Bio-Homology-InterologWalk
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scripts/Data/psi-mi.obo view on Meta::CPAN
[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 []
scripts/Data/psi-mi.obo view on Meta::CPAN
[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
scripts/Data/psi-mi.obo view on Meta::CPAN
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
scripts/Data/psi-mi.obo view on Meta::CPAN
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 []
scripts/Data/psi-mi.obo view on Meta::CPAN
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 []
scripts/Data/psi-mi.obo view on Meta::CPAN
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
scripts/Data/psi-mi.obo view on Meta::CPAN
[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
scripts/Data/psi-mi.obo view on Meta::CPAN
[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 []
scripts/Data/psi-mi.obo view on Meta::CPAN
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
scripts/Data/psi-mi.obo view on Meta::CPAN
[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
scripts/Data/psi-mi.obo view on Meta::CPAN
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
scripts/Data/psi-mi.obo view on Meta::CPAN
[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 []
scripts/Data/psi-mi.obo view on Meta::CPAN
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
scripts/Data/psi-mi.obo view on Meta::CPAN
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 []
scripts/Data/psi-mi.obo view on Meta::CPAN
[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
scripts/Data/psi-mi.obo view on Meta::CPAN
[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
scripts/Data/psi-mi.obo view on Meta::CPAN
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 []
scripts/Data/psi-mi.obo view on Meta::CPAN
[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
scripts/Data/psi-mi.obo view on Meta::CPAN
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 []
scripts/Data/psi-mi.obo view on Meta::CPAN
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
scripts/Data/psi-mi.obo view on Meta::CPAN
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
scripts/Data/psi-mi.obo view on Meta::CPAN
[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
scripts/Data/psi-mi.obo view on Meta::CPAN
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
scripts/Data/psi-mi.obo view on Meta::CPAN
[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 []
scripts/Data/psi-mi.obo view on Meta::CPAN
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
scripts/Data/psi-mi.obo view on Meta::CPAN
[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 []
scripts/Data/psi-mi.obo view on Meta::CPAN
[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
scripts/Data/psi-mi.obo view on Meta::CPAN
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 []
scripts/Data/psi-mi.obo view on Meta::CPAN
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 []
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