Saint: A lightweight SBML annotation integration environment

Allyson Lister

CISBAN, Newcastle University

This post is an homage to Ally’s own herculean note taking style, since she can’t blog her own talk.

Saint has been developed to help modellers get information into their SBML models really quickly. Ally shows a picture of a model describing neuromuscular junctions (standard biomodel). This model contains terms which are descriptions, and the mathematical model. The maths doesn’t know anything about the underlying biology. For example, actin is just a label, there is no implicit knowledge contained in that label (ie actin is a protein, invoved in the cytoskeleton etc).

Short intro to SBML: SBML is a standard format, which is widely used. it stores the maths and enables linking to the underlying biology.

So what do we know about actin –

  • its a protein (UniProt)
  • interactions? (Pathway Commons, STRING)
  • reactions and parameters (SABIO-RK, BRENDA, KEGG)
  • vocab (SBO, GO)

Now we can use the MIRIAM standard to annotate the model with the above information.

When building a model, you need to add info to things like species, name, reaction, compartment
Annotation and SBO term sit between the model and the biology information – these can be used to retrieve the information from the databases. This has to be done manually currently, this is hard and is often not done exhausively, or even at all.

Saint enables automation of this procedure. It already links to a number of data sources – MIRIAM, UniProt, STRING, SBO, Pathway Commons. Reduces effort on the part of the modeller. Saint is lightweight and easy-to-use. Useful as a first pass annotation tool, or to add annotation to an existing model.

How Saint works:

  • import SBML into Saint
  • Saint then searches for appropriate annotation
  • and presents this annotation, and allows to to accept or reject the changes

Ally is using a model produced by Carole Proctor in CISBAN as an example run-through of Saint.

Saint does some validation via libsbml on import of an SBML model. The tool then presents a list of species found in the model, these can be hidden if you don’t want to retrieve information on them. Zoom into ‘Ctelo’ for an example – a plus next to the name of the species shows the annotation already available in the SBML model (‘known’ information). So we can se that Ctelo is a Capped Telomere. You can decide which species you want to annotate, and which datasources you want to retrieve that annotation from.

Queries are made from datasources by a Master Asynchronous Query Service – once information becomes available, it is immediately visible in the UI (as an ‘inferred’ tab), and you see a ‘New Annotation found’ message. Once Saint has retrieved annotation, the user can choose which annotation he wants to keep, and how this information links to the species in the model (is, part etc – MIRIAM terms)

CDC13 = polypeptide chain, nuclear telomere cap complex, protein binding, single-stranded telomeric DNA binding, telomerase inhibitor activity.

Future work – more data sources, use of species type, better support for non-systematic names, adding software source attribution, incorporation of SBGN (Systems Biology Graphical Notation) for better display.

Personal comments – good job Ally – hope I did it justice!

Ally’s standard disclaimer:

Please note that this post is merely my notes on the presentation. They are not guaranteed to be correct, and unless explicitly stated are not my opinions. They do not reflect the opinions of my employers. Any errors you can happily assume to be mine and no-one else’s. I’m happy to correct any errors you may spot – just let me know!


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