Core terms status

[Chris Stoeckert]

Dear DENRIErs,

We are scheduled to have a call on Thursday Jan 22 to discuss the core terms. Below is a summary of the recent email discussions  that I propose placing here: http://obi-ontology.org/page/Core_terms#DENRIE 

For our Thursday call, I suggest we decide what changes are needed to the summary and any points that should be presented at the workshop in Vancouver.

Thanks,

Chris

Note that DENRIE email threads are all available at http://groups.google.com/group/obi-denrie-branch/

 

1. datum/ data; dataset; data structure:

Data item refers to a fact usually collected as the result of experience, observation or experiment, or processes within a computer system, or a set of premises. This may be a number, word, or image, particularly as a measurement or observation of a set of variables.”

Data set is a data item with some bundling of other data items for some purpose, without implication of homogeneity or  other structural   
constraints, at least at the broadest level. 

Remaining issues:

Need a definition for data structure. Is it an information content entity? Or is it a different type of generically dependent continuant?

 If IAO needs a generic data item that is unfettered by process, should OBI create a more specific one corresponding to experimental, corroborated data which are output of an observation or measurement (actually in the OBI scope, they would be output of data transformation and/or assay only) 

2, 3, 6, 7, 8. narrative object - textual & figure, hypothesis, result, conclusion. 

information content entity 
    report (purpose of information for the author and audience) 
       journal article 
       patent application 
       grant progress report 
       patient record 
    proposition (relation of information to reality according to the author) 
        conclusion 
        hypothesis 
        result   
    information entity about a realizable 
              text format 
             figure format 
             audio format 
             table format 
             html spec 
             pdf spec 

A report is an ICE describing findings of some individual or group. It usually is made up of a set of propositions, and can be written,   
spoken or encoded digitally. Its content is reflective of an investigation, and it's purpose is to inform an audience. (from http://www.google.ca/search?q=define%3Areport, Bjoern, and current definition of narrative object) 

A proposition is an ICE that affirms or denies something and is either true or false. A proposition represents the relation of the   
information to reality according to the author. alternative term: statement  (from http://www.google.ca/search?q=define%3Aproposition and Bjoern) 

Remaining issues:

Create additional distinction of: 

       human format specification (format of information as seen by humans) 

        digital format specification (format of information as seen by computers) 

Remaining definitions

4. Software

Software entity: series of encoded instructions that can be directly executed by a CPU, or transformed in to a form that can be. For 
programming texts that are syntactically correct and which are in a language that can be executed by an interpreter this would correspond 
to the tokenized version of the text stripped of comments. 

Remaining issues: merge with SepCV definition?

5. variable.

status of variable is that it is stuck by a limitation of BFO. Variable is a term in PATO as a quality.

Agreement that OBI should contain an experimental variable. Could be a type of investigation specification (plan).

9. objective specification

modify current definition to: An objective specification is an information entity which can serve as the aim or purpose towards which the realization of the plan is directed.

10. study design

Agree with approval by Plan and Planned Process branch. Updated definition from BP is: A study design is a plan comprising of protocols and/or data transformations that are executed as part of an investigation. The objective of the study design is to produce results (information). The study design specifies how the different data produced in the execution of the investigation are related, how they are interpreted, and what are the desired results. 

11. value/ unit

Needs discussion. Here's a starting proposal:

A mouse is on a weight scale that reads out 5 grams. 
The 5 grams is a recording of a measurement and constitutes a data item. The information content of the data item is encoded as the numeral 5 (value). The quality that the measurement data item is about is grams (which is a quantification of the quality of weight and drawn from the units of measurement ontology).