Computable evolutionary phenotype knowledge: a hands-on workshop

 community, Informatics, Knowledge Base, knowledgebase, Outreach, Software, Workshops  Comments Off on Computable evolutionary phenotype knowledge: a hands-on workshop
Sep 302017
 

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: https://hackmd.io/s/Sk6Xa7Eq-#

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.


Filed under: Informatics, Knowledge Base, Outreach, Workshops Tagged: community, knowledgebase, Software, Workshops

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

 Phenex, Phylogenetics, Teleosts, Workshops  Comments Off on Tree of life and data integration challenges at the first FuturePhy workshop
Apr 062016
 

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.

The catfish team (John Lundberg, Mariangeles Arce, Jim Balhoff, Brian Sidlauskas, Ricardo Betancur, Laura Jackson, Kole Kubicek, Kyle Luckenbill, and myself, Wasila Dahdul) included participants with expertise in catfish anatomy, phylogenetics (molecular and morphological), development, bioinformatics, and digital imaging. We were motivated to build on the work of the All Catfish Species Inventory to achieve a more complete understanding of catfish diversification by integrating published phylogenies, 2D and 3D images in various online repositories, and thousands of computable phenotypes for catfishes in Phenoscape.

Screen Shot 2016-04-06 at 9.58.44 AM

We held several hands-on sessions on tree grafting (using Mesquite, R, and Arbor), data annotation (using Phenex), and tree submission to Open Tree.  We also examined an automatically generated supermatrix for 18 published catfish matrices in the Phenoscape KB (generated using the OntoTrace tool), and prototype data visualizations for supermatrices developed by Curt Lisle in Arbor. We used Mesquite to manually create a draft megatree, and in parallel, uploaded trees to Open Tree, which automatically synthesized a megatree for catfishes. Our plan is to compare the output of manual tree-building in Mesquite with the automated tree from Open Tree.

Among the issues and priorities that emerged during the workshop was the need for inclusion of the authoritative Catalog of Fishes taxonomy in Open Tree, and allowing the addition of unnamed or uncertainly identified taxa commonly used in matrices. We also discussed challenges in automated character consolidation across multiple studies, and the reuse of images across multiple online archives.

We left with a plan to continue tree building and data layer integration post-workshop, with the aim of publishing the catfish megatree (including the methods and remaining challenges) and the integration of data layers via interactions between Arbor, Open Tree, and Phenoscape.


Filed under: Phenex, Phylogenetics, Teleosts, Workshops
Feb 212014
 

Dear all,

We are pleased to announce a Uberon workshop, satellite of the Biocuration2014 meeting, to be held in Toronto, Canada, on the 5th and 6th April 2014.

Uberon is an integrated cross-species anatomy ontology, representing a variety of entities classified according to traditional anatomical criteria such as structure, function, and developmental lineage. Uberon provides a necessary bridge between anatomical structures in different taxa for cross-species inference, allowing integration of model organism, human, and comparative morphology data.

This workshop will be user-oriented, and will be devoted to introducing and training participants to the use of Uberon. For more information and schedule, please see the workshop website:
http://edu.isb-sib.ch/course/view.php?id=167

Attendance is limited, and places will be allocated on a first come, first served basis. The estimated registration fee is C$200. The registration page is available at:
http://www.isb-sib.ch/edu/Registration/SIB_courses.php?id=234

For more information about the Biocuration conference, please see:
http://biocuration2014.events.oicr.on.ca/biocuration

Looking forward to meeting you in Toronto,

The organizers: Chris Mungall, Melissa Haendel, and Frederic Bastian

Oct 292013
 

by Karen Eilbeck

One of our tasks at the SO-GENO phenotype workshop in Portland this fall, was to formalize the description of phenotypic data in genomic annotation. Previously we had written instructions in the use of phenotype ontologies such as HPO when creating variant file annotations in Genome Variation Format (GVF). GVF is a tab delimited variant file for the detailed annotation of sequence variants, and the specification is managed as part of the Sequence Ontology. Our revised guidelines were split into human and non-human recommendations to reflect the diversity in phenotypic annotation resources. We address best practices for annotation, provide easy to follow examples, and discuss the process for requesting new terms from the phenotype resources. The recommendations are available here and have been registered with Biosharing as a reporting guideline. Biosharing is a website to register and track well-constituted efforts to develop standards for describing and sharing biosciences experiments; see more here.

Oct 292013
 

by Matthew Brush

In September 2013, the Phenotype RCN sponsored a three-day workshop at Oregon Health & Science University to align sequence feature and genetic variation representation and thereby support phenotype data integration. Participants included developers of the Sequence Ontology  (SO) [1] (Karen Eilbeck, Mike Bada, and Bret Heale), and members of the ontology team from the Monarch Initiative [2] who have been developing a genotype ontology called GENO (Matthew Brush, Melissa Haendel, and Chris Mungall).

Background

One of the goals of the Phenotype RCN is to promote coordination and standardization of phenotype-related data. A standardized representation of genotype information is required for integrating genetically-linked phenotype data from diverse sources  including model organism, human variation, livestock, and evolutionary databases.  A particular challenge relates to harmonizing phenotype annotations where they are linked to genetic variations at different levels of granularity – from complete strain genotypes, to specific gene alleles, to single nucleotide polymorphisms.

Monarch and SO Projects

The Monarch Initiative is a new effort that aims to integrate genotype-to-phenotype and related data from numerous sources under a common semantic framework, and develop tools and services for user-guided exploration and analysis. Towards this end, Monarch required development of new modeling for genotypes (housed in GENO), which was lacking in the ontology landscape. The scope of GENO necessarily overlaps with that of the Sequence Ontology, but has a unique perspective on sequence features as they relate to linking different scales of genetic variation and to organismal phenotypes. The need to align modeling between SO and GENO motivated our collaboration, which was particularly timely as the SO had recently initiated a refactoring to accommodate use cases beyond its initial charge of genome annotation. This refactoring aimed to  define the context of the SO with respect to the Basic Formal Ontology (BFO) and other OBO ontologies, enhance representation of sequence variation, and develop a parallel representation of material sequence features (MSO) to complement the abstract feature representation in the existing SO. These goals were consistent with those of Monarch to support better phenotype data integration and therefore a workshop was funded by the Phenotype RCN.

Genetic Variation in GENO

The genotype information modeled in GENO is broadly conceived to include any variation in gene expression that is tied to an observed phenotypic effect. Two types of ‘genetic variation’ are explicitly distinguished in GENO: (1) ‘Sequence-variation’ describes changes in the sequence of an organism’s genome, which are captured in the traditional genotypes shared by biologists. In this context, ‘sequence variant genes’ are heritable changes in genomic DNA, and include things like point mutations, SNPs, or transgenic insertions that are represented in SO. (2) ‘Expression-variation’ relates to experimental alterations in the expression-level of genes that are not due to changes in the sequence of the subjects’ genome. Here, ‘expression variant gene’ are genes that are altered in the level of their expression as a result of some experimental intervention such as targeted gene knock-down using reagents such as morpholinos and RNAi, or transient expression from DNA constructs. Like sequence variants, these expression variants change what is expressed in an organism and can lead to measurable phenotypic outcomes.  The GENO ontology aims to re-use and co-develop the SO sequence variation model, but the notion of expression variation was concluded to be outside the SO scope. Modeling in GENO will extend and be logically consistent with the SO approach and will leverage links to orthogonal ontologies to place variation in a broader biological context [3]. Additional information about the SO and GENO models and their interaction can be found in the presentation posted here [4].

Workshop Goals and Outcomes

One of the immediate goals of our workshop was to find consensus on high-level ontological issues that have yet to be resolved in the development of these and other OBO Foundry ontologies and document these decisions for the community.  Many such issues have been broadly debated for years, and our outcomes may be relevant for other domains or applications in biomedical research. Much progress was made in resolving key issues, and a plan was established for ongoing collaborative work.  Some outcomes are below, and more detailed notes can be found here [5].

  1. Terminological standardization of core terms.  Terms such as ‘sequence’, ‘gene’, ‘allele’, variant’, ‘reference’, ‘mutant’, ‘genetic’ are variably and ambiguously used across communities, and required precise definitions and consistent use.  Work is ongoing to craft such definitions, which will be reflected in our respective ontologies as they are refined and vetted.
  2. The ontological nature of sequences and sequence features (and their place in the BFO/IAO framework).  Specific topics included: (1) the merits and implications of modeling sequence features as generically dependent continuants, or more specifically as information content entities, (2) defining identity criteria for sequence features to include their sequence and their position (as opposed to sequence only), (3) how to model attributes of sequence features such as biological activity, experimental provenance, reference status, and zygosity, and (4) the ways in which sequence features are considered to vary with respect each other (e.g. wild-type vs mutant sequences, reference vs alternate sequences).
  3. Gene representation, and modeling the central dogma. We debated strategies to provide an OWL-based ontological representation and identifiers for genes and their variants, that would serve SO, Monarch, and the broader phenotype community.  Related discussions focused on how to build from this gene representation to link to derived sequences at RNA and protein levels, and describe properties that emerge in this derivation.
  4. Variant representation.  A precise and explicit account of how the concept of ‘sequence variation’ should be defined across SO and GENO was established. In this model, a ‘variant’ is any sequence feature that varies_with some other instance of the same feature.  So sequence variants are considered to be ‘variant_with’ any other version of that feature, rather than ‘variants_of’ some reference. But we will also represent more specific types of the ‘variant_with’ relation that describe the different ways biologists consider sequences to vary with each other based on the roles that the variants in this relation hold (including where one is reference and another alternate versions, or one is wild-type and the other mutant). This is a critical facet of relating phenotypes to genotypes.
  5. Integration of expression-level variation modeling in GENO with sequence-variation modeling in SO.  Here, the high level approach for representing expression variation in terms of genetic sequences that are altered in their expression was reviewed and vetted by members of Monarch and SO teams.  Several approaches for conceptual integration of the expression and sequence variation models are under consideration.
  6. Technical approaches for coordinated development.  Topics included how to manage parallel construction and coordination of abstract SO and physical MSO ontologies – where strategies for automated derivation of the SO from the MSO were reviewed.  In addition, we discussed how to manage community development of SO and GENO as integrated but separate ontologies, using existing platforms, tools, and standards for software development (Google projects, trackers, list-serves, build and QA tools, etc).

As noted above, more details on each of these topics, as well as many others, can be found in the document here [5].  Participation of the broader community is encouraged through feedback on this document or participation in ongoing coordination calls (contact brushm@ohsu.edu for info).

References

  1. http://www.sequenceontology.org/
  2. http://monarchinitiative.org/
  3. ICBO 2013 conference paper – http://www2.unb.ca/csas/data/ws/icbo2013/papers/ec/icbo2013_submission_60.pdf
  4. Presentation to the Phenotype RCN, October 2013 – http://www.slideshare.net/mhb120/phenotype-rcn-sogenoworkshopshared
  5. Google doc summarizing workshop outcomes – https://docs.google.com/document/d/1AUEVX0Sx_iy9mTI6F59Yo7ZCXu4zv5uSk28AHid5zhc/edit#
Oct 122013
 

On Monday, October 7, the Phenotype RCN hosted a cross-working group call featuring presentations by Pier Luigi Buttigieg on the Environment Ontology and by Matthew Brush on a workshop focused on genetic variation representation.

Dr. Buttigieg, a post-doctoral research associate at the Alfred Wegener Institute Helmholtz Centre for Polar and Marine Research, gave an overview of the structure and applications of the Environment Ontology (EnvO), a community ontology for the concise, controlled description of environments. It contains terms at the levels of biomes, environmental features, and environmental material. He talked about EnvO’s sister project, GAZ, an open-source gazetteer built on ontological principles, and EnvO’s adoption by the Encyclopedia of Life (EOL) to provide environmental context to taxon information. EnvO is of particular interest to the RCN because we would like to further explore capturing environments in relation to phenotype.

Matthew Brush, a member of the Ontology Development Group at Oregon Health & Science University, reported on a RCN-sponsored workshop to align genetic variation representation across the Sequence Ontology and Monarch Initiative, in support of efforts to link phenotypes to genotype data. There will be more posted on the RCN blog soon about the workshop and its outcomes.

The Phenotype RCN plans to host monthly calls the first Monday of every month at 8 a.m. Pacific / 11 a.m. Eastern time. If you would like to receive invitations to join via WebEx, please email Erik Segerdell. Suggestions for topics and volunteers for presenters are welcome!

An announcement for the next meeting, November 4, is coming soon.

California Dreaming

 Evolution, Knowledge Base, Outreach, Science, Workshops  Comments Off on California Dreaming
Mar 282013
 

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.

clay1postitsspeed_dating2karl

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.


Filed under: Evolution, Knowledge Base, Outreach, Science, Workshops
Mar 152013
 

By Peter Midford and George Gkoutos

We held a one-day behavior ontologies workshop on Sunday, February 24, immediately prior to this
year’s RCN summit. Our goals were to bring ontology developers and behavioral biologists together
to review the NBO (NeuroBehavior Ontology) as well as discuss its use and interoperability with other
ontologies. We started the day with a series of short talks: George Gkoutos and Robert Hoehndorf
explaining the development and initial applications of the NBO, followed by six speakers who
volunteered to discuss related topics.

Beorn Brembs presented a data workflow that captured Drosophila movements in the course of
a ‘choice’ experiment. The flow went from raw video to depositing data in figshare, via R, and finished
by showing the role of NBO annotations in the final deposit. Melissa Haendel raised several issues
related to capturing behavior observations using ontologies: What does behavior inhere in? How to
relate observations across species? How do measurements and observations relate to phenotypes
or conditions? David Osumi-Sutherland discussed the application of behavior terms in annotations
within the Virtual Fly Brain (http://www.virtualflybrain.org). Janna Hastings discussed two new
ontologies for Emotions (https://code.google.com/p/emotion-ontology/) and Mental Functioning
(https://code.google.com/p/mental-functioning-ontology/) and both their relationships to the NBO and
their application to mental disease. Christine Wall introduced an ontology of processes involved in
mammalian feeding, which looked like a good candidate for inclusion in NBO and raised important
questions of representation of sequential behavior events and behaviors existing on a continuum.
Finally, Allan Kalueff introduced a community developed catalog of zebrafish behavior.

We followed this with a morning breakout session with groups selected by areas of taxonomic focus:
arthropods, non-mammalian vertebrates, non-human mammals, and humans. When the breakout
groups reported out, there were some common concerns about taxon specificity of terms, both in text
definitions and in their placement in the hierarchy – the later potentially leading to incorrect inferences
for taxa not considered during development of the ontology. There were questions about behaviors,
social and otherwise, involving more than one organism, and the role of abnormal and ‘clinic’ behavior
phenotypes. Finally one group looked at several previous efforts to construct behavior ontologies (e.g.,
the ABO constructed at a series of workshops, and David Shotton’s SABO project).

After lunch, we proposed and discussed topics for a new set of breakouts, and settled on Application
to Behavioral Ecology, Representing Affective Behavior, and a group reviewing the behavior process
branch, with NBO developers George Gkoutos and Robert Hoehndorf soliciting suggestions for high
priority changes.

The Behavioral Ecology session brought a group of behavioral ecologists together with Chris Mungall
to discuss the ABO ontology and how it might be integrated with the NBO. Anne Clark and Sue
Margulis discussed how the ABO had been used in the development of the Ethosearch tool, an online
collection of text ethograms indexed with terms from the ABO. They had also written, and offered
to contribute a collection of text definitions they had developed during the Ethosearch effort. The
consensus was that the ontologies were fairly compatible and that it would be desirable to graft portions
of the NBO in the ABO. The group also agreed that the learning and cognition sections of the NBO
should be a priority area for review as both structure and definitions suffered from species specificity.

The review group wound up focussing on terms for voluntary and involuntary movement, an issue that
came up in the invertebrate morning breakout as well. There was discussion of reflexes, of which the
NBO has a large number, many of which are human or mammal specific, but of significant clinical
interest.

The report-out from the affective behavior group generated a lively discussion that started by
addressing the conflation between observable behavior (e.g., smiling) and an inferred diagnosis
(emotional happiness). Although this distinction between observable behavior and inferred emotion
(which might belong in the emotion-ontology) is straightforward, other behavior terms (‘agoraphobic
behavior’) conflate behavior and diagnosis. There was also discussion of fear-related terms in general
and whether these might be too human-centric and what the scope of the NBO was; in particular
would the NBO apply to plants or even paramecia, which have been the subject of multiple ethograms
in the past 15 years. The consensus appeared to be that NBO should apply to animals with nervous
systems, that other types of behavior ought to be welcome additions to the Biological Process branch
of the Gene Ontology. There was also discussion of terms of the form ‘behavioral control of x’ where
x was a process, such as defecation or lacrimation, was meaningfully different from the underlying
physiological process.

The discussion of affective terms provided a nice transition to Barry Smith’s presentation ‘On the
Future of the NeuroBehavior Ontology and Its Relation to the Mental Functioning Ontology.’ After
reviewing the partitioning of domains of biological knowledge by various OBO ontologies, Barry
made the case that the portion of Biological Process that applied to whole organisms needed to be
split between the NBO for observable behavior and the complementary Mental Functioning Ontology
(MFO). The MFO will cover terms related to mental states and processes, for example sensory
perception. Perception is not an observable behavior, though there are behaviors associated with
perception (e.g., head turning, flehman response). He recommended that NBO retain the prefix NBO,
but be considered the (narrow) Behavior Ontology. He also recommended that the feeding ontology
developed by the FEED project be incorporated into NBO, that merging the ABO ontology should
be explored, perhaps scoping behavioral terms taxonomically (e.g, with ‘occurs-in-taxon’) when
appropriate, and to create a separate version of the NBO that marks the human-specific terms. He also
thought we shouldn’t be spending a lot of time discussing what is and isn’t behavior.

We finished the day with a discussion of next steps and deciding what are the best routes for providing
feedback to the NBO developers. In regard to feedback routes, we looked at several options: the OBO-
behavior list, the tracker associated with the NBO repository on google-code, as well as the notes
mechanism within the NCBO Bioportal and Ontobee. We decided that the OBO-behavior list and the
google tracker were adequate at this time. George also said he would add some new committers to
facilitate additions from the FEED ontology, the ABO, as well as terms from the community-developed
list of zebrafish terms in collaboration with ZFIN (this has been done).

We discussed next steps, in terms of ontology work, publications and funding. There was interest
in proposing a behavior ontology focussed RCN to fund workshops. There is interest in among the
behavioral ecology attendees in proposing two followups, the first being a hackathon for ontology
developers (perhaps 3 days) to clear up the ontology issues in the NBO (such as the relation between
the process and phenotype branches) which could be followed up by a workshop for a review from
the perspective of behavioral biology, perhaps in the space between ISBE and ABS in summer 2014.
There is sense that prior to seeking major funding, we should generate more publications, and that the
data and use cases are there to demonstrate the value of behavior ontologies, as several presentations
during the day had already demonstrated. One suggestion was to look at disease terms in the NBO
and look for clusters of behavior phenotypes associated with those terms. Given the importance of
behavior in model organism communities, the group expected that both the NIH and EU funding
agencies would be interested in supporting further work with the NBO.

We broke up shortly before 6 PM, though the behavior thread continued throughout the RCN summit. The application of ontologies to behavior still lags behind the use of anatomy ontologies, but combining the opportunities to benefit from the experiences with anatomical ontologies and the enthusiasm expressed at the workshop, there is reason to be optimistic about the future development and application of behavior ontologies.

Homology in anatomy ontologies: Report from a Phenotype RCN meeting

 Anatomy Ontology, Homology, Vertebrates, Workshops  Comments Off on Homology in anatomy ontologies: Report from a Phenotype RCN meeting
Feb 262013
 

At the end of October 2012, the working groups of the Phenotype Research Coordination Network (RCN) all met at the Asilomar Conference Center, in Pacific Grove, CA. One of the groups, the Vertebrate working group, made it their goal to discuss methods of representing phylogenetic and serial homology in anatomy ontologies, an issue that is central to Phenoscape as well. Though common ancestry is implicit in the semantics of many classes and subclass relationships (see for example the ‘homology_notes’ for digit in Uberon), most multispecies anatomy ontologies, including Uberon, VSAO, and TAO, do not assert homology relationships between anatomical entities.  Nonetheless, homology is central to comparative biology, and therefore to enriching computations across data types, species, and evolutionary change.


The working group used ontological relationships, phenotypes, and homology assertions across a small set of skeletal elements from vertebrate fins and limbs as a test case to identify requirements for making and reasoning over homology assertions. These included both positive (data expected to be returned) and negative (data expected not to be returned) results for particular queries involving phylogenetic and serial homology.  The group developed a number of such queries across subtype (is_a) and partonomy (part_of) relationships.  One example is that without homology assertions a query for phenotypes involving the ‘humerus’ would not retrieve phenotypes for ‘femur’.  Asserting that the ‘forelimb skeleton’ is serially homologous to the ‘hindlimb skeleton’ would not remedy this, because doing so would not imply that their parts (humerus and femur, respectively) would be homologous as well.  Instead, serial homology must be directly asserted between entities, even when they are parts of other already homologous structures (i.e., in this case humerus and femur have to also be directly asserted to be serial homologues).  Conversely, it was determined that homology relations, both serial and phylogenetic, should propagate to subclasses. For example, to return phenotypes for types of both the ‘paired fin skeleton’ and the ‘skeleton of limb’ in a query for either requires asserting phylogenetic homology only for these high-level classes. With this assertion propagating to all their subclasses, such as  ‘pectoral fin skeleton’, ‘hindlimb skeleton’, or ‘autopodial skeleton’, phenotypes for any of their subtypes would then also be returned.  The group also discussed how to define the identity of elements of a series consistently and ideally, universally.  The consensus was to specify subsets of digits for different taxa with different conventions, e.g., a basal tetrapod subset and a bird subset.

In summary, as identified at the workshop the requirements for reasoning over both phylogenetic and serial homology turned out to be fully consistent with standard OWL property semantics. Furthermore, the recommendations that emerged from the workshop for defining elements in a repeated series are fully in line with the goal of defining classes in anatomy ontologies such that they can be applied unambiguously, including in a manner that is not inconsistent with knowledge of developmental and evolutionary origin.

Aside from several Phenoscape personnel (Jim Balhoff,  David Blackburn, Alex Dececchi, Hilmar Lapp, Paula Mabee, Chris Mungall), participants in the meeting included Eric KansaHans Larsson and Karen Sears, who were new to the RCN (and Phenoscape). We are grateful to them for helping us work through the questions in a way that kept it grounded in enabling science.


Filed under: Anatomy Ontology, Homology, Ontology, Vertebrates, Workshops

Call for Participants: Workshop on New Tools for Studying Phenotype Evolution in the Vertebrates

 Evolution, Knowledge Base, Science, Workshops  Comments Off on Call for Participants: Workshop on New Tools for Studying Phenotype Evolution in the Vertebrates
Jul 232012
 

What new research opportunities are opened up by the power to compute over phenotype information from thousands of species of vertebrates, particularly when that information is combined with phenotype and expression information for thousands of genes in multiple model organisms? The Phenoscape project invites you to be among the pioneers in opening up this research.

The first release of the Phenoscape Knowledgebase includes over 500K species phenotypes linked to 4,000+ genes from zebrafish, and is currently being extended to capture phenotype data from other vertebrates and linked to phenotype and expression data for other model organisms (including mouse and Xenopus).

We are looking for participants for a small, 3-day workshop, February 8-10 (to be held at the California Academy of Sciences, San Francisco) who are interested in engaging in creative problem-solving directed at this outstanding problem and initiating collaborations. The outcome is expected to be several collaborative projects whose goals would drive the development of the Phenoscape tool set/interface and would present new and creative ways to deepen understanding of phenotypic evolution. Phenoscape aims to support the initial steps in these activities. We are particularly interested in a broad approach to this problem and welcome interest from scientists with backgrounds in computational and systems biology, mathematics, development, genomics, and evolution.

If you are interested, please contact Paula Mabee or Todd Vision.


Filed under: Evolution, Knowledge Base, Science, Workshops