Today was a highly informative combination of talks and further improvement of OBI. Hopefully, you'll find these musings on the day's work helpful at either jogging your own memory of the events, or in giving you an idea what went on in our heads.
Ontologies – How do we integrate and/or make use of them?
Can we, at the moment or in future, place
parent classes for all OBO ontologies in OBI? Definitely not now, as they don't share the same ULO (Upper Level Ontology). Some work is being done by the OBO-UBO group on mapping OBO ontologies to ULOs like BFO. (See the OBO-UBO web page for more information)
In a related question, should all OBO
ontologies use BFO? It would make integration a much more straightforward process. In my opinion, this would be a great idea in the long term, however practicalities may prevent it. 🙂
Should things like
BioTop (http://www.ifomis.uni-saarland.de/biotop/) be integrated
into OBO, under BFO but before OBI? In my opinion (though today was the first time I have read about BioTop so it isn't the most informed one), in our case probably not, as resolving the three may be problematic. However, some terms or ideas might be useful to share.
Formal OWL, aka making OBI Formally correct
Should be assigned
to someone/some people for later, after more classes have been
created. There is simply too much flux in the file at the moment. Get the graphs in place first, perhaps working on some
complex relations as you go. Further, the definitions must explicitly hold information
on creating these relations, irrespective of whether or not you make the relationships as you go or at the end.
BFO and OBI use
different metadata tags, and there should be a
shared set of tags.
The metadata tags
used in BFO are part of snap/span, I think. Would need to bring up the idea of metadata resolution (if possible, and we all agree it should be pursed) with that group too.
Barry Smith will bring OBI's information object and plan terms to the BFO group.
A milestone has been added (see the OBI Wiki) to
hammer out exact implementation of the metadata list, and to work
with other communities as appropriate (e.g. BFO, OBO Foundry =
Barry, M Ashburner, Suzie, Chris M.).
Ontology – Simona Carini & Barry Smith
Rctbank is a
clinical trail db – information on all published clinical trials.
(from journal articles)
Its purpose is to provide enough
information to allow evaluation of these trials
RCT = randomized
Epoch and Clinical
Trial Ontology (CTO) are the other two that are being developed.
Barry Smith is involved in CTO, and therefore is built with OBI
in mind, but is still very small
RCT and Epoch
aren’t close to being OBO/OBI compliant.
Their choices are
in conflict with the choices we’ve made
- that does NOT mean that they aren't imminently useful (which they are), just that merging would be problematic
There has been
agreement between Epoch and RCT that all should work towards a CTO
that will work within the OBI framework
reconciliation is one of the goals of the CTO workshop in May.
There are people
claiming to develop a CTO but it is actually a CT database
ontology (I missed the name of the people being referred to here). It isn’t
the same beast. Understanding the data is not equivalent to
understanding the processes in a trial.
RCT Schema – Barry
independently of OWL or protégé, and is more correctly
a database schema, though it is called an ontology.
Not the right way
to do it – it is unbalanced: no place for a study, though is a
place for a 2o study.
2o study seems to
be at the wrong level in the hierarchy
it is unclear what
trial details means
When the same term (or portion of a term) is repeated
over and over, it is often the a sign of a mistake, of redundancy
One of the
children of population concept is population.
An ontology is
important for reasoning using the is_a hierarchy, which can be reasoned
over: Population is NOT a population concept and is NOT a concept
blocked here “from both directions”
Further, a recruitment
flowchart is not a population concept
These things, like
population concept, are headers/labels/conveniences, but they are not
ontological forms. Some options for restructuring could be the following two things:
is_a continuant is_a entity
occurrent is_a entity
Not all RCT terms have
Epoch Ontology (Dave
Parrish in charge of it) – Barry Smith
There are parts of
this ontology that don’t belong in the CTO, but do belong in OBI
developed to support the immune tolerance network (ITN), a big
clinical trial resource: they fund, implement, monitor and assess
clinical trials, and provide data services.
of ITN perform operations (generation and collection) -> data
management -> analysis
They have an
ontology of the kind of analytical steps their software needs to
perform, and it helps them configure the software application.
For example, elements are claimed to be
nouns, and represent the physical objects of the system. Classes of
elements are domain types, containers, relationships. These are not
physical objects always – they’re sometimes processes. Also,
they are not always nouns.
Fits in with the
community milestones, i.e. we could get many terms from the clinical trials community.
Branches have been assigned. See the OBI Branches Wiki Page for up to date information.
current terms in various OBO ontologies to BFO
biological process is_a span:process
already developed an environmental ontology in a plant context,
which we should remember and hopefully incorporate useful terms in the first round of community term dates.
Have moved all terms
that would fall under PATO out of the ontology, e.g. state and
anything under quality.
Do we really need
"in vitro state" as well as "in vitro"? Terms such as
these are always tied to objects like cells – these are not design
as much as the state of the cells.
Is in vivo
a location or a state? You can take in vitro cells and put
them into “vivo”, and they are still in vitro cells,
which means in vitro is a BFO quality.
The interior of
your gut is the site for your gut bacteria. The interior of gut (IG)
is also a type/node in the FMA (as a location). IG has qualities
(shape, etc). In addition to these qualities it has others that
determine its roles (having certain pressure, pH value). How to
distinguish what FMA means from what an environment ontology means?
If we remove
in-vivo_state, we run into problems with multiple inheritance. We
needed to separate out the state of a biomaterial from the
biomaterial itself, i.e. don’t have in-vivo_material as a child of
What terms do we
need to use to describe diseases?
Disease (hook for
disease ontology), disease_symptoms, disease_stages,
Ended up going through the entire ontology, resolving many problems. There is a new OWL file, but it is not yet ready for public consumption therefore it won't be posted here until it is available from the official OBI pages.
There is general consensus among the workshop attendees that a very large amount of work is getting done, and there is a lot of positive feeling that the Milestones developed this week are giving us hard dates for inclusion of many more terms. The addition of terms can only truly start once the high-level structure has been decided, and this workshop has moved in great leaps and bounds towards a final structure of the higher levels of OBI. The "higher levels" have been generally defined at this meeting as the top two levels of OBI below BFO. This is what was completed today: the two levels directly below BFO have been studied by the group and cleaned.