IAO tracker

[Melanie Courtot]

Hi,

Terms have been submitted on the IAO tracker, see http://code.google.com/p/information-artifact-ontology/issues/list
Please follow discussion on the IAO mailing list at http://groups.google.com/group/information-ontology
- the tracker automatically emails the list on submission, but I was
unable to add the denrie group as cc on the mail.

Thanks,
Melanie

---
Mélanie Courtot
TFL- BCCRC
675 West 10th Avenue
Vancouver, BC
V5Z 1L3, Canada

[Chris Stoeckert]

Melanie,
Thanks for taking care of that.

In response to the action item from today's developers call, here is
my understanding of where we stand.
- data/ data item, measured data item, derived data item: already
added by James and discussed
- data format specification, objective format specification, study
design: agree with Plan and Planned Process proposals - letting them
add to OBI
- software: already in OBI. No changes based on OBI Workshop.
- independent variable specification has already been added in IAO,
see http://purl.obofoundry.org/obo/iao.owl, as IAO_0000011. Definition
source: Bjoern Peters.
- hypothesis, data representational model, study result - added by
Melanie
- conclusion (study interpretation), narrative object (report),
measurement unit label, scalar measurement datum have been submitted
to IAO tracker by Melanie.

I think that takes care of all DENRIE core terms except:
report element # would replace report display element
subclass of: information content entity
definition: A report element is an information content entity in which
information is presented and consumed by a human being. Examples of
report elements are figure (dot plot), table, text portion … (may
include a movie or audio clip on a web page).
editor note: needs some more work (clarify relations).
definition source :GROUP:OBI" with an editor note "2009-xx-xx: work on
this term has been finalized during the OBI workshop winter 2009"

Thanks.
Chris

[Melanie Courtot]

Hi all,

We just had a long discussion with Alan and proposed a list of
modifications to IAO addressing the DENRIE terms.
Please check and comment on them directly on the tracker at
http://code.google.com/p/information-artifact-ontology/issues/list
(Issues 10 to 14 included).
I also copy the summary below.

I will allow a bit of time for others to comment and will take care of
the changes hopefully Monday.

Thanks,
Melanie



Proposed resolutions following discussion Alan/Melanie Wednesday 11th
March

1. study interpretation - http://code.google.com/p/information-artifact-ontology/issues/detail?id=10

study interpretation is_a narrative object, and part_of report

subclass of: narrative object
definition: Study interpretation is a narrative object interpreting a
study result. Examples include whether a hypothesis is false, the
study failed to address the hypothesis, the study results have led to
new hypotheses.
editor note: 2009-xx-xx: definition was " a narrative object which can
be published in a report summarizing and interpreting a protocol
application"
alternative term: conclusion
definition source: GROUP:OBI
editor note "2009-xx-xx: work has been done on this term during during
the OBI workshop winter 2009 and the current definition was considered
acceptable for use in OBI. If there is a need to modify this
definition please notify OBI"

Note: "paper publication" as currently in the definition of
"conclusion" was used liberally and means any kind of report (e.g.
includes lab notebooks)

2. narrative object/report - http://code.google.com/p/information-artifact-ontology/issues/detail?id=11

Narrative object include fiction (e.g. novel) and reports: report is a
subclass of narrative object, but doesn't replace it.

report
subclass of: narrative object
definition: A report is a narrative object assembled by an author for
the purpose of providing information for the audience. A report is the
output of a documenting process and has the objective to be consumed
by a specific audience. Topic of the report is on something that has
completed. A report is not a single figure. Examples of reports are
journal article, patent application, grant progress report, case
report (not patient record)
definition source: GROUP:OBI
editor note "2009-xx-xx: work has been done on this term during during
the OBI workshop winter 2009 and the current definition was considered
acceptable for use in OBI. If there is a need to modify this
definition please notify OBI"


3. update measurement unit label -
http://code.google.com/p/information-artifact-ontology/issues/detail?id=12


measurement unit label
subclass of: label
definition: A measurement unit label is as a label that is part of a
scalar measurement data item and denotes a unit of measure.
editor note: instances of unit label would be drawn from the PATO
units of measurement ontology or equivalent.


- This term doesn't have a definition source: definition of definition
source annotation property reads :"formal citation, e.g. identifier in
external database to indicate / attribute source(s) for the
definition. Free text indicate / attribute source(s) for the
definition. EXAMPLE: Author Name, URI, MeSH Term C04, PUBMED ID, Wiki
uri on 31.01.2007". This term was proposed by Alan and accepted by
OBI.
- we add editor note: "2009-xx-xx: review of this  term done during
the OBI workshop winter 2009 leading to it being considered an
acceptable term for use in OBI. If there is a need to modify this
definition please notify OBI"
- This term has been modified up to a point where it is different from
the original term OBI_0000176, measurement unit.
An editor note will be added: "provenance: a term measurement unit was
proposed for OBI (OBI_0000176) , edited by Chris Stoeckert and
Cristian Cocos, and subsequently moved to IAO where the objective for
which the original term was defined was satisfied with the definition
of this, different, term. "


4. update label of scalar measurement datum -
http://code.google.com/p/information-artifact-ontology/issues/detail?id=13

Terms datum and data item were deemed synonyms as they were both
alternative terms for data item, however they are not exact synonyms,
as datum refers specifically to the singular form.

Data item:
remove alternative term datum from data item
adding editor note saying "2009-xx-xx: removed datum as alternative
term as datum specifically refers to singular form, and is thus not an
exact synonym"
adding editor note saying "data item deliberatly ambiguous: we merged
data set and datum to be one entity, no knowing how to define singular
versus plural. So data item is more general than datum. "

scalar measurement datum:
we decided to keep datum singular in scalar measurement datum, as in
this case we explicitly refer to the singular form


5. report element - http://code.google.com/p/information-artifact-ontology/issues/detail?id=14

report element # would replace report display element

subclass of: narrative object
definition: A report element is a narrative object in which
information is presented and consumed by a human being, and is part of
a report. Examples of report elements are figure (dot plot), table,

text portion … (may include a movie or audio clip on a web page).
editor note: needs some more work (clarify relations).
definition source :GROUP:OBI

editor note "2009-xx-xx: work has been done on this term during during
the OBI workshop winter 2009 and the current definition was considered
acceptable for use in OBI. If there is a need to modify this
definition please notify OBI"


report element is a subclass of narrative object and part_of report

On Mar 4, 2:26 pm, Chris Stoeckert <stoec...@pcbi.upenn.edu> wrote:
> Melanie,
> Thanks for taking care of that.
>
> In response to the action item from today's developers call, here is  
> my understanding of where we stand.
> - data/ data item, measured data item, derived data item: already  
> added by James and discussed
> - data format specification, objective format specification, study  
> design: agree with Plan and Planned Process proposals - letting them  
> add to OBI
> - software: already in OBI. No changes based on OBI Workshop.
> - independent variable specification has already been added in IAO,  

> seehttp://purl.obofoundry.org/obo/iao.owl, as IAO_0000011. Definition  

> source: Bjoern Peters.
> - hypothesis, data representational model, study result - added by  
> Melanie
> - conclusion (study interpretation), narrative object (report),  
> measurement unit label, scalar measurement datum have been submitted  
> to IAO tracker by Melanie.
>
> I think that takes care of all DENRIE core terms except:
> report element # would replace report display element
> subclass of: information content entity
> definition: A report element is an information content entity in which
> information is presented and consumed by a human being. Examples of
> report elements are figure (dot plot), table, text portion … (may
> include a movie or audio clip on a web page).
> editor note: needs some more work (clarify relations).
> definition source :GROUP:OBI" with an editor note "2009-xx-xx: work on
> this term has been finalized during the OBI workshop winter 2009"
>
> Thanks.
> Chris
>
> On Mar 4, 2009, at 12:12 PM, Melanie Courtot wrote:
>
>
>
> > Hi,
>

> > Terms have been submitted on the IAO tracker, seehttp://code.google.com/p/information-artifact-ontology/issues/list
> > Please follow discussion on the IAO mailing list athttp://groups.google.com/group/information-ontology

[Chris Stoeckert]

Hi Melanie,
Thanks for doing this. At first glance, I'm OK with the results but
will add any comments by Monday.
Chris