en $Revision$ a dependent continuant or its bearer that is created as the result of one or more intentional processes. Examples: uniprot, the english language, the contents of this document or a printout of it, the temperature measurements from a weather balloon. has measurement unit label specifically denotes c specifically denotes r =def r is a portion of reality & c is a particular quality & c depends specifically on some independent continuant b & b acquired c as the result of the achievement of an objective to enable pointing to r repeatedly. Marked means there is a changed or additional quality of the bearer - the quality is the information carrier. Case 1 Memory trace as mark created when reading some description of some friend. The trace can denote. Case 2 Pattern of ink arrayed on paper as mark when writing down a friend's name Case 3 Pattern of magnetic domains on scattered pieces of a hard disk platter as mark when saving a file. Smith, Ceusters, Ruttenberg, 2000 years of philosophy Alan Ruttenberg The process of creation is, for example, writing down on paper the name of a friend by deliberately creating a certain pattern using ink. Here the ink + paper is the independent continuant and the carrier is the pattern in the ink. c = pattern in the ink b = paper + ink r = friend is about person:Alan Ruttenberg This document is about information artifacts and their representations a representation is_about anything exactly when some part of the information_artifact denotes the entity Smith, Ceusters, Ruttenberg, 2000 years of philosophy generically denotes Smith, Ceusters, Ruttenberg, 2000 years of philosophy The word Boston on a traffic signn in Massachusetts generically denotes the city of Boston g generically denotes r =def r is a portion of reality there is some c that is a concretization of g every c that is a concretization of g specifically denotes r person:Alan Ruttenberg materially denotes is quality measurement of m is a quality measurement of q at t when q is a determinable quality there is a measurement process p that has_output m m has a value part that together with the units of the value of q at t. p is a assay assay: process and has_input some material entity and has_output some information content entity and which is such that instances of this process type reliably generate outputs that describes the input. a is a magnitude means a is a determinate quality particular inhering in some bearer b existing at a time t that can be represented/denoted by an information content entity e that has parts denoting a unit of measure, a number, and b. The unit of measure is an instance of the determinable quality. unit of measure is a quality, e.g. the length of a ruler. a represents b means either a denotes b or a describes describe: a describes b means a is about b and a allows an inference of at least one quality of b Example: q = height of barry p is the process using a tape measure extend across the longer part of barry and reading off the number at the far end. v is that number # dimension is height unit of measure is inches We have had a long discussion about denotes versus describes. This one is the one we are struggling with at the moment. The issue is what a measurement measures. On the one hand saying that it measures the quality would include it "measuring" the bearer = referring to the bearer in the measurement. However this makes comparisons of two different things not possible. On the other hand not having it inhere in the bearer, on the face of it, breaks the audit trail. Werner suggests a solution based on "Magnitudes" a proposal for which we are awaiting details. describes represents There is controversy about this relation intended to represent the relation between some arbitrary physical thing that is used as a represention/proxy/pointer to something else has measurement value conditional specification OBI branch derived OBI_0000349 PlanAndPlannedProcess Branch instruction trigger is information about a realizable that specifies that what should happen if the trigger condition is fulfilled measurement unit label remove? See unit of measure. OBI_0000176 A measurement unit label is an label that is part of a measurement datum and denotes a unit of measure. Examples of measurement unit labels are liters, inches, weight per volume. measurement unit label person:Alan Ruttenberg objective specification Barry Smith OBI_0000217 Alan Ruttenberg An objective specification is an information entity about a realizable entity that describes a intended process endpoint. When part of a plan specification the concretization is realized in a planned process in which the bearer tries to effect the world so that the process endpoint is achieved. Answers the question, why did you do this experiment? Jennifer Fostel OBI Plan and Planned Process/Roles Branch objective specification purpose of a study; support of hypothesis, discovery of new information narrative object OBI_0000013 A narrative object is an information content entity that is a set of propositions. Examples of narrative objects are reports, journal articles, and patents submission. agree - DENRIE. Issue(alan) do we only mean text? What about a story told by mime. Does music count? (no) what about an oral report. Regarding definition, saying it is a set of propositions means we loose the idea that wording matters. Maybe adjust saying a narrative object has some relationshop to a set of propositions group:OBI narrative object person:Chris Stoeckert action specification Alan Ruttenberg An action specification is information about a realizable that describes an action the bearer will take OBI Plan and Planned Process branch Pour the contents of flask 1 into flask 2 artifact An artifact is an independent continuant that is the intended output of an objective driven process There is not yet consensus this term label http://www.golovchenko.org/cgi-bin/wnsearch?q=label#4n A label is a symbol that is part of some other datum and is used to either partially define the denotation of that datum or to provide a means for identifying the datum as a member of the set of data with the same label software GROUP: OBI PERSON: Alan Ruttenberg PERSON: Bjoern Peters PERSON: Chris Stoeckert PERSON: Melanie Courtot 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. see sourceforge tracker discussion at http://sourceforge.net/tracker/index.php?func=detail&aid=1958818&group_id=177891&atid=886178 software digital entity 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. OBI_0000261 digital entity group:OBI person:Chris Stoeckert journal article content Journal article content is a narrative object that is the information content encoded in a article published in a serious, scholarly publication, most often peer-reviewed. OBI_0000159 Examples of encodings of journal article content are articles published in the journals, Nature and Science. The content can often be cited by reference to a paper based encoding, e.g. Authors, Title of article, Journal name, date or year of publication, volume and page number. group:OBI journal article content person:Alan Ruttenberg person:Chris Stoeckert information carrier Alan Ruttenberg an information carrier is that quality of an information bearer that imparts the information content The pattern in ink on a page of a paperback novel. Smith, Ceusters, Ruttenberg, 2000 years of philosophy binary digital entity OBI_0000244 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. MS Word document, ZIP file, DICOM file, JPEG file binary digital entity digital_entity group:OBI person:Chris Stoeckert unit of measure Alan Ruttenberg 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. Smith, Ceusters, Ruttenberg, 2000 years of philosophy programming language OBI_0000058 A language in which source code is written, intended to executed/run by a software interpreter. Programming languages are ways to write instructions that specify what to do, and sometimes, how to do it. R, Perl, Java group:OBI person:Alan Ruttenberg person:Chris Stoeckert programming language data item JAR: datum -- well, this will be very tricky to define, but maybe some information-like stuff that might be put into a computer and that is meant, by someone, to denote and/or to be interpreted by some process... I would include lists, tables, sentences... I think I might defer to Barry, or to Brian Cantwell Smith JAR: A data item is an approximately justified approximately true approximate belief a data item is an information content entity that is intended to be a truthful statement about something (modulo, e.g., measurement precision or other systematic errors) and is constructed/acquired by a method which reliably tends to produce (approximately) truthful statements. Jonathan Rees data datum symbol Jonathan Rees a smallish, word-like datum... numeral Jonathan Rees a symbol that denotes a number Examples of information content entites include journal articles, data, graphical layouts, and graphs. OBI_0000142 an information content entity is an entity that is generically dependent on some artifact and stands in relation of aboutness to some entity information content entity information_content_entity 'is_encoded_in' some digital_entity in obi before split (040907). information_content_entity 'is_encoded_in' some physical_document in obi before split (040907). Previous. An information content entity is a non-realizable information entity that 'is encoded in' some digital or physical entity. integer numeral Jonathan Rees a numeral that denotes an integer scalar measurement datum 1 1 Would write this as: has_part some 'measurement unit label' and has_part some numeral and has_part exactly 2, except for the fact that this won't let us take advantage of OWL reasoning over the numbers. Instead use has measurment value property to represent the same. Use has measurement unit label (subproperty of has_part) so we can easily say that there is only one of them. a scalar measurement datum is a measurement datum that is composed of two parts, a single numeral and a unit label. 10 feet. 3 ml. Alan Ruttenberg information entity about a realizable Werner pushed back on calling it realizable information entity as it isn't realizable. However this name isn't right either. An example would be a recipe. The realizable entity would be a plan, but the information entity isn't about the plan, it, once concretized, *is* the plan. -Alan An information entity about a realizable is an information content entity about a realizable. Alan Ruttenberg time trigger OBI branch derived OBI_0000331 PlanAndPlannedProcess Branch revisit? time trigger conclusion OBI_0000005 A conclusion is a narrative object which can be published in a paper summerizing and interpreting a protocol application. Jennifer Fostel conclusion dot plot OBI_0000123 A dot plot is a report graph which is a graphical representation of data where each data point is represented by a single dot placed on coordinates corresponding to data point values in particular dimensions. Dot plot of SSC-H and FSC-H. dot plot group:OBI person:Allyson person:Chris Stoeckert report graph OBI_0000240 group:OBI A report graph is a report figure that presents one or more tuples of information my mapping those tuples in to a two dimensional space in a non arbitrary way. person:Alan Ruttenberg person:Allyson Lister report graph text based digital entity A text based digital entity is a digital entity that is encoded so that it only contains text characters. OBI_0000132 XML file, C++ source code file digital_entity group:OBI person:Chris Stoeckert text based digital entity rule OBI_0500021 MSI PRS PRS a rule is an executable which guides, defines, restricts actions example to be added rule contour plot OBI_0000246 Contour plot of SSC-H, FSC-H, and FL1-H. contour plot generically_dependent_continuants group:Flow Cytometry community person:Allyson person:Chris Stoeckert report figure 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 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 OBI_0000027 group:OBI person:Alan Ruttenberg person:Allyson Lister report figure algorithm OBI_0000270 PMID: 18378114.Genomics. 2008 Mar 28. LINKGEN: A new algorithm to process data in genetic linkage studies. Philippe Rocca-Serra PlanAndPlannedProcess Branch adapted from discussion on OBI list (Matthew Pocock, Christian Cocos, Alan Ruttenberg) algorithm an algorithm is a plan which describes inputs, output of mathematical functions as well as workflow of execution for achieving an predefined objective. Algorithms are realized usually by means of implementation as computer programs for execution by automata. software interpreter OBI_0000199 A software interpreter is a generically dependent realizable entity that takes, as input, some digital entity, and takes action driven by the information content of that digital entity Do we care? Jennifer: Yes, there was a particular version of R that had a bug and it was fixed later. That would imply that we mean specific version of an interpreter. So an instance of this would be a particular version of the interpreter R program, Perl interpreter, Java virtual machine group:OBI person:Alan Ruttenberg person:Chris Stoeckert software interpreter density plot OBI_0000179 A density plot is a report graph which is a graphical representation of data where the tint of a particular pixel corresponds to some kind of function corresponding the the amount of data points relativelly with their distance from the the pixel. Density plot of SSC-H and FSC-H. density plot group:Flow Cytometry community person:Allyson person:Chris Stoeckert report of results Examples of reports are gene lists and investigation reports. These are not published (journal) articles but may be included in a journal article. OBI_0000099 A report is a narrative object that is a formal statement of the results of an investigation, or of any matter on which definite information is required, made by some person or body instructed or required to do so. disagreement about where reports go. alan: only some gene lists are reports. Is a report all the content of some document? The example of usage suggests that a report may be part of some article. Term needs clarification group:OBI person:Chris Stoeckert report of results report display element 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. OBI_0000001 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 group:OBI person:Alan Ruttenberg person:Allyson Lister report display element binary executable 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) OBI_0000222 binary executable group:OBI person:Jennifer Fostel source code module OBI_0000039 A source code module is an information content entity that specifies, using a programming language, some algorithm. The written source code that implements part of an algorithm. Test - if you know that it was written in a specific language, then it can be source code module. We mean here, roughly, the wording of a document such as a perl script. group:OBI person:Alan Ruttenberg person:Chris Stoeckert source code module 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 OBI_0000265 group:OBI person:Alan Ruttenberg person:Allyson Lister report table data format specification OBI_0000187 A data format specification is the information content borne by the document published defining the specification. blah: for organizing information artifacts. Example: The ISO document specifying what encompasses an XML document; The instructions in a XSD file OBI branch derived PlanAndPlannedProcess Branch data format specification data set OBI_0000042 A data set is an information content entity that is an aggregate of other information_content_entities that have something in common and are considered to form a unit. data set group:OBI person:Allyson person:Chris Stoeckert image OBI_0000030 An image is an information content entity which provides a visual representation of for the result of a measurement. group:OBI image person:Allyson person:Chris Stoeckert plan specification OBI_0000344 A plan specification is an information entity about a realizable entity. The specification includes parts such as objective specification, action specifications and conditional specifications. When concretized it is realized in a process in which the bearer tries to achieve the objectives, in part by taking the actions specified. Alan Ruttenberg Alternative previous definition: a plan is a set of instructions that specify how an objective should be achieved OBI Plan and Planned Process branch PMID: 18323827.Nat Med. 2008 Mar;14(3):226.New plan proposed to help resolve conflicting medical advice. plan specification digital document 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. OBI_0000195 digital document group:OBI person:Jennifer Fostel measurement datum A measurement datum is an information content entity that is a recording of the output of a measurement such as produced by an instrument. OBI_0000305 Examples of measurement data are the recoding of the weight of a mouse as {40,mass,"grams"}, the recording of an observation of the behavior of the mouse {,process,"agitated"}, the recording of the expression level of a gene as measured through the process of microarray experiment {3.4,luminosity,}. group:OBI measurement datum person:Chris Stoeckert _identifier _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. version number A version number is an information content entity which is a sequence of characters borne by part of each of a class of manufactured products or its packaging and indicates its order within a set of other products having the same name. Note: we feel that at the moment we are happy with a general version number, and that we will subclass as needed in the future. For example, see 7. genome sequence version serial number A serial number is an information content entity which is a unique sequence of characters borne by part of manufactured product or its packaging that is assigned to each individual in some class of products, and so can serve as a way to identify an individual product within the class. Serial numbers can be encoded in a variety of other information objects, such as bar codes, numerals, or patterns of dots. Note: during the call there was some confusion between serial number and model number. We agreed that it would be very helpful for all those terms to have example of usages - please add if you have any :-) lot number batch number A lot number is an information content entity which is an identical sequence of character borne by part of manufactured product or its packaging for each instances of a product class in a discrete batch of an item. Lot numbers are usually assigned to each separate production run of an item. Manufacturing as a lot might be due to a variety of reasons, for example, a single process during which many individuals are made from the same portion of source material. Lot numbers can be encoded in a pattern of other information objects, such as bar codes, numerals, or patterns of dots. setting datum Alan grouped these in placeholder for the moment. Name by analogy to measurement datum. A settings datum is a datum that denotes some configuration of an instrument. digital quality Need to rework digital entity. Digital quality was suggested by Barry. material information bearer An information bearer is an artifact, such as a hard drive, upon which an information content entity generically depends. histogram A histogram is a report graph which is a statistical description of a distribution in terms of occurrence frequencies of different event classes. GROUP:OBI PERSON:Chris Stoeckert PERSON:James Malone PERSON:Melanie Courtot histogram heatmap A heatmap is a report graph which is a graphical representation of data where the values taken by a variable(s) are shown as colors in a two-dimensional map. GROUP:OBI PERSON:Chris Stoeckert PERSON:James Malone PERSON:Melanie Courtot heatmap Venn diagram A Venn diagram is a report graph showing all hypothetically possible logical relations between a finite collection of sets. PERSON:Chris Stoeckert PERSON:James Malone PERSON:Melanie Courtot Venn diagram WEB: http://en.wikipedia.org/wiki/Venn_diagram survival curve A survival curve is a report graph which is a graphical representation of data where the percentage of survival is plotted as a function of time. PERSON:Chris Stoeckert PERSON:James Malone PERSON:Melanie Courtot WEB: http://www.graphpad.com/www/book/survive.htm survival curve dendrogram A dendrogram is a report graph which is a tree diagram frequently used to illustrate the arrangement of the clusters produced by a clustering algorithm. Dendrograms are often used in computational biology to illustrate the clustering of genes. PERSON:Chris Stoeckert PERSON:James Malone PERSON:Melanie Courtot WEB: http://en.wikipedia.org/wiki/Dendrogram dendrogram scatterplot A scatterplot is a report graph which uses Cartesian coordinates to display values for two variables for a set of data. The data is displayed as a collection of points, each having the value of one variable determining the position on the horizontal axis and the value of the other variable determining the position on the vertical axis. PERSON:Chris Stoeckert PERSON:James Malone PERSON:Melanie Courtot WEB: http://en.wikipedia.org/wiki/Scatterplot scattergraph scatterplot