format-version: 1.2 ontology: http://www.semanticweb.org/coss/ontologies/2020/2/untitled-ontology-2 owl-axioms: Prefix(owl:=)\nPrefix(rdf:=)\nPrefix(xml:=)\nPrefix(xsd:=)\nPrefix(rdfs:=)\n\n\nOntology(\nDeclaration(AnnotationProperty())\n\n\nAnnotationAssertion( \"ProtProcessMovies\"^^xsd:string)\n) [Term] id: Acquisition comment: Contains acquisition parameters such as magnification, voltage, spherical aberration, amplitude contrast, dose per frame and inital dose, optics group, and beam tilt is_a: EMObject [Term] id: AtomStruct comment: File representing an atomic structure (PDB, mmCIF, ...) is_a: EMObject property_value: hasVolume "Volume" [Term] id: Average is_a: Image2D [Term] id: CTFModel comment: Contains a minimum description of the Microscope Contrast Transfer Function with parameters like the two defoci, the defocus angle, phase shift and an image of the Power Spectrum Density. is_a: EMObject [Term] id: Class2D comment: This is a set of particles and its 2D representative is_a: SetOfParticles property_value: hasRepresentative "Average" property_value: isASetOf "Particle" [Term] id: Class3D comment: This is a set of particles and its 3D representative is_a: SetOfParticles property_value: hasRepresentative "Volume" property_value: isASetOf "Particle" [Term] id: ClassVol comment: This is a set of volumes and its 3D representative is_a: SetOfVolumes property_value: hasRepresentative "Volume" [Term] id: Coordinate comment: x,y coordinate of a particle in a micrograph is_a: EMObject [Term] id: DefocusGroup comment: Defines a min and maximum defocus that belongs to this group. is_a: EMObject property_value: hasRelation "Micrograph" [Term] id: EMSet is_a: EMObject [Term] id: FSC comment: Fourier Shell Correlation is_a: EMObject property_value: hasVolume "Volume" [Term] id: Image comment: It has an index and filename to point to the physical image. Contains sampling rate. It refers to 2D or 3D. is_a: EMObject property_value: hasTransform "Transform" [Term] id: Image2D is_a: Image [Term] id: Image3D is_a: Image [Term] id: Mask comment: Mask 2D is_a: Image2D [Term] id: Micrograph is_a: Image2D property_value: hasAcquisition "Acquisition" [Term] id: Movie is_a: Image2D property_value: hasAcquisition "Acquisition" [Term] id: MovieParticle comment: This is a set of images corresponding to a single particle in each ones of the frames. is_a: Particle [Term] id: NormalMode comment: This is the result of a normal mode analysis on an atomic or pseudoatomic structure is_a: EMObject property_value: hasRelation "AtomStruct" [Term] id: Particle is_a: Image2D property_value: hasAcquisition "Acquisition" property_value: hasCoordinate "Coordinate" property_value: hasCTF "CTFModel" property_value: hasTransform "Transform" [Term] id: Prot2D is_a: EMProtocol [Term] id: Prot3D is_a: EMProtocol [Term] id: ProtAlign2D comment: Aligns a set of 2D images is_a: ProtAnalysis2D property_value: hasOutput "SetOfParticles" [Term] id: ProtAlignMovies comment: Aligns a set of movies into a set of micrographs is_a: ProtMovies property_value: hasOutput "SetOfMicrographs" [Term] id: ProtAlignVolume comment: Align volumes is_a: ProtVolume property_value: hasOutput "Volume" [Term] id: ProtAlignmentAssign comment: Assigns a 2D alignment to a SetOfParticles is_a: ProtAlign2D [Term] id: ProtAnalysis2D comment: Performs some other kind of 2D analysis is_a: ProtParticles property_value: hasInput "SetOfParticles" [Term] id: ProtAnalysis3D comment: Performs any 3D analysis on a set of particles is_a: Prot3D property_value: hasInput "SetOfParticles" [Term] id: ProtAverageFrames comment: Computes the average of a set of movies into a set of micrographs is_a: ProtMovies property_value: hasOutput "SetOfMicrographs" [Term] id: ProtCTFAssign comment: Assigns an already computed set of CTFs to a set of Micrographs or Particles is_a: ProtMicrographs property_value: hasInput "SetOfCTF" property_value: hasInput "SetOfParticles" property_value: hasOutput "SetOfMicrographs" property_value: hasOutput "SetOfParticles" [Term] id: ProtCTFMicrographs comment: Computes the CTF of a set of micrographs is_a: ProtMicrographs property_value: hasInput "SetOfMicrographs" property_value: hasOutput "SetOfCTF" [Term] id: ProtClassesConsensus comment: Creates a consensus of a set of classes is_a: ProtOther property_value: hasInput "SetOfClasses" property_value: hasOutput "SetOfClasses" [Term] id: ProtClassify2D comment: Classifies a set of particles in 2D classes is_a: ProtAnalysis2D property_value: hasOutput "SetOfClasses2D" [Term] id: ProtClassify3D is_a: ProtAnalysis3D property_value: hasOutput "SetOfClasses3D" [Term] id: ProtCoords is_a: EMProtocol [Term] id: ProtCreateFSC comment: Creates an FSC is_a: ProtOther property_value: hasOutput "FSC" [Term] id: ProtCreateMask comment: Special protocol used in batch mode is_a: ProtCreateMask2D [Term] id: ProtCreateMask2D comment: Creates a 2D mask is_a: Prot2D property_value: hasOutput "Mask" [Term] id: ProtCreateMask3D comment: Create a 3D mask is_a: ProtVolume property_value: hasOutput "VolumeMask" [Term] id: ProtExtractCoords comment: Extracts coordinates from a set of particles is_a: ProtCoords property_value: hasInput "SetOfParticles" property_value: hasOutput "SetOfCoordinates" [Term] id: ProtExtractMovieParticles comment: Extracts a set of MovieParticles from a set of Movies and a set of Particles is_a: ProtMovies property_value: hasInput "SetOfParticles" property_value: hasOutput "SetOfMovieParticles" [Term] id: ProtExtractParticles comment: Takes a set of micrographs and coordinates and extract the particles is_a: ProtParticles property_value: hasInput "SetOfCoordinates" property_value: hasInput "SetOfMicrographs" property_value: hasOutput "SetOfParticles" [Term] id: ProtExtractParticlesPair comment: Extracts particles from a set of tilt pairs is_a: ProtExtractParticles [Term] id: ProtFilterParticles comment: Applies a filter is_a: ProtProcessParticles [Term] id: ProtFilterVolumes comment: Filter volumes is_a: ProtVolume property_value: hasOutput "Volume" [Term] id: ProtFitting3D is_a: Prot3D property_value: hasInput "AtomStruct" property_value: hasInput "Volume" [Term] id: ProtImport comment: Any import protocol is_a: EMProtocol [Term] id: ProtImportAverages comment: Imports a set of averages is_a: ProtImport property_value: hasOutput "SetOfAverages" [Term] id: ProtImportCTF comment: Imports a set of CTFs and assigns it to a set of micrographs is_a: ProtImport property_value: hasInput "SetOfMicrographs" property_value: hasOutput "SetOfCTF" [Term] id: ProtImportCoordinates comment: Produces a set of coordinates is_a: ProtImport property_value: hasInput "SetOfMicrographs" property_value: hasOutput "SetOfCoordinates" [Term] id: ProtImportCoordinatesPairs comment: Importing coordinates for tilt pairs is_a: ProtImportCoordinates [Term] id: ProtImportMask comment: Imports a 2D or 3D mask. is_a: ProtImport property_value: hasOutput "Mask" property_value: hasOutput "VolumeMask" [Term] id: ProtImportMicrographs comment: Imports a set of micrographs is_a: ProtImport property_value: hasOutput "SetOfMicrographs" [Term] id: ProtImportMicrographsTiltPairs comment: Import micrographs tilt pairs is_a: ProtImport property_value: hasOutput "SetOfMicrographs" [Term] id: ProtImportMovies comment: Imports a set of movies is_a: ProtImport property_value: hasOutput "SetOfMovies" [Term] id: ProtImportParticles comment: Import a set of particles is_a: ProtImport property_value: hasOutput "SetOfParticles" [Term] id: ProtImportPdb comment: Imports an atomic structure is_a: ProtImport property_value: hasOutput "AtomStruct" [Term] id: ProtImportSequence comment: Imports sequence is_a: ProtImport property_value: hasOutput "Sequence" [Term] id: ProtImportVolumes comment: Imports a volume is_a: ProtImport property_value: hasOutput "Volume" [Term] id: ProtInitialVolume comment: The input may be a set of particles or a set of averages (which can be regarded as a summary of a set of particles) is_a: ProtAnalysis3D property_value: hasInput "SetOfAverages" property_value: hasOutput "SetOfVolumes" property_value: hasOutput "Volume" [Term] id: ProtMaskParticles comment: Applies a mask is_a: ProtProcessParticles [Term] id: ProtMaskVolumes comment: Apply a mask to a volume (the mask can be defined by a description, for instance, a geometrical object) is_a: ProtVolume property_value: hasInput "VolumeMask" property_value: hasOutput "Volume" [Term] id: ProtMicrographs comment: Any operation on a set of micrographs is_a: EMProtocol [Term] id: ProtMovieAssignGain comment: Assigns a gain to a set of movies is_a: ProtMovies property_value: hasOutput "SetOfMovies" [Term] id: ProtMovies comment: Any protocol that takes a set of movies is_a: EMProtocol property_value: hasInput "SetOfMovies" [Term] id: ProtOperateParticles comment: Other operations on a SetOfParticles not considered on the other branches is_a: ProtProcessParticles [Term] id: ProtOperateVolumes comment: Performs an operation with one or two volumes (calculator) is_a: ProtVolume property_value: hasOutput "Volume" [Term] id: ProtOther is_a: EMProtocol [Term] id: ProtParticlePicking comment: Takes a set of micrographs and produces a set of coordinates with particle candidates is_a: ProtCoords property_value: hasInput "SetOfMicrographs" property_value: hasOutput "SetOfCoordinates" [Term] id: ProtParticlePickingAuto comment: A subclass of particle picking algorithms that can perform this operation completely automatically. is_a: ProtParticlePicking [Term] id: ProtParticles comment: Protocols dealing with particles and restricted to 2D is_a: Prot2D [Term] id: ProtPickingDifference comment: Produces a difference between two sets of coordinates is_a: ProtCoords property_value: hasInput "SetOfCoordinates" property_value: hasOutput "SetOfCoordinates" [Term] id: ProtPreprocessMicrographs comment: Operations like cropping, resizing, inverting contrast, ... is_a: ProtMicrographs property_value: hasInput "SetOfMicrographs" property_value: hasOutput "SetOfMicrographs" [Term] id: ProtPreprocessVolumes comment: Preprocess volumes (filters, ...) is_a: ProtVolume property_value: hasOutput "Volume" [Term] id: ProtProcessParticles comment: Any protocol that applies a transformation to a SetOfParticles is_a: ProtAnalysis2D property_value: hasOutput "SetOfParticles" [Term] id: ProtReconstruct3D comment: Reconstruct a map from a set of particles is_a: ProtAnalysis3D property_value: hasOutput "Volume" [Term] id: ProtRefine3D comment: Refine the angular alignment of a set of particles is_a: ProtAnalysis3D property_value: hasOutput "Volume" [Term] id: ProtSets comment: Operations on sets is_a: EMProtocol [Term] id: ProtSplitSet comment: Splits a set into several pieces is_a: ProtSets [Term] id: ProtSubSet comment: Computes a subset of a set is_a: ProtSets [Term] id: ProtSubSetByMic comment: Computes a subset of particles according to a set of micrographs is_a: ProtSubSet property_value: hasInput "SetOfMicrographs" property_value: hasInput "SetOfParticles" property_value: hasOutput "SetOfParticles" [Term] id: ProtUnionSet comment: Computes the union of several sets is_a: ProtSets [Term] id: ProtUserSubSet comment: Computes a subset of another set by a graphical intervention of the user is_a: ProtSubSet [Term] id: ProtVolume comment: Protocols whose main input is a volume or a set of volumes is_a: Prot3D property_value: hasInput "Volume" [Term] id: Sequence comment: Protein sequence is_a: EMObject property_value: hasRelation "AtomStruct" [Term] id: SetOfAtomStructs is_a: EMSet property_value: isASetOf "AtomStruct" [Term] id: SetOfAverages comment: This is a set of 2D averages is_a: SetOfImages2D property_value: isASetOf "Particle" [Term] id: SetOfCTF is_a: EMSet property_value: isASetOf "CTFModel" [Term] id: SetOfClasses comment: This is a set of classes 2D, 3D or Vol is_a: EMSet [Term] id: SetOfClasses2D is_a: SetOfClasses property_value: isASetOf "Class2D" [Term] id: SetOfClasses3D is_a: SetOfClasses property_value: isASetOf "Class3D" [Term] id: SetOfClassesVol is_a: SetOfClasses property_value: isASetOf "ClassVol" [Term] id: SetOfCoordinates is_a: EMSet property_value: isASetOf "Coordinate" [Term] id: SetOfDefocusGroup is_a: EMSet property_value: isASetOf "DefocusGroup" [Term] id: SetOfFSCs is_a: EMSet property_value: isASetOf "FSC" [Term] id: SetOfImages is_a: EMSet property_value: hasAcquisition "Acquisition" property_value: isASetOf "Image" [Term] id: SetOfImages2D is_a: SetOfImages property_value: isASetOf "Image2D" [Term] id: SetOfImages3D is_a: SetOfImages property_value: isASetOf "Image3D" [Term] id: SetOfMicrographs is_a: SetOfImages2D property_value: isASetOf "Micrograph" [Term] id: SetOfMovieParticles is_a: SetOfParticles property_value: isASetOf "MovieParticle" [Term] id: SetOfMovies is_a: SetOfImages2D property_value: isASetOf "Movie" [Term] id: SetOfNormalModes is_a: EMSet property_value: isASetOf "NormalMode" [Term] id: SetOfParticles is_a: SetOfImages2D property_value: isASetOf "Particle" [Term] id: SetOfSequences is_a: EMSet property_value: isASetOf "Sequence" [Term] id: SetOfVolumes is_a: SetOfImages3D [Term] id: Transform comment: Transformation matrix. It is valid for images and volumes is_a: EMObject [Term] id: Volume comment: Map is_a: Image3D [Term] id: VolumeMask comment: Mask 3D is_a: Image3D