Denrie

Digital Entity and Non-realizable Information Entity Branch
The Digital Entity and Non-realizable Information Entity Branch is an OBI Branch concerned with identifying entities and relations used in biological and biomedical investigations to describe information entities that can be interpreted by a computer or documented and communicated.

<<Back to Homepage

Scope
The scope of the Digital Entity and Non-realizable Information Entity branch is to identify essential entities to describe the output of measurements, types of files, and information content. The scope of DENRIE is restricted to biological and biomedical investigations. The Information Artifact Ontology is the source for general Information entities and will be imported into OBI. Terms with OBI IDs will be specific to investigations.

Digital Entity and Non-realizable Information Entity conference calls
Notes and schedule for calls can be found at the |Digital Entity and Non-realizable Information Entity conference call page>>

Latest Digital Entity and Non-realizable Information Entity branch .owl file
https://obi.svn.sourceforge.net/svnroot/obi/trunk/src/ontology/branches/DigitalEntityPlus.owl

Current OBI types

 * "digital_entity" Def: digital entity is an information entity which is a collection of bits that can be interpreted by a computer.
 * "non-realizable_information_entity" Def: an information entity is a dependent_continuant which conveys meaning and can be documented and communicated.

Use cases and term submission
List of Digital Entity and Non-realizable Information Entity Terms from Communities:


 * Tab delimited file with terms from flow cytometry: [[Media:DigitalEntity-FlowCytometry-2007-03-30.txt]]
 * Tab delimited file generated by the review of ~ExperimentDesignType terms in the MGED Ontology by the OBI Developers and the MGED Ontology developers in Spring, 2006: [[Media:moObjectiveTerms.txt]]
 * [[Media:GenericallyDepCont_to-DENIE-FlowCytometry-reorg.txt]]
 * [[Media:Terms_from_DataTransf_for_DENRIE.doc]]

Updated term collection

 * http://spreadsheets.google.com/ccc?key=p5JLniV3bk-edIPKOziyXfA&hl=en

Current outstanding issues
Action items related to DENRIE from Vancouver Workshop
 * Related discussion: https://wiki.cbil.upenn.edu/obiwiki/index.php/MondayJan28Notes
 * Point 7: Alan Ruttenberg, DENRI ppt http://ashby.csail.mit.edu/presentations/DenrieReport.pdf
 * Point 9: James Malone - Flow Cytometry Data Transformation Use Case
 * Related discussion: https://wiki.cbil.upenn.edu/obiwiki/index.php/TuesdayJan29Notes
 * Point 1: Plan Branch - Philippe Rocca Serra: first part down to Children of Protocol Application
 * relationships between DENRIE and Plan
 * issues with objectives, hypotheses, conclusions
 * Melanie Courtot - Quality
 * terms from DENRI - voltage etc need better definitions - the definitions were old for datum. They agreed that these are qualities. AR thinks they are dispositions.


 * General items
 * Branch/Individual review of other branches by March DL:Mar 15
 * Items involving DENRIE
 * Make the connection between the visulation between table and graph that comes out of this process currently that is in the DENRI branch. A cross branch issue. DT, DENRI. JM. DL:Feb 15
 * issue that we need a quality like thing of 'Gifness' and how works with DENRI. could also be solved by using feature om OBI as above, again a work around BS/AR: DL:?When info ontology is tackled?
 * Types can bear quality like things features and mathematical function and this is a workaround here where classes are created in OBI for math entities. Outside BFO so needs to be OBI and would mean that we don't need a relation. New class called feature - has_feature relates a type to a feature, all base, degree and number are features of type. DT branch and CC, AR, BS. DL:21 Feb phone call
 * Alan will generate a list of problems and solutions with DENRI for discussion on a conference call. Info ontology. DL: Dealt with in calls
 * BS will provide a better name for MeasurementUnit as Units pre-exist in the world outside data and so the name is bad. DL:May 1
 * Items involving DENRIE marked as DONE
 * Edit:InformationEntity will be renamed plan, synonym RealizableInformationEntity
 * Edit:DigitalEntity->child of NonRealizableInfoEntity, Plan will be a sibling of NonRealizeableInfoEntity, both children of InfoEntity
 * EDIT:Objective now child of InfoEntity
 * EDIT:Define Objective add a definition, synonym is GOAL

Previous posted issues
 * Discuss presentation by Barry Smith provided by Alan Ruttenberg
 * http://mumble.net/~alanr/Partitions_quantities_BuffaloNov06.ppt
 * Identify terms that need to be submitted to other branches
 * Chris S. attempt [[Image:digital entity-cs.xls]]
 * Review Software Ontology
 * Bill Bug wrote on July 10, 2007 to the OBI-developers list:

Here's the currently published version of the NCBC-wide Software/Resource Ontology: http://bioontology.org/projects/ontologies/SoftwareOntology/

This is an ongoing project to provide a shared semantic framework & lexicon for describing the software tools being hosted or developed by the collection of NCBCs: http://na-mic.org/Wiki/index.php/SDIWG:_NCBC_Resource_Yellow_Pages_and_Software_Ontologies

The ontology NCBCs are developing for this purpose is indirectly linked to the effort across NCBCs to come to an agreement as to what ontologies/terminologies/classification schemes NCBC's collectively agree to use to cover their annotation requirements: http://www.berkeleybop.org/sowg/table.cgi http://www.na-mic.org/Wiki/index.php/PrelimResultsSOWG1 I've also been meaning to bring up the issue of what they've been trying to do on this front in the BioMOBY project (something I assume has come up before in the context of MGED work): listings: objects http://mobycentral.icapture.ubc.ca:8090/sswap/RESOURCES/MOBY-S/Objects/listing.html namespaces http://mobycentral.icapture.ubc.ca:8090/sswap/RESOURCES/MOBY-S/Namespaces/listing.html
 * Bill Bug also wrote on July 27, 2007 to the OBI-developers list:

ontology (viewable in SWOOP): http://biomoby.org/RESOURCES/MOBY-S/Objects

I think there are pros & cons to the way they are currently proceeding, but its clear many of their objects are certainly entities we want to cover in this branch of OBI.

Mailing list
For the latest news and updates on the Digital Entity and Non-realizable Information Entity Branch sign-up at the mailing list at DENRIE Mailing List

Editors
Editors for the Digital Entity and Non-realizable Information Entity branch are as follows:


 * Bill Bug
 * Kevin Clancy
 * Cristian Cocos
 * Melanie Courtot
 * Jennifer Fostel
 * Allyson Lister
 * Alan Ruttenberg
 * Chris Stoeckert

Related Links
* OBI Branches