3rd OBI Workshop: Day 4

Day 4 consisted mainly of discussions regarding the nature of a study versus investigation. These terms themselves are loaded, and what one person thinks of and calls a study may be exactly what others call investigation. In the end, after about 3/4 of the day devoted to the subject, the answer was…. ah, but that would be telling! Read through the notes of the day, and then at the end, all will be revealed.

  • those on the instrument branch (and more generally, all OBI development branches where appropriate) should remember the following:
    • don't ignore what the vendors are doing – they'll have term lists
    • don't ignore what the communities have done (ie metabolomics and proteomics)
  • The full specification for who is assigned to which branches, and how we will physically create the branches, is available on the branch OBI Wiki page.

Study Design Use Case – Drawing terms from the Community – Phillippe Rocca-Serra

  • Very interesting, but I wasn't able to take many notes due to updating the OBI wiki on the Branch implementation. If anyone has any good notes, either let me know and I'll include them here, or add them yourself as a comment!
  • The take-home message is that trying to reconcile many groups' different meanings for the same words is difficult, but drawing a large set of terms from literature and communities is very important.
  • By showing us what he has done, it gives all branch groups an idea of the work involved in working on their branches.

Branch best-practices

  • If a relation is missing while developing a branch, should it be referred to the relation ontology immediately?
    •  Try and define it as a group before submitting to RO, and ask for help if required. definition includes restrictions on where these relations can connect to and from.
    • far too many ontology projects collapse because they have far to many relations.
  • Should put a use-case of OBI on the wiki, for example, post use-cases of composition of study design
  • When branches create terms, at the same time as they make the terms, useful community alternative terms should be added. When you get an OBI term, you will immediately get many other associated terms.
  • Not only would you have a special interface for the biologists, but you would also be able to have computer people have a special structured interface to the literature via these alternative terms

Finding a real home for Information_Entities

  • At the moment BFO has qualities, information entities (generically dependent) and realizable entities (specifically dependent) as children of dependent continuant (DC). But generically dependent is not the same as the current definition of DC, and therefore needs to be made a sibling called generically_dependent_continuant.
    • Digital objects can exist in many different places and be identical. No other DC objects can be identical in this way.
    • DC and GDC will be disjoint.

Solving Study versus Investigation

  • If we are doing OBI, then we need an investigation design
  • Consensus was quickly reached on what an Investigation is:
    • Investigation is a process in which data are gathered from one or more protocol applications with the goal of reaching conclusions. It is guided by the realization of a investigation_design.
  • However, whether or not a study was necessary at all was a real debate.
    • One group thought a study was just a smaller version of an Investigation, and could therefore be dealt with by having investigations within investigations.
    • The other defined a study as everything done to materials prior to actually doing the assays
  • Therefore, a child of protocol_application was created for this purpose.
    • A sample_preparation_for_assay is a protocol_application including material_enrollments and biomaterial_transformations. There is alternative_term for this called "study".

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