3rd OBI Workshop: Day 3

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.

Outside OBO
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.).

Clinical Trial
Ontology – Simona Carini
& Barry Smith

  • http://rctbank.ucsf.edu/ontology/outline/index.htm

  • 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
    controlled trials

  • 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.

    • Developed
      independently

    • 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

    • This necessary
      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
Smith

  • Built
    independently of OWL or protégé, and is more correctly
    a database schema, though it is called an ontology.

  • Top-level class:
    root

    • 2o study

    • Trial-details

    • Trial

    • Concept

      • Subclasses

  • 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

    • Reasoning is
      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:

  • Population/protocol/design
    is_a continuant is_a entity

  • Trial is_a
    occurrent is_a entity

  • Not all RCT terms have
    definitions

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

  • Originally
    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.

    • Informatics dept
      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.

OBO-UBO

http://berkeleybop.org/ubo/

  • Mapping between
    current terms in various OBO ontologies to BFO

    • E.g. GO
      biological process is_a span:process

  • Gramene has
    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.

More general
discussion

  • 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
    biomaterial_entity.

  • What terms do we
    need to use to describe diseases?

    • Disease (hook for
      disease ontology), disease_symptoms, disease_stages,
      disease_course.

  • 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.

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