Jan 092015

Figure assembled by Anya Broverman-Wray (CC BY 2.0) doi: 10.1371/journal.pbio.1002033.g001

In case you missed it, our latest Phenotype RCN publication came out this week in PLoS Biology. In this perspective we argue for more investment in the infrastructure needed to make phenotypes more accessible. Check it out!

Abstract.—Despite a large and multifaceted effort to understand the vast landscape of phenotypic data, their current form inhibits productive data analysis. The lack of a community-wide, consensus-based, human- and machine-interpretable language for describing phenotypes and their genomic and environmental contexts is perhaps the most pressing scientific bottleneck to integration across many key fields in biology, including genomics, systems biology, development, medicine, evolution, ecology, and systematics. Here we survey the current phenomics landscape, including data resources and handling, and the progress that has been made to accurately capture relevant data descriptions for phenotypes. We present an example of the kind of integration across domains that computable phenotypes would enable, and we call upon the broader biology community, publishers, and relevant funding agencies to support efforts to surmount today’s data barriers and facilitate analytical reproducibility.

Deans AR, Lewis SE, Huala E, Anzaldo SS, Ashburner M, Balhoff JP, Blackburn DC, Blake JA, Burleigh JG, Chanet B, Cooper LD, Courtot M, Csösz S, Cui H, Dahdul W, Das S, Dececchi TA, Dettai A, Diogo R, Druzinsky RE, Dumontier M, Franz NM, Friedrich F, Gkoutos GV, Haendel M, Harmon LJ, Hayamizu TF, He Y, Hines HM, Ibrahim N, Jackson LM, Jaiswal P, James-Zorn C, Köhler S, Lecointre G, Lapp H, Lawrence CJ, Le Novère N, Lundberg JG, Macklin J, Mast AR, Midford PE, Mikó I, Mungall CJ, Oellrich A, Osumi-Sutherland D, Helen Parkinson, Ramírez MJ, Richter S, Robinson PN, Ruttenberg A, Schulz KS, Segerdell E, Seltmann KC, Sharkey MJ, Smith AD, Smith B, Specht CD, Squires RB, Thacker RW, Thessen A, Fernandez-Triana J, Vihinen M, Vize PD, Vogt L, Wall CE, Walls RL, Westerfeld M, Wharton RA, Wirkner CS, Woolley JB, Yoder MJ, Zorn AM, Mabee PM. (2015) Finding our way through phenotypes. PLoS Biology 13(1): e1002033. DOI: 10.1371/journal.pbio.1002033

Dec 072014

euroevodevoVienna2014In late July, the Phenotype RCN and Phenoscape co-sponsored several speakers in the symposium “What should Bioinformatics do for EvoDevo?” co-organized by Günter Plickert, Mark Blaxter, Paula Mabee and Ann Burke. The symposium was part of the European Society for Evolutionary Developmental Biology (EED) meeting, held in Vienna. The organizers brought together speakers whose research and perspectives provided examples of how EvoDevo data integration is necessary for discoveries.  Several speakers presented new insights into EvoDevo that were directly derived from sequencing genomes or transcriptomes.   Others showed how by using semantic methods to represent species phenotypes, they could be linked to genetic and developmental data, and the research questions that they addressed. This well-attended symposium met its goals, which were to:

  • promote awareness of new and developing resources and methods as well as EvoDevo uses of existing ones.
  • promote discussions in the EvoDevo community that value input of bioinformatics to EvoDevo questions.
  • invite the audience to share their ideas of how to move the integration forward

The excellent organization of this conference and the wonderful venue helped spark several new collaborations and grant proposals.  Talks and speakers in this symposium included (full program found here):

  1. Bioinformatics for EvoDevo: Connecting evolutionary morphology and model organism genetics, presented by Paula Mabee (University of South Dakota, Vermillion, SD, USA)
  2. Insights into the evolution and development of planarian regeneration from the genome of the flatworm, Girardia tigrina, presented by Sujai Kumar (University of Oxford, GBR)
  3. From the wet lab to the computer and back: A stage specific RNAseq analysis elucidates the molecular underpinnings and evolution of Hydrozoan development, presented by Philipp Schiffer (University of Cologne, GER)
  4. Insights into the evolution of early development of parthenogenetic nematodes by second generation sequencing, presented by Christopher Kraus (University of Cologne, GER)
  5. Petaloidy, polarity and pollination: The evolution of organ morphology networks, presented by Chelsea Specht (University of California Berkeley, CA, USA)
  6. Aligning phonemes and genomes to understand the evolution of multicellular organisms, presented by Philip Donoghue (University of Bristol, GBR)
  7. Online databases provide critical insights into the evolution of appendage modularity during the fin to limb transition, presented by Karen Sears (University of Illinois, Urbana, IL, USA)
  8. Evolutionally conserved mechanisms of regeneration in chordates: Uncovering pathways active during WBR in Botrylloides leachi, presented by Lisa Zondag (University of Otago, Dunedin, NZL)
  9. Phylogenomics of MADS-box genes in flowering plants to identify EvoDevo genes, presented by Guenter Theissen (Friedrich Schiller University Jena, GER)
  10. Illuminating the evolutionary origin of the turtle shell by a comparative tissue-specific transcriptome analysis, presented by Juan Pascual-Anaya (RIKEN Center for Developmental Biology, Kobe, JPN)
  11. Blastodermal segmentation in the milkweed bug, Oncopeltus facsiatus, presented by Ariel Chipman (The Hebrew University of Jerusalem, ISR)
  12. The origins of arthropod innovations: Insights from the noninsect arthropods, the cherry shrimp and rusty millipede, presented by Nathan Kenny (The Chinese University of Hong Kong, HKG)
 Posted by on December 7, 2014 at 4:52 pm
Nov 142014

Figure3-Revised.copyDo sponges have true tissues? This fundamental question is just one of the controversial topics that Phenotype RCN team members encountered as they constructed a new ontology to describe the unique features of sponge anatomy. As you can see from the diagram below, the team opted to describe “functional layers” of sponge cells, re-using the CARO class ‘portion of tissue’ to contain these layers.

The recently published Porifera ontology (PORO) is an outcome of Phenotype RCN meetings that matched experts in creating ontologies with taxonomists seeking to improve phenotype descriptions and databases. Sponge biologists Bob Thacker, Cristina Díaz, Adeline Kerner, and Régine Vignes-Lebbe teamed up with information scientists Chris Mungall, Melissa Haendel, and Erik Segerdell to generate the ontology from an existing thesaurus of anatomical terms. The ontology is currently being used to allow natural language processing software to efficiently extract morphological characters from taxonomic monographs.

Citation: Thacker RW, Díaz MC, Kerner A, Vignes-Lebbe R, Segerdell E, Haendel MA, Mungall CJ. 2014. The Porifera Ontology (PORO): enhancing sponge systematics with an anatomy ontology. Journal of Biomedical Semantics 5:39. doi: 10.1186/2041-1480-5-39.

Agelas conifera 14Jan06 066 copy 2.jpg

 Posted by on November 14, 2014 at 2:40 am
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.



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

Half-duck, half-crocodile, and bigger than T. Rex: a giant semiaquatic predatory dinosaur

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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

Phenoscape poster at Evolution 2014

 Conferences, Curation Tools, Data Curation  Comments Off on Phenoscape poster at Evolution 2014
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.


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:


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:


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!