now browsing by category


BioPortal ontology support

The functionality for reading of the ontology directly from the BioPortal web was implemented. The user can simply define the path to several of the ontologies stored in BioPortal repository. The terms from the ontology can be used in the process of design of experimental protocol for experiment description. Standardization of terminology used for experiment description based on evaluated ontology is the best way how to properly describe and share experimental protocols.

We are still adding the support for the main repositories in the field.

BioWES Poster from ICSB 2013

Poster ICSB 2013 JPEG

BioWES on ICSB 2013

The pilot version of BioWES data storage system was demonstrated on 14th International Conference on Systems Biology in Copenhagen. The main purpose of the specialized workshop organized within the conference was to receive the feedback of the participating system biologists. Further development of the system as well as its testing and presentation is planned in Autumn.


Aquaculture Europe 2013

Aquaculture Europe – the annual meeting of the European Aquaculture Society – takes place at the Norwegian University of Science and Technology in Trondheim in August 9 – 12, 2013. The theme – Making Sense of Science – will focus on knowledge management to support technological development and innovation. The plenary sessions will provide delegates the examples from various sectors. Abstracts for the parallel sessions will focus on demonstrating the practical implications and application of results.

Sessions and abstracts are to be focused on following questions:

  • What is driving innovation? Theory & Practice – and including closed versus open innovation, the utilization of networks, organic organizations and the balance between exploration and exploitation, and paradigm shifts for breakthrough and acceptance.
  • Mapping genomes – what impact for the sector? Status and future of mapping fish, algae, bacteria and other genomes. Modern molecular biology techniques for genetic mapping can create new breakthroughs in revealing breeding efficiency and adaptation of physiological responses. What impacts could this have for the cultivation of aquatic organisms?
  • Maximising impact of research – How can we secure optimal transfer of new scientific knowledge into use in the sector? How do we set priorities – before, during and after programs, evaluations and in consortia? How do we communicate better to different users of new knowledge?

Conferences in 2014

20th International Mass Spectrometry Conference will take place in Geneva, Switzerland, August 24-29, 2014. Geneva was selected as host city of the 20th IMSC, which will be taking place at the Centre International de Conférences Genève (CICG).


The 5th Conference on Systems Biology of Mammalian Cells (SBMC) 2014 will be held in Germany in July 2014.

The Open Biological and Biomedical Ontologies

Ascomycete phenotype ontology was added into OBO CVS repository.

The ontology serve as a structured controlled vocabulary for the phenotypes of Ascomycete fungi. The ontology is related to the Saccharomyces genome database. You can find more details about the database here:

Pilot of protocol designer

The discussion with partners involved in the testing of the BioWes system identified the bottle necks of the developing solution. The definition of the electronic template of the protocol was the main issue. The XML language was originally used for the definition of the protocol template. This way of definition is very beneficial from standardization point of view but it is not very user friendly. Therefore the WYSIWYG (graphical user interface) editor Protocol designer has been developed to solve this issue. Using the Protocol designer, every technician can prepare the protocol template and use it for description of experiments.


New ontology focused on the fish production was developed in the frame of Aquaexcel projects (

The goal of the AQUAEXCEL-ATOL ontology is to define and organize livestock traits, with a focus on the main types of fish production (meat, feed and fertility) in accordance with societal priorities (animal welfare, product quality, etc.).

This ontology will be a reference for semantic search tools in order to improve queries on bibliographic resources about livestock animal phenotypes. Making homogeneous database annotation, it opens the possibility for meta-analysis and modeling.

Follow the link to access the ontology tool:

A tutorial on the tool can be found at:

Protocol generator testing

BioWes testing at the Core Facility Cell Imaging and Ultrastructure Research of University of Vienna.

The prototype of the Protocol generator and the Local database was installed in the Cell physiology and scientific film laboratory of Core Facility Cell Imaging and Ultrastructure Research of University of Vienna. The laboratory seeks the way how to contribute to the understanding of the organization and dynamics of plant cells under various physiological and ecological conditions. The laboratory will use the system of electronic protocols for description of the advanced video light and electron microscopy combined with fluorescence techniques.