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What is an ontology?
Why an ontology about the Cell Cycle?
How can I benefit from the project?
How can I contribute to the project?
What is OWL?
What is RDF?
What is OBO?
What does a CCO id mean?
Which organisms does CCO cover?
What is the scope of CCO?
How can I cite CCO?
Do I need a license to use CCO and/or integrate it into my database/ontology?
Can I use data from CCO to build other resources?
Where is my question? What is an ontology?
The short answer is that, as Gruber first stated, an ontology is a specification of a conceptualization of a knowledge domain. An ontology is a controlled vocabulary that describes objects and the relations between them in a formal way, and has a grammar for using the vocabulary terms to express something meaningful within a specified domain of interest. The vocabulary is used to make queries and assertions. Ontological commitments are agreements to use the vocabulary in a consistent way for knowledge sharing. TOP Why an Ontology about the Cell Cycle?
Because there is no efficient computational representation of the knowledge about the Cell Cycle. TOP How can I benefit from the project?
Depending on who are you and what you need, the benefit you can obtain can be found in different levels (see this diagram). For example, if you are a Biologist, you may be interested in answering some questions you have about your favourite cell cycle protein. If you are a programmer who has to build an application that does something interesting with articles that refer the to the cell cycle, you may want to use the ontology as a help or data model. Perhaps you are a programmer and you need to deal with OBO ontologies in a simple and straight forward way, so in that case you would be interested in the APIs and tools. And so on.TOP How can I contribute to the project?
You can contribute in different areas: - Using the ontology and telling us what is lacking on it or how we could improve it.
- Using the APIs and other resources (plugins, ...) and telling us whether you find any bugs or possible improvements.
- Improving the APIs or contributing with more code or ideas.
- ...
All the suggestions can be sent to the mailing list (ccofriends @ psb.ugent.be) or the email address (cco @ psb.ugent.be).TOP What is OWL?
OWL stands for Web Ontology Language. It is an official W3C reccomendation for knowledge representation (i.e. ontology building) in the semantic web. It is and open and widely accepted standard, it is very expressive, it has strict semantics, and it has a sound formal basis. This allows for reasoning, thus for better maintenance and querying of CCO. TOP What is RDF?
RDF (Resource Description Framework) is a knowledge representation language proposed by the W3C for knowledge integration in the semantic web. RDF has a very basic model behind, based on triples, offering "light-weight" semantics: it is not as expressive as OWL but it is suitable for "fast and cheap" knowledge integration and querying.TOP What is OBO?
OBO stands for Open Biomedical Ontologies and it is the name of the OBO file format as well. It is, like OWL, a knowledge representation language for building ontologies. It is widely accepted in the Biologists' community because it is very intuitive, although it doesn't have the same formal advantages of OWL.TOP What does a CCO id mean?
Each element has a unique identifier of the form CCO:cnnnnnnn. CCO indicates that the concept belongs to the CCO ontology (CCO is also known as the ontology namespace), c denotes de sub-namespace: C (cellular component), P (biological process), F (molecular function), R (reference), T (taxon), I (interaction), B (protein) and G (gene). Finally, nnnnnnn consists of 7 numerical characters.TOP Which organisms does CCO cover?
For the moment the following: Arabidopsis thaliana, Homo sapiens,Saccharomyces cerevisiae and Schizosaccharomyces pombe.TOP What is the scope of CCO?
CCO basically contains genes, proteins, interactions (comprising genes or proteins that participate in them), processes from the cell cycle subtree of GO, molecular functions (GO), taxa, and ontological constructs (like an upper level ontology and relationships) to stick everything together. The knowledge represented in the system is expected to grow in quantity (integrating more data and different resources) and quality (organizing everything with Ontology Design Patterns and new relationships).TOP How can I cite CCO?
Please cite: A cell-cycle knowledge integration framework. DILS 2006, LNBI 4075, pp. 19-34, 2006. (SpringerLink). You should please cite the CCO web site as well (http://www.cellcycleontology.org).TOP Do I need a license to use CCO and/or integrate it into my database/ontology?
The CCO is available to both public and private sector users with no licensing requirements. However, we would ask you to cite the CCO web site (http://www.cellcycleontology.org). Due to its integrative nature, there are components within CCO which may call for a different licensing approach. We have acknowledged them and created cross references to the original entities.TOP Can I use data from CCO to build other resources?
Yes, in fact CCO does it with other resources. You can do it as long as you cite the paper mentioned in the prior question and this webpage.TOP Where is my question?
If you don't find the question you are looking for, please send an email to cco @ psb.ugent.be.TOP
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