Ontobras 2019 - Tutorial: Transforming clinical and clinical research data to ontology-driven linked data
By Mathias Brochhausen
(Slides available)
*My own comments are marked with an asterisk
Ontological reasoning may be used to assist in completeness in querying datasets. A real experiment showed an improvement in the retrieval of data regarding children living in a smoking household.
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Platform for imaging in Precision Medicine:
- efficiency and sustainability
- new tools for analysis
- improving ability to manage and analyze integrated datasets
- making clinical data available, both for text and image-based data
According to Mathias, the biggest problem he sees in data management is not related to how types are related, but the fact that many data managers do not account for the instances. He believes that OWL-based ontologies should not allow relations between types. The "arrows" should relate instances (or groups of instances).
*This is a bottom-up approach: from the data to the model
*When applying OntoUML, we actually take a top-down approach: from the model to the data. Perhaps because we often do not have the data to start with, and we are actually concentrating on understanding the domain.
João Paulo (JP): This discussion has also a lot to do with notation. Type relations are not a limitation for OWL Full.
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For heterogeneous bases, it is hard and costly to deal with mappings from all kinds of data formats. In his experience, using a triple store is the best way, if you need ontology-based reasoning over the data. He presented a case on the use of RDF-based data:
Building a Pattern Repository for Instantiation of Patterns
- Patterns may help with reuse
- Which patterns should we store?
There are different ways to express the same knowledge. None of them is glaringly wrong. Some might be preferred over others for certain uses (e.g. for being quicker). If the patterns are all equally valid, I should prefer to use a patterns that other people are already using (that is what patterns are about, i.e. reuse, so that we do not all end up with different ontologies)
- They already have an ontology use pattern repository for which one may contribute and also use the existing patterns.
- These patterns differ from the ones provided at www.ontologydesignpatterns.org because while the latter aims at informing the design, the former is focused on informing how to instantiate the data.
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Representational Accuracy for Informed Consent Data
His group is involved with some case studies regarding the use of Biobanks' data. One thing that is very important is to acquire the consent of the owners of the medical material stored in these repositories.
By Mathias Brochhausen
(Slides available)
*My own comments are marked with an asterisk
Ontological reasoning may be used to assist in completeness in querying datasets. A real experiment showed an improvement in the retrieval of data regarding children living in a smoking household.
----
Platform for imaging in Precision Medicine:
- efficiency and sustainability
- new tools for analysis
- improving ability to manage and analyze integrated datasets
- making clinical data available, both for text and image-based data
According to Mathias, the biggest problem he sees in data management is not related to how types are related, but the fact that many data managers do not account for the instances. He believes that OWL-based ontologies should not allow relations between types. The "arrows" should relate instances (or groups of instances).
*This is a bottom-up approach: from the data to the model
*When applying OntoUML, we actually take a top-down approach: from the model to the data. Perhaps because we often do not have the data to start with, and we are actually concentrating on understanding the domain.
João Paulo (JP): This discussion has also a lot to do with notation. Type relations are not a limitation for OWL Full.
----
For heterogeneous bases, it is hard and costly to deal with mappings from all kinds of data formats. In his experience, using a triple store is the best way, if you need ontology-based reasoning over the data. He presented a case on the use of RDF-based data:
----
Building a Pattern Repository for Instantiation of Patterns
- Patterns may help with reuse
- Which patterns should we store?
There are different ways to express the same knowledge. None of them is glaringly wrong. Some might be preferred over others for certain uses (e.g. for being quicker). If the patterns are all equally valid, I should prefer to use a patterns that other people are already using (that is what patterns are about, i.e. reuse, so that we do not all end up with different ontologies)
- They already have an ontology use pattern repository for which one may contribute and also use the existing patterns.
- These patterns differ from the ones provided at www.ontologydesignpatterns.org because while the latter aims at informing the design, the former is focused on informing how to instantiate the data.
----
Representational Accuracy for Informed Consent Data
His group is involved with some case studies regarding the use of Biobanks' data. One thing that is very important is to acquire the consent of the owners of the medical material stored in these repositories.
- Related work: existing ontology on Inform Consent (Lin at al, 2013)
*full reference on slides
- For their specific case studies, they needed to specify rights and obligations, which was not contemplated in the work of (Lin et al, 2013).
*This work could evolve by using UFO-L
JP: the permission relation is an example of how type-type relation could be useful.
Mathias answered that it would indeed be easier to express it that way, but because they are limited by OWL-DL, they still take the approach of relating the instances instead of the types.
Gian: Do you see the need for a relator, i.e. an object that persists in time an is related to the event of giving consent?
Mathias answered that they are kind of "reductionist" in this sense, representing roles and events, but not relators. In the end of the discussion, he said he would need to think about the use of relators in his work.
One important disclamer that Mathias does is that not everything about consent is in the ontology.
*This is in fact compliant with the OWL's open world assumption.
A glimpse of how they used d-act may be seen in the figures below:
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