Frequently Asked Questions
What is SBO, and who should use it?
- What is SBO, and what does it stand for?
- What is SBO used for, and why was it created?
- Is SBO use restricted to the field of Systems Biology?
- Is there a particular modelling format within which SBO should be used?
- Who should annotate a model, and what purpose does it serve?
What does SBO describe, and what does it look like?
- What does the ontology look like?
- What information do the separate branches hold?
- How are SBO terms linked to each other?
- What does an SBO identifier look like?
- How do I access a specific SBO term?
- Are there any relationships between terms originating from different branches of the ontology?
SBO - Questions about term and ontology stability
- How stable are SBO identifiers?
- What is obsoletion?
- Is there a versioning systems for SBO?
- How do I know what has changed recently in the ontology?
What information is available, and what is the best way to access it?
- What information is stored with each entry
- How do I search SBO for a term?
- Where can I download SBO?
- Under which license is SBO distributed?
- Which components of SBO can be accessed through web services?
Suggesting new terms for SBO, reporting bugs, citations and contacts
- What is the best way to suggest a term for inclusion in SBO?
- How do I report an error in an SBO term?
- How do I contact you with other concerns or issues?
- How do I cite SBO?
More specific questions about SBO and modeling
What is SBO, and what does it stand for?
SBO is an acronym for Systems Biology Ontology. It is one of a number of OBO Foundry candidate ontologies , and is freely available for anyone to use. It is composed of hierarchically arranged sets of controlled vocabularies that are commonly used in mathematical modelling. Information on the individual branches can be found here.
What is SBO used for, and why was it created?
SBO is used primarily used in the annotation of mathematical models, as a way to provide additional semantic information. This semantic layer of information is not required for simulations instantiated from a model, but can provide additional information to the modeler about, for example, the roles of participants in particular reactions, the framework that the model was conceived in, or the specific mathematical rules that modeler has determined to govern the behavior of the instantiated system. It was created in response to the growing desire of the mathematical modelling community to incorporate semantic information into mathematical models.
Is SBO use restricted to the field of Systems Biology?
As mentioned, the use of SBO, whilst primarily being in the modelling field, is not restricted to it. As with other OBO ontologies, SBO can be freely used to annotate information, where a suitable term can be found.
Is there a particular modelling format within which SBO should be used?
There exist a number of defined formats within which mathematical models can be encoded. These include, for example, SBML, CellML, and GENESIS. SBO terms can be used in any of these formats, or indeed in any structured format. SBML itself, however, does provide a specific manner in which SBO terms can be integrated into the file format; Since Level 2 Version 2, SBML has incorporated a specific attribute, sboTerm, specifically for the purpose of linking SBO term annotations with model components.
Who should annotate a model, and what purpose does it serve?
A model can essentially be annotated with SBO at any time during its lifecycle. The model creator may annotate a model at the time of creation to provide information regarding how it was constructed, thereby providing unambiguous information on any in-built assumptions, or to define the precise framework within which the model was constructed. A subsequent modeler, having run various simulations, may choose to provide additional information in the model itself, perhaps more precisely defining the nature of the parameters or about specific rate laws that can be applied. A biological investigator may provide information on the roles particular participants play within reactions encoded in the model, to integrate a biological perspective into the model. The short answer is that SBO terms can be added at all stages of the model's lifecycle, and by anyone who harbors an interest. The additional semantic information added in this way increases the usability, and reusability, of the model, as well as allowing models themselves to be converted from one framework to another, or indeed from one formal representational format to another.
What does the ontology look like?
SBO is actually composed of seven orthogonal vocabularies, each represented by a 'branch' of the ontology, and each related to the root 'sbo term' through an 'is_a' relationship. More information about this type of relationship can be reached from here. The SBO branch structure can be viewed from the main page.
The tree itself is fully navigable, and branches can be expanded and collapsed using the '+' and '-' icons, respectively, on the left side of each sub-tree.
What information do the separate branches hold?
Each of the seven branches of the ontology represent different aspects/concepts:
- 'entity' branch : hierarchically arranged set of terms to represent either 'material' entities (e.g. 'macromolecule' and 'simple chemical'), or functional entities (e.g. 'enzyme' and 'receptor').
- 'interaction' branch : hierarchically arranged set of terms to represent types of process, (e.g. 'transport reaction'), and the relationship an entity has to another (e.g.'inhibition')
- 'mathematical expression' branch : hierarchically arranged set of terms which successively refine various mathematical expressions contained within a model (e.g. enzymatic rate law')
- 'metadata representation' branch : hierarchically arranged set of terms which define the different types of metadata which are commonly provided with model components (e.g. bibliographical reference')
- 'modelling framework' branch : hierarchically arranged set of terms precisely define the framework within which the model was constructed, which is crucial to understand its limitations under various simulation conditions (e.g. discrete framework')
- 'participant role' branch : hierarchically arranged set of terms which specify precisely the role played by model components, whether they be, for example, a functional compartment, or competitive inhibitor
- 'quantitative parameter' branch : hierarchically arranged set of terms which precisely numerical parameter that are used in quantitative models (e.g. kinetic constants' and 'biochemical coefficient')
It is noteworthy that terms in the 'quantitative parameter' and 'mathematical expression' branches contain mathematical expressions encoded in MathML 2.0. These serve to relate the symbols used in the mathematical expressions in the model to the actual parameter intended to be referenced in the ontology, thereby removing any ambiguity in the semantic meaning.
How are SBO terms linked to each other?Within each branch, the hierarchically arranged terms are related by subclassing (aka hyponymy or subsumption). In this way, each term is_a particular version of the parent term.
What does an SBO identifier look like?
SBO identifiers take the following form: 'SBO' prefix, a colon separator, trailed by a 7 digit identifier. e.g SBO:1234567.
Once assigned, an identifier perennially identifies a concept within the ontology. Some of the information associated with an SBO term may change, for example where a term is refined, or where it is made obsolete.
How do I access a specific SBO term?
The previous access URL is also still functional: http://www.ebi.ac.uk/sbo/main/entry.do?sboId=SBO:0000029.
Are there any relationships between terms originating from different branches of the ontology?
SBO contains only is_a relationships (subsumption), where the terms of the various vocabularies are not directly linked as in some "classical" ontologies. Some branches of the ontology do however contain MathML lambda functions, within which there are links to terms in the other branches. For instance, here is the MathML for the "Henri-Michaelis-Menten rate law":
|<semantics definitionURL="http://biomodels.net/SBO/#SBO:0000062">||targets continuous framework (modelling framework branch)|
|<bvar><ci definitionURL="http://biomodels.net/SBO/#SBO:0000025">kcat</ci></bvar>||targets catalytic rate constant (quantitative parameter)|
|<bvar><ci definitionURL="http://biomodels.net/SBO/#SBO:0000505">Et</ci></bvar>||targets concentration of enzyme (quantitative parameter branch)|
|<bvar><ci definitionURL="http://biomodels.net/SBO/#SBO:0000015">S</ci></bvar>||targets concentration of substrate (quantitative parameter branch)|
|<bvar><ci definitionURL="http://biomodels.net/SBO/#SBO:0000373">Ks</ci></bvar>||targets Michaelis constant in fast equilibrium (quantitative parameter branch)|
How stable are SBO identifiers?
As previously stated, once assigned, and identifier is permanently associated with an SBO concept. Some changes may be made, however, to a term name, its definition, or to some of the other fields associated with the term. These do not affect the central concept represented by the term, but should serve only to clarify the existing term, or to refine it. Practically, such changes are required when new terms are introduced into the ontology and relationships with existing 'child' or 'parent' terms need to be further refined to allow conceptual distinction between them.
What is obsoletion?
There are rare occasions where a term no longer fits within the SBO domain. This could occur where:
- a term is superseded
- the concept for a term is made redundant by the use of an improved representational approach
- more than one term is found to cover the same concept space
- a term is erroneously created
In each case, the redundant term is made 'obsolete' and withdrawn from the visible ontology, although it does still exist and can be searched for. This helps prevent reuse of the obsolete term for new annotations, while retaining the term for previously created annotations. Obsolete terms in the ontology are clearly marked, in red on the term view, as "(OBSOLETE TERM)" beside the SBO identifier. Where appropriate, alternative terms that can be used in place of those that have been made obsolete are suggested. These are listed as either 'consider using' or 'replaced by', indicating a refinement of that section of the ontology.
Is there a versioning systems for SBO?
There is currently no versioning system for the ontology, although we do plan to add such a feature. While each individual term in the ontology has a modification log, the only current way to identify a 'version' of the ontology itself is by looking at the 'data-version' field in the download file. This identifies the collected data set comprising the ontology by date.
How do I know what has changed recently in the ontology?
A list of the most recent changes to the ontology can be found here. This provides the same information as is available through the history field in an SBO entry, as well as a 'comment', providing information summarising why the change was made.
What information is stored with each entry
Clicking on a term generates a pop up display containing the following information, also known as the entry view:
- Identifier: The SBO identifier appears at the top of the pop up display.
- Name: The full name of the SBO term.
- (optional) Synonyms: Known synonyms for the term name.
- Definition: Textual definition describing the precise meaning and context of use for the selected term.
- (optional) MathML: A standardised XML-based mathematical definition of the term.
- (optional) Rendered equation: The graphically rendered representation of the mathematical definition presented in the MathML field, if applicable.
- Comment: Clarification comments inserted by the curator to further define or clarify the use of the term.
- Miscellaneous: Creation and last modification dates for the term.
- Parents: Hyperlinked SBO identifier(s), and term name(s) of the immediate parent(s) of the displayed term.
- Children: Hyperlinked SBO identifier(s), and term name(s) of the immediate children of the displayed term.
- History: Lists the dates, actions and details of all changes to the displayed term, since its introduction to the ontology.
In the case of obsolete terms, the identifier at the top of the pop up is clearly marked obsolete.
How do I search SBO for a term?
Search results are returned as a series of tables, differentiated on the basis of where in the term information the keyword was located. Each table lists the SBO Accession ('identifier'), 'term name', and clickable links to both the 'tree view' and the 'entry view'. Up to four tables are displayed, depending on where the search term was matched:
- Table 1 - search keyword matched with an SBO 'accession'.
- Table 2 - search keyword matched with an SBO 'term name'.
- Table 3 - search keyword matched with either 'definition', 'comment' or 'MathML'.
- Table 4 - search keyword matched with a 'synonym'.
If more than one keyword is entered for search, the results page lists only terms where all keywords appear within an SBO term. We aim to increase the functionality of the search to allow 'OR' and other logical combinations.
Where can I download SBO?
SBO can be downloaded here. It is available in 3 different formats: OBO, OWL or XML file. An export of each file format is generated each day (7.00 GMT) for direct download, and is available under the 'Instant exports' heading. Alternatively, a downloadable file can be generated on request under the 'Generate exports' heading. The 'SBO Statistics' summary display on the download page (top, right side) indicates the date of the last modification to the ontology. This may be useful in determining whether you wish to download an instant or generated export. A more extensive list of changes to the ontology can be found through the 'Recent changes'.
Under which license is SBO distributed?
SBO is distributed under the Artistic License 2.0.
Which components of SBO can be accessed through web services?
A list of the Web Services available for SBO data access can be found here. These can be used to programmatically access various information about terms available in the ontology, or even to retrieve information on sub-trees. Services include the ability to search for terms based on synonyms, retrieval of term information based on provision of an identifier, and the ability to retrieve parent/child relationships for a given SBO term. The WSDL describing the services is available here, while the java library required is available from links here. Tutorials are also available from this page to demonstrate use of the Web Services.
What is the best way to suggest a term for inclusion in SBO?
SBO is an open source project, and is listed on SourceForge. Both term and feature requests can be submitted from this page. Once submitted, each request is assessed by an SBO curator. This may require the curator to contact the submitter to clarify the request, or to obtain further information. It is therefore very helpful to provide a contact email address with any submitted tracker items. For other concerns, please use one of the alternative means of contact.
How do I report an error in an SBO term?
How do I contact you with other concerns or issues?
For all other queries or concerns you may have, that are not addressed by this FAQ, you may contact us for further assistance using the most appropriate link on this page. This page includes links to various mailing lists.
How do I cite SBO?
A paper has been published which covers the ontologies developed by BioModels.net, and is the reference community paper:
Courtot M., Juty N., Knüpfer C., Waltemath D., Zhukova A., Dräger A., Dumontier M., Finney A., Golebiewski M., Hastings J., Hoops S., Keating S., Kell D.B., Kerrien S., Lawson J., Lister A., Lu J., Machne R., Mendes P., Pocock M., Rodriguez N., Villeger A., Wilkinson D.J., Wimalaratne S., Laibe C., Hucka M., Le Novère N. (2011), Model storage, exchange and integration. Molecular Systems Biology, 7:543DOI MSB
Alternatively, please quote either of the following:
Le Novère N, Courtot M, Laibe C (2007), Adding semantics in kinetics models of biochemical pathways. Proceedings of the 2nd International ESCEC Symposium on Experimental Standard Conditions on Enzyme Characterizations. Article
Is SBO only relevant for continuous approaches?
The Systems Biology Ontology is meant to enhance the semantics of models, regardless of the modelling approach used in their creation. Actually, the conversion between continuous and discrete models was one of the main motivations behind the creation of the ontology itself. If terms are missing to properly annotate your model, you are most welcome to propose their addition via the tracker.
Is SBO only relevant for Computational Modeling?
No, although it was its primary goal. SBO can be used in any situation of Biology where mathematical expressions relate participants and parameters. For instance, one can use SBO to automatically generate the necessary containers to store parameters derived from a curve fitting. It is more generically useful since there is always a mathematical model behind an "experimental measurement", whether a transformation signal intensity to optical density, a frequency-spectrum to a concentration or a dose-response to a thermodynamic parameter, etc. SBO can also be used as a semantic glue between different formal representations.