Bio-Homology-InterologWalk
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scripts/Data/psi-mi.obo view on Meta::CPAN
[Term]
id: MI:0002
name: participant identification method
def: "Method to determine the molecules involved in the interaction." [PMID:14755292]
subset: PSI-MI slim
synonym: "participant detection" EXACT PSI-MI-alternate []
synonym: "participant ident" EXACT PSI-MI-short []
relationship: part_of MI:0000 ! molecular interaction
[Term]
id: MI:0003
name: feature detection method
def: "Method to determine the features of the proteins involved in the interaction." [PMID:14755292]
subset: PSI-MI slim
synonym: "feature detection" EXACT PSI-MI-short []
relationship: part_of MI:0000 ! molecular interaction
[Term]
id: MI:0004
name: affinity chromatography technology
def: "This class of approaches is characterised by the use of affinity resins as tools to purify molecule of interest (baits) and their binding partners. The baits can be captured by a variety of high affinity ligands linked to a resin - for example,...
subset: PSI-MI slim
synonym: "affinity chrom" EXACT PSI-MI-short []
synonym: "Affinity purification" EXACT PSI-MI-alternate []
is_a: MI:0091 ! chromatography technology
is_a: MI:0400 ! affinity technology
[Term]
id: MI:0005
name: alanine scanning
def: "This approach is used to identify the residues that are involved in an interaction. Several variants of the native protein are prepared by sequentially mutating each residue of interest to an alanine. The mutated proteins are expressed and pro...
subset: PSI-MI slim
is_a: MI:0810 ! substitution analysis
[Term]
id: MI:0006
name: anti bait coimmunoprecipitation
def: "A specific antibody for the molecule of interest (bait) is available, this is used to generate a high affinity resin to capture the endogenous bait present in a sample." [PMID:7708014]
subset: PSI-MI slim
synonym: "anti bait coip" EXACT PSI-MI-short []
is_a: MI:0019 ! coimmunoprecipitation
[Term]
id: MI:0007
name: anti tag coimmunoprecipitation
def: "A specific antibody for the molecule of interest is not available, therefore the bait protein is expressed as a hybrid protein fused to a tag peptide/protein for which efficient and specific antibodies or a specific ligand are available." [PMID...
subset: PSI-MI slim
synonym: "anti tag coip" EXACT PSI-MI-short []
is_a: MI:0019 ! coimmunoprecipitation
[Term]
id: MI:0008
name: array technology
def: "In this class of methodologies, the molecules to be tested are presented ordered in an array format (typically at high density) on planar supports. The characteristics and chemical nature of the planar support can vary. This format permits the ...
subset: PSI-MI slim
is_a: MI:0400 ! affinity technology
[Term]
id: MI:0009
name: bacterial display
def: "The protein of interest is presented on the outer membrane of Gram negative bacteria by expressing it as a fusion partner to peptide signals that direct heterologous proteins to the cell surface. For instance, a single chain Fv (scFv) antibody ...
subset: PSI-MI slim
is_a: MI:0034 ! display technology
is_a: MI:0054 ! fluorescence-activated cell sorting
[Term]
id: MI:0010
name: beta galactosidase complementation
def: "Beta-galactosidase activity can be used to monitor the interaction of chimeric proteins. Pairs of inactive beta gal deletion mutants are capable of complementing to restore activity when fused to interacting protein partners. Critical to the su...
subset: PSI-MI slim
synonym: "beta galactosidase" EXACT PSI-MI-short []
is_a: MI:0228 ! cytoplasmic complementation assay
[Term]
id: MI:0011
name: beta lactamase complementation
def: "This strategy is based on a protein fragment complementation assay (PCA) of the enzyme TEM-1 beta-lactamase. The approach includes a simple colorimetric in vitro assays using the cephalosporin nitrocefin and assays in intact cells using the flu...
subset: PSI-MI slim
synonym: "beta lactamase" EXACT PSI-MI-short []
is_a: MI:0228 ! cytoplasmic complementation assay
[Term]
id: MI:0012
name: bioluminescence resonance energy transfer
def: "In this variation of the FRET assay the donor fluorophore is replaced by a luciferase (typically Renilla luciferase). In the presence of its substrate, the luciferase catalyses a bioluminescent reaction that excites the acceptor fluorophore thr...
subset: PSI-MI slim
synonym: "BRET" EXACT PSI-MI-alternate []
synonym: "bret" EXACT PSI-MI-short []
synonym: "LRET" EXACT PSI-MI-alternate []
is_a: MI:0051 ! fluorescence technology
[Term]
id: MI:0013
name: biophysical
def: "The application of physical principles and methods to biological experiments." [PMID:14755292]
subset: PSI-MI slim
is_a: MI:0045 ! experimental interaction detection
[Term]
id: MI:0014
name: adenylate cyclase complementation
def: "Adenylate cyclase is encoded by the cyaA gene and contains a catalytic domain which can be proteolytically cleaved into two complementary fragments, T25 and T18, which remain associated in the presence of calmodulin in a fully active ternary co...
subset: PSI-MI slim
synonym: "adenylate cyclase" EXACT PSI-MI-short []
synonym: "bacterial two-hybrid" EXACT PSI-MI-alternate []
is_a: MI:0228 ! cytoplasmic complementation assay
[Term]
id: MI:0016
name: circular dichroism
def: "Circular dichroism (CD) is observed when optically active molecules absorb left and right hand circularly polarized light slightly differently. Linearly polarized light can be viewed as a superposition of two components of circularly polarized ...
subset: PSI-MI slim
synonym: "CD" EXACT PSI-MI-alternate []
synonym: "cd" EXACT PSI-MI-short []
is_a: MI:0013 ! biophysical
[Term]
id: MI:0017
name: classical fluorescence spectroscopy
def: "Proteins contain endogenous fluorophores such as tryptophan residue and heme or flavins groups. Protein folding and protein-protein interaction can be studied by monitoring changes in the tryptophan environment detected by changes in its intrin...
subset: PSI-MI slim
synonym: "fluorescence spectr" EXACT PSI-MI-short []
is_a: MI:0051 ! fluorescence technology
[Term]
id: MI:0018
name: two hybrid
def: "The classical two-hybrid system is a method that uses transcriptional activity as a measure of protein-protein interaction. It relies on the modular nature of many site-specific transcriptional activators (GAL 4) , which consist of a DNA-bindin...
subset: PSI-MI slim
synonym: "2 hybrid" EXACT PSI-MI-short []
synonym: "2-hybrid" EXACT PSI-MI-alternate []
synonym: "2H" EXACT PSI-MI-alternate []
synonym: "2h" EXACT PSI-MI-alternate []
synonym: "classical two hybrid" EXACT PSI-MI-alternate []
synonym: "Gal4 transcription regeneration" EXACT PSI-MI-alternate []
synonym: "two-hybrid" EXACT PSI-MI-alternate []
synonym: "yeast two hybrid" EXACT PSI-MI-alternate []
is_a: MI:0232 ! transcriptional complementation assay
[Term]
id: MI:0019
name: coimmunoprecipitation
def: "In this approach an antibody, specific for the molecule of interest (bait) or any tag expressed within a fusion protein, is used to separate the bait from a protein mixture or a cell lysate and to capture its ligand simultaneously. The partners...
subset: PSI-MI slim
synonym: "co-immunoprecipitation" EXACT PSI-MI-alternate []
synonym: "Co-IP" EXACT PSI-MI-alternate []
synonym: "CoIp" EXACT PSI-MI-alternate []
synonym: "coip" EXACT PSI-MI-short []
synonym: "immunoprecipitation" EXACT PSI-MI-alternate []
is_a: MI:0004 ! affinity chromatography technology
[Term]
id: MI:0020
name: transmission electron microscopy
def: "During the treatment for microscope analysis a tissue section is incubated with high-specificity antibodies coupled to heavy metals (gold). Any tissue section can then be analysed by electron microscopy to localise the target proteins within th...
subset: PSI-MI slim
synonym: "tem" EXACT PSI-MI-short []
is_a: MI:0040 ! electron microscopy
[Term]
id: MI:0021
name: colocalization by fluorescent probes cloning
scripts/Data/psi-mi.obo view on Meta::CPAN
[Term]
id: MI:0025
name: copurification
def: "Approaches designed to separate cell components on the basis of their physicochemical properties. The observation that two or more proteins copurify in one or several conditions is taken as an indication that they form a molecular complex.\nOBS...
subset: PSI-MI slim
is_obsolete: true
[Term]
id: MI:0026
name: correlated mutations
def: "Pairs of multiple alignments of orthologous sequences are used to identify potential interacting partners as proteins that show covariation of their residue identities between different species. Proteins displaying inter-protein correlated muta...
subset: PSI-MI slim
is_a: MI:0101 ! sequence based prediction
is_a: MI:0660 ! feature prediction
[Term]
id: MI:0027
name: cosedimentation
def: "Separation of a protein mixture under the influence of artificial gravity." [PMID:14755292]
subset: PSI-MI slim
is_a: MI:0401 ! biochemical
[Term]
id: MI:0028
name: cosedimentation in solution
def: "The ultracentrifuge can be used to characterise and/or purify macromolecules in solution according to their mass and hydrodynamic properties. Sedimentation studies provide information about the molecular weight and shape of a molecule. It is al...
subset: PSI-MI slim
synonym: "solution sedimentati" EXACT PSI-MI-short []
is_a: MI:0027 ! cosedimentation
[Term]
id: MI:0029
name: cosedimentation through density gradient
def: "Sedimentation through a density gradient measures the sedimentation rate of a mixture of proteins through either a glycerol or sucrose gradient. Two interacting proteins will sediment mostly as a complex at concentrations above the binding cons...
subset: PSI-MI slim
synonym: "density sedimentatio" EXACT PSI-MI-short []
is_a: MI:0027 ! cosedimentation
[Term]
id: MI:0030
name: cross-linking study
def: "Analysis of complexes obtained by chemical treatments that promote the formation of covalent bonds among molecules in close proximity." [PMID:14755292]
subset: PSI-MI slim
synonym: "crosslink" EXACT PSI-MI-short []
is_a: MI:0401 ! biochemical
[Term]
id: MI:0031
name: protein cross-linking with a bifunctional reagent
def: "A cross-linker is a bifunctional molecule having two reactive ends linked by a spacer, often containing a disulfide bond. Cross-linkers induce the formation of covalent bonds among proteins that are neighbours. When a reducing agent is added th...
subset: PSI-MI slim
synonym: "Label transfer techniques" EXACT PSI-MI-alternate []
synonym: "Photoaffinity labelling" EXACT PSI-MI-alternate []
synonym: "protein crosslink" EXACT PSI-MI-short []
is_a: MI:0030 ! cross-linking study
[Term]
id: MI:0032
name: de novo protein sequencing by mass spectrometry
def: "The strategy to determine the complete amino acid sequence of a protein by mass spectrometry relies on the generation of a nested set of fragments differing by one amino acid. This reveals the identity of the residue that has been removed at ea...
subset: PSI-MI slim
synonym: "ms protein sequence" EXACT PSI-MI-short []
synonym: "MS/MS" RELATED []
is_a: MI:0093 ! protein sequence identification
is_a: MI:0427 ! Identification by mass spectrometry
is_a: MI:0659 ! experimental feature detection
[Term]
id: MI:0033
name: deletion analysis
def: "In this approach, once a molecule is demonstrated to participate in an interaction, several deletion derivatives are produced and tested in the binding assay to identify the minimal fragment (domain) that can still support the interaction." [PM...
subset: PSI-MI slim
is_a: MI:0074 ! mutation analysis
[Term]
id: MI:0034
name: display technology
def: "All the methods that permit the physical linking of a protein/peptide to its coding sequence. As a consequence affinity purification of the displayed peptide results in the genetic enrichment of its coding sequence. By these technologies genes ...
subset: PSI-MI slim
is_a: MI:0400 ! affinity technology
[Term]
id: MI:0035
name: docking
def: "Predicts the structure of a molecular complex from the unbound structures of its components. The initial approach in the majority of docking procedures is based largely on the 'rigid-body' assumption, whereby the proteins are treated as solid o...
subset: PSI-MI slim
is_a: MI:0105 ! structure based prediction
is_a: MI:0577 ! feature prediction from structure
[Term]
id: MI:0036
name: domain fusion
def: "The rosetta stone, or domain fusion procedure, is based on the assumption that proteins whose homologues in other organisms happen to be fused into a single protein chain are likely to interact or to be functionally related." [PMID:10573422]
subset: PSI-MI slim
synonym: "Rosetta Stone" EXACT PSI-MI-alternate []
is_a: MI:0058 ! genome based prediction
is_a: MI:0101 ! sequence based prediction
[Term]
id: MI:0037
name: domain profile pairs
def: "This approach uses a protein interaction network of a given organism to infer interaction in another organism using information about the interacting region. The regions or domains involved in interactions are clustered if they share sequence s...
subset: PSI-MI slim
is_a: MI:0046 ! experimental knowledge based
is_a: MI:0101 ! sequence based prediction
is_a: MI:0660 ! feature prediction
[Term]
id: MI:0038
name: dynamic light scattering
def: "In dynamic light scattering, particle diffusion in solution gives rise to fluctuations in the intensity of the scattered light on the microsecond scale. The hydrodynamic radius of the particles can be easily calculated." [PMID:9013660]
subset: PSI-MI slim
synonym: "dls" EXACT PSI-MI-short []
is_a: MI:0067 ! light scattering
[Term]
id: MI:0039
name: edman degradation
def: "In this procedure the N-terminus amino acid is cleaved from a polypeptide and identified by high-pressure liquid chromatography. The cycle is repeated on the ever-shortening polypeptide until all the residues are identified. On average only 20-...
subset: PSI-MI slim
is_a: MI:0433 ! partial identification of protein sequence
[Term]
id: MI:0040
name: electron microscopy
def: "Electron microscopy methods provide insights into the structure of biological macromolecules and their supramolecular assemblies. Resolution is on average around 10 Angstroms but can reach the atomic level when the samples analysed are 2D cryst...
subset: PSI-MI slim
synonym: "Electron cryomicroscopy" EXACT PSI-MI-alternate []
synonym: "Electron crystallography" EXACT PSI-MI-alternate []
is_a: MI:0428 ! imaging technique
[Term]
id: MI:0041
name: electron nuclear double resonance
def: "A combination of NMR and EPR. The lines in the EPR spectrum that are caused by coupling of an unpaired electron nearby nuclei change in intensity when these nuclei are excited at their NMR frequency." [PMID:11817959, PMID:11988476, PMID for app...
subset: PSI-MI slim
synonym: "ENDOR" EXACT PSI-MI-alternate []
synonym: "endor" EXACT PSI-MI-short []
is_a: MI:0043 ! electron resonance
[Term]
id: MI:0042
name: electron paramagnetic resonance
def: "EPR (also called ESR, Electron Spin Resonance) spectroscopy is analogous to NMR, but is based on the excitation of unpaired electrons instead of nuclei. Unpaired (single) electrons are only found in radicals and some metal ions (paramagnetic sp...
subset: PSI-MI slim
synonym: "EPR" EXACT PSI-MI-alternate []
synonym: "epr" EXACT PSI-MI-short []
synonym: "ESR" EXACT PSI-MI-alternate []
is_a: MI:0043 ! electron resonance
[Term]
id: MI:0043
name: electron resonance
def: "A form of spectroscopy in which the absorption of microwave by a sample in a strong magnetic field is used to study atoms or molecules with unpaired electrons." [PMID:14755292]
subset: PSI-MI slim
is_a: MI:0013 ! biophysical
is_a: MI:0659 ! experimental feature detection
[Term]
id: MI:0045
name: experimental interaction detection
def: "Methods based on laboratory experiments to determine an interaction." [PMID:14755292]
subset: PSI-MI slim
synonym: "experimental interac" EXACT PSI-MI-short []
is_a: MI:0001 ! interaction detection method
[Term]
id: MI:0046
name: experimental knowledge based
def: "Predictive algorithms that rely on the information obtained by experimental results." [PMID:14755292]
subset: PSI-MI slim
synonym: "experimental info" EXACT PSI-MI-short []
is_a: MI:0063 ! interaction prediction
[Term]
id: MI:0047
name: far western blotting
def: "Proteins are fractionated by PAGE (SDS-polyacrylamide gel electrophoresis), transferred to a nitrocellulose membrane and tested for the ability to bind to a protein, a peptide, or any other ligand. Cell lysates can also be fractionated before g...
subset: PSI-MI slim
synonym: "Affinity blotting" EXACT PSI-MI-alternate []
is_a: MI:0892 ! solid phase assay
[Term]
id: MI:0048
name: filamentous phage display
def: "Filamentous phages (M13, f1, fd) have been extensively used to develop and implement the technology of phage display. Repertoires of relatively short peptides of random amino acid sequences or cDNA libraries have been constructed and searched s...
subset: PSI-MI slim
synonym: "filamentous phage" EXACT PSI-MI-short []
is_a: MI:0084 ! phage display
[Term]
id: MI:0049
name: filter binding
def: "A method in which separation depends upon the ability of one participant to bind to a filter or membrane which the other participants do not. Molecules interacting with the bound molecule will also be retain on the filter. For example, proteins...
subset: PSI-MI slim
synonym: "Filter overlay assay" EXACT PSI-MI-alternate []
is_a: MI:0892 ! solid phase assay
[Term]
id: MI:0050
name: flag tag coimmunoprecipitation
def: "The protein of interest is expressed as a fusion to the peptide DYKDDDDKV for which antibodies are commercially available. Sometimes multiple copies of the peptide are fused in tandem.\nOBSOLETE redundant term. Map to feature type: flag-tagged ...
subset: PSI-MI slim
synonym: "flag tag coip" EXACT PSI-MI-short []
is_obsolete: true
[Term]
id: MI:0051
name: fluorescence technology
def: "Techniques based upon the measurement of the emission of one or more photons by a molecule activated by the absorption of a quantum of electro-magnetic radiation. Typically the emission, which is characterised by a wavelength that is longer tha...
subset: PSI-MI slim
synonym: "fluorescence" EXACT PSI-MI-short []
is_a: MI:0013 ! biophysical
[Term]
id: MI:0052
name: fluorescence correlation spectroscopy
def: "FCS monitors the random motion of fluorescently labelled molecules inside a defined volume irradiated by a focused laser beam. These fluctuations provide information on the rate of diffusion or diffusion time of a particle and this is directly ...
subset: PSI-MI slim
synonym: "FCS" EXACT PSI-MI-alternate []
synonym: "fcs" EXACT PSI-MI-short []
is_a: MI:0051 ! fluorescence technology
[Term]
id: MI:0053
name: fluorescence polarization spectroscopy
def: "Because of the long lifetimes of excited fluorescent molecules (nanoseconds), fluorescence can be used to monitor the rotational motion of molecules, which occurs on this timescale. This is accomplished experimentally by excitation with plane-p...
subset: PSI-MI slim
synonym: "Fluorescence anisotropy" EXACT PSI-MI-alternate []
synonym: "FPS" EXACT PSI-MI-alternate []
synonym: "fps" EXACT PSI-MI-short []
is_a: MI:0051 ! fluorescence technology
[Term]
id: MI:0054
name: fluorescence-activated cell sorting
def: "Cells in suspension flow through a laser beam, the scattered light or emitted fluorescence is measured, filtered and converted to digital values. Cells can be sorted according to their properties. Using flow cytometry, any fluorescent or light ...
subset: PSI-MI slim
synonym: "FACS" EXACT PSI-MI-alternate []
synonym: "facs" EXACT PSI-MI-short []
synonym: "Flow cytometry" EXACT PSI-MI-alternate []
is_a: MI:0051 ! fluorescence technology
[Term]
id: MI:0055
name: fluorescent resonance energy transfer
def: "FRET is a quantum mechanical process involving the radiationless transfer of energy from a donor fluorophore to an appropriately positioned acceptor fluorophore. The fluorophores are genetically fused to the protein in analysis and cotransfecte...
subset: PSI-MI slim
synonym: "FRET" EXACT PSI-MI-alternate []
synonym: "fret" EXACT PSI-MI-short []
synonym: "FRET analysis" EXACT PSI-MI-alternate []
synonym: "RET" EXACT PSI-MI-alternate []
is_a: MI:0051 ! fluorescence technology
[Term]
id: MI:0056
name: full identification by DNA sequencing
def: "Sequencing occurs during the course of the experiment. The DNA to be sequenced is used as template for the in vitro synthesis, by DNA polymerase, of a set of partial replicas, all beginning at the same place, but terminating at different points...
subset: PSI-MI slim
synonym: "full dna sequence" EXACT PSI-MI-short []
is_a: MI:0078 ! nucleotide sequence identification
is_a: MI:0659 ! experimental feature detection
[Term]
id: MI:0057
name: gene neighbourhood
def: "Gene pairs that show a conserved topological neighbourhood in many prokaryotic genomes are considered by this approach to encode interacting or functionally related proteins. By measuring the physical distance of any given gene pair in differen...
subset: PSI-MI slim
is_a: MI:0058 ! genome based prediction
[Term]
id: MI:0058
name: genome based prediction
def: "Methods that require fully sequenced genomes either because they are based on the comparison of genome topology or on the identification of orthologous sequences in different genomes." [PMID:14755292]
subset: PSI-MI slim
synonym: "genome prediction" EXACT PSI-MI-short []
is_a: MI:0063 ! interaction prediction
[Term]
id: MI:0059
name: gst pull down
def: "The bait protein is expressed and purified as a fusion to the glutathione S-tranferase protein. The bait protein is normally attached to a glutathione sepharose resin or alternatively to a support containing an anti-GST antibody.\nOBSOLETE redu...
subset: PSI-MI slim
is_obsolete: true
[Term]
id: MI:0060
name: ha tag coimmunoprecipitation
def: "The protein of interest is expressed as a fusion to the peptide YPYDVPDYA (a fragment of the influenza hemaglutinin protein) for which antibodies are commercially available.\nOBSOLETE redundant term. Map to feature type : ha-tagged (MI:0520) an...
subset: PSI-MI slim
synonym: "ha tag coip" EXACT PSI-MI-short []
is_obsolete: true
[Term]
id: MI:0061
name: his pull down
def: "The bait protein is expressed and purified fused to an amino or carboxyterminal tail containing a variable number of histidines. The bait protein is normally attached to a metal (usually nickel) resin.\nOBSOLETE redundant term. Map to feature t...
subset: PSI-MI slim
is_obsolete: true
[Term]
id: MI:0062
name: his tag coimmunoprecipitation
def: "The protein of interest is expressed as a fusion to a poly-His tail. This permits purification by chromatography over a metal column or by binding to commercially available anti poly-His antibodies.\nOBSOLETE redundant term. Map to feature type...
subset: PSI-MI slim
synonym: "his tag coip" EXACT PSI-MI-short []
is_obsolete: true
[Term]
id: MI:0063
name: interaction prediction
def: "Computational methods to predict an interaction." [PMID:14755292]
subset: PSI-MI slim
synonym: "in silico methods" EXACT PSI-MI-alternate []
synonym: "predicted interac" EXACT PSI-MI-short []
is_a: MI:0001 ! interaction detection method
[Term]
id: MI:0064
name: interologs mapping
def: "Protein interactions, experimentally detected in an organism, are extended to a second organism assuming that homologue proteins, in different organisms, maintain their interaction properties." [PMID:11731503]
subset: PSI-MI slim
synonym: "Homology based interaction prediction" EXACT PSI-MI-alternate []
is_a: MI:0046 ! experimental knowledge based
is_a: MI:0101 ! sequence based prediction
[Term]
id: MI:0065
name: isothermal titration calorimetry
def: "Isothermal titration calorimetry (ITC) measures directly the energy associated with a chemical reaction triggered by the mixing of two components. A typical ITC experiment is carried out by the stepwise addition of one of the reactants (~10-6 L...
subset: PSI-MI slim
synonym: "ITC" EXACT PSI-MI-alternate []
synonym: "itc" EXACT PSI-MI-short []
is_a: MI:0013 ! biophysical
[Term]
id: MI:0066
name: lambda phage display
def: "Morphologically classified as one of the siphoviridae, lambda is a temperate bacteriophage of E.coli, with a double-stranded DNA genome. It has an icosahedral head attached to a flexible helical tail. Both the tail protein pV and the head prote...
subset: PSI-MI slim
synonym: "lambda phage" EXACT PSI-MI-short []
is_a: MI:0084 ! phage display
[Term]
id: MI:0067
name: light scattering
def: "Dynamic and static laser light scattering probes the size, shape, and structure of biological macromolecules or of their assemblies. A beam is focused on an optically clear cylindrical cell containing the sample. Most of the light passes direct...
subset: PSI-MI slim
is_a: MI:0013 ! biophysical
[Term]
id: MI:0068
name: mass detection of residue modification
def: "Mass spectrometry can be used to characterise chemical modifications within peptides. One approach consists in the observation of a mass difference when a sample is treated with an enzyme that can specifically remove a peptide modification, for...
subset: PSI-MI slim
synonym: "modified residue ms" EXACT PSI-MI-short []
is_a: MI:0659 ! experimental feature detection
[Term]
id: MI:0069
name: mass spectrometry studies of complexes
def: "Mass spectrometric approaches to the study of protein in complexes permits the identification of subunit stoichiometry and transient associations. By preserving complexes intact in the mass spectrometer, mass measurement can be used for monitor...
subset: PSI-MI slim
synonym: "ms of complexes" EXACT PSI-MI-short []
is_a: MI:0943 ! detection by mass spectrometry
[Term]
id: MI:0070
name: mobility shift
def: "Protein modifications can be identified by gel electrophoresis since any change in the mass and/or the charge of the protein can alter its mobility in PAGE. Although this method does not allow the unequivocal identification of the type of modif...
subset: PSI-MI slim
is_a: MI:0659 ! experimental feature detection
[Term]
id: MI:0071
name: molecular sieving
def: "In sizing columns (gel filtration), the elution position of a protein or of a complex depends on its Stokes radius. Molecules with a radius that is smaller than the bead size are retained and retarded by the interaction with the matrix. The obs...
subset: PSI-MI slim
synonym: "Gel Filtration" EXACT PSI-MI-alternate []
synonym: "Siezing column" EXACT PSI-MI-alternate []
synonym: "Size Exclusion Chromatography" EXACT PSI-MI-alternate []
is_a: MI:0013 ! biophysical
is_a: MI:0091 ! chromatography technology
[Term]
id: MI:0072
name: monoclonal antibody western blot
def: "Western blot assay carried out using monospecific antibodies produced in the supernatant of a cell line obtained by fusing a lymphocyte B to a myeloma cell line or selected by phage display technology." [PMID:14755292]
subset: PSI-MI slim
synonym: "monoclonal western" EXACT PSI-MI-short []
is_a: MI:0113 ! western blot
[Term]
id: MI:0073
name: mrna display
def: "This method relies on the covalent coupling of mRNA to the nascent polypeptide. The mRNA (natural or artificial) is first covalently linked to a short DNA linker carrying a puromycin moiety. The mRNA mixture is then translated in vitro. When th...
subset: PSI-MI slim
is_a: MI:0034 ! display technology
[Term]
id: MI:0074
name: mutation analysis
def: "Mutant molecules are produced by random or directed techniques and assayed for their ability to support binding." [PMID:14755292]
subset: PSI-MI slim
is_a: MI:0659 ! experimental feature detection
[Term]
id: MI:0075
name: myc tag coimmunoprecipitation
def: "The protein of interest is expressed as a fusion to the peptide EUKLISEED (a fragment of the Myc oncogene protein) for which antibodies are commercially available. Sometimes multiple copies of the peptide are fused in tandem.\nOBSOLETE redundan...
subset: PSI-MI slim
synonym: "myc tag coip " EXACT PSI-MI-short []
is_obsolete: true
[Term]
id: MI:0076
name: neural network on interface properties
def: "Neural networks are trained on the properties of residues belonging to a cluster of residues that are neighbours in space on protein surface. The predictor permits the inference of the residues that are likely to be on an interaction interface....
subset: PSI-MI slim
synonym: "interface predictor" EXACT PSI-MI-short []
is_a: MI:0577 ! feature prediction from structure
[Term]
id: MI:0077
name: nuclear magnetic resonance
def: "NMR requires a small volume of concentrated compound solution that is placed in a strong magnetic field. Certain atomic nuclei, and in particular hydrogen, have a magnetic moment or spin; that is, they have an intrinsic magnetisation, like a ba...
subset: PSI-MI slim
synonym: "NMR" EXACT PSI-MI-alternate []
synonym: "nmr" EXACT PSI-MI-short []
is_a: MI:0013 ! biophysical
is_a: MI:0659 ! experimental feature detection
[Term]
id: MI:0078
name: nucleotide sequence identification
def: "Identification of a nucleotide sequence. Depending on the experimental design, nucleotide sequence can be determined before the interaction detection while building a collection of clones or after the selection of randomly generated clones." [P...
subset: PSI-MI slim
synonym: "nucleotide sequence" EXACT PSI-MI-short []
synonym: "sequence cloning" EXACT PSI-MI-alternate []
is_a: MI:0661 ! experimental participant identification
[Term]
id: MI:0079
name: other biochemical technologies
def: "Experimental methods that could not be assigned to the other large group of technologies.\nOBSOLETE use biochemical (MI:0401) instead." [PMID:14755292]
subset: PSI-MI slim
synonym: "other biochemic tech" EXACT PSI-MI-short []
is_obsolete: true
[Term]
id: MI:0080
name: partial dna sequence identification by hybridization
def: "Genes are recognised by hybridization of a probe with a fragment of the gene sequence." [PMID:14755292]
subset: PSI-MI slim
synonym: "partial dna sequence" EXACT PSI-MI-short []
is_a: MI:0078 ! nucleotide sequence identification
[Term]
id: MI:0081
name: peptide array
def: "The peptide synthesis methods offer numerous opportunities to synthesise and subsequently screen large arrays of synthetic peptides on planar cellulose supports. Discrete spots are arranged as arrays on membrane sheets where each spot is indivi...
subset: PSI-MI slim
is_a: MI:0008 ! array technology
[Term]
id: MI:0082
name: peptide massfingerprinting
def: "This approach leads to protein identification by matching peptide masses, as measured by mass spectrometry, to the ones calculated from in silico fragmentation of a protein sequence database. A peptide mixture from a tryptic digest is analysed ...
subset: PSI-MI slim
synonym: "fingerprinting" EXACT PSI-MI-short []
is_a: MI:0427 ! Identification by mass spectrometry
is_a: MI:0433 ! partial identification of protein sequence
is_a: MI:0815 ! confirmation by molecular weight
[Term]
id: MI:0083
name: peptide synthesis
def: "When one of the partners participates in the interaction with a relatively short peptide fragment, it is often convenient to precisely identify the minimal region that supports the interaction by synthesising a series of overlapping peptides an...
subset: PSI-MI slim
is_a: MI:0093 ! protein sequence identification
[Term]
id: MI:0084
name: phage display
def: "Peptide sequences or entire proteins can be displayed on phage capsids by fusion to coat proteins to generate a library of fusion phages each displaying a different peptide. Such a library can then be exploited to identify specific phages that ...
subset: PSI-MI slim
is_a: MI:0034 ! display technology
[Term]
id: MI:0085
name: phylogenetic profile
def: "The phylogenetic profile of a protein stores information about the presence and the absence of that protein in a set of genomes. By clustering identical or similar profiles, proteins with similar functions and potentially interacting are identi...
subset: PSI-MI slim
is_a: MI:0058 ! genome based prediction
[Term]
id: MI:0086
name: polyclonal antibody western blot
def: "Western blot assay carried out using a mixture of different antibodies that represent the immune response, normally in an experimental animal, to the protein of interest." [PMID:14755292]
subset: PSI-MI slim
synonym: "polyclonal western" EXACT PSI-MI-short []
is_a: MI:0113 ! western blot
[Term]
id: MI:0087
name: predictive text mining
def: "Methods based on natural language processing to detect possible interactions between proteins (direct physical interactions or indirect genetic interactions). This includes the detection of non ambiguous protein or gene names and analysis of th...
subset: PSI-MI slim
synonym: "predictive tm" EXACT PSI-MI-short []
is_a: MI:0110 ! text mining
[Term]
id: MI:0088
name: primer specific pcr
def: "Sequences can be identified in a DNA mixture by launching a PCR (Polymerase Chain Reaction) controlled by sequence specific primers. Such reaction starts only when the hybridization of the primer with a complementary sequence occurs." [PMID:147...
subset: PSI-MI slim
is_a: MI:0080 ! partial dna sequence identification by hybridization
[Term]
id: MI:0089
name: protein array
def: "The protein array technology allows the screening of biochemical activities or binding abilities of hundreds or thousands of protein samples in parallel. After synthesis and purification by high-throughput methodologies, the proteins are printe...
subset: PSI-MI slim
is_a: MI:0008 ! array technology
[Term]
id: MI:0090
name: protein complementation assay
def: "The function of numerous proteins or ribonucleic particles (enzymes, transcription factors, and others) can be rationally dissected into two fragments that fold autonomously but cannot complement to reconstitute the complex function, unless the...
subset: PSI-MI slim
synonym: "complementation" EXACT PSI-MI-short []
synonym: "PCA" EXACT PSI-MI-alternate []
is_a: MI:0045 ! experimental interaction detection
[Term]
id: MI:0091
name: chromatography technology
def: "Used to separate and/or analyse complex mixtures. The components to be separated are distributed between two phases: a stationary phase (bed) and a mobile phase which percolates through the stationary bed. The nature of the two phases determine...
subset: PSI-MI slim
synonym: "chromatography" EXACT PSI-MI-short []
synonym: "column chromatography" EXACT PSI-MI-alternate []
is_a: MI:0401 ! biochemical
[Term]
id: MI:0092
name: protein in situ array
def: "Protein In Situ Array is a method by which protein arrays are rapidly generated in one step directly from DNA, by cell-free protein expression and simultaneous in situ immobilisation at a surface. Individual genes or fragments are produce by PC...
subset: PSI-MI slim
synonym: "PISA" EXACT PSI-MI-alternate []
synonym: "pisa" EXACT PSI-MI-short []
is_a: MI:0089 ! protein array
[Term]
id: MI:0093
name: protein sequence identification
def: "Single amino acid identification along a protein sequence." [PMID:14755292]
subset: PSI-MI slim
synonym: "protein sequence" EXACT PSI-MI-short []
is_a: MI:0661 ! experimental participant identification
[Term]
id: MI:0094
name: protein staining
def: "A wide range of dyes have been used over the years to visualise proteins in polyacrylamide gels - Coomasie Blue and silver-staining being two classical methods. Fluorescent dyes such as Nile Red and SYPRO Orange are now increasingly used due to...
subset: PSI-MI slim
is_a: MI:0659 ! experimental feature detection
[Term]
id: MI:0095
name: proteinchip(r) on a surface-enhanced laser desorption/ionization
def: "ProteinChip(r) Array technology is a surface-enhanced laser desorption/ionization (SELDI) approach (Ciphergen Biosystems Inc. Fremont, CA, USA) for sample fractionation accomplished by retentate chromatography. Retentate chromatography is perfo...
subset: PSI-MI slim
synonym: "seldi chip" EXACT PSI-MI-short []
synonym: "SELDI ProteinChip" EXACT PSI-MI-alternate []
is_a: MI:0089 ! protein array
[Term]
id: MI:0096
name: pull down
def: "A specific affinity chromatography method where a molecule of interest (bait) is expressed as a fusion to an affinity tag (GST, HIS tag and others) and binds to a support that has affinity for the tag. The protein may be expressed and purified ...
subset: PSI-MI slim
is_a: MI:0004 ! affinity chromatography technology
[Term]
id: MI:0097
name: reverse ras recruitment system
def: "In this complementation approach the bait can be any membrane protein (for example a receptor or a channel protein), the prey is cloned as a fusion protein of any cDNA from a library and the coding sequence of cytoplasmic RAS (cdc25 in yeast). ...
subset: PSI-MI slim
synonym: "reverse RRS" EXACT PSI-MI-alternate []
synonym: "reverse rrs" EXACT PSI-MI-short []
is_a: MI:0228 ! cytoplasmic complementation assay
[Term]
id: MI:0098
name: ribosome display
def: "This method permits the coupling of phenotype to genotype via the formation of a non-covalent ternary complex between mRNAs and their encoded polypeptides while they are translated in an in vitro system. As a first step a cDNA library is constr...
subset: PSI-MI slim
is_a: MI:0034 ! display technology
[Term]
id: MI:0099
name: scintillation proximity assay
def: "SPA relies upon the fact that a beta particle emitted from a radioisotope decay can excite a fluorophore only when it is at a very short distance in water solution (few micrometers). The ligand is labelled with a radioactive atom and its potent...
subset: PSI-MI slim
synonym: "RIA Radio Immuno Assay" EXACT PSI-MI-alternate []
synonym: "SPA" EXACT PSI-MI-alternate []
synonym: "spa" EXACT PSI-MI-short []
is_a: MI:0013 ! biophysical
[Term]
id: MI:0100
name: sequence based phylogenetic profile
def: "Multiple alignments of orthologous sequences in the same species and their corresponding phylogenetic trees are built. Every phylogenetic tree is computed as a matrix of distances between all possible protein pairs. The covariation of the dista...
subset: PSI-MI slim
synonym: "sequence phylogeny" EXACT PSI-MI-short []
is_a: MI:0058 ! genome based prediction
is_a: MI:0101 ! sequence based prediction
[Term]
id: MI:0101
name: sequence based prediction
def: "Computational methods based on evolutionary hypothesis, used as criteria to browse sequences and predict interacting pairs." [PMID:14755292]
subset: PSI-MI slim
synonym: "predict from sequenc" EXACT PSI-MI-short []
is_a: MI:0063 ! interaction prediction
[Term]
id: MI:0102
name: sequence tag identification
def: "This approach leads to protein identification by combining mass measurement and short amino acid sequence information obtained by tandem mass spectrometry. This information is then used to automatically find the best match in a sequence databas...
subset: PSI-MI slim
synonym: "sequence tag" EXACT PSI-MI-short []
is_a: MI:0427 ! Identification by mass spectrometry
is_a: MI:0433 ! partial identification of protein sequence
[Term]
id: MI:0103
name: southern blot
def: "A standard procedure to identify DNA fragments containing specific gene sequences. In this procedure i) a genome is fragmented using a restriction enzyme ii) the generated fragments are separated by electrophoresis iii) the fragments are transf...
subset: PSI-MI slim
is_a: MI:0080 ! partial dna sequence identification by hybridization
[Term]
id: MI:0104
name: static light scattering
def: "In static light scattering, the average intensity of scattered light at multiple angles is measured. The data yield information on particle molecular weight, particle size and shape, and particle-particle interactions." [PMID:9013660]
subset: PSI-MI slim
synonym: "sls" EXACT PSI-MI-short []
is_a: MI:0067 ! light scattering
[Term]
id: MI:0105
name: structure based prediction
def: "Methods based on 3D structure information." [PMID:14755292]
subset: PSI-MI slim
synonym: "predict from struct" EXACT PSI-MI-short []
is_a: MI:0063 ! interaction prediction
[Term]
id: MI:0106
name: surface patches
def: "Surface patches are built using 6 criteria: solvation potential, residue interface propensity, hydrophobicity, planarity, protrusion and accessible surface area. Protein structures having similar patches are likely to have the same interactions...
subset: PSI-MI slim
is_a: MI:0577 ! feature prediction from structure
[Term]
id: MI:0107
name: surface plasmon resonance
def: "This method measures formation of complex by monitoring changes in the resonance angle of light impinging on a gold surface as a result of changes in the refractive index of the surface. A ligand of interest (small molecule, peptide, protein, s...
subset: PSI-MI slim
synonym: "BIAcore(r)" EXACT PSI-MI-alternate []
synonym: "Optical biosensor" EXACT PSI-MI-alternate []
synonym: "spr" EXACT PSI-MI-short []
is_a: MI:0013 ! biophysical
[Term]
id: MI:0108
name: t7 phage display
def: "T7 is a double stranded DNA bacteriophage with a thin-walled icosahedral capsid, ~550 Angstrom in diameter, which is decorated by 415 copies of the capsid protein, the product of gene 10. gp10 can tolerate insertions at the carboxyterminus with...
comment: Reference not index in medline: Rosenberg, A, Griffin, K, Studier, WS, McCormick, M, Berg, J, Novy, R, Mierendorf, R inNovations, 1996, 6, 1.
subset: PSI-MI slim
synonym: "t7 phage" EXACT PSI-MI-short []
is_a: MI:0084 ! phage display
[Term]
id: MI:0109
name: tap tag coimmunoprecipitation
def: "The TAP method involves the fusion of the TAP tag (encoding a calmodulin binding peptide, a TEV cleavage site, and the Staphylococcus aureus Protein A) to the target protein and the introduction of the construct into the host cell or organism, ...
subset: PSI-MI slim
synonym: "tap tag coip" EXACT PSI-MI-short []
is_obsolete: true
[Term]
id: MI:0110
name: text mining
def: "Text mining methods can be used to predict or confirm interactions by automated processing of scientific literature. Co-occurrence in the same sentence of an abstract of gene products labels are analysed to evaluate whether it represents a vali...
subset: PSI-MI slim
is_a: MI:0046 ! experimental knowledge based
[Term]
id: MI:0111
name: dihydrofolate reductase reconstruction
def: "The gene for DHFR is rationally dissected into two fragments called F[1,2] and F[3]. Two proteins or protein domains that are thought to bind to each other can then be fused to either of the two DHFR fragments. Reconstitution of enzyme activity...
subset: PSI-MI slim
synonym: "dhfr reconstruction" EXACT PSI-MI-short []
is_a: MI:0228 ! cytoplasmic complementation assay
[Term]
id: MI:0112
name: ubiquitin reconstruction
def: "In this method the two proteins, whose interaction is under investigation, (in this case mostly membrane proteins) are fused to an terminal fragment (Nub) and to a C-terminal fragment of ubiquitin (Cub). The two fragments do not associate to fo...
subset: PSI-MI slim
synonym: "ub reconstruction" EXACT PSI-MI-short []
is_a: MI:0228 ! cytoplasmic complementation assay
[Term]
id: MI:0113
name: western blot
def: "Western blot is a procedure to identify and quantify proteins. A mixture of protein is first submitted to an electrophoresis in denaturing condition and then electro-transferred from the gel to a membrane. The membrane is then incubated with a ...
subset: PSI-MI slim
synonym: "Immuno blot" EXACT PSI-MI-alternate []
is_a: MI:0421 ! identification by antibody
is_a: MI:0659 ! experimental feature detection
[Term]
id: MI:0114
name: x-ray crystallography
def: "Analysis of a diffraction pattern generated by a single crystal. X-rays have a wavelength, typically around 1 Angstrom (the diameter of a hydrogen atom). If a narrow parallel beam of X-rays is directed at a sample of a pure protein, most of the...
subset: PSI-MI slim
synonym: "X-ray" EXACT PSI-MI-alternate []
synonym: "x-ray diffraction" EXACT PSI-MI-short []
is_a: MI:0013 ! biophysical
is_a: MI:0659 ! experimental feature detection
[Term]
id: MI:0115
name: yeast display
def: "The proteins are displayed on the surface of the yeast S. cerevisiae by fusion to signal sequences for protein secretion. This method is limited by the low efficiency of the yeast display system but can take full advantage of exploiting cell so...
subset: PSI-MI slim
is_a: MI:0034 ! display technology
is_a: MI:0054 ! fluorescence-activated cell sorting
[Term]
id: MI:0116
name: feature type
def: "Property of a subsequence that may interfere with the binding of a molecule." [PMID:14755292]
subset: PSI-MI slim
relationship: part_of MI:0000 ! molecular interaction
[Term]
id: MI:0117
name: binding site
def: "A region of a molecule identified as being involved in an interaction." [PMID:14755292]
subset: PSI-MI slim
is_a: MI:0252 ! biological feature
[Term]
id: MI:0118
name: mutation
def: "Sequence variation due to insertion, deletion or substitution event." [PMID:14755292]
subset: PSI-MI slim
is_a: MI:0252 ! biological feature
[Term]
id: MI:0119
name: mutation decreasing interaction
def: "Region of a molecule whose mutation or deletion decreases significantly interaction strength." [PMID:14755292]
subset: PSI-MI slim
synonym: "hotspot" EXACT PSI-MI-alternate []
synonym: "mutation decreasing" EXACT PSI-MI-short []
is_a: MI:0118 ! mutation
scripts/Data/psi-mi.obo view on Meta::CPAN
synonym: "palmitoylation" EXACT PSI-MI-short []
is_a: MI:0211 ! lipid addition
[Term]
id: MI:0217
name: phosphorylation reaction
def: "Reversible reaction that can affect D,C,H,S,T,Y,R residues." [GO:0016310, PMID:14755292, RESID:AA0033, RESID:AA0034, RESID:AA0035, RESID:AA0036, RESID:AA0037, RESID:AA0038, RESID:AA0039, RESID:AA0222]
subset: PSI-MI slim
synonym: "phosphorylation" EXACT PSI-MI-short []
is_a: MI:0414 ! enzymatic reaction
[Term]
id: MI:0218
name: physical interaction
def: "Interaction among molecules that can be direct or indirect.\nOBSOLETE: splitted to 'association' MI:0914 and 'physical association' MI:0915. For remapping consider the experimental setting of an interaction. For bulk remapping a possible criter...
is_obsolete: true
[Term]
id: MI:0219
name: synthetic lethal
def: "Death phenotype observed on cells carrying combination of two independently silent mutations.\nOBSOLETE: remap to CV intraction type 'synthetic interaction' MI:0794 and external CV for phenotype description (lethal FBcv:0000351)" [PMID:15608217...
subset: PSI-MI slim
is_obsolete: true
[Term]
id: MI:0220
name: ubiquitination reaction
def: "Reversible reaction that create a covalent bond between a C-terminus G of ubiquitin and a K residue of the target." [GO:0016567, PMID:11583613, RESID:AA0125]
subset: PSI-MI slim
synonym: "ubiquitination" EXACT PSI-MI-short []
is_a: MI:0414 ! enzymatic reaction
[Term]
id: MI:0221
name: expression level
def: "Synthesis rate of a molecule under investigation described in comparison with its naturally occurring expression level in a cell." [PMID:14755292]
subset: PSI-MI slim
is_a: MI:0346 ! experimental preparation
[Term]
id: MI:0222
name: physiological level
def: "A molecule whose synthesis is under control of its natural gene promoter or estimated to be expressed at a similar rate." [PMID:14755292]
subset: PSI-MI slim
synonym: "endogenous" EXACT PSI-MI-alternate []
synonym: "endogenous level" EXACT PSI-MI-alternate []
is_a: MI:0221 ! expression level
[Term]
id: MI:0223
name: under expressed level
def: "A molecule is estimated to be expressed at lower levels than in physiological condition." [PMID:14755292]
subset: PSI-MI slim
synonym: "under-expressed" EXACT PSI-MI-short []
is_a: MI:0221 ! expression level
is_a: MI:0803 ! expression level alteration
[Term]
id: MI:0225
name: chromatin immunoprecipitation array
def: "The method combines a modified chromatin immunoprecipitation (ChIP) procedure, with DNA microarray analysis. Cells are fixed with formaldehyde, harvested, and disrupted by sonication. The DNA fragments cross-linked to a protein of interest are ...
subset: PSI-MI slim
synonym: "chip-chip" EXACT PSI-MI-short []
is_a: MI:0008 ! array technology
is_a: MI:0402 ! chromatin immunoprecipitation assay
[Term]
id: MI:0226
name: ion exchange chromatography
def: "Stable complexes and their component proteins can be separated on the basis of their net charge by ion-exchange chromatography. If a protein has a net positive charge at pH 7, it will usually bind to a column of beads containing carboxylate gro...
subset: PSI-MI slim
synonym: "IEC" EXACT PSI-MI-alternate []
synonym: "ion exchange chrom" EXACT PSI-MI-short []
is_a: MI:0091 ! chromatography technology
[Term]
id: MI:0227
name: reverse phase chromatography
def: "Reverse phase chromatography operates on the basis of hydrophilicity and lipophilicity. The stationary phase consists of silica based packings with n-alkyl chains covalently bound. For example, C-8 signifies an octyl chain and C-18 an octadecyl...
subset: PSI-MI slim
synonym: "reverse phase chrom" EXACT PSI-MI-short []
is_a: MI:0091 ! chromatography technology
[Term]
id: MI:0228
name: cytoplasmic complementation assay
def: "Protein complementation assay performed by dissecting a cytoplasmic protein activity and restoring it through the two hybrid proteins interaction." [PMID:14755292]
subset: PSI-MI slim
synonym: "cytoplasmic compl" EXACT PSI-MI-short []
is_a: MI:0090 ! protein complementation assay
[Term]
id: MI:0229
name: green fluorescence protein complementation assay
def: "Protein-protein interaction trap based on fusions of bait and prey protein to two dissected fragment of GFP. The system implemented in E. coli, allow screening of partners, including membrane proteins and also detect transient interaction that ...
subset: PSI-MI slim
synonym: "gfp complementation" EXACT PSI-MI-short []
is_a: MI:0228 ! cytoplasmic complementation assay
[Term]
id: MI:0230
name: membrane bound complementation assay
def: "Protein complementation assay based on dissection of a membrane protein." [PMID:14755292]
subset: PSI-MI slim
synonym: "membrane compl" EXACT PSI-MI-short []
is_a: MI:0090 ! protein complementation assay
[Term]
id: MI:0231
name: mammalian protein protein interaction trap
def: "The MAPPIT(mammalian protein-protein interaction Trap) is a screening method for protein-protein interaction in mammalian cells, based on the reconstitution of a membrane STAT (signal transducers and activators of transcription) receptor. The b...
subset: PSI-MI slim
synonym: "mappit" EXACT PSI-MI-short []
is_a: MI:0230 ! membrane bound complementation assay
[Term]
id: MI:0232
name: transcriptional complementation assay
def: "Protein complementation assay performed by dissecting a transcription factor activity (DNA binding domain and transcription activation domain) its restoration through the two hybrid proteins interaction that lead to a reporter gene expression."...
subset: PSI-MI slim
synonym: "transcription compl" EXACT PSI-MI-short []
is_a: MI:0090 ! protein complementation assay
[Term]
id: MI:0233
name: protein dna complex
def: "A stable set of interacting protein and DNA that can be copurified and operate as a functional unit." [PMID:14755292]
subset: PSI-MI slim
is_a: MI:0314 ! complex
[Term]
id: MI:0234
name: 131i radiolabel
def: "Molecule labelled with 131 radio isotope of iodine atoms." [PMID:14755292]
subset: PSI-MI slim
synonym: "131I" EXACT PSI-MI-alternate []
synonym: "I131" EXACT PSI-MI-alternate []
is_a: MI:0517 ! radiolabel
[Term]
id: MI:0235
name: 14c radiolabel
def: "Molecule labelled with the radio isotope 14 of carbon atoms." [PMID:14755292]
subset: PSI-MI slim
synonym: "14C" EXACT PSI-MI-alternate []
synonym: "C14" EXACT PSI-MI-alternate []
is_a: MI:0517 ! radiolabel
[Term]
id: MI:0236
name: 32p radiolabel
def: "Molecule labelled with the radio isotope 32 of phosphorus atoms." [PMID:14755292]
subset: PSI-MI slim
synonym: "32P" EXACT PSI-MI-alternate []
synonym: "P32" EXACT PSI-MI-alternate []
scripts/Data/psi-mi.obo view on Meta::CPAN
[Term]
id: MI:0387
name: alexa 488 label
def: "Alexa fluorescent dye analogue to Oregon Green 488 with an approximate excitation wavelength maximum of 488 nm." [PMID:10449539]
subset: PSI-MI slim
is_a: MI:0384 ! alexa label
[Term]
id: MI:0388
name: alexa 532 label
def: "Alexa fluorescent dye analogue to Rhodamine 6G with an approximate excitation wavelength maximum of 532nm." [PMID:10449539]
subset: PSI-MI slim
is_a: MI:0384 ! alexa label
[Term]
id: MI:0389
name: alexa 546 label
def: "Alexa fluorescent dye analogue to Cy3 with an approximate excitation wavelength maximum of 546nm." [PMID:10449539]
subset: PSI-MI slim
is_a: MI:0384 ! alexa label
[Term]
id: MI:0390
name: alexa 568 label
def: "Alexa fluorescent dye analogue to Rhodamine Red-X with an approximate excitation wavelength maximum of 568nm." [PMID:10449539]
subset: PSI-MI slim
is_a: MI:0384 ! alexa label
[Term]
id: MI:0391
name: alexa 594 label
def: "Alexa fluorescent dye analogue to Texas Red-X with an approximate excitation wavelength maximum of 594nm." [PMID:10449539]
subset: PSI-MI slim
is_a: MI:0384 ! alexa label
[Term]
id: MI:0396
name: predetermined participant
def: "Molecule whose sequence identity is not checked and has been assumed from external or previous experimental evidence(s)." [PMID:14755292]
subset: PSI-MI slim
synonym: "predetermined" EXACT PSI-MI-short []
is_a: MI:0661 ! experimental participant identification
[Term]
id: MI:0397
name: two hybrid array
def: "Two-hybrid screening can be done in a colony array format, in which each colony expresses a defined pair of proteins. Because the particular protein pair expressed in each colony is defined by its position in the array, positive signals identif...
subset: PSI-MI slim
is_a: MI:0018 ! two hybrid
[Term]
id: MI:0398
name: two hybrid pooling approach
def: "In the pooling strategy the sets of bait and prey hybrid vectors are randomly mated. The positives double hybrid clones are the interacting partners." [PMID:12634794, PMID for application instance:11283351]
subset: PSI-MI slim
synonym: "two hybrid pooling" EXACT PSI-MI-short []
is_a: MI:0018 ! two hybrid
[Term]
id: MI:0399
name: two hybrid fragment pooling approach
def: "This two hybrid approach involves the screening of a large number of individual proteins against a comprehensive library of randomly generated fragment as prey. The usage of degenerated fragment allows identification of the minimal protein regi...
subset: PSI-MI slim
synonym: "2h fragment pooling" EXACT PSI-MI-short []
is_a: MI:0398 ! two hybrid pooling approach
[Term]
id: MI:0400
name: affinity technology
def: "Techniques which depend upon the strength of the interaction between two entities." [PMID:14755292]
subset: PSI-MI slim
synonym: "affinity techniques" EXACT PSI-MI-short []
is_a: MI:0401 ! biochemical
[Term]
id: MI:0401
name: biochemical
def: "The application of chemical principles and methods to biological experiments to demonstrate an interaction." [PMID:14755292]
subset: PSI-MI slim
is_a: MI:0045 ! experimental interaction detection
[Term]
id: MI:0402
name: chromatin immunoprecipitation assay
def: "Chromatin immunoprecipitation (ChIP) is a powerful approach that allows one to define the interaction of factors with specific chromosomal sites in living cells. ChIP involves treating cells or tissue briefly with formaldehyde to crosslink prot...
subset: PSI-MI slim
synonym: "ch-ip" EXACT PSI-MI-short []
is_a: MI:0400 ! affinity technology
[Term]
id: MI:0403
name: colocalization
def: "Coincident occurrence of molecules in a given subcellular fraction observed with a low resolution methodology from which a physical interaction among those molecules cannot be inferred." [PMID:14755292]
subset: PSI-MI slim
is_a: MI:0190 ! interaction type
[Term]
id: MI:0404
name: comigration in non denaturing gel electrophoresis
def: "comigration by non denaturing gel electrophoresis." [PMID:14755292]
subset: PSI-MI slim
synonym: "comig non denat gel" EXACT PSI-MI-short []
is_a: MI:0807 ! comigration in gel electrophoresis
[Term]
id: MI:0405
name: competition binding
def: "Competitive binding experiments measure equilibrium binding of a single concentration of ligand at various concentrations of an unlabeled competitor. Analysis of these data gives the affinity of the receptor for the competitor." [PMID:14755292]
subset: PSI-MI slim
is_a: MI:0400 ! affinity technology
[Term]
id: MI:0406
name: deacetylase assay
def: "Measures the catalysis of the hydrolysis of an acetyl group or groups from a substrate molecule." [PMID:14755292]
subset: PSI-MI slim
is_a: MI:0415 ! enzymatic study
[Term]
id: MI:0407
name: direct interaction
def: "Interaction that is proven to involve only its interactors." [PMID:14755292]
subset: PSI-MI slim
is_a: MI:0915 ! physical association
[Term]
id: MI:0408
name: disulfide bond
def: "Covalent bond mediated by 2 sulfur atoms." [PMID:14755292]
subset: PSI-MI slim
is_a: MI:0195 ! covalent binding
[Term]
id: MI:0409
name: dna footprinting
def: "Experimental method used to identify the region of a nucleic acid involved in an interaction with a protein. One sample of a radiolabeled nucleic acid of known sequence is submitted to partial digestion. A second sample is incubated with its in...
subset: PSI-MI slim
is_obsolete: true
[Term]
id: MI:0410
name: electron tomography
def: "Electron tomography is a general method for three-dimensional (3D) reconstruction of single, transparent objects from a series of projection images (i.e. from a tilt series) recorded with a transmission electron microscope. It offers the opport...
subset: PSI-MI slim
synonym: "sem" EXACT PSI-MI-short []
is_a: MI:0040 ! electron microscopy
[Term]
id: MI:0411
name: enzyme linked immunosorbent assay
def: "Following non-covalent binding of a purified primary ligand to a solid phase, a blocking reagent is added to prevent any non-specific binding. A specific antigen is then allowed to bind to the primary ligand. Unbound antigen is removed by washi...
subset: PSI-MI slim
synonym: "ELISA" EXACT PSI-MI-alternate []
synonym: "elisa" EXACT PSI-MI-short []
is_a: MI:0421 ! identification by antibody
is_a: MI:0892 ! solid phase assay
[Term]
id: MI:0412
name: electrophoretic mobility supershift assay
def: "The EMSA supershift is a EMSA experiment carried out using a third lane loaded with the radiolabeled nucleic acid, a protein mixture and an antibody for a specific protein. If an extra retardation is observed, this is due to the formation of a ...
subset: PSI-MI slim
synonym: "emsa supershift" EXACT PSI-MI-short []
is_a: MI:0413 ! electrophoretic mobility shift assay
[Term]
id: MI:0413
name: electrophoretic mobility shift assay
def: "This method proves the interaction between a nucleic acid and a protein partner. On the same electrophoresis gel 1 lane is loaded with a radiolabeled nucleic acid of known sequence, a second lane is loaded with the same nucleic acid together wi...
subset: PSI-MI slim
synonym: "band shift" EXACT PSI-MI-alternate []
synonym: "emsa" EXACT PSI-MI-short []
synonym: "Gel retardation assay" EXACT PSI-MI-alternate []
is_a: MI:0892 ! solid phase assay
[Term]
id: MI:0414
name: enzymatic reaction
def: "terms aiming to represent biochemical reactions referring to their resulting product modifications." [PMID:14755292]
subset: PSI-MI slim
synonym: "Biochemical reaction" EXACT PSI-MI-alternate []
is_a: MI:0407 ! direct interaction
[Term]
id: MI:0415
name: enzymatic study
def: "Participants are enzyme or substrate in a biochemical reaction." [PMID:14755292]
subset: PSI-MI slim
is_a: MI:0401 ! biochemical
[Term]
id: MI:0416
name: fluorescence microscopy
def: "Fluorescent microscopy uses a high intensity light to illuminate the sample. This light excites fluorescence species in the sample, which then emit light of a longer wavelength. A fluorescent microscope also produces a magnified image of the sa...
subset: PSI-MI slim
synonym: "fluorescence imaging" EXACT PSI-MI-short []
scripts/Data/psi-mi.obo view on Meta::CPAN
name: collagen film assay
def: "Measures the amount of radiolabel released into the medium when enzyme is added onto a film of isotope-labelled collagen." [PMID:6247938]
subset: PSI-MI slim
is_a: MI:0435 ! protease assay
[Term]
id: MI:0514
name: in gel phosphatase assay
def: "Substrate protein pre-radiolabelled either synthetically or through the action of a kinase transferring an isotope of phosphate from a nucleotide. Substrate then exposed to phosphate under assay conditions. Substrate isolated by gel electrophor...
subset: PSI-MI slim
synonym: "in gel phosphatase" EXACT PSI-MI-short []
is_a: MI:0434 ! phosphatase assay
[Term]
id: MI:0515
name: methyltransferase assay
def: "Measures the catalysis of the transfer of a methyl group to an acceptor molecule." [PMID:14755292]
subset: PSI-MI slim
synonym: "methyltransferase as" EXACT PSI-MI-short []
is_a: MI:0415 ! enzymatic study
[Term]
id: MI:0516
name: methyltransferase radiometric assay
def: "Measures the transfer of a radiolabelled methyl group of a donor, for example S-adenosyl-L-methionine (SAM) to a carboxyl group of an acceptor." [PMID:14755292]
subset: PSI-MI slim
synonym: "radiolabeled methyl" EXACT PSI-MI-short []
is_a: MI:0515 ! methyltransferase assay
[Term]
id: MI:0517
name: radiolabel
def: "A radiolabelled molecule has radio isotopes among its constituent atoms that can be used to identify, localize or quantify the full molecule." [PMID:14755292]
subset: PSI-MI slim
synonym: "radiolabeled" EXACT PSI-MI-alternate []
synonym: "radiolabelled" EXACT PSI-MI-short []
is_a: MI:0253 ! isotope label
[Term]
id: MI:0518
name: flag tag
def: "The protein of interest is expressed as a fusion to the peptide DYKDDDDKV for which antibodies are commercially available. Sometimes multiple copies of the peptide are fused in tandem." [PMID:14755292]
subset: PSI-MI slim
synonym: "DYKDDDDKV epitope tag" EXACT PSI-MI-alternate []
synonym: "FLAG" EXACT PSI-MI-alternate []
synonym: "FLAG-tagged" EXACT PSI-MI-alternate []
is_a: MI:0507 ! tag
[Term]
id: MI:0519
name: glutathione s tranferase tag
def: "The protein is expressed and purified as a fusion to the glutathione S-tranferase protein." [PMID:14755292]
subset: PSI-MI slim
synonym: "glutathione S-tranferase tag" EXACT PSI-MI-alternate []
synonym: "gst tag" EXACT PSI-MI-short []
is_a: MI:0365 ! enzyme tag
[Term]
id: MI:0520
name: ha tag
def: "The protein of interest is expressed as a fusion to the peptide YPYDVPDYA (a fragment of the influenza hemagglutinin protein) for which antibodies are commercially available." [PMID:14755292]
subset: PSI-MI slim
synonym: "YPYDVPDYA epitope tag" EXACT PSI-MI-alternate []
is_a: MI:0507 ! tag
[Term]
id: MI:0521
name: his tag
def: "The protein of interest is expressed as a fusion to a poly-His tail. This permits purification by chromatography over a metal column or by binding to commercially available anti poly-His antibodies." [PMID:14755292]
subset: PSI-MI slim
synonym: "6-His-tag" EXACT PSI-MI-alternate []
synonym: "Hexa-His-tag" EXACT PSI-MI-alternate []
synonym: "Histidine-tag" EXACT PSI-MI-alternate []
is_a: MI:0507 ! tag
[Term]
id: MI:0522
name: myc tag
def: "The protein of interest is expressed as a fusion to the peptide EUKLISEED (a fragment of the Myc oncogene protein) for which antibodies are commercially available. Sometimes multiple copies of the peptide are fused in tandem." [PMID:14755292]
subset: PSI-MI slim
synonym: "EUKLISEED epitope tag" EXACT PSI-MI-alternate []
is_a: MI:0507 ! tag
[Term]
id: MI:0523
name: t7 tag
def: "The protein of interest is expressed as a fusion to the peptide MASMTGGQQMG for which antibodies are commercially available." [PMID:14755292]
subset: PSI-MI slim
synonym: "MASMTGGQQMG epitope tag" EXACT PSI-MI-alternate []
is_a: MI:0507 ! tag
[Term]
id: MI:0524
name: calmodulin binding peptide plus protein a tag
def: "Tag encoding a calmodulin binding peptide, a TEV cleavage site, and the Staphylococcus aureus Protein A fused to a target protein and the introduction of the construct into the host cell or organism, maintaining the expression of the fusion pro...
subset: PSI-MI slim
synonym: "CBP-ProtA tagged" EXACT PSI-MI-alternate []
synonym: "tap tagged" EXACT PSI-MI-short []
is_a: MI:0677 ! tandem tag
[Term]
id: MI:0525
name: v5 tag
def: "The protein of interest is expressed as a fusion to the peptide GKPIPNPLLGLDST for which antibodies are commercially available." [PMID:14755292]
subset: PSI-MI slim
synonym: "GKPIPNPLLGLDST epitope tag" EXACT PSI-MI-alternate []
is_a: MI:0507 ! tag
[Term]
id: MI:0526
name: n-acetyl-lysine
def: "Residue modification." [PMID:14755292, RESID:AA0048, RESID:AA0055]
subset: PSI-MI slim
synonym: "acetyllysine" EXACT PSI-MI-short []
is_a: MI:0121 ! acetylated residue
[Term]
id: MI:0527
name: adp ribosylated residue
def: "Residue modification." [PMID:14755292]
subset: PSI-MI slim
synonym: "adp-ribosylated" EXACT PSI-MI-short []
is_a: MI:0120 ! post translation modification
[Term]
id: MI:0528
name: omega-n-(adp-ribosyl)-arginine
def: "Residue modification." [PMID:14755292, RESID:AA0168]
subset: PSI-MI slim
synonym: "(S)-2-amino-5-([imino([adenosine 5'-(trihydrogen diphosphate) 5'->5'-ester with alpha-D-ribofuranosyl]amino)methyl]amino)pentanoic acid" EXACT PSI-MI-alternate []
synonym: "adp-ribosylarginine" EXACT PSI-MI-short []
synonym: "N(omega)-[alpha-D-ribofuranoside 5'->5'-ester with adenosine 5'-(trihydrogen diphosphate)]-L-arginine" EXACT PSI-MI-alternate []
synonym: "N(omega)-alpha-D-ribofuranosyl-L-arginine 5'->5'-ester with adenosine 5'-(trihydrogen diphosphate)" EXACT PSI-MI-alternate []
synonym: "omega-N-(ADP-ribosyl)-L-arginine" EXACT PSI-MI-alternate []
is_a: MI:0527 ! adp ribosylated residue
[Term]
id: MI:0529
name: s-(adp-ribosyl)-cysteine
scripts/Data/psi-mi.obo view on Meta::CPAN
synonym: "NG-methylarginine;" EXACT PSI-MI-alternate []
synonym: "omega-N-methyl-L-arginine" EXACT PSI-MI-alternate []
is_a: MI:0563 ! methylated arginine
[Term]
id: MI:0565
name: neddylated lysine
def: "Residue modification due to a cross-link between a lysine and a glycine from the Nedd8 protein family." [PMID:111]
subset: PSI-MI slim
is_a: MI:0179 ! other modification
[Term]
id: MI:0566
name: sumoylation reaction
def: "Reversible reaction that create a covalent bond between a C-terminus G of an ubiquitine like sumo protein and a K residue of the target." [GO:0016925, PMID:15985640]
subset: PSI-MI slim
synonym: "sumoylation" EXACT PSI-MI-short []
is_a: MI:0414 ! enzymatic reaction
[Term]
id: MI:0567
name: neddylation reaction
def: "Reversible reaction that create a covalent bond between a Glycine residue of an ubiquitine like NEDD8 protein and a lysine residue of the target." [GO:0045116, PMID:16127432]
subset: PSI-MI slim
synonym: "neddylation" EXACT PSI-MI-short []
is_a: MI:0414 ! enzymatic reaction
[Term]
id: MI:0568
name: desumoylation reaction
def: "Cleavage of the G-K bond and release of the SUMO ubiquitin like proteins." [GO:0016926, PMID:15985640]
subset: PSI-MI slim
synonym: "desumoylation" EXACT PSI-MI-short []
is_a: MI:0414 ! enzymatic reaction
[Term]
id: MI:0569
name: deneddylation reaction
def: "Cleavage of the G-K bond and release of the NEDD8 ubiquitin like proteins. Deneddylation, which removes the NEDD8 moiety, requires the isopeptidase activity of the COP9 signalosome." [GO:0000338, PMID:16127432]
subset: PSI-MI slim
synonym: "deneddylation" EXACT PSI-MI-short []
is_a: MI:0414 ! enzymatic reaction
[Term]
id: MI:0570
name: protein cleavage
def: "Covalent modification of a polypeptide occuring during its maturation or its proteolytic degradation." [PMID:14744292]
subset: PSI-MI slim
is_a: MI:0194 ! cleavage reaction
[Term]
id: MI:0571
name: mrna cleavage
def: "Any process by which a pre-mRNA or mRNA molecule is cleaved at specific sites or in a regulated manner." [GO:0006379, PMID:14681407]
subset: PSI-MI slim
is_a: MI:0902 ! rna cleavage
[Term]
id: MI:0572
name: dna cleavage
def: "Covalent bond breakage of a DNA molecule leading to the formation of smaller fragments." [PMID:14755292]
subset: PSI-MI slim
is_a: MI:0910 ! nucleic acid cleavage
[Term]
id: MI:0573
name: mutation disrupting interaction
def: "Region of a molecule whose mutation or deletion totally disrupts an interaction." [PMID:14755292]
subset: PSI-MI slim
synonym: "mutation disrupting" EXACT PSI-MI-short []
is_a: MI:0119 ! mutation decreasing interaction
[Term]
id: MI:0574
name: digital object identifier
def: "Identifier of a publication prior to pubmed indexing." [PMID:14755292]
subset: PSI-MI slim
synonym: "doi" EXACT PSI-MI-short []
xref: id-validation-regexp:\"\\d+.\\d+/[a-zA-Z0-9\\.\\\:\]+\"
xref: search-url: "http://dx.doi.org/${ac}"
is_a: MI:0445 ! literature database
[Term]
id: MI:0575
name: alliance for cellular signaling
def: "Alliance for Cellular Signaling (AfCS -Nature) store yeast 2-hybrid Interaction data and expression data. Information and data are freely available to all.\nhttp://www.signaling-gateway.org" [PMID:14755292]
subset: PSI-MI slim
synonym: "AfCS" EXACT PSI-MI-alternate []
synonym: "afcs" EXACT PSI-MI-short []
xref: id-validation-regexp:\"[0-9\]+\"
xref: search-url: "http://www.signaling-gateway.org/data/Y2H/cgi-bin/y2h_int.cgi?id=${ac}"
is_a: MI:0461 ! interaction database
is_a: MI:0489 ! source database
[Term]
id: MI:0576
name: structural proximity
def: "Method to identify domain-domain interactions within the same resolved structure. Domains are first projected onto a pdb structure and then the distance between all pairs of residues in different domains are calculated. When the distance betwee...
subset: PSI-MI slim
is_a: MI:0577 ! feature prediction from structure
[Term]
id: MI:0577
name: feature prediction from structure
def: "Group of method taking advantage of 3D structure to calculate and infer the feature of interacting molecules." [PMID:14755292]
subset: PSI-MI slim
synonym: "feature struct pred" EXACT PSI-MI-short []
is_a: MI:0660 ! feature prediction
[Term]
id: MI:0578
name: maltose binding protein tag
def: "The protein is expressed and purified as a fusion to the glutathione maltose-binding protein (MBP). The MBP-fusion protein can be purified by affinity chromatography using an amylose resin." [PMID:14755292]
subset: PSI-MI slim
synonym: "maltose binding protein tag" EXACT PSI-MI-alternate []
synonym: "mbp tag" EXACT PSI-MI-short []
is_a: MI:0240 ! fusion protein
[Term]
id: MI:0579
name: electron donor
scripts/Data/psi-mi.obo view on Meta::CPAN
[Term]
id: MI:0596
name: experimental form description
def: "Free text description of all the tags and artificial process undergone by a molecule during an experiment." [PMID:14755292]
subset: PSI-MI slim
synonym: "experimental form de" EXACT PSI-MI-short []
is_a: MI:0666 ! participant attribute name
[Term]
id: MI:0597
name: feature description
def: "The feature text description may include information about the feature detection method." [PMID:14755292]
subset: PSI-MI slim
is_a: MI:0668 ! feature attribute name
[Term]
id: MI:0598
name: feature constraint
def: "The feature constraint free text will specificity whether a biological feature is shown to be possible (just observed) or required (experimentally demonstrated to be necessary for an interaction)." [PMID:14755292]
subset: PSI-MI slim
is_a: MI:0668 ! feature attribute name
[Term]
id: MI:0599
name: figure legend
def: "Text pointing to a specific paper figure legend where the experimental evidences for an interaction are to be found." [PMID:14755292]
subset: PSI-MI slim
is_a: MI:0664 ! interaction attribute name
is_a: MI:0665 ! experiment attibute name
[Term]
id: MI:0600
name: conditional synthetic lethal nutrition-sensitivity
def: "Two silent mutations show a nutrition sensitive lethal phenotype when they co-occur on the same cell.\nOBSOLETE: remap to CV intraction type 'synthetic interaction' MI:0794 and external CV for phenotype description." [PMID:15608217]
subset: PSI-MI slim
synonym: "nutrition synt letal" EXACT PSI-MI-short []
is_obsolete: true
[Term]
id: MI:0601
name: sequence ontology
def: "The Sequence Ontology (SO) is a structured controlled vocabulary for the parts of a genomic annotation. SO provides a common set of terms and definitions that will facilitate the exchange, analysis and management of genomic data." [PMID:1589287...
subset: PSI-MI slim
synonym: "so" EXACT PSI-MI-short []
xref: id-validation-regexp:\"SO\:[0-9\]\{7}\"
is_a: MI:0447 ! feature database
is_a: MI:0473 ! participant database
[Term]
id: MI:0602
name: chemical footprinting
def: "Binding sites are identified by altered reactivity of a complex to a chemical treatment compared to the unbound molecules. Residues in close contact with the binding partner are protected from cleavage by the enzyme. When these chemicals are ad...
subset: PSI-MI slim
synonym: "chemical footprint" EXACT PSI-MI-short []
is_a: MI:0417 ! footprinting
[Term]
id: MI:0603
name: dimethylsulphate footprinting
def: "Dimethylsulphate (DMS) is the most commonly used chemical to study DNA-protein interactions. DMS induces methylation of guanine residues so DNA interaction with protein binding to AT rich sequences or to the phosphate backbone may be not detect...
subset: PSI-MI slim
synonym: "dms footprinting" EXACT PSI-MI-short []
is_a: MI:0602 ! chemical footprinting
[Term]
id: MI:0604
name: potassium permanganate footprinting
def: "Potassium permanganate bind to single-stranded pyrimidine residues, it is commonly used to detect promoters opening regions in vivo. KMnO4 treatment of cells, followed by treatment with piperidine, followed by either PCR and/or acrylamide gel e...
subset: PSI-MI slim
synonym: "k-mn-04 footprinting" EXACT PSI-MI-short []
is_a: MI:0602 ! chemical footprinting
[Term]
id: MI:0605
name: enzymatic footprinting
def: "Binding sites are identified by altered reactivity of a complex to an enzymatic probe compared to the unbound molecules. Residues in close contact with the binding partner are protected from cleavage by the enzyme. When these enzymes are admini...
subset: PSI-MI slim
synonym: "enzymatic footprint" EXACT PSI-MI-short []
is_a: MI:0417 ! footprinting
[Term]
id: MI:0606
name: DNase I footprinting
def: "Deoxyribonuclease I (DNase I) do not have high specificity for given sequences or residues, thus footprinting with DNase I permits the exact delineation of the protein-DNA binding site. Moreover DNase I, can be used for in vivo footprinting by ...
subset: PSI-MI slim
synonym: "dnase 1 footprinting" EXACT PSI-MI-short []
is_a: MI:0605 ! enzymatic footprinting
[Term]
id: MI:0607
name: small nuclear rna
def: "These RNA molecules are relatively short (less than 200 nucleotides each), and there are five of them (U1, U2, U4, U5, and U6) involved in the major form of pre-mRNA splicing. Known as snRNAs (small nuclear RNAs), each is complexed with at leas...
subset: PSI-MI slim
synonym: "snRNA" EXACT PSI-MI-alternate []
synonym: "snrna" EXACT PSI-MI-short []
is_a: MI:0320 ! ribonucleic acid
[Term]
id: MI:0608
name: ribosomal rna
def: "RNA that is transcribed from the DNA of the nucleolus and is found, together with characteristic proteins, in the ribosomes." [PMID:14755292]
subset: PSI-MI slim
synonym: "rRNA" EXACT PSI-MI-alternate []
synonym: "rrna" EXACT PSI-MI-short []
is_a: MI:0320 ! ribonucleic acid
[Term]
id: MI:0609
name: small nucleolar rna
def: "The small nucleolar RNAs, are stable RNA contained in the nucleoli and these RNAs exist as snoRNA: protein complexes called snoRNPs (also called 'snorps'). The snoRNPs function is in the maturation of ribosomal RNA and other RNAs, by: creating ...
subset: PSI-MI slim
synonym: "snoRNA" EXACT PSI-MI-alternate []
synonym: "snorna" EXACT PSI-MI-short []
is_a: MI:0320 ! ribonucleic acid
[Term]
id: MI:0610
name: small interfering rna
def: "Ribonucleic acid used in RNAi study. These RNA have the reverse complementary sequence of a target gene's mRNA transcript and inhibit its expression." [PMID:10542148]
subset: PSI-MI slim
scripts/Data/psi-mi.obo view on Meta::CPAN
subset: PSI-MI slim
synonym: "enhancement" EXACT PSI-MI-short []
is_obsolete: true
[Term]
id: MI:0803
name: expression level alteration
def: "Synthesis rate of a molecule under investigation differs from its naturally occurring expression level in a cell." [PMID:14755292]
subset: PSI-MI slim
synonym: "expression modif" EXACT PSI-MI-short []
is_a: MI:0787 ! genetic experimental form
[Term]
id: MI:0804
name: mutated gene
def: "The gene is mutated in some unknown manner" [PMID:14755292]
subset: PSI-MI slim
is_a: MI:0787 ! genetic experimental form
[Term]
id: MI:0805
name: wwpdb
def: "The Worldwide Protein Data Bank (wwPDB) consists of organizations that act as deposition, data processing and distribution centers for PDB data. The founding members are RCSB PDB (USA), MSD-EBI (Europe) and PDBj (Japan). The BMRB (USA) group jo...
subset: Drugable
subset: PSI-MI slim
synonym: "wwPDB" EXACT PSI-MI-alternate []
xref: id-validation-regexp:\"[0-9\][a-zA-Z0-9\]\{3}\"
is_a: MI:0447 ! feature database
is_a: MI:0461 ! interaction database
is_a: MI:0489 ! source database
[Term]
id: MI:0806
name: pdbj
def: "PDBj(Protein Data Bank Japan) maintains the database for the protein structures with financial assistance from the Institute for Bioinformatics Research and Development of Japan Science and Technology Corporation(BIRD-JST), collaborating with t...
subset: PSI-MI slim
synonym: "PDBj" EXACT PSI-MI-alternate []
xref: id-validation-regexp:\"[0-9\][a-zA-Z0-9\]\{3}\"
xref: search-url: "http://pdbjs3.protein.osaka-u.ac.jp/xPSSS/DetailServlet?PDBID=${ac}&PAGEID=Summary"
is_a: MI:0805 ! wwpdb
[Term]
id: MI:0807
name: comigration in gel electrophoresis
def: "The interaction of two molecules is determine by their very close proximity or the overlap of their relative bands in a gel." [PMID:14755292]
subset: PSI-MI slim
synonym: "comigration in gel" EXACT PSI-MI-short []
is_a: MI:0401 ! biochemical
[Term]
id: MI:0808
name: comigration in sds page
def: "Method allowing the detection of strong interactions between two molecules by their very close proximity or the overlap of their relative bands in a denaturing SDS gel." [PMID:14755292, PMID:16732283]
subset: PSI-MI slim
synonym: "comigration in sds" EXACT PSI-MI-short []
is_a: MI:0807 ! comigration in gel electrophoresis
[Term]
id: MI:0809
name: bimolecular fluorescence complementation
def: "The bimolecular fluorescence complementation (BiFC) is an assay for determination of the locations of protein interactions in living cells. This approach is based on complementation between two non fluorescent fragments of the yellow fluorescen...
subset: PSI-MI slim
synonym: "bifc" EXACT PSI-MI-short []
is_a: MI:0051 ! fluorescence technology
is_a: MI:0090 ! protein complementation assay
[Term]
id: MI:0810
name: substitution analysis
def: "In this approach, once a molecule is demonstrated to participate in an interaction, several substitution mutants are produced and tested in the binding assay to identify the residues which identity is crucial for the interaction." [PMID:1475529...
subset: PSI-MI slim
synonym: "substitut analysis" EXACT PSI-MI-short []
is_a: MI:0074 ! mutation analysis
[Term]
id: MI:0811
name: insertion analysis
def: "In this approach, once a molecule is demonstrated to participate in an interaction, several insertion derivatives are produced and tested in the binding assay to detect the regions that are important for the interaction." [PMID:14755292]
subset: PSI-MI slim
is_a: MI:0074 ! mutation analysis
[Term]
id: MI:0812
name: calmodulin binding protein tag
def: "The protein is expressed and purified as a fusion to the calmoduling-binding protein. The fusion protein can be purified by affinity chromatography using a calmodulin resin." [PMID:14755292]
subset: PSI-MI slim
synonym: "cam tag" EXACT PSI-MI-short []
is_a: MI:0240 ! fusion protein
[Term]
id: MI:0813
name: proximity enzyme linked immunosorbent assay
def: "Method allowing efficient and precise interaction detection, along with extensive repertoires of specific binding reagents. It is based on proximity a ligation mechanism that enables sensitive high-capacity protein measurements by converting t...
subset: PSI-MI slim
synonym: "p elisa" EXACT PSI-MI-short []
synonym: "pELISA" EXACT PSI-MI-alternate []
is_a: MI:0400 ! affinity technology
is_a: MI:0421 ! identification by antibody
[Term]
id: MI:0814
name: protease accessibility laddering
def: "In protease accessibility laddering (PAL) tagged proteins are purified on magnetic beads in their natively folded state. While attached to the beads, proteins are probed with proteases. Proteolytic fragments are eluted and detected by immunobl...
subset: PSI-MI slim
synonym: "pal" EXACT PSI-MI-alternate []
synonym: "protease access" EXACT PSI-MI-short []
is_a: MI:0605 ! enzymatic footprinting
[Term]
id: MI:0815
name: confirmation by molecular weight
def: "Molecule whose sequence identity is derived from their molecular weight" [PMID:14755292]
subset: PSI-MI slim
synonym: "weight identificat" EXACT PSI-MI-short []
is_a: MI:0396 ! predetermined participant
[Term]
id: MI:0816
name: molecular weight estimation by staining
def: "Molecule whose sequence identity is derived from their molecular weight after a comigration in a gel with molecular weight marker." [PMID:14755292]
subset: PSI-MI slim
synonym: "weight by staining" EXACT PSI-MI-short []
is_a: MI:0815 ! confirmation by molecular weight
[Term]
id: MI:0817
name: molecular weight estimation by silver staining
def: "Molecule whose sequence identity is derived from their molecular weight after a comigration in a gel with molecular weight marker and staining of the molecules with silver." [PMID:14755292]
subset: PSI-MI slim
synonym: "weight silver stain" EXACT PSI-MI-short []
is_a: MI:0816 ! molecular weight estimation by staining
[Term]
id: MI:0818
name: molecular weight estimation by coomasie staining
def: "Molecule whose sequence identity is derived from their molecular weight after a comigration in a gel with molecular weight marker and staining of the molecules with comassie dye." [PMID:14755292]
subset: PSI-MI slim
synonym: "weight by comassie" EXACT PSI-MI-short []
is_a: MI:0816 ! molecular weight estimation by staining
[Term]
id: MI:0819
name: molecular weight estimation by bromide staining
def: "Molecule whose sequence identity is derived from their molecular weight after a comigration in a gel with molecular weight marker and staining of the molecules with bromide dyes." [PMID:14755292]
subset: PSI-MI slim
synonym: "weight by bromide" EXACT PSI-MI-short []
is_a: MI:0816 ! molecular weight estimation by staining
[Term]
id: MI:0820
name: molecular weight estimation by sybr staining
def: "Molecule whose sequence identity is derived from their molecular weight after a comigration in a gel with molecular weight marker and staining of the molecules with sybr dyes." [PMID:14755292]
subset: PSI-MI slim
synonym: "safe DNA gel stain" EXACT PSI-MI-alternate []
synonym: "weight by sybr" EXACT PSI-MI-short []
is_a: MI:0816 ! molecular weight estimation by staining
[Term]
id: MI:0821
name: molecular weight estimation by autoradiography
def: "Molecule whose sequence identity is derived from their molecular weight after a comigration in a gel with molecular weight marker and staining by autoradiography." [PMID:14755292]
subset: PSI-MI slim
synonym: "weight autoradiogra" EXACT PSI-MI-short []
is_a: MI:0815 ! confirmation by molecular weight
[Term]
id: MI:0822
name: molecular weight estimation by hoechst staining
def: "Molecule whose sequence identity is derived from their molecular weight after a comigration in a gel with molecular weight marker and staining of the molecules with Hoechst dyes." [PMID:14755292]
subset: PSI-MI slim
synonym: "weight by hoechst" EXACT PSI-MI-short []
is_a: MI:0816 ! molecular weight estimation by staining
[Term]
id: MI:0823
name: predetermined feature
def: "Feature detection not verified in the context of an experiment but assumed from external or previous experimental evidence(s)." [PMID:14755292]
subset: PSI-MI slim
synonym: "predetermined featur" EXACT PSI-MI-short []
is_a: MI:0093 ! protein sequence identification
is_a: MI:0427 ! Identification by mass spectrometry
is_a: MI:0659 ! experimental feature detection
[Term]
id: MI:0824
name: x-ray powder diffraction
def: "Analysis of a diffraction pattern generated by an isotropic sample composed of many randomly oriented crystals." [PMID:14755292]
subset: PSI-MI slim
synonym: "X-ray" EXACT PSI-MI-alternate []
synonym: "x-ray powder diffrac" EXACT PSI-MI-short []
is_a: MI:0114 ! x-ray crystallography
[Term]
id: MI:0825
name: x-ray fiber diffraction
def: "Analysis of the diffraction pattern of a partially ordered sample composed of fibers oriented parallel to each other using X-ray." [PMID:14755292]
subset: PSI-MI slim
synonym: "X-ray" EXACT PSI-MI-alternate []
synonym: "x-ray fiber diffrac" EXACT PSI-MI-short []
is_a: MI:0114 ! x-ray crystallography
[Term]
id: MI:0826
name: x ray scattering
def: "Method where the internal structure of a sample is derived from the intensity distribution of the scattered monochromatic X-ray beam at very low scattering angles." [PMID:14755292]
subset: PSI-MI slim
synonym: "saxs" EXACT PSI-MI-short []
is_a: MI:0067 ! light scattering
[Term]
id: MI:0827
name: x-ray tomography
def: "X-ray Tomography is a branch of X-ray microscopy. A series of projection images are used to calculate a three dimensional reconstruction of an object. The technique has found many applications in materials science and later in biology and biome...
subset: PSI-MI slim
is_a: MI:0428 ! imaging technique
[Term]
id: MI:0828
name: polyprotein fragment
def: "Subpart of a polyprotein that is naturally cleaved in vivo." [PMID:14577292]
subset: PSI-MI slim
synonym: "chain" RELATED []
synonym: "polyprotein frag" EXACT PSI-MI-short []
is_a: MI:0252 ! biological feature
[Term]
id: MI:0829
name: multiple parent reference
def: "This qualifier is used for hybrid or composite molecules with more than one cross-reference to parent molecules." [PMID:14755292]
subset: PSI-MI slim
synonym: "multiple parent" EXACT PSI-MI-short []
is_a: MI:0353 ! cross-reference type
[Term]
id: MI:0830
name: tissue list
def: "List of tissue used as topic in UniProt RC line.\nhttp://www.expasy.org/cgi-bin/lists?tisslist.txt" [PMID:14755292]
subset: PSI-MI slim
is_a: MI:0473 ! participant database
[Term]
id: MI:0831
name: cell ontology
def: "Ontology of cell types.\nhttp://obo.sourceforge.net/cgi-bin/detail.cgi?cell" [PMID:16381901]
subset: PSI-MI slim
is_a: MI:0473 ! participant database
[Term]
id: MI:0832
name: half cystine
def: "A protein modification that is effectively either one half of a cystine cross-link, or a cysteine residue with one hydrogen atom or proton removed" [MOD:00798, RESID:AA0025]
subset: PSI-MI slim
synonym: "Half of a disulfide bridge" EXACT PSI-MI-alternate []
is_a: MI:0179 ! other modification
[Term]
id: MI:0833
name: autoradiography
def: "Experimental method by which radiolabel is detected by exposure to a photographic emulsion forming a pattern on the film." [PMID:14755292]
subset: PSI-MI slim
is_a: MI:0659 ! experimental feature detection
is_a: MI:0866 ! tag visualisation
[Term]
id: MI:0834
name: ka
def: "Association rate constant or rate of complex formation. Unit MOLE per SECOND (M-1 s-1)" [PMID:14755292]
subset: PSI-MI slim
synonym: "kon" EXACT PSI-MI-short []
is_a: MI:0640 ! parameter type
[Term]
id: MI:0835
name: kd
def: "Dissociation rate constant measuring the stability of a complex. Unit SECOND (s-1)" [PMID:14755292]
subset: PSI-MI slim
synonym: "koff" EXACT PSI-MI-short []
is_a: MI:0640 ! parameter type
[Term]
id: MI:0836
name: temperature of interaction
def: "Temperature at which interaction was determined. Unit KELVIN (K)" [PMID:14755292]
scripts/Data/psi-mi.obo view on Meta::CPAN
subset: PSI-MI slim
synonym: "pHint" EXACT PSI-MI-alternate []
is_a: MI:0640 ! parameter type
[Term]
id: MI:0838
name: kelvin
def: "A scale that measures an object's temperature over absolute zero, the theoretical coolest temperature where all molecular and atomic motion ceases. On the Kelvin scale, the freezing point of water is 273 (273 K = 0 o C = 32 o F)." [PMID:1475529...
subset: PSI-MI slim
synonym: "K" EXACT PSI-MI-alternate []
is_a: MI:0647 ! parameter unit
[Term]
id: MI:0839
name: mole per second
def: "Per mole per second, unit for association rate constant" [PMID:14755292]
subset: PSI-MI slim
synonym: "M-1s-1" EXACT PSI-MI-alternate []
is_a: MI:0647 ! parameter unit
[Term]
id: MI:0840
name: stimulator
def: "Molecule stimulating an interaction by interacting with one or more of the participants." [PMID:14755292]
subset: PSI-MI slim
is_a: MI:0500 ! biological role
[Term]
id: MI:0841
name: phosphotransfer assay
def: "Measures the rate of a phosphate transfer between two proteins" [PMID:14755292]
subset: PSI-MI slim
synonym: "phosphotransfer assa" EXACT PSI-MI-short []
is_a: MI:0415 ! enzymatic study
[Term]
id: MI:0842
name: phosphate donor
def: "Any molecule that is able to transfer an phosphate to another chemical species." [PMID:14755292]
subset: PSI-MI slim
is_a: MI:0918 ! donor
[Term]
id: MI:0843
name: phosphate acceptor
def: "Molecule to which a phosphate may be transferred from a phosphate donor." [PMID:14755292]
subset: PSI-MI slim
is_a: MI:0919 ! acceptor
[Term]
id: MI:0844
name: phosphotransfer reaction
def: "Reaction where a phosphate is transferred between two proteins of a phosphorelay system. " [PMID:14755292, PMID:16712436]
subset: PSI-MI slim
synonym: "phosphotransfer" EXACT PSI-MI-short []
is_a: MI:0414 ! enzymatic reaction
[Term]
id: MI:0845
name: spin label
def: "Paramagnetic fragment, most often a cyclic nitroxide derivative, covalently attached to a molecule of interest." [PMID:10966640]
subset: PSI-MI slim
is_a: MI:0505 ! experimental feature
[Term]
id: MI:0846
name: r1 spin label
def: "Paramagnetic molecule (1-oxyl-2,2,5,5-tetramethylpyrroline-\n3-methyl)-methanethiosulfonate. that can be covalently attached to any cysteine aminoacid producing a nitroxide\nside chain designated R1." [PMID:10966640]
subset: PSI-MI slim
is_a: MI:0845 ! spin label
[Term]
id: MI:0847
name: dansyl tag
def: "Dansyl is fluorescent tag. Dansyl is the acronyme of 5-dimethylaminonaphthalene-1-sulfonyl radical group reacting with any NH2 groups." [PMID:14755292]
subset: PSI-MI slim
synonym: "5-dimethylaminonaphthalene-1-sulfonyl tag" EXACT PSI-MI-alternate []
synonym: "dansyl label" EXACT PSI-MI-alternate []
is_a: MI:0857 ! fluorescent dye label
[Term]
id: MI:0848
name: 125i radiolabel
def: "Molecule labelled with 125 radio isotope of iodine atoms." [PMID:14755292]
subset: PSI-MI slim
synonym: "125I" EXACT PSI-MI-alternate []
synonym: "I125" EXACT PSI-MI-alternate []
is_a: MI:0517 ! radiolabel
[Term]
id: MI:0849
name: ncbi taxonomy
def: "The NCBI taxonomy database indexes over 55 000 organisms that are represented in the sequence databases with at least one nucleotide or protein sequence. The Taxonomy Browser can be used to view the taxonomic position or retrieve sequence and s...
subset: PSI-MI slim
xref: id-validation-regexp:\"[0-9\]+\"
xref: search-url: "http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&id=${ac}&lvl=3&lin=f&keep=1&srchmode=1&unlock"
is_a: MI:0473 ! participant database
[Term]
id: MI:0850
name: encode
def: "ENCODE (the Encyclopedia Of DNA Elements) seeks to identify all protein-coding genes. The current ENCODE data set is derived from 1% of the human genome and has been selected for analysis in the pilot phase of the project.\nhttp://www.genome.go...
subset: PSI-MI slim
synonym: "ENCODE" EXACT PSI-MI-alternate []
synonym: "Encyclopedia Of DNA Elements" EXACT PSI-MI-alternate []
is_a: MI:0683 ! sequence database
[Term]
id: MI:0851
name: protein genbank identifier
def: "GenBank Identifier or GI numbers for proteins." [PMID:17170002]
subset: PSI-MI slim
synonym: "GenBank Protein GI" EXACT PSI-MI-alternate []
synonym: "genbank protein gi" EXACT PSI-MI-alternate []
synonym: "genbank_protein_gi" EXACT PSI-MI-short []
xref: id-validation-regexp:\"[0-9\]+\"
xref: search-url: "http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=protein&cmd=Retrieve&dopt=Graphics&list_uids=${ac}"
is_a: MI:0860 ! genbank indentifier
[Term]
id: MI:0852
scripts/Data/psi-mi.obo view on Meta::CPAN
subset: PSI-MI slim
synonym: "HAt" EXACT PSI-MI-alternate []
synonym: "hat" EXACT PSI-MI-short []
is_a: MI:0889 ! acetylation assay
[Term]
id: MI:0888
name: small angle neutron scattering
def: "During a SANS experiment a beam of neutrons is directed at a sample. The neutrons are elastically scattered by a sample and the resulting scattering pattern is analyzed to provide information about the size, shape and orientation of some compon...
subset: PSI-MI slim
synonym: "SANS" EXACT PSI-MI-alternate []
synonym: "sans" EXACT PSI-MI-short []
is_a: MI:0013 ! biophysical
[Term]
id: MI:0889
name: acetylation assay
def: "Measures the catalysis of the addition of an acetyl group to a target molecule." [PMID:14755292]
subset: PSI-MI slim
is_a: MI:0415 ! enzymatic study
[Term]
id: MI:0890
name: qdot
def: "Qdot are nanocrystals fluorophores . Nanocrystals a are extremely efficient materials for generating and they have a highly customizable surface for directing their bioactivity, producing a fluorescent probe that outperforms traditional dyes in...
subset: PSI-MI slim
is_a: MI:0857 ! fluorescent dye label
[Term]
id: MI:0891
name: neutron fiber diffraction
def: "Analysis of diffraction pattern of a partially ordered sample composed of fibers oriented parallel to each other using neutron beam." [PMID:10771422, PMID:15272083, PMID:15546977, PMID:15914673, PMID:16041074, PMID:16707576]
subset: PSI-MI slim
synonym: "neutron fiber diff" EXACT PSI-MI-short []
is_a: MI:0013 ! biophysical
[Term]
id: MI:0892
name: solid phase assay
def: "Assay where at least one molecule under analysis is bound to a solid surface, such as a microplate wall or the sides of a tube, the other reactants being free in solution." [PMID:14755292]
subset: PSI-MI slim
is_a: MI:0400 ! affinity technology
[Term]
id: MI:0893
name: neutron diffraction
def: "Analysis of diffraction pattern using neutron beam" [PMID:10771422, PMID:15272083, PMID:15546977, PMID:15914673, PMID:16041074, PMID:16707576]
subset: PSI-MI slim
is_a: MI:0013 ! biophysical
[Term]
id: MI:0894
name: electron diffraction
def: "Analysis of diffraction pattern using electron beam." [PMID:10949309, PMID:11034202, PMID:11171962, PMID:11532455, PMID:11700061, PMID:15141214, PMID:16325200]
subset: PSI-MI slim
is_a: MI:0013 ! biophysical
[Term]
id: MI:0895
name: protein kinase A complementation
def: "This method uses Renilla luciferase (Rluc)-based protein fragment complementation assay (PCA) that is designed specifically to investigate dynamic protein complexes (association and dissociation). It is chose to generate a PCA based on the Rluc...
subset: PSI-MI slim
synonym: "pka complementation" EXACT PSI-MI-short []
is_a: MI:0228 ! cytoplasmic complementation assay
[Term]
id: MI:0896
name: renilla luciferase protein tag
def: "Renilla luciferase, is an enzyme of the sea pansy catalyzing the oxidation of the lucifering pigment (reaction with ATP or oxigen) that produces light. This protein is often used as a vizualisation tag because compare to many fluorescent tag i...
subset: PSI-MI slim
synonym: "renilla lucirefase" EXACT PSI-MI-short []
is_a: MI:0240 ! fusion protein
[Term]
id: MI:0897
name: protein modification ontology
def: "Catalogue of covalent modification of, or a change resulting in an alteration of the measured molecular mass of, a peptide or protein amino acid residue." [PMID:14755292]
subset: PSI-MI slim
synonym: "psi-mod" EXACT PSI-MI-short []
xref: id-validation-regexp:\"MOD\:[0-9\]\{5}\"
is_a: MI:0447 ! feature database
[Term]
id: MI:0898
name: putative self
def: "Molecule that is reported to self-interact but the experimental condition does not allow to resolve whether the interaction is intramolecular (true self interaction) or intermolecular (homodimer)." [PMID:14755292]
subset: PSI-MI slim
is_a: MI:0495 ! experimental role
is_a: MI:0500 ! biological role
[Term]
id: MI:0899
name: p3 filamentous phage display
def: "pIII is one of the minor coat proteins that decorates in five copies the emerging tip of filamentous phage. Similarly to pVIII pIII also tolerates peptide insertions at the amino-terminus. The sequences to be displayed can either be encoded in ...
subset: PSI-MI slim
synonym: "low valency display" EXACT PSI-MI-alternate []
synonym: "p3 filamentous phage" EXACT PSI-MI-short []
is_a: MI:0048 ! filamentous phage display
[Term]
id: MI:0900
name: p8 filamentous phage display
def: "pVIII is the major coat protein of filamentous phage. Its amino-terminus is exposed to solvent and tolerates the insertion of relatively large peptide fragments. By inserting the peptide coding sequence into the phage copy of the pVIII gene up ...
subset: PSI-MI slim
synonym: "high valency display" EXACT PSI-MI-alternate []
synonym: "p8 filamentous phage" EXACT PSI-MI-short []
is_a: MI:0048 ! filamentous phage display
[Term]
id: MI:0901
name: isotope label footprinting
def: "Exposed amino acid residues undergo a rapid exchange of a specific radio-isotope e.g. hydrogen/deuterium. Residues involved in a molecular interaction are protected from this exchange and exhibit a much slower rate of exchange. This method of b...
subset: PSI-MI slim
synonym: "isotope footprinting" EXACT PSI-MI-short []
is_a: MI:0605 ! enzymatic footprinting
[Term]
id: MI:0902
name: rna cleavage
def: "Any process by which an RNA molecule is cleaved at specific sites or in a regulated manner." [GO:0006396, PMID:14681407]
subset: PSI-MI slim
is_a: MI:0910 ! nucleic acid cleavage
[Term]
id: MI:0903
name: mpidb
def: "The microbial protein-protein interactions database (MPDIB) aims to collect and provide all known physical prokaryotic interactions." [PMID:14755292]
subset: PSI-MI slim
synonym: "MPDIB" EXACT PSI-MI-alternate []
is_a: MI:0461 ! interaction database
[Term]
id: MI:0904
name: polysaccharide
def: "A polysaccharide is a complex polymer of carbohydrate monormers. They are polymers made up of many monosaccharides joined together by glycosidic bonds. They are therefore very large, often branched, macromolecules." [PMID:14755292]
subset: PSI-MI slim
is_a: MI:0383 ! biopolymer
[Term]
id: MI:0905
name: amplified luminescent proximity homogeneous assay
def: "AlphaScreen relies on the use of Donor and Acceptor beads that are coated with a layer of hydrogel providing functional groups for bioconjugation. When a biological interaction between molecules brings the beads into proximity, a cascade of che...
subset: PSI-MI slim
synonym: "alfa-screen" EXACT PSI-MI-short []
synonym: "AlphaScreen" EXACT PSI-MI-alternate []
is_a: MI:0013 ! biophysical
[Term]
id: MI:0906
name: au1 tag
def: "The protein of interest is expressed as a fusion to the peptide DTYRYI for which antibodies are commercially available." [PMID:18216269]
subset: PSI-MI slim
synonym: "DTYRYI epitope tag" EXACT PSI-MI-alternate []
is_a: MI:0507 ! tag
[Term]
id: MI:0907
name: conformational status
def: "Statement about the native/denatured conformation of the protein." [PMID:14755292]
subset: PSI-MI slim
synonym: "conformation" EXACT PSI-MI-short []
is_a: MI:0346 ! experimental preparation
[Term]
id: MI:0908
name: denatured
def: "Altered conformation state of the protein as a result of heat or chemical modification resulting in a changed structure of the protein." [PMID:14755292]
subset: PSI-MI slim
is_a: MI:0907 ! conformational status
[Term]
id: MI:0909
name: native
def: "State of the protein without interference i.e. the natural form." [PMID:14755292]
subset: PSI-MI slim
is_a: MI:0907 ! conformational status
[Term]
id: MI:0910
name: nucleic acid cleavage
def: "Covalent bond breakage of a nucleic acid molecule leading to the formation of smaller fragments." [PMID:14755292]
subset: PSI-MI slim
synonym: "ncl acid cleavage" EXACT PSI-MI-short []
is_a: MI:0194 ! cleavage reaction
[Term]
id: MI:0911
name: cross linker
def: "A variety of crosslinkers are used to analyze subunit structure of proteins, protein interactions and various parameters of protein function. Subunit structure is deduced since crosslinkers only bind surface amino residues in relatively close p...
subset: PSI-MI slim
synonym: "crosslinker" EXACT PSI-MI-alternate []
is_a: MI:0505 ! experimental feature
[Term]
id: MI:0912
name: spdp cross linker
def: "N -Succinimidyl 3-(2-pyridyldithio)-propionate, is heterobifunctional, thiol-cleavable \nand membrane permeable crosslinkers. It contains an amine-reactive N-hydroxysuccinimide (NHS) ester \nthat will react with lysine residues to form a stable...
subset: PSI-MI slim
synonym: "N -Succinimidyl 3-(2-pyridyldithio)-propionate" EXACT PSI-MI-alternate []
is_a: MI:0911 ! cross linker
[Term]
id: MI:0913
name: lc-spdp cross linker
def: "Succinimidyl 6-(3-[2-pyridyldithio]-propionamido)hexanoate, is an heterobifunctional, thiol-cleavable \nand membrane permeable crosslinkers. It contains an amine-reactive N-hydroxysuccinimide (NHS) ester \nthat will react with lysine residues t...
subset: PSI-MI slim
synonym: "Succinimidyl 6-(3-[2-pyridyldithio]-propionamido)hexanoate" EXACT PSI-MI-alternate []
is_a: MI:0912 ! spdp cross linker
[Term]
id: MI:0914
name: association
def: "Molecules that are experimentally shown to be associated potentially by sharing just one interactor. Often associated molecules are co-purified by a pull-down or coimmunoprecipitation and share the same bait molecule." [PMID:14755292]
subset: PSI-MI slim
is_a: MI:0190 ! interaction type
[Term]
id: MI:0915
name: physical association
def: "Molecules that are experimentally shown to belong to the same functional or structural complex." [PMID:14755292]
subset: PSI-MI slim
is_a: MI:0914 ! association
[Term]
id: MI:0916
name: lexa vp16 complementation
def: "Yeast two-hybrid system using Escherichia coli LexA amino acids 1-202 as the DNA-binding domain (BD), and a transcriptional activation domain from the herpes simplex virus protein VP16 (either aa 411-490 or aa 411-455) that can specifically act...
subset: PSI-MI slim
synonym: "lexa vp16 complement" EXACT PSI-MI-short []
synonym: "LexA VP16 transcription complementation" EXACT PSI-MI-alternate []
is_a: MI:0018 ! two hybrid
[Term]
id: MI:0917
name: matrixdb
def: "Knowledgebase of the extracellular matrix storing experimentally determined interactions involving extracellular biomolecules. It includes protein-protein, protein-polysaccharide, and protein-lipid interactions." [PMID:19147664]
subset: PSI-MI slim
is_a: MI:0461 ! interaction database
is_a: MI:0489 ! source database
[Term]
id: MI:0918
name: donor
def: "Molecule which emits electrons or ions that are transfered to an acceptor molecule." [PMID:14755292]
subset: PSI-MI slim
is_a: MI:0500 ! biological role
[Term]
id: MI:0919
name: acceptor
def: "Molecule able to receive electrons or ions from a donor molecule." [PMID:14755292]
subset: PSI-MI slim
is_a: MI:0500 ! biological role
[Term]
id: MI:0920
name: ribonuclease assay
def: "Measures the catalysis of the hydrolysis of phosphodiester bonds in chains of RNA." [PMID:14755292]
subset: PSI-MI slim
is_a: MI:0415 ! enzymatic study
[Term]
id: MI:0921
name: surface plasmon resonance array
def: "This array technology allows the screening of binding abilities of hundreds or thousands of biomolecules (small molecule, peptide, protein, sugar, lipid, nucleic acid, and their fragments) printed onto the gold-coated chip by using an instrumen...
subset: PSI-MI slim
synonym: "Biacore Flexchip(r)" EXACT PSI-MI-alternate []
synonym: "spr array" EXACT PSI-MI-short []
synonym: "SPRi-Plex " EXACT PSI-MI-alternate []
synonym: "SPRImager" EXACT PSI-MI-alternate []
is_a: MI:0008 ! array technology
is_a: MI:0107 ! surface plasmon resonance
[Term]
id: MI:0922
name: imex evidence
def: "Experimental evidence supporting an interaction curated and released under the IMEx agreement." [PMID:14755292]
subset: PSI-MI slim
is_a: MI:0353 ! cross-reference type
[Term]
id: MI:0923
name: irefindex
def: "iRefIndex provides an index of protein interactions available in a number of primary interaction databases including BIND, BioGRID, DIP, HPRD, IntAct, MINT, MPact, MPPI and OPHID. This index allows the user to search for a protein and retrieve...
subset: PSI-MI slim
synonym: "iRefIndex" EXACT PSI-MI-alternate []
is_a: MI:0461 ! interaction database
is_a: MI:0489 ! source database
[Term]
id: MI:0924
name: camjedb
def: "Camjedb is a comprehensive database for information on the genome of Campylobacter jejuni.\nhttp://www.sanger.ac.uk/Projects/C_jejuni/" [PMID:106882042]
subset: PSI-MI slim
is_a: MI:0683 ! sequence database
[Term]
id: MI:0925
name: observed ptm
def: "Post translational modification observed on a protein in the context of an interaction." [PMID:14755292]
subset: PSI-MI slim
is_a: MI:0668 ! feature attribute name
[Term]
id: MI:0926
name: fiash label
def: "This fluorescent label is a small ligand membrane-permeant and nonfluorescent until it binds with high affinity and specificity to the tetracysteine domain. Such in situ labeling adds much less mass than does green fluorescent protein and offe...
subset: PSI-MI slim
synonym: "4',5'-bis(1,3,2-dithioarsolan-2-yl)fluorescein " EXACT PSI-MI-alternate []
synonym: "FIAsH label" EXACT PSI-MI-alternate []
is_a: MI:0857 ! fluorescent dye label
[Term]
id: MI:0927
name: iaedans label
def: "IAEDANS is fluorescent tag that bind to cysteines. IAEDANS is the acronyme of (5((((2-iodoacetyl)amino)ethyl)amino)-naphthalene-1-sulfonic acid) with free SH groups." [PMID:11052891]
subset: PSI-MI slim
synonym: "(5((((2-iodoacetyl)amino)ethyl)amino)-naphthalene-1-sulfonic acid) " EXACT PSI-MI-alternate []
synonym: "1,5-IAEDANS" EXACT PSI-MI-alternate []
synonym: "IAEDANS" EXACT PSI-MI-alternate []
is_a: MI:0857 ! fluorescent dye label
[Term]
id: MI:0928
name: filter trap assay
def: "Biomolecules are mixed in a buffer and the resulting mixture is\npassed through a filter. Large\naggregates are retained on the filter and the pariticipants may then be identified." [PMID:10859365]
subset: PSI-MI slim
synonym: "<new synonym>" RELATED []
synonym: "filter binding" EXACT []
synonym: "filter retardation assay" RELATED []
synonym: "Filter retention assay" EXACT PSI-MI-alternate []
is_a: MI:0013 ! biophysical
is_a: MI:0091 ! chromatography technology
[Term]
id: MI:0929
name: nothern blot
def: "A standard procedure to identify RNA fragments containing specific\nsequences. In this procedure RNA fragments are separated by\nelectrophoresis, the fragments are transferred to a membrane and the\nmembrane is incubated with a radio labelled p...
subset: PSI-MI slim
synonym: "northen" EXACT PSI-MI-alternate []
is_a: MI:0078 ! nucleotide sequence identification
[Term]
id: MI:0930
name: epistatic genetic interaction
def: "The genetic interaction between a group of genes, in which the effects of an allele of one member gene of the group hide the effects of alleles of other genes in the group." [PMID:11988766]
subset: PSI-MI slim
synonym: "epistatis" EXACT PSI-MI-short []
is_a: MI:0935 ! positive genetic interaction
[Term]
id: MI:0931
name: genetic interaction defined by inequality
def: "Two genes A and B present an genetic interaction defined by inequality if the phenotypes of the two single mutants a and b, the double mutant ab and the wild-type WT can be measured quantitatively and described relative to each other by an i...
subset: PSI-MI slim
synonym: "genetic inequality" EXACT PSI-MI-short []
is_a: MI:0208 ! genetic interaction
[Term]
id: MI:0932
name: noninteractive genetic interaction defined by inequality
def: "Mutation that has no effect in the WT and b backgrounds, or b has no effect in the a and WT backgrounds, or both hold true. E. g., WT = a > b = ab." [PMID:15833125]
subset: PSI-MI slim
synonym: "noninteractive" EXACT PSI-MI-short []
synonym: "noninteractive genetic interaction (sensu inequality)" EXACT PSI-MI-alternate []
is_a: MI:0931 ! genetic interaction defined by inequality
is_a: MI:0934 ! neutral genetic interaction
[Term]
id: MI:0933
name: negative genetic interaction
def: "The phenotype of the double mutant ab is stronger than expected from the combination of the individual effects of a and b." [PMID:14755292]
subset: PSI-MI slim
synonym: "negative gen int" EXACT PSI-MI-short []
is_a: MI:0208 ! genetic interaction
[Term]
id: MI:0934
name: neutral genetic interaction
def: "The phenotype of the double mutant ab is equal to the phenotype expected from the combination of the individual effects of a and b." [PMID:14755292]
subset: PSI-MI slim
synonym: "neutral gent int" EXACT PSI-MI-short []
is_a: MI:0208 ! genetic interaction
[Term]
id: MI:0935
name: positive genetic interaction
def: "The phenotype of the double mutant ab is weaker than expected from the combination of the individual effects of a and b." [PMID:14755292]
subset: PSI-MI slim
synonym: "positive gent int" EXACT PSI-MI-short []
is_a: MI:0208 ! genetic interaction
[Term]
id: MI:0936
name: emdb
def: "The Electron Microscopy Data Bank (EMDB) contains experimentally determined three-dimensional maps and associated experimental data and files." [PMID:14643225]
subset: PSI-MI slim
synonym: "Electron Microscopy Data Bank" EXACT PSI-MI-alternate []
synonym: "eMDB" EXACT PSI-MI-short []
is_a: MI:0472 ! pdbe
[Term]
id: MI:0937
name: glu tag
def: "This peptide is a 314 to 319 amino acids fragment of the middle T antigen of mouse polymavirus. Glu-Glu epitope peptide." [PMID:8077219]
subset: PSI-MI slim
synonym: "glu tag" EXACT PSI-MI-short []
is_a: MI:0507 ! tag
[Term]
id: MI:0938
name: rheology measurement
def: "Characterization of viscoelastic properties of biomolecule solution is used to infer interactions between molecules." [PMID:18445655]
subset: PSI-MI slim
synonym: "rheology" EXACT PSI-MI-short []
is_a: MI:0013 ! biophysical
[Term]
id: MI:0939
name: fluorescein label
def: "Fluorescence label used to monitor the presence of a protein." [PMID:14755292]
subset: PSI-MI slim
synonym: "fluorescein" EXACT PSI-MI-short []
is_a: MI:0857 ! fluorescent dye label
[Term]
id: MI:0940
name: fluorescein-5-maleimide label
def: "Fluorescein-5-maleimide is one of the most popular fluorescent dyes for thiol modifications of proteins at cysteine residues that either are intrinsically present or result from reduction of cystines. Unlike iodoacetamides, maleimides do not re...
subset: PSI-MI slim
synonym: "fluor-5-maleimide" EXACT PSI-MI-short []
is_a: MI:0939 ! fluorescein label
[Term]
id: MI:0941
name: competitor
def: "Binds to the bait molecule in competition with other prey molecules, for example at a shared binding site." [PMID:14755292]
subset: PSI-MI slim
synonym: "competitor" EXACT PSI-MI-short []
is_a: MI:0500 ! biological role
[Term]
id: MI:0942
name: uniprot taxonomy
def: "Based on NCBO Taxonomy but adapted for UniProt\nhttp://www.uniprot.org/taxonomy/" [PMID:18836194]
subset: PSI-MI slim
synonym: "uniprot taxon" EXACT PSI-MI-alternate []
xref: id-validation-regexp:\"[0-9\]+\"
xref: search-url: "http://www.uniprot.org/taxonomy/${ac}"
is_a: MI:0473 ! participant database
[Term]
id: MI:0943
name: detection by mass spectrometry
def: "'Study of interactions by an analytical technique based on measurements of mass-to-charge ratio of charged particles in a mass spectrometer." [PMID:14755292]
subset: PSI-MI slim
synonym: "ms interact detect" EXACT PSI-MI-short []
is_a: MI:0013 ! biophysical
[Term]
id: MI:0944
name: mass spectrometry study of hydrogen/deuterium exchange
def: "Mass spectroscopy based measurement of the rate and/or extent of the hydrogen/deuterium exchange." [PMID:18948593]
subset: PSI-MI slim
synonym: "h1-h2 ms" EXACT PSI-MI-short []
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