Sasso C, Maganuco S, Fabbri M, Martill DM, Zouhri S, Myhrvold N, Iurino DA (2014) Semiaquatic adaptations in a giant predatory dinosaur. Science. http://doi.org/10.1126/science.1258750.


Filed under: Uncategorized
Sep 252014
 

[written by Matt Yoder. Posted by Andy Deans]

Regular RCN attendees Matt Yoder, István Mikó and Andy Deans attended ICIM3 in Berlin, Germany on August 3rd–7th. The congress brought together world leaders in invertebrate morphology for a week of presentations and discussion on the campus of the Humboldt University in Berlin. Logistics were flawless, with ample food and drink to wet interactions (e.g., endless beer and pretzels for the poster session!). The conference was truly a showcase of phenotypes and was fascinating from the standpoint of just seeing examples of life evolving. For those of us interested in semantically describing morphological diversity, the myriad approachs to representing morphology as data was extremely informative and indicative of the challenges we face.

people stand around, talking in a room full of posters

Morphologists talk phenotype, over endless pretzels and beer. Photo by Andy Deans (CC BY 2.0).

In addition to generally absorbing the goings on, Yoder and Deans participated in a eMorphology symposium led by Lars Vogt, one of the PIs of MorphDBase. Deans presented on the state of semantic phenotype representation, with particular attention to its role in taxonomy (Deans ICIM3 slideshow), a follow-up to a presentation and panel discussion from the last ICIM (Deans ICIM2 slideshow). Yoder delivered a talk (http://dx.doi.org/10.6084/m9.figshare.1127970) on behalf of Jim Balhoff et al., on presence/absence inference utilizing Phenoscape KB. Balhoff has written tools that utilize inference to expand the knowledge provided by curators into much larger datasets asserting the presence or absence of anatomical features across taxa. These tools also find logical inconsistencies with curator made statements, and are a great example of a practical approach to computing on phenotypes.

A meeting highlight was the opportunity to see the latest and greatest imaging technologies within a special symposium on advances in microscopy. Speakers highlighted advances in 3D and 4D imaging, with systems capable of generating massive datasets—easily rivaling the big-data world of genomics. Handling these data has become a science itself. It was great to see open-source software and hardware(!) initiatives leading the field in this regard. Stephen Saalfeld’s talk on image alignment was amazing, a presentation similar to that given at ICIM3 is available on Youtube. Pavel Tomancak’s description of light-sheet microscopy using OpenSpim was also inspirational.

non-hexapod pancrustaceans in vials of ethanol

Arthropod phenotypes on display in the halls. Ready access to specimens and hand-blown glass models (see below) catalyzed several discussions about the evolution of form and function in this phylum. Photo by Andy Deans (CC BY 2.0).

Finally, the meeting was flush with opportunities for developing longer term collaborations. The curators of MorphDBase and the recent initiative TaxonWorks spent significant time discussing the possibility of sharing a code-base and thus greatly extending their resources. We hope that this collaboration comes to fruition and that it becomes an important component of “phenotype-handling” in the future.

A special thanks to the Phenotype RCN PIs for supporting, in part, our attendance.

museum case full of boxes that contain glass models of organisms

Glass models of invertebrates, on display at the Humboldt University, in Berlin. Photo by Andy Deans (CC BY 2.0).

 Posted by on September 25, 2014 at 1:04 am
Aug 272014
 

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.


Filed under: Conferences, Curation Tools, Data Curation
Aug 262014
 

Our new paper describing the Biological Spatial Ontology has just been published in the Journal of Biomedical Semantics: http://www.jbiomedsem.com/content/5/1/34

Differences in the position and orientation of anatomical structures among species, or between mutant and wildtype organisms, is a frequently described source of phenotypic variation in the literature. For example, pectoral fins can be located anteriorly or posteriorly on a fish’s body, and their bases can be inclined vertically or horizontally. Although widely used in phenotypic descriptions, the application of spatial descriptors can differ across fields of biology, causing confusion when one attempts to compare anatomy across species. We developed the BSPO to standardize the description of spatial terminology across taxa and to enable spatial reasoning.

image1

Fig 1. Comparison of primary organismal axes designated in a diversity of species and their representation in BSPO

BSPO contains 146 classes and 58 relations representing anatomical axes, gradients, regions, sections, sides, and surfaces that apply to whole organisms and their parts:

fig2

Fig 2. Organization of high-level spatial classes in BSPO and some of their children.

We describe the challenges in designating positional terminology across the wonderful diversity of body forms, including headless animals and those with the anus adjacent to its mouth:

fig3

Fig 3. An individual zooid of the colonial ectoproct Bugula.

The BSPO is currently used by projects that require positional representation in anatomy ontologies and phenotype annotation. Terms in the BSPO are most developed for animals and, to a lesser extent, plants. We welcome feedback from the community, particularly to improve the taxonomic coverage of spatial terms in the ontology.

Aug 172014
 

April 29th, San Diego, CA

A mini-symposium, entitled ANATOMY ONTOLOGIES: BIOINFORMATICS IN THE ANATOMICAL SCIENCES, was held at the Annual Meeting of the American Association of Anatomists (AAA) a few months ago. I was very pleased to assemble a wonderful group of speakers for the symposium, which was supported by grants from AAA and Phenotype RCN.  My purpose for organizing the symposium was to introduce cutting edge tools of bioinformatics to my anatomy colleagues. Although the talks were as good as I could have hoped, the attendance at the meeting was a bit poor, likely because of the many concurrent sessions (see program). Here is the line-up for the six talks. Clicking on the title will take you to the abstract.

Computing on the anatomical form for disease discovery.
M.A. Haendel and C.J. Mungall. Oregon Health & Science University and Lawrence Berkeley National Laboratory.

The scourge of neuroanatomical nomenclature: use of neuroanatomical ontologies within the Neuroscience Information Framework.  M. Martone. UC San Diego Health Sciences.

Textpresso for oro-pharyngeal anatomy: a system for searching the full text of anatomy literatures.
K. Van Auken, R. Druzinsky, J. Done, P.W. Sternberg and H-M. Mueller. California Institute of Technology and University of Illinois.

An anatomy ontology for oro-pharyngeal muscles and the logical underpinnings of comparative anatomy.  R.E. Druzinsky. University of Illinois.

The modern character synthesis: Using semantic tools to aggregate morphological characters across studies.
A. Dececchi, P. Mabee and J. Balhoff. University of South Dakota and NESCent.

Big anatomy: the new views from integrated anatomy, development, and genes.  P. Mabee (on behalf of Phenoscape team). University of South Dakota.

Submitted by Robert Druzinsky.

 

Jul 212014
 

Over the years, a number of different vertebrate anatomy ontologies have been developed. Some of these are dedicated to a single model species, or to human. Others have been developed to describe phenotypic variation across species, and these cover a broad range of species. In particular:

This lead to considerable duplication of effort, as common anatomical
structures such as ‘pectoral girdle‘ were represented in all five ontologies
(as well as their single species counterparts):

Haendel et al fig 1

Pectoral girdle and related concepts in Uberon, with cross-references to other ontologies shown (Fig 1, Haendel et al)

It was difficult for the Phenoscape group to integrate data across all these ontologies, as this required that curators kept mutual cross-references up to date, a time-consuming and error-prone task.

As a result, the maintainers of these ontologies agreed to join forces and build a common ontology.This work is described in a new paper in the ontologies special issue of the Journal of Biomedical Semantics:

Haendel MA, Balhoff JP, Bastian FB et al  Unification of multi-species vertebrate anatomy ontologies for comparative biology in Uberon Journal of Biomedical Semantics 2014, 5:21  doi:10.1186/2041-1480-5-21

The group selected Uberon as the core ontology, as it had the broadest coverage, was already well-integrated with the single-species ontologies, and was adapted for OWL reasoning. The curators of these ontologies worked long and hard to integrate their work, with input from anatomy experts and developers of single-species ontologies, revealing many interesting differences in the way structures are represented across species along the way. For example, the representation of teeth in the combined ontology had to be flexible enough to accommodate teeth that are in widely variable locations and configurations:

Figure 4. Diversity of tooth locations

The number of classes merged is shown in figure 2 of the paper:

Figure 2. Overlap and contributions from source ontologies. A) Venn diagram showing the extent of cross-referenced content between msAOs prior to the merge.. B) Ontology evolution and integration into Uberon

 

As a result of this effort, we have a common anatomy ontology with broad and deep coverage for vertebrate anatomy. For a variety of viewing options, see the Uberon website. For examples of use for data integration see:

Like most ontologies, work is ongoing and we are constantly striving to improve depth, coverage and quality. We’re currently actively improving the representation of facial muscles in the ontology based on the FEED ontology. We are also working on a federated approach for bringing in invertebrate anatomy ontologies, many of which are developed under the auspices of the Phenotype RCN  including the Arthropod Anatomy Ontology, the Poriferan anatomy ontology [Thacker et al, accepted, JBMS], the cephalopod  ontology and the ctenophore ontology. We welcome feedback from everyone!

Jun 182014
 

This spring saw three related meetings (two workshops and a hackathon) aimed at advancing development of the Biological Collections Ontology (BCO) and the Population and Community Ontology (PCO) and developing tools to annotate data using those and other ontologies. The first two meetings were held from February 18-20, 2014 in the iPlant offices in Tucson, AZ, right before the Phenotype RCN annual meeting, and were supported in part by the Phenotype RCN. The third meeting was held concurrently with the 16th Genomics Standards Consortium (GSC) Meeting at Pembroke College in Oxford, England from March 31 – April 2. Additional support for all three meetings was provided by EAGER: An Interoperable Information Infrastructure for Biodiversity Research, RCN4GSC: A Research Coordination Network for the Genomic Standards Consortium, and BiSciCol Tracker: Towards a tagging and tracking infrastructure for biodiversity science collections, with logistic support from iPlant and the GSC.

At the first meeting, ten in-person and three remote participants gathered use cases to help grow the PCO, a relatively new ontology that describes collections of organisms such as populations and communities as well as qualities and processes related to those collections. The PCO can be used to describe any collection of organisms (or viruses or viroids), from microbes to humans, whether the collection consists of one or multiple taxa. During one and half days, we came up with a preliminary list of factors by which organisms are grouped into populations or communities, developed an ontology design pattern for how to describe membership in a group of organisms, defined several new PCO terms for specific use cases, made decisions about modeling challenging concepts such as ecological niche (spanning both only PCO and ENVO), and decided to provide pre-composed terms for those characteristics of populations that are not taxon specific and cannot be defined as derived from individual measurements. In addition, there were many lively discussions about the nature of an organism or population and how our expanding knowledge of the microbial world might turn everything we know on its head.

The second workshop focused on mapping datasets to ontology terms and converting them to Resource Description Framework (RDF), using the BCO, an ontology that describes field-based biological sampling processes and observations, as well as material entities and roles associated with those processes. During another intense one and a half days, 18 in-person and one remote participants coordinated development among BCO, OBI, and ENVO, created a concept map for DNA marker gene studies that led to new terms for OBI and a manuscript submitted to the International Conference on Biomedical Ontologies, and did a first pass mapping of Darwin Core terms to ontology terms. In addition, we mapped three data sets to the BCO, converted them to RDF triple stores, and ran preliminary queries. At the end of the third day, about half of the participants climbed into a van to take part in another three jam-packed days of meetings Biosphere 2, hosted by the Phenotype RCN. Our northern European colleagues were particularly happy to see the sunshine for the first time in months.

To help counteract the pleasant weather in Arizona and follow-up on some of the ideas generated during the workshop in Tucson, we decided to hold a BCO hackathon in Oxford six weeks later. In our honor, temperatures in the UK jumped 20 degrees (Fahrenheit) the week we were there, sparing me total weather shock. The hackathon was smaller (7 full time participants plus a few part time), and focused on generating concrete products. Over the course of four days, we coded an additional dataset to RDF, developed a Material Sample Core for the Global Biodiversity Information Framework (GBIF), created a Web Ontology Language (OWL) file for importing Darwin Core classes and properties into BCO, developed a workflow for converting biodiversity data among formats, prepared an updated version of the BCO for release, and completed a proof-of-concept conversion tool that converts existing RDF outputs to Darwin Core Archive format using an ontology specification. We also took part in several of the main meeting sessions of the GSC and reported on our work to the larger group.

A more detailed report describing these three meetings has been submitted to Standards in Genomic Science.

Submitted by Ramona Walls, on behalf of co-organizers John Deck and Rob Guralnick and all of the participants.

 Posted by on June 18, 2014 at 2:14 pm
Jun 102014
 

Calling all Phenotype RCNer’s and anyone else who works with phenotype data – We want your name on a manuscript supporting a computable phenotypes future! (If you read and agree of course.)

Over the past four years of sponsoring meetings, courses, and exchanges, we have, with your help and participation, developed a comprehensive understanding of where the phenotype community is at, what is needed for integration of phenotypes with other data, and a vision of the science that could be achieved with this integration. In this article, we attempt to educate researchers, granting agencies, and policy makers on the current ‘non-computable’ state of phenotypic data across various life science domains, and we try to motivate them to use, develop, and advocate for semantic methods. Because of the relevance of this work to most areas of biological sciences and because it relates specifically to creating interdisciplinary knowledge—and especially because it is open access—PLoS Biology is our target journal.

  1. The link to manuscript is here: http://bit.ly/PhenotypeMS (Google doc). And a Word version (.docx) with line numbers is available if you prefer.
  2. The form to add your comments, suggestions, references, and especially your author information is here: http://bit.ly/PhenotypeComments

Please respond by 18 June 2014 (next Wednesday). We will post updates here on our blog.

‘Branching’ phenotypes are not easily recovered from free text (far right column), the format in which most organismal phenotypes are recorded. (top row) Bee setae are usually modified in a way that presumably facilitates pollen collection, a €153 billion ecosystem service. This relatively simple phenotype has been described in myriad ways. Photo of bumble bee covered in pollen by Thomas Bresson (source). Photo of seta interacting with pollen grain by István Mikó (source). (middle row) Plant trichomes take on many forms and likewise are described using many lexicons. Photo of Arabidopsis plants covered in hair-like structures (trichomes) by BlueRidgeKitties (source). Scanning electron micrograph of Arabidopsis trichome by Heiti Paves (source). (bottom) In zebrafish larvae, angiogenesis starts with vessels branching to form a network (right image) that is referred in disparate ways. Zebrafish embryo photo by MichianaSTEM (source). Zebrafish blood vessels image is Figure 5A from Alvarez et al. 2009.

 Posted by on June 10, 2014 at 2:46 am
May 302014
 

Dear Phenotype RCN community.  Please take a moment to help NSF identify priorities for investment in Genome-Phenome research.  These will be translated into funding solicitations relevant to you!

John Wingfield, Assistant Director of the National Science Foundation Directorate for Biological Sciences (BIO), is pleased to announce the posting of a Wiki to seek community input on the grand challenge of understanding the complex relationship between genomes and phenomes.  The Wiki is intended to facilitate discussion among researchers in diverse disciplines that intersect with biology, such as computation, mathematics, engineering, physics, and chemistry. The Wiki format encourages open communication, captures new viewpoints, and promotes free exchange of ideas about the bottlenecks that impede progress on the genomes-phenomes grand challenge and approaches or strategies to overcome these challenges. Information provided through the Wiki will help inform BIO’s future research investments and activities relevant to understanding genomes-phenomes relationships.

To provide comments, ask questions and view input from and interact with other community members, first-time users should sign up for an account via this link: Sign-up.  Once registered, users will be directed to the main page of the NSF Wiki to accept the terms and conditions before proceeding.  Additional guidance and subsequent visits can be accessed via this link: Genomes-Phenomes Wiki.Community members should feel free to forward notice of this to anyone they think might be interested in contributing to the discussion. Questions regarding the Wiki should be sent to bio-gen-phen@nsf.gov.

 Posted by on May 30, 2014 at 7:39 pm