A strong requirement to organize any filed of knowledge is the agreement in the terminology used. This has been a concern in Bioinformatics and has led to the development of a number of ontologies describing several aspects of the discipline (6, 7, 8, 9). Here we have developed a partial ontology to describe Nucleic Acids simulations. Its contents are used to qualify simulations, and power the search facility. Simulation browser tables, and simulation details (Figure S1B) include the set of keywords derived from the ontology. In its present state ontology represents merely a set of normalized terms, but it has been developed in a separate project and will be documented elsewhere.
Table of ontology terms (view in a ontology viewer)
| Hierarchic Id | Label | Description | |||||
| 1 | System | Composition of simulated system | |||||
| 101 | NA_Type | Type of Nucleic Acid | |||||
| 10101 | DNA | DNA | |||||
| 10102 | RNA | RNA | |||||
| 10103 | DNA-RNA_Hybrid | DNA-RNA Hybrid | |||||
| 10104 | PNA | PNA | |||||
| 10199 | OtherNAType | Other NA Types | |||||
| 102 | Structure_Type | Structure of the nucleic acid | |||||
| 10201 | SingleStrand | Single Strand | |||||
| 1020101 | Unpaired | Single Strand with no WC pairing | |||||
| 1020102 | Hairpin | Hairpin, WC pairing | |||||
| 10202 | Duplex | Duplex | |||||
| 1020201 | Canonical | Canonical WC pairing | |||||
| 102020101 | Linear | Linear duplex | |||||
| 10202010101 | Unpaired | Linear duplex with unpaired ends | |||||
| 10202010102 | BulgedLin | Linear duplex with unpaired fragments | |||||
| 102020102 | Circular | Circular duplex | |||||
| 1020202 | Hogsteen | Hogsteen pairing | |||||
| 10203 | Triplex | Triplex | |||||
| 1020301 | ParallelTrip | Parallel Triplex | |||||
| 1020302 | AntiParallelTrip | Antiparallel Triplex | |||||
| 10204 | Quadruplex | Quadruplex | |||||
| 1020401 | Gloop | Gloop | |||||
| 1020402 | ParallelQuad | Parallel Quadruplex | |||||
| 1020403 | AntiparallelQuad | Antiparallel Quadruplex | |||||
| 1020404 | IDNA | I-DNA | |||||
| 10205 | HollidayJnt | Holliday junction | |||||
| 10206 | 3WayJnt | 3-Way junction | |||||
| 10207 | Loop | Loop | |||||
| 10299 | OtherStructureType | Other structure types | |||||
| 103 | System_Type | Type of complex involving NA | |||||
| 10301 | Naked | Naked, uncomplexed | |||||
| 10302 | Complex | Complexed Nuc. Acid | |||||
| 1030201 | Protein-nuc | Complex Protein Nucl. Acid | |||||
| 103020101 | Enzymes | Complexed with Enzyme | |||||
| 103020102 | Binding | Binding Proteins | |||||
| 10302010201 | Regulatory | Regulatory Proteins (Trans Factors, etc) | |||||
| 10302010202 | SstrandBind | Single Strand Binders | |||||
| 10302010203 | Nucleosome | Nucleosome proteins | |||||
| 10302010299 | OtherBindProt | Other binding proteins | |||||
| 1030202 | Ligand-nuc | Ligand Nucleic Acid complexes | |||||
| 103020201 | Intercalator | Intercalator | |||||
| 103020202 | MinGBinder | Minor groove binder | |||||
| 103020203 | MajGBinder | Major groove binder | |||||
| 103020204 | HybridBinder | Hybrid binders | |||||
| 104 | OriginalHelicalConformation | Original helical conformation of the Nucleic Acids | |||||
| 10401 | A | A | |||||
| 10402 | B | B | |||||
| 10403 | Z | Z | |||||
| 10404 | Hogsteen | Hogsteen | |||||
| 10405 | MixedHConf | Mixed conformations | |||||
| 10499 | OtherHConf | Other Conformations | |||||
| 105 | SequenceModifications | Modifications of Nucleic Acids Sequence | |||||
| 10501 | ModifiedNucleotides | Modified Nucleotides | |||||
| 10502 | CrossLinked | CrossLinked | |||||
| 10503 | EpigeneticVariants | EpigeneticVariants | |||||
| 10504 | SequenceMismatches | Sequence Mismatches | |||||
| 10599 | OtherSeqMod | Other modifications | |||||
| 106 | SequenceFeatures | Relevant features related to sequence | |||||
| 10601 | PolyA | Poly A Track | |||||
| 1060101 | BrokenPolyA | Broken Poly A Track | |||||
| 10602 | PolyG | Poly G Track | |||||
| 10603 | DrewDickersonD | Drew Dickerson Dodecamer | |||||
| 10604 | SeqMismatch | Sequence Mismatches | |||||
| 2 | Simulation | Simulation Data | |||||
| 201 | SimConditions | Simulation settings | |||||
| 20101 | ForceField | ForceField | |||||
| 2010101 | Amber | Cornell ForceField family | |||||
| 201010101 | Parm99 | Parm99 | |||||
| 201010102 | ParmBSC0 | ParmBSC0 | |||||
| 201010103 | ParmBSC1 | ParmBSC1 | |||||
| 201010104 | ParmBSC0-OL1 | ParmBSC0-OL1 | |||||
| 201010105 | ParmBSC0-OL4 | ParmBSC0-OL4 | |||||
| 201010106 | ParmBSC0-OL1-OL4 | ParmBSC0-OL1-OL4 | |||||
| 201010107 | ParmBSC0-CG | ParmBSC0-Cheng/Garcia | |||||
| 2010102 | Charmm | Charmm ForceField family | |||||
| 201010201 | Charmm36 | Charm66 | |||||
| 2010199 | OtherFF | Other forcefields | |||||
| 20102 | Length | Length of simulations | |||||
| 2010201 | NanoSecondRange | Between 1 ns and 1 us | |||||
| 2010202 | MicroSecondRange | Over 1 us | |||||
| 20103 | Temperature | Simulation temperature | |||||
| 2010301 | Physiological | Physiological (around 298, 300K) | |||||
| 2010302 | NonPhysiological | NonPhysiological | |||||
| 20104 | Solvent | Solvent used in the simulation | |||||
| 2010401 | Water | Water only | |||||
| 2010402 | Mixed | Mixture water and other solvent | |||||
| 201040201 | Wat-Ethanol | Water Ethanol mixture | |||||
| 20105 | Charge | Charge model | |||||
| 2010501 | Electroneutral | Counter ions to compensate NA charge | |||||
| 2010502 | AddedSalt | Added counterions over charge compensation | |||||
| 201050201 | Physiological | Physiological (0.15M) | |||||
| 201050202 | NonPhysiological | NonPhysiological | |||||
| 20106 | IonParam | Parameter used for ion description | |||||
| 2010601 | Dang | Dang | |||||
| 2010602 | Cheatham | Cheatham | |||||
| 202 | TrajectoryType | Type of trajectory related to conformation changes | |||||
| 20201 | Equilibrium | Equilibrium (thermal fluctuations without major conf. Changes) | |||||
| 20202 | Folding | Folding or Unfolding | |||||
| 20203 | Transition | Transition between known conformations | |||||
| 20299 | OtherTrajType | Other type of trajectory | |||||
| 3 | Analysis | Analysis: any data derived from trajectories (simulated or experimental ensembles) | |||||
| 301 | TimeScope | Time scope of the analysis | |||||
| 30101 | Snapshot | Analysis made on a single snapshot | |||||
| 30102 | TimeAvg | Time averaged analysis | |||||
| 302 | FragmentScope | Fragment scope of the analysis | |||||
| 30201 | SingleBase | Analysis done on a single residue (base) | |||||
| 30202 | GroupAvg | Analysis done on a group of residues | |||||
| 3020201 | BP | Analysis done on a base pair (considering the main NA pairing) | |||||
| 3020202 | BPStep | Analysis done on a base pair step (2 consequent base pairs, considering the main pairing) | |||||
| 3020203 | SeqFragment | Analysis done on other sequence fragments | |||||
| 30203 | FullSystem | Analysis done on the complete system | |||||
| 30204 | Metatrajectory | Analysis done on a group of trajectories | |||||
| 30205 | ExpStructure | Analysis done on a experimental structure | |||||
| 303 | AnalysisType | Type of analysis | |||||
| 30301 | BackboneTorsions | Backbone Torsions | |||||
| 3030101 | BI/BIIPopulation | Proportion of BI/BII population | |||||
| 3030102 | SugarPuckering | Sugar puckering populations (N,E,S,W) | |||||
| 3030103 | AGCanonical | Proportion of canonical alpha/gamma torsions | |||||
| 30302 | HelicalParam | Helical parameters | |||||
| 3030201 | AxisBP | Base Pair Axis parameters | |||||
| 303020101 | AxisBPTras | Traslational Base Pair Axis parameters | |||||
| 30302010101 | Xdisp | X-Displacement | |||||
| 30302010102 | Ydisp | Y-Displacement | |||||
| 303020102 | AxisBPRot | Rotational Base Pair Axis parameters | |||||
| 30302010201 | Inclination | Inclination | |||||
| 30302010202 | Tip | Tip | |||||
| 3030202 | HelicalBP | Base Pair Helical parameters | |||||
| 303020201 | HelicalBPTrans | Translational Base Pair Helical parameters | |||||
| 30302020101 | Shear | Shear | |||||
| 30302020102 | Stretch | Stretch | |||||
| 30302020103 | Stagger | Stagger | |||||
| 303020202 | HelicaBRRot | Rotational Base Pair Helical parameters | |||||
| 30302020201 | Buckle | Buckle | |||||
| 30302020202 | Opening | Opening | |||||
| 30302020203 | Propeller | Propeller | |||||
| 3030203 | HelicalBPStep | Base Pair Step Helical parameters | |||||
| 303020301 | HelicaBPStepTrans | Translational Base Pair Step Helical parameters | |||||
| 30302030101 | Rise | Rise | |||||
| 30302030102 | Slide | Slide | |||||
| 30302030103 | Shift | Shift | |||||
| 303020302 | HelicaBPStepRot | Rotational Base Pair Step Helical parameters | |||||
| 30302030201 | Roll | Roll | |||||
| 30302030202 | Tilt | Tilt | |||||
| 30302030203 | Twist | Twist | |||||
| 30303 | GrooveAnalysis | Groove analysis | |||||
| 3030301 | MajorGroove | Major Groove | |||||
| 303030101 | MajGDepth | Depth of the Major Groove | |||||
| 303030102 | MinGWidth | Width of the Major Groove | |||||
| 3030302 | MinorGroove | Minor Groove | |||||
| 303030201 | MinGDepth | Depth of the Minor Groove | |||||
| 303030202 | MinGWidth | Width of the Mino Groove | |||||
| 30304 | Interactions | Analysis of interactions | |||||
| 3030401 | Hbonds | Hydrogen bonds (distances) | |||||
| 303040101 | WC | Watson-Crick Hydrogen Bonds | |||||
| 303040199 | Other | Other Hydrogend Bonds | |||||
| 3030402 | Stacking | Stacking interactions | |||||
| 303040201 | Wstrand | Stacking on the Watson Strand | |||||
| 303040202 | Cstrand | Stacking on the Crick Strand | |||||
| 303040203 | Crossed | Stacking between strands | |||||
| 30305 | NMR | NMR observables | |||||
| 3030501 | NOE | NOE | |||||
| 3030502 | JC | J-Couplings | |||||
| 30306 | Stiffness | Stiffness analysis | |||||
| 3030601 | ForceConstant | Force Constants | |||||
| 303060101 | Fctwist | Fctwist | |||||
| 303060102 | Fcroll | Fcroll | |||||
| 303060103 | Fctilt | Fctilt | |||||
| 303060104 | Fcrise | Fcrise | |||||
| 303060105 | Fcshift | Fcshift | |||||
| 303060106 | Fcslide | Fcslide | |||||
| 3030602 | ForceMatrix | Matrix of stiffness constants (twist, roll, tilt, rise, shift, slide) | |||||
| 3030603 | ForceProduct | DiagonalProduct | |||||
| 30307 | TrajectoryVideo | Video of Trajectory in standard formats | |||||
| 30308 | TrajectoryData | Trajectory data | |||||
| 3030801 | PCAZip | Trajectory in PCZ format | |||||
| 30309 | Cartesian | Cartesian analysis | |||||
| 3030901 | RMSd | Root Mean Square Deviation (RMSd) | |||||
| 3030902 | RMSf | Root Mean Square Fluctuation (RMSf) | |||||
| 3030903 | RadGyration | Radius of Gyration | |||||
| 3030904 | Bfactor | B - Factor | |||||
| 3030905 | AvgStruct | Average structure | |||||
| 30310 | PCAnalysis | Principal Component analysis | |||||
| 3031001 | EigenValues | PCA EigenValues | |||||
| 3031002 | NumberEV | Number of PCA EigenValues for a given variance | |||||
| 3031003 | EigenVal | Vector of eigenValues | |||||
| 3031002 | EigenVector | PCA EigenVectors | |||||
| 3031003 | TrajectoryProj | Projections of trajectory | |||||
| 3031004 | Animated trajectory | Trajectory animated following given eigenvectors | |||||
| 3031005 | Entropy | Entropy prediction | |||||
| 3031005 | Schlitter | Schlitter | |||||
| 303100502 | Androcioaei | Entropy prediction using Androcioaei protocol | |||||
| 3031006 | Variance | Variance measured in the trajectory | |||||
| 30311 | ContactMaps | Contact Maps | |||||