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