2010 Semantic Web Workshop

June 16, 2010

I recently attended the 2010 Semantic Web Workshop in Santa Fe, hosted by the SSWAP project and iPlant, at St. John’s College.  This was a two-day workshop, June 7-8, introducing semantic web technologies and applications to biological data and service integration.  The first day was scheduled to be a whirlwind overview of semantic web technologies, beginning with a lecture on the foundations of web logic and reasoning in classic formal logic and moving through RDF, RDFS, and OWL.  However, air travel problems led me to miss the entire first day of the workshop.  Fortunately Damian Gessler, the workshop organizer, provided me with all the slides for the first day upon my arrival, and I was able to somewhat catch up before day 2.  These slides are really a great overview of semantic web technologies and will be a useful resource.

The second day focused on applications to biological data and web services.  A discussion on “taxonomic intelligence” was particularly illuminating.  It provided an example of how different communities can share a set of identifiers for species, for example, yet provide their own set of statements about the taxonomy relating those species.  Each community can draw conclusions relevant to its preferred taxonomy using data associated with the same species.

The afternoon focused on the SSWAP project, led by Damian Gessler.  SSWAP is a protocol which uses OWL documents to describe the inputs and outputs relevant to a web service.  Interestingly, users of these web services would submit their input in the very same OWL model used for service descriptions.

In Phenoscape, we are using OBO ontologies rather than RDF and OWL and storing our ontological annotations in OBD, a datastore tailored for OBO technologies which provides its own very effective reasoner.  However, this workshop provided a great opportunity to stay up to date with semantic web standards and explore how to make our data compatible with and part of the global semantic web.  In addition, St. John’s College was a great meeting location – it is a small college with a wonderful natural landscape in the hills outside of Santa Fe.

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Posted by Jim

Vertebrate skeletal anatomy workshop

May 4, 2010

Probably the most important branch of an anatomy ontology for vertebrates – at least from the standpoint of comparative morphologists, paleontologists, systematists – is the skeleton.  We invited a small group of bone and cartilage experts to come to a workshop at NESCent April 9-10, 2010, with the goal of reviewing, revising, and altogether enhancing the skeletal branch of the various vertebrate anatomy ontologies.  We had representation from the amphibian and teleost multispecies anatomy ontologies, the vertebrate model organism ontologies (zebrafish, Xenopus, mouse), and the cell ontology, as well as expert ontologists to advise on best representation (see our wiki page for their names and slides from their brief introductory presentations).  The workshop was productive beyond our expectations: we produced a ‘generic’ skeletal ontology that can be plugged into all vertebrate anatomy ontologies.  The files (including the useful cmap files) are under review by workshop participants at the moment, and we will be posting the outcome as a Vertebrate Skeletal Ontology in the obo foundry within the month.  Let us know if you want to review some giant spreadsheets of bone terms and relationships in the next few weeks….

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Posted by pmabee

Phenoscape solicits feedback on new interfaces at AmphibAnat Kansas City meeting

December 4, 2009

In early November Wasila and I attended the AmphibAnat workshop in Kansas City, MO (Nov. 5-8) that was organized by Anne Maglia. As you may know, Phenoscape has a close relationship with this group, not only because they work on herps (ichthyologists and herpetologists have a long tradition of working together…), but because they are also developing ontologies to annotate the published comparative anatomical literature. I presented the status of our work in Phenoscape to the large group (~40) of amphibian development and anatomy experts who were present. As these folks added new terms, synonyms, and images to the amphibian ontologies over the course of the next few days, we solicited comments on the prototypes of three new interfaces for the Phenoscape Knowledgebase. Using both images and paper copies of these prototypes, we invited people to sit down with us on a one-on-one basis and describe in detail what worked and what was missing or unclear. The feedback was extremely useful, and we appreciated the AmphibAnat time. We have now gone over all the comments within Phenoscape and logged them individually to FogBugz, our internal tracking system. We’ll be generating new versions of these prototypes through early February, when we plan a formal round of usability testing.

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Posted by pmabee

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 »

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Posted by pmidford

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 »

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Posted by tjvision

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 »

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Posted by pmabee

Second “Evolutionary Biology & Ontologies” workshop

January 9, 2009

Our second “Evolutionary Biology & Ontologies Workshop” was held at the Society of Integrative and Comparative Biology (SICB) meetings in Boston (January 5, 2009).  It was organized by the Phenoscape PIs (Paula Mabee, Todd Vision, Monte Westerfield), NESCent and Barry Smith from the National Center for Biomedical Ontologies (NCBO).  In our morning of talks, our speakers provided the audience with a solid introduction to ontologies, annotations, curation tools, databases, and examples of the integrative questions that can be answered using them.   The speakers, titles, and slides for these talks are available through the links below, and they provide an instructive resource for the community. Read the rest of this entry »

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Posted by pmabee

Report from the Phenoscape Data Roundup

October 24, 2008

“…where the buffalo roam and the data are rounded up-up all day….”

A few weeks ago, from Sep 27 to Oct 1, we met in the Black Hills of South Dakota with a group of guest data curators and outside advisors to curate high priority papers, refine the curation workflow and Phenex interface, and evaluate the first prototypes for the web-based user interface to the database. Not only did the workshop end up highly productive (see below), we also had a chance to observe the annual roundup of the largest herd of buffalo in North America, swim in cold Sylvan lake, and see Mount Rushmore one evening. Read the rest of this entry »

2 Comments | Curation Tools, Data Curation, Informatics, Workshops | Tagged: , , | Permalink
Posted by pmabee

Evolutionary Biology & Ontologies Workshop report

July 11, 2008

Our first educational and outreach event “Evolutionary Biology & Ontologies Workshop” was held at the Evolution meetings in Minneapolis, Minnesota (June 20, 2008), and we felt it was a big success.  We had lots of enthusiasm and over 50 attendees for this all day workshop, which was organized by the Phenoscape PIs (Paula Mabee, Todd Vision, Monte Westerfield), NESCent and Barry Smith from the National Center for Biomedical Ontologies (NCBO). 

We need to especially thank all our speakers for their excellent presentations, They not only gave the audience a varied introduction to ontologies, but also a set of examples of the integrative questions that can be answered using them.   The slideshows for all of these talks are on our wiki but I thought I would provide a brief overview of each one right below as a summary of the workshop. The use of ontologies is just emerging in evolutionary biology, and it is an exciting time to be involved in this field.  As we move forward to use ontologies in evolutionary biology, we discover new requirements and challenges — for example, the challenge of how we create ontologies that are interoperable — so that we can ask big questions that span not only taxonomic groups (such as bees and fishes and mouse and fly) but different knowledge domains (such as phenotype, evolution, and genetics, genomics, medicine). Read the rest of this entry »

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Posted by pmabee

Our first Data Jamboree is beginning

April 18, 2008

The first Phenoscape Data Jamboree (we are scheduled to have one each year) is starting today at NESCent. The event brings three fish morphologists external to the project (Miles Coburn, Kevin Conway, Mário de Pinna) together with our morphologist, ontology, and informatics personnel. In addition, Nicole Washington (NCBO) and Martin Ringwald (Jackson Laboratory), two experts from communities that have made considerable strides in bringing ontology-driven and semantically explicit approaches to bear on annotating gene function and mouse phenotypes and gene expression, respectively, are here to serve in an advisory role.

Read the rest of this entry »

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Posted by Hilmar

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