Irene Sanchez Lopez Carlos Oscar Sorzano Ontology that describes data types and image processing operations in Cryo Electron Microscopy of Single Particles Cryo Electron Microscopy ontology 2021-03-09 hasAcquisition hasCoordinate hasInput hasOutput hasRelation hasRepresentative hasTransform hasVolume isASetOf hasCTF has_obo_format_version EMThing EMObject EMProtocol Contains acquisition parameters such as magnification, voltage, spherical aberration, amplitude contrast, dose per frame and inital dose, optics group, and beam tilt Acquisition http://scipion.i2pc.es/ontology/CRYOEM_0000075 File representing an atomic structure (PDB, mmCIF, ...) AtomStruct x,y coordinate of a particle in a micrograph Coordinate 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 CTFModel Defines a min and maximum defocus that belongs to this group. DefocusGroup EMSet http://scipion.i2pc.es/ontology/CRYOEM_0000075 Fourier Shell Correlation FSC It has an index and filename to point to the physical image. Contains sampling rate. It refers to 2D or 3D. Image http://scipion.i2pc.es/ontology/CRYOEM_0000005 This is the result of a normal mode analysis on an atomic or pseudoatomic structure NormalMode http://scipion.i2pc.es/ontology/CRYOEM_0000005 Protein sequence Sequence Transformation matrix. It is valid for images and volumes Transform Prot2D Prot3D ProtCoords Any import protocol ProtImport Any operation on a set of micrographs ProtMicrographs Any protocol that takes a set of movies ProtProcessMovies ProtMovies ProtOther Operations on sets ProtSets SetOfAtomStructs This is a set of classes 2D, 3D or Vol SetOfClasses SetOfCoordinates SetOfCTF SetOfDefocusGroup SetOfFSCs SetOfImages SetOfNormalModes SetOfSequences Image2D Image3D http://scipion.i2pc.es/ontology/CRYOEM_0000071 Creates a 2D mask ProtCreateMask2D Protocols dealing with particles and restricted to 2D ProtParticles Performs any 3D analysis on a set of particles ProtAnalysis3D http://scipion.i2pc.es/ontology/CRYOEM_0000005 ProtFitting3D Protocols whose main input is a volume or a set of volumes ProtVolume Extracts coordinates from a set of particles ProtExtractCoords Takes a set of micrographs and produces a set of coordinates with particle candidates ProtParticlePicking Produces a difference between two sets of coordinates ProtPickingDifference Imports a set of averages ProtImportAverages Produces a set of coordinates ProtImportCoordinates Imports a set of CTFs and assigns it to a set of micrographs ProtImportCTF Imports a 2D or 3D mask. ProtImportMask Imports a set of micrographs ProtImportMicrographs Import micrographs tilt pairs ProtImportMicrographsTiltPairs Imports a set of movies ProtImportMovies Import a set of particles ProtImportParticles http://scipion.i2pc.es/ontology/CRYOEM_0000005 Imports an atomic structure ProtImportPdb Imports sequence ProtImportSequence Imports a volume ProtImportVolumes Assigns an already computed set of CTFs to a set of Micrographs or Particles ProtCTFAssign Computes the CTF of a set of micrographs ProtCTFMicrographs Operations like cropping, resizing, inverting contrast, ... ProtPreprocessMicrographs Aligns a set of movies into a set of micrographs ProtAlignMovies Computes the average of a set of movies into a set of micrographs ProtAverageFrames http://scipion.i2pc.es/ontology/CRYOEM_0000106 Extracts a set of MovieParticles from a set of Movies and a set of Particles ProtExtractMovieParticles Assigns a gain to a set of movies ProtMovieAssignGain Creates a consensus of a set of classes ProtClassesConsensus Creates an FSC ProtCreateFSC Splits a set into several pieces ProtSplitSet Computes a subset of a set ProtSubSet Computes the union of several sets ProtUnionSet http://scipion.i2pc.es/ontology/CRYOEM_0000104 SetOfClasses2D http://scipion.i2pc.es/ontology/CRYOEM_0000105 SetOfClasses3D SetOfClassesVol SetOfImages2D SetOfImages3D Average Mask 2D Mask Micrograph Movie Particle Map Volume Mask 3D VolumeMask Special protocol used in batch mode ProtCreateMask Performs some other kind of 2D analysis ProtAnalysis2D Takes a set of micrographs and coordinates and extract the particles ProtExtractParticles ProtClassify3D 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) ProtInitialVolume Reconstruct a map from a set of particles ProtReconstruct3D Refine the angular alignment of a set of particles ProtRefine3D Align volumes ProtAlignVolume Create a 3D mask ProtCreateMask3D Filter volumes ProtFilterVolumes http://scipion.i2pc.es/ontology/CRYOEM_0000076 http://scipion.i2pc.es/ontology/CRYOEM_0000075 Apply a mask to a volume (the mask can be defined by a description, for instance, a geometrical object) ProtMaskVolumes http://scipion.i2pc.es/ontology/CRYOEM_0000075 Preprocess volumes (filters, ...) ProtPreprocessVolumes http://scipion.i2pc.es/ontology/CRYOEM_0000075 Performs an operation with one or two volumes (calculator) ProtOperateVolumes A subclass of particle picking algorithms that can perform this operation completely automatically. ProtParticlePickingAuto Importing coordinates for tilt pairs ProtImportCoordinatesPairs Computes a subset of particles according to a set of micrographs ProtSubSetByMic Computes a subset of another set by a graphical intervention of the user ProtUserSubSet This is a set of 2D averages SetOfAverages SetOfMicrographs SetOfMovies SetOfParticles SetOfVolumes This is a set of images corresponding to a single particle in each ones of the frames. MovieParticle Aligns a set of 2D images ProtAlign2D Classifies a set of particles in 2D classes ProtClassify2D Any protocol that applies a transformation to a SetOfParticles ProtProcessParticles Extracts particles from a set of tilt pairs ProtExtractParticlesPair This is a set of particles and its 2D representative Class2D http://scipion.i2pc.es/ontology/CRYOEM_0000075 This is a set of particles and its 3D representative Class3D SetOfMovieParticles This is a set of volumes and its 3D representative ClassVol Assigns a 2D alignment to a SetOfParticles ProtAlignmentAssign Applies a filter ProtFilterParticles Applies a mask ProtMaskParticles Other operations on a SetOfParticles not considered on the other branches ProtOperateParticles