IBO is a biomedical ontology that enables the annotation of imaging biomarker data (e.g., measurement processes, measures, clinical processes, imaging datasets, etc.). BFO 2 Reference: BFO does not claim to provide complete coverage of entities of all types. It seeks only to provide coverage of those entities studied by empirical science together with those entities which affect or are involved in human activities such as data processing and planning - coverage that is sufficiently broad to provide assistance to those engaged in building domain ontologies for purposes of data annotation. BFO 2 Reference: BFO's treatment of continuants and occurrents - as also its treatment of regions, rests on a dichotomy between space and time, and on the view that there are two perspectives on reality - earlier called the 'SNAP' and 'SPAN' perspectives, both of which are essential to the non-reductionist representation of reality as we understand it from the best available science. BFO 2 Reference: For both terms and relational expressions in BFO, we distinguish between primitive and defined. 'Entity' is an example of a primitive term. Primitive terms in a highest-level ontology such as BFO are terms that are so basic to our understanding of reality that there is no way of defining them in a non-circular fashion. For these, therefore, we can provide only elucidations, supplemented by examples and by axioms. Alan Ruttenberg Albert Goldfain Barry Smith Bill Duncan Bjoern Peters Chris Mungall David Osumi-Sutherland Fabian Neuhaus Holger Stenzhorn James A. Overton Janna Hastings Jie Zheng Jonathan Bona Larry Hunter Leonard Jacuzzo Ludger Jansen Mark Ressler Mathias Brochhausen Mauricio Almeida Melanie Courtot Pierre Grenon Randall Dipert Ron Rudnicki Selja Seppälä Stefan Schulz Thomas Bittner Werner Ceusters Yongqun "Oliver" He 10/04/2018 Emna Amdouni and Bernard Gibaud Please see the project site https://github.com/BFO-ontology/BFO, the bfo2 owl discussion group http://groups.google.com/group/bfo-owl-devel, the bfo2 discussion group http://groups.google.com/group/bfo-devel, the tracking google doc http://goo.gl/IlrEE, and the current version of the bfo2 reference http://purl.obolibrary.org/obo/bfo/dev/bfo2-reference.docx. This ontology is generated from a specification at https://github.com/BFO-ontology/BFO/tree/master/src/ontology/owl-group/specification/ and with the code that generates the OWL version in https://github.com/BFO-ontology/BFO/tree/master/src/tools/. A very early version of BFO version 2 in CLIF is at http://purl.obolibrary.org/obo/bfo/dev/bfo.clif. The BSD license on the BFO project site refers to code used to build BFO. This BFO 2.0 version represents a major update to BFO and is not strictly backwards compatible with BFO 1.1. The previous OWL version of BFO, version 1.1.1 will remain available at http://ifomis.org/bfo/1.1 and will no longer be updated. The BFO 2.0 OWL is a classes-only specification. The incorporation of core relations has been held over for a later version. Relates an entity in the ontology to the name of the variable that is used to represent it in the code that generates the BFO OWL file from the lispy specification. Really of interest to developers only BFO OWL specification label Relates an entity in the ontology to the term that is used to represent it in the the CLIF specification of BFO2 Person:Alan Ruttenberg Really of interest to developers only BFO CLIF specification label editor preferred term example of usage definition editor note term editor alternative term definition source curator note imported from elucidation has associated axiom(nl) has associated axiom(fol) has axiom label 'is estimated from' is a specification of the relationship 'is about' and it serves to link an 'information content entity' to another 'information content entity'. PERSONS: Emna Amdouni, Yanncik Morvan and Bernard Gibaud 27/11/2015 This relationship can be used to denotes how a particular information content entity was been derived from another 'information content entity'. is_estimated_from Emna Amdouni, Yannick Morvan and Bernard Gibaud is_process_profile_measurement_of MR dataset http://neurolog.unice.fr/ontoneurolog/v3.0/OntoSpec-documentation.zip Farooq Ahmad , Michel Dojat, Bernard Gibaud, Gilles Kassel, Lynda Temal September 30th, 2008 A MR DATASET is either a RECONSTRUCTED DATASET or a NON- RECONSTRUCTED DATASET. However, the applications considered in the context of the Neurolog project concern essentially RECONTRUCTED MR DATASETS. So, for simplicity, all the specializations of MR DATASETS currently defined in the ontology are RECONSTRUCTED DATASETS. This choice will be reconsidered later on to take into account both RECONTRUCTED and NON-RECONSTRUCTED MR DATASETS. MR dataset 1.1 dataset A DATASET is a PROPOSITION. [EP/ER] Every DATASET has for proper part exactly one DATASET SET OF VALUES during a TIME INTERVAL. [EP/ER] Every DATASET has for proper part exactly one DATASET META-DATA during a TIME INTERVAL. [EP/ER] Every DATASET is expressed by at least one DATASET EXPRESSION at a TIME INTERVAL. [EP/ER] Every DATASET is physically realized by at least one FILE at a TIME INTERVAL. [EP/ICL] No DATASET is a DATASET META-DATA. [EP/ICL] No DATASET is a DATASET SET OF VALUES. http://neurolog.unice.fr/ontoneurolog/v3.0/OntoSpec-documentation.zip September 30th, 2008 DATASETS are divided among MR DATASETS, PET DATASETS, CT DATASETS, SPECT DATASETS, MEG DATASETS, and EEG DATASETS according to their modality. We chose to restrict the definition of these modality DATASETS. All the parameters derived from such modality DATASETS, such as QUANTITATIVE T1 DATASET, etc., are not considered as modality DATASETS. [SA] DATASETS are divided among SINGLE SUBJECT DATASETS and MULTIPLE SUBJECT DATASETS according to whether they refer to one SUBJECT or not. [SA] DATASETS are divided among ANATOMICAL DATASETS, FUNCTIONAL DATASETS, METABOLIC DATASETS, and HEMODYNAMIC DATASETS according to the kind of entity they explore. [SA] DATASETS are divided among REGISTRATION DATASETS, SEGMENTATION DATASETS, TEMPLATE DATASETS, etc., according to the kind of processing they are the result of. [SA] DATASETS are divided among RECONSTRUCTED DATASETS and NON-RECONSTRUCTED DATASETS whether they provide measurements at well-identified locations in 3D space. dataset 1.1 dataset metadata Every DATASET META-DATA is a proper part of exactly one DATASET during a TIME INTERVAL. No DATASET META-DATA is a DATASET. No DATASET META-DATA is a DATASET SET OF VALUES. http://neurolog.unice.fr/ontoneurolog/v3.0/OntoSpec-documentation.zip PERSONS: Emna Amdouni and Bernrad Gibaud September 30th, 2008 dataset metadata 1.1 data set of values A DATASET SET OF VALUES is a PROPOSITION. Every DATASET SET OF VALUES is a proper part of only one DATASET during a TIME INTERVAL. No DATASET SET OF VALUES is a DATASET. No DATASET SET OF VALUES is a DATASET META-DATA. http://neurolog.unice.fr/ontoneurolog/v3.0/OntoSpec-documentation.zip PERSONS: Emna Amdouni and Bernrad Gibaud September 30th, 2008 dataset set of values 1.1 hemodynamic dataset A HEMODYNAMIC DATASET is a DATASET which explores a blood flow. http://neurolog.unice.fr/ontoneurolog/v3.0/OntoSpec-documentation.zip Farooq Ahmad , Michel Dojat, Bernard Gibaud, Gilles Kassel, Lynda Temal September 30th, 2008 hemodynamic dataset 1.1 parameter quantification dataset http://neurolog.unice.fr/ontoneurolog/v3.0/OntoSpec-documentation.zip Farooq Ahmad , Michel Dojat, Bernard Gibaud, Gilles Kassel, Lynda Temal September 30th, 2008 This class of PARAMETER QUANTIFICATION DATASETS subsumes all the RECONSTRUCTED DATASETS that measure clinically relevant biological quantities of the tissues, such as T1 value, regional cerebral blood volume, fractional anisotropy, etc. They generally result of post-processing of acquired images, based on some estimation model. The values represented in those datasets are considered as measures because they are supposed to be “reproducible when measured again, and also comparable with measurements made by others in others locations” parameter quantification dataset 1.1 segmentation dataset segmentation-dataset is a dataset is a dataset which is the result of a segmentation at a time interval. Every segmentation dataset can be superimpposed with another reconstructed dataset or segmentation dataset or statistical dataset or parameter qunatification dataset. Based on AIM model definition, segmentation is a result segmentation of segmentation process where segmenting or partitioning digital image (s) in to a set of pixels. These pixels are stored in a separate file from the original image(s). http://neurolog.unice.fr/ontoneurolog/v3.0/OntoSpec-documentation.zip Farooq Ahmad , Michel Dojat, Bernard Gibaud, Gilles Kassel, Lynda Temal September 30th, 2008 segmentation dataset 1.1 single subject dataset http://neurolog.unice.fr/ontoneurolog/v3.0/OntoSpec-documentation.zip Farooq Ahmad , Michel Dojat, Bernard Gibaud, Gilles Kassel, Lynda Temal September 30th, 2008 single subject dataset 1.1 template dataset A TEMPLATE DATASET is a STATISTICAL DATASET which is a result of a DATASETS MEAN CALCULATION at a TIME INTERVAL. [CP/SL] Every TEMPLATE DATASET is a STATISTICAL DATASET. [CP/ER] Every TEMPLATE DATASET refers to a GROUP OF SUBJECTS. http://neurolog.unice.fr/ontoneurolog/v3.0/OntoSpec-documentation.zip Farooq Ahmad , Michel Dojat, Bernard Gibaud, Gilles Kassel, Lynda Temal September 30th, 2008 template dataset 1.1 http://neurolog.unice.fr/ontoneurolog/v3.0/OntoSpec-documentation.zip PERSONS: Emna Amdouni and Bernard Gibaud October 16th, 2008 calibration model application dataset processing is a data transformation process that represents the process of extracting clinically relevant information or knowledge from medical images. While closely related to the field of medical imaging, data processing focuses on the computational analysis of the images, not their acquisition. The methods can be grouped into several broad categories: image segmentation, image registration, image-based physiological modeling, and others. Medical image computing http://neurolog.unice.fr/ontoneurolog/v3.0/OntoSpec-documentation.zip PERSONS: Emna Amdouni and Bernard Gibaud October 16th, 2008 dataset processing A FRACTIONAL ANISOTROPY CALCULATION is a QUANTITATIVE PARAMETER ESTIMATION. [CP/EVR] Every FRACTIONAL ANISOTROPY CALCULATION has for data only a DIFFUSION TENSOR DATASET at a TIME INTERVAL. [EP/ER] Every FRACTIONAL ANISOTROPY CALCULATION has for result a FRACTIONAL ANISOTROPY DATASET at a TIME INTERVAL. http://neurolog.unice.fr/ontoneurolog/v3.0/OntoSpec-documentation.zip PERSONS: Farooq Ahmad, Michel Dojat, Bernard Gibaud, Gilles Kassel, Lynda Temal fractional anisotropy calculation medical image segmentation A SEGMENTATION is a DATASET PROCESSING. [EP/ER] Every SEGMENTATION has for result at least one SEGMENTATION DATASET at a TIME INTERVAL. [CP/EVR] No SEGMENTATION has for data an EEG DATASET or a MEG DATASET or a NON-RECONSTRUCTED DATASET or a REGISTRATION DATASET or a MESH DATASET or a SEGMENTATION DATASET or a CALIBRATION DATASET at a TIME INTERVAL. ONL-DP http://neurolog.unice.fr/ontoneurolog/v3.0/OntoSpec-documentation.zip PERSONS: Farooq Ahmad, Michel Dojat, Bernard Gibaud, Gilles Kassel, Lynda Temal October 16th, 2008 image segmentation A MEAN DIFFUSIVITY CALCULATION is a QUANTITATIVE PARAMETER ESTIMATION. [CP/EVR] Every MEAN DIFFUSITY CALCULATION has for data only a DIFFUSION TENSOR DATASET at a TIME INTERVAL. [EP/ER] Every MEAN DIFFUSIVITY CALCULATION has for result a MEAN DIFFUSIVITY DATASET at a TIME INTERVAL. http://neurolog.unice.fr/ontoneurolog/v3.0/OntoSpec-documentation.zip PERSONS: Farooq Ahmad, Michel Dojat, Bernard Gibaud, Gilles Kassel, Lynda Temal October 16th, 2008 mean diffusivity calculation quantitative parameter estimation A QUANTITATIVE PARAMETER ESTIMATION is a medical image analysis. [EP/ER] Every QUANTITATIVE PARAMETER ESTIMATION has for result a PARAMETER QUANTIFICATION DATASET at a TIME INTERVAL. http://neurolog.unice.fr/ontoneurolog/v3.0/OntoSpec-documentation.zip PERSONS: Farooq Ahmad, Michel Dojat, Bernard Gibaud, Gilles Kassel, Lynda Temal October 16th, 2008 Quantitative parameter estimation is the procedure that leads to the quantitative estimation of a specific physiological parameter. quantitative parameter estimation image reconstruction A RECONSTRUCTION is a DATASET PROCESSING. [EP/ER] Every RECONSTRUCTION has for data exactly one NON-RECONSTRUCTED DATASET at a TIME INTERVAL. [EP/ER] Every RECONSTRUCTION has for result exactly one RECONSTRUCTED DATASET at a TIME INTERVAL. image reconstruction http://neurolog.unice.fr/ontoneurolog/v3.0/OntoSpec-documentation.zip PERSONS: Farooq Ahmad, Michel Dojat, Bernard Gibaud, Gilles Kassel, Lynda Temal October 16th, 2008 resampling statistical analysis http://neurolog.unice.fr/ontoneurolog/v3.0/OntoSpec-documentation.zip statistical analysis BFO:0000001 entity Entity Julius Caesar Verdi’s Requiem the Second World War your body mass index BFO 2 Reference: In all areas of empirical inquiry we encounter general terms of two sorts. First are general terms which refer to universals or types:animaltuberculosissurgical procedurediseaseSecond, are general terms used to refer to groups of entities which instantiate a given universal but do not correspond to the extension of any subuniversal of that universal because there is nothing intrinsic to the entities in question by virtue of which they – and only they – are counted as belonging to the given group. Examples are: animal purchased by the Emperortuberculosis diagnosed on a Wednesdaysurgical procedure performed on a patient from Stockholmperson identified as candidate for clinical trial #2056-555person who is signatory of Form 656-PPVpainting by Leonardo da VinciSuch terms, which represent what are called ‘specializations’ in [81 Entity doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. For example Werner Ceusters 'portions of reality' include 4 sorts, entities (as BFO construes them), universals, configurations, and relations. It is an open question as to whether entities as construed in BFO will at some point also include these other portions of reality. See, for example, 'How to track absolutely everything' at http://www.referent-tracking.com/_RTU/papers/CeustersICbookRevised.pdf An entity is anything that exists or has existed or will exist. (axiom label in BFO2 Reference: [001-001]) entity Entity doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. For example Werner Ceusters 'portions of reality' include 4 sorts, entities (as BFO construes them), universals, configurations, and relations. It is an open question as to whether entities as construed in BFO will at some point also include these other portions of reality. See, for example, 'How to track absolutely everything' at http://www.referent-tracking.com/_RTU/papers/CeustersICbookRevised.pdf per discussion with Barry Smith An entity is anything that exists or has existed or will exist. (axiom label in BFO2 Reference: [001-001]) BFO:0000002 continuant Continuant BFO 2 Reference: Continuant entities are entities which can be sliced to yield parts only along the spatial dimension, yielding for example the parts of your table which we call its legs, its top, its nails. ‘My desk stretches from the window to the door. It has spatial parts, and can be sliced (in space) in two. With respect to time, however, a thing is a continuant.’ [60, p. 240 Continuant doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. For example, in an expansion involving bringing in some of Ceuster's other portions of reality, questions are raised as to whether universals are continuants A continuant is an entity that persists, endures, or continues to exist through time while maintaining its identity. (axiom label in BFO2 Reference: [008-002]) if b is a continuant and if, for some t, c has_continuant_part b at t, then c is a continuant. (axiom label in BFO2 Reference: [126-001]) if b is a continuant and if, for some t, cis continuant_part of b at t, then c is a continuant. (axiom label in BFO2 Reference: [009-002]) if b is a material entity, then there is some temporal interval (referred to below as a one-dimensional temporal region) during which b exists. (axiom label in BFO2 Reference: [011-002]) (forall (x y) (if (and (Continuant x) (exists (t) (continuantPartOfAt y x t))) (Continuant y))) // axiom label in BFO2 CLIF: [009-002] (forall (x y) (if (and (Continuant x) (exists (t) (hasContinuantPartOfAt y x t))) (Continuant y))) // axiom label in BFO2 CLIF: [126-001] (forall (x) (if (Continuant x) (Entity x))) // axiom label in BFO2 CLIF: [008-002] (forall (x) (if (Material Entity x) (exists (t) (and (TemporalRegion t) (existsAt x t))))) // axiom label in BFO2 CLIF: [011-002] continuant Continuant doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. For example, in an expansion involving bringing in some of Ceuster's other portions of reality, questions are raised as to whether universals are continuants A continuant is an entity that persists, endures, or continues to exist through time while maintaining its identity. (axiom label in BFO2 Reference: [008-002]) if b is a continuant and if, for some t, c has_continuant_part b at t, then c is a continuant. (axiom label in BFO2 Reference: [126-001]) if b is a continuant and if, for some t, cis continuant_part of b at t, then c is a continuant. (axiom label in BFO2 Reference: [009-002]) if b is a material entity, then there is some temporal interval (referred to below as a one-dimensional temporal region) during which b exists. (axiom label in BFO2 Reference: [011-002]) (forall (x y) (if (and (Continuant x) (exists (t) (continuantPartOfAt y x t))) (Continuant y))) // axiom label in BFO2 CLIF: [009-002] (forall (x y) (if (and (Continuant x) (exists (t) (hasContinuantPartOfAt y x t))) (Continuant y))) // axiom label in BFO2 CLIF: [126-001] (forall (x) (if (Continuant x) (Entity x))) // axiom label in BFO2 CLIF: [008-002] (forall (x) (if (Material Entity x) (exists (t) (and (TemporalRegion t) (existsAt x t))))) // axiom label in BFO2 CLIF: [011-002] BFO:0000003 occurrent Occurrent BFO 2 Reference: every occurrent that is not a temporal or spatiotemporal region is s-dependent on some independent continuant that is not a spatial region BFO 2 Reference: s-dependence obtains between every process and its participants in the sense that, as a matter of necessity, this process could not have existed unless these or those participants existed also. A process may have a succession of participants at different phases of its unfolding. Thus there may be different players on the field at different times during the course of a football game; but the process which is the entire game s-depends_on all of these players nonetheless. Some temporal parts of this process will s-depend_on on only some of the players. Occurrent doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. An example would be the sum of a process and the process boundary of another process. Simons uses different terminology for relations of occurrents to regions: Denote the spatio-temporal location of a given occurrent e by 'spn[e]' and call this region its span. We may say an occurrent is at its span, in any larger region, and covers any smaller region. Now suppose we have fixed a frame of reference so that we can speak not merely of spatio-temporal but also of spatial regions (places) and temporal regions (times). The spread of an occurrent, (relative to a frame of reference) is the space it exactly occupies, and its spell is likewise the time it exactly occupies. We write 'spr[e]' and `spl[e]' respectively for the spread and spell of e, omitting mention of the frame. An occurrent is an entity that unfolds itself in time or it is the instantaneous boundary of such an entity (for example a beginning or an ending) or it is a temporal or spatiotemporal region which such an entity occupies_temporal_region or occupies_spatiotemporal_region. (axiom label in BFO2 Reference: [077-002]) Every occurrent occupies_spatiotemporal_region some spatiotemporal region. (axiom label in BFO2 Reference: [108-001]) b is an occurrent entity iff b is an entity that has temporal parts. (axiom label in BFO2 Reference: [079-001]) (forall (x) (if (Occurrent x) (exists (r) (and (SpatioTemporalRegion r) (occupiesSpatioTemporalRegion x r))))) // axiom label in BFO2 CLIF: [108-001] (forall (x) (iff (Occurrent x) (and (Entity x) (exists (y) (temporalPartOf y x))))) // axiom label in BFO2 CLIF: [079-001] occurrent Occurrent doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. An example would be the sum of a process and the process boundary of another process. per discussion with Barry Smith Simons uses different terminology for relations of occurrents to regions: Denote the spatio-temporal location of a given occurrent e by 'spn[e]' and call this region its span. We may say an occurrent is at its span, in any larger region, and covers any smaller region. Now suppose we have fixed a frame of reference so that we can speak not merely of spatio-temporal but also of spatial regions (places) and temporal regions (times). The spread of an occurrent, (relative to a frame of reference) is the space it exactly occupies, and its spell is likewise the time it exactly occupies. We write 'spr[e]' and `spl[e]' respectively for the spread and spell of e, omitting mention of the frame. An occurrent is an entity that unfolds itself in time or it is the instantaneous boundary of such an entity (for example a beginning or an ending) or it is a temporal or spatiotemporal region which such an entity occupies_temporal_region or occupies_spatiotemporal_region. (axiom label in BFO2 Reference: [077-002]) Every occurrent occupies_spatiotemporal_region some spatiotemporal region. (axiom label in BFO2 Reference: [108-001]) b is an occurrent entity iff b is an entity that has temporal parts. (axiom label in BFO2 Reference: [079-001]) (forall (x) (if (Occurrent x) (exists (r) (and (SpatioTemporalRegion r) (occupiesSpatioTemporalRegion x r))))) // axiom label in BFO2 CLIF: [108-001] (forall (x) (iff (Occurrent x) (and (Entity x) (exists (y) (temporalPartOf y x))))) // axiom label in BFO2 CLIF: [079-001] BFO:0000004 ic IndependentContinuant a chair a heart a leg a molecule a spatial region an atom an orchestra. an organism the bottom right portion of a human torso the interior of your mouth b is an independent continuant = Def. b is a continuant which is such that there is no c and no t such that b s-depends_on c at t. (axiom label in BFO2 Reference: [017-002]) For any independent continuant b and any time t there is some spatial region r such that b is located_in r at t. (axiom label in BFO2 Reference: [134-001]) For every independent continuant b and time t during the region of time spanned by its life, there are entities which s-depends_on b during t. (axiom label in BFO2 Reference: [018-002]) (forall (x t) (if (IndependentContinuant x) (exists (r) (and (SpatialRegion r) (locatedInAt x r t))))) // axiom label in BFO2 CLIF: [134-001] (forall (x t) (if (and (IndependentContinuant x) (existsAt x t)) (exists (y) (and (Entity y) (specificallyDependsOnAt y x t))))) // axiom label in BFO2 CLIF: [018-002] (iff (IndependentContinuant a) (and (Continuant a) (not (exists (b t) (specificallyDependsOnAt a b t))))) // axiom label in BFO2 CLIF: [017-002] independent continuant b is an independent continuant = Def. b is a continuant which is such that there is no c and no t such that b s-depends_on c at t. (axiom label in BFO2 Reference: [017-002]) For any independent continuant b and any time t there is some spatial region r such that b is located_in r at t. (axiom label in BFO2 Reference: [134-001]) For every independent continuant b and time t during the region of time spanned by its life, there are entities which s-depends_on b during t. (axiom label in BFO2 Reference: [018-002]) (forall (x t) (if (IndependentContinuant x) (exists (r) (and (SpatialRegion r) (locatedInAt x r t))))) // axiom label in BFO2 CLIF: [134-001] (forall (x t) (if (and (IndependentContinuant x) (existsAt x t)) (exists (y) (and (Entity y) (specificallyDependsOnAt y x t))))) // axiom label in BFO2 CLIF: [018-002] (iff (IndependentContinuant a) (and (Continuant a) (not (exists (b t) (specificallyDependsOnAt a b t))))) // axiom label in BFO2 CLIF: [017-002] BFO:0000006 s-region SpatialRegion BFO 2 Reference: Spatial regions do not participate in processes. Spatial region doesn't have a closure axiom because the subclasses don't exhaust all possibilites. An example would be the union of a spatial point and a spatial line that doesn't overlap the point, or two spatial lines that intersect at a single point. In both cases the resultant spatial region is neither 0-dimensional, 1-dimensional, 2-dimensional, or 3-dimensional. A spatial region is a continuant entity that is a continuant_part_of spaceR as defined relative to some frame R. (axiom label in BFO2 Reference: [035-001]) All continuant parts of spatial regions are spatial regions. (axiom label in BFO2 Reference: [036-001]) (forall (x y t) (if (and (SpatialRegion x) (continuantPartOfAt y x t)) (SpatialRegion y))) // axiom label in BFO2 CLIF: [036-001] (forall (x) (if (SpatialRegion x) (Continuant x))) // axiom label in BFO2 CLIF: [035-001] spatial region Spatial region doesn't have a closure axiom because the subclasses don't exhaust all possibilites. An example would be the union of a spatial point and a spatial line that doesn't overlap the point, or two spatial lines that intersect at a single point. In both cases the resultant spatial region is neither 0-dimensional, 1-dimensional, 2-dimensional, or 3-dimensional. per discussion with Barry Smith A spatial region is a continuant entity that is a continuant_part_of spaceR as defined relative to some frame R. (axiom label in BFO2 Reference: [035-001]) All continuant parts of spatial regions are spatial regions. (axiom label in BFO2 Reference: [036-001]) (forall (x y t) (if (and (SpatialRegion x) (continuantPartOfAt y x t)) (SpatialRegion y))) // axiom label in BFO2 CLIF: [036-001] (forall (x) (if (SpatialRegion x) (Continuant x))) // axiom label in BFO2 CLIF: [035-001] BFO:0000008 t-region TemporalRegion Temporal region doesn't have a closure axiom because the subclasses don't exhaust all possibilites. An example would be the mereological sum of a temporal instant and a temporal interval that doesn't overlap the instant. In this case the resultant temporal region is neither 0-dimensional nor 1-dimensional A temporal region is an occurrent entity that is part of time as defined relative to some reference frame. (axiom label in BFO2 Reference: [100-001]) All parts of temporal regions are temporal regions. (axiom label in BFO2 Reference: [101-001]) Every temporal region t is such that t occupies_temporal_region t. (axiom label in BFO2 Reference: [119-002]) (forall (r) (if (TemporalRegion r) (occupiesTemporalRegion r r))) // axiom label in BFO2 CLIF: [119-002] (forall (x y) (if (and (TemporalRegion x) (occurrentPartOf y x)) (TemporalRegion y))) // axiom label in BFO2 CLIF: [101-001] (forall (x) (if (TemporalRegion x) (Occurrent x))) // axiom label in BFO2 CLIF: [100-001] temporal region Temporal region doesn't have a closure axiom because the subclasses don't exhaust all possibilites. An example would be the mereological sum of a temporal instant and a temporal interval that doesn't overlap the instant. In this case the resultant temporal region is neither 0-dimensional nor 1-dimensional per discussion with Barry Smith A temporal region is an occurrent entity that is part of time as defined relative to some reference frame. (axiom label in BFO2 Reference: [100-001]) All parts of temporal regions are temporal regions. (axiom label in BFO2 Reference: [101-001]) Every temporal region t is such that t occupies_temporal_region t. (axiom label in BFO2 Reference: [119-002]) (forall (r) (if (TemporalRegion r) (occupiesTemporalRegion r r))) // axiom label in BFO2 CLIF: [119-002] (forall (x y) (if (and (TemporalRegion x) (occurrentPartOf y x)) (TemporalRegion y))) // axiom label in BFO2 CLIF: [101-001] (forall (x) (if (TemporalRegion x) (Occurrent x))) // axiom label in BFO2 CLIF: [100-001] BFO:0000009 2d-s-region TwoDimensionalSpatialRegion an infinitely thin plane in space. the surface of a sphere-shaped part of space A two-dimensional spatial region is a spatial region that is of two dimensions. (axiom label in BFO2 Reference: [039-001]) (forall (x) (if (TwoDimensionalSpatialRegion x) (SpatialRegion x))) // axiom label in BFO2 CLIF: [039-001] two-dimensional spatial region A two-dimensional spatial region is a spatial region that is of two dimensions. (axiom label in BFO2 Reference: [039-001]) (forall (x) (if (TwoDimensionalSpatialRegion x) (SpatialRegion x))) // axiom label in BFO2 CLIF: [039-001] BFO:0000011 st-region SpatiotemporalRegion the spatiotemporal region occupied by a human life the spatiotemporal region occupied by a process of cellular meiosis. the spatiotemporal region occupied by the development of a cancer tumor A spatiotemporal region is an occurrent entity that is part of spacetime. (axiom label in BFO2 Reference: [095-001]) All parts of spatiotemporal regions are spatiotemporal regions. (axiom label in BFO2 Reference: [096-001]) Each spatiotemporal region at any time t projects_onto some spatial region at t. (axiom label in BFO2 Reference: [099-001]) Each spatiotemporal region projects_onto some temporal region. (axiom label in BFO2 Reference: [098-001]) Every spatiotemporal region occupies_spatiotemporal_region itself. Every spatiotemporal region s is such that s occupies_spatiotemporal_region s. (axiom label in BFO2 Reference: [107-002]) (forall (r) (if (SpatioTemporalRegion r) (occupiesSpatioTemporalRegion r r))) // axiom label in BFO2 CLIF: [107-002] (forall (x t) (if (SpatioTemporalRegion x) (exists (y) (and (SpatialRegion y) (spatiallyProjectsOntoAt x y t))))) // axiom label in BFO2 CLIF: [099-001] (forall (x y) (if (and (SpatioTemporalRegion x) (occurrentPartOf y x)) (SpatioTemporalRegion y))) // axiom label in BFO2 CLIF: [096-001] (forall (x) (if (SpatioTemporalRegion x) (Occurrent x))) // axiom label in BFO2 CLIF: [095-001] (forall (x) (if (SpatioTemporalRegion x) (exists (y) (and (TemporalRegion y) (temporallyProjectsOnto x y))))) // axiom label in BFO2 CLIF: [098-001] spatiotemporal region A spatiotemporal region is an occurrent entity that is part of spacetime. (axiom label in BFO2 Reference: [095-001]) All parts of spatiotemporal regions are spatiotemporal regions. (axiom label in BFO2 Reference: [096-001]) Each spatiotemporal region at any time t projects_onto some spatial region at t. (axiom label in BFO2 Reference: [099-001]) Each spatiotemporal region projects_onto some temporal region. (axiom label in BFO2 Reference: [098-001]) Every spatiotemporal region s is such that s occupies_spatiotemporal_region s. (axiom label in BFO2 Reference: [107-002]) (forall (r) (if (SpatioTemporalRegion r) (occupiesSpatioTemporalRegion r r))) // axiom label in BFO2 CLIF: [107-002] (forall (x t) (if (SpatioTemporalRegion x) (exists (y) (and (SpatialRegion y) (spatiallyProjectsOntoAt x y t))))) // axiom label in BFO2 CLIF: [099-001] (forall (x y) (if (and (SpatioTemporalRegion x) (occurrentPartOf y x)) (SpatioTemporalRegion y))) // axiom label in BFO2 CLIF: [096-001] (forall (x) (if (SpatioTemporalRegion x) (Occurrent x))) // axiom label in BFO2 CLIF: [095-001] (forall (x) (if (SpatioTemporalRegion x) (exists (y) (and (TemporalRegion y) (temporallyProjectsOnto x y))))) // axiom label in BFO2 CLIF: [098-001] BFO:0000015 process Process a process of cell-division, \ a beating of the heart a process of meiosis a process of sleeping the course of a disease the flight of a bird the life of an organism your process of aging. p is a process = Def. p is an occurrent that has temporal proper parts and for some time t, p s-depends_on some material entity at t. (axiom label in BFO2 Reference: [083-003]) BFO 2 Reference: The realm of occurrents is less pervasively marked by the presence of natural units than is the case in the realm of independent continuants. Thus there is here no counterpart of ‘object’. In BFO 1.0 ‘process’ served as such a counterpart. In BFO 2.0 ‘process’ is, rather, the occurrent counterpart of ‘material entity’. Those natural – as contrasted with engineered, which here means: deliberately executed – units which do exist in the realm of occurrents are typically either parasitic on the existence of natural units on the continuant side, or they are fiat in nature. Thus we can count lives; we can count football games; we can count chemical reactions performed in experiments or in chemical manufacturing. We cannot count the processes taking place, for instance, in an episode of insect mating behavior.Even where natural units are identifiable, for example cycles in a cyclical process such as the beating of a heart or an organism’s sleep/wake cycle, the processes in question form a sequence with no discontinuities (temporal gaps) of the sort that we find for instance where billiard balls or zebrafish or planets are separated by clear spatial gaps. Lives of organisms are process units, but they too unfold in a continuous series from other, prior processes such as fertilization, and they unfold in turn in continuous series of post-life processes such as post-mortem decay. Clear examples of boundaries of processes are almost always of the fiat sort (midnight, a time of death as declared in an operating theater or on a death certificate, the initiation of a state of war) (iff (Process a) (and (Occurrent a) (exists (b) (properTemporalPartOf b a)) (exists (c t) (and (MaterialEntity c) (specificallyDependsOnAt a c t))))) // axiom label in BFO2 CLIF: [083-003] process p is a process = Def. p is an occurrent that has temporal proper parts and for some time t, p s-depends_on some material entity at t. (axiom label in BFO2 Reference: [083-003]) (iff (Process a) (and (Occurrent a) (exists (b) (properTemporalPartOf b a)) (exists (c t) (and (MaterialEntity c) (specificallyDependsOnAt a c t))))) // axiom label in BFO2 CLIF: [083-003] BFO:0000016 disposition Disposition an atom of element X has the disposition to decay to an atom of element Y certain people have a predisposition to colon cancer children are innately disposed to categorize objects in certain ways. the cell wall is disposed to filter chemicals in endocytosis and exocytosis BFO 2 Reference: Dispositions exist along a strength continuum. Weaker forms of disposition are realized in only a fraction of triggering cases. These forms occur in a significant number of cases of a similar type. b is a disposition means: b is a realizable entity & b’s bearer is some material entity & b is such that if it ceases to exist, then its bearer is physically changed, & b’s realization occurs when and because this bearer is in some special physical circumstances, & this realization occurs in virtue of the bearer’s physical make-up. (axiom label in BFO2 Reference: [062-002]) If b is a realizable entity then for all t at which b exists, b s-depends_on some material entity at t. (axiom label in BFO2 Reference: [063-002]) (forall (x t) (if (and (RealizableEntity x) (existsAt x t)) (exists (y) (and (MaterialEntity y) (specificallyDepends x y t))))) // axiom label in BFO2 CLIF: [063-002] (forall (x) (if (Disposition x) (and (RealizableEntity x) (exists (y) (and (MaterialEntity y) (bearerOfAt x y t)))))) // axiom label in BFO2 CLIF: [062-002] disposition b is a disposition means: b is a realizable entity & b’s bearer is some material entity & b is such that if it ceases to exist, then its bearer is physically changed, & b’s realization occurs when and because this bearer is in some special physical circumstances, & this realization occurs in virtue of the bearer’s physical make-up. (axiom label in BFO2 Reference: [062-002]) If b is a realizable entity then for all t at which b exists, b s-depends_on some material entity at t. (axiom label in BFO2 Reference: [063-002]) (forall (x t) (if (and (RealizableEntity x) (existsAt x t)) (exists (y) (and (MaterialEntity y) (specificallyDepends x y t))))) // axiom label in BFO2 CLIF: [063-002] (forall (x) (if (Disposition x) (and (RealizableEntity x) (exists (y) (and (MaterialEntity y) (bearerOfAt x y t)))))) // axiom label in BFO2 CLIF: [062-002] BFO:0000017 realizable RealizableEntity the disposition of this piece of metal to conduct electricity. the disposition of your blood to coagulate the function of your reproductive organs the role of being a doctor the role of this boundary to delineate where Utah and Colorado meet To say that b is a realizable entity is to say that b is a specifically dependent continuant that inheres in some independent continuant which is not a spatial region and is of a type instances of which are realized in processes of a correlated type. (axiom label in BFO2 Reference: [058-002]) All realizable dependent continuants have independent continuants that are not spatial regions as their bearers. (axiom label in BFO2 Reference: [060-002]) (forall (x t) (if (RealizableEntity x) (exists (y) (and (IndependentContinuant y) (not (SpatialRegion y)) (bearerOfAt y x t))))) // axiom label in BFO2 CLIF: [060-002] (forall (x) (if (RealizableEntity x) (and (SpecificallyDependentContinuant x) (exists (y) (and (IndependentContinuant y) (not (SpatialRegion y)) (inheresIn x y)))))) // axiom label in BFO2 CLIF: [058-002] realizable entity To say that b is a realizable entity is to say that b is a specifically dependent continuant that inheres in some independent continuant which is not a spatial region and is of a type instances of which are realized in processes of a correlated type. (axiom label in BFO2 Reference: [058-002]) All realizable dependent continuants have independent continuants that are not spatial regions as their bearers. (axiom label in BFO2 Reference: [060-002]) (forall (x t) (if (RealizableEntity x) (exists (y) (and (IndependentContinuant y) (not (SpatialRegion y)) (bearerOfAt y x t))))) // axiom label in BFO2 CLIF: [060-002] (forall (x) (if (RealizableEntity x) (and (SpecificallyDependentContinuant x) (exists (y) (and (IndependentContinuant y) (not (SpatialRegion y)) (inheresIn x y)))))) // axiom label in BFO2 CLIF: [058-002] BFO:0000018 0d-s-region ZeroDimensionalSpatialRegion A zero-dimensional spatial region is a point in space. (axiom label in BFO2 Reference: [037-001]) (forall (x) (if (ZeroDimensionalSpatialRegion x) (SpatialRegion x))) // axiom label in BFO2 CLIF: [037-001] zero-dimensional spatial region A zero-dimensional spatial region is a point in space. (axiom label in BFO2 Reference: [037-001]) (forall (x) (if (ZeroDimensionalSpatialRegion x) (SpatialRegion x))) // axiom label in BFO2 CLIF: [037-001] BFO:0000019 quality Quality the ambient temperature of this portion of air the color of a tomato the length of the circumference of your waist the mass of this piece of gold. the shape of your nose the shape of your nostril a quality is a specifically dependent continuant that, in contrast to roles and dispositions, does not require any further process in order to be realized. (axiom label in BFO2 Reference: [055-001]) If an entity is a quality at any time that it exists, then it is a quality at every time that it exists. (axiom label in BFO2 Reference: [105-001]) (forall (x) (if (Quality x) (SpecificallyDependentContinuant x))) // axiom label in BFO2 CLIF: [055-001] (forall (x) (if (exists (t) (and (existsAt x t) (Quality x))) (forall (t_1) (if (existsAt x t_1) (Quality x))))) // axiom label in BFO2 CLIF: [105-001] quality a quality is a specifically dependent continuant that, in contrast to roles and dispositions, does not require any further process in order to be realized. (axiom label in BFO2 Reference: [055-001]) If an entity is a quality at any time that it exists, then it is a quality at every time that it exists. (axiom label in BFO2 Reference: [105-001]) (forall (x) (if (Quality x) (SpecificallyDependentContinuant x))) // axiom label in BFO2 CLIF: [055-001] (forall (x) (if (exists (t) (and (existsAt x t) (Quality x))) (forall (t_1) (if (existsAt x t_1) (Quality x))))) // axiom label in BFO2 CLIF: [105-001] BFO:0000020 sdc SpecificallyDependentContinuant Reciprocal specifically dependent continuants: the function of this key to open this lock and the mutually dependent disposition of this lock: to be opened by this key of one-sided specifically dependent continuants: the mass of this tomato of relational dependent continuants (multiple bearers): John’s love for Mary, the ownership relation between John and this statue, the relation of authority between John and his subordinates. the disposition of this fish to decay the function of this heart: to pump blood the mutual dependence of proton donors and acceptors in chemical reactions [79 the mutual dependence of the role predator and the role prey as played by two organisms in a given interaction the pink color of a medium rare piece of grilled filet mignon at its center the role of being a doctor the shape of this hole. the smell of this portion of mozzarella b is a specifically dependent continuant = Def. b is a continuant & there is some independent continuant c which is not a spatial region and which is such that b s-depends_on c at every time t during the course of b’s existence. (axiom label in BFO2 Reference: [050-003]) Specifically dependent continuant doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. We're not sure what else will develop here, but for example there are questions such as what are promises, obligation, etc. (iff (SpecificallyDependentContinuant a) (and (Continuant a) (forall (t) (if (existsAt a t) (exists (b) (and (IndependentContinuant b) (not (SpatialRegion b)) (specificallyDependsOnAt a b t))))))) // axiom label in BFO2 CLIF: [050-003] specifically dependent continuant b is a specifically dependent continuant = Def. b is a continuant & there is some independent continuant c which is not a spatial region and which is such that b s-depends_on c at every time t during the course of b’s existence. (axiom label in BFO2 Reference: [050-003]) Specifically dependent continuant doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. We're not sure what else will develop here, but for example there are questions such as what are promises, obligation, etc. per discussion with Barry Smith (iff (SpecificallyDependentContinuant a) (and (Continuant a) (forall (t) (if (existsAt a t) (exists (b) (and (IndependentContinuant b) (not (SpatialRegion b)) (specificallyDependsOnAt a b t))))))) // axiom label in BFO2 CLIF: [050-003] BFO:0000023 role Role John’s role of husband to Mary is dependent on Mary’s role of wife to John, and both are dependent on the object aggregate comprising John and Mary as member parts joined together through the relational quality of being married. the priest role the role of a boundary to demarcate two neighboring administrative territories the role of a building in serving as a military target the role of a stone in marking a property boundary the role of subject in a clinical trial the student role BFO 2 Reference: One major family of examples of non-rigid universals involves roles, and ontologies developed for corresponding administrative purposes may consist entirely of representatives of entities of this sort. Thus ‘professor’, defined as follows,b instance_of professor at t =Def. there is some c, c instance_of professor role & c inheres_in b at t.denotes a non-rigid universal and so also do ‘nurse’, ‘student’, ‘colonel’, ‘taxpayer’, and so forth. (These terms are all, in the jargon of philosophy, phase sortals.) By using role terms in definitions, we can create a BFO conformant treatment of such entities drawing on the fact that, while an instance of professor may be simultaneously an instance of trade union member, no instance of the type professor role is also (at any time) an instance of the type trade union member role (any more than any instance of the type color is at any time an instance of the type length).If an ontology of employment positions should be defined in terms of roles following the above pattern, this enables the ontology to do justice to the fact that individuals instantiate the corresponding universals – professor, sergeant, nurse – only during certain phases in their lives. b is a role means: b is a realizable entity & b exists because there is some single bearer that is in some special physical, social, or institutional set of circumstances in which this bearer does not have to be& b is not such that, if it ceases to exist, then the physical make-up of the bearer is thereby changed. (axiom label in BFO2 Reference: [061-001]) (forall (x) (if (Role x) (RealizableEntity x))) // axiom label in BFO2 CLIF: [061-001] role b is a role means: b is a realizable entity & b exists because there is some single bearer that is in some special physical, social, or institutional set of circumstances in which this bearer does not have to be& b is not such that, if it ceases to exist, then the physical make-up of the bearer is thereby changed. (axiom label in BFO2 Reference: [061-001]) (forall (x) (if (Role x) (RealizableEntity x))) // axiom label in BFO2 CLIF: [061-001] BFO:0000024 fiat-object-part FiatObjectPart or with divisions drawn by cognitive subjects for practical reasons, such as the division of a cake (before slicing) into (what will become) slices (and thus member parts of an object aggregate). However, this does not mean that fiat object parts are dependent for their existence on divisions or delineations effected by cognitive subjects. If, for example, it is correct to conceive geological layers of the Earth as fiat object parts of the Earth, then even though these layers were first delineated in recent times, still existed long before such delineation and what holds of these layers (for example that the oldest layers are also the lowest layers) did not begin to hold because of our acts of delineation.Treatment of material entity in BFOExamples viewed by some as problematic cases for the trichotomy of fiat object part, object, and object aggregate include: a mussel on (and attached to) a rock, a slime mold, a pizza, a cloud, a galaxy, a railway train with engine and multiple carriages, a clonal stand of quaking aspen, a bacterial community (biofilm), a broken femur. Note that, as Aristotle already clearly recognized, such problematic cases – which lie at or near the penumbra of instances defined by the categories in question – need not invalidate these categories. The existence of grey objects does not prove that there are not objects which are black and objects which are white; the existence of mules does not prove that there are not objects which are donkeys and objects which are horses. It does, however, show that the examples in question need to be addressed carefully in order to show how they can be fitted into the proposed scheme, for example by recognizing additional subdivisions [29 the FMA:regional parts of an intact human body. the Western hemisphere of the Earth the division of the brain into regions the division of the planet into hemispheres the dorsal and ventral surfaces of the body the upper and lower lobes of the left lung BFO 2 Reference: Most examples of fiat object parts are associated with theoretically drawn divisions b is a fiat object part = Def. b is a material entity which is such that for all times t, if b exists at t then there is some object c such that b proper continuant_part of c at t and c is demarcated from the remainder of c by a two-dimensional continuant fiat boundary. (axiom label in BFO2 Reference: [027-004]) (forall (x) (if (FiatObjectPart x) (and (MaterialEntity x) (forall (t) (if (existsAt x t) (exists (y) (and (Object y) (properContinuantPartOfAt x y t)))))))) // axiom label in BFO2 CLIF: [027-004] fiat object part b is a fiat object part = Def. b is a material entity which is such that for all times t, if b exists at t then there is some object c such that b proper continuant_part of c at t and c is demarcated from the remainder of c by a two-dimensional continuant fiat boundary. (axiom label in BFO2 Reference: [027-004]) (forall (x) (if (FiatObjectPart x) (and (MaterialEntity x) (forall (t) (if (existsAt x t) (exists (y) (and (Object y) (properContinuantPartOfAt x y t)))))))) // axiom label in BFO2 CLIF: [027-004] BFO:0000026 1d-s-region OneDimensionalSpatialRegion an edge of a cube-shaped portion of space. A one-dimensional spatial region is a line or aggregate of lines stretching from one point in space to another. (axiom label in BFO2 Reference: [038-001]) (forall (x) (if (OneDimensionalSpatialRegion x) (SpatialRegion x))) // axiom label in BFO2 CLIF: [038-001] one-dimensional spatial region A one-dimensional spatial region is a line or aggregate of lines stretching from one point in space to another. (axiom label in BFO2 Reference: [038-001]) (forall (x) (if (OneDimensionalSpatialRegion x) (SpatialRegion x))) // axiom label in BFO2 CLIF: [038-001] BFO:0000027 object-aggregate ObjectAggregate a collection of cells in a blood biobank. a swarm of bees is an aggregate of members who are linked together through natural bonds a symphony orchestra an organization is an aggregate whose member parts have roles of specific types (for example in a jazz band, a chess club, a football team) defined by fiat: the aggregate of members of an organization defined through physical attachment: the aggregate of atoms in a lump of granite defined through physical containment: the aggregate of molecules of carbon dioxide in a sealed container defined via attributive delimitations such as: the patients in this hospital the aggregate of bearings in a constant velocity axle joint the aggregate of blood cells in your body the nitrogen atoms in the atmosphere the restaurants in Palo Alto your collection of Meissen ceramic plates. An entity a is an object aggregate if and only if there is a mutually exhaustive and pairwise disjoint partition of a into objects BFO 2 Reference: object aggregates may gain and lose parts while remaining numerically identical (one and the same individual) over time. This holds both for aggregates whose membership is determined naturally (the aggregate of cells in your body) and aggregates determined by fiat (a baseball team, a congressional committee). ISBN:978-3-938793-98-5pp124-158#Thomas Bittner and Barry Smith, 'A Theory of Granular Partitions', in K. Munn and B. Smith (eds.), Applied Ontology: An Introduction, Frankfurt/Lancaster: ontos, 2008, 125-158. b is an object aggregate means: b is a material entity consisting exactly of a plurality of objects as member_parts at all times at which b exists. (axiom label in BFO2 Reference: [025-004]) (forall (x) (if (ObjectAggregate x) (and (MaterialEntity x) (forall (t) (if (existsAt x t) (exists (y z) (and (Object y) (Object z) (memberPartOfAt y x t) (memberPartOfAt z x t) (not (= y z)))))) (not (exists (w t_1) (and (memberPartOfAt w x t_1) (not (Object w)))))))) // axiom label in BFO2 CLIF: [025-004] object aggregate An entity a is an object aggregate if and only if there is a mutually exhaustive and pairwise disjoint partition of a into objects An entity a is an object aggregate if and only if there is a mutually exhaustive and pairwise disjoint partition of a into objects ISBN:978-3-938793-98-5pp124-158#Thomas Bittner and Barry Smith, 'A Theory of Granular Partitions', in K. Munn and B. Smith (eds.), Applied Ontology: An Introduction, Frankfurt/Lancaster: ontos, 2008, 125-158. b is an object aggregate means: b is a material entity consisting exactly of a plurality of objects as member_parts at all times at which b exists. (axiom label in BFO2 Reference: [025-004]) (forall (x) (if (ObjectAggregate x) (and (MaterialEntity x) (forall (t) (if (existsAt x t) (exists (y z) (and (Object y) (Object z) (memberPartOfAt y x t) (memberPartOfAt z x t) (not (= y z)))))) (not (exists (w t_1) (and (memberPartOfAt w x t_1) (not (Object w)))))))) // axiom label in BFO2 CLIF: [025-004] BFO:0000028 3d-s-region ThreeDimensionalSpatialRegion a cube-shaped region of space a sphere-shaped region of space, A three-dimensional spatial region is a spatial region that is of three dimensions. (axiom label in BFO2 Reference: [040-001]) (forall (x) (if (ThreeDimensionalSpatialRegion x) (SpatialRegion x))) // axiom label in BFO2 CLIF: [040-001] three-dimensional spatial region A three-dimensional spatial region is a spatial region that is of three dimensions. (axiom label in BFO2 Reference: [040-001]) (forall (x) (if (ThreeDimensionalSpatialRegion x) (SpatialRegion x))) // axiom label in BFO2 CLIF: [040-001] BFO:0000029 site Site Manhattan Canyon) a hole in the interior of a portion of cheese a rabbit hole an air traffic control region defined in the airspace above an airport the Grand Canyon the Piazza San Marco the cockpit of an aircraft the hold of a ship the interior of a kangaroo pouch the interior of the trunk of your car the interior of your bedroom the interior of your office the interior of your refrigerator the lumen of your gut your left nostril (a fiat part – the opening – of your left nasal cavity) b is a site means: b is a three-dimensional immaterial entity that is (partially or wholly) bounded by a material entity or it is a three-dimensional immaterial part thereof. (axiom label in BFO2 Reference: [034-002]) (forall (x) (if (Site x) (ImmaterialEntity x))) // axiom label in BFO2 CLIF: [034-002] site b is a site means: b is a three-dimensional immaterial entity that is (partially or wholly) bounded by a material entity or it is a three-dimensional immaterial part thereof. (axiom label in BFO2 Reference: [034-002]) (forall (x) (if (Site x) (ImmaterialEntity x))) // axiom label in BFO2 CLIF: [034-002] BFO:0000030 object Object atom cell cells and organisms engineered artifacts grain of sand molecule organelle organism planet solid portions of matter star BFO 2 Reference: BFO rests on the presupposition that at multiple micro-, meso- and macroscopic scales reality exhibits certain stable, spatially separated or separable material units, combined or combinable into aggregates of various sorts (for example organisms into what are called ‘populations’). Such units play a central role in almost all domains of natural science from particle physics to cosmology. Many scientific laws govern the units in question, employing general terms (such as ‘molecule’ or ‘planet’) referring to the types and subtypes of units, and also to the types and subtypes of the processes through which such units develop and interact. The division of reality into such natural units is at the heart of biological science, as also is the fact that these units may form higher-level units (as cells form multicellular organisms) and that they may also form aggregates of units, for example as cells form portions of tissue and organs form families, herds, breeds, species, and so on. At the same time, the division of certain portions of reality into engineered units (manufactured artifacts) is the basis of modern industrial technology, which rests on the distributed mass production of engineered parts through division of labor and on their assembly into larger, compound units such as cars and laptops. The division of portions of reality into units is one starting point for the phenomenon of counting. BFO 2 Reference: Each object is such that there are entities of which we can assert unproblematically that they lie in its interior, and other entities of which we can assert unproblematically that they lie in its exterior. This may not be so for entities lying at or near the boundary between the interior and exterior. This means that two objects – for example the two cells depicted in Figure 3 – may be such that there are material entities crossing their boundaries which belong determinately to neither cell. Something similar obtains in certain cases of conjoined twins (see below). BFO 2 Reference: To say that b is causally unified means: b is a material entity which is such that its material parts are tied together in such a way that, in environments typical for entities of the type in question,if c, a continuant part of b that is in the interior of b at t, is larger than a certain threshold size (which will be determined differently from case to case, depending on factors such as porosity of external cover) and is moved in space to be at t at a location on the exterior of the spatial region that had been occupied by b at t, then either b’s other parts will be moved in coordinated fashion or b will be damaged (be affected, for example, by breakage or tearing) in the interval between t and t.causal changes in one part of b can have consequences for other parts of b without the mediation of any entity that lies on the exterior of b. Material entities with no proper material parts would satisfy these conditions trivially. Candidate examples of types of causal unity for material entities of more complex sorts are as follows (this is not intended to be an exhaustive list):CU1: Causal unity via physical coveringHere the parts in the interior of the unified entity are combined together causally through a common membrane or other physical covering\. The latter points outwards toward and may serve a protective function in relation to what lies on the exterior of the entity [13, 47 BFO 2 Reference: an object is a maximal causally unified material entity BFO 2 Reference: ‘objects’ are sometimes referred to as ‘grains’ [74 b is an object means: b is a material entity which manifests causal unity of one or other of the types CUn listed above & is of a type (a material universal) instances of which are maximal relative to this criterion of causal unity. (axiom label in BFO2 Reference: [024-001]) object b is an object means: b is a material entity which manifests causal unity of one or other of the types CUn listed above & is of a type (a material universal) instances of which are maximal relative to this criterion of causal unity. (axiom label in BFO2 Reference: [024-001]) BFO:0000031 gdc GenericallyDependentContinuant The entries in your database are patterns instantiated as quality instances in your hard drive. The database itself is an aggregate of such patterns. When you create the database you create a particular instance of the generically dependent continuant type database. Each entry in the database is an instance of the generically dependent continuant type IAO: information content entity. the pdf file on your laptop, the pdf file that is a copy thereof on my laptop the sequence of this protein molecule; the sequence that is a copy thereof in that protein molecule. b is a generically dependent continuant = Def. b is a continuant that g-depends_on one or more other entities. (axiom label in BFO2 Reference: [074-001]) (iff (GenericallyDependentContinuant a) (and (Continuant a) (exists (b t) (genericallyDependsOnAt a b t)))) // axiom label in BFO2 CLIF: [074-001] generically dependent continuant (iff (GenericallyDependentContinuant a) (and (Continuant a) (exists (b t) (genericallyDependsOnAt a b t)))) // axiom label in BFO2 CLIF: [074-001] b is a generically dependent continuant = Def. b is a continuant that g-depends_on one or more other entities. (axiom label in BFO2 Reference: [074-001]) BFO:0000034 function Function the function of a hammer to drive in nails the function of a heart pacemaker to regulate the beating of a heart through electricity the function of amylase in saliva to break down starch into sugar BFO 2 Reference: In the past, we have distinguished two varieties of function, artifactual function and biological function. These are not asserted subtypes of BFO:function however, since the same function – for example: to pump, to transport – can exist both in artifacts and in biological entities. The asserted subtypes of function that would be needed in order to yield a separate monoheirarchy are not artifactual function, biological function, etc., but rather transporting function, pumping function, etc. A function is a disposition that exists in virtue of the bearer’s physical make-up and this physical make-up is something the bearer possesses because it came into being, either through evolution (in the case of natural biological entities) or through intentional design (in the case of artifacts), in order to realize processes of a certain sort. (axiom label in BFO2 Reference: [064-001]) (forall (x) (if (Function x) (Disposition x))) // axiom label in BFO2 CLIF: [064-001] function A function is a disposition that exists in virtue of the bearer’s physical make-up and this physical make-up is something the bearer possesses because it came into being, either through evolution (in the case of natural biological entities) or through intentional design (in the case of artifacts), in order to realize processes of a certain sort. (axiom label in BFO2 Reference: [064-001]) (forall (x) (if (Function x) (Disposition x))) // axiom label in BFO2 CLIF: [064-001] BFO:0000035 p-boundary ProcessBoundary the boundary between the 2nd and 3rd year of your life. p is a process boundary =Def. p is a temporal part of a process & p has no proper temporal parts. (axiom label in BFO2 Reference: [084-001]) Every process boundary occupies_temporal_region a zero-dimensional temporal region. (axiom label in BFO2 Reference: [085-002]) (forall (x) (if (ProcessBoundary x) (exists (y) (and (ZeroDimensionalTemporalRegion y) (occupiesTemporalRegion x y))))) // axiom label in BFO2 CLIF: [085-002] (iff (ProcessBoundary a) (exists (p) (and (Process p) (temporalPartOf a p) (not (exists (b) (properTemporalPartOf b a)))))) // axiom label in BFO2 CLIF: [084-001] process boundary p is a process boundary =Def. p is a temporal part of a process & p has no proper temporal parts. (axiom label in BFO2 Reference: [084-001]) Every process boundary occupies_temporal_region a zero-dimensional temporal region. (axiom label in BFO2 Reference: [085-002]) (forall (x) (if (ProcessBoundary x) (exists (y) (and (ZeroDimensionalTemporalRegion y) (occupiesTemporalRegion x y))))) // axiom label in BFO2 CLIF: [085-002] (iff (ProcessBoundary a) (exists (p) (and (Process p) (temporalPartOf a p) (not (exists (b) (properTemporalPartOf b a)))))) // axiom label in BFO2 CLIF: [084-001] BFO:0000038 1d-t-region OneDimensionalTemporalRegion the temporal region during which a process occurs. BFO 2 Reference: A temporal interval is a special kind of one-dimensional temporal region, namely one that is self-connected (is without gaps or breaks). A one-dimensional temporal region is a temporal region that is extended. (axiom label in BFO2 Reference: [103-001]) (forall (x) (if (OneDimensionalTemporalRegion x) (TemporalRegion x))) // axiom label in BFO2 CLIF: [103-001] one-dimensional temporal region A one-dimensional temporal region is a temporal region that is extended. (axiom label in BFO2 Reference: [103-001]) (forall (x) (if (OneDimensionalTemporalRegion x) (TemporalRegion x))) // axiom label in BFO2 CLIF: [103-001] BFO:0000040 material MaterialEntity a flame a forest fire a human being a hurricane a photon a puff of smoke a sea wave a tornado an aggregate of human beings. an energy wave an epidemic the undetached arm of a human being BFO 2 Reference: Material entities (continuants) can preserve their identity even while gaining and losing material parts. Continuants are contrasted with occurrents, which unfold themselves in successive temporal parts or phases [60 BFO 2 Reference: Object, Fiat Object Part and Object Aggregate are not intended to be exhaustive of Material Entity. Users are invited to propose new subcategories of Material Entity. BFO 2 Reference: ‘Matter’ is intended to encompass both mass and energy (we will address the ontological treatment of portions of energy in a later version of BFO). A portion of matter is anything that includes elementary particles among its proper or improper parts: quarks and leptons, including electrons, as the smallest particles thus far discovered; baryons (including protons and neutrons) at a higher level of granularity; atoms and molecules at still higher levels, forming the cells, organs, organisms and other material entities studied by biologists, the portions of rock studied by geologists, the fossils studied by paleontologists, and so on.Material entities are three-dimensional entities (entities extended in three spatial dimensions), as contrasted with the processes in which they participate, which are four-dimensional entities (entities extended also along the dimension of time).According to the FMA, material entities may have immaterial entities as parts – including the entities identified below as sites; for example the interior (or ‘lumen’) of your small intestine is a part of your body. BFO 2.0 embodies a decision to follow the FMA here. A material entity is an independent continuant that has some portion of matter as proper or improper continuant part. (axiom label in BFO2 Reference: [019-002]) Every entity which has a material entity as continuant part is a material entity. (axiom label in BFO2 Reference: [020-002]) every entity of which a material entity is continuant part is also a material entity. (axiom label in BFO2 Reference: [021-002]) (forall (x) (if (MaterialEntity x) (IndependentContinuant x))) // axiom label in BFO2 CLIF: [019-002] (forall (x) (if (and (Entity x) (exists (y t) (and (MaterialEntity y) (continuantPartOfAt x y t)))) (MaterialEntity x))) // axiom label in BFO2 CLIF: [021-002] (forall (x) (if (and (Entity x) (exists (y t) (and (MaterialEntity y) (continuantPartOfAt y x t)))) (MaterialEntity x))) // axiom label in BFO2 CLIF: [020-002] material entity A material entity is an independent continuant that has some portion of matter as proper or improper continuant part. (axiom label in BFO2 Reference: [019-002]) Every entity which has a material entity as continuant part is a material entity. (axiom label in BFO2 Reference: [020-002]) every entity of which a material entity is continuant part is also a material entity. (axiom label in BFO2 Reference: [021-002]) (forall (x) (if (MaterialEntity x) (IndependentContinuant x))) // axiom label in BFO2 CLIF: [019-002] (forall (x) (if (and (Entity x) (exists (y t) (and (MaterialEntity y) (continuantPartOfAt x y t)))) (MaterialEntity x))) // axiom label in BFO2 CLIF: [021-002] (forall (x) (if (and (Entity x) (exists (y t) (and (MaterialEntity y) (continuantPartOfAt y x t)))) (MaterialEntity x))) // axiom label in BFO2 CLIF: [020-002] BFO:0000140 cf-boundary ContinuantFiatBoundary b is a continuant fiat boundary = Def. b is an immaterial entity that is of zero, one or two dimensions and does not include a spatial region as part. (axiom label in BFO2 Reference: [029-001]) BFO 2 Reference: In BFO 1.1 the assumption was made that the external surface of a material entity such as a cell could be treated as if it were a boundary in the mathematical sense. The new document propounds the view that when we talk about external surfaces of material objects in this way then we are talking about something fiat. To be dealt with in a future version: fiat boundaries at different levels of granularity.More generally, the focus in discussion of boundaries in BFO 2.0 is now on fiat boundaries, which means: boundaries for which there is no assumption that they coincide with physical discontinuities. The ontology of boundaries becomes more closely allied with the ontology of regions. BFO 2 Reference: a continuant fiat boundary is a boundary of some material entity (for example: the plane separating the Northern and Southern hemispheres; the North Pole), or it is a boundary of some immaterial entity (for example of some portion of airspace). Three basic kinds of continuant fiat boundary can be distinguished (together with various combination kinds [29 Continuant fiat boundary doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. An example would be the mereological sum of two-dimensional continuant fiat boundary and a one dimensional continuant fiat boundary that doesn't overlap it. The situation is analogous to temporal and spatial regions. Every continuant fiat boundary is located at some spatial region at every time at which it exists (iff (ContinuantFiatBoundary a) (and (ImmaterialEntity a) (exists (b) (and (or (ZeroDimensionalSpatialRegion b) (OneDimensionalSpatialRegion b) (TwoDimensionalSpatialRegion b)) (forall (t) (locatedInAt a b t)))) (not (exists (c t) (and (SpatialRegion c) (continuantPartOfAt c a t)))))) // axiom label in BFO2 CLIF: [029-001] continuant fiat boundary b is a continuant fiat boundary = Def. b is an immaterial entity that is of zero, one or two dimensions and does not include a spatial region as part. (axiom label in BFO2 Reference: [029-001]) Continuant fiat boundary doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. An example would be the mereological sum of two-dimensional continuant fiat boundary and a one dimensional continuant fiat boundary that doesn't overlap it. The situation is analogous to temporal and spatial regions. (iff (ContinuantFiatBoundary a) (and (ImmaterialEntity a) (exists (b) (and (or (ZeroDimensionalSpatialRegion b) (OneDimensionalSpatialRegion b) (TwoDimensionalSpatialRegion b)) (forall (t) (locatedInAt a b t)))) (not (exists (c t) (and (SpatialRegion c) (continuantPartOfAt c a t)))))) // axiom label in BFO2 CLIF: [029-001] BFO:0000141 immaterial ImmaterialEntity BFO 2 Reference: Immaterial entities are divided into two subgroups:boundaries and sites, which bound, or are demarcated in relation, to material entities, and which can thus change location, shape and size and as their material hosts move or change shape or size (for example: your nasal passage; the hold of a ship; the boundary of Wales (which moves with the rotation of the Earth) [38, 7, 10 immaterial entity BFO:0000142 1d-cf-boundary OneDimensionalContinuantFiatBoundary The Equator all geopolitical boundaries all lines of latitude and longitude the line separating the outer surface of the mucosa of the lower lip from the outer surface of the skin of the chin. the median sulcus of your tongue a one-dimensional continuant fiat boundary is a continuous fiat line whose location is defined in relation to some material entity. (axiom label in BFO2 Reference: [032-001]) (iff (OneDimensionalContinuantFiatBoundary a) (and (ContinuantFiatBoundary a) (exists (b) (and (OneDimensionalSpatialRegion b) (forall (t) (locatedInAt a b t)))))) // axiom label in BFO2 CLIF: [032-001] one-dimensional continuant fiat boundary a one-dimensional continuant fiat boundary is a continuous fiat line whose location is defined in relation to some material entity. (axiom label in BFO2 Reference: [032-001]) (iff (OneDimensionalContinuantFiatBoundary a) (and (ContinuantFiatBoundary a) (exists (b) (and (OneDimensionalSpatialRegion b) (forall (t) (locatedInAt a b t)))))) // axiom label in BFO2 CLIF: [032-001] BFO:0000144 process-profile ProcessProfile On a somewhat higher level of complexity are what we shall call rate process profiles, which are the targets of selective abstraction focused not on determinate quality magnitudes plotted over time, but rather on certain ratios between these magnitudes and elapsed times. A speed process profile, for example, is represented by a graph plotting against time the ratio of distance covered per unit of time. Since rates may change, and since such changes, too, may have rates of change, we have to deal here with a hierarchy of process profile universals at successive levels One important sub-family of rate process profiles is illustrated by the beat or frequency profiles of cyclical processes, illustrated by the 60 beats per minute beating process of John’s heart, or the 120 beats per minute drumming process involved in one of John’s performances in a rock band, and so on. Each such process includes what we shall call a beat process profile instance as part, a subtype of rate process profile in which the salient ratio is not distance covered but rather number of beat cycles per unit of time. Each beat process profile instance instantiates the determinable universal beat process profile. But it also instantiates multiple more specialized universals at lower levels of generality, selected from rate process profilebeat process profileregular beat process profile3 bpm beat process profile4 bpm beat process profileirregular beat process profileincreasing beat process profileand so on.In the case of a regular beat process profile, a rate can be assigned in the simplest possible fashion by dividing the number of cycles by the length of the temporal region occupied by the beating process profile as a whole. Irregular process profiles of this sort, for example as identified in the clinic, or in the readings on an aircraft instrument panel, are often of diagnostic significance. The simplest type of process profiles are what we shall call ‘quality process profiles’, which are the process profiles which serve as the foci of the sort of selective abstraction that is involved when measurements are made of changes in single qualities, as illustrated, for example, by process profiles of mass, temperature, aortic pressure, and so on. b is a process_profile =Def. there is some process c such that b process_profile_of c (axiom label in BFO2 Reference: [093-002]) b process_profile_of c holds when b proper_occurrent_part_of c& there is some proper_occurrent_part d of c which has no parts in common with b & is mutually dependent on b& is such that b, c and d occupy the same temporal region (axiom label in BFO2 Reference: [094-005]) (forall (x y) (if (processProfileOf x y) (and (properContinuantPartOf x y) (exists (z t) (and (properOccurrentPartOf z y) (TemporalRegion t) (occupiesSpatioTemporalRegion x t) (occupiesSpatioTemporalRegion y t) (occupiesSpatioTemporalRegion z t) (not (exists (w) (and (occurrentPartOf w x) (occurrentPartOf w z))))))))) // axiom label in BFO2 CLIF: [094-005] (iff (ProcessProfile a) (exists (b) (and (Process b) (processProfileOf a b)))) // axiom label in BFO2 CLIF: [093-002] process profile b is a process_profile =Def. there is some process c such that b process_profile_of c (axiom label in BFO2 Reference: [093-002]) b process_profile_of c holds when b proper_occurrent_part_of c& there is some proper_occurrent_part d of c which has no parts in common with b & is mutually dependent on b& is such that b, c and d occupy the same temporal region (axiom label in BFO2 Reference: [094-005]) (forall (x y) (if (processProfileOf x y) (and (properContinuantPartOf x y) (exists (z t) (and (properOccurrentPartOf z y) (TemporalRegion t) (occupiesSpatioTemporalRegion x t) (occupiesSpatioTemporalRegion y t) (occupiesSpatioTemporalRegion z t) (not (exists (w) (and (occurrentPartOf w x) (occurrentPartOf w z))))))))) // axiom label in BFO2 CLIF: [094-005] (iff (ProcessProfile a) (exists (b) (and (Process b) (processProfileOf a b)))) // axiom label in BFO2 CLIF: [093-002] BFO:0000145 r-quality RelationalQuality John’s role of husband to Mary is dependent on Mary’s role of wife to John, and both are dependent on the object aggregate comprising John and Mary as member parts joined together through the relational quality of being married. a marriage bond, an instance of requited love, an obligation between one person and another. b is a relational quality = Def. for some independent continuants c, d and for some time t: b quality_of c at t & b quality_of d at t. (axiom label in BFO2 Reference: [057-001]) (iff (RelationalQuality a) (exists (b c t) (and (IndependentContinuant b) (IndependentContinuant c) (qualityOfAt a b t) (qualityOfAt a c t)))) // axiom label in BFO2 CLIF: [057-001] relational quality b is a relational quality = Def. for some independent continuants c, d and for some time t: b quality_of c at t & b quality_of d at t. (axiom label in BFO2 Reference: [057-001]) (iff (RelationalQuality a) (exists (b c t) (and (IndependentContinuant b) (IndependentContinuant c) (qualityOfAt a b t) (qualityOfAt a c t)))) // axiom label in BFO2 CLIF: [057-001] BFO:0000146 2d-cf-boundary TwoDimensionalContinuantFiatBoundary a two-dimensional continuant fiat boundary (surface) is a self-connected fiat surface whose location is defined in relation to some material entity. (axiom label in BFO2 Reference: [033-001]) (iff (TwoDimensionalContinuantFiatBoundary a) (and (ContinuantFiatBoundary a) (exists (b) (and (TwoDimensionalSpatialRegion b) (forall (t) (locatedInAt a b t)))))) // axiom label in BFO2 CLIF: [033-001] two-dimensional continuant fiat boundary a two-dimensional continuant fiat boundary (surface) is a self-connected fiat surface whose location is defined in relation to some material entity. (axiom label in BFO2 Reference: [033-001]) (iff (TwoDimensionalContinuantFiatBoundary a) (and (ContinuantFiatBoundary a) (exists (b) (and (TwoDimensionalSpatialRegion b) (forall (t) (locatedInAt a b t)))))) // axiom label in BFO2 CLIF: [033-001] BFO:0000147 0d-cf-boundary ZeroDimensionalContinuantFiatBoundary the geographic North Pole the point of origin of some spatial coordinate system. the quadripoint where the boundaries of Colorado, Utah, New Mexico, and Arizona meet zero dimension continuant fiat boundaries are not spatial points. Considering the example 'the quadripoint where the boundaries of Colorado, Utah, New Mexico, and Arizona meet' : There are many frames in which that point is zooming through many points in space. Whereas, no matter what the frame, the quadripoint is always in the same relation to the boundaries of Colorado, Utah, New Mexico, and Arizona. a zero-dimensional continuant fiat boundary is a fiat point whose location is defined in relation to some material entity. (axiom label in BFO2 Reference: [031-001]) (iff (ZeroDimensionalContinuantFiatBoundary a) (and (ContinuantFiatBoundary a) (exists (b) (and (ZeroDimensionalSpatialRegion b) (forall (t) (locatedInAt a b t)))))) // axiom label in BFO2 CLIF: [031-001] zero-dimensional continuant fiat boundary zero dimension continuant fiat boundaries are not spatial points. Considering the example 'the quadripoint where the boundaries of Colorado, Utah, New Mexico, and Arizona meet' : There are many frames in which that point is zooming through many points in space. Whereas, no matter what the frame, the quadripoint is always in the same relation to the boundaries of Colorado, Utah, New Mexico, and Arizona. requested by Melanie Courtot a zero-dimensional continuant fiat boundary is a fiat point whose location is defined in relation to some material entity. (axiom label in BFO2 Reference: [031-001]) (iff (ZeroDimensionalContinuantFiatBoundary a) (and (ContinuantFiatBoundary a) (exists (b) (and (ZeroDimensionalSpatialRegion b) (forall (t) (locatedInAt a b t)))))) // axiom label in BFO2 CLIF: [031-001] BFO:0000148 0d-t-region ZeroDimensionalTemporalRegion a temporal region that is occupied by a process boundary right now the moment at which a child is born the moment at which a finger is detached in an industrial accident the moment of death. temporal instant. A zero-dimensional temporal region is a temporal region that is without extent. (axiom label in BFO2 Reference: [102-001]) (forall (x) (if (ZeroDimensionalTemporalRegion x) (TemporalRegion x))) // axiom label in BFO2 CLIF: [102-001] zero-dimensional temporal region A zero-dimensional temporal region is a temporal region that is without extent. (axiom label in BFO2 Reference: [102-001]) (forall (x) (if (ZeroDimensionalTemporalRegion x) (TemporalRegion x))) // axiom label in BFO2 CLIF: [102-001] BFO:0000182 history History A history is a process that is the sum of the totality of processes taking place in the spatiotemporal region occupied by a material entity or site, including processes on the surface of the entity or within the cavities to which it serves as host. (axiom label in BFO2 Reference: [138-001]) history A history is a process that is the sum of the totality of processes taking place in the spatiotemporal region occupied by a material entity or site, including processes on the surface of the entity or within the cavities to which it serves as host. (axiom label in BFO2 Reference: [138-001]) CHEBI:15354 CHEBI:16919 CHEBI:16953 CHEBI:17268 CHEBI:18059 CHEBI:23367 CHEBI:24996 CHEBI:33893 CHEBI:35204 CHEBI:35210 CHEBI:35211 CHEBI:37335 MRI contrast agent MRI contrast agent is a pharmaceuical agent that represents contrast media used to improve the visibility of internal body structures in magnetic resonance imaging (MRI). The most commonly used compounds for contrast enhancement are gadolinium-based. Such MRI contrast agents shorten the relaxation times of atoms within body tissues following oral or intravenous administration. WEB: https://en.wikipedia.org/wiki/MRI_contrast_agent CHEBI:50408 CHEBI:52217 CHEBI:77746 GO:0008150 GO:0051211 IAO:0000003 IAO:0000009 labeled symbol IAO:0000027 IAO:0000030 IAO:0000032 lesion size, tumor volume, etc measurements can be described as scalar quantities. IAO:0000064 IAO:0000088 IAO:0000100 IAO:0000109 IAO:0000309 IAO:0000408 OBCS:0000090 Examples include temperature with the Celsius scale, which has two defined points (the freezing and boiling point of water at specific conditions) and then separated into 100 intervals, date when measured from an arbitrary epoch (such as AD), percentage such as a percentage return on a stock, and direction measured in degrees from true or magnetic north. interval scale OBI:0000011 OBI:0000047 OBI:0000066 OBI:0000093 OBI:0000272 OBI:0000319 OBI:0000471 OBI:0000679 in this context this term is used to represent the mean of grey levels' values. OBI:0000963 OBI:0000968 OBI:0000970 OBI:0000984 OBI:0000988 OBI:0001007 medical image creation OBI:0001028 OBI:0001554 OBI:0001573 OBI:0001930 OBI:0001931 OBI:0001933 OBI:0200000 OBI:0200029 OBI:0302838 OBI:0302867 OBI:0302910 we have reused this term to define process that have as gaol to evaluate risk intervention. we have reused this term to define process that have as goal to evaluate risk intervention (predict the consequence of an intervention) OBI:0302911 OBI:0500000 OBI:0600002 PERSON: Andrew J.Buckler OBI:1110108 OGMS:0000019 PATO:0000047 biological sex PATO:0000122 PATO:0000918 PATO:0001019 PATO:0001241 PATO:0001323 PATO:0001739 PATO:0001740 PATO:0002129 PATO:0002242 REO:0000280 UO:0000001 UO:0000047 UO:0000052 UO:0000060 UO:0000095 UO:0000128 UO:0000270 UO:0000319 radioactivity concentration anatomical:structure anatomical structure obo:cell homo:sapiens obo:organism QIBO:Cellular_Target cellular target http://purl.bioontology.org/ontology/QIBO PERSONS: Emna Amdouni and Bernard Giabud cellular target QIBO:Ex_vivo_subject ex vivo subject 'ex vivo subject' is an 'imaging subject' that refers to living tissue, substance or cells that can be extracted from an organism in order to realize some experimentations / measurements. WEB: https://en.wikipedia.org/wiki/Ex_vivo http://purl.bioontology.org/ontology/QIBO PERSON: Andrew J.Buckler We have based our definition on the information presented in Wikipedia. QIBO:Imaging_Agent imaging agent 'Imaging agent' is a 'material to be added' that represents chemicals designed to allow clinicians to determine whether a mass is benign or malignant and locate metastatic cancer sites in the body. 'Imaging agent' is a 'material to be added' that represents chemicals designed to allow clinicians to determine whether a mass is benign or malignant and locate metastatic cancer sites in the body. WEB: https://en.wikipedia.org/wiki/Imaging_agent http://purl.bioontology.org/ontology/QIBO http://purl.bioontology.org/ontology/QIBO PERSON: Andrew J.Buckler The development of an imaging agent involves synthesizing the agent to target a particular tumor or process, after which the imaging instruments can be adjusted to neutralize the target. Such agents are first examined via preclinical animal studies before engaging in early-phase human clinical studies. QIBO:Imaging_Subject imaging subject http://purl.bioontology.org/ontology/QIBO PERSON: Andrew J.Buckler QIBO:In_vitro_subject in vitro subject for example proteins are examined in solution, or cells in artificial culture medium. 'in vitro subject' is an 'imaging subject' that represents cells or biological molecules that are studied outside their normal biological context. http://purl.bioontology.org/ontology/QIBO https://en.wikipedia.org/wiki/In_vitro PERSON: Andrew J.Buckler QIBO:In_vivo_subject in vivo subject 'in vivo subject' is a 'subject' that is used in an vivo study. In vivo studies are those in which the effects of various biological entities are tested on whole, living organisms usually animals including humans, and plants as opposed to a partial or dead organism, or those done in vitro ("within the glass"), i.e., in a laboratory environment using test tubes, petri dishes etc. Examples of investigations in vivo include: the pathogenesis of disease by comparing the effects of bacterial infection with the effects of purified bacterial toxins; the development of antibiotics, antiviral drugs, and new drugs generally; and new surgical procedures. http://purl.bioontology.org/ontology/QIBO Wikipedia page: https://en.wikipedia.org/wiki/In_vivo PERSON: Andrew J.Buckler QIBO:Metastasis metastasis PERSONS: Emna Amdouni and Bernard Gibaud metastasis QIBO:Molecular_Target molecular target http://purl.bioontology.org/ontology/QIBO PERSONS: Emna Amdouni and Bernard Giabud molecular target QIBO:Parameter_Extraction_Algorithm PERSON: Emna Amdouni parameter extraction algorithm QIBO:Phantom_experimental_subject imaging phantom experimental subject 'phantom experimental subject' is an 'imaging subject' is a specially designed object that is scanned or imaged in the field of medical imaging to evaluate, analyze, and tune the performance of various imaging devices. A phantom is more readily available and provides more consistent results than the use of a living subject or cadaver, and likewise avoids subjecting a living subject to direct risk. Phantoms were originally employed for use in 2D x-ray based imaging techniques such as radiography or fluoroscopy, though more recently phantoms with desired imaging characteristics have been developed for 3D techniques such as MRI, CT, Ultrasound, PET, and other imaging methods or modalities. WEB: https://en.wikipedia.org/wiki/Imaging_phantom PERSON: Andrew J.Buckler QIBO:Predicting_response_to_therapy predicting response to therapy QIBO: http://bioportal.bioontology.org/ontologies/QIBO PERSON: Andrew J.Buckler QIBO:Prognosis medical prognosis QIBO: http://bioportal.bioontology.org/ontologies/QIBO http://medical-dictionary.thefreedictionary.com/prognosis PERSONS: Emna Amdouni and Bernard Gibaud A prognosis is a prediction of the probable course and outcome of a disease. QIBO:Quantitation_Algorithm PERSON: Emna Amdouni quantitation algorithm QIBO:Screening screening Screening in medicine, is a strategy used in a population to identify the possible presence of an as-yet-undiagnosed disease in individuals without signs or symptoms. QIBO: http://bioportal.bioontology.org/ontologies/QIBO https://en.wikipedia.org/wiki/Screening_(medicine) PERSON: Andrew J.Buckler QIBO:Staging staging satging is the determination of distinct phases or periods in the course of a disease, the life history of an organism, or any biological process. QIBO: http://bioportal.bioontology.org/ontologies/QIBO http://medical-dictionary.thefreedictionary.com/ PERSON: Andrew J.Buckler staging QIBO:Treatment_assessment treatment assessment QIBO: http://bioportal.bioontology.org/ontologies/QIBO PERSONS: Emna Amdouni and Bernard Gibaud http://www.radlex.org/RID/RID11590 RID11590 air contrast RID11590 annotator role PERSONS: Emna Amdouni and Bernard Gibaud annotator role http://www.radlex.org/RID/RID11652 RID11652 attapulgite RID11652 http://www.radlex.org/RID/RID11685 RID11685 b-19036 RID11685 http://www.radlex.org/RID/RID11587 RID11587 barium contrast agent RID11587 http://www.radlex.org/RID/RID11588 RID11588 barium sulfate suspension RID11588 http://www.radlex.org/RID/RID11654 RID11654 bentonite RID11654 http://www.radlex.org/RID/RID11661 RID11661 blood pool contrast agent RID11661 http://www.radlex.org/RID/RID11591 RID11591 carbon dioxide contrast RID11591 http://www.radlex.org/RID/RID11664 RID11664 chromium labeled red blood cells RID11664 http://www.radlex.org/RID/RID11683 RID11683 chromium diethyl hia meglumine RID11683 http://www.radlex.org/RID/RID11651 RID11651 clay suspension RID11651 http://www.radlex.org/RID/RID11648 RID11648 combination of oil emulsion and paramagnetic substance RID11648 http://www.radlex.org/RID/RID38684 RID38684 conray RID38684 http://www.radlex.org/RID/RID38686 RID38686 conray 30 RID38686 http://www.radlex.org/RID/RID38687 RID38687 conray 43 RID38687 http://www.radlex.org/RID/RID38685 RID38685 cysto conray ii RID38685 http://www.radlex.org/RID/RID38680 RID38680 cystografin RID38680 http://www.radlex.org/RID/RID38681 RID38681 cystografin dilute RID38681 http://www.radlex.org/RID/RID38676 RID38676 diatrizoate RID38676 http://www.radlex.org/RID/RID11605 RID11605 drug delivery microbbubles RID11605 http://www.radlex.org/RID/RID11649 RID11649 emulsion containing baby formula with ferrous sulfate RID11649 http://www.radlex.org/RID/RID11650 RID11650 emulsion containing corn oil and ferric ammonium citrate RID11650 http://www.radlex.org/RID/RID11601 RID11601 encapsulated microbubbles RID11601 FDA validated imaging biomarker measurement protocol function Emna Amdouni and Bernard Gibaud FDA validated imaging biomarker measurement protocol function http://www.radlex.org/RID/RID11612 RID11612 ferric ammonium citrate RID11612 http://www.radlex.org/RID/RID11611 RID11611 ferric chloride RID11611 http://www.radlex.org/RID/RID11675 RID11675 ferrioxamine RID11675 http://www.radlex.org/RID/RID11676 RID11676 ferrioamine methanesulfonate RID11676 http://www.radlex.org/RID/RID11643 RID11643 ferixan RID11643 http://www.radlex.org/RID/RID11644 RID11644 ferumoxides RID11644 http://www.radlex.org/RID/RID11647 RID11647 ferumoxtran 10 RID11647 May include marker clips, coils, wires, catheter sleeves, injected or leaked silicone, metal or glass related to trauma, and implants. 'foreign matter','fb','foreign object' http://www.radlex.org/RID/RID5425 Radlex PERSONS: Emna Amdouni and Bernard Giabud RID5425 foreign body Objects that inadvertently enter the body or body cavities from the environment. RID5425 http://www.radlex.org/RID/RID11622 RID11622 gadobenate dimeglumine RID11622 http://www.radlex.org/RID/RID11636 RID11636 gadobutrol RID11636 http://www.radlex.org/RID/RID11629 RID11629 gadodiamide RID11629 http://www.radlex.org/RID/RID11626 RID11626 gadofosveset trisodium RID11626 http://www.radlex.org/RID/RID11662 RID11662 gadolinium labeled albumin RID11662 http://www.radlex.org/RID/RID11663 RID11663 gadolinium labeled dextran RID11663 A gadolinium chelate is a contrast agent which combines ion and ligand molecule, also known as the chelate complex. A ligand is the molecule that is used to bind the ion, in this case Gadolinium http://www.radlex.org/RID/RID11613 RID11613 gadolinium chelate RID11613 http://www.radlex.org/RID/RID11689 RID11689 gadolinium oxide RID11689 gadopentetate dimeglumine http://www.radlex.org/RID/RID11616 RID11616 gadoterate meglumine RID11616 http://www.radlex.org/RID/RID11634 RID11634 gadoteridol RID11634 http://www.radlex.org/RID/RID11631 RID11631 gadoversetamide RID11631 http://www.radlex.org/RID/RID11624 RID11624 gadoxetic acid disodium salt RID11624 http://www.radlex.org/RID/RID11589 RID11589 gas contrast RID11589 http://www.radlex.org/RID/RID38678 RID38678 gastrografin RID38678 geometrical shape a 'geometrical shape' is an 'image markup' which represents the shape of graphical drawing placed on a region of interest (ROI). Annotation and Image Markup (AIM) model: https://wiki.nci.nih.gov/display/AIM/Annotation+and+Image+Markup+-+AIM PERSONS: Emna Amdouni and Bernard Giabud geometrical shape http://www.radlex.org/RID/RID11593 RID11593 helium contrast RID11593 http://www.radlex.org/RID/RID11680 RID11680 hepatobiliary chelate RID11680 http://www.radlex.org/RID/RID11677 RID11677 hepatobiliary contrast agent RID11677 CT numbers a 'Hounsfield scale' is a 'quantitative scale' for describing radiodensity. This scale represents a linear transformation of the original linear attenuation coefficient measurement in one in which the radiodensity of distilled water at standard pressure and temperature (STP) is defined as zero Hounsfield units (HU), while the radiodensity of air at STP is defined as -1000 HU. WEB: https://en.wikipedia.org/wiki/Hounsfield_scale PERSONS: Emna Amdouni and Bernard Gibaud hounsfield scale hounsfield scale hounsfield unit http://www.owl-ontologies.com/Ontology1415135201.owl#RID39161 Radlex PERSON: Emna Amdouni PERSONS: Emna Amdouni and Bernard Gibaud RID39161 hounsfield unit RID39161 http://www.radlex.org/RID/RID38682 RID38682 hypaque RID38682 screening based on imaging biomarker 'screening based on imaging biomarker' is a 'screening' process that uses diagnostic biomarkers to detect and treat early stage disease in the asymptomatic population. Book title: evaluation of biomarkers and surrogate endpoints in chronic disease link: https://books.google.fr/books?hl=fr&lr=&id=lVpopHW10dUC&oi=fnd&pg=PT1&dq=Evaluation+of+biomarkers+and+surrogate+endpoints+in+chronic+disease.+National+Academies+Press.&ots=5VC5wGE0x9&sig=QBHnoM0DvthLJKveycIaJN0u1Js#v=onepage&q=Evaluation%20of%20biomarkers%20and%20surrogate%20endpoints%20in%20chronic%20disease.%20National%20Academies%20Press.&f=false PERSONS: Emna Amdouni and Bernard Gibaud screening based on imaging biomarker image markup an 'image markup' is an 'image annoatation' which represents graphical drawing and textual description that can be placed on image. Annotation and Image Markup model (AIM): https://wiki.nci.nih.gov/display/AIM/Annotation+and+Image+Markup+-+AIM PERSONS: Emna Amdouni and Bernard Giabud image markup http://www.radlex.org/RID/RID11583 RID11583 iodinated contrast agent RID11583 http://www.radlex.org/RID/RID12959 RID12959 iodized oil RID12959 http://www.radlex.org/RID/RID11614 RID11614 ionic gadolinium chelate RID11614 http://www.radlex.org/RID/RID38675 RID38675 ionic high osmolality monomeric contrast agent RID38675 http://www.radlex.org/RID/RID11585 RID11585 ionic iodinated contrast agent RID11585 http://www.radlex.org/RID/RID11618 RID11618 ionic linear gadolinium chelate RID11618 http://www.radlex.org/RID/RID11621 RID11621 ionic linear gadolinium chelate with protein binding RID11621 http://www.radlex.org/RID/RID11615 RID11615 ionic macrocyclic gadolinium chelate RID11615 http://www.radlex.org/RID/RID38683 RID38683 iothalamate RID38683 http://www.radlex.org/RID/RID38688 RID38688 ioxithalamate RID38688 http://www.radlex.org/RID/RID38692 RID38692 isopaque RID38692 Transfer constant K-trans is an 'imaging biomarker volume measurement datum' that represents the volume transfer constant between blood plasma and EES. http://pfeifer.phas.ubc.ca/refbase/files/Tofts-JMRI-1999-10-223.pdf PERSONS: Emna Amdouni and Bernard Gibaud. K_trans Transfer constant measurement datum http://www.radlex.org/RID/RID11653 RID11653 kaolin pectate RID11653 http://www.radlex.org/RID/RID11690 RID11690 liposome RID11690 image creation Log PERSONS: Emna Amdouni and Bernrad Gibaud image creation Log MR proton spectroscopy metabolites PERSONS: Emna Amdouni and Bernard Giabud MR proton spectroscopy metabolites http://www.radlex.org/RID/RID11639 RID11639 magnetite albumin microspheres RID11639 http://www.radlex.org/RID/RID38677 RID38677 MD 76 R RID38677 http://www.radlex.org/RID/RID38679 RID38679 MD gastroview RID38679 http://www.radlex.org/RID/RID11669 RID11669 metalloporphyrin RID11669 http://www.radlex.org/RID/RID38691 RID38691 metrizoate RID38691 http://www.radlex.org/RID/RID11599 RID11599 microbubbles contrast RID11599 http://www.radlex.org/RID/RID11597 RID11597 mineral oil contrast RID11597 Antibodies produced by clones of cells such as those isolated after hybridization of activated b lymphocytes with neoplastic cells. These hybrids are often referred to as hybridomas. [MeSH] http://www.radlex.org/RID/RID11667 RID11667 monoclonal antibody RID11667 http://www.radlex.org/RID/RID11672 RID11672 nitroxide RID11672 http://www.radlex.org/RID/RID11673 RID11673 nitroxide stable free radicals RID11673 none label option PERSONS: Emna Amdouni and Bernard Giabud none label option http://www.radlex.org/RID/RID11600 RID11600 nonencapsulated microbbubbles RID11600 http://www.radlex.org/RID/RID11627 RID11627 nonionic gadolinium chelate RID11627 http://www.radlex.org/RID/RID11628 RID11628 nonionic linear gadolinium chelate RID11628 http://www.radlex.org/RID/RID11633 RID11633 nonionic macrocyclic gadolinium chelate RID11633 http://www.radlex.org/RID/RID11596 RID11596 oil contrast RID11596 http://www.radlex.org/RID/RID11598 RID11598 oil emulsion contrast RID11598 oral magnetic particles http://www.radlex.org/RID/RID11610 RID11610 paramagnetic agent RID11610 http://www.radlex.org/RID/RID11656 RID11656 perfluorochemical RID11656 PERSONS: Emna Amdouni and Bernard Gibaud prognostic imaging biomarker role 'prognostic imaging biomarker role' is a 'role' that inheres in prognostic process, when used it enables the identification of patients with differing risks of a specific outcome. Thus, in rognostic process imaging biomarkers are used as a markers to differentiate categories of patients various risks for a fixed change , regardless of choice of the treatment (or choosing not to administer treatment) imaging biomarkers are mainly used in the clinical context, to: *Diagnosis process *Prognosis *Assesment of response to therapeutic intervention *Prediction of the outcome of a therapeutic intervention, reccurence and survival ========================================================= A list of examples of use of imaging biomarkers are given in these refrences: *Publication: Medical imaging in personalised medicine: a white paper of the research committee of the European Society of Radiology (ESR): http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4376812/ (see table 2) *Book: Evaluation of Biomarkers and surrogate endpoints in chronic disease (institute of medicine) imaging biomarker application is a 'data transformation' which represents imaging biomarker's role in a decision model context. This class defines the possible PERSONS: Emna Amdouni and Bernard Gibaud imaging biomarker application An 'imaging biomarker application model' is an 'algorithm' that defines the different evaluation criteria that must be tested in order to make a decision. These criteria may include, patient age, type and number of therapies that have been realized, therapeutic response, etc. An 'imaging biomaker application model' is, thus, concretizied by an 'imaging biomarker application' . PERSON: Emna Amdouni imaging biomarker application model imaging biomarker assesment investigation We validate a biomarker for a particular role and population. PERSONS: Emna Amdouni and Bernard Gibaud imaging biomarker assesment investigation http://www.radlex.org/RID/RID39165 PERSON: Emna Amdouni RID39165 imaging biomarker average value calculation algorithm RID39165 diagnostic process based on imaging biomarker 'diagnostic process based on imaging biomarker' is a 'performing a diagnosis' process that definitively establish the presence or not of a disease. Book title: evaluation of biomarkers and surrogate endpoints in chronic disease link: https://books.google.fr/books?hl=fr&lr=&id=lVpopHW10dUC&oi=fnd&pg=PT1&dq=Evaluation+of+biomarkers+and+surrogate+endpoints+in+chronic+disease.+National+Academies+Press.&ots=5VC5wGE0x9&sig=QBHnoM0DvthLJKveycIaJN0u1Js#v=onepage&q=Evaluation%20of%20biomarkers%20and%20surrogate%20endpoints%20in%20chronic%20disease.%20National%20Academies%20Press.&f=false PERSONS: Emna Amdouni and Bernard Gibaud diagnostic process based on imaging biomarker investigation based on imaging biomarker imaging biomarker based investigation is an investiagtion that represents biomarker investigations in clinical trial and practice. PERSONS: Emna Amdouni and Bernard Gibaud investigation based on imaging biomarker predicting response to therapy based on imaging biomarker PERSON: Emna Amdouni PERSONS: Emna Amdouni and Bernard Gibaud predicting response to therapy based on imaging biomarker prognosis based on imaging biomarker PERSONS: Emna Amdouni and Bernard Gibaud prognosis based on imaging biomarker staging based on imaging biomarker PERSONS: Emna Amdouni and Bernard Gibaud staging based on imaging biomarker survival estimation based on imaging biomarker survival estimation based on imaging biomarker is a survival estimation entity that represents the action of predicting organism's survival period. PERSONS: Emna Amdouni and Bernard Gibaud survival estimation based on imaging biomarker imaging biomarker based treatment assessment PERSONS: Emna Amdouni and Bernard Gibaud imaging biomarker based treatment assessment http://www.radlex.org/RID/RID39224 PERSON: Emna Amdouni RID39224 imaging biomarker mean value calculation algorithm RID39224 imaging biomarker measurement process imaging biomarker measurement process is a planned process which represents the set of realized actions that have to be executed to generate a biomarker value. PERSONS: Emna Amdouni and Bernard Gibaud imaging biomarker measurement process imaging biomarker measurement protocol QIBA Profile: FDG-PET/CT as an Imaging Biomarker measuring Response to Cancer Therapy https://www.rsna.org/uploadedFiles/RSNA/Content/Science_and_Education/QIBA/QIBA_FDG-PET_Profile_v105_Publicly_Reviewed_Version_FINAL_11Dec2013.pdf An 'imaging biomarker protocol' is a 'protocol' that describes and defines the procedure of measurement, the calibrated measuring system parameters and the measurement conditions, to a generate a biomarker use with an intended role. Imaging process standards help sponsors ensure that imaging data are obtained in a manner that complies in a manner that complies with a trial's protocol, that the quality of imaging data is maintained within among clinical sites, and that there is a verifiable record of the imaging process. PERSON: Emna Amdouni imaging biomarker measurement protocol imaging biomarker measurement protocol function PERSONS: Emna Amdouni and Bernard Gibaud imaging biomarker measurement protocol function http://www.radlex.org/RID/RID12781 PERSON: Emna Amdouni RID12781 imaging biomarker region of interest calculation algorithm RID12781 imaging biomarker response to therapeutic intervention imaging biomarker response to therapeutic intervention is a 'response to therapeutic intervention' that determines whether a therapy is having the intended effect on a disease and whether adverse effects arise. Book title: evaluation of biomarkers and surrogate endpoints in chronic disease link: https://books.google.fr/books?hl=fr&lr=&id=lVpopHW10dUC&oi=fnd&pg=PT1&dq=Evaluation+of+biomarkers+and+surrogate+endpoints+in+chronic+disease.+National+Academies+Press.&ots=5VC5wGE0x9&sig=QBHnoM0DvthLJKveycIaJN0u1Js#v=onepage&q=Evaluation%20of%20biomarkers%20and%20surrogate%20endpoints%20in%20chronic%20disease.%20National%20Academies%20Press.&f=false PERSONS: Emna Amdouni and Bernard Gibaud imaging biomarker response to therapeutic intervention imaging biomarker value tumor volume, length, degree of contrast enhancement, necrosis, mass effect, contrast /T2 ratio, tumor heterogeneity (T2 heterogeneity), contrast/necrosis ratio , etc. an 'imaging biomarker value' is a measurement datum generated by an image analysis process which is the final part of a potentially complex measurement process. This complex measurement process may involve image creation, reconstruction, processing, etc, according to the defined protocol. Imaging biomarker values are classified into different categories based on their data types. Thus, we distinguish between quantitative and qualitative values. *Imaging biomarker value represents imaging biomarker values that composed of a solely measured quality e.g. tumor volume and imaging biomarkers that are functions of a measured quality and other factors (see ref1). *Imaging biomarker value entity covers qualitative and quantitative imaging biomarkers. *We can know the kind of the quality (anatomical, functional or molecular) that is studied by the biomarker value by refering to the nature of the imaging data set and this can be done thanks to the relationship 'is_estiamted_from'. Reference (ref1) page 3 of QIBA group, 'The emerging science of quantitative imaging biomarkers terminology and definitions for scientific studies and regulatory submissions'. PERSONS: Emna Amdouni and Bernrad Gibaud imaging biomarker value 'ROI delimitation' is a 'study design' execution that describes the process of delimitation of a certain region of interest that we want to study. This class regroups two categories of delimitation: manual and automatic delimitation. PERSONS: Emna Amdouni and Bernard Gibaud ROI delimitation ROI manuel drawing ROI manuel drawing is an ROI delimitation process that represents manuel drawing of ROIs arround the identified region by the imaging experts. The image analysis workstation enables imaging expert to define both 2D and 3D region of interest (ROIs). [QIBA page 45] PERSONS: Emna Amdouni and Bernard Gibaud ROI manuel drawing Rate constant between EES and blood plasma http://pfeifer.phas.ubc.ca/refbase/files/Tofts-JMRI-1999-10-223.pdf PERSONS: Emna Amdouni and Bernard Gibaud K_ep k21, k2, 1/tc K_ep = k_tans / v_e unit: min ^(-1) Rate constant between EES and blood plasma http://www.radlex.org/RID/RID11688 RID11688 reticuloendothelial contrast agent RID11688 standard uptake value The standardized uptake value (SUV) is often used in positron emission tomography (PET) imaging for a simple semiquantitative analysis. Its use is particularly common in the analysis of fluorodeoxyglucose (FDG) images of cancer patients. The SUV is calculated either pixel-wise yielding a parametric image, or over a region of interest (ROI). This may be done for any image acquired at time point t, or for all images of a dynamic series acquired at multiple time points. The SUV is commonly defined as the ratio of (1) the tissue radioactivity concentration c (e.g. in MBq/kg = kBq/g) at time point t, and (2) the injected activity (e.g. in MBq, extrapolated to the same time t) divided by the body weight (e.g. in kg): SUV = C(T)/[injection dose (MBq)/patient's weight (kg)] SUVs are a convenient measure for the evaluation of [18F]FDG PET images within a subject to study therapy monitoring/therapy response, and also for comparison between subjects. WEB: https://en.wikipedia.org/wiki/Standardized_uptake_value PERSONS: Emna Amdouni and Bernard Gibaud Standard uptake value standardized uptake value body surface area PERSONS: Emna Amdouni and Bernrad Gibaud standardized uptake value body surface area standardized uptake value body weight PERSONS: Emna Amdouni and Bernard Gibaud SUVbw standardized uptake value body weight males: 48.0 + 1.06 * (height - 152) females: 45.5 + 0.91 * (height - 152) PERSONS: Emna Amdouni and Bernard Gibaud SUVibw Standardized Uptake Value ideal body weight Standardized Uptake Value lean body mass males: 1.10 * weight – 120 * (weight/height)^2 females: 1.07 * weight – 148 * (weight/height)^2 PERSONS: Emna Amdouni and Bernard Gibaud SUVlbm standardized uptake value lean body mass http://www.radlex.org/RID/RID11655 RID11655 sucrose polyester RID11655 http://www.radlex.org/RID/RID11638 RID11638 superparamagnetic contrast agent RID11638 http://www.radlex.org/RID/RID11641 RID11641 superparamagnetic iron oxide RID11641 PERSONS: Emna Amdouni, yannick Morvan and Bernard Gibaud T2 star weighted dataset T2 star weighted template dataset PERSONS: Emna Amdouni and Bernrad Gibaud T2 star weighted template dataset http://www.radlex.org/RID/RID11604 RID11604 targeted microbbubles RID11604 http://www.radlex.org/RID/RID38689 RID38689 telebrix RID38689 http://www.radlex.org/RID/RID38690 RID38690 telebrix 350 RID38690 therapy monitoring PERSONS: Emna Amdouni and Bernard Gibaud therapy monitoring http://www.radlex.org/RID/RID11666 RID11666 tumor specific agent RID11666 http://www.radlex.org/RID/RID11645 RID11645 ultrasmall superparamagnetic iron oxide RID11645 X-ray attenuation coefficient 'X-ray attenuation coefficient' is an 'attenuation coefficient measurement datum' is a coefficient that describes the fraction of a beam of X-rays or gamma rays that is absorbed or scattered per unit thickness of the absorber. This value basically accounts for the number of atoms in a cubic cm volume of material and the probability of a photon being scattered or absorbed from the nucleus or an electron of one of these atoms. DICOM CP 1390 page 9 PERSONS: Emna Amdouni and Bernrad Gibaud X-ray attenuation coefficient x ray attenuation PERSONS: Emna Amdouni and Bernard Gibaud x ray attenuation http://www.radlex.org/RID/RID11594 RID11594 xenon contrast RID11594 activity measurement datum An activity measurement datum is a scalar measurement which is the result of the activity quality measurement. This measure calculate the number of particles dacaying per unit time. Its unit of measure is becquerel. PERSONS: Emna Amdouni, Yannick Morvan and Bernard Gibaud PERSONS: Emna Amdouni and Bernard Gibaud activity measurement datum all label option PERSONS: Emna Amdouni and Bernard Gibaud 17 December 2015 all label option apparent diffusion coefficient dataset PERSONS: Emna Amdouni and Bernrad Gibaud apparent diffusion coefficient dataset apparent diffusion coefficient measurement datum PERSONS: Emna Amdouni and Bernard Gibaud 13/01/2016 apparent diffusion coefficient measurement datum area measurement datum An 'area measurement datum' is a scalar measurement datum that is the result of the measurement of an area. PERSONS: Emna Amdouni and Bernard Gibaud area measurement datum attenuation coefficient measurement datum PERSONS: Emna Amdouni and Bernard Gibaud https://en.wikipedia.org/wiki/Attenuation_coefficient Attenuation coefficient describes the extent to which the radiant flux of a beam is reduced as it passes through a specific material. It is used in the context of *X-rays or Gamma rays, where it is denoted μ and measured in cm−1; *Neutrons and nuclear reactors, where it is called macroscopic cross section (although actually it is not a section dimensionally speaking), denoted Σ and measured in m−1; *Solar and infrared radiative transfer in the atmosphere, albeit usually denoted with another symbol (given the standard use of μ = cos θ for slant paths); *Ultrasound attenuation, where it is denoted α and measured in dB·cm−1·MHz−1; *Acoustics for characterizing particle size distribution, where it is denoted α and measured in m−1. Usually attenuation coefficient is expressed in Hounsfield units. attenuation coefficient measurement datum 'attenuation coefficient measurement datum' is a 'scalar measurement datum' that represents a quantitative numerical statement of the relative attenuation of the X-Ray beam at a specified point. An attenuation coefficient of the volume of a material characterizes how easily it can be penetrated by a beam of light, sound, particles, or other energy or matter. A small attenuation coefficient indicates that the material in question is relatively transparent, while a larger value indicates greater degrees of opacity. The attenuation coefficient is dependent upon the type of material and the energy of the radiation. between 34 and 67 percent label option PERSONS: Emna Amdouni and Bernard Gibaud 17 December 2015 between 34 and 67 percent label option between 68 and 95 percent label option PERSONS: Emna Amdouni and Bernard Gibaud 17 December 2015 between 68 and 95 percent label option between 6 and 33 percent label option PERSONS: Emna Amdouni and Bernard Gibaud 17 December 2015 between 6 and 33 percent label option binary categorical imaging biomarker measurement datum VASARI MR feature key: cyst ('yes', 'no'), hemorrhage ('yes', 'no'), cortical involvement ('yes', 'no'), deep WM invasion ('yes', 'no'), etc. a 'binary categorical imaging biomarker measurement datum' is a binary categorical measurement that represent only two possible categorical values (labels) that can be assigned to an imaging biomarker value. PERSONS: Emna Amdouni and Bernrad Gibaud dichotomous imaging biomarker measurement datum dichotomous measurement datum e.g. male/female. A 'dichotomous measurement datum' is a 'categorical measurement datum' that represents categorical data that can take one value between two labels. PERSONS: Emna Amdouni and Bernrad Gibaud binary categorical measurement datum dichotomous measurement datum binary discrete measurement datum Smoking status: smoker, non-smoker. Attendance: present, absent. Class: lower classman, upper classman. A binary discrete measurement datum is a discrete measurement datum that represents categorical data in which there are only two categories. Emna Amdouni and Bernard Gibaud binary discrete measurement datum imaging biomarker application role 'imaging biomarker application role' is a 'role' that inheres in an 'imaging biomarker value that is realized in an 'imaging biomarker application' in which an 'information content entity' (predicted value, conclusion, etc) is generated about the interpreted biomarker value. PERSONS: Emna Amdouni and Bernard Gibaud imaging biomarker application role males & females: weight^0.425 * height^0.725 * 0.007184 PERSONS: Emna Amdouni and Bernard Gibaud 01/12/2015 BSA – body surface area body surface area brainstem categorical label option PERSONS: Emna Amdouni and Bernard Gibaud 17 December 2015 brainstem categorical label option VASARI criteria PERSONS: Emna Amdouni and Bernrad Gibaud 17 December 2015 categorical VASARI criteria categorical imaging biomarker measurement datum for example VASARI criteria: side of tumor epicenter ('right', 'center/bilateral', 'left'), enhancement quality ('None', 'mild/minimal', 'Marked'), cyst ('No', 'Yes'), thickness of enhancing margin ('n/a', 'well defined', 'poorly defined'). a 'categorical imaging biomarker measurement' is a 'categorical measurement datum' that represents nominal imaging biomarker values. Categorical imaging biomarker measurements are entities that fall into unordered categories. PERSONS: Emna Amdouni and Bernrad Gibaud categorical imaging biomarker measurement datum Categorical measurement datum hair color: blonde, brown, red, black, etc. smoking status: smoker, non-smoker, etc. A 'categorical measurement datum' is a 'measurement datum' that is reported on a categorical scale. nominal mesurement datum PERSON: Bjoern Peters http://purl.obolibrary.org/obo/OBI_0000938 nominal mesurement datum categorical measurement datum http://purl.obolibrary.org/obo/OBI_0000938 cellular proliferation PERSONS: Emna Amdouni and Bernard Gibaud cellular proliferation center categorical label PERSONS: Emna Amdouni and Bernard Gibaud 17 December 2015 center categorical label option cerebellum categorical label option PERSONS: Emna Amdouni and Bernard Gibaud 17 December 2015 cerebellum categorical label option cerebral blood flow measurement datum A 'cerebral blood flow measurement datum' is a 'volume blood flow measurement datum' that estimates the blood supply to the brain in a given period of time. An adult, CBF is typically 750 millilitres per minute or 15% of the cardiac output. This equates to an average perfusion of 50 to 54 millilitres of blood per 100 grams of brain tissue per minute. CBF is tightly regulated to meet the brain's metabolic demands.[ WEB: https://en.wikipedia.org/wiki/Cerebral_blood_flow PERSONS: Emna Amdouni and Bernard Gibaud Cerebral blood flow measurement datum is used as an indicator for tissue perfusion and vessel density. cerebral blood flow measurement datum cerebral blood volume measurement datum PERSONS: Emna Amdouni and Bernard Gibaud CBV is an important parameter for quantitative functional MRI (fMRI) and investigation of the blood oxygenation level-dependent (BOLD) signal mechanism. cerebral blood volume measurement datum clinical practice investigation based on imaging biomarker PERSONS: Emna Amdouni and Bernard Gibaud clinical practice investigation based on imaging biomarker clinical trial investigation based on imaging biomarker PERSONS: Emna Amdouni and Bernrad Gibaud clinical trial investigation based on imaging biomarker continuous imaging biomaker measurement datum A 'continuous imaging biomarker measurement datum' is a 'continuous measurement datum' that represents imaging biomarker value as a continuous variable. PERSONS: Emna Amdouni and Bernrad Gibaud continuous imaging biomarker measurement datum continuous measurement datum For example, between 62 and 82 inches, there are a lot of possibilities: one participant might be 64.03891 inches tall, and another person might be 72.67025 inches tall. And there are literally millions of other possible heights between 62 and 82 inches. A 'continuous measurement datum' is a 'numerical measurement datum' that can take any value between two numbers. Any value within an interval is possible with a fine enough measuring device. For example, blood pressure is usually measured to the nearest 2mm Hg, but could be measured with much greater resolution of difference. The interval measurement scale is intended for continuous data. Sometimes continuous data are given discrete values at certain thresholds, for example age a last birthday is a discrete value but age itself is a continuous quantity; in these situations it is reasonable to treat discrete values as continuous. Remember that information is lost when continuous data are recorded only in ranges (ordered categories), and the statistical analysis of continuous data is more powerful than that of categorical data. WEB: http://www.statsdirect.com/help/default.htm#basics/measurement_scales.htm PERSONS: Emna Amdouni and Bernrad Gibaud continuous measurement datum cortical involvement VASARI criteria non enhancing or enhancing tumor extending to the cortical mantle, or cortex is no longer distinguishable relative to subjacent tumor. possible values are: 0._/ 1.no/ 2.yes PERSONS: Emna Amdouni and Bernrad Gibaud 23 December 2015 cortical involvement VASARI criteria cortical involvement label option PERSONS: Emna Amdouni and Bernard Gibaud 23 December 2015 cortical involvement label option cortical involvement value specification PERSONS: Emna Amdouni and Bernard Giabud 23 December 2015 cortical involvement value specification count measurement datum 'discrete measurement datum' is a 'numerical measurement datum' that represents a simple count of things, natural numbers.Discrete data arise from observations that can only take certain numerical values, usually counts such as number of children or number of patients attending a clinic in a year. WEB: http://www.statsdirect.com/help/default.htm#basics/measurement_scales.htm PERSONS: Emna Amdouni and Bernard Gibaud Ordered categorical data are sometimes treated as discrete data, this is wrong. For example, using the Registrar General's classification of social class, it would be wrong to say that class I is five times the socio-economic status as class V, as there is not a strict numerical relationship between these categories. Thus, ordered categorical data should not be treated as discrete data for statistical analysis. Discrete data may be treated as ordered categorical data in statistical analysis, but some information is lost in doing so. discrete measurement datum 1 count value specification A 'count value specification' is a ' numerci value specification' that represents a natural number. PERSONS: Emna Amdouni and Bernard Giabud 17 December 2015 count value specification cyst a 'cyst' is a 'pathological structure' is a closed sac, having a distinct membrane and division compared to the nearby tissue. Hence, it is a cluster of cells that have grouped together to form a sac (not unlike the manner in which water molecules group together, forming a bubble) Radlex Emna Amdouni and Bernard Gibaud cyst cyst VASARI criteria 'cyst criteria' is a 'categorical VASARI criteria' that describes cysts if they are well defined, rounded, often eccentric regions of very bright T2W signal and low T1W signal essentially matching CSF signal intensity, with very thin, regular, smooth, no enhancing or regular enhancing walls, possibly with thin, regular, internal. possible values: 0._/ 1.no/ 2.yes PERSONS: Emna Amdouni and Bernrad Gibaud 17 December 2015 cyst VASARI criteria cyst label PERSONS: Emna Amdouni and Bernard Gibaud 17 December 2015 cyst label cyst value specification PERSONS: Emna Amdouni and Bernard Giabud 17 December 2015 cyst value specification deep WM invasion VASARI criteria enhancing or nCET tumor extending into the internal capsule or brainstem. possible values are: 0._/ 1.no/ 2.yes PERSONS: Emna Amdouni and Bernrad Gibaud 23 December 2015 deep WM invasion VASARI criteria deep WM invasion label option PERSONS: Emna Amdouni and Bernard Gibaud 23 December 2015 deep WM invasion label option deep WM invasion value specification PERSONS: Emna Amdouni and Bernard Giabud 23 December 2015 deep WM invasion value specification derived measurement datum PERSONS: Emna Amdouni and Bernard Gibaud derived measurement unit label descriptive statistics A descriptive statistic parameter is a data item that describes a feature of a collection of information, or the quantitative description itself. descriptive statistics are distinguished from inferential statistics (or inductive statistics), in that descriptive statistics aim to summarize a sample, rather than use the data to learn about the population that the sample of data is thought to represent. This generally means that descriptive statistics, unlike inferential statistics, are not developed on the basis of probability theory. Even when a data analysis draws its main conclusions using inferential statistics, descriptive statistics are generally also presented. Wikipedia page: https://en.wikipedia.org/wiki/Descriptive_statistics PERSONS: Emna Amdouni and Bernrad Gibaud Wikipedia descriptive statistic parameter diagnostic imaging biomarker role 'diagnostic imaging biomarker role' is a 'role' that inheres in diagnostic process PERSONS: Emna Amdouni and Bernard Gibaud diagnostic imaging biomarker role diffusion anisotropy PERSONS: Emna Amdouni and Bernard Gibaud diffusion anisotropy diffusion characteristics VASARI criteria predominantly facilitated or restricted diffusion in the enhancing or nCET portion of the tumor. (based on ADC map). equivocal is neither. No ADC, use no-image, proportion of tissue not relevant. PERSONS: Emna Amdouni and Bernrad Gibaud 23 December 2015 diffusion characteristics VASARI criteria diffusion characteristics label option PERSONS: Emna Amdouni and Bernard Gibaud 23 December 2015 diffusion characteristics label option diffusion characteristics value specification PERSONS: Emna Amdouni and Bernard Giabud 23 December 2015 diffusion characteristics value specification diffusion imaging biomarker measurement datum PERSONS: Emna Amdouni and Bernard Gibaud 13/01/2016 diffusion imaging biomarker measurement datum diffusion measurement datum PERSONS: Emna Amdouni and Bernard Gibaud diffusion measurement datum PERSONS: Emna Amdouni and Bernard Gibaud 13/01/2016 diffusion of water molecules PERSONS: Emna Amdouni and Bernard Gibaud this term can be used to represent the ability of a material to create an ultrasound return echo. edema crosses midline VASARI criteria 'edema crosses midline VASARI criteria' is a 'categorical VASARI criteria' that represents a nCET crosses into contralateral hemisphere through white matter commissures (exclusive of herniated ipsilateral tissue). possible values are: 0._/ 1.n/a/ 2.no/ 3.yes PERSONS: Emna Amdouni and Bernrad Gibaud 23 December 2015 edema crosses midline VASARI criteria edema crosses midline midline label option PERSONS: Emna Amdouni and Bernard Gibaud 23 December 2015 edema crosses midline midline label option edema crosses midline value specification PERSONS: Emna Amdouni and Bernard Giabud 23 December 2015 edema crosses midline value specification edema proportion VASARI criteria PERSONS: Emna Amdouni and Bernrad Gibaud 23 December 2015 edema proportion VASARI criteria edema proportion label option PERSONS: Emna Amdouni and Bernard Gibaud 23 December 2015 edema proportion label option edema proportion value specification PERSONS: Emna Amdouni, Yannick Morvan and Bernrad Gibaud 23 December 2015 edema proportion value specification PERSONS: Emna Amdouni and Bernard Gibaud tis term can be used to represent elastic properties of the tissue eloquent brain VASARI criteria 'eloquent brain criteria' is a 'categorical VASARI criteria' that evaluates if the geographic center or the enhancing component involve eloquent cortex (motor, language, vision) or key underlying white matter? 0._/ 1.none/ 2.speech motor/ 3.speech receptive/ 4.motor/ 5.vision VASARI PERSONS: Emna Amdouni and Bernrad Gibaud 17 December 2015 eloquent brain VASARI criteria eloquent brain label PERSONS: Emna Amdouni and Bernard Gibaud 17 December 2015 eloquent brain label eloquent brain value specification PERSONS: Emna Amdouni and Bernard Giabud 17 December 2015 eloquent brain value specification enhancement quality VASARI criteria 'enhancement quality' is an 'ordered and categorical imaging biomarker measurement' that refers to the qualitative degree of contrast enhancement. The qualitative degree of contrast enhancement is defined as having all or portions of the tumor that demonstrate significantly higher signal on the post contrast T1W images compared to pre contrast T1W images. possible values: 0._/ 1.none/ 2.mild/ 3.marked PERSONS: Emna Amdouni and Bernrad Gibaud 17 December 2015 enhancement quality VASARI criteria enhancement quality label PERSONS: Emna Amdouni and Bernad Gibaud 17 December 2015 enhancement quality label enhancement quality value specification PERSONS: Emna Amdouni, Yannick Morvan and Bernard Gibaud 17 December 2015 enhancement quality value specification enhancing margin definition VASARI criteria 'enhancing margin definition VASARI criteria' is an 'ordred and categorical imaging biomarker measurement datum' that assess if most of the outside margin of the enhancement is well defined or poorly defined. PERSONS: Emna Amdouni and Bernrad Gibaud 23 December 2015 the scoring is not applicable (n/a) if there is no contrast enhancement. enhancing margin definition VASARI criteria enhancing margin definition label option PERSONS: Emna Amdouni and Bernard Gibaud 23 December 2015 enhancing margin definition label option enhancing margin definition value specification PERSONS: Emna Amdouni and Bernard Giabud 23 December 2015 enhancing margin definition value specification ependymal invasion VASARI criteria invasion of any adjacent ependymal surface in continuity with enhancing or non-enhancing tumor matrix. possible values are: 0._/ 1.no/ 2.yes PERSONS: Emna Amdouni and Bernrad Gibaud 23 December 2015 ependymal invasion VASARI criteria ependymal invasion label option PERSONS: Emna Amdouni and Bernard Gibaud 23 December 2015 ependymal invasion label option ependymal invasion value specification PERSONS: Emna Amdouni and Bernard Giabud 23 December 2015 ependymal invasion value specification expansive label option PERSONS: Emna Amdouni and Bernard Gibaud 17 December 2015 expansive label option EES extravascular extracellular space calculates the volume of extravascular extracellular space per unit volume of tissue. http://pfeifer.phas.ubc.ca/refbase/files/Tofts-JMRI-1999-10-223.pdf PERSONS: Emna Amdouni and Bernard Gibaud V_e unit: volume of tissue ve (0 <ve < 1) extravascular extracellular space measurement datum facilitated label option PERSONS: Emna Amdouni and Bernard Gibaud 23 December 2015 facilitated label option first order feature extraction PERSONS: Emna Amdouni and Bernard Gibaud first order feature extraction fraction measurement datum contrast/necrosis ratio, contrast/T2 ratio T1/FLAIR ratio aproximates size of FLAIR abnormality. A 'fraction measurement datum' is a 'numerical measurement datum' that represents represents a part of a whole or, more generally, any number of equal parts. When spoken in everyday English, a fraction describes how many parts of a certain size there are, for example, one-half, eight-fifths, three-quarters. simple fraction (examples: 1/2 and 24/7 consists of an integer numerator, displayed above a line (or before a slash), and a non-zero integer denominator, displayed below (or after) that line. Numerators and denominators are also used in fractions that are not common, including compound fractions, complex fractions, and mixed numerals. WEB: https://en.wikipedia.org/wiki/Fraction_(mathematics) PERSONS: Emna Amdouni and Bernard Gibaud / fraction measurement datum fractional anisotropy measurement datum Fractional anisotropy (FA) is a scalar value between zero and one that describes the degree of anisotropy of a diffusion process. A value of zero means that diffusion is isotropic, i.e. it is unrestricted (or equally restricted) in all directions. A value of one means that diffusion occurs only along one axis and is fully restricted along all other directions. FA is a measure often used in diffusion imaging where it is thought to reflect fiber density, axonal diameter, and myelination in white matter. https://en.wikipedia.org/wiki/Fractional_anisotropy Emna Amdouni and Bernard Gibaud FA value FA measure is a coefficient reflecting the fractional anisotropy of the tissues, derived from a diffusion weighted MR image. Fractional anisotropy is proportional to the square root of the variance of the eigen values divided by the square root of the sum of the squares of the eigen values. fractional anisotropy measurement datum fractional anisotropy value variability PERSONS: Emna Amdouni and Bernard Gibaud fractional anisotropy value variability frontal categorical label option PERSONS: Emna Amdouni and Bernard Gibaud 17 December 2015 frontal categorical label option gliomatosis label option PERSONS: Emna Amdouni and Bernard Gibaud 17 December 2015 gliomatosis label option global intensity distribution PERSONS: Emna Amdouni and Bernard Gibaud global intensity distribution glycolysis the amount glycolysis activity summed across all voxels in a defined region or within a defined range of SUV (on FDG-PET). PERSONS: Emna Amdouni and Bernard Gibaud glycolysis measurement datum hemorrhage VASARI criteria intrinsic hemorrhage in the tumor matrix. Any intrinsic foci of low signal on 12WI or high signal on T1WI (use B0 image if necessary for confirmation). possible values are: 0._/ 1.no/ 2.yes PERSONS: Emna Amdouni and Bernrad Gibaud 23 December 2015 hemorrhage VASARI criteria hemorrhage label option PERSONS: Emna Amdouni and Bernard Gibaud 23 December 2015 hemorrhage label option hemorrhage value specification PERSONS: Emna Amdouni and Bernard Giabud 23 December 2015 hemorrhage value specification human PERSONS: Emna Amdouni and Bernard Gibaud human medical image annotation creation 'image annotation' describes the action of adding textual information or graphical markups (annotation) to the image in order to enrich its semantic and facilitate its analysis by the other users. PERSONS: Emna Amdouni and Bernard Gibaud image annotation creation image analysis PERSONS: Emna Amdouni and Bernard Gibaud image analysis 'image analysis protocol' is a 'protocol' that defines PERSON: Emna Amdouni image analysis protocol image analysis workstation image analysis workstation is a device that have the ability to receive and propagate the data output (imaging and metadata) collected from the image acquisition, reconstruction and post-processing activities. With the input data, the analysis workstation (and software analysis tools) will be able to make use of certain attribute values to perform certain measurements and computational analysis. QIBA profiles PERSONS: Emna Amdouni and Bernard Gibaud image analysis workstation image annotation an 'image annotation' is an 'information content entity' that annotates images. Annotation and Image Markup (AIM) model: https://wiki.nci.nih.gov/display/AIM/Annotation+and+Image+Markup+-+AIM PERSONS: Emna Amdouni and Bernard Giabud image annotation 'image creation protocol' is a 'protocol' that describes procedures that shall be performed and that precise how subjects should be imaged and how to parametrize the imaging devices so as to achieve reproducible quantitative endpoints. PERSON: Emna Amdouni As it has been explained in QIBA profile FDG/PET CT, the motivation of controlling the image acquisition is that over the course of a trial, hardware and software updates will occur. The intent of the profile is to ensure the instrument gives the same results over the duration of the trial. QIBA profiles are available from: RSNA.ORG/QIBA. image creation protocol PERSON: Emna Amdouni image post processing protocol PERSON: Emna Amdouni image processing protocol PERSON: Emna Amdouni image reconstruction protocol region of interest Image region is 'data set' that represents a subset of pixels of some image and that is identified for a particular purpose. Image region may be associated with one or more measurements QIBA: http://qibawiki.rsna.org/images/5/58/ClinicalTrialResults_20121229_QIBA.doc PERSONS: Emna Amdouni and Bernrad Gibaud image region region of interest imaging agent injected dose 'imaging agent injected dose' is a 'dose' that indicates the volume of the injected imaging agent during patient preparation step. PERSONS: Emna Amdouni and Bernrad Gibaud imaging agent injected dose imaging biomarker activity measurement datum Emna Amdouni and Bernard Gibaud imaging biomarker activity measurement datum imaging biomarker area measurement datum 'imaging biomarker area measurement datum' is an 'area measurement datum' that represents imaging biomarker that calculates the area quality. Emna Amdouni and Bernard Gibaud imaging biomarker area measurement datum imaging biomarker attenuation coefficient measurement Emna Amdouni and Bernard Gibaud imaging biomarker attenuation coefficient measurement imaging biomarker count measurement datum PERSONS: Emna Amdouni and Bernard Gibaud discrete imaging biomarker measurement datum imaging biomarker fraction measurement datum PERSONS: Emna Amdouni and Bernard Gibaud imaging biomarker fraction measurement datum imaging biomarker length measurement datum PERSONS: Emna Amdouni and Bernrad Gibaud imaging biomarker length measurement datum mass density imaging biomarker measurement datum 'mass density imaging biomarker measurement datum' is a 'mass density measurement datum' that represents imaging biomarker that calculates the mass density quality of a certain independent continuant. PERSONS: Emna Amdouni and Bernard Gibaud mass density imaging biomarker measurement datum imaging biomarker numerical score measurement datum VASARI MR features 'imaging biomarker numerical score measurement datum' is a 'numerical score measurement datum' that represents imaging biomarkers' values that are based on aggregated scores. PERSONS: Emna Amdouni and Bernrad Gibaud imaging biomarker numerical score measurement datum imaging biomarker percent measurement datum VASARI MR Feautres: proportion nCET, 'imaging biomarker percent measurement datum' is a 'percent measurement datum' that represents imaging biomarker value that is expressed as a percent. Emna Amdouni and Bernard Gibaud imaging biomarker percent measurement datum imaging biomarker ratio measurement datum 'imaging biomarker ratio measurement datum' is a 'ratio mesaurement datum' that represent imaging biomarker value that is a ratio. PERSONS: Emna Amdouni and Bernrad Gibaud imaging biomarker ratio measurement datum imaging biomarker scalar score composite inputs PERSONS: Emna Amdouni and Bernard Gibaud imaging biomarker scalar score from composite inputs imaging biomarker volume measurement datum PERSONS: Emna Amdouni and Bernard Gibaud imaging biomarker volume measurement datum imaging characteristic PERSONS: Emna Amdouni and Bernard Gibaud imaging characteristic "spiculated, "dense", "hypoechoic", "heterogeneous, ... Imaging observation characteristic is a descriptors of imaging observation. Annotation Image Markup (AIM) model PERSONS: Emna Amdouni and Bernard Gibaud imaging observation characteristic imaging physical characteristic PERSONS: Emna Amdouni and Bernard Gibaud imaging physical characteristic imaging subject homo_sapiens PERSONS: Emna Amdouni and Bernard Gibaud imaging subject homo_sapiens imaging subject PERSONS: Emna Amdouni and Bernard Giabud imaging subject human imaging subject role an imaging subject role is a role that inheres in an imaging subject and is realized by the process being imaged by an image acquisition device. PERSONS: Emna Amdouni and Bernard Gibaud imaging subject role indeterminate label option PERSONS: Emna Amdouni and Bernard Gibaud 17 December 2015 indeterminate label option infiltrative label option PERSONS: Emna Amdouni and Bernard Gibaud 17 December 2015 infiltrative label option insular categorical label option PERSONS: Emna Amdouni and Bernard Gibaud 17 December 2015 insular categorical label option intensity distribution PERSONS: Emna Amdouni and Bernard Gibaud intensity distribution intervention effect assessment role PERSONS: Emna Amdouni and Bernard Gibaud intervention effect assessment role irregular label option PERSONS: Emna Amdouni and Bernard Gibaud 23 December 2015 irregular label option kurtosis value a 'kurtosis value' is a 'statistical shape distribution parameter' that gives an indication on the sharp and disentangled aspect or rather flattened of histogram, i.e. we search how uniform is the grey level distribution. In probability theory and statistics, kurtosis (from Greek: κυρτός, kyrtos or kurtos, meaning "curved, arching") is a measure of the "tailedness" of the probability distribution of a real-valued random variable. In a similar way to the concept of skewness, kurtosis is a descriptor of the shape of a probability distribution and, just as for skewness, there are different ways of quantifying it for a theoretical distribution and corresponding ways of estimating it from a sample from a population. There are various interpretations of kurtosis, and of how particular measures should be interpreted; these are primarily tail weight, peakedness (width of peak), and lack of shoulders (distribution primarily peak and tails, not in between). Wikipedia page: https://en.wikipedia.org/wiki/Kurtosis PERSONS: Emna Amdouni and Bernrad Gibaud Wikipedia kurtosis value less than 5 percent label option PERSONS: Emna Amdouni and Bernard Gibaud 17 December 2015 less than 5 percent label option less than 95 percent label option PERSONS: Emna Amdouni and Bernard Gibaud 17 December 2015 less than 95 percent label option local intensity distribution PERSONS: Emna Amdouni and Bernard Gibaud local intensity distribution In computing, a logfile is a file that records either events that occur in an operating system or other software runs, or messages between different users of a communication software. Wikipedia web page: https://en.wikipedia.org/wiki/Logfile wikipedia PERSONS: Emna Amdouni and Bernard Gibaud logfile image analysis Log image analysis log is a logfile that records how an image analysis process has been realized. For our context, we will need to save the method used to define ROI and to extract the imaging biomarker value, setting parameters of the image analysis workstation. PERSONS: Emna Amdouni and Bernrad Gibaud image analysis Log image post processing Log PERSONS: Emna Amdouni and Bernard Giabud image processing Log image reconstruction Log PERSONS: Emna Amdouni and Bernard Giabud image reconstruction Log subject preparation Log PERSONS: Emna Amdouni and Bernard Giabud subject preparation Log long axis long axis measurement datum VASARI MR Feautres: lesion size represents largest perpendicular (x-y) cross-sectional diameter of T2 signal abnormality (longest dimension X perpendicular dimension) measured on a single axial image only. long axis measurement datum is a scalar measurement datum that represents the measurement result of long axis quality. PERSONS: Emna Amdouni and Bernard Gibaud long axis measurement datum marked label option PERSONS: Emna Amdouni and Bernard Gibaud 17 December 2015 marked label option mass density measurement datum mass density measurement datum is a scalar measurement datum that is the result of mass density quality measurement. PERSONS: Emna Amdouni and Bernard Gibaud mass density measurement datum mass imaging biomarker measurement datum PERSONS: Emna Amdouni and Bernard Gibaud mass imaging biomarker measurement datum mass measurement datum a mass measurement datum is a scalar measurement datum that is the result of measurement of mass quality PERSONS: Emna Amdouni and Bernard Gibaud mass measurement datum mass [PIRADS] A three-dimensional space occupying structure resulting from an accumulation of neoplastic cells, inflammatory cells, or cystic changes. focus,density,lesion,nodule,vague density http://www.radlex.org/RID/RID3874 Emna Amdouni and Bernard Gibaud RID3874 mass structure RID3874 mean cerebral blood flow value PERSONS: Emna Amdouni and Bernrad Gibaud 27/11/2015 mean cerebral blood flow value mean cerebral blood volume value PERSONS: Emna Amdouni and Bernrad Gibaud 27/11/2015 mean cerebral blood volume value the volume of a lesion (e.g, a tumor) ascertained through information about its metabolic activity (e.g., SUV on PET) DICOM CP 1386 metabolic volume metabolic volume The volume of a lesion (e.g., a tumor) ascertained through information about its metabolic activity (e.g., SUV on PET). PERSONS: Emna Amdouni and Bernrad Gibaud Metabolic Tumor Volume (MTV) metabolic volume mild label option PERSONS: Emna Amdouni and Bernard Gibaud 17 December 2015 mild label option mixed label option PERSONS: Emna Amdouni and Bernard Gibaud 17 December 2015 mixed label option motor label option PERSONS: Emna Amdouni and Bernard Giabud 17 December 2015 motor label option PERSONS: Emna Amdouni and Bernard Gibaud 13/01/2016 movement of water molecules multicentric label option PERSONS: Emna Amdouni and Bernard Gibaud 17 December 2015 multicentric label option multifocal label option PERSONS: Emna Amdouni and Bernard Gibaud 17 December 2015 multifocal label option multifocal or multicentric VASARI criteria 'multifocal or multicentric criteria' is a 'categorical VASARI criteria' that represents if lesion is multifocal or multicentric. Multifocal is defined as having at least one region of tumor, either enhancing or nonenhancing which is not contiguous with the dominant lesion and is outside the region abnormality (edema) surrounding the dominant mass. This can be defined as those resulting from dissemination or growth by an established route, spread via commissural or other pathways, or via CSF channels or local metastases, whereas multicentric are widely separated lesions in different lobes or different hemispheres that cannot be attributed to one of the previously mentioned pathways. Gliomatosis refers to generalized neoplastic transformation of the white matter of most of a hemisphere. possible values are: 0._/ 1.n/a/ 2.multifocal/ 3.multicentric/ 4.gliomatosis PERSONS: Emna Amdouni and Bernrad Gibaud 17 December 2015 multifocal or multicentric VASARI criteria multifocal or multicentric label PERSONS: Emna Amdouni and Bernard Gibaud 17 december 2015 multifocal or multicentric label multifocal or multicentric value specification PERSONS: Emna Amdouni and Bernard Giabud 17 December 2015 multifocal or multicentric value specification neither label option PERSONS: Emna Amdouni and Bernard Gibaud 23 December 2015 neither label option no PERSONS: Emna Amdouni and Bernard Gibaud 17 December 2015 no label option no image label option PERSONS: Emna Amdouni and Bernard Gibaud 23 December 2015 no image label option non-enhancing margin definition VASARI criteria 'non-enhancing margin definition VASARI criteria' is a 'categorical VASARI criteria' that express if most of the outside non-enhancing margin of the tumor is well defined and smooth (geographic), versus if the margin is ill-defined and irregular. PERSONS: Emna Amdouni and Bernrad Gibaud 23 December 2015 non-enhancing margin definition VASARI criteria non-enhancing margin definition label option PERSONS: Emna Amdouni and Bernard Gibaud 23 December 2015 non-enhancing margin definition label option non enhancing margin definition value specification PERSONS: Emna Amdouni and Bernard Giabud 23 December 2015 non enhancing margin definition value specification none label option PERSONS: Emna Amdouni and Bernard Gibaud 17 December 2015 none label option not available label option PERSONS: Emna Amdouni and Bernard Gibaud 17 December 2015 not available label option numeric imaging biomarker measurement datum PERSONS: Emna Amdouni and Bernard Gibaud numerical imaging biomarker measurement datum numeric value specification A 'numeric value specification' is a 'value specification' that specifies the representation format of numeric measurement datum. PERSONS: Emna Amdouni and Bernard Giabud 17 December 2015 numeric value specification numerical measurement datum cholesterol level, height , age, number of students late for class, time to complete a homework assignment 'numerical measurement datum' is an 'measurement datum' that represents quantitative values and that are expressed by numbers. Here, the objects being studied are “measured” based on some quantitative trait. The resulting data are set of numbers. quantitative value or variable PERSONS: Emna Amdouni and Bernrad Gibaud numerical measurement datum numerical score measurement datum APACHE score (acute physiological assessment and chronic health evaluation) a widely used method for assessing severity of illness in acutely ill patients in intensive care units, taking into account a variety of routine physiological parameters. Stroke score any of various scoring systems that seek to characterize a patient's clinical state following a stroke. VASARI scores http://medical-dictionary.thefreedictionary.com/score PERSONS: Emna Amdouni and Bernard Gibaud numerical score measurement datum Numerical score measurement datum is a continuous measurement datum that represents a rating, usually expressed numerically, based on specific achievement or the degree to which certain qualities are manifest. occipital categorical label option PERSONS: Emna Amdouni and Bernard Gibaud 17 December 2015 occipital categorical label option ordered and categorical imaging biomarker measurement datum VASARI MR Feautres: thickness of enhancing margin ('none', 'thin', 'solid'), definition of margin ('well defined', poorly defined'). an 'ordinal and categorical imaging biomarker measurement datum' is an 'ordinal and categorical measurement datum' that represents nominal imaging biomarker values that are arranged according to some categorical scale. PERSONS: Emna Amdouni and Bernrad Gibaud ordered and categorical imaging biomarker measurement datum ordered categorical measurement datum an 'ordinal categorical measurement datum' is a 'categorical measurement datum' which represents nominal entities that are arranged according to some categorical scale. Here, data ordering is important. PERSONS: Emna Amdouni and Bernrad Gibaud ordered categorical measurement datum ordinal categorical value specification PERSONS: Emna Amdouni and Bernard Giabud 17 December 2015 ordinal categorical value specification PERSONS: Emna Amdouni and Bernard Gibaud parameter estimation parietal categorical label option PERSONS: Emna Amdouni and Bernard Gibaud 17 December 2015 parietal categorical label option pathological structure 'pathological structure' is a 'material entity' that represents abnormal entities that we visualize on medical images. These structures can denotes the presence or absence of a certain pathology. PERSON: Emna Amdouni and Bernard Gibaud pathological structure percent measurement datum error in measurement, percent measurement datum is a ratio measurement that denotes numbers as fractions of 100. PERSONS: Emna Amdouni and Bernard Gibaud % percent measurement datum 2 percent value specification A 'percent value specification' is a 'fraction value specification' that represents fractions that their dominator is e qual to 100. These fractions can be written explicitly without using explicit numerators or denominators, by using decimals, percent signs or negative exponents. PERSONS: Emna Amdouni and Bernard Giabud 17 December 2015 0.01, 1%, and 10−2 respectively, all of which are equivalent to 1/100 percent value specification PERSONS: Emna Amdouni and Bernard Gibaud this term can be used todescribe the volume of blood perfusing ino tissue phantom PERSONS: Emna Amdouni and Bernard Gibaud phantom pial invasion VASARI criteria enhancement of the overlying pia in continuity with enhancing or non enhancing tumor. possible values are: 0._/ 1.no/ 2.yes PERSONS: Emna Amdouni and Bernrad Gibaud 23 December 2015 pial invasion VASARI criteria pial invasion label option PERSONS: Emna Amdouni and Bernard Gibaud 23 December 2015 pial invasion label option pial invasion value specification PERSONS: Emna Amdouni and Bernard Giabud 23 December 2015 pial invasion value specification poorly defined option label PERSONS: Emna Amdouni and Bernard Gibaud 23 December 2015 poorly defined option label portion enhancing label 'proportion enhancing label' is a 'categorical label' that represents what proportion of the entire tumor is enhancing (assuming that the entire abnormality may be comprised of: 1) an enhancing component 2) a non-enhancing component 3) a necrotic component and 4) a edema component.) PERSONS: Emna Amdouni and Bernard Gibaud 17 December 2015 proportion enhancing label predictive imaging biomarker role 'predictive imaging biomarker role' is a 'role' that inheres in prediction process, imaging biomarker values are used in this context to predict the potential benefits (effectiveness) risks ( toxicity) treatment according to the status of the marker. PERSONS: Emna Amdouni and Bernard Gibaud predictive imaging biomarker role proportion enhancing value specification PERSONS: Emna Amdouni, Yannick Morvan and Bernard Gibaud 23 December 2015 proportion enhancing value specification proportion nCET label option PERSONS: Emna Amdouni and Bernard Gibaud 17 December 2015 proportion nCET label option proportion necrosis VASARI criteria 'proportion necrosis criteria' is an 'ordered and categorical imaging biomarker measurement' that describes necrotic zone. Necrosis is defined as a region within the tumor that does not enhance or shows markedly diminished enhancement, is high on T2W and proton density images, is low on T1W images, and has an irregular border. Assuming that the entire abnormality may be comprised of: 1) an enhancing component, 2) a non-enhancing component, 3) a necrotic component and 4) edema component. PERSONS: Emna Amdouni and Bernrad Gibaud 17 December 2015 proportion necrosis VASARI criteria proportion necrosis label option PERSONS: Emna Amdouni and Bernrad Gibaud 17 December 2015 proportion necrosis label option proportion necrosis value specification PERSONS: Emna Amdouni, Yannick Morvan and Bernard Gibaud 17 December 2015 proportion necrosis value specification qualitative image analysis PERSONS: Emna Amdouni and Bernard Giabud qualitative image analysis PERSONS: Emna AMDOUNI and Bernard Gibaud qualitative parameter estimation quality process profile PERSONS: Emna Amdouni and Bernard Gibaud quality process profile quantitative image analysis image analysis is a study design execution that extracts meaningful information from images (ROIs measurements); mainly from digital images by means of digital image processing techniques. PERSONS: Emna Amdouni and Bernard Gibaud quantitative image analysis radioactivity imaging biomarker measurement datum Standardized uptake value 'radioactivity imaging biomarker measurement datum' is a 'radioactivity imaging biomarker measurement datum' that represents imaging biomarker value that measures radioactivity quality. PERSONS: Emna Amdouni and Bernard Gibaud radioactivity imaging biomarker measurement datum radioactivity measurement datum Radioactivity measurement datum is a scalar measurement datum that is the result of measurement of radiation quality. It measures the amount of energy absorbed by biological tissue from ionizing radiation per unit mass. PERSONS: Emna Amdouni and Bernard Gibaud radioactivity measurement datum rate imaging biomarker measurement datum 'rate imaging biomarker measurement datum' is a 'rate measurement datum' that represents biomarkers that calcualtes the number of PERSONS: Emna Amdouni and Bernard Gibaud rate imaging biomarker measurement datum ratio measurement datum For example, if a bowl of fruit contains eight oranges and six lemons, then the ratio of oranges to lemons is eight to six (that is, 8:6, which is equivalent to the ratio 4:3). Thus, a ratio can be a fraction as opposed to a whole number. Also, in this example the ratio of lemons to oranges is 6:8 (or 3:4), and the ratio of oranges to the total amount of fruit is 8:14 (or 4:7). 'ratio measurement datum' is a 'continuous measurement datum' that describes is a relationship between two numbers indicating how many times the first number contains the second. This measurement datum summarises two pieces of information, namely their constituent numerator and denominator values. Simple ratios (0 to 1, i.e. the denominator is the maximum possible value that the numerator can take) can be treated as continuous data. More difficult to analyse data arise when the ratio represents a change, and the value can be negative. Ratios of observations compared with reference values, e.g. height relative to the mean of a reference population for a given sex and age, are difficult to handle as values may fall either side of 1 (100%). Wikipedia page: https://en.wikipedia.org/wiki/Ratio WEB: http://www.statsdirect.com/help/default.htm#basics/measurement_scales.htm PERSONS: Emna Amdouni and Bernard Gibaud ratio measurement datum ratio variable Ratio variable is a quality that is attributed to a variable that the difference between any two measures is meaningful and any two values have a meaningfull ratio, making the operations of multiplication and division meaningful. A ratio variable possesses a meaningful zero value. [VIM] International vocabulary of metrology (VIM) PERSONS: Emna Amdouni and Bernard Gibaud Mathematical parametres that can be computed from this variable are: frequency distribution, median and percentiles, addition or substraction, mean, standard deviation, standard error of the mean, ratio or cofficient of variation. ratio variable reduction of fractional anisotropy value PERSONS: Emna Amdouni and Bernard Gibaud reduction of fractional anisotropy value regional cerebral blood volume measurement datum PERSONS: Emna Amdouni and Bernard Gibaud regional cerebral blood volume measurement datum regional cerebral blood volume dataset PERSONS: Emna AMDOUNI, Yannick Morvan and Bernard Gibaud regional cerebral blood volume dataset regional intensity distribution PERSONS: Emna Amdouni and Bernard Gibaud regional intensity distribution PERSONS: Emna Amdouni and Bernard Gibaud relative anisotropy reponse to therapeutic inervention PERSONS: Emna Amdouni and Bernard Gibaud response to therapeutic intervention restricted label option PERSONS: Emna Amdouni and Bernard Gibaud 23 December 2015 restricted label option right categorical label PERSONS: Emna Amdouni and Bernard Gibaud 17 December 2015 right categorical label option scalar imaging biomarker measurement datum lesion size, An 'imaging biomarker measurement datum' is a 'scalar measurement datum' that represents imaging biomarker value that refers to quantity consisting of a single real number used to measured magnitude (for example, size). PERSONS: Emna Amdouni and Bernard Gibaud scalar imaging biomarker measurement datum set of molecular entities PERSONS: Emna Amdouni and Bernard Gibaud 13/01/2016 set of molecular entities short axis short axis measurement datum long axis measurement datum is a scalar measurement datum that represents the measurement result of xxx. PERSONS: Emna Amdouni and Bernard Gibaud short axis measurement datum side of lesion epicenter VASARI criteria side of lesion epicenter' is a 'categorical VASARI criteria' that represents the side of lesion epicenter. VASARI PERSONS: Emna Amdouni and Bernrad Gibaud 17 December 2015 side of lesion epicenter VASARI criteria side of lesion epicenter. The possible values are: 0._/ 1.right/ 2.center/ 3.left PERSONS: Emna Amdouni and Bernrad Gibaud side of tumor epicenter VASARI criteria side of lesion epicenter label PERSONS: Emna Amdouni and Bernard Gibaud 17 December 2015 side of tumor epicenter label side of tumor epicenter value specification PERSONS: Emna Amdouni and Bernard Giabud 17 December 2015 side of tumor epicenter value specification skewness value a 'skewness value' is a 'statistical shape distribution parameter' that measures the dissimilarity of the grey level histogram (if it is well balanced around its mean or if it is more directed to the left or to the right with regard to its mean). It is a reponse to the question: are the intensities usually darker or lighter than the mean? In probability theory and statistics, skewness is a measure of the asymmetry of the probability distribution of a real-valued random variable about its mean. The skewness value can be positive or negative, or even undefined. Wikipedia page https://en.wikipedia.org/wiki/Skewness PERSONS: Emna Amdouni and Bernrad Gibaud skewness value slice of interest selection represents the step of the user selection of one image, generally it is the most informative image, among other a set of images. PERSONS: Emna Amdouni and Bernard Gibaud slice of interest selection slice of interest selection smooth label option PERSONS: Emna Amdouni and Bernard Gibaud 23 December 2015 smooth label option speech motor label option PERSONS: Emna Amdouni and Bernard Giabud 17 December 2015 speech motor label option speech receptive label option PERSONS: Emna Amdouni and Bernard Giabud 17 December 2015 speech receptive label option standard deviation value a 'standard deviation value' is a 'statistical dispersion parameter' that measures the distribution of grey levels around the mean. It manifests region roughness. PERSONS: Emna Amdouni and Bernrad Gibaud 27/11/2015 standard deviation value statistical dispersion parameter 'statistical dispersion parameter' is a 'descriptive dispersion parameter' that describes a distribution. In statistics, dispersion (also called variability, scatter, or spread) denotes how stretched or squeezed a distribution (theoretical or that underlying a statistical sample) is. Common examples of measures of statistical dispersion are the variance, standard deviation and interquartile range. Wikipedia page: https://en.wikipedia.org/wiki/Statistical_dispersion PERSONS: Emna Amdouni and Bernrad Gibaud Dispersion is contrasted with location or central tendency, and together they are the most used properties of distributions. statistical dispersion parameter statistical location parameter a 'statistical location parameter' is a 'descriptive statistic parameter' that describes a probability distributions that is parametrized by a scalar- or vector-valued parameter x_0, which determines the "location" or shift of the distribution. https://en.wikipedia.org/wiki/Location_parameter PERSONS: Emna Amdouni and Bernrad Gibaud Wikipedia statistical location parameter statistical shape distribution parameter a 'statistical shape distribution parameter' is any parameter of a probability distribution that is neither a location parameter nor a scale parameter (nor a function of either or both of these only, such as a rate parameter). Such a parameter must affect the shape of a distribution rather than simply shifting it (as a location parameter does) or stretching/shrinking it (as a scale parameter does). Wikipedia page: https://en.wikipedia.org/wiki/Shape_parameter PERSONS: Emna Amdouni and Bernrad Gibaud Wikipedia statistical shape distribution parameter statistical variance PERSONS: Emna Amdouni and Bernrad Gibaud statistical variance subject participation role PERSONS: Emna Amdouni and Bernard Gibaud subject participation role subject preparation subject preparation describes the process of patient management in order to enable him to realize a certain medical exam. This process may include: imaging agent administration and injection, patient handling, etc. PERSONS: Emna Amdouni and Bernard Gibaud subject preparation PERSON: Emna Amdouni subject preparation protocol A sum of the longest diameter (LD) for all target lesions is calculated and reported as the baseline sum LD. The baseline sum LD will be used as reference by which to characterize the objective tumor response. https://en.wikipedia.org/wiki/Response_Evaluation_Criteria_in_Solid_Tumors PERSONS: Emna Amdouni and Bernard Gibaud sum of the longest diameter sum of the product of the short and long diameters PERSONS: Emna Amdouni and Bernard Gibaud sum of the product of the short and long diameters Category markers intended to replace an evaluation criterion clinic designed to determine the clinical benefit or risk from epidemiological, therapeutic or pathophysiological PERSONS: Emna Amdouni and Bernard Gibaud surrogate endpoint imaging biomarker role survival estimation PERSON: Emna Amdouni and Bernard Gibaud survival estimation temporal categorical label option PERSONS: Emna Amdouni and Bernard Gibaud 17 December 2015 temporal categorical label option textural features PERSONS: Emna Amdouni and Bernard Gibaud textural features texture PERSONS: Emna Amdouni and Bernard Gibaud texture thickness of enhancing margin VASARI criteria 'thickness of enhancing margin VASARI criteria' is an 'ordered and categorical imaging biomarker measurement datum' that describes the enhancing margin. If the enhancing rim is thin, regular and measures < 3 mm in thickness and has homogenous enhancement the grade is thin. If most of the rim demonstrates nodular and/or thick enhancement, the grade is thick. If there is only solid enhancement and no rim, the grade is solid. possible values are 0._/ 1.n/a/ 2.none/ 3.thin/ 4.thick PERSONS: Emna Amdouni and Bernrad Gibaud 23 December 2015 The scoring is not applicable if there is no contrast enhancement. thickness of enhancing margin VASARI criteria thickness of enhancing margin label option PERSONS: Emna Amdouni and Bernard Gibaud 23 December 2015 thickness of enhancing margin label option thickness of enhancing margin value specification PERSONS: Emna Amdouni, Yannick Morvan and Bernard Gibaud 23 December 2015 thickness of enhancing margin value specification thin label option PERSONS: Emna Amdouni and Bernard Gibaud 23 December 2015 thin label option three dimension ellipse a 'three dimension ellipse' is a 'three dimension geometrical shape' that represents an ellipse defined by four (x,y,z) triplets, the two first triplets specifying the endpoints of the major axis and the second two triplets specifying the endpoints of the minor axis. Annotation Image Markup (AIM) model https://wiki.nci.nih.gov/display/AIM/Annotation+and+Image+Markup+-+AIM PERSONS: Emna Amdouni and Bernard Giabud three dimension ellipse three dimension ellipsoid a 'three dimension ellipsoid' is a 'three dimension geometrical shape' that represents a 'three dimension geometrical shape' that represents a three dimensional geometric surface whose plane sections are either ellipses or circles and contains three intersecting orthogonal axes "a","b" and "c". The ellipsoid is defined by six (x,y,z) triplets, the first and second triplets specifying the endpoints of axis "a", the third and fourth triplets specifying the endpoints of axis "b", and the fifth and sixt triplets specifing the endpoints of axis "c". Annotation Image Markup (AIM) model: https://wiki.nci.nih.gov/display/AIM/Annotation+and+Image+Markup+-+AIM PERSONS: Emna Amdouni and Bernard Gibaud three dimension ellipsoid three dimension geometric shape a 'three dimension geometric shape' is a 'geometrical shape' which represents three dimension coordinates of a graphical drawing that can be placed on an image to identify a region of interest (ROI). Annotation Image Markup (AIM model): https://wiki.nci.nih.gov/display/AIM/Annotation+and+Image+Markup+-+AIM PERSONS: Emna Amdouni and Bernard Giabud three dimension geometrical shape three dimension multipoint a 'three dimension multi-point' is a 'three dimension geometrical shape' that represents a mulile locations each denoed by an (x,y,z) triplet. The points need not be coplanar. Annotation Image Markup (AIM) model: https://wiki.nci.nih.gov/display/AIM/Annotation+and+Image+Markup+-+AIM PERSONS: Emna Amdouni and Bernard Gibaud three dimension multi-point three dimension point a 'three dimension point' is a 'three dimension geometrical shape' that represents a single location denoted by a single (x,y,z) triplet. Annotation Image Markup (AIM) model: https://wiki.nci.nih.gov/display/AIM/Annotation+and+Image+Markup+-+AIM PERSONS: Emna Amdouni and Bernard Gibaud three dimension point three dimension polygon a 'three dimension polygon' is a 'three dimension geometrical shape' that represents a series of connected line segments with ordered vertices denoted by (x,y,z) triplets, where the first and last vertices shall be the same forming a polygon; the points shall be coplaner. Annotation Image Markup (AIM model): https://wiki.nci.nih.gov/display/AIM/Annotation+and+Image+Markup+-+AIM PERSONS: Emna Amdouni and Bernard Gibaud three dimension polygon three dimension polyline a 'three dimension polyline' is a 'three dimension geometrical shape' that represents a series of connected line segments with ordered vertices by (x,y,z) triples, the points need not be coplanar. Annotation Image Markup (AIM) model: https://wiki.nci.nih.gov/display/AIM/Annotation+and+Image+Markup+-+AIM PERSONS: Emna Amdouni and Bernard Gibaud three dimension polyline three dimension spatial coordinate Annotation Image Markup (AIM) model: https://wiki.nci.nih.gov/display/AIM/Annotation+and+Image+Markup+-+AIM PERSONS: Emna Amdouni and Bernard Gibaud three dimension spatial coordinate total lesion glycolysis The total activity of a lesion obtained as the product of its volume and its glycolytic activity (on FDG-PET). The volume may be defined on the same modality (e.g., the MV on FDG-PET) or another spatially registred modality (e.g., the lesion outline segmented on CT or MR). Does not apply to other radiopharmaceuticals than those involved in glucose metabolism. Emna Amdouni and Bernard Gibaud total lesion glycolysis tumor grading based on imaging biomarker PERSONS: Emna Amdouni and Bernard Gibaud tumor grading based on imaging biomarker tumor location VASARI criteria tumor location' is a 'VASARI criteria' that represents the location of lesion geographic epicenter (not all areas of involvement). possible values are: 0._/ 1.frontal/2.temporal/ 3.insular/ 4.parietal/ 5. occipital/ 6.brainstem/ 7.cerebellum VASARI PERSONS: Emna Amdouni and Bernrad Gibaud 17 December 2015 tumor location VASARI criteria tumor location label PERSONS: Emna Amdouni and Bernard Gibaud 17 December 2015 tumor location label tumor location value specification PERSONS: Emna Amdouni and Bernard Giabud 17 December 2015 tumor location value specification two dimension circle a 'two dimension circle' is a 'two dimension geometrical shape' that represents a circle that is defined by two (column, row) pairs. The first point is the central pixel. The second is a pixel on the perimeter of the circle. Annotation Image Markup (AIM) model: https://wiki.nci.nih.gov/display/AIM/Annotation+and+Image+Markup+-+AIM PERSONS: Emna Amdouni and Bernard Gibaud two dimension circle two dimension ellipse a 'two dimension ellipse' is a 'two dimension geometrical shape' that represents a two dimension ellipse that is defined by four pixel (column, row pairs), the first two points specifying the endpoints of the major axis and the second two points specifying the endpoints of the minor axis of an ellipse. Annotation Image Markup (AIM) model: https://wiki.nci.nih.gov/display/AIM/Annotation+and+Image+Markup+-+AIM PERSONS: Emna Amdouni and Bernard Gibaud two dimension ellipse two dimension geometric shape Annotation Image Markup (AIM) model: https://wiki.nci.nih.gov/display/AIM/Annotation+and+Image+Markup+-+AIM PERSONS: Emna Amdouni and Bernard Gibaud two dimension geometrical shape a 'two dimension geometric shape' is a 'geometrical shape' that represents two dimension coordiantes of a graphical drawing that can be placed on an image to identify a region of interest (ROI). two dimension multi point a 'two dimension multi point' is a 'two dimension geometrical shape' that represents a two dimension geometric shape that represents multiple pixels each denoted by an column, row) pair. Annotation Image Markup (AIM) model: https://wiki.nci.nih.gov/display/AIM/Annotation+and+Image+Markup+-+AIM PERSONS: Emna Amdouni and Bernard Gibaud two dimension multi point two dimension point a 'two dimension point' is 'two dimension geometrical shape' that represents a two dimension geometric shape that represents a single point denoted by a single (column, row) pair. Annotation Image Markup (AIM) model: https://wiki.nci.nih.gov/display/AIM/Annotation+and+Image+Markup+-+AIM PERSONS: Emna Amdouni and Bernard Gibaud two dimension point two dimension polyline a 'two dimesnion polyline' is a 'two dimension geometrical shape' that represents two dimension polyline that represents a series of connected line segments with ordred vertices denoted by (column, row) pair; if the first and last vertices are the same it is a closed polygon. Annotation Image Markup (AIM) model: https://wiki.nci.nih.gov/display/AIM/Annotation+and+Image+Markup+-+AIM PERSONS: Emna Amdouni and Bernard Gibaud two dimension polyline two dimension spatial coordinate a 'two dimension spatial coordinate' is a 'two dimension geometrical shape' that represents a two dimension geometric shape that represents the 2D coordinates of the shape. Annotation Image Markup (AIM) model: https://wiki.nci.nih.gov/display/AIM/Annotation+and+Image+Markup+-+AIM PERSONS: Emna Amdouni and Bernard Gibaud two dimension spatial coordinate variance value a 'variance value' is a 'statistical shape distribution' that measures how far a set of numbers is spread out. A variance of zero indicates that all the values are identical. Variance is always non-negative: a small variance indicates that the data points tend to be very close to the mean (expected value) and hence to each other, while a high variance indicates that the data points are very spread out around the mean and from each other. Wikipedia page: https://en.wikipedia.org/wiki/Variance PERSONS: Emna Amdouni and Bernrad Gibaud 27/11/2015 Wikipedia variance value velocity Emna Amdouni and Bernard Gibaud this term can be used to represent tissue or flow velocity velocity velocity measurement datum PERSON: Emna Amdouni and Bernard Gibaud velocity measurement datum vision label option PERSONS: Emna Amdouni and Bernard Giabud 17 December 2015 vision label option volume measurement datum For example the volume of a given tumor, 2.0 cm3 is an imaging biomarker value. volume masurement datum is a scalar measurement datum that is the result of measurement of voume quality PERSONS: Emna Amdouni and Bernard Gibaud volume measurement datum volumetric flow rate measurement datum volumetric flow rate measurement datum is a scalar measurement datum that is the result of measurement of voumteric flow rate quality PERSONS: Emna Amdouni and Bernard Gibaud volumetric flow rate measurement datum well defined option label PERSONS: Emna Amdouni and Bernard Gibaud 23 December 2015 well defined option label yes PERSONS: Emna Amdouni and Bernard Gibaud 17 December 2015 yes label option imaging biomarker volumetric flow rate datum PERSONS: Emna Amdouni and Bernrad Gibaud imaging biomarker volumetric flow rate datum choline/creatine ratio for single-proton MR spectroscopy, the ratio between the choline and creatine resonance peaks. DICOM standard, Part 16 PERSONS: Emna Amdouni and Bernrad Gibaud choline/creatine ratio measurement datum N-acetylaspartate/choline ratio measurement datum PERSONS: Emna Amdouni and Bernard Gibaud N-acetylaspartate/creatine ratio measurement datum T1/FLAIR ratio label PERSONS: Emna Amdouni and Bernard Gibaud T1/FLAIR ratio label T1/FLAIR ratio value specification 17 December 2015 PERSONS: Emna Amdouni and Bernard Giabud T1/FLAIR ratio value specification T1/FLAIR ratio VASARI criteria 'T1/FLAIR ratio VASARI criteria' is a 'categorical VASARI criteria' that represents tumor feature summary. ============================================================ *Expansive= size of pre-contrast T1 abnormality (exclusive of signal intensity) approximates size of FLAIR abnormality. *Mixed= size of T1 abnormality moderately less than FLAIR envelope. *Infiltrative= size of pre-contrast T1 abnormality much smaller than size of FLAIR abnormality (use T2 if FLAIR is not provided). possible values: 0._/ 1.exapnsive/ 2.mixed/ 3. infiltrative PERSONS: Emna Amdouni and Bernrad Gibaud 17 December 2015 T1/FLAIR ratio VASARI criteria creatine+choline / citrate ratio measurement datum PERSONS: Emna Amdouni and Bernard Gibaud creatine+choline / citrate ratio measurement datum N-acetylaspartate/creatine ratio measurement datum PERSONS: Emna Amdouni and Bernard Gibaud N-acetylaspartate/creatine ratio measurement datum thick/solid label option PERSONS: Emna Amdouni and Bernard Gibaud 23 December 2015 thick/solid label option owl:Thing CT dataset http://neurolog.unice.fr/ontoneurolog/v3.0/OntoSpec-documentation.zip Farooq Ahmad , Michel Dojat, Bernard Gibaud, Gilles Kassel, Lynda Temal September 30th, 2008 COMPUTED TOMOGRAPHY (CT) COMPUTED TOMOGRAPHY (CT) is an imaging method in which a cross-sectional image of the structures in a body plane is reconstructed by a computer program from the x-ray absorption of beams projected through the body in the image plane. CT dataset 1.1 EEG dataset An EEG DATASET is a DATASET which is the result of either an EEG DATASET ACQUISITION or a DATASET PROCESSING which processes an EEG DATASET as data and keeps the same nature to the DATASET result. http://neurolog.unice.fr/ontoneurolog/v3.0/OntoSpec-documentation.zip Farooq Ahmad , Michel Dojat, Bernard Gibaud, Gilles Kassel, Lynda Temal September 30th, 2008 Electro encephalography (EEG) Electro encephalography (EEG) is the measurement of electrical activity produced by the brain as recorded from electrodes placed on the scalp. EEG dataset 1.1 H1 MR spectroscopy dataset A H1 MR SPECTROSCOPY DATASET is a MR SPECTROSCOPY DATASET. http://neurolog.unice.fr/ontoneurolog/v3.0/OntoSpec-documentation.zip Farooq Ahmad , Michel Dojat, Bernard Gibaud, Gilles Kassel, Lynda Temal September 30th, 2008 H1 MR spectroscopy dataset 1.1 H1 chemical shift imaging dataset an H1 CHEMICAL SHIFT IMAGING DATASET is an H1 MR SPECTROSCOPY DATASET. http://neurolog.unice.fr/ontoneurolog/v3.0/OntoSpec-documentation.zip Farooq Ahmad , Michel Dojat, Bernard Gibaud, Gilles Kassel, Lynda Temal September 30th, 2008 H1 chemical shift imaging dataset 1.1 H1 single voxel spectroscopy dataset A H1 SINGLE VOXEL SPECTROSCOPY DATASET is an H1 MR SPECTROSCOPY DATASET. http://neurolog.unice.fr/ontoneurolog/v3.0/OntoSpec-documentation.zip Farooq Ahmad , Michel Dojat, Bernard Gibaud, Gilles Kassel, Lynda Temal September 30th, 2008 H1 single voxel spectroscopy dataset 1.1 MEG dataset http://neurolog.unice.fr/ontoneurolog/v3.0/OntoSpec-documentation.zip Farooq Ahmad , Michel Dojat, Bernard Gibaud, Gilles Kassel, Lynda Temal September 30th, 2008 Magneto encephalography (MEG) is an imaging technique used to measure the magnetic fields produced by electrical activity in the brain via extremely sensitive devices such as superconducting quantum interference devices (SQUIDs). MEG dataset 1.1 MR spectroscopy dataset http://neurolog.unice.fr/ontoneurolog/v3.0/OntoSpec-documentation.zip Farooq Ahmad , Michel Dojat, Bernard Gibaud, Gilles Kassel, Lynda Temal September 30th, 2008 MR spectroscopy dataset 1.1 PET dataset POSITRON EMISSION TOMOGRAPHY (PET) is a nuclear medicine imaging method similar to computed tomography, except that the image shows the tissue concentration of a positron-emitting radioisotope. http://neurolog.unice.fr/ontoneurolog/v3.0/OntoSpec-documentation.zip Farooq Ahmad , Michel Dojat, Bernard Gibaud, Gilles Kassel, Lynda Temal September 30th, 2008 A PET DATASET is a DATASET which is the result of either a PET DATASET ACQUISITION or a DATASET PROCESSING which processes a PET DATASET as data and keeps the same nature to the DATASET result. PET dataset 1.1 SPECT dataset http://neurolog.unice.fr/ontoneurolog/v3.0/OntoSpec-documentation.zip Farooq Ahmad , Michel Dojat, Bernard Gibaud, Gilles Kassel, Lynda Temal September 30th, 2008 SPECT dataset 1.1 T1 weighted DCE-MR dataset http://neurolog.unice.fr/ontoneurolog/v3.0/OntoSpec-documentation.zip Farooq Ahmad , Michel Dojat, Bernard Gibaud, Gilles Kassel, Lynda Temal September 30th, 2008 T1 weighted DCE-MR dataset 1.1 T1 weighted MR dataset A T1 WEIGHTED MR DATASET is a MR DATASET. [EP/SL] Every T1 WEIGHTED MR DATASET is an ANATOMICAL DATASET. [EP/SL] Every T1 WEIGHTED MR DATASET is a RECONSTRUCTED DATASET. http://neurolog.unice.fr/ontoneurolog/v3.0/OntoSpec-documentation.zip Farooq Ahmad , Michel Dojat, Bernard Gibaud, Gilles Kassel, Lynda Temal September 30th, 2008 T1 weighted MR dataset 1.1 T1 weighted template dataset A T1 WEIGHTED MR TEMPLATE DATASET is a T1 WEIGHTED MR DATASET which is a TEMPLATE DATASET. http://neurolog.unice.fr/ontoneurolog/v3.0/OntoSpec-documentation.zip Farooq Ahmad , Michel Dojat, Bernard Gibaud, Gilles Kassel, Lynda Temal September 30th, 2008 T1 weighted MR template dataset 1.1 T2 star weighted DCE-MR dataset A T2 STAR WEIGHTED DCE MR DATASET is a DYNAMIC CONTRAST-ENHANCED MR DATASET. http://neurolog.unice.fr/ontoneurolog/v3.0/OntoSpec-documentation.zip Farooq Ahmad , Michel Dojat, Bernard Gibaud, Gilles Kassel, Lynda Temal September 30th, 2008 A T2 and T2 STAR WEIGHTED DCE MR DATASET reflects the T2 and T2 STAR of tissue decrease as the Gd contrast agent bolus passes through the brain. From the changes along time reflecting how the Gd contrast agent bolus passes through the brain, it is possible to estimate the cerebral blood flow (represented in milliliters of blood per gram of tissue per minute) as well as the cerebral blood volume (represented in milliliters of blood per gram of tissue). However, absolute quantification of perfusion is unreliable since the arterial input function is not well characterized and the relaxivity is unknown. T2 star weighted DCE-MR dataset 1.1 T2 star weighted MR dataset http://neurolog.unice.fr/ontoneurolog/v3.0/OntoSpec-documentation.zip Farooq Ahmad , Michel Dojat, Bernard Gibaud, Gilles Kassel, Lynda Temal September 30th, 2008 T2 star weighted MR dataset 1.1 T2 weighted DCE-MR dataset A T1 WEIGHTED DCE MR DATASET is a DYNAMIC CONTRAST-ENHANCED MR DATASET. http://neurolog.unice.fr/ontoneurolog/v3.0/OntoSpec-documentation.zip Farooq Ahmad , Michel Dojat, Bernard Gibaud, Gilles Kassel, Lynda Temal September 30th, 2008 A T1 WEIGHTED DCE MR DATASET reflects the dynamics of diffusion of the exogenous contrast media from the blood pool into the extra vascular extracellular space (EES) of the brain at a rate determined by the blood flow to the tissue, the permeability of the Brain Blood Barrier (BBB), and the surface area of the perfusing vessels. T2 weighted DCE-MR dataset 1.1 T2 weighted MR dataset A T2 WEIGHTED MR DATASET is a MR DATASET. [EP/SL] Every T2 WEIGHTED MR DATASET is an ANATOMICAL DATASET. [EP/SL] Every T2 WEIGHTED MR DATASET is a RECONSTRUCTED DATASET. http://neurolog.unice.fr/ontoneurolog/v3.0/OntoSpec-documentation.zip Farooq Ahmad , Michel Dojat, Bernard Gibaud, Gilles Kassel, Lynda Temal September 30th, 2008 T2 weighted MR dataset 1.1 T2 weighted template dataset A T2 WEIGHTED MR TEMPLATE DATASET is a T2 WEIGHTED MR DATASET which is a TEMPLATE DATASET. http://neurolog.unice.fr/ontoneurolog/v3.0/OntoSpec-documentation.zip Farooq Ahmad , Michel Dojat, Bernard Gibaud, Gilles Kassel, Lynda Temal September 30th, 2008 T2 weighted template dataset 1.1 absolute metabolite concentration dataset An ABSOLUTE METABOLITE CONCENTRATION DATASET is a PARAMETER QUANTIFICATION DATASET which is a result of an ABSOLUTE METABOLITE CONCENTRATION ESTIMATION at a TIME INTERVAL. [EP/SL] Every ABSOLUTE METABOLITE CONCENTRATION DATASET is a METABOLIC DATASET. http://neurolog.unice.fr/ontoneurolog/v3.0/OntoSpec-documentation.zip Farooq Ahmad , Michel Dojat, Bernard Gibaud, Gilles Kassel, Lynda Temal September 30th, 2008 absolute metabolite concentration dataset 1.1 absolute proton density dataset http://neurolog.unice.fr/ontoneurolog/v3.0/OntoSpec-documentation.zip Farooq Ahmad , Michel Dojat, Bernard Gibaud, Gilles Kassel, Lynda Temal September 30th, 2008 The absolute proton concentration [1H] of a tissue defines the number of protons per unit volume of tissue. The absolute proton density of a tissue refers to the concentration of protons in this tissue, relative to that of the same volume of water at the same temperature. It is expressed in pu (percent units). absolute proton density dataset 1.1 anatomical dataset An ANATOMICAL DATASET is a DATASET which explores a brain anatomical structure. http://neurolog.unice.fr/ontoneurolog/v3.0/OntoSpec-documentation.zip Farooq Ahmad , Michel Dojat, Bernard Gibaud, Gilles Kassel, Lynda Temal September 30th, 2008 anatomical dataset 1.1 bias field dataset A BIAS FIELD DATASET is a CALIBRATION DATASET which is a result of a BIAS FIELD ESTIMATION at a TIME INTERVAL. http://neurolog.unice.fr/ontoneurolog/v3.0/OntoSpec-documentation.zip Farooq Ahmad , Michel Dojat, Bernard Gibaud, Gilles Kassel, Lynda Temal September 30th, 2008 bias field dataset 1.1 bload dataset http://neurolog.unice.fr/ontoneurolog/v3.0/OntoSpec-documentation.zip Farooq Ahmad , Michel Dojat, Bernard Gibaud, Gilles Kassel, Lynda Temal September 30th, 2008 bload dataset 1.1 calibration dataset http://neurolog.unice.fr/ontoneurolog/v3.0/OntoSpec-documentation.zip Farooq Ahmad , Michel Dojat, Bernard Gibaud, Gilles Kassel, Lynda Temal September 30th, 2008 A CALIBRATION DATASET serves for calibration purposes. It represents a model that enables to transform non-calibrated data into calibrated data. For instance, in MR, a Field Map can be acquired for estimating the modification of the field B0 (Static Magnetic Field) or B1 (Radiofrequency Transmit Field) induced by the presence of the subject (i.e. the magnetic susceptibility of the tissues). From this data (called Magnetic Field Quality datasets) a transformation may be computed in order to compensate for this non-uniformity of the field: this transformation is a CALIBRATION DATASET. calibration dataset 1.1 contrast agent angio MR dataset A CONTRAST AGENT ANGIO MR DATASET is a MR DATASET. [EP/SL] Every CONTRAST AGENT ANGIO MR DATASET is a HEMODYNAMIC DATASET. [EP/SL] Every CONTRAST AGENT ANGIO MR DATASET is a RECONSTRUCTED DATASET. http://neurolog.unice.fr/ontoneurolog/v3.0/OntoSpec-documentation.zip Farooq Ahmad , Michel Dojat, Bernard Gibaud, Gilles Kassel, Lynda Temal September 30th, 2008 contrast agent angio MR dataset 1.1 diffusion tensor dataset A DIFFUSION TENSOR DATASET is a PARAMETER QUANTIFICATION DATASET which is a result of a DIFFUSION TENSOR CALCULATION at a TIME INTERVAL. [EP/SL] Every DIFFUSION TENSOR DATASET is an ANATOMICAL DATASET. http://neurolog.unice.fr/ontoneurolog/v3.0/OntoSpec-documentation.zip Farooq Ahmad , Michel Dojat, Bernard Gibaud, Gilles Kassel, Lynda Temal September 30th, 2008 The DIFFUSION TENSOR DATASET reflects the directional dependence of the diffusion properties, independently of the orientation of the tissue with respect to the directions of measurements. D is calculated from a non diffusion-weighted image plus six or more diffusion-weighted measurements along non collinear directions. diffusion tensor dataset 1.1 diffusion weighted MR dataset A DIFFUSION WEIGHTED MR DATASET is a MR DATASET. [EP/SL] Every DIFFUSION WEIGHTED MR DATASET is an ANATOMICAL DATASET. [EP/SL] Every DIFFUSION WEIGHTED MR DATASET is a RECONSTRUCTED DATASET. http://neurolog.unice.fr/ontoneurolog/v3.0/OntoSpec-documentation.zip Farooq Ahmad , Michel Dojat, Bernard Gibaud, Gilles Kassel, Lynda Temal September 30th, 2008 The Stejskal-Tanner imaging sequence is used to exploit diffusion of water molecules. Tissues with highly mobile water, such as cerebrospinal fluid (CSF) (strong diffusion) appear dark on images acquired in the presence of strong diffusion gradients, reflecting the dephasing of the contributing spins. A diffusion map can be calculated by combining at least two diffusion-weighted images that are differently sensitized to diffusion but remain identical with respect to the other parameters, spin density, T1, T2, TR, and TE. By using, for instance, the image S0 without diffusion weighting (b=0) and one diffusion-weighted image (b > 0), we can calculate a D value for each pixel. A parametric image containing these data is called a diffusion map or apparent diffusion map (ADC). The latter term emphasizes the fact that the D values obtained with this procedure depend on the experimental conditions (eg, direction of the sensitizing gradient and diffusion time delta). diffusion weighted MR dataset 1.1 displacement field dataset http://neurolog.unice.fr/ontoneurolog/v3.0/OntoSpec-documentation.zip Farooq Ahmad , Michel Dojat, Bernard Gibaud, Gilles Kassel, Lynda Temal September 30th, 2008 displacement field dataset 1.1 dynamic contrast enhanced MR dataset http://neurolog.unice.fr/ontoneurolog/v3.0/OntoSpec-documentation.zip Farooq Ahmad , Michel Dojat, Bernard Gibaud, Gilles Kassel, Lynda Temal September 30th, 2008 A DYNAMIC CONTRAST-ENHANCED MR DATASET reflects the dynamics of exogenous extracellular contrast media. dynamic contrast enhanced MR dataset 1.1 field map dataset A FIELD MAP DATASET is a PARAMETER QUANTIFICATION DATASET which is a result of a FIELD MAP ESTIMATION at a TIME INTERVAL. [EP/SL] Every FIELD MAP DATASET is a CALIBRATION DATASET. http://neurolog.unice.fr/ontoneurolog/v3.0/OntoSpec-documentation.zip Farooq Ahmad , Michel Dojat, Bernard Gibaud, Gilles Kassel, Lynda Temal September 30th, 2008 field map dataset 1.1 floating dataset http://neurolog.unice.fr/ontoneurolog/v3.0/OntoSpec-documentation.zip Farooq Ahmad , Michel Dojat, Bernard Gibaud, Gilles Kassel, Lynda Temal September 30th, 2008 A DATASET is used as a FLOATING DATASET in the context of a Registration Data Processing. During the registration, the FLOATING DATASET (also called source) is resampled in the sampling grid provided by the REFERENCE DATASET. floating dataset 1.1 fractional anisotropy dataset http://neurolog.unice.fr/ontoneurolog/v3.0/OntoSpec-documentation.zip Farooq Ahmad , Michel Dojat, Bernard Gibaud, Gilles Kassel, Lynda Temal September 30th, 2008 fractional anisotropy dataset 1.1 functional dataset A DATASET is used as a FLOATING DATASET in the context of a Registration Data Processing. During the registration, the FLOATING DATASET (also called source) is resampled in the sampling grid provided by the REFERENCE DATASET. http://neurolog.unice.fr/ontoneurolog/v3.0/OntoSpec-documentation.zip Farooq Ahmad , Michel Dojat, Bernard Gibaud, Gilles Kassel, Lynda Temal September 30th, 2008 functional dataset 1.1 magnetic field quality dataset http://neurolog.unice.fr/ontoneurolog/v3.0/OntoSpec-documentation.zip Farooq Ahmad , Michel Dojat, Bernard Gibaud, Gilles Kassel, Lynda Temal September 30th, 2008 A MAGNETIC FIELD QUALITY DATASET is an MR DATASET acquired to measure the non-uniformity of the static magnetic field B0 and linearity of its gradients, or to measure the radiofrequency field inhomogeneities. Such DATASETS are used to create FIELD MAP DATASETS and VOXEL DISPLACEMENT MAPS (which are CALIBRATION DATASETS) that are used to correct the deformation induced by those inhomogeneities. magnetic field quality dataset 1.1 magnetic field quality dataset long echo time A MAGNETIC FIELD QUALITY DATASET LONG ECHO TIME is a MAGNETIC FIELD QUALITY DATASET. http://neurolog.unice.fr/ontoneurolog/v3.0/OntoSpec-documentation.zip Farooq Ahmad , Michel Dojat, Bernard Gibaud, Gilles Kassel, Lynda Temal September 30th, 2008 magnetic field quality dataset long-echo-time 1.1 magnetic field quality dataset short echo time A MAGNETIC FIELD QUALITY DATASET SHORT ECHO TIME is a MAGNETIC FIELD QUALITY DATASET. http://neurolog.unice.fr/ontoneurolog/v3.0/OntoSpec-documentation.zip Farooq Ahmad , Michel Dojat, Bernard Gibaud, Gilles Kassel, Lynda Temal September 30th, 2008 magnetic field quality dataset short echo-time 1.1 magnetization transfer ratio dataset http://neurolog.unice.fr/ontoneurolog/v3.0/OntoSpec-documentation.zip Farooq Ahmad , Michel Dojat, Bernard Gibaud, Gilles Kassel, Lynda Temal September 30th, 2008 The Magnetization Transfer Ratio may be defined as MTR=100x(M0-Ms)/M0 pu, where M0 represents the signal measured in absence of saturation, and Ms the signal in the presence of saturation applied to the bound proton pool. It is expressed as percentage units (pu). A magnetization transfer ratio dataset “gives an indication of the quantity of bound protons present in tissue; it is reduced in many pathologies, particularly de-myelinisation, and provides different information from conventional parameters such as T2”. (Tofts, 2004). magnetization transfer ratio dataset 1.1 mean diffusivity dataset A MEAN DIFFUSIVITY DATASET is PARAMETER QUANTIFICATION DATASET which is a result of a MEAN DIFFUSIVITY CALCULATION at a TIME INTERVAL. [EP/SL] Every MEAN DIFFUSIVITY DATASET is an ANATOMICAL DATASET http://neurolog.unice.fr/ontoneurolog/v3.0/OntoSpec-documentation.zip Farooq Ahmad , Michel Dojat, Bernard Gibaud, Gilles Kassel, Lynda Temal September 30th, 2008 The mean diffusivity is the average value of the diffusion coefficients at this voxel. This can be estimated by the average of the eigen values of the diffusion tensor. mean diffusivity dataset 1.1 mesh dataset A MESH DATASET is a DATASET which is a result of a MESH GENERATION at a TIME INTERVAL. http://neurolog.unice.fr/ontoneurolog/v3.0/OntoSpec-documentation.zip Farooq Ahmad , Michel Dojat, Bernard Gibaud, Gilles Kassel, Lynda Temal September 30th, 2008 mesh dataset 1.1 metabolic dataset A METABOLIC DATASET is a DATASET which explores a brain metabolic process. http://neurolog.unice.fr/ontoneurolog/v3.0/OntoSpec-documentation.zip Farooq Ahmad , Michel Dojat, Bernard Gibaud, Gilles Kassel, Lynda Temal September 30th, 2008 metabolic dataset 1.1 metabolite concentration ratio dataset A METABOLITE CONCENTRATION RATIO DATASET is a PARAMETER QUANTIFICATION DATASET which is a result of a METABOLITE CONCENTRATION RATIO ESTIMATION at a TIME INTERVAL. [EP/SL] Every METABOLITE CONCENTRATION RATIO DATASET is a METABOLIC DATASET. http://neurolog.unice.fr/ontoneurolog/v3.0/OntoSpec-documentation.zip Farooq Ahmad , Michel Dojat, Bernard Gibaud, Gilles Kassel, Lynda Temal September 30th, 2008 metabolite concentration ratio dataset 1.1 multiple subject dataset http://neurolog.unice.fr/ontoneurolog/v3.0/OntoSpec-documentation.zip Farooq Ahmad , Michel Dojat, Bernard Gibaud, Gilles Kassel, Lynda Temal September 30th, 2008 A MULTIPLE SUBJECTS DATASET is a dataset that does not refer to a single subject. For example, datasets that result from the statistical analysis of many datasets referring to multiple subjects are MULTIPLE SUBJECTS DATASETS. Such datasets may refer to multiple subjects, or may refer to a GROUP OF SUBJECTS. multiple subjects dataset 1.1 multiple subjects template dataset A MULTIPLE SUBJECTS TEMPLATE DATASET is a TEMPLATE DATASET which is a MULTIPLE SUBJECTS DATASET. http://neurolog.unice.fr/ontoneurolog/v3.0/OntoSpec-documentation.zip Farooq Ahmad , Michel Dojat, Bernard Gibaud, Gilles Kassel, Lynda Temal September 30th, 2008 multiple subjects template dataset 1.1 non reconstructed dataset http://neurolog.unice.fr/ontoneurolog/v3.0/OntoSpec-documentation.zip Farooq Ahmad , Michel Dojat, Bernard Gibaud, Gilles Kassel, Lynda Temal September 30th, 2008 A NON-RECONSTRUCTED DATASET provides measurements that do not relate to a precise 3D location, such as measurements in Fourier space, or integration along a projection line (e.g. projection image in SPECT or CT). In contrast, a RECONTRUCTED DATASET provides a measurement of a quality of the explored object (e.g. brain tissues) at well-identified locations in 3D space, usually organized as a 2D and 3D regular sampling grid. non reconstructed dataset 1.1 nuclear medicine projection datset A NUCLEAR MEDICINE PROJECTION DATASET is a SPECT DATASET. [EP/SL] Every NUCLEAR MEDICINE PROJECTION DATASET is a METABOLIC DATASET. [EP/SL] Every NUCLEAR MEDICINE PROJECTION DATASET is a NON-RECONSTRUCTED DATASET. http://neurolog.unice.fr/ontoneurolog/v3.0/OntoSpec-documentation.zip Farooq Ahmad , Michel Dojat, Bernard Gibaud, Gilles Kassel, Lynda Temal September 30th, 2008 nuclear medicine projection dataset 1.1 nuclear medicine tomo dataset A NUCLEAR MEDICINE TOMO DATASET is a SPECT DATASET. [EP/SL] Every NUCLEAR MEDICINE TOMO DATASET is a METABOLIC DATASET. [EP/SL] Every NUCLEAR MEDICINE TOMO DATASET is a RECONSTRUCTED DATASET. http://neurolog.unice.fr/ontoneurolog/v3.0/OntoSpec-documentation.zip Farooq Ahmad , Michel Dojat, Bernard Gibaud, Gilles Kassel, Lynda Temal September 30th, 2008 nuclear medicine tomo dataset 1.1 proton density weighted MR dataset A PROTON DENSITY WEIGHTED MR DATASET is a MR DATASET. [EP/SL] Every PROTON DENSITY WEIGHTED MR DATASET is an ANATOMICAL DATASET. [EP/SL] Every PROTON DENSITY WEIGHTED MR DATASET is a RECONSTRUCTED DATASET. http://neurolog.unice.fr/ontoneurolog/v3.0/OntoSpec-documentation.zip Farooq Ahmad , Michel Dojat, Bernard Gibaud, Gilles Kassel, Lynda Temal September 30th, 2008 All images have intensity proportional to proton density. Images with very little T1 or T2 weighting are called ‘PD-weighted’. proton density weighted MR dataset 1.1 proton density weighted MR template dataset A PROTON DENSITY WEIGHTED MR TEMPLATE DATASET is a PROTON DENSITY WEIGHTED MR DATASET which is a TEMPLATE DATASET. http://neurolog.unice.fr/ontoneurolog/v3.0/OntoSpec-documentation.zip Farooq Ahmad , Michel Dojat, Bernard Gibaud, Gilles Kassel, Lynda Temal September 30th, 2008 All images have intensity proportional to proton density. Images with very little T1 or T2 weighting are called ‘PD-weighted’. proton density weighted MR template dataset 1.1 quality procedure dataset http://neurolog.unice.fr/ontoneurolog/v3.0/OntoSpec-documentation.zip Farooq Ahmad , Michel Dojat, Bernard Gibaud, Gilles Kassel, Lynda Temal September 30th, 2008 A QUALITY PROCEDURE DATASET is a DATASET which was acquired to assess the quality of the data produced by a piece of imaging equipment. It may also be used to produce a CALIBRATION DATASET. For example, a phantom may be scanned to measure spatial scaling. quality procedure dataset 1.1 quantitative T1 dataset A QUANTITATIVE T1 DATASET is a PARAMETER QUANTIFICATION DATASET which is a result of a QUANTITATIVE T1 ESTIMATION at a TIME INTERVAL. [EP/SL] Every QUANTITATIVE T1 DATASET is an ANATOMICAL DATASET. http://neurolog.unice.fr/ontoneurolog/v3.0/OntoSpec-documentation.zip Farooq Ahmad , Michel Dojat, Bernard Gibaud, Gilles Kassel, Lynda Temal September 30th, 2008 longitudinal relaxation time (in milliseconds) T1, also called longitudinal relaxation time (in milliseconds), is an intrinsic biophysical property of the tissue, related to macromolecule concentration, water binding and water content. quantitative T1 dataset 1.1 quantitative T2 dataset QUANTITATIVE T2 DATASET is a PARAMETER QUANTIFICATION DATASET which is a result of a QUANTITATIVE T2 ESTIMATION at a TIME INTERVAL. http://neurolog.unice.fr/ontoneurolog/v3.0/OntoSpec-documentation.zip Farooq Ahmad , Michel Dojat, Bernard Gibaud, Gilles Kassel, Lynda Temal September 30th, 2008 transverse relaxation time (in milliseconds) T2, also called transverse relaxation time (in milliseconds), is an intrinsic biophysical property of the tissues, also related to the bulk water content of the tissue. quantitative T2 dataset 1.1 quantitative T2 star dataset A QUANTITATIVE T2 DATASET is a PARAMETER QUANTIFICATION DATASET which is a result of a QUANTITATIVE T2 ESTIMATION at a TIME INTERVAL. http://neurolog.unice.fr/ontoneurolog/v3.0/OntoSpec-documentation.zip Farooq Ahmad , Michel Dojat, Bernard Gibaud, Gilles Kassel, Lynda Temal September 30th, 2008 T2, also called transverse relaxation time (in milliseconds), is an intrinsic biophysical property of the tissues, also related to the bulk water content of the tissue. quantitative T2 star dataset 1.1 reconstructed dataset http://neurolog.unice.fr/ontoneurolog/v3.0/OntoSpec-documentation.zip Farooq Ahmad , Michel Dojat, Bernard Gibaud, Gilles Kassel, Lynda Temal September 30th, 2008 reconstructed dataset 1.1 reference dataset http://neurolog.unice.fr/ontoneurolog/v3.0/OntoSpec-documentation.zip Farooq Ahmad , Michel Dojat, Bernard Gibaud, Gilles Kassel, Lynda Temal September 30th, 2008 reference dataset 1.1 regional cerebral blood flow dataset http://neurolog.unice.fr/ontoneurolog/v3.0/OntoSpec-documentation.zip Farooq Ahmad , Michel Dojat, Bernard Gibaud, Gilles Kassel, Lynda Temal September 30th, 2008 Cerebral blood flow (represented in milliliters of blood per gram of tissue per minute) can be calculated from diverse measurements, such as a T2 or T2 STAR WEIGHTED DCE MR DATASET, or a SPIN TAGGING PERFUSION MR DATASET. regional cerebral blood flow dataset 1.1 regional cerebral blood volume dataset http://neurolog.unice.fr/ontoneurolog/v3.0/OntoSpec-documentation.zip Farooq Ahmad , Michel Dojat, Bernard Gibaud, Gilles Kassel, Lynda Temal September 30th, 2008 Cerebral blood volume (represented in milliliters of blood per gram of tissue) can be calculated from diverse measurements, such as a T2 or T2 STAR WEIGHTED DCE MR DATASET. regional cerebral blood volume dataset 1.1 regional mean transit time dataset http://neurolog.unice.fr/ontoneurolog/v3.0/OntoSpec-documentation.zip Farooq Ahmad , Michel Dojat, Bernard Gibaud, Gilles Kassel, Lynda Temal September 30th, 2008 The regional mean transit time, rMTT, is the average time it takes the tracer substance to pass through the vascular bed within the voxel (rMTT= rCBV/rCBF). regional mean transit time dataset 1.1 registration dataset A REGISTRATION DATASET is a DATASET which is a result of a REGISTRATION at a TIME INTERVAL. http://neurolog.unice.fr/ontoneurolog/v3.0/OntoSpec-documentation.zip Farooq Ahmad , Michel Dojat, Bernard Gibaud, Gilles Kassel, Lynda Temal September 30th, 2008 registration dataset 1.1 relative anisotropy dataset A RELATIVE ANISOTROPY DATASET is a PARAMETER QUANTIFICATION DATASET which is a result of a RELATIVE ANISOTROPY CALCULATION at a TIME INTERVAL. [EP/SL] Every RELATIVE ANISOTROPY DATASET is an ANATOMICAL DATASET. http://neurolog.unice.fr/ontoneurolog/v3.0/OntoSpec-documentation.zip Farooq Ahmad , Michel Dojat, Bernard Gibaud, Gilles Kassel, Lynda Temal September 30th, 2008 relative anisotropy dataset 1.1 single subject template dataset A SINGLE SUBJECT TEMPLATE DATASET is a TEMPLATE DATASET which is a SINGLE SUBJECT DATASET. http://neurolog.unice.fr/ontoneurolog/v3.0/OntoSpec-documentation.zip Farooq Ahmad , Michel Dojat, Bernard Gibaud, Gilles Kassel, Lynda Temal September 30th, 2008 single subject template dataset 1.1 spin tagging perfusion MR dataset http://neurolog.unice.fr/ontoneurolog/v3.0/OntoSpec-documentation.zip Farooq Ahmad , Michel Dojat, Bernard Gibaud, Gilles Kassel, Lynda Temal September 30th, 2008 Spin tagging is a technique of measurement of blood perfusion, based on magnetically labeled arterial blood water as an endogenous tracer. SPIN TAGGING PERFUSION MR allows to obtain absolute values of perfusion of brain tissue by blood (cerebral blood flow) in ml blood/g tissue/ min. spin tagging perfusion MR dataset 1.1 statistical dataset A STATISTICAL DATASET is a DATASET which is a result of a DATASET STATISTICAL ANALYSIS at a TIME INTERVAL. [CP/EER] Every STATISTICAL DATASET can be superimposed with another RECONSTRUCTED DATASET or SEGMENTATION DATASET or STATISTICAL DATASET or PARAMETER QUANTIFICATION DATASET. http://neurolog.unice.fr/ontoneurolog/v3.0/OntoSpec-documentation.zip Farooq Ahmad , Michel Dojat, Bernard Gibaud, Gilles Kassel, Lynda Temal September 30th, 2008 statistical dataset 1.1 time of flight angio MR dataset http://neurolog.unice.fr/ontoneurolog/v3.0/OntoSpec-documentation.zip Farooq Ahmad , Michel Dojat, Bernard Gibaud, Gilles Kassel, Lynda Temal September 30th, 2008 Time-of-flight (TOF) is based on the phenomenon of flow-related enhancement of spins entering into an imaging slice. As a result of being unsaturated, these spins give more signal that surrounding stationary spins. With 2-D TOF, multiple thin imaging slices are acquired with a flow-compensated gradient-echo sequence. These images can be combined by using a technique of reconstruction such as maximum intensity projection (MIP), to obtain a 3-D image of the vessels analogous to conventional angiography. With 3-D TOF, a volume of images is obtained simultaneously by phase-encoding in the slice-select direction. time of flight angio MR dataset 1.1 velocity encoded angio MR dataset http://neurolog.unice.fr/ontoneurolog/v3.0/OntoSpec-documentation.zip Farooq Ahmad , Michel Dojat, Bernard Gibaud, Gilles Kassel, Lynda Temal September 30th, 2008 Spins that are moving in the same direction as a magnetic field gradient develop a phase shift that is proportional to the velocity of the spins. This is the basis of phase-contrast angiography. Phase-contrast pulse sequence is used to encode the velocity of the spins. Stationary spins undergo no net change in phase after the two gradients are applied. Moving spins will experience a different magnitude of the second gradient compared to the first, because of its different spatial position. This results in a net phase shift. This information can be used directly to determine the velocity of the spins. Alternatively, the image can be subtracted from one acquired without the velocity encoding gradients to obtain an angiogram. velocity encoded angio MR dataset 1.1 voxel displacement map dataset A VOXEL DISPLACEMENT MAP DATASET is a CALIBRATION DATASET which is a result of a VOXEL DISPLACEMENT MAP ESTIMATION at a TIME INTERVAL. http://neurolog.unice.fr/ontoneurolog/v3.0/OntoSpec-documentation.zip Farooq Ahmad , Michel Dojat, Bernard Gibaud, Gilles Kassel, Lynda Temal September 30th, 2008 voxel displacement map datset 1.1 An ABSOLUTE METABOLITE CONCENTRATION ESTIMATION is a QUANTITATIVE PARAMETER ESTIMATION. [CP/EVR] Every ABSOLUTE METABOLITE CONCENTRATION ESTIMATION has for data only a H1 CHEMICAL SHIFT IMAGING DATASET at a TIME INTERVAL. [EP/ER] Every ABSOLUTE METABOLITE CONCENTRATION ESTIMATION has for result an ABSOLUTE METABOLITE CONCENTRATION DATASET at a TIME INTERVAL. http://neurolog.unice.fr/ontoneurolog/v3.0/OntoSpec-documentation.zip PERSONS: Farooq Ahmad, Michel Dojat, Bernard Gibaud, Gilles Kassel, Lynda Temal October 16th, 2008 absolute metabolite concentration estimation An ABSOLUTE PROTON DENSITY ESTIMATION is a QUANTITATIVE PARAMETER ESTIMATION. [EP/ER] Every ABSOLUTE PROTON DENSITY ESTIMATION has for data at least two PROTON DENSITY WEIGHTED MR DATASET at a TIME INTERVAL. [EP/ER] Every ABSOLUTE PROTON DENSITY ESTIMATION has for result an ABSOLUTE PROTON DENSITY DATASET at a TIME INTERVAL. http://neurolog.unice.fr/ontoneurolog/v3.0/OntoSpec-documentation.zip PERSONS: Farooq Ahmad, Michel Dojat, Bernard Gibaud, Gilles Kassel, Lynda Temal October 16th, 2008 The specific procedure that leads to the quantitative estimation of the proton density defined tissue or structure. absolute proton density estimation An AFFINE NON-RIGID REGISTRATION is an AFFINE REGISTRATION. http://neurolog.unice.fr/ontoneurolog/v3.0/OntoSpec-documentation.zip PERSONS: Farooq Ahmad, Michel Dojat, Bernard Gibaud, Gilles Kassel, Lynda Temal October 16th, 2008 affine non rigid registration An AFFINE REGISTRATION, or LINEAR REGISTRATION, is a REGISTRATION. http://neurolog.unice.fr/ontoneurolog/v3.0/OntoSpec-documentation.zip PERSONS: Farooq Ahmad, Michel Dojat, Bernard Gibaud, Gilles Kassel, Lynda Temal October 16th, 2008 affine registration http://neurolog.unice.fr/ontoneurolog/v3.0/OntoSpec-documentation.zip PERSONS: Farooq Ahmad, Michel Dojat, Bernard Gibaud, Gilles Kassel, Lynda Temal October 16th, 2008 A BIAS-CORRECTION is a RESTORATION that focuses on the compensation of bias. bias correction October 16th, 2008 bias field estimation A BLOOD OXYGEN LEVEL DEPENDENT SIGNAL CHANGES ESTIMATION is a QUANTITATIVE PARAMETER ESTIMATION. [CP/EVR] Every BLOOD OXYGEN LEVEL DEPENDENT SIGNAL CHANGES ESTIMATION has for data only a T2 STAR WEIGHTED MR DATASET at a TIME INTERVAL. [EP/ER] Every BLOOD OXYGEN LEVEL DEPENDENT SIGNAL CHANGES ESTIMATION has for result a BOLD DATASET at a TIME INTERVAL. http://neurolog.unice.fr/ontoneurolog/v3.0/OntoSpec-documentation.zip PERSONS: Farooq Ahmad, Michel Dojat, Bernard Gibaud, Gilles Kassel, Lynda Temal October 16th, 2008 blood oxygen level dependent signal changes estimation A BOUNDARY SURFACE AND REGION BASED SEGMENTATION is a SEGMENTATION. A BOUNDARY SURFACE BASED SEGMENTATION is a SEGMENTATION. PERSONS: Farooq Ahmad, Michel Dojat, Bernard Gibaud, Gilles Kassel, Lynda Temal October 16th, 2008 boundary surface and region based segmentation PERSONS: Farooq Ahmad, Michel Dojat, Bernard Gibaud, Gilles Kassel, Lynda Temal October 16th, 2008 boundary surface based segmentation A TISSUES SEGMENTATION is a SEGMENTATION. PERSONS: Farooq Ahmad, Michel Dojat, Bernard Gibaud, Gilles Kassel, Lynda Temal October 16th, 2008 brain segmentation http://neurolog.unice.fr/ontoneurolog/v3.0/OntoSpec-documentation.zip October 16th, 2008 calibration model estimation October 16th, 2008 closing coefficient of variation calculation coefficient of variation calculation October 16th, 2008 convolution http://neurolog.unice.fr/ontoneurolog/v3.0/OntoSpec-documentation.zip PERSONS: Farooq Ahmad, Michel Dojat, Bernard Gibaud, Gilles Kassel, Lynda Temal October 16th, 2008 A CROPPING is a resampling that affects only the domain of the mathematical function associated to the dataset “to be cropped”, by defining a subset of this domain, more precisely by reducing the number of samples and changing the upper and lower limit of one or more intervals of this domain. The values taken by the function associated to the dataset are not changed. cropping http://neurolog.unice.fr/ontoneurolog/v3.0/OntoSpec-documentation.zip October 16th, 2008 dataset arithmetical operation http://neurolog.unice.fr/ontoneurolog/v3.0/OntoSpec-documentation.zip October 16th, 2008 dataset transformation October 16th, 2008 dataset addition October 16th, 2008 datasets blending October 16th, 2008 datasets division October 16th, 2008 datasets logical operation October 16th, 2008 datasets multiplication October 16th, 2008 datasets subtraction http://neurolog.unice.fr/ontoneurolog/v3.0/OntoSpec-documentation.zip PERSONS: Farooq Ahmad, Michel Dojat, Bernard Gibaud, Gilles Kassel, Lynda Temal A DENOISING is a RESTORATION that focuses on the compensation of noise. denoising A DIFFUSION TENSOR CALCULATION is a QUANTITATIVE PARAMETER ESTIMATION. [CP/EVR] Every DIFFUSION TENSOR CALCULATION has for data only a DIFFUSION WEIGHTED MR DATASET at a TIME INTERVAL. [EP/ER] Every DIFFUSION TENSOR CALCULATION has for result a DIFFUSION TENSOR DATASET at a TIME INTERVAL. http://neurolog.unice.fr/ontoneurolog/v3.0/OntoSpec-documentation.zip PERSONS: Farooq Ahmad, Michel Dojat, Bernard Gibaud, Gilles Kassel, Lynda Temal October 16th, 2008 diffusion tensor calculation October 16th, 2008 dilation October 16th, 2008 distance transform processing A DISTORTION-CORRECTION is a RESTORATION. [EP/SL] Every DISTORTION-CORRECTION is a CALIBRATION MODEL APPLICATION. http://neurolog.unice.fr/ontoneurolog/v3.0/OntoSpec-documentation.zip PERSONS: Farooq Ahmad, Michel Dojat, Bernard Gibaud, Gilles Kassel, Lynda Temal October 16th, 2008 A DISTORTION-CORRECTION is a RESTORATION that focuses on the compensation of a distortion, based on a calibration model. distortion correction October 16th, 2008 erosion A FIELD MAP ESTIMATION is a QUANTITATIVE PARAMETER ESTIMATION. [EP/SL] A FIELD MAP ESTIMATION is a CALIBRATION MODEL ESTIMATION. [CP/ER] Every FIELD MAP ESTIMATION has for data exactly one MAGNETIC FIELD QUALITY DATASET LONG ECHO TIME at a TIME INTERVAL. [CP/ER] Every FIELD MAP ESTIMATION has for data exactly one MAGNETIC FIELD QUALITY DATASET SHORT ECHO TIME at a TIME INTERVAL. [EP/ER] Every FIELD MAP ESTIMATION has for result a FIELD MAP DATASET at a TIME INTERVAL. http://neurolog.unice.fr/ontoneurolog/v3.0/OntoSpec-documentation.zip PERSONS: Farooq Ahmad, Michel Dojat, Bernard Gibaud, Gilles Kassel, Lynda Temal October 16th, 2008 field map estimation http://neurolog.unice.fr/ontoneurolog/v3.0/OntoSpec-documentation.zip October 16th, 2008 filtering October 16th, 2008 fourrier transformation October 16th, 2008 high pass filtering An INTENSITY NORMALIZATION is a RESAMPLING. http://neurolog.unice.fr/ontoneurolog/v3.0/OntoSpec-documentation.zip PERSONS: Farooq Ahmad, Michel Dojat, Bernard Gibaud, Gilles Kassel, Lynda Temal October 16th, 2008 An INTENSITY MODIFICATION is a resampling that affects only the range of the values taken by the mathematical function associated to the dataset “to be intensity-normalized”. Examples are: Bias field correction (with respect to an estimated bias); Histogram equalization; Intensity normalization (with respect to a reference); Image contrast adjustment (window / level); Image inversion. intensity normalization PERSONS: Farooq Ahmad, Michel Dojat, Bernard Gibaud, Gilles Kassel, Lynda Temal October 16th, 2008 A lesion segmentation is a segmentation that extracts structures such as tumours, or multiple sclerosis white matter lesions. lesion segmentation October 16th, 2008 low pass filtering A MAGNETIZATION TRANSFER RATIO CALCULATION is a QUANTITATIVE PARAMETER ESTIMATION. [CP/EVR] Every MAGNETIZATION TRANSFER RATIO CALCULATION has for data only T1 WEIGHTED MR DATASETS or T2 WEIGHTED MR DATASETS or T2 STAR WEIGHTED MR DATASETS at a TIME INTERVAL. [EP/ER] Every MAGNETIZATION TRANSFER RATIO CALCULATION has for result a MAGNETIZATION TRANSFER RATIO DATASET at a TIME INTERVAL. http://neurolog.unice.fr/ontoneurolog/v3.0/OntoSpec-documentation.zip PERSONS: Farooq Ahmad, Michel Dojat, Bernard Gibaud, Gilles Kassel, Lynda Temal October 16th, 2008 magnetization transfer ratio calculation October 16th, 2008 mathematical morphology filtering mean calculation mean calculation http://neurolog.unice.fr/ontoneurolog/v3.0/OntoSpec-documentation.zip October 16th, 2008 mesh-generation A METABOLITE CONCENTRATION RATIO ESTIMATION is a QUANTITATIVE PARAMETER ESTIMATION. [CP/EVR] Every METABOLITE CONCENTRATION RATIO ESTIMATION has for data only a SPECTROSCOPIC IMAGING DATASET at a TIME INTERVAL. [EP/ER] Every METABOLITE CONCENTRATION RATIO ESTIMATION has for result a METABOLITE CONCENTRATION RATIO DATASET at a TIME INTERVAL. http://neurolog.unice.fr/ontoneurolog/v3.0/OntoSpec-documentation.zip PERSONS: Farooq Ahmad, Michel Dojat, Bernard Gibaud, Gilles Kassel, Lynda Temal October 16th, 2008 metabolite concentration ratio estimation A MONO MODALITY AFFINE NON-RIGID REGISTRATION is an AFFINE NON-RIGID REGISTRATION. http://neurolog.unice.fr/ontoneurolog/v3.0/OntoSpec-documentation.zip PERSONS: Farooq Ahmad, Michel Dojat, Bernard Gibaud, Gilles Kassel, Lynda Temal October 16th, 2008 A MONO MODALITY AFFINE NON-RIGID REGISTRATION is an affine registration which estimates an affine but non-rigid geometrical transformation, in which the reference and the floating image have the same modality, which means that they represent the same kind of information, e.g. a T1-weighted MR signal. mono-modality affine non regid registration A MONO MODALITY NON-AFFINE REGISTRATION is a NON-AFFINE REGISTRATION. http://neurolog.unice.fr/ontoneurolog/v3.0/OntoSpec-documentation.zip PERSONS: Farooq Ahmad, Michel Dojat, Bernard Gibaud, Gilles Kassel, Lynda Temal October 16th, 2008 mono-modality non affine registration A mono modality rigid registration is a rigid registration in which the reference and the floating image have the same modality, which means that they represent the same kind of information, e.g. a T1-weighted MR signal. http://neurolog.unice.fr/ontoneurolog/v3.0/OntoSpec-documentation.zip PERSONS: Farooq Ahmad, Michel Dojat, Bernard Gibaud, Gilles Kassel, Lynda Temal October 16th, 2008 mono modality rigid registration A MULTI MODALITY AFFINE NON-RIGID REGISTRATION is an AFFINE NON-RIGID REGISTRATION. http://neurolog.unice.fr/ontoneurolog/v3.0/OntoSpec-documentation.zip PERSONS: Farooq Ahmad, Michel Dojat, Bernard Gibaud, Gilles Kassel, Lynda Temal October 16th, 2008 multi-modality affine non rigid registration A MULTI MODALITY NON-AFFINE REGISTRATION is a NON-AFFINE REGISTRATION. http://neurolog.unice.fr/ontoneurolog/v3.0/OntoSpec-documentation.zip PERSONS: Farooq Ahmad, Michel Dojat, Bernard Gibaud, Gilles Kassel, Lynda Temal October 16th, 2008 multi-modality non affine registration A MULTI MODALITY RIGID COREGISTRATION is a RIGID REGISTRATION. http://neurolog.unice.fr/ontoneurolog/v3.0/OntoSpec-documentation.zip PERSONS: Farooq Ahmad, Michel Dojat, Bernard Gibaud, Gilles Kassel, Lynda Temal October 16th, 2008 multi-modality rigid coregistration A NON-AFFINE REGISTRATION, or NON-LINEAR REGISTRATION, is a REGISTRATION. http://neurolog.unice.fr/ontoneurolog/v3.0/OntoSpec-documentation.zip PERSONS: Farooq Ahmad, Michel Dojat, Bernard Gibaud, Gilles Kassel, Lynda Temal October 16th, 2008 non affine registration A NORMALIZATION, or ACROSS-SUBJECT REGISTRATION, is a REGISTRATION. http://neurolog.unice.fr/ontoneurolog/v3.0/OntoSpec-documentation.zip PERSONS: Farooq Ahmad, Michel Dojat, Bernard Gibaud, Gilles Kassel, Lynda Temal October 16th, 2008 October 16th, 2008 opening PERMUTATION is a RESAMPLING http://neurolog.unice.fr/ontoneurolog/v3.0/OntoSpec-documentation.zip PERSONS: Farooq Ahmad, Michel Dojat, Bernard Gibaud, Gilles Kassel, Lynda Temal October 16th, 2008 permutation A QUANTITATIVE T1 ESTIMATION is a QUANTITATIVE PARAMETER ESTIMATION. [EP/ER] Every QUANTITATIVE T1 ESTIMATION has for data at least two T1 WEIGHTED MR DATASET at a TIME INTERVAL. [EP/ER] Every QUANTITATIVE T1 ESTIMATION has for result a QUANTITATIVE T1 DATASET at a TIME INTERVAL. http://neurolog.unice.fr/ontoneurolog/v3.0/OntoSpec-documentation.zip PERSONS: Farooq Ahmad, Michel Dojat, Bernard Gibaud, Gilles Kassel, Lynda Temal October 16th, 2008 quantitative T1 estimation A QUANTITATIVE T2 ESTIMATION is a QUANTITATIVE PARAMETER ESTIMATION. [EP/ER] Every QUANTITATIVE T2 ESTIMATION has for data at least two T2 WEIGHTED MR DATASET at a TIME INTERVAL. [EP/ER] Every QUANTITATIVE T2 ESTIMATION has for result a QUANTITATIVE T2 DATASET at a TIME INTERVAL. http://neurolog.unice.fr/ontoneurolog/v3.0/OntoSpec-documentation.zip PERSONS: Farooq Ahmad, Michel Dojat, Bernard Gibaud, Gilles Kassel, Lynda Temal October 16th, 2008 Several methods can be used for the quantitative estimation of T2 in a defined tissue or structure. based on the use of a spin echo sequence and the acquisition of several T2-weighted images at different echo time during the recovery of the transverse magnetic component. quantitative T2 estimation A QUANTITATIVE T2 STAR CALCULATION is a QUANTITATIVE PARAMETER ESTIMATION. [EP/ER] Every QUANTITATIVE T2 STAR ESTIMATION has for data at least two T2 STAR WEIGHTED MR DATASET at a TIME INTERVAL. [EP/ER] Every QUANTITATIVE T2 STAR ESTIMATION has for result a QUANTITATIVE T2 STAR DATASET at a TIME INTERVAL. http://neurolog.unice.fr/ontoneurolog/v3.0/OntoSpec-documentation.zip PERSONS: Farooq Ahmad, Michel Dojat, Bernard Gibaud, Gilles Kassel, Lynda Temal October 16th, 2008 qunatitative T2 star estimation REORIENTATION is a RESAMPLING http://neurolog.unice.fr/ontoneurolog/v3.0/OntoSpec-documentation.zip PERSONS: Farooq Ahmad, Michel Dojat, Bernard Gibaud, Gilles Kassel, Lynda Temal October 16th, 2008 reorientation A REGION BASED SEGMENTATION is a SEGMENTATION. PERSONS: Farooq Ahmad, Michel Dojat, Bernard Gibaud, Gilles Kassel, Lynda Temal October 16th, 2008 region based segmentation A REGIONAL CEREBRAL BLOOD FLOW ESTIMATION is a QUANTITATIVE PARAMETER ESTIMATION. [CP/EER] Every REGIONAL CEREBRAL BLOOD FLOW ESTIMATION has for data a T2 WEIGHTED DCE MR DATASET or a T2 STAR WEIGHTED DCE MR DATASET or a SPIN TAGGING PERFUSION MR DATASET at a TIME INTERVAL. [EP/ER] Every REGIONAL CEREBRAL BLOOD FLOW ESTIMATION has for result a REGIONAL CEREBRAL BLOOD FLOW DATASET at a TIME INTERVAL. http://neurolog.unice.fr/ontoneurolog/v3.0/OntoSpec-documentation.zip PERSONS: Farooq Ahmad, Michel Dojat, Bernard Gibaud, Gilles Kassel, Lynda Temal October 16th, 2008 regional cerebral blood flow estimation A REGIONAL CEREBRAL BLOOD VOLUME ESTIMATION is a QUANTITATIVE PARAMETER ESTIMATION. [CP/EER] Every REGIONAL CEREBRAL BLOOD VOLUME ESTIMATION has for data a T2 WEIGHTED DCE MR DATASET or a T2 STAR WEIGHTED DCE MR at a TIME INTERVAL. [EP/ER] Every REGIONAL CEREBRAL BLOOD VOLUME ESTIMATION has for result a REGIONAL CEREBRAL BLOOD VOLUME DATASET at a TIME INTERVAL. http://neurolog.unice.fr/ontoneurolog/v3.0/OntoSpec-documentation.zip PERSONS: Farooq Ahmad, Michel Dojat, Bernard Gibaud, Gilles Kassel, Lynda Temal October 16th, 2008 regional cerebral blood volume estimation A REGIONAL MEAN TRANSIT TIME CALCULATION is a QUANTITATIVE PARAMETER ESTIMATION. [CP/ER] Every REGIONAL MEAN TRANSIT TIME CALCULATION has for data exactly one REGIONAL CEREBRAL BLOOD VOLUME DATASET at a TIME INTERVAL. [CP/EVR] Every REGIONAL MEAN TRANSIT TIME CALCULATION has for data exactly one REGIONAL CEREBRAL BLOOD FLOW DATASET at a TIME INTERVAL. [EP/ER] Every REGIONAL MEAN TRANSIT TIME CALCULATION has for result a REGIONAL MEAN TRANSIT TIME DATASET at a TIME INTERVAL. http://neurolog.unice.fr/ontoneurolog/v3.0/OntoSpec-documentation.zip PERSONS: Farooq Ahmad, Michel Dojat, Bernard Gibaud, Gilles Kassel, Lynda Temal October 16th, 2008 regional mean transit time calculation medical image registration http://neurolog.unice.fr/ontoneurolog/v3.0/OntoSpec-documentation.zip PERSONS: Farooq Ahmad, Michel Dojat, Bernard Gibaud, Gilles Kassel, Lynda Temal October 16th, 2008 registration A REGISTRATION WITH DISTORTION CORRECTION is a REGISTRATION which has for part a DISTORTION CORRECTION. [EP/ER] Every REGISTRATION WITH DISTORTION CORRECTION has for data at least one CALIBRATION DATASET or PARAMETER QUANTIFICATION DATASET at a TIME INTERVAL. http://neurolog.unice.fr/ontoneurolog/v3.0/OntoSpec-documentation.zip PERSONS: Farooq Ahmad, Michel Dojat, Bernard Gibaud, Gilles Kassel, Lynda Temal October 16th, 2008 registration with distortion correction A RELATIVE ANISOTROPY CALCULATION is a QUANTITATIVE PARAMETER ESTIMATION. [CP/EVR] Every RELATIVE ANISOTROPY CALCULATION has for data only a DIFFUSION TENSOR DATASET at a TIME INTERVAL. [EP/ER] Every RELATIVE ANISOTROPY CALCULATION has for result a RELATIVE ANISOTROPY DATASET at a TIME INTERVAL. http://neurolog.unice.fr/ontoneurolog/v3.0/OntoSpec-documentation.zip PERSONS: Farooq Ahmad, Michel Dojat, Bernard Gibaud, Gilles Kassel, Lynda Temal October 16th, 2008 relative anisostropy calculation http://neurolog.unice.fr/ontoneurolog/v3.0/OntoSpec-documentation.zip PERSONS: Farooq Ahmad, Michel Dojat, Bernard Gibaud, Gilles Kassel, Lynda Temal October 16th, 2008 resolution modification medical image restoration http://neurolog.unice.fr/ontoneurolog/v3.0/OntoSpec-documentation.zip PERSONS: Farooq Ahmad, Michel Dojat, Bernard Gibaud, Gilles Kassel, Lynda Temal October 16th, 2008 restoration A RIGID REGISTRATION is a REGISTRATION. http://neurolog.unice.fr/ontoneurolog/v3.0/OntoSpec-documentation.zip PERSONS: Farooq Ahmad, Michel Dojat, Bernard Gibaud, Gilles Kassel, Lynda Temal October 16th, 2008 rigid registration October 16th, 2008 skeletonizing October 16th, 2008 smoothing standard deviation calculation standard deviation calculation October 16th, 2008 structured mesh-generation A SUBCORTICAL SEGMENTATION is a SEGMENTATION. PERSONS: Farooq Ahmad, Michel Dojat, Bernard Gibaud, Gilles Kassel, Lynda Temal October 16th, 2008 subcortical segmentation October 16th, 2008 thickening October 16th, 2008 thinning October 16th, 2008 thresholding PERSONS: Farooq Ahmad, Michel Dojat, Bernard Gibaud, Gilles Kassel, Lynda Temal October 16th, 2008 A tissues segmentation is a segmentation that extracts the tissues such as grey matter, white matter, cerebro-spinal fluid. tissues segmentation October 16th, 2008 unstructured mesh-generation October 16th, 2008 voxel displacement map claculation October 16th, 2008 wavelet transformation radioactive imaging agent radioactive tracer or radioactive label WEB: https://en.wikipedia.org/wiki/Radioactive_tracer A radioactive imaging agent is a chemical compound in which one or more atoms have been replaced by a radioisotope so by virtue of its radioactive decay it can be used to explore the mechanism of chemical reactions by tracing the path that the radioisotope follows from reactants to products. Radiolabeling is thus the radioactive form of isotopic labeling. Contrast-enhanced ultrasound clavicle hepatocyte subdivision of thorax subdivision of body proper tarsal bone calcaneus anterior chest elbow knee segment of neuraxis subdivision of trunck proper coronary artery bone organ brain lobular organ corticomedullary organ organ with organ cavity region of pectoral part of chest systemic artery endo-epithelial cell heart stomach neck liver pancreas kidney long bone mononuclear phagocyte system abdomen pelvis breast adrenal gland thymus femur cellular component measurement scale nominal scale ordinal scale ratio scale We have added the term value to the name of this entity that is extracted from OBCS. We have added the term value to the name of this entity that is extracted from OBCS. image creation device disorder normal value A role played by a part of a molecular entity distinguishable by the observer but not by the system and used to identify a tracer. [CHEBI ontology] We have changed the initial BFO definition of the relation 'has role'. We have define that every continuant (dependent or independent) are authorized to inheres a role when it participate in a given process. Imaging biomarker values have their associated roles which can be a diagnostic, predictive, prognosis and surrogate endpoint role. We have added the term value to the name of this entity that is extracted from OBCS. BFO 2 Reference: BFO does not claim to provide complete coverage of entities of all types. It seeks only to provide coverage of those entities studied by empirical science together with those entities which affect or are involved in human activities such as data processing and planning - coverage that is sufficiently broad to provide assistance to those engaged in building domain ontologies for purposes of data annotation. BFO 2 Reference: BFO's treatment of continuants and occurrents - as also its treatment of regions, rests on a dichotomy between space and time, and on the view that there are two perspectives on reality - earlier called the 'SNAP' and 'SPAN' perspectives, both of which are essential to the non-reductionist representation of reality as we understand it from the best available science. BFO 2 Reference: For both terms and relational expressions in BFO, we distinguish between primitive and defined. 'Entity' is an example of a primitive term. Primitive terms in a highest-level ontology such as BFO are terms that are so basic to our understanding of reality that there is no way of defining them in a non-circular fashion. For these, therefore, we can provide only elucidations, supplemented by examples and by axioms. Alan Ruttenberg Albert Goldfain Barry Smith Bill Duncan Bjoern Peters Chris Mungall David Osumi-Sutherland Fabian Neuhaus Holger Stenzhorn James A. Overton Janna Hastings Jie Zheng Jonathan Bona Larry Hunter Leonard Jacuzzo Ludger Jansen Mark Ressler Mathias Brochhausen Mauricio Almeida Melanie Courtot Pierre Grenon Randall Dipert Ron Rudnicki Selja Seppälä Stefan Schulz Thomas Bittner Werner Ceusters Yongqun "Oliver" He Please see the project site https://github.com/BFO-ontology/BFO, the bfo2 owl discussion group http://groups.google.com/group/bfo-owl-devel, the bfo2 discussion group http://groups.google.com/group/bfo-devel, the tracking google doc http://goo.gl/IlrEE, and the current version of the bfo2 reference http://purl.obolibrary.org/obo/bfo/dev/bfo2-reference.docx. This ontology is generated from a specification at https://github.com/BFO-ontology/BFO/tree/master/src/ontology/owl-group/specification/ and with the code that generates the OWL version in https://github.com/BFO-ontology/BFO/tree/master/src/tools/. A very early version of BFO version 2 in CLIF is at http://purl.obolibrary.org/obo/bfo/dev/bfo.clif. The BSD license on the BFO project site refers to code used to build BFO. This BFO 2.0 version represents a major update to BFO and is not strictly backwards compatible with BFO 1.1. The previous OWL version of BFO, version 1.1.1 will remain available at http://ifomis.org/bfo/1.1 and will no longer be updated. The BFO 2.0 OWL is a classes-only specification. The incorporation of core relations has been held over for a later version. We have added the term value to the name of this entity that is extracted from OBCS. We have added the term value to the name of this entity that is extracted from OBCS. We have added the term value to the name of this entity that is extracted from OBCS. We have added the term value to the name of this entity that is extracted from OBCS. We have added the term value to the name of this entity that is extracted from OBCS. We have added the term value to the name of this entity that is extracted from OBCS. We have added the term value to the name of this entity that is extracted from OBCS. We have added the term value to the name of this entity that is extracted from OBCS. We have added the term value to the name of this entity that is extracted from OBCS. We have added the term value to the name of this entity that is extracted from OBCS. We have added the term value to the name of this entity that is extracted from OBCS. We have added the term value to the name of this entity that is extracted from OBCS. We have added the term value to the name of this entity that is extracted from OBCS. We have added the term value to the name of this entity that is extracted from OBCS. We have added the term value to the name of this entity that is extracted from OBCS. We have added the term value to the name of this entity that is extracted from OBCS. We have added the term value to the name of this entity that is extracted from OBCS. We have added the term value to the name of this entity that is extracted from OBCS. We have added the term value to the name of this entity that is extracted from OBCS. We have added the term value to the name of this entity that is extracted from OBCS. We have added the term value to the name of this entity that is extracted from OBCS. We have added the term value to the name of this entity that is extracted from OBCS. minibody PERSON: Andrew J.Buckler albumin PERSON: Andrew J.Buckler minibody PERSON: Andrew J.Buckler minibody PERSON: Andrew J.Buckler biological macromolecule A macromolecule is a very large molecule commonly created by polymerization of smaller subunits (monomers). They are typically composed of thousands or more atoms. The most common macromolecules in biochemistry are biopolymers (nucleic acids, proteins, carbohydrates and polyphenols) and large non-polymeric molecules (such as lipids and macrocycles).Synthetic macromolecules include common plastics and synthetic fibres as well as experimental materials such as carbon nanotubes. Wikipedia page: https://en.wikipedia.org/wiki/Macromolecule http://purl.bioontology.org/ontology/QIBO PERSON: Andrew J.Buckler carbohydrate PERSON: Andrew J.Buckler cell line 'cell line' is an 'in vitro cell' that represents cells that grow in the first or later subculture from a primary culture. http://purl.bioontology.org/ontology/QIBO http://medical-dictionary.thefreedictionary.com/cell+line PERSON: Andrew J.Buckler http://purl.bioontology.org/ontology/QIBO DNA__ PERSON: Andrew J.Buckler dextran PERSON: Andrew J.Buckler minibody PERSON: Andrew J.Buckler disease diagnostic disease staging ex vivo bodily substance http://purl.bioontology.org/ontology/QIBO PERSON: Andrew J.Buckler ex vivo cells http://purl.bioontology.org/ontology/QIBO PERSON: Andrew J.Buckler ex vivo tissue biopsy An ex vivo tissue biopsy is an ex vivo subject that represents an amount of tissue that is removed by the doctor in order to be studied. http://purl.bioontology.org/ontology/QIBO PERSON: Andrew J.Buckler minibody PERSON: Andrew J.Buckler glycosaminoglycan PERSON: Andrew J.Buckler in vitro cell in vitro cell is an in vivo subject that represents living cells that are maintained in vitro in artificial media of serum and nutrients for the study and growth of certain strains of microorganisms or for experiments in controlling diseases, such as cancer. They are routinely used to culture viruses that infect patients. WEB: http://medical-dictionary.thefreedictionary.com/cell+culture http://purl.bioontology.org/ontology/QIBO PERSON: Andrew J.Buckler in vitro primary cell PERSON: Andrew J.Buckler in vitro tissue biopsy PERSON: Andrew J.Buckler lipid PERSON: Andrew J.Buckler Lipid Microbubble PERSON: Andrew J.Buckler minibody PERSON: Andrew J.Buckler monoclonal Antibody PERSON: Andrew J.Buckler nucleic acid PERSON: Andrew J.Buckler oligonucleotide PERSON: Andrew J.Buckler http://purl.bioontology.org/ontology/QIBO http://purl.bioontology.org/ontology/QIBO polysaccharide PERSON: Andrew J.Buckler proteins and polypeptide PERSON: Andrew J.Buckler http://purl.bioontology.org/ontology/QIBO transducted cell 'transduced cell' is a 'cell line' that is caused by a transduction. A transduction is the process by which DNA is transferred from one bacterium to another by a virus. It also refers to the process whereby foreign DNA is introduced into another cell via a viral vector. Wikipedia page: https://en.wikipedia.org/wiki/Transduction_(genetics) PERSON: Andrew J.Buckler http://purl.bioontology.org/ontology/QIBO photoactivatable imaging agent PERSONS: Emna Amdouni, Yannick Morvan and Bernard Giabud minibody PERSON: Andrew J.Buckler IBO is a biomedical ontology that enables the annotation of imaging biomarker data (e.g., measurement processes, measures, clinical processes, imaging datasets, etc.). 10/04/2018 Emna Amdouni and Bernard Gibaud