Core terms

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A list of core terms will be compiled by each branch and added here, by the end of the year (2008).


Biomaterial

terms description - discussion
1. material entity definition: currently union of 3 types of BFO objects

new proposed definition: material entity def A "snap:IndependentContinuant" ("independent_continuant") that is spatially extended, and its identity of is independent of that of other entities and can be maintained through time. ex of usage: collection of random bacteria, a chair, dorsal surface of the body (examples chosen to cover the 3 cases)

2. organism - Homo sapiens alternative term natural person, alt term human person is subject to confusion, e.g. as legal term "This is a common offshore legal term meaning a living breathing person as opposed to an unnatural person such as a corporation", thus we chose to have natural person as alternative term

- organism should include dead ones as well

3. organization - We added an instance organization Affymetrix to serve as model/

template for other branches. For example the instrument branch needs to represent manufacturers. Instances will be added in a separate file - Affymetrix has been added in the Biomaterial branch file just as an example how we proceed. Role branch will add a manufacturer role Relation branch: there is a relation is_manufactured_by, do we need the inverse is_manufacturer_of? do we need a more generic one is_supplier and then use roles?

4. molecular entities - instead of adding our own label and preferred term to get rid of

plural form, we should contact external resource and ask for modification according to OBO Foundry principles. Adding our own form is not very efficient, and create double display of labels in protege if both lang tags are set to "en"

Process of adding new subclasses to molecular entities case of "huge" resources e.g. melanie has a list of 600 fluorochromes and bjoern a list of 1000 peptides Proposal is to store these very specific resources in external files (Bjoern may not want to get 600 fluorochromes when downloading OBI)

5. chemical entities in solution (mixtures) concentration proposal form BP and AR

- has been discussed in Karlsruhe with Stefan Schulz, Marijke Keet -> seems to lean towards Bjoern's proposal - AI for Bjoern: send email including description of his proposal - AI for all: encode one example properly in OWL file before workshop

6. environmental matter - link to envo

- http://www.ebi.ac.uk/ontology-lookup/browse.do?ontName=ENVO&termId=ENVO%3A00010483&termName=environmental%20matter - possibility: mireot environmental matter - issue: current children of ENVO too broad for us (e.g. bone) - AI for JM to send email to envo/biomaterial with proposal (change environmental matter to "material entity", subclasses, and then have defined class environmental matter, which has quality/role of being able to host organisms)

7. macroscopic part of organism parasites, fetus etc are macroscopic part or organism too, even

though they are organisms - JM: parasitic could be disposition? - virus? not macroscopic (macroscopic= multicellular or similar size) - issue of canonical part: parasites yes or no? - current pb: heart on table => process changing nature of the input -> conferred quality, TBD in Vancouver

8. artifact object - issue= an output of mat transfo is artifact - ex: collect something

from street, is it artifact? - process branch needs to say what mat transformation is (note: has been renamed artifact material creation) - e.g. we don't want collection there - we agree that all output of artifact material creatio will be artifact object - AI for BP: work on artifact material creation and check classification - AI for BIomaterial branch: review what falls under there

9. EOO (entity of organismal origin) - all EOO should be artifact objects

- "artifact of organismal origin": intent to collect sthg that was part of organism - blood serum should be linked to blood as macroscopic part of organism - BP: extracted heart is no longer an heart, as parthood relation don't hold anymore other example: finger part of hand not true anymore if severed finger - we need relation "severed finger used to be finger" - Alan's proposal: having finger (anat structure) and subclasses finger in vivo and severed finger - other anatomy ontology don't work that way -> would create issues in re using them - AI for BP: have one example blood and heart/finger


DENRIE

terms description - discussion
1. datum/ data; dataset; data structure data item is an information content entity that is intended to be a truthful statement about something (modulo , e.g. measurement imprecision or unintended error) and is constructed/acquired by a method which reliably tends to produce (approximately) truthful statements. (synonym datum, data).

editor note: truth fulness is supposed to differentiate lies from facts. It is not meant to indicate that the data item represents an absolute truth. The processes that 'tend to reliably produce truthful statements' need to be spelled out. One of them should be assay. editor note: alternative def: 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 bundling of data items without implication of homogeneity or other structural constraints, at least at the broadest level. editor note: Originally included the bundling was for some purpose but that requires a matching logical definition.

data structure is specification of relationships between data items. editor note: term label may actually be data structure specification

also see http://groups.google.com/group/obi-denrie-branch/browse_thread/thread/579eed73373feca8?hl=en and http://groups.google.com/group/information-ontology/browse_thread/thread/24694b46a1239912?hl=en

2. narrative object - textual report (purpose of information for the author and audience)
       journal article 
       patent application 
       grant progress report 
       patient record 

see also http://groups.google.com/group/obi-denrie-branch/browse_thread/thread/be1021bf8ed390f6?hl=en

3. narrative object - figure 'report element format' is a format in which information is presented

and consumed by a human being.

   figure format
       dot plot
       [...]
   table format
   text format
   audio format
   movie format

Needs some more work (keep 'format' or not, clarify relations).

see also http://groups.google.com/group/obi-denrie-branch/browse_thread/thread/be1021bf8ed390f6?hl=en

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.

editor note: also a definition available from SepCV

see also http://groups.google.com/group/information-ontology/browse_thread/thread/81adc82d0c5d0a39?hl=en and http://code.google.com/p/information-artifact-ontology/issues/detail?id=7

5. variable - could be plan experimental factor is a specification that is varied within an experiment (signifying, for example, the 'control' and 'experimental' groups) synonym is independent variable

dependent variable is a data item that is simply a measurement derived from instruments with no manipulations derived variable is a data item that has been obtained through processing of other data. proxy variable is a data item where one variable is linked to another via a vague or non-specific relation (i.e., 'time-spent freezing' is a proxy for 'fear', which may contribute to the high-level interpretation of a study).

see also http://groups.google.com/group/obi-denrie-branch/browse_thread/thread/411a13f034737c1d

6. hypothesis hypothesis is a proposition

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) editor note: Alan is concerned that he doesn't understand what instances of hypotheses are and would prefer to have them the narrative style definitions of the terms conclusion, hypothesis, result, and would like to not have proposition as a term as it looks like the definition is coincident with data item

see also http://groups.google.com/group/obi-denrie-branch/browse_thread/thread/b0825584009fb768

7. result result is a proposition
8. conclusion conclusion is a proposition
9. objective specification - research objective An objective specification is an information entity which can serve as the aim or purpose towards which the realization of the plan is directed.

editor note: waiting for Plan and Planned process branch

see also http://groups.google.com/group/obi-denrie-branch/browse_thread/thread/d088883005df2d87

10. study design - technical approach 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 scalar measurement datum is_a data item and has part unit label and has part numeral.

editor note: measurement datum is an information content entity that is a recording of the output of a measurement such as as produced by an instrument. (Given the discussions on data/ datum this should be relabeled as "measurement data item." )

numeral which is a symbol that denotes a number.

measurement unit label is as a label that is part of a measurement datum and denotes a unit of measure. (labels are a type of symbol so it is of the same type as numeral). editor note: instances of unit label would be drawn from the PATO units of measurement ontology or equivalent

see also http://groups.google.com/group/obi-denrie-branch/browse_thread/thread/e64016e158bd6a6c


Role

terms description - discussion
1. analyte role
2. protocol participant role
3. specified input role
4. specified output role
5. evaluant role
6. reagent role
7. Reference Role
8. Study Personnel Role
9. Study Subject Role
10. Subject Specimen Role


Plan and Planned Process

terms description - discussion
1. investigation status: branch approved
2. study design status: branch approved
3. protocol status: branch approved
4. assay status: branch approved. Should have more children added, e.g. non analyte-measuring assays
5. analyte measuring assay status: branch approved
6. material administration status: first branch review done.
7. objective driven process, planned process, and protocol application status: branch approved. merged objective driven with planned process.
8. objective specification, plan specification status: branch approved
9. material transformation = artifact creation status: first branch review done. After switch to 'artifact creation', we need to when we want something to be a transformation only, and when something is a newly created artifact.
10. material separation status: not reviewed
11. manufacturing process status: first branch review done


Data Transformation

terms description - discussion
1. data transformation A data transformation is a protocol application which produces output data from input data - e.g. the application of a clustering protocol to microarray data or the application of a statistical testing method on a primary data set to determine a p-value.
2. data transformation objective A data transformation objective is an objective specification that a data transformation may have towards which the realization of that transformation is directed.
3. has_objective This sits outside of DT branch but still lacks a definition.
4. has_specified_input_data A relation between a process and a participant in that process, that consumes a data set . The process is the realization of a concretization of a realizable information entity (objective specification or plan specification). In general, not all data present at the beginning of the process are specified_data.
5. has_specified_output_data A relation between a participant in a process, that produces a data set . The process is the realization of a concretization of a realizable information entity (objective specification or plan specification). In general, not all data present at the end of the process are specified_data.
6. data item Awaiting definition from IAO
7. data set Awaiting definition from IAO
8. report figure - linking to a visualization (is_rendered_by) A report figure is a report display element that has some aspect of illustration, but may be a composite of figures, images, and other elements Part of IAO
9. software IAO. 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. Need instructions on be subclassing this so we can add relevant DT/OBI classes.
10. 'roles for data' and variable Still not clear how to represent these.


Instrument

terms description - discussion
1. device
2. instrument
3. platform
4. artifact object
5. device function
6. _canonical realization of device function
7. produce data function
8. information processor function
9. process
10. protocol