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 scipion:CRYOEM_0000001 EMThing scipion:CRYOEM_0000002 EMObject scipion:CRYOEM_0000003 EMProtocol scipion:CRYOEM_0000004 Contains acquisition parameters such as magnification, voltage, spherical aberration, amplitude contrast, dose per frame and inital dose, optics group, and beam tilt Acquisition scipion:CRYOEM_0000005 File representing an atomic structure (PDB, mmCIF, ...) http://scipion.i2pc.es/ontology/CRYOEM_0000075 AtomStruct scipion:CRYOEM_0000006 x,y coordinate of a particle in a micrograph Coordinate scipion:CRYOEM_0000007 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 scipion:CRYOEM_0000008 Defines a min and maximum defocus that belongs to this group. DefocusGroup scipion:CRYOEM_0000009 EMSet scipion:CRYOEM_0000010 Fourier Shell Correlation http://scipion.i2pc.es/ontology/CRYOEM_0000075 FSC scipion:CRYOEM_0000011 It has an index and filename to point to the physical image. Contains sampling rate. It refers to 2D or 3D. Image scipion:CRYOEM_0000012 This is the result of a normal mode analysis on an atomic or pseudoatomic structure http://scipion.i2pc.es/ontology/CRYOEM_0000005 NormalMode scipion:CRYOEM_0000013 Protein sequence http://scipion.i2pc.es/ontology/CRYOEM_0000005 Sequence scipion:CRYOEM_0000014 Transformation matrix. It is valid for images and volumes Transform scipion:CRYOEM_0000015 Prot2D scipion:CRYOEM_0000016 Prot3D scipion:CRYOEM_0000017 ProtCoords scipion:CRYOEM_0000018 Any import protocol ProtImport scipion:CRYOEM_0000019 Any operation on a set of micrographs ProtMicrographs scipion:CRYOEM_0000020 Any protocol that takes a set of movies ProtProcessMovies ProtMovies scipion:CRYOEM_0000021 ProtOther scipion:CRYOEM_0000022 Operations on sets ProtSets scipion:CRYOEM_0000023 SetOfAtomStructs scipion:CRYOEM_0000024 This is a set of classes 2D, 3D or Vol SetOfClasses scipion:CRYOEM_0000025 SetOfCoordinates scipion:CRYOEM_0000026 SetOfCTF scipion:CRYOEM_0000027 SetOfDefocusGroup scipion:CRYOEM_0000028 SetOfFSCs scipion:CRYOEM_0000029 SetOfImages scipion:CRYOEM_0000030 SetOfNormalModes scipion:CRYOEM_0000031 SetOfSequences scipion:CRYOEM_0000032 Image2D scipion:CRYOEM_0000033 Image3D scipion:CRYOEM_0000034 Creates a 2D mask http://scipion.i2pc.es/ontology/CRYOEM_0000071 ProtCreateMask2D scipion:CRYOEM_0000035 Protocols dealing with particles and restricted to 2D ProtParticles scipion:CRYOEM_0000036 Performs any 3D analysis on a set of particles ProtAnalysis3D scipion:CRYOEM_0000037 http://scipion.i2pc.es/ontology/CRYOEM_0000005 ProtFitting3D scipion:CRYOEM_0000038 Protocols whose main input is a volume or a set of volumes ProtVolume scipion:CRYOEM_0000039 Extracts coordinates from a set of particles ProtExtractCoords scipion:CRYOEM_0000040 Takes a set of micrographs and produces a set of coordinates with particle candidates ProtParticlePicking scipion:CRYOEM_0000041 Produces a difference between two sets of coordinates ProtPickingDifference scipion:CRYOEM_0000042 Imports a set of averages ProtImportAverages scipion:CRYOEM_0000043 Produces a set of coordinates ProtImportCoordinates scipion:CRYOEM_0000044 Imports a set of CTFs and assigns it to a set of micrographs ProtImportCTF scipion:CRYOEM_0000045 Imports a 2D or 3D mask. ProtImportMask scipion:CRYOEM_0000046 Imports a set of micrographs ProtImportMicrographs scipion:CRYOEM_0000047 Import micrographs tilt pairs ProtImportMicrographsTiltPairs scipion:CRYOEM_0000048 Imports a set of movies ProtImportMovies scipion:CRYOEM_0000049 Import a set of particles ProtImportParticles scipion:CRYOEM_0000050 Imports an atomic structure http://scipion.i2pc.es/ontology/CRYOEM_0000005 ProtImportPdb scipion:CRYOEM_0000051 Imports sequence ProtImportSequence scipion:CRYOEM_0000052 Imports a volume ProtImportVolumes scipion:CRYOEM_0000053 Assigns an already computed set of CTFs to a set of Micrographs or Particles ProtCTFAssign scipion:CRYOEM_0000054 Computes the CTF of a set of micrographs ProtCTFMicrographs scipion:CRYOEM_0000055 Operations like cropping, resizing, inverting contrast, ... ProtPreprocessMicrographs scipion:CRYOEM_0000056 Aligns a set of movies into a set of micrographs ProtAlignMovies scipion:CRYOEM_0000057 Computes the average of a set of movies into a set of micrographs ProtAverageFrames scipion:CRYOEM_0000058 Extracts a set of MovieParticles from a set of Movies and a set of Particles http://scipion.i2pc.es/ontology/CRYOEM_0000106 ProtExtractMovieParticles scipion:CRYOEM_0000059 Assigns a gain to a set of movies ProtMovieAssignGain scipion:CRYOEM_0000060 Creates a consensus of a set of classes ProtClassesConsensus scipion:CRYOEM_0000061 Creates an FSC ProtCreateFSC scipion:CRYOEM_0000062 Splits a set into several pieces ProtSplitSet scipion:CRYOEM_0000063 Computes a subset of a set ProtSubSet scipion:CRYOEM_0000064 Computes the union of several sets ProtUnionSet scipion:CRYOEM_0000065 http://scipion.i2pc.es/ontology/CRYOEM_0000104 SetOfClasses2D scipion:CRYOEM_0000066 http://scipion.i2pc.es/ontology/CRYOEM_0000105 SetOfClasses3D scipion:CRYOEM_0000067 SetOfClassesVol scipion:CRYOEM_0000068 SetOfImages2D scipion:CRYOEM_0000069 SetOfImages3D scipion:CRYOEM_0000070 Average scipion:CRYOEM_0000071 Mask 2D Mask scipion:CRYOEM_0000072 Micrograph scipion:CRYOEM_0000073 Movie scipion:CRYOEM_0000074 Particle scipion:CRYOEM_0000075 Map Volume scipion:CRYOEM_0000076 Mask 3D VolumeMask scipion:CRYOEM_0000077 Special protocol used in batch mode ProtCreateMask scipion:CRYOEM_0000078 Performs some other kind of 2D analysis ProtAnalysis2D scipion:CRYOEM_0000079 Takes a set of micrographs and coordinates and extract the particles ProtExtractParticles scipion:CRYOEM_0000080 ProtClassify3D scipion:CRYOEM_0000081 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 scipion:CRYOEM_0000082 Reconstruct a map from a set of particles ProtReconstruct3D scipion:CRYOEM_0000083 Refine the angular alignment of a set of particles ProtRefine3D scipion:CRYOEM_0000084 Align volumes ProtAlignVolume scipion:CRYOEM_0000085 Create a 3D mask ProtCreateMask3D scipion:CRYOEM_0000086 Filter volumes ProtFilterVolumes scipion:CRYOEM_0000087 Apply a mask to a volume (the mask can be defined by a description, for instance, a geometrical object) http://scipion.i2pc.es/ontology/CRYOEM_0000076 http://scipion.i2pc.es/ontology/CRYOEM_0000075 ProtMaskVolumes scipion:CRYOEM_0000088 Preprocess volumes (filters, ...) http://scipion.i2pc.es/ontology/CRYOEM_0000075 ProtPreprocessVolumes scipion:CRYOEM_0000089 Performs an operation with one or two volumes (calculator) http://scipion.i2pc.es/ontology/CRYOEM_0000075 ProtOperateVolumes scipion:CRYOEM_0000090 A subclass of particle picking algorithms that can perform this operation completely automatically. ProtParticlePickingAuto scipion:CRYOEM_0000091 Importing coordinates for tilt pairs ProtImportCoordinatesPairs scipion:CRYOEM_0000092 Computes a subset of particles according to a set of micrographs ProtSubSetByMic scipion:CRYOEM_0000093 Computes a subset of another set by a graphical intervention of the user ProtUserSubSet scipion:CRYOEM_0000094 This is a set of 2D averages SetOfAverages scipion:CRYOEM_0000095 SetOfMicrographs scipion:CRYOEM_0000096 SetOfMovies scipion:CRYOEM_0000097 SetOfParticles scipion:CRYOEM_0000098 SetOfVolumes scipion:CRYOEM_0000099 This is a set of images corresponding to a single particle in each ones of the frames. MovieParticle scipion:CRYOEM_0000100 Aligns a set of 2D images ProtAlign2D scipion:CRYOEM_0000101 Classifies a set of particles in 2D classes ProtClassify2D scipion:CRYOEM_0000102 Any protocol that applies a transformation to a SetOfParticles ProtProcessParticles scipion:CRYOEM_0000103 Extracts particles from a set of tilt pairs ProtExtractParticlesPair scipion:CRYOEM_0000104 This is a set of particles and its 2D representative Class2D scipion:CRYOEM_0000105 This is a set of particles and its 3D representative http://scipion.i2pc.es/ontology/CRYOEM_0000075 Class3D scipion:CRYOEM_0000106 SetOfMovieParticles scipion:CRYOEM_0000107 This is a set of volumes and its 3D representative ClassVol scipion:CRYOEM_0000108 Assigns a 2D alignment to a SetOfParticles ProtAlignmentAssign scipion:CRYOEM_0000109 Applies a filter ProtFilterParticles scipion:CRYOEM_0000110 Applies a mask ProtMaskParticles scipion:CRYOEM_0000111 Other operations on a SetOfParticles not considered on the other branches ProtOperateParticles 2021-03-09 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