en obsolete classes from the information artifact ontology. see http://code.google.com/p/information-artifact-ontology/ 2009-11-06 This file is based on checkout of our SVN repository revision $Revision: 2489 $ has curation status definition editor note in branch example of usage definition editor editor preferred term alternative term definition source has obsolescence reason describes obsolete_artifact represents obsolete2_digital entity OBI_0000261 3/22/2009 Alan Ruttenberg, obsoleted per http://groups.google.com/group/information-ontology/browse_thread/thread/789ad4b7708d5cf4 Superclass was 'digitial quality' A digital entity is an information entity which is a collection of bits that can be interpreted by a computer. Two digital entities are the same if they are bitwise identical. group:OBI obsolete_digital entity person:Chris Stoeckert obsolete_material_entity obsolete2_binary digital entity OBI_0000244 3/22/2009 Alan Ruttenberg, obsoleted per http://groups.google.com/group/information-ontology/browse_thread/thread/789ad4b7708d5cf4 Superclass was 'digital entity' A binary digital entity is a digital entity that is encoded in a way that is not easily human readable and that contains other than text characters. binary digital entity digital_entity group:OBI person:Chris Stoeckert obsolete2_text based digital entity OBI_0000132 group:OBI 3/22/2009 Alan Ruttenberg, obsoleted per http://groups.google.com/group/information-ontology/browse_thread/thread/789ad4b7708d5cf4 superclass was 'digital document' A text based digital entity is a digital entity that is encoded so that it only contains text characters. digital_entity person:Chris Stoeckert text based digital entity obsolete2_binary executable OBI_0000222 3/22/2009 Alan Ruttenberg, obsoleted per http://groups.google.com/group/information-ontology/browse_thread/thread/789ad4b7708d5cf4 superclass was 'digital entity' Binary executable is a digital entity consisting of the binary representation of machine instructions of a specific processor or they may be binary pseudocode for a virtual machine. A non-source executable file is also called an object program. It is assumed that the binary executable file contains properly-formatted computer instructions. (derived from Wikipedia, Nov 1, 2007) binary executable group:OBI person:Jennifer Fostel obsolete2_digital document OBI_0000195 3/22/2009 Alan Ruttenberg, obsoleted per http://groups.google.com/group/information-ontology/browse_thread/thread/789ad4b7708d5cf4 superclass was 'digial entity' A digital document is a digital entity consisting of an electronic file which can be rendered into human-readable form by one or more computational applications. The digital document does not refer to the information content of the document but to an instance of the file. digital document group:OBI person:Jennifer Fostel obsolete_digital quality Need to rework digital entity. Digital quality was suggested by Barry. 3/22/2009 Alan Ruttenberg, obsoleted per http://groups.google.com/group/information-ontology/browse_thread/thread/789ad4b7708d5cf4 obsolete_unit of measure Alan Ruttenberg Smith, Ceusters, Ruttenberg, 2000 years of philosophy The length of a ruler. a unit of measure is the quality of some material entity compared to which another quality is some multiple of. MS Word document, ZIP file, DICOM file, JPEG file XML file, C++ source code file I prepended the 'report ' to make it clear that we mean parts of reports here. We may want a more generic version of 'figure', in which case this would become a defined class - figure and part_of some report report figure person:Alan Ruttenberg 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 person:Allyson Lister OBI_0000027 Replaced by defined version of figure group:OBI obsolete2_report figure obsolete_imported from GROUP:OBI:<http://purl.obolibrary.org/obo/obi> For external terms/classes, the ontology from which the term was imported. obsolete_imported from Replaced by IAO_0000412 group:OBI 2009-08-10 Alan Ruttenberg: Larry Hunter suggests that this be obsoleted and replaced by 'textual entity table'. Alan restored as there are OBI dependencies and this merits further discussion OBI_0000265 person:Allyson Lister obsolete_report table report table A report table is a report display element consisting of a matrix of cells layed out in a grid, some set of which are filled with some information content person:Alan Ruttenberg A study interpretation is a textual entity about the implications of a study result. Examples include discussion of whether a hypothesis is false, whether the study failed to address the hypothesis, and whether the study results have led to new hypotheses 2009-03-16: 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. conclusion OBI_0000005 obsolete_study interpretation The obsoleting of narrative object required a modest change in the definition of this term. Circularity with "interpretation... interprets" has been removed, using "about the implications" instead. Lawrence Hunter obsolete_study interpretation PERSON: Alan Ruttenberg 2009-03-16: definition was "A conclusion is a narrative object which can be published in a paper summerizing and interpreting a protocol application." PERSON: Melanie Courtot PERSON: Jennifer Fostel _identifier is a container under information content entity for collecting types of terms to indicate a specific instance or clas of what was used or participated in an investigation. Identifiers are borne by a product or its packaging, and can be encoded in a variety of other information objects, such as bar codes, numerals, or patterns of dots. Note: everybody agreed that identifier is probably a too general term. We however felt that it would be appropriate to group "identifiying" terms under some kind of umbrella. We therefore propose to use _identifier for that purpose. As per OBI conventions, the _ prefixing identifier indicates that this is a helper class and shouldn't be considered as final. obsolete_identifier OBI_0000001 2009-03-16: was report display element with definition: A report display element is a narrative object that is part of a report. Report display elements are set off from the textual parts of a report and are typically given a label(e.g. Figure 2) which is used to refer to the element from the text. Typically the 2d layout is part of the identity of such elements. Replaced by textual entity and figure PERSON: Allyson Lister report element 2009-03-16: needs some more work (clarify relations). 2009-08-10 Alan Ruttenberg: Larry Hunter suggests that this be obsoleted and replaced by 'textual entity' and 'figure'. Alan restored as there are OBI dependencies and this merits further discussion PERSON: Melanie Courtot 2009-03-16: 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. There will be some issue here about whether these are defined classes. As intended these are meant to denote the parts of the report that are not textual but are typically boxed and set within the text, labelled with some identifier, and referred to in the text PERSON: Alan Ruttenberg obsolete_report element 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). GROUP:OBI has obsolescence reason has curation status editor note example of usage editor preferred term alternative term definition in branch definition source definition editor