[Obi-devel] Minutes OBI call 2013-04-29
Alejandra Gonzalez-Beltran
Dear All,
Please, find below the minutes of yesterday’s call.
Attendees:
James Overton, Bjoern Peters, Randi Vita, Alejandra Gonzalez-Beltran, Philippe Rocca-Serra, Jie Zheng, Chris Stoeckert, Michel Dumontier,Jennifer Fostel, Alan Ruttenberg.
1. Assign chairs for the following calls.
May 6th: Bjoern Peters - it was pointed out that it is a holiday in the UK
May 13th:Philippe Rocca-Serra
May 20th: James Overton
May 27th: It was pointed out that it is a holiday in the US, so there will be no call.
Philippe updated the wiki page with this information:
http://obi-ontology.org/page/Conference_call_developers_agenda
2. OBI metadata in Bioportal
The Bioportal metadata for OBI is incorrect., e.g. OBI is showing up under CTSA. Philippe mentioned that he contacted Trish Whetzel and that the issue should be included in their tracker.
3. Discuss about the agenda for an IAO-related call.
It had been proposed that 1 in 3 OBI calls could be dedicated to IAO. To allow for greater participation of IAO developers, we created a doodle poll to decide which of the following three calls will deal with IAO issues.
Action Item: Please, fill in your availability at:
http://www.doodle.com/ge3e4vaedrnadz75
It was emphasised that issues should be added to the tracker, ideally before the call dedicated for IAO discussions.
Action Item: All to go over IAO version currently used by OBI and file any issue + feature request
for instance:
http://code.google.com/p/information-artifact-ontology/issues/detail?id=112&q=concretize
from OBI tracker:
http://sourceforge.net/tracker/?func=detail&aid=3603259&group_id=177891&atid=886178
4. Philippe and I would like to discuss the coding measurements in OBI at instance level, as part of creating
documentation/guidelines for using OBI.
We presented the following document:
where we specified options for representing measurements at the instance level in OBI, as we think it would be useful to have documentation about specific patterns for these representations that would allow to pose the same types of (SPARQL or DL) queries over instance data.
The need for this arose from discussions with James Overton and Jennifer Fostel, who also required these kind of modelling in their project.
Alan suggested to look at the QUDT ontology for units, rather than UO.
Some notes:
- QUDT requires accepting the licensing terms, see information from Bioportal :
http://bioportal.bioontology.org/ontologies/49774?p=terms and terms don’t resolve
it is under CC-BY-SA license
- neither QUDT nor UO use BFO as TLO.
Jie pointed to this link, where there are examples of using OBI measurements:
From her experience, she discouraged use of ‘float’ as a datatype as would cause problems later when performing reasoning: resolution = use xsd:double or xsd:decimal instead. It would be great to document these reasons further.
Unfortunately, we did not get too far in describing the document as other topics were raised such as BFO1.2/BFO2 discussion.
Hi Jie,
I presume you are referring to why OBI consortium isn't showing up under
'Groups' instead of "CTSA". I was very surprised on that too.
I will email Trish now.
For the records, please find enclose the information OBI vetted and sent
to the OBO Foundry when filing a request for review:
----------------------------
Dear OBO foundry,
I am submitting the following request for review on the behalf of OBI
-ontology name: Ontology for Biomedical Investigation
-contact person name: OBI developers ; Bjoern Peters
-contact person email: obi-...@lists.sourceforge.net; bpe...@liai.org
-scope of ontology:
(taken from http://obi-ontology.org/page/Main_Page "What is it?:
"The Ontology for Biomedical Investigations (OBI) project is developing
an integrated ontology for the description of biological and clinical
investigations. This includes a set of 'universal' terms, that are
applicable across various biological and technological domains, and
domain-specific terms relevant only to a given domain. This ontology
will support the consistent annotation of biomedical investigations,
regardless of the particular field of study. The ontology will represent
the design of an investigation, the protocols and instrumentation used,
the material used, the data generated and the type analysis performed on
it. Currently OBI is being built under the Basic Formal Ontology (BFO).
Develop an Ontology for Biomedical Investigations in collaboration with
groups representing different biological and technological domains
involved in Biomedical Investigations
Make OBI compatible with other bio-ontologies
Develop OBI using an open source approach
Create a valuable resource for the biomedical communities to provide a
source of terms for consistent annotation of investigations"
-link to stable version of the ontology:
http://purl.obolibrary.org/obo/obi.owl
-link to ontology documentation (e.g., web or wiki page):
http://obi-ontology.org/page/Main_Page
-other important links (describe):
svn repository: http://obi.svn.sourceforge.net/svnroot/obi/
issue tracker: https://sourceforge.net/tracker/?group_id=177891&atid=886178
-date of previous review request (if applicable):
OBI was reviewed last in February 2010
(http://obi-ontology.org/page/OBOFoundry_Meeting_2010_Feb)
http://www.obofoundry.org/wiki/index.php/OBO_Foundry_Workshop_2010/outcomes/monday
----------------------------
> ------------------------------------------------------------------------------
On 29/04/2013 14:13, jiez...@pcbi.upenn.edu wrote:
> Can we go through the metadata of OBI posted on the Bioportal web site
> together?
>
> Thanks,
>
> Jie
>
> Quoting Alejandra Gonzalez-Beltran <alejandra.gon...@gmail.com>:
>
>> Dear All,
>>
>> I will be chairing the call today.
>>
>> As agenda items, we have:
>>
>> 1. Assign chairs for the following calls.
>>
>> 2. Discuss about the agenda for an IAO-related call.
>>
>> 3. Philippe and I would like to discuss the coding measurements in OBI at
>> instance level, as part of creating documentation/guidelines for using OBI.
>>
>> Please, let me know if there is something else we should discuss.
>>
>> Best regards,
>>
>> Alejandra
>>
>
>
>
>
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>
Alejandra Gonzalez-Beltran, PhD
Senior Software Engineer, ISATeam
University of Oxford Tel: +44(0)1865 610688
Oxford e-Research Centre Fax: +44(0)1865 610624
7 Keble Road, Oxford Skype: agbeltran
OX1 3QG, UK http://uk.linkedin.com/in/agbeltran
--
Michel Dumontier
Jie pointed to this link, where there are examples of using OBI measurements:
From her experience, she discouraged use of ‘float’ as a datatype as would cause problems later when performing reasoning: resolution = use xsd:double or xsd:decimal instead. It would be great to document these reasons further.
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