1st - 2nd of February 2010, Rostock (Germany)
Modeling biological systems: Bio-model similarities and differences based on semantic information
General Information
Date: Monday, 1st – Tuesday 2nd of February 2010Organization: Dipl.-Inf. Dagmar Waltemath, Graduate school dIEM oSiRiS, Rostock University
Workshop location: Rostock University, Ulmenstrasse 69, Haus 1, room SR118
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Questions to be addressed during the workshop
- Semantics, annotations and meta-information - what is this all about? What are the relations between these notions?
- What is the current state-of-the-art regarding the use of bio-model meta-information?
- What approaches exist for the annotation of models? What is annotated and how is annotation done technically?
- Who is annotating? What resources can be used?
- What concepts exist to determine bio-model similarities (in biology vs information retrieval)?
- What implementations exist to calculate bio-model similarities?
- How can we enhance work on model similarities using existing work on meta-information (e.g. annotations)?
Aim
The main aim is to share our knowledge on model "semantics", use it to develop ideas on how to determine model similarities/differences, discuss open issues, and investigate how to bring together the different projects we are working on.Therefore, the schedule is not considered "fixed" but rather as a guideline. Feel free to make comments and suggest further topics!
Wiki page
linkSchedule
The meeting will start on Monday, 1st of February 2010 at 11am.- Invited speakers: Nicolas Le Novère and Patrick Lambrix
- Attendees will have 5 minutes (and 1 slide) for introduction and presentation of their work. Please try to communicate especially what you would need for your work and what you think you can provide to the others.
- Remaining time will be dedicated to discussions. The given slots are no must. Lively discussions, also in smaller groups and on different issues, are always welcome!
| time slot | session |
| 11:00-12:00 | Patrick Lambrix: Ontology alignment and applications.
Abstract The use of ontologies is a key technology for the Semantic Web and in particular in the biomedical field many ontologies have already been developed. Many of these ontologies, however, contain overlapping information and to make full use of the advantages of ontologies it is important to know the inter-ontology relationships, i.e. we need to align the ontologies. Knowledge of these alignments would lead to improvements in search, integration and analysis of biomedical data. In this talk we give an overview of techniques for ontology alignment with a focus on approaches that compute similarity values between terms in the different ontologies. Further, we discuss the results of evaluations of these techniques using biomedical ontologies. We also give examples of the use of ontology alignment in applications such as literature search. slides |
12:00-13:00 | l-u-n-c-h at Mensa (not funded) |
| 13:00-14:00 | Nicolas Le Novère: Toward a consistent set of interoperable standards to represent models and simulations.
Abstract A decade ago, the creation of the Systems Biology Markup Language (SBML) changed the way people exchanged, verified and re-used models in systems biology. The robustness and versatility of this standard format, coupled to a wide software support fostered the emergence of a whole area of research centred on model processing such as encoding, annotation, merging, comparison and integration with other datasets. Other community standards of representation were created in computational systems biology, and a vertical organisation is emerging, with different layers of descriptions. While the model structure is covered by SBML and similar efforts, the biological semantics can be described using BioPAX while models and pathways can be graphically represented using the languages of the Systems Biology Graphical Notation (SBGN). Computing glues permit to relate the components of the different layers. For instance one can generate SBGN maps from SBML using the Systems Biology Ontology (SBO) and convert SBML into BioPAX using the controlled MIRIAM annotations. Independently to the systems biology community, other scientists developed their own standards of representations, such as CellML (physiology), NeuroML (neurophysiology), SimileXML (ecology), with more on the way. More recently, new languages appeared that complement the model description, such as SED-ML to describe the simulation experiments or SBRML to encode the numerical results. The developers of all those initiatives are now in contact, and try to improve the interoperability of the languages. One can hope to see, in a not too elusive future, the creation of a coherent set of non-overlapping standards, similar to the W3C standards for the World Wide Web, that will cover the various modeling approaches and scales, but also the different levels of discourse and representation in Systems Biology. slides |
| 14:30-15:30 | Presentation round (5 minutes for each participant) Dagmar Waltemath |
| 15:30-16:00 | c-o-f-f-e-e |
| 16:00-17:30 | On annotations: How are models annotated? What are the techniques behind? Which resources exist and how could we make use of each other's work? Introduction by Christian Knüpfer |
| 19:00 - ?? | Dinner at Heumond in the city (student restaurant, not funded) |
Tuesday, 2nd of February
| time slot | session |
| 9:00-10:30 | (continuing on yesterday's first session) Short discussion of the main issues of the following sessions |
| 10:30-11:00 | c-o-f-f-e-e |
| 11:00-12:30 | Data and Models / Model Versions and Annotations of annotations |
| 12:30-13:30 | l-u-n-c-h at Mensa (not funded) |
| 13:30-15:00 | Model Features / Model similarity /Ontology Alignment |
| 15:00-15:30 | c-o-f-f-e-e |
| 15:30-16:30 | How to write the annotation spec? |
| 16:30-17:00 | Conclusions. |
| 19:00 | Meet at Greifennest for a walk through the city. |
| 20:00 | Dinner at Carlo 615 at the harbour. |
Confirmed participants
- Patrick Lambrix, Linköpings Universitet (Sweden) homepage
- Nicolas Le Novère, European Bioinformatics Institute (UK) homepage
- Ron Henkel, Universität Rostock homepage
- Christian Knüpfer, Friedrich-Schiller-Universität Jena homepage
- Falko Krause, Humboldt-Universität zu Berlin homepage
- Wolfram Liebermeister, Humboldt-Unisversität zu Berlin homepage
- Allyson Lister, Newcastle University (UK) homepage
- Marvin Schulz, Humboldt-Universität zu Berlin homepage
- Neil Swainston, University of Manchester homepage
- Dagmar Waltemath, Universität Rostock homepage
- Sarala Wimalaratne, European Bioinformatics Institute (UK) homepage
Directions
Model meeting locations show on a bigger map
University Campus Ulmenstrasse: The meeting takes place in house 1, which is the one located on Ulmenstrasse.
There is a couple of places around to have breakfast (e.g. Humboldt), lunch (e.g. Mensa), or just a coffee.
Wireless Lan is available on the campus.
Hotel Greifennest: August-Bebel-Strasse 49b, 18055 Rostock map
To get to the University campus Ulmenstrasse, take but no. 25 from Schröderplatz towards Thomas-Morus-Strasse until Saarplatz (1 stop), or walk downhill August-Bebel-Strasse, uphill Arnold-Bernhard-Strasse towards Saarplatz. Walk down Ulmenstrasse. (10-15 min)
Intercity Hotel: Herweghstraße 51, 18055 Rostock (located directly at the train station)
To get to the University campus Ulmenstrasse, take the S-Bahn (fast train) from the train station (track 1 or 2) towards Warnemünde. Get off the first station, Parkstrasse. Walk towards the campus. (10 min)