Beta release of the Phenoscape Knowledgebase

October 12, 2009

We are pleased to announce the beta release of the Phenoscape Knowledgebase (KB) at http://kb.phenoscape.org/ and would like to solicit feedback.

Phenoscape KB integrates phenotypic data from genetic studies of zebrafish with evolutionarily variable phenotypes from the literature of fishes. It currently contains 333,987 phenotype statements about 2,310 taxa (mainly ostariophysan fishes), from 51 publications, and 11,267 phenotype statements about 2,953 genes retrieved from ZFIN (zfin.org). You can explore these data by searching for anatomical terms, taxa (by Latin name), or genes (by ZFIN gene symbol).

You will notice that entering search terms is simplified by auto-completion, so typing the first few letters of a term, taxon, or gene symbol often suffices. There is also a “tag cloud” on the front page that shows the terms most frequently occurring in the KB – click on a term to search for data relevant to that term.

The beta release was first announced at the ASIH meetings in Portland, Oregon this past summer in connection with “Ontologies for Ichthyology and Herpetology” workshop (https://www.phenoscape.org/wiki/ASIH09_workshop).

We expect to make a broader release announcement in February 2010, after we have incorporated the feedback from early users and implemented a number of important features that did not make it into the beta release.

So please take a few minutes to explore Phenoscape KB and send us your feedback and ideas (help@phenoscape.org).


Our summer of code project

August 27, 2009

Phenoscape has mentored, under the auspices of NESCent, another Google Summer of Code student this year.  Kasia Hayden developed a plugin package for Mesquite that allows users to view character matrices and EQ (ontology-based) annotations produced using the Phenex tool.  The primary purpose was to allow curators to share their annotation work with others in the context of a more familiar tool.  Users can select cells in a Mesquite character matrix and, using two new cell tools, see EQ annotations either as text in the bottom pane of the matrix window, or as a graph in a separate pop-up window.

This project also served as an important use-case for the NeXML phylogenetics exchange language.  Although Phenex has used NeXML for over a year, the annotations it generated were not readable by the NeXML package for Mesquite. During and after the database interoperability hackathon last spring, the NeXML developers worked out a standard for annotation and a common java library for parsing NeXML.  Kasia’s project served as a test of that interoperability, and the final product demonstrates that we have achieved it.

Although I was the primary mentor for this project, it would not have been possible without the contributions of Jim, who was co-mentor and who made some Phenex changes to support us, or of Rutger Vos, who pulled the annotation format together and provided us with lots of advice on the NeXML language and library implementation.

Finally, check out Kasia’s walk through of the projectHer blog also traces the progress and frustrations of learning about ontologies, Mesquite, NeXML and the GraphViz Dot language, all in one summer.  Thank you Kasia!

NeXMLAnnotations_MesquiteNexmlViewer


Summer Curation Drive

August 24, 2009

On March 29, 2009, we initiated an ambitious goal (informally dubbed the ‘5K Karacters Kuration Goal’) to curate over 5,000 characters for 3,500 species from 50 papers by June 15. The reason for this annotation push was the planned beta release of the Phenoscape Knowledgebase at the Joint Meeting of Ichthyologists and Herpetologists (22-27 July 2009) in Portland, Oregon. We formed a curator team including Jeff Engeman, Terry Grande, Eric Hilton, John Lundberg, and Paula Mabee, and we each took on a significant chunk (either 500 or 1000 characters) of the ichthyological literature.   Read the rest of this entry »


New fossil tells how piranhas got their teeth

August 16, 2009

A recent publication on Megapiranha paranensis from Phenoscape curators Wasila Dahdul and John Lundberg is in the news!

click for full-zise image

DURHAM, N.C. — How did piranhas — the legendary freshwater fish with the razor bite — get their telltale teeth? Researchers from Argentina, the United States and Venezuela have uncovered the jawbone of a striking transitional fossil that sheds light on this question. Named Megapiranha paranensis, this previously unknown fossil fish bridges the evolutionary gap between flesh-eating piranhas and their plant-eating cousins.

Present-day piranhas have a single row of triangular teeth, like the blade on a saw, explained the researchers. But their closest relatives — a group of fishes commonly known as pacus — have two rows of square teeth, presumably for crushing fruits and seeds. “In modern piranhas the teeth are arranged in a single file,” said Wasila Dahdul, a visiting scientist at the National Evolutionary Synthesis Center in North Carolina. “But in the relatives of piranhas — which tend to be herbivorous fishes — the teeth are in two rows,” said Dahdul.

Megapiranha shows an intermediate pattern: it’s teeth are arranged in a zig-zag row. This suggests that the two rows in pacus were compressed to form a single row in piranhas. “It almost looks like the teeth are migrating from the second row into the first row,” said John Lundberg, curator at the Academy of Natural Sciences in Philadelphia and a co-author of the study.

If this is so, Megapiranha may be an intermediate step in the long process that produced the piranha’s distinctive bite. To find out where Megapiranha falls in the evolutionary tree for these fishes, Dahdul examined hundreds of specimens of modern piranhas and their relatives. “What’s cool about this group of fish is their teeth have really distinctive features. A single tooth can tell you a lot about what species it is and what other fishes they’re related to,” said Dahdul. Her phylogenetic analysis confirms their hunch — Megapiranha seems to fit between piranhas and pacus in the fish family tree.

The Megapiranha fossil was originally collected in a riverside cliff in northeastern Argentina in the early 1900s, but remained unstudied until paleontologist Alberto Cione of Argentina’s La Plata Museum rediscovered the startling specimen — an upper jaw with three unusually large and pointed teeth — in the 1980s in a museum drawer.

Cione’s find suggests that Megapiranha lived between 8-10 million years ago in a South American river system known as the Parana. But you wouldn’t want to meet one today. If the jawbone of this fossil is any indication, Megapiranha was a big fish. By comparing the teeth and jaw to the same bones in present-day species, the researchers estimate that Megapiranha was up to 1 meter (3 feet) in length. That’s at least four times as long as modern piranhas. Although no one is sure what Megapiranha ate, it probably had a diverse diet, said Cione.

Other riddles remain, however. “Piranhas have six teeth, but Megapiranha had seven,” said Dahdul. “So what happened to the seventh tooth?”

“One of the teeth may have been lost,” said Lundberg. “Or two of the original seven may have fused together over evolutionary time. It’s an unanswered question. Maybe someday we’ll find out.”

********************

The team’s findings were published in the June 2009 issue of the Journal of Vertebrate Paleontology.

CITATION: Cione, A., W. Dahdul, J. Lundberg, and A. Machado-Allison. (2009). “Megapiranha paranensis, a new genus and species of Serrasalmidae (Characiformes, Teleostei) from the upper Miocene of Argentina.” Journal of Vertebrate Paleontology 29(2): 350-358.

Image Credits:
Artwork by Ray Troll, 2005


Phenex 1.0-beta24 released

August 14, 2009

Phenex 1.0-beta24 is now available for download.

This release has a few new features and a number of bug fixes:

Features:

  • The Search panel from OBO-Edit is now available in Phenex, under the View > Ontology menu.  This allows the user to do a textual search of all loaded terms, and view a results list.
  • There is a “quick editing” mode for the character matrix interface.  The user can type the name of a state symbol, without first double-clicking the cell, and Tab or Return to the next cell to edit.
  • If the quality “count” has been used in a phenotype for any state for a character, it will be auto-filled for subsequent states.
  • Open/Save panel starts at the previously visited directory.

Bugs fixed:

  • Copy and paste of terms in the Phenotypes table works consistently now.
  • The post-composition editor no longer disappears after tabbing out of the genus field when running on Java 6.
  • The menubar no longer disappears after using the post-composition editor.

ICBO Summary

August 12, 2009
While the rest of Phenoscape was at ASIH running the ontology workshop and announcing the database and website release, I was across the country, representing Phenoscape at the International Conference on Biomedical Ontologies in Buffalo, NY.
ICBO covered 2-3/4 days (July 24-26) of presentations with two evening poster sessions.  There were
also software demos during the lunch breaks, and two panel discussions.
Although there were several sessions devoted to ontologies of disease and clinical practice, there
were a number of talks of interest to Phenoscapers.  Among these were several alignment talks, including
one from the BGEE group on Homonto and Chris Mungall’s on cross products and Uberon.  There were also sessions
on annotation and natural language processing (NLP), including Mike Bada’s talk on developing a corpus for testing NLP based annotation.
There were also two talks specifically about ontologies and physiology, one by John Gennari focused on integrating
existing anatomy ontologies (e.g., FMA) with physiological simulations, though he specifically ducked ontological
modeling of physiology as process.  The other was an ‘old school AI’ simulation of a patient, that includes models of
physiology, cognition, and NLP.
There was also some promising activity on behavior ontologies, including a poster by Tim Beck, a postdoc from the UK on a mammalian behavior ontology
and a ‘behavior lunch’ on the second day, with Tim, Judy Blake, David Shotton (ABO collaborator from Oxford), Mary Shimoyama (RGD), and several others.
There is a European plan to develop a new OWL-based general behavior ontology, and Chris Mungall has recently established an OBO-behavior list ().
There was also a lot of discussion generated by the proposed ontology of homology relations (the 1.0 version; 1.1 released recently(http://bgee.unil.ch/bgee/download/homology_ontology_v1.1.obo)), although the consensus from the numerous people I discussed
it with was that it needed more work (which is happening).
Other interesting ontologies included an ontology of Evolutionary processes presented in a poster by Adam Goldstein (Iona University).  He’s since been in
contact with Hilmar, and I believe with representatives of CDAO and Dryad.  Phenoscape was also represented by a poster.
There were two panels, one focussing on Ontology and Publishing.  Although the lineup, which included
a representative from Elsevier (Jabe Wilson) and Alan Ruttenberg from Science Commons suggested a discussion
on open publishing, the Elsevier representation was quiet restrained, and it was Larry Hunter who made the strongest argument that publishers currently
provide little value to academics.  David Shotton discussed his semantic annotation of a randomly selected paper on an infectous disease.
The second panel was on the Future (and past) of ontologies and knowledge representation.  I think the two memorable claims from this discussion
were the call to expand the A-box (since the T-box is really less than most people think) and Barry Smith’s claim that in 25 years consulting ontologies
will be as common in biology and medical departements as statisticians are today.
The text from all the presentations and posters will be made available at Nature Proceedings (http://precedings.nature.com/collections/icbo-2009).  There was
also an ICBO group on FriendFeed (http://friendfeed.com/icbo) with other attendee’s tweets from the conference and preceeding tutorial sessions.  Finally, I will
be posted a more detailed report on my personal blog (http://ontethology.blogspot.com).

While the rest of Phenoscape was at the ASIH meeting, involved with the ontology workshop and the release of the database and website, I was across the country, representing Phenoscape at the International Conference on Biomedical Ontologies (ICBO) in Buffalo, NY.  ICBO covered 2-3/4 days (July 24-26) of presentations with two evening poster sessions. There were also software demos during the lunch breaks, and two panel discussions.

Although many of the sessions were devoted to ontologies of disease and clinical practice, there were a number of talks of interest to Phenoscapers. Read the rest of this entry »


Postdoctoral opportunity: The genetics and evolution of anatomical diversity in fishes

June 16, 2009

An NSF-funded postdoctoral position is available in the laboratory of Monte Westerfield (University of Oregon, Institute of Neuroscience) to study experimentally candidate genes for the diversification of skeletal architecture in fish species related to zebrafish.

The position is available through the Phenoscape project, a collaboration among evolutionary and model organism biologists (including Paula Mabee of the University of South Dakota, Monte Westerfield of the Zebrafish Information Network, and Todd Vision of the National Evolutionary Synthesis Center). Read the rest of this entry »


Joint Phenoscape and AmphibAnat Workshop at ASIH, July 25th in Portland, Oregon

May 28, 2009

ASIH 2009 workshop banner

Ontologies, controlled vocabularies with well-defined relations among terms, are a key tool in scientific data integration. By using ontologies, scientists from different disciplines can know when they are referring to the same entity by different names, and new discoveries are enabled by computer software being able to reason across disciplines and over large datasets. Already widely used in genomics, ontologies are of growing importance in systematics, ecology, behavior, genetics, morphology and physiology. This workshop aims to explore the utility of ontologies for ichthyology and herpetology, using the Teleost Anatomy Ontology and the Amphibian Anatomy Ontology as case studies of community resources that are being actively developed and used by members of ASIH. Read the rest of this entry »


Meeting with Deep Fin and other fishy folk

April 17, 2009

Phenoscapers met with Deep Fin and several associated fish groups in late February for ontology development, curation, web interface development and outreach. We had lots of good interactions with the 30+ ichthyologists attending. Read below for the details. Read the rest of this entry »


Summer Training Opportunities

February 1, 2009

We are offering summer traineeships for graduate students and postdocs interested in gaining expertise in informatics and the application of ontologies to evolutionary, anatomical, developmental, and genetic data.

Opportunities are available to work as part of the Phenoscape team on data curation or open source software/database development. Participants would be located at the National Evolutionary Synthesis Center or the University of South Dakota. Stipends of $5,000 will be given to participants to cover travel, room and board for 10-12 weeks. Read the rest of this entry »