These are my notes for the third session of talks at the UK Ontology Network Meeting on 14 April, 2016.
Ontology-driven Applications with MEKON and HOBO
Currently used in a sepsis prediction system and a clinical trials design / design-retrieval system (early prototypes). MEKON is based around a generic frames model with a plugin framework which allows the incorporation of ontology-like knowledge sources and associated reasoning mechanisms. HOBO extends MEKON to enable the creation of domain specific object models, bound to appropriately populated frames models, Instantiations of object models operate in tandem with instantiations of bound frames models.
They come with instance store mechanisms, delivered via plugins. Current plugins are based on OWL DL, RDF + SPARQL and the XML database BaseX. They also come with a Model Explorer GUI to allow the model developer to browse, explore dynamic behaviour of specific instantiations, and exercise the instance store (store instances and execute queries).
MEKON and HOBO provide layered architecture (structured means of combining generic knowledge sources and reasoners, and domain specific processing), handle much of the dirty work, and provide client access via appropriate APIs (generic frames model, domain-specific object models).
MEKON enables the creation of a skeleton application without having to write a single line of code.
The Synthetic Biology Open Language
Goksel Misrili, James Alastair McLaughlin, Matthew Pocock, Anil Wipat
Synthetic biology aims to engineer novel and predictable biological systems through existing engineering paradigms. Lots of information is required, including DNA sequence info, regulatory elements, molecular interactions and more. They are currently using SBOL 2.0. Modules allow hierarchical representation of computational and biological systems. A biological example would be a subtilin sensor.
SBOL utilises existing SW resources, e.g. BioPAX, SO, SBO, EDAM, Dublin Core, Provenance Ontology. SBOL is serialized as XML. SBOL allows the unambiguous exchange of synthetic biology designs, and is developed by a large consortium.
ConSBOL: A terminology for biopolymer design
Matthew Pocock, Chris Taylor, James Alastair McLaughlin, Anil Wipat
The presenter was unable to make the workshop today.
Please note that this post is merely my notes on the presentation. I may have made mistakes: these notes are not guaranteed to be correct. Unless explicitly stated, they represent neither my opinions nor the opinions of my employers. Any errors you can assume to be mine and not the speaker’s. I’m happy to correct any errors you may spot – just let me know!