Phenotype RCN

Plant Working Group at the Phenotype RCN

May 092012

Left: Maize de*-N738A (Allele) selfed colorless flint M2 origin ear showing thin collapsed defective kernels (cp*-N738A), also segregating for pitted discolored defective kernels (ptd*-N738B) (courtesy of Carolyn Lawrence, MaizeGDB). Center: Tomato mutant n2326m1 showing low fertility (courtesy of Naama Menda, SGN). Right: Aborted seed phenotype of Arabidopsis hisn2-1 heterozygote with mutant seeds (white, brown) arrested at a preglobular stage of embryo development (courtesy of David Meinke, Oklahoma State University).

The plant working group had a productive meeting as part of the second Phenotype RCN summit meeting in February at NESCent. We succeeded in bringing some new people into the plant working group while still continuing momentum from our two previous meetings in 2011.

Our discussion continued a thread from previous meetings on how to develop a pilot project that could serve to demonstrate the usefulness of describing plant phenotypes using a common ontology such as the Plant Ontology (PO). Our goal is to show how a set of phenotype annotations from several species, made using a shared set of ontology terms, can be used to transfer knowledge across species and answer questions that require cross-species comparison. We came up with a concrete plan for a pilot project that involves gathering a test set of phenotype annotations associated to genes for several plant species and analyzing the resulting dataset. The plan expands somewhat on our earlier idea to focus on a use case for leaves, and leverages work published recently by David Meinke (Lloyd and Meinke, 2012) to gather a dataset of phenotypes for 2400 Arabidopsis genes ( as well as the efforts by several plant databases to collect phenotype data.

Specific tasks we hope to complete by the next WG meeting in October:

Assemble existing sets of phenotype data for five plant taxa (Arabidopsis, tomato, maize, rice and legumes)
Convert these existing phenotype datasets to entity/quality format, using PO and GO terms for entity and PATO for quality
Calculate ortholog sets for the species included in the phenotype data

We hope to use the fall working group meeting to explore the predictive power of the dataset and plan an analysis phase for the pilot project.

Phenotype RCN Annual Summit meeting 2012

Announcements, Conference, Uncategorized, Workshops, phenotype ontology research collaboration network; phenotype ontology rcn; phenotype ontology; anatomy ontology No Responses »

Mar 192012

The second annual summit meeting of the Phenotype RCN was held February 23-25, 2012 at the National Evolutionary Synthesis Center (NESCent) in Durham, North Carolina. It included 61 participants, 12 of whom were from countries outside the USA, including Canada, France, Germany, UK, Switzerland, and Venezuela. NESCent generously opened its doors to us once again, and our big and happy group made use of the entire facility including the large auditorium downstairs and all the breakout rooms and conversation areas.

We focused this meeting on the research and reasoning applications of phenotype ontologies, how to build them, and how to annotate phenotypic data. Please see the slides from the excellent presentations from the meeting. The desired outcome of the workshop was that people would take something tangible home with them: an idea, a method, or a collaboration that would help them with existing or new research. Anticipating that almost half of the people attending were new to ontologies, we designed two hands-on exercises for the first day to give participants experience with ontology building (using Vue) and annotation (using a Phenote interface that was customized for the RCN meeting). We met in small (4-5 person) groups and used images of dogs and humans to serve as a focus for the kinds of issues that arise, e.g., ‘What is a snout?’ and ‘Can the same anatomy ontology be used for dogs and humans?’. On the second day of the workshop we focused on the kinds of discoveries that could be made with phenotypic data made computable with ontologies. We broke out in challenge-centered groups (e.g., how to express complex and quantitative phenotypes?) as well as along taxonomic lines (plants, vertebrates, arthropods and now poriferans and fungi). As documented in the working group reports, critical directions for new research were identified, and several collaborating groups were formed to moved ahead with prototyping or otherwise investigating opportunities for this work.

The RCN PIs (me, Eva, Andy, and Suzi) felt that this meeting was particularly successful, and that there was a palpable sense of momentum. Participants departed with new colleagues and collaborations, and new ideas of how to interact effectively with ontologies and how using them can advance their science. We are looking forward to our next chance to meet! Let me know if you have any questions about this workshop or have interest in meeting with us in the future. Please also consider applying for the new Anatomy Ontology course this summer.

Paula (pmabee@usd.ed)

Adding Amphibians to Phenoscape

Uncategorized Comments Off

Mar 072012

On 15–16 February 2012, I visited NESCent to work with Peter Midford, Jim Balhoff, and, especially, Wasila Dahdul. The focus of my trip was to push forward on the continued development of the Amphibian Anatomical Ontology and the integration of phenotypic data for amphibians into the larger Phenoscape project.

With Peter Midford, I worked to make a significant update to the Amphibian Taxonomy Ontology based largely on a recent revision to the higher-level taxonomy used on AmphibiaWeb (for which I am part of the steering committee). AmphibiaWeb provides an excellent resource for Phenoscape and other related projects because it provides a list of currently recognized species of living amphibians and is updated daily.

The majority of my visit was spent working with Wasila Dahdul on issues related to the Amphibian Anatomy Ontology (AAO) and on curating our first evolutionary dataset related to the fin–limb transition (Ruta et al., 2003). During this work, we plowed through a significant portion of AAO terms lacking parent terms (either adding parents or synonymizing the terms with others in either VAO or AAO). We also evaluated whether to add terms to the AAO that are present in the Xenopus Anatomy Ontology (XAO; Xenopus is a genus of African frogs used as a model system) but absent in the AAO. In some cases, this led to recommending that those terms be removed from the XAO. As we have started to curate morphological characters related to the limbs from the study by Ruta et al. (2003), we encountered many terms not present in existing anatomy ontologies, such as AAO or the Vertebrate Anatomy Ontology. Some terms had been slated for inclusion in the Amniote Anatomy Ontology (AmAO) being developed by Nizar Ibrahim and Paul Sereno (University of Chicago). Because these terms are also present in non-amniotes, we are recommending that they be migrated from the AmAO to the higher-level VAO.

As we start to focus on curating phenotypes from the literature of vertebrate paleontology, a few issues are emerging. One important issue is that curation of data from paleontological studies will likely necessitate adding a field to our information for specimens to accommodate free text alongside museum abbreviations and catalog numbers. The reason for this is that paleontological studies can rely on a combination of materials, including both specimens and examination of literature. We will also need to add to and refine the collection of museum codes used to curate specimen data. These last points about accurately curating data related to specimens examined are important if we are to use the Phenoscape knowledgebase to point to records for those same specimens in on-line databases, or if databases (such as those for museum collections) want to point to records of specimens in the Phenoscape knowledgebase.

Filed under: Uncategorized

RCN Neural Crest Workshop Report

Anatomy Ontology, Morphology, Uncategorized No Responses »

Mar 062012

The RCN hosted a one-day workshop at NESCent on Feb 22nd on ontological representation of neural crest and its development. Domain experts and ontology representatives from different anatomy ontologies came together to provide a cross-ontology perspective, with the goal of having an integrated set of ontologies to better represent neural crest development and thereby query developmental and evolutionary data. The group will continue refining the ontologies and are developing use cases to evaluate the approach.

Some of the highlights were:

1. We need to represent pre-migratory (part_of neural crest), migratory and post migratory neural crest cells

2. The neural crest is a regional, differentiating part of the neurectoderm, and is a region of the embryo (not as trivial as it sounds!)

3. What we think of as “neural crest cells” are migratory neural crest cells that have migrated out of the neural crest

4. Differential representation of migratory cell populations as 3-D “slugs” in the cranial region vs. “sheets” or “streams” in the trunk

5. Representation of mesenchyme is conflated in most existing ontologies. We need to differentiate embryonic mesenchyme from adult mesenchyme

6. Evidence and attribution about which structures are neural crest derived in any given species would be a very valuable addition to the community, this will be a goal for the working group to pursue

7. What is the neural crest a type of? The neural crest has attributes of a fourth (secondary, or tertiary?) germ layer in that it is not preformed but is rather formed via inductive interactions. This is a controversial idea and potentially not very useful in an ontology given how germ layer classification is not used consistently. But fun to think about . TO DO: Further discussion is necessary to identify the most useful mechanisms to classify neural crest, germ layers, placodes, and their derivatives.

8. Pre-gastrulation, “proto-neural crest”, and Rohon-Beard neurons (or other NC related cells that do not leave the neurectoderm) are not currently represented, classified, or related very well

A high level overview of some of our work:

Diagram highlights neural crest as part of the neurectoderm, which gives rise to migrating streams in the cranial region, or cells along a given path in the trunk region.

Full meeting notes and more figures are available here:

https://docs.google.com/document/d/1-4QZnWGIBZBKLsOccd6mcB44BREv5bhHamCBVWnQAQ4/edit

Participants and agenda are here:

http://wiki.phenotypercn.org/wiki/Neural_Crest_Workshop

Arthropod Working Group at the Phenotype RCN

Anatomy Ontology No Responses »

Mar 052012

External male (left) and female (right) genitalia of ceraphronoid wasps, as visualized using laser confocal microscopy. Which parts of these anatomical complexes are true 'appendages' and why? How do we define an arthropod 'segment'?

It’s been just over a week since our grand Phenotype RCN summit meeting at NESCent, and now that the dust has settled it’s a good time to report on some progress and future directions of the Arthropod Working Group (AWG). The AWG is one of four somewhat loose-knit working groups, organized under the Phenotype RCN umbrella, and our primary goal is to develop a common anatomy ontology for Arthropoda (CAAO, for now). This summit meeting was the third opportunity for us arthroöntologists (pretty sure that wasn’t a real word, until now) to meet since the RCN began last year, and we capitalized on the positive vibe permeating through the greater meeting to discuss five main questions:

1) What resources do we have already to move this effort forward in an organized, robust way? We itemized the various communication and ontology development tools we have at our disposal: Arthropod Anatomy email list (not used much yet, but could blossom), an arthropod anatomy ontology Google Code site with issue tracker, ontology development tools (primarily Protégé and mx), and Skype (of course!)

2) Given these resources, how do we envision the workflow unfolding? We’ve been working in a somewhat piecemeal fashion for the last year, which made progress a bit … slow. Given the varied informatics expertise of our group we still need to discuss mechanisms that will allow everyone to contribute in a relatively flexible way – e.g., some people could checkout the ontology and refine it using Protégé, whereas others will want simply to send requests via email. This discussion is ongoing.

3) Ontology development should be guided by real use cases. What are ours? Our working group (n=17 so far) is populated by systematists, comparative morphologists, neuro-anatomists, and evolutionary developmental biologists. And our study organisms ranged from established models (Drosophila) to emerging models (Parhyale, Gryllus) to fossils. Accordingly, our use cases were quite diverse: connecting behavior to anatomy (For any given behavior, what structures are implicated in clades X and Y?), discovering homology across Arthropoda (e.g., topologically same structure but named differently in different clades), understanding the context of internal arthropod anatomy (in which clades are the ovaries dorsally located anterior to segment X?), standardizing descriptions of comparative anatomy results (making descriptions explicit and logical), query for data about homologous or similar anatomical structures in related species (e.g., gene expression, phenotype, electrophysiology data), make data collected in one domain available/queryable to all other relevant domains (e.g., from descriptive taxonomy to genome-phenome researchers).

4) Given these use cases, how do we prioritize ontology development or otherwise partition its development? This discussion is ongoing, but we tossed around options for recruiting more experts to contribute for certain high priority anatomical systems. E.g., if we see immediate payoff for implementing the CAAO in the context of ovarian phenotypes we could organize a push to recruit more arthropod ovary experts for a working group.

5) What are our action items? We definitely need to organize regular virtual meetings, either as Skype chats/calls or regular conference calls. We’re scheduling the first chat soon and will post here when we finalize the date/time!

So, that’s the quick summary of our working group meeting. Expect more news soon, right here on this blog. In the meantime, if you crave a more detailed report of the AWG activities so far, and you seek to get more involved, don’t hesitate to contact Andy Deans (adeans @ gmail . com) – especially if you think you know the answers to the questions highlighted in the image caption above!

OBO OWL primer

Development, Informatics, OWL 2.0, Software, web ontology language No Responses »

Mar 012012

On the last day of a very successful Phenotype RCN meeting at Nescent last week , we held an impromptu session on OBO to OWL mappings. This was based on the a recent workshop run for GO curators by myself (David Osumi-Sutherland), Chris Mungall, Simon Jupp and Jane Lomax. By popular demand, I’ve posted my slides on slideshare.

The original workshop also included an intro to Protégé 4 by Simon Jupp [warning: word doc] as well as a set of problem solving exercises consisting of a set of folders each featuring one or more test ontologies and a README with instructions. For best results, you should checkout the whole repository of exercises using an svn client: svn checkout http://oboformat.googlecode.com/svn/docs/tutorial/ obo2owl_tut_read_only

Details of the software required for these exercises can be found at http://tinyurl.com/86w9xud

New summer course on anatomy ontologies

Uncategorized Comments Off

Feb 272012

A summer course on anatomy ontologies is being offered for the first time through the NESCent Academy and the Phenotype Ontology Research Coordination Network. The intended audience is postgraduate researchers in evolutionary biology and informatics – including students, postdocs and faculty – who are relative newcomers to ontologies. It will be held from 30-Jul to 3-Aug 2012 in Durham, NC. Spread the word, and if you are interested be sure to apply before the deadline of 6-Apr. [Full disclosure: a number of long-time friends of Phenoscape are among the instructors].

From the course website:

Evolutionary research has been revolutionized by the explosion of genetic information available, and anatomy ontologies must play a central crucial in relating this knowledge to observable diversity. Anatomy ontologies and vocabularies are widely used to index data and are critical for relating gene expression and phenotype data across taxa. Within a single species, anatomy ontologies provide scaffolding that interconnects many kinds of observations; across species, they provide evolutionary, developmental, and mechanistic insights. In order for anatomy ontologies to successfully serve all of these purposes, they must be constructed consistently so that they can be utilized and understood by both researcher and software alike. This course aims to teach proper ontology design principles and practices such that anatomical interoperability across evolutionarily disparate taxa is achieved. It further seeks to promote community growth and adoption of ontology-based methods and tools. The subsequent benefit is in the form of shared access to the unique data store of each community (e.g. genetic, genomic, developmental, and evolutionary data).

The course covers a basic introduction to ontology design principles and usage, specific ontology considerations for anatomy, application of anatomy ontologies in the context of evolutionary phenotype comparison, and use of anatomy ontologies for image annotation in different taxa. There will be strong emphasis on hands-on exercises that will develop ontology skills and provide exposure to different software applications that are useful in variety of areas of evolutionary biology.

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Integrating the Paleobiology Database (PaleoDB) into our taxonomy workflow

Data Curation, Taxonomy Ontology, fossils, paleobiology database, taxonomy Comments Off

Feb 142012

In the original Phenoscape project, our focus was on asking comparative questions regarding living taxa. Although we added fossil taxa to the Teleost Taxonomy Ontology (TTO) when our publications included them, we had no general need to add fossil taxa to the contemporary groups provided by the Catalog of Fishes. However, in our renewal, the focus has both expanded taxonomically (to all vertebrates) and narrowed to the evolution of fins and limbs. The evolution of limbs from fins occurred over 300 million years ago, meaning the morphological data for this transition exists only in the fossil record. Therefore, including fossil data and taxonomy has become essential.

These fossil taxa are not available in the major online sources of names, whether taxon-specific, such as Catalog of Fishes, or general such as Catalog of Life or the NCBI taxonomy. Although NCBI includes some fossil taxa, taxa are only included when a related molecular sequence is submitted, which will never be the case for the vast majority of fossil taxa. These latter taxa will only ever be represented as morphological remains.

This need for fossil data, along with the absence of names from recognized sources, requires us to either add names (and hopefully plausible taxonomy) as curators encounter them in papers, or find an alternative source for names of fossil taxa. Although we have and will continue to add fossil taxa to our taxonomy, we do not, and did not intend to become a name or taxonomy authority in our own right. In light of the strengths and weaknesses of the Phenoscape team allying with a recognized source of fossil taxonomy seems the best option.

The Paleobiology database also called PaleoDB or simply PBDB is an online repository covering a wide range of paleontological data across all taxa represented in the fossil record. These data include names as well as taxonomic opinions appearing in paleontology publications. These data are available and queryable on the PBDB website and are also available for bulk download. As part of developing the Vertebrate Taxonomy Ontology (VTO), an expansion of the TTO to cover all vertebrates and several chordate groups of interest, I have implemented a tool that adds the content of these bulk downloads to a taxonomy ontology. The process of updating from PBDB was designed to minimize disruption to the existing taxonomy by only adding new taxa from PBDB along with whatever taxonomic lineage is required to link each new taxon to a taxon already known to the existing taxonomy. This way, updating from PBDB does not disrupt any existing taxonomic hierarchy we have either incorporated from other resources or were the result of prior curators’ efforts.

However, no taxonomic resource is ever complete. As our term of curators annotate publications, they are encountering fossil taxa unknown to PBDB, and have begun contributing the publication and taxonomy information back to the PBDB. John Alroy and the PBDB board have accepted several project members as authorizers and enterers of data into the PBDB. This allows us to give back to the PBDB as well as simplify the process of adding fossil taxa to our vertebrate taxonomy. We have developed a workflow where a curator can enter publications, names, and taxonomic opinions directly into the PBDB. This immediately makes our additions visible to a wider community and the opportunity to engage expertise we may not have known existed. Subsequent PBDB bulk downloads will include these new names and reflect any changes to the taxonomic opinions entered during curation. These will then be added to the next update of the VTO.

Filed under: Data Curation, Taxonomy Ontology, Uncategorized Tagged: fossils, paleobiology database, taxonomy

Collaborative editing in Phenex 1.2

Curation Tools, Phenex Comments Off

Feb 132012

We have recently released version 1.2.1 of our Phenex annotation software. This release adds some functionality for easier collaborative editing of data files. While our curators have used Subversion revision control software in the past, the new features make it more reliable to share Phenex data files with user-friendly file synchronization software such as Dropbox. While a NeXML document is open in Phenex, the application monitors for changes to the document file in the background. If the file is being shared via Dropbox and is simultaneously edited by someone else, Phenex will alert the user that the file has changed and offer to load the new version. If there are no unsaved edits then Phenex will reload the file automatically. Phenex 1.2 also provides an autosave feature which saves the document after every edit—this reduces the chance that the file might be edited elsewhere while one has unsaved changes, avoiding complicated file merges.

Filed under: Curation Tools, Phenex

NCBO Webinar: Wed, Feb. 15

Webinar No Responses »

Feb 122012

NCBO Webinar: Wed, Feb. 15, 10:00am PT

Michel Dumontier, Formalization of models and simulation results in systems biology.

“NCBO Webinar Series presentations occur via the Web and teleconference at 10:00 am PT on the 1st and 3rd Wednesday of every month. This series aims to showcase new projects, technologies and ideas in biomedical ontology.”

Phenotype RCN

Welcome

Plant Working Group at the Phenotype RCN

Phenotype RCN Annual Summit meeting 2012

Adding Amphibians to Phenoscape

RCN Neural Crest Workshop Report

Arthropod Working Group at the Phenotype RCN

OBO OWL primer

New summer course on anatomy ontologies

Integrating the Paleobiology Database (PaleoDB) into our taxonomy workflow

Collaborative editing in Phenex 1.2

NCBO Webinar: Wed, Feb. 15

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