format-version: 1.0
date: 11:03:2009 20:53
saved-by: dg
auto-generated-by: OBO-Edit 1.101
default-namespace: PAR

[Term]
id: PAR:0001
name: interaction detection method
def: "Method to generate of characterize a binder." [pubmed:14755292 "primary-reference"]
exact_synonym: "interaction detect" []
relationship: part_of PAR:1004 ! PROTEIN AFFINITY REAGENT CV

[Term]
id: PAR:0002
name: participant identification method
def: "Method to determine the proteins involved in the interaction." [pubmed:14755292 "primary-reference"]
related_synonym: "participant detection" []
exact_synonym: "participant ident" []
relationship: part_of PAR:1004 ! PROTEIN AFFINITY REAGENT CV

[Term]
id: PAR:0003
name: feature detection method
def: "Method to determine the features of the proteins involved in the interaction." [pubmed:14755292 "primary-reference"]
exact_synonym: "feature detection" []
relationship: part_of PAR:1004 ! PROTEIN AFFINITY REAGENT CV

[Term]
id: PAR: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, antibodies specific for the bait itself, antibodies for specific tags engineered to be expressed as part of the bait or other high affinity binders such as glutathione resins for GST fusion proteins, metal resins for histidine-tagged proteins." [pubmed:7708014 "primary-reference"]
related_synonym: "Affinity purification" []
exact_synonym: "affinity chrom" []
is_a: PAR:0091 ! chromatography technology
is_a: PAR:0661 ! experimental participant identification

[Term]
id: PAR: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 mutating each residue of interest to an alanine. The mutated proteins are expressed, tested for proper folding and probed in the binding assay." [pubmed:14755292 "primary-reference"]
is_a: PAR:0810 ! substitution analysis

[Term]
id: PAR: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 simultaneous assay, in controlled conditions, of several thousand proteins/peptides/nucleic acids for different functions, for instance their ability to bind any given molecule." [pubmed:14755292 "primary-reference"]
is_a: PAR:0401 ! biochemical

[Term]
id: PAR: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 fragment, consisting of the variable heavy and variable light domains from two separate anti-digoxin monoclonal antibodies, was displayed on the outer membrane of Escherichia coli by fusing it to an Lpp-OmpA. Similar systems have also been developed for gram positive bacteria. Fluorescence-activated cell sorting (FACS), is used to specifically select clones displaying a protein binding to scFv-producing cells." [pubmed:10436088 "primary-reference", pubmed:8248129 "method reference"]
is_a: PAR:0034 ! display technology
is_a: PAR:0054 ! fluorescence-activated cell sorting

[Term]
id: PAR: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 through a resonance energy transfer mechanism. As with FRET the energy transfer occurs only if the protein fused to the luciferase and the one fused to the acceptor fluorophore are in close proximity (10-100 Angstrom)." [pubmed:10725388 "see-also", pubmed:9874787 "primary-reference"]
related_synonym: "BRET" []
related_synonym: "LRET" []
exact_synonym: "bret" []
is_a: PAR:0051 ! fluorescence technology

[Term]
id: PAR:0013
name: biophysical
def: "The application of physical principles and methods to biological experiments." [pubmed:14755292 "primary-reference"]
is_a: PAR:0001 ! interaction detection method

[Term]
id: PAR: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 light of equal amplitude and phase but opposite handness. When this light passes through an optically active sample the two polarized components are absorbed differently. The difference in left and right handed absorbance A(l)- A(r) is the signal registered in CD spectra. This signal displays distinct features corresponding to different secondary structures present in peptides, proteins and nucleic acids. The analysis of CD spectra can therefore yield valuable information about the secondary structure of biological macromolecules and the interactions among molecules that influence their structure." [pubmed:11578931 "primary-reference"]
related_synonym: "CD" []
exact_synonym: "cd" []
is_a: PAR:0013 ! biophysical

[Term]
id: PAR: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 intrinsic fluorescence. Changes in the fluorescence emission spectrum on complex formation can occur either due to a shift in the wavelength of maximum fluorescence emission or by a shift in fluorescence intensity caused by the mixing of two proteins. The interaction of two proteins causes a shift in the fluorescence emission spectrum relative to the sum of the individual fluorescence spectra, resulting in a difference spectrum [F (complex)-2 F (sum)], which is a measurable effect of the interaction. Loss of fluorescence signal from a substrate can be used to measure protein cleavage." [pubmed:7708014 "primary-reference"]
exact_synonym: "fluorescence spectr" []
is_a: PAR:0051 ! fluorescence technology

[Term]
id: PAR: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 the cell. This method supports very high resolution colocalisation of different molecules in a cell." [pubmed:14755292 "primary-reference"]
exact_synonym: "tem" []
is_a: PAR:0040 ! electron microscopy

[Term]
id: PAR:0027
name: cosedimentation
def: "Separation of a protein mixture under the influence of artificial gravity." [pubmed:14755292 "primary-reference"]
is_a: PAR:0401 ! biochemical

[Term]
id: PAR: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 also possible to measure the association state of the sample. Both the mass of a molecule and its shape, that influences the friction forces and diffusion that counterbalances gravity, determine the sedimentation speed." [pubmed:10410796 "primary-reference"]
exact_synonym: "solution sedimentati" []
is_a: PAR:0027 ! cosedimentation

[Term]
id: PAR: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 constant. By varying the concentration of one or both of the complex constituents and taking into account the dilution of the species during sedimentation, one can reasonably accurately estimate the binding constant." [pubmed:10410796 "primary-reference"]
exact_synonym: "density sedimentatio" []
is_a: PAR:0027 ! cosedimentation

[Term]
id: PAR: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." [pubmed:14755292 "primary-reference"]
exact_synonym: "crosslink" []
is_a: PAR:0401 ! biochemical

[Term]
id: PAR: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 the disulfide bridge is cleaved, the cross-linked pairs are released and can be identified. There are various classes of cross-linkers, the most common are those having photoreactive groups that become reactive fluorophores when activated by UV light thereby resulting in photolabeling the cross-linked moieties." [pubmed:10679368 "primary-reference", pubmed:7708014 "method reference"]
related_synonym: "Label transfer techniques" []
related_synonym: "Photoaffinity labelling" []
exact_synonym: "protein crosslink" []
is_a: PAR:0030 ! cross-linking study

[Term]
id: PAR: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 permits to reveal the identity of the residue that has been removed at each degradation step by measuring the mass difference of fragments differing of one residue. Peptide fragments can be obtained by protease treatment combined with the fragmentation promoted by collision (or other methods) within a tandem mass spectrometer. This approach can be carried out with LC MS/MS (Liquid Chromatography Tandem Mass Spectrometry), nanoESI MS/MS (nanoElectrospray Ionisation tandem mass spectrometry), or FTMS (Fourier Transform mass spectrometry) instruments." [pubmed:10984529 "primary-reference"]
exact_synonym: "ms protein sequence" []
is_a: PAR:0093 ! protein sequence identification
is_a: PAR:0427 ! mass spectrometry

[Term]
id: PAR: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." [pubmed:14755292 "primary-reference"]
is_a: PAR:0074 ! mutation analysis

[Term]
id: PAR: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 encoding a peptide with desired binding properties can be selected over an excess of up to 1012 unrelated molecules." [pubmed:14755292 "primary-reference"]
is_a: PAR:0401 ! biochemical

[Term]
id: PAR: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." [pubmed:9013660 "primary-reference"]
exact_synonym: "dls" []
is_a: PAR:0067 ! light scattering

[Term]
id: PAR: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 20-30 consecutive cycles can be performed and lead to amino acid identification. Longer polypeptides or full length proteins must be cleaved by specific protease before Edman degradation and their sequences built by fragment overlapping." [pubmed:14755292 "primary-reference"]
is_a: PAR:0433 ! partial identification of protein sequence

[Term]
id: PAR: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 crystals. Different types of samples can be analysed by electron microscopy: crystals, single particles like viruses, macromolecular complexes or entire cells and tissue sections. Samples can be chemically fixed or vitrified by rapid freezing in liquid ethane, and then transferred into the electron microscope. Data collection consists of the recording of electron diffraction data (2D crystals) and images. Depending on the type of sample, different approaches are used to analyse and merge images and electron diffraction data." [pubmed:11785754 "primary-reference"]
related_synonym: "Electron cryomicroscopy" []
related_synonym: "Electron crystallography" []
is_a: PAR:0428 ! imaging techniques

[Term]
id: PAR: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." [pubmed:11817959 "primary-reference", pubmed:11988476 "method reference", pubmed:12186859 "see-also"]
related_synonym: "ENDOR" []
exact_synonym: "endor" []
is_a: PAR:0043 ! electron resonance

[Term]
id: PAR: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 species); the EPR spectrum provides information about the environment and mobility of the paramagnetic species. The magnetic interaction of two paramagnetic centres in a protein can be used to calculate the distance between them; this allows studies of the movements and interactions of protein segments. In proteins without any intrinsic unpaired electrons it is possible to attach a radical probe (spin label). Stable nitroxide radicals can be bound to amino acid residues, in analogy with fluorescent probes. In combination with site directed mutagenesis this method is used in particular to study structure and assembly of membrane proteins, by measuring with EPR whether an amino acid is in a polar or non polar environment." [pubmed:11817959 "primary-reference"]
related_synonym: "EPR" []
related_synonym: "ESR" []
exact_synonym: "epr" []
is_a: PAR:0043 ! electron resonance

[Term]
id: PAR: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." [pubmed:14755292 "primary-reference"]
is_a: PAR:0013 ! biophysical

[Term]
id: PAR: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 gel electrophoresis to increase the sensitivity of the method for detecting interactions with rare proteins. Denaturants are removed during the blotting procedure, which allows many proteins to recover (or partially recover) activity. However, if biological activity is not recoverable, the proteins can be fractionated by a non denaturing gel system. This variation of the method eliminates the problem of activity regeneration and allows the detection of binding when the presence of a protein complex is required for binding. The protein probe can be prepared by any one of several procedures, while fusion affinity tags greatly facilitate purification. Synthesis in E. coli with a GST fusion, epitope tag, or other affinity tag is most commonly used. The protein of interest can then be radioactively labelled, biotinylated, or used in the blotting procedure as an unlabeled probe that is detected by a specific antibody." [pubmed:7708014 "primary-reference"]
related_synonym: "Affinity blotting" []
is_a: PAR:0401 ! biochemical

[Term]
id: PAR: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 successfully. Most experiments have taken advantage of the ability to assemble phages decorated with hybrid versions of the receptor protein pIII or of the major coat protein pVIII. Both systems allow the display of foreign peptides by fusion to the amino-terminus of the capsid protein but differ in the number of peptide copies that can be displayed on each phage particle. Display libraries of very diverse protein fragments have been constructed by fusing either genomic or cDNA fragments to gene III or gene VIII." [pubmed:7682645 "primary-reference"]
exact_synonym: "filamentous phage" []
is_a: PAR:0084 ! phage display

[Term]
id: PAR: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 expressed by different clones of an expression library are bound to a nitrocellulose membrane, by colony (bacterial library) or plaque (phage library) blotting. A labelled protein can then be used as a probe to identify clones expressing proteins that interact with the probe. Interactions occur on the nitrocellulose filters. The method is highly general and therefore widely applicable. A variety of approaches can be used to label the ligand, alternatively the ligand can be detected by a specific antibody. " [pubmed:7708014 "primary-reference"]
related_synonym: "Filter overlay assay" []
is_a: PAR:0401 ! biochemical

[Term]
id: PAR: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 than the one of excitatory radiation, occurs within 10-8 seconds." [pubmed:14755292 "primary-reference"]
exact_synonym: "fluorescence" []
is_a: PAR:0013 ! biophysical

[Term]
id: PAR: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 dependent on the particle mass. As a consequence, any increase in the mass of a biomolecule, e.g. as a result of an interaction with a second molecule, is readily detected as an increase in the diffusion time of the particle. From these results the concentration of the different molecules can be calculated as well as their binding constant." [pubmed:10733953 "primary-reference"]
related_synonym: "FCS" []
exact_synonym: "fcs" []
is_a: PAR:0051 ! fluorescence technology

[Term]
id: PAR: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-polarized light, followed by measurement of the emission at parallel and perpendicular planes. Since rotational correlation times depend on the size of the molecule, this method can be used to measure the binding of two proteins because the observed polarization increase when a larger complex is formed. A fluorescence anisotropy experiment is normally carried out with a protein bearing a covalently added fluorescent group, which increases both the observed fluorescence lifetime of the excited state and the intensity of the fluorescent signal. Residue modification can be assessed by addition of an antibody which binds to the modified residue and alters the molecular weight of the complex. A variation of this technique has been used to show interaction of a DNA binding protein with another protein. In this case the DNA rather than protein is fluorescently labelled." [pubmed:12805227 "primary-reference", pubmed:7708014 "method reference"]
related_synonym: "Fluorescence anisotropy" []
related_synonym: "FPS" []
exact_synonym: "fps" []
is_a: PAR:0051 ! fluorescence technology

[Term]
id: PAR: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 scattering experiment can be carried out on entire cells. With this instrument, interactions occurring either on cell surfaces or in any other subcellular location can be studied by using suitable fluorescent labels." [pubmed:11988464 "primary-reference"]
related_synonym: "FACS" []
related_synonym: "Flow cytometry" []
exact_synonym: "facs" []
is_a: PAR:0051 ! fluorescence technology

[Term]
id: PAR: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 cotransfected. Three basic conditions must be fulfilled for FRET to occur between a donor molecule and acceptor molecule. First, the donor emission spectrum must significantly overlap the absorption spectrum of the acceptor. Second, the distance between the donor and acceptor fluorophores must fall within the range 20 to 100 Angstrom. Third, the donor and acceptor fluorophores must be in favourable orientations." [pubmed:11558993 "primary-reference"]
related_synonym: "FRET" []
related_synonym: "FRET analysis" []
related_synonym: "RET" []
exact_synonym: "fret" []
is_a: PAR:0051 ! fluorescence technology

[Term]
id: PAR:0056
name: full identification by 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 along the DNA chain. The key to this method is the use of dideoxyribonucleoside triphosphates in which the deoxyribose 3'-OH group present in normal nucleotides is missing; when such a modified nucleotide is incorporated into a DNA chain, it blocks the elongation of the chain. To determine the full sequence, the four different chain-terminating dideoxyribonucleosides are used in competition with an excess of deoxyribonucleosides in separate DNA synthesis reactions on the same DNA template. When the products of these four reactions are analysed by electrophoresis in four parallel lanes of a denaturing polyacrylamide gel, the DNA sequence can be derived. Every lane displays a family of DNA fragments of different lengths, reflecting the different sites at which a specific residue occurs in the original DNA." [pubmed:14755292 "primary-reference"]
exact_synonym: "full dna sequence" []
is_a: PAR:0078 ! nucleotide sequence identification

[Term]
id: PAR: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 per injection) into the reaction cell (~1mL) containing the second reactant. The chemical reaction occurring after each injection either releases or absorbs heat (qi) proportional to the amount of ligand that binds to the protein with a characteristic binding enthalpy (DH). As modern ITC instruments operate on the heat compensation principle, the instrumental response (measured signal) is the amount of power (microcalories per second) necessary to maintain constant the temperature difference between the reaction and the reference cells. Because the amount of uncomplexed protein available progressively decreases after each successive injection, the magnitude of the peaks becomes progressively smaller until complete saturation is achieved. The difference between the concentration of bound ligand in the ith and (i-1)th injections depends on the binding constant Ka and the total ligand injected. The calculations depend on the binding model (number of substrates). Analysis of the data yields DH and DG = -RTlnKa. The entropy change is obtained by using the standard thermodynamic expression DG = DH-TDS." [pubmed:11785756 "primary-reference"]
related_synonym: "ITC" []
exact_synonym: "itc" []
is_a: PAR:0013 ! biophysical

[Term]
id: PAR: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 protein pD have been used for displaying (C or N terminally) foreign peptides on the viral capsid." [pubmed:7682645 "primary-reference"]
exact_synonym: "lambda phage" []
is_a: PAR:0084 ! phage display

[Term]
id: PAR: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 directly through the sample. A small portion of the light is scattered; the scattered light intensity containing information about the scattering particle is detected at an angle (typically in the range 15-180degrees) from the direction of the incident beam." [pubmed:9013660 "primary-reference"]
is_a: PAR:0013 ! biophysical

[Term]
id: PAR: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 instance a phosphatase. The mass difference corresponds to the mass of the chemical group covalently linked to a residue. Such experiments carried out with a MALDI-TOF (Matrix-assisted laser desorption ionization time-of-flight ) do not allow the mapping of the modification site within the sequence, whereas any tandem mass spectrometer (LC MS/MS Liquid Chromatography Tandem Mass Spectrometry, nanoESI MS/MS nanoElectrospray Ionisation tandem mass spectrometry, FTMS Fourier Transform mass spectrometry) provide such information. A second approach consists of the direct mass measurement of the ionized chemical group dissociated from the residue within a tandem mass spectrometer. Both approaches need a prior enrichment of the modified peptide population in the samples with IMAC (Immobilized Metal Affinity Chromatography)or specific anti-modification antibodies." [pubmed:11395414 "primary-reference", pubmed:11875433 "see-also"]
exact_synonym: "modified residue ms" []
is_a: PAR:0659 ! experimental feature detection

[Term]
id: PAR: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 monitoring changes in different experimental conditions, or to investigate how variations of collision energy affect their dissociation. Complexes can be transferred into the gas phase by a nanoflow ESI (Electrospray Ionisation) ionisation device. This is the method of choice for the investigation of the higher-order structure of biomolecules because it allows direct analysis of dilute aqueous solutions and the desolvation process is efficient and closer to the native-like solution environment. Mass measurements of intact macromolecular complexes is largely the domain of time of-flight (TOF) MS. This is mostly due to the high sensitivity and speed of TOF analysis, as well as the virtually unlimited m/z range. Quadrupole TOF (Q-TOF) type mass spectrometers combine a quadrupole mass filter with an orthogonal TOF analyser. These spectrometers provide supplementary structural information for ions isolated in the quadrupole and analysed in the TOF. This allows complexes well in excess of 60 kDa to be dissociated and consequently their subunit composition can be determined." [pubmed:12057199 "see-also", pubmed:12504676 "primary-reference"]
exact_synonym: "ms of complexes" []
is_a: PAR:0013 ! biophysical

[Term]
id: PAR: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 unequivocally identification of the type of modification that has caused the shift, it is possible, by combining this approach with more direct methods, to correlate the extent of the shift to a specific modification." [pubmed:14755292 "primary-reference"]
is_a: PAR:0659 ! experimental feature detection

[Term]
id: PAR: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 observation that two proteins, loaded on a sieving column, elute in a fraction(s) corresponding to a MW that is larger than the MW of either protein may be taken as an indication that the two proteins interact. Furthermore this technique provides a conceptually simple method for evaluating the affinity of the interaction." [pubmed:7708014 "primary-reference"]
related_synonym: "Gel Filtration" []
related_synonym: "Siezing column" []
related_synonym: "Size Exclusion Chromatography" []
is_a: PAR:0013 ! biophysical
is_a: PAR:0091 ! chromatography technology

[Term]
id: PAR: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." [pubmed:14755292 "primary-reference"]
exact_synonym: "monoclonal western" []
is_a: PAR:0113 ! western blot

[Term]
id: PAR: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 the ribosome reaches the RNA-DNA junction the ribosome stalls and the puromycin moiety enters the peptidyltransferase site of the ribosome and forms a covalent linkage to the nascent polypeptide. As a result the protein and the mRNA are covalently joined and can be isolated from the ribosome and purified. In the current protocol, a cDNA strand is then synthesised to form a less sticky RNA-DNA hybrid and these complexes are finally used for affinity selection. As in most display approaches, several selections cycles (3-6) are sufficient to enrich for mRNAs encoding ligand proteins." [pubmed:11551470 "primary-reference"]
is_a: PAR:0034 ! display technology

[Term]
id: PAR:0074
name: mutation analysis
def: "Several mutant molecules are produced by random or directed techniques and assayed for their ability to support binding. Mutants defective in binding are tested for correct folding to pinpoint the residues that are directly involved in binding." [pubmed:14755292 "primary-reference"]
is_a: PAR:0659 ! experimental feature detection

[Term]
id: PAR:0077
name: nuclear magnetic resonance
def: "NMR requires a small volume of concentrated protein 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 bar magnet. The spin aligns along the strong magnetic field, but can be changed to a misaligned excited state in response to applied radio frequency (RF) pulses of electromagnetic radiation. When the excited hydrogen nuclei relax to their aligned state, they emit RF radiation, which can be measured and displayed as a spectrum. The nature of the emitted radiation depends on the environment of each hydrogen nucleus, and if one nucleus is excited, it will influence the absorption and emission of radiation by other nuclei that lie close to it. It is consequently possible, by an ingenious elaboration of the basic NMR technique known as two-dimensional NMR, to distinguish the signals from hydrogen nuclei in different amino acid residues and to identify and measure the small shifts in these signals that occur when these hydrogen nuclei lie close enough to interact: the size of such a shift reveals the distance between the interacting pair of hydrogen atoms. In this way NMR can give information about the distances between the parts of the protein molecule. NMR provides information about interacting atoms thereby permitting to obtain information about protein structure and protein-protein interaction." [pubmed:12062432 "see-also", pubmed:12120505 "primary-reference"]
related_synonym: "NMR" []
exact_synonym: "nmr" []
is_a: PAR:0013 ! biophysical

[Term]
id: PAR: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." [pubmed:14755292 "primary-reference"]
related_synonym: "sequence cloning" []
exact_synonym: "nucleotide sequence" []
is_a: PAR:0661 ! experimental participant identification

[Term]
id: PAR:0080
name: partial dna sequence identification by hybridization
def: "Genes are recognised by hybridization of a probe with a fragment of the gene sequence." [pubmed:14755292 "primary-reference"]
exact_synonym: "partial dna sequence" []
is_a: PAR:0078 ! nucleotide sequence identification

[Term]
id: PAR: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 individually accessed by manual or automated delivery of the appropriate reagent solutions. Over the past few years protein-protein recognition, peptide-metal ion interactions, peptide-nucleic acid binding, enzymatic modification of peptides experiments, have been explored using synthetic peptide arrays on planar support." [pubmed:11167074 "primary-reference"]
is_a: PAR:0008 ! array technology

[Term]
id: PAR: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 by MALDI-MS (Matrix-assisted laser desorption ionization mass spectrometry). The list of peptide masses obtained by MALDI MS is automatically compared to the calculated masses of the predicted peptide fragments for each entry in the database. High mass accuracy is very important in order to obtain a statistically significant and unambiguous match This method is best applied to completely sequenced genomes and well characterised proteomes. However, depending on the data quality, proteins that are highly homologous to already characterised proteins (greater than 80 to 90% sequence identity) can also be identified. The retrieved sequence are evaluated by mass accuracy of the peptides, matching of additional peptide masses in the MALDI spectrum after accounting for common modifications such as oxidation, acrylamidation of cysteine and missed cleavages and the use of secondary information (apparent isoelectric point and molecular weight). If any ambiguity about the identification by MALDI-MS still exists, the results must verified by an other identification method. Peptide mass fingerprint is generally carried out with a MALDI-TOF (Matrix-assisted laser desorption ionization time-of-flight ) instrument but can also be achieved ESI-TOF (Electrospray Ionisation time-of-flight) or LC-MS (Liquid Chromatography-Mass Spectrometry) mass spectrometer." [pubmed:10967324 "primary-reference", pubmed:11752590 "method reference", pubmed:11805826 "see-also"]
exact_synonym: "fingerprinting" []
is_a: PAR:0427 ! mass spectrometry
is_a: PAR:0433 ! partial identification of protein sequence
is_a: PAR:0815 ! confirmation by molecular weight

[Term]
id: PAR: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 and by testing them in the binding assay. Synthetic peptides that are identical with peptides synthesised in vivo are useful experimental tools for such studies. Peptides are routinely synthesised in a test tube from monomeric amino acids by condensation reactions that form peptide bonds. Peptides are constructed sequentially by coupling the C-terminus of a monomeric amino acid to the N-terminus of the growing peptide. To prevent unwanted reactions involving the amino groups and carboxyl groups of the side chains during the coupling steps, a protecting (blocking) group is attached to the side chains. Without these protecting groups, branched peptides would be generated. In the last steps of synthesis, the side chain-protecting groups are removed and the peptide is cleaved from the resin on which synthesis occurs." [pubmed:14755292 "primary-reference"]
is_a: PAR:0093 ! protein sequence identification
is_a: PAR:1075 ! chemical synthesis

[Term]
id: PAR: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 display peptides that bind to any given bait molecule for instance an antibody. The selection is performed by a series of cycles of affinity purification known as panning. The bait protein, immobilized on a solid support (plastic, agarose, sepharose, magnetic beads and others) is soaked in the phage mixture and that phage that remains attached to the bait is amplified and carried through a further affinity purification step. Each cycle results in an approximately 1,000-fold enrichment of specific phage and after a few selection rounds (2-4), DNA sequencing of the tight-binding phage reveals only a small number of sequences. Phage display panning experiments can be carried out either on libraries of peptides of random amino acid sequence or on libraries of displaying natural peptides obtained by inserting cDNA fragments into the phage vector (cDNA libraries). Libraries have been assembled on several different phages (Fd, Lambda or T7)." [pubmed:10975452 "primary-reference", pubmed:7708014 "method reference"]
is_a: PAR:0034 ! display technology

[Term]
id: PAR: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." [pubmed:14755292 "primary-reference"]
exact_synonym: "polyclonal western" []
is_a: PAR:0113 ! western blot

[Term]
id: PAR: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." [pubmed:14755292 "primary-reference"]
is_a: PAR:0080 ! partial dna sequence identification by hybridization

[Term]
id: PAR: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 printed onto the chip by using an instrument (micro-arrayer) that is capable of spotting liquid samples in a reproducible manner onto a planar support. The ordered protein array can then be probed with labelled molecules to identify proteins that bind to the bait." [pubmed:10976071 "primary-reference", pubmed:12067604 "method reference"]
is_a: PAR:0008 ! array technology

[Term]
id: PAR: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 determines the separation criteria exploited by the column such as affinity, ionic charges, size or hydrophobicity of the molecules under analysis. Each type of column can be implemented with the mobile phase under atmospheric or high pressure condition. In this later case columns are designated as High Pressure Liquid Chromatography (HPLC)." [pubmed:14755292 "primary-reference"]
related_synonym: "column chromatography" []
exact_synonym: "chromatography" []
is_a: PAR:0401 ! biochemical

[Term]
id: PAR: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 PCR or RT-PCR depending on the source of genetic material using properly designed primers. The PISA is generated by cell-free protein synthesis using coupled transcription and translation to produce a double HexaHis-tagged protein, the reaction being carried out on a surface to which the protein adheres as soon as it is synthesised." [pubmed:11470888 "primary-reference"]
related_synonym: "PISA" []
exact_synonym: "pisa" []
is_a: PAR:0008 ! array technology

[Term]
id: PAR:0093
name: protein sequence identification
def: "Single amino acid identification along a protein sequence." [pubmed:14755292 "primary-reference"]
exact_synonym: "protein sequence" []
is_a: PAR:0661 ! experimental participant identification

[Term]
id: PAR: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 their superior dynamic range. Use of non-denaturing gels can allow visualisation of protein protein interactions. Several dyes can be used to specifically indicate residue modification, however this methodology will give no information as the number of residues modified or their position within the protein sequence. Examples include the use of acid fuscian or the fluorescent dansyl hydrazine to show protein glycosylation." [pubmed:12015990 "primary-reference"]
is_a: PAR:0659 ! experimental feature detection

[Term]
id: PAR: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 performed on ProteinChip Arrays with varying chromatographic properties (e.g. anion exchange, cation exchange, metal affinity and reverse phase). By utilising arrays with differing surface chemistries in parallel and in series, a complex mixture of proteins, as from cells or body fluids, can be resolved into subsets of proteins with common properties. Specific analytes can also be examined by using preactivated arrays to which a bait molecule (such as an antibody or biotinylated DNA) is immobilized and a solution containing the binding partner(s) is presented to the array. This array-based immunoprecipitation or protein-binding experiment has been used with good success to study DNA-binding proteins, receptor-ligand interactions, and protein complexes. Any ligand retained on a SELDI chip can directly be identified by mass spectrometry." [pubmed:11827829 "primary-reference"]
related_synonym: "SELDI ProteinChip" []
exact_synonym: "seldi chip" []
is_a: PAR:0008 ! array technology

[Term]
id: PAR:0096
name: pull down
def: "A specific affinity chromatography method where a protein of interest (bait) is expressed as a fusion to an affinity tag (GST, HIS tag and others) and linked at high concentration to a support that has affinity for the tag. Purified proteins or cellular extracts are then adsorbed to the resin and the retained binding proteins are identified. Thus, in this approach, the protein that has affinity for the solid support (bait) is expressed and purified first, often in an heterologous system, and then challenged with a solution containing the candidate partner proteins. no antibodies to retain bait but other affinity stuffs." [pubmed:14755292 "primary-reference"]
is_a: PAR:0004 ! affinity chromatography technology

[Term]
id: PAR: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 constructed that encodes chimeric proteins in which the natural proteins or protein domains are fused to a C-terminal tether. As a consequence when the mRNA is translated in vitro the domain can fold while the tether is still in the ribosomal tunnel. Furthermore this chimeric mRNAs lack a stop codon, thus preventing release of the mRNA and the polypeptide from the ribosome. High concentrations of magnesium and low temperature further stabilise the ternary complex. Similarly to phage display, these complexes can be used directly to select for nucleic acids encoding proteins with desired properties." [pubmed:11551470 "primary-reference", pubmed:12167034 "see-also"]
is_a: PAR:0034 ! display technology

[Term]
id: PAR: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 potential partner is fixed to fluorophore containing beads, the emitted fluorescence proving their interaction can be measured in a scintillation counter. The scintillator measures only the amount of bound radiolabelled ligand. Competition experiment with cold competitor can be done to estimate the binding affinities (50% inhibitory concentration [IC50], cold ligand versus labelled ligand). Loss of signal can also be used to measure substrate cleavage by an enzyme, and labelled antibodies used to titrate the degree of modified residue present." [pubmed:3866247 "primary-reference"]
related_synonym: "RIA Radio Immuno Assay" []
related_synonym: "SPA" []
exact_synonym: "spa" []
is_a: PAR:0013 ! biophysical

[Term]
id: PAR: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 database. A mixture of peptides derived from a protease digestion is analysed by nanoelectrospray LC-MS/MS (Liquid Chromatography Tandem Mass Spectrometer or nanoESI MS/MS) mass spectrometry. Electrospray mass spectrometry cannot be applied to dilute samples and is affected by high salt. As a consequence peptides, normally extracted from acrylamide gels by in situ proteolysis, are desalted and concentrated on a microcolumn followed by elution into a capillary used for nanoelectrospray tandem mass spectrometry. A first mass spectrum (Normal mass spectrum or Q1 mass spectrum) gives information about the masses of all the peptides. Peptides observed in the normal mass spectrum are isolated in turn and dissociated into fragments by collision with gas molecules within the mass spectrometer. Some of the fragments obtained from a peptide constitute a nested set, differing by one amino acid, and the mass difference between them allows assignment of a partial sequence. The masses of the fragments define the position of the partial sequence in the peptide. Together with the cleavage specificity of the protease used to cleave the protein, and mass information such sequence tag provides much higher search specificity to match the a database entry. The procedure is repeated with several peptides from the digest, resulting in multiple identifications of the same protein or identification of several proteins from the peptide mixture. Unknown proteins can easily be identified by using the high specificity of the peptide sequence tag for searches in most sequence databases including EST or genome databases." [pubmed:10967324 "primary-reference", pubmed:11752590 "method reference", pubmed:11805837 "see-also"]
exact_synonym: "sequence tag" []
is_a: PAR:0427 ! mass spectrometry
is_a: PAR:0433 ! partial identification of protein sequence

[Term]
id: PAR: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 transferred to a membrane iv)the membrane is incubated with a radio labelled probe that hybridises any complementary subsequence." [pubmed:14755292 "primary-reference"]
is_a: PAR:0080 ! partial dna sequence identification by hybridization

[Term]
id: PAR: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." [pubmed:9013660 "primary-reference"]
exact_synonym: "sls" []
is_a: PAR:0067 ! light scattering

[Term]
id: PAR: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 (peptide or protein) is immobilized on a dextran polymer, and a solution of interacting protein is passed over it through a cell, with a gold wall coated with this polymer. Macromolecules that interact with the immobilized ligand are retained on the polymer surface, and alter the resonance angle of impinging light as a result of the change in refractive index brought about by the increased protein mass retained on the polymer surface. Since all proteins have the same refractive index and since there is a linear correlation between resonance angle shift and protein concentration near the surface, this allows one to measure changes in protein concentration at the surface as a consequence of protein interaction. Furthermore, this can be done in real time, allowing direct measurement of both the on rate and the off rate of complex formation." [pubmed:11896282 "primary-reference", pubmed:12120258 "method reference", pubmed:16338355 "method reference"]
related_synonym: "BIAcore(r)" []
related_synonym: "Optical biosensor" []
exact_synonym: "spr" []
is_a: PAR:0013 ! biophysical

[Term]
id: PAR: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 without loosing its ability to be inserted into functional phage capsids. Both low density and high density display (albeit only with short peptides) can be achieved." [pubmed:14755292 "primary-reference"]
exact_synonym: "t7 phage" []
xref_analog: comment:Reference not index in medline \: Rosenberg\, A.\, Griffin\, K.\, Studier\, W.S.\, McCormick\, M.\, Berg\, J.\, Novy\, R.\, Mierendorf\, R. inNovations\, 1996\, 6\, 1. "ANNOTATION"
is_a: PAR:0084 ! phage display

[Term]
id: PAR:0113
name: western blot
def: "Western blot is a procedure to identify and quantify a binder protein interaction. 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 primary antibody specific for a given protein or a specific residue modification in the sample under analysis. A secondary antibody, radiolabelled or fused to fluorophore or to a chromogenic enzyme, targets the first antibody and allows the visualisation of the protein band on the membrane." [pubmed:14755292 "primary-reference"]
related_synonym: "Immuno blot" []
is_a: PAR:0401 ! biochemical
is_a: PAR:0421 ! identification by antibody
is_a: PAR:0659 ! experimental feature detection

[Term]
id: PAR: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 X-rays will pass straight through it. A small fraction, however, will be scattered by the atoms in the sample. If the sample is a well-ordered crystal, the scattered waves will reinforce one another at certain points and will appear as diffraction spots when the X-rays are recorded by a suitable detector. The position and intensity of each spot in the X-ray diffraction pattern contain information about the position and nature of the atoms in the crystal. The three-dimensional structure of a large molecule can be deduced from the electron-density map of its crystal. In recent years X-ray diffraction analysis has become increasingly automated, and now the slowest step is likely to be the production of suitable protein crystals. This requires high concentration of very pure protein and empirical searching for the proper crystallisation conditions." [pubmed:14755292 "primary-reference"]
related_synonym: "X-ray" []
related_synonym: "x-ray crystallography" []
exact_synonym: "x-ray diffraction" []
is_a: PAR:0013 ! biophysical

[Term]
id: PAR: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 sorting methods (FACS) to isolate cells that display molecules with desired binding properties." [pubmed:9181578 "primary-reference"]
is_a: PAR:0034 ! display technology
is_a: PAR:0054 ! fluorescence-activated cell sorting

[Term]
id: PAR:0116
name: feature type
def: "Property of a subsequence that may interfere with the binding of a molecule." [pubmed:14755292 "primary-reference"]
relationship: part_of PAR:1004 ! PROTEIN AFFINITY REAGENT CV

[Term]
id: PAR:0117
name: binding site
def: "A sequence range within a protein identified as involved in an interaction." [pubmed:14755292 "primary-reference"]
is_a: PAR:0252 ! biological feature

[Term]
id: PAR:0118
name: mutation
def: "Sequence variation due to insertion, deletion or substitution event." [pubmed:14755292 "primary-reference"]
is_a: PAR:0252 ! biological feature

[Term]
id: PAR:0119
name: mutation decreasing interaction
def: "Residue of a protein whose identity mutation or deletion decreases significantly interaction strength." [pubmed:14755292 "primary-reference"]
related_synonym: "hotspot" []
exact_synonym: "mutation decreasing" []
is_a: PAR:0118 ! mutation

[Term]
id: PAR:0120
name: post translation modification
def: "Residue covalent modifications occurring in the specific protein form involved in an interaction.  See also:" [pubmed:14755292 "primary-reference"]
exact_synonym: "ptm" []
xref_analog: url:http\://www.ebi.ac.uk/ontology-lookup/browse.do?ontName=MOD "ANNOTATION"
is_a: PAR:0252 ! biological feature

[Term]
id: PAR:0121
name: acetylated residue
def: "residue modification." [pubmed:11125103 "primary-reference"]
is_a: PAR:0120 ! post translation modification

[Term]
id: PAR:0122
name: n-acetyl-alanine
def: "residue modification." [pubmed:11125103 "primary-reference", resid:AA0041 "identity"]
related_synonym: "(S)-2-(acetylamino)propanoic acid" []
related_synonym: "[A:ac]" []
related_synonym: "AAC" []
related_synonym: "acetylalanine" []
related_synonym: "N-acetyl-L-alanine" []
exact_synonym: "acetylalanine" []
is_a: PAR:0121 ! acetylated residue

[Term]
id: PAR:0123
name: n2-acetyl-arginine
def: "residue modification." [pubmed:11125103 "primary-reference", resid:AA0354 "identity"]
related_synonym: "[R:ac]" []
related_synonym: "acetylarginine" []
related_synonym: "alpha-acetylamino-delta-guanidinovaleric acid" []
related_synonym: "N2-acetyl-L-arginine" []
related_synonym: "RAC" []
exact_synonym: "acetylarginine" []
is_a: PAR:0121 ! acetylated residue

[Term]
id: PAR:0124
name: n-acetyl-asparagine
def: "residue modification." [pubmed:11125103 "primary-reference"]
related_synonym: "[N:ac]" []
related_synonym: "N-acetyl-L-asparagine" []
related_synonym: "NAC" []
exact_synonym: "acetylasparagine" []
is_a: PAR:0121 ! acetylated residue

[Term]
id: PAR:0125
name: n-acetyl-aspartic acid
def: "residue modification." [pubmed:11125103 "primary-reference", resid:AA0042 "identity"]
related_synonym: "(S)-2-(acetylamino)butanedioic acid" []
related_synonym: "[D:ac]" []
related_synonym: "acetylaspartic acid" []
related_synonym: "DAC" []
related_synonym: "N-acetyl-L-aspartic acid" []
exact_synonym: "acetylaspartate" []
is_a: PAR:0121 ! acetylated residue

[Term]
id: PAR:0126
name: n-acetyl-cysteine
def: "residue modification." [pubmed:11125103 "primary-reference", resid:AA0043 "identity"]
related_synonym: "(R)-2-acetylamino-3-sulfanylpropanoic acid" []
related_synonym: "2-acetylamino-3-mercaptopropanoic acid" []
related_synonym: "[C:ac]" []
related_synonym: "CAC" []
related_synonym: "N-acetyl-L-cysteine" []
related_synonym: "N-acetylcysteine" []
exact_synonym: "acetylcysteine" []
is_a: PAR:0121 ! acetylated residue

[Term]
id: PAR:0127
name: n-acetyl-glutamine
def: "residue modification." [pubmed:11125103 "primary-reference", resid:AA0045 "identity"]
related_synonym: "(S)-2-acetylamino-5-pentanediamic acid" []
related_synonym: "[Q:ac]" []
related_synonym: "acetylglutamine" []
related_synonym: "N-acetyl-L-glutamine" []
related_synonym: "QAC" []
exact_synonym: "acetylglutamine" []
is_a: PAR:0121 ! acetylated residue

[Term]
id: PAR:0128
name: n-acetyl-glutamic acid
def: "residue modification." [pubmed:11125103 "primary-reference", resid:AA0044 "identity"]
related_synonym: "(S)-2-(acetylamino)pentanedioic acid" []
related_synonym: "[E:ac]" []
related_synonym: "acetylglutamic acid" []
related_synonym: "EAC" []
related_synonym: "N-acetyl-L-glutamic acid" []
exact_synonym: "acetylglutamate" []
is_a: PAR:0121 ! acetylated residue

[Term]
id: PAR:0129
name: n-acetylglycine
def: "residue modification." [pubmed:11125103 "primary-reference", resid:AA0046 "identity"]
related_synonym: "2-(acetylamino)ethanoic acid" []
related_synonym: "[G:ac]" []
related_synonym: "aceturic acid" []
related_synonym: "GAC" []
related_synonym: "N-acetylglycine" []
exact_synonym: "acetylglycine" []
is_a: PAR:0121 ! acetylated residue

[Term]
id: PAR:0130
name: n-acetyl-histidine
def: "residue modification." [pubmed:11125103 "primary-reference"]
related_synonym: "[H:ac]" []
related_synonym: "HAC" []
related_synonym: "N-acetyl-L-histidine" []
exact_synonym: "acetylhistidine" []
is_a: PAR:0121 ! acetylated residue

[Term]
id: PAR:0131
name: n-acetyl-isoleucine
def: "residue modification." [pubmed:11125103 "primary-reference", resid:AA0047 "identity"]
related_synonym: "(2S,3S)-2-acetylamino-3-methylpentanoic acid" []
related_synonym: "[I:ac]" []
related_synonym: "acetylisoleucine" []
related_synonym: "IAC" []
related_synonym: "N-acetyl-L-isoleucine" []
exact_synonym: "acetylisoleucine" []
is_a: PAR:0121 ! acetylated residue

[Term]
id: PAR:0132
name: n-acetyl-leucine
def: "residue modification." [pubmed:11125103 "primary-reference"]
related_synonym: "[L:ac]" []
related_synonym: "LAC" []
related_synonym: "N-acetyl-L-leucine" []
exact_synonym: "acetylleucine" []
is_a: PAR:0121 ! acetylated residue

[Term]
id: PAR:0133
name: n2-acetyl-lysine
def: "residue modification." [pubmed:11125103 "primary-reference", resid:AA0048 "identity"]
related_synonym: "(S)-2-acetylamino-6-aminohexanoic acid" []
related_synonym: "[K:ac]" []
related_synonym: "KAC" []
related_synonym: "N2-acetyl-L-lysine" []
related_synonym: "N2-acetyllysine" []
exact_synonym: "n2-acetyllysine" []
is_a: PAR:0526 ! n-acetyl-lysine

[Term]
id: PAR:0134
name: n6-acetyl-lysine
def: "residue modification." [pubmed:11125103 "primary-reference", resid:AA0055 "identity"]
related_synonym: "(S)-2-amino-6-(acetylamino)hexanoic acid" []
related_synonym: "[K:N6ac]" []
related_synonym: "epsilon-acetyllysine" []
related_synonym: "KA6" []
related_synonym: "N(zeta)-acetyllysine" []
related_synonym: "N6-acetyl-L-lysine" []
exact_synonym: "n6-acetyllysine" []
is_a: PAR:0526 ! n-acetyl-lysine

[Term]
id: PAR:0135
name: n-acetyl-methionine
def: "residue modification." [pubmed:11125103 "primary-reference", resid:AA0049 "identity"]
related_synonym: "(S)-2-acetylamino-4-(methylsulfanyl)butanoic acid" []
related_synonym: "2-acetylamino-4-(methylthio)butanoic acid" []
related_synonym: "[M:ac]" []
related_synonym: "acetylmethionine" []
related_synonym: "MAC" []
related_synonym: "methionamine" []
related_synonym: "N-acetyl-L-methionine" []
exact_synonym: "acetylmethionine" []
is_a: PAR:0121 ! acetylated residue

[Term]
id: PAR:0136
name: n-acetyl-phenylalanine
def: "residue modification." [pubmed:11125103 "primary-reference"]
related_synonym: "[F:ac]" []
related_synonym: "FAC" []
related_synonym: "N-acetyl-L-phenylalanine" []
exact_synonym: "acetylphenylalanine" []
is_a: PAR:0121 ! acetylated residue

[Term]
id: PAR:0137
name: n-acetyl-proline
def: "residue modification." [pubmed:11125103 "primary-reference", resid:AA0050 "identity"]
related_synonym: "(2S)-1-acetyl-2-pyrrolidinecarboxylic acid" []
related_synonym: "[P:ac]" []
related_synonym: "acetylproline" []
related_synonym: "N-acetyl-L-proline" []
related_synonym: "PAC" []
exact_synonym: "acetylproline" []
is_a: PAR:0121 ! acetylated residue

[Term]
id: PAR:0138
name: n-acetyl-serine
def: "residue modification." [pubmed:11125103 "primary-reference", resid:AA0051 "identity"]
related_synonym: "(S)-2-acetylamino-3-hydroxypropanoic acid" []
related_synonym: "[S:ac]" []
related_synonym: "N-acetyl-L-serine" []
related_synonym: "N-acetylserine" []
related_synonym: "SAC" []
exact_synonym: "acetylserine" []
is_a: PAR:0121 ! acetylated residue

[Term]
id: PAR:0139
name: n-acetyl-threonine
def: "residue modification." [pubmed:11125103 "primary-reference", resid:AA0052 "identity"]
related_synonym: "(2S,3R)-2-acetylamino-3-hydroxybutanoic acid" []
related_synonym: "[T:ac]" []
related_synonym: "N-acetyl-L-threonine" []
related_synonym: "N-acetylthreonine" []
related_synonym: "TAC" []
exact_synonym: "acetylthreonine" []
is_a: PAR:0121 ! acetylated residue

[Term]
id: PAR:0140
name: n-acetyl-tryptophan
def: "residue modification." [pubmed:11125103 "primary-reference"]
related_synonym: "[W:ac]" []
related_synonym: "N-acetyl-L-tryptophan" []
related_synonym: "WAC" []
exact_synonym: "acetyltryptophan" []
is_a: PAR:0121 ! acetylated residue

[Term]
id: PAR:0141
name: n-acetyl-tyrosine
def: "residue modification." [pubmed:11125103 "primary-reference", resid:AA0053 "identity"]
related_synonym: "(S)-2-acetylamino-3-(4-hydoxyphenyl)propanoic acid" []
related_synonym: "[Y:ac]" []
related_synonym: "N-acetyl-L-tyrosine" []
related_synonym: "N-acetyltyrosine" []
related_synonym: "YAC" []
exact_synonym: "acetyltyrosine" []
is_a: PAR:0121 ! acetylated residue

[Term]
id: PAR:0142
name: n-acetyl-valine
def: "residue modification." [pubmed:11125103 "primary-reference", resid:AA0054 "identity"]
related_synonym: "(S)-2-acetylamino-3-methylbutanoic acid" []
related_synonym: "[V:ac]" []
related_synonym: "N-acetyl-L-valine" []
related_synonym: "N-acetylvaline" []
related_synonym: "VAC" []
exact_synonym: "acetylvaline" []
is_a: PAR:0121 ! acetylated residue

[Term]
id: PAR:0143
name: amidated residue
def: "residue modification." [pubmed:11125103 "primary-reference"]
is_a: PAR:0120 ! post translation modification

[Term]
id: PAR:0144
name: alanine amide
def: "residue modification." [pubmed:14755292 "primary-reference"]
related_synonym: "(S)-2-aminopropanamide" []
related_synonym: "[A:am]" []
related_synonym: "AAM" []
related_synonym: "alaninamide" []
related_synonym: "L-alanine amide" []
exact_synonym: "alanineamide" []
is_a: PAR:0143 ! amidated residue

[Term]
id: PAR:0145
name: arginine amide
def: "residue modification." [pubmed:11125103 "primary-reference", resid:AA0082 "identity"]
related_synonym: "(S)-2-amino-5-guanidinopentanamide" []
related_synonym: "[R:am]" []
related_synonym: "argininamide" []
related_synonym: "L-arginine amide" []
related_synonym: "RAM" []
exact_synonym: "arginineamide" []
is_a: PAR:0143 ! amidated residue

[Term]
id: PAR:0146
name: formylated residue
def: "residue modification." [pubmed:11125103 "primary-reference"]
is_a: PAR:0120 ! post translation modification

[Term]
id: PAR:0147
name: n-formyl-methionine
def: "residue modification." [pubmed:11125103 "primary-reference", resid:AA0021 "identity"]
related_synonym: "(S)-2-formylamino-4-(methylsulfanyl)butanoic acid" []
related_synonym: "2-formylamino-4-(methylthio)butanoic acid" []
related_synonym: "[M:form]" []
related_synonym: "MFM" []
related_synonym: "N-formyl-L-methionine" []
exact_synonym: "formylmethionine" []
is_a: PAR:0146 ! formylated residue

[Term]
id: PAR:0148
name: hydroxylated residue
def: "residue modification." [pubmed:11125103 "primary-reference"]
is_a: PAR:0120 ! post translation modification

[Term]
id: PAR:0149
name: 4-hydroxy-proline
def: "residue modification." [pubmed:11125103 "primary-reference", resid:AA0030 "identity"]
related_synonym: "4-hydroxy-L-proline" []
related_synonym: "[P:hy_g]" []
related_synonym: "HYP" []
exact_synonym: "4hydroxyproline" []
is_a: PAR:0148 ! hydroxylated residue

[Term]
id: PAR:0150
name: lipid modification
def: "residue modification." [pubmed:11125103 "primary-reference"]
is_a: PAR:0120 ! post translation modification

[Term]
id: PAR:0151
name: s-farnesyl-cysteine
def: "residue modification." [pubmed:11125103 "primary-reference", resid:AA0102 "identity"]
related_synonym: "(R,E,E)-2-amino-3-(3,7,11-trimethyl-2,6,10-dodecatrienylsulfanyl)propanoic acid" []
related_synonym: "2-amino-3-(3,7,11-trimethyl-2,6,10-dodecatrienylthio)propanoic acid" []
related_synonym: "[C:farn]" []
related_synonym: "CFN" []
related_synonym: "S-farnesyl-L-cysteine" []
exact_synonym: "farnesylcysteine" []
is_a: PAR:0547 ! s-prenyl-cysteine

[Term]
id: PAR:0152
name: s-geranylgeranyl-cysteine
def: "residue modification." [pubmed:11125103 "primary-reference", resid:AA0104 "identity"]
related_synonym: "(R,E,E,E)-2-amino-3-(3,7,11,15-tetramethyl-2,6,10,14-hexadecatetraenylsulfanyl)propanoic acid" []
related_synonym: "2-amino-3-(3,7,11,15-tetramethyl-2,6,10,14-hexadecatetraenylthio)propanoic acid" []
related_synonym: "[C:ger]" []
related_synonym: "CGR" []
related_synonym: "S-geranylgeranyl-L-cysteine" []
exact_synonym: "geranylgeranylcys" []
is_a: PAR:0547 ! s-prenyl-cysteine

[Term]
id: PAR:0153
name: n-palmitoyl-cysteine
def: "residue modification." [pubmed:11125103 "primary-reference", resid:AA0060 "identity"]
related_synonym: "(R)-2-hexadecanoylamino-3-sulfanylpropanoic acid" []
related_synonym: "2-hexadecanoylamino-3-mercaptopropanoic acid" []
related_synonym: "[C:palm_n]" []
related_synonym: "CPN" []
related_synonym: "N-(1-oxahexadecyl)-L-cysteine" []
related_synonym: "N-palmitoyl-L-cysteine" []
exact_synonym: "n-palmitoylcysteine" []
is_a: PAR:0561 ! palmitoylated residue

[Term]
id: PAR:0154
name: s-palmitoyl-cysteine
def: "residue modification." [pubmed:11125103 "primary-reference", resid:AA0106 "identity"]
related_synonym: "(R)-2-amino-3-(hexadecanoylsulfanyl)propanoic acid" []
related_synonym: "2-amino-3-(hexadecanoylthio)propanoic acid" []
related_synonym: "[C:palm_s]" []
related_synonym: "CPS" []
related_synonym: "cysteine hexadecanoate thioester" []
related_synonym: "cysteine palmitate thioester" []
related_synonym: "S-palmitoyl-L-cysteine" []
exact_synonym: "s-palmitoylcysteine" []
is_a: PAR:0561 ! palmitoylated residue

[Term]
id: PAR:0155
name: n-myristoyl-glycine
def: "residue modification." [pubmed:11125103 "primary-reference", resid:AA0059 "identity"]
related_synonym: "[G:myr]" []
related_synonym: "GMY" []
related_synonym: "N-myristoyl-glycine" []
exact_synonym: "myristoylglycine" []
is_a: PAR:0560 ! myristoylated residue

[Term]
id: PAR:0156
name: n6-myristoyl-lysine
def: "residue modification." [pubmed:11125103 "primary-reference", resid:AA0078 "identity"]
related_synonym: "(S)-2-amino-6-(tetradecanoylamino)hexanoic acid" []
related_synonym: "[K:myr]" []
related_synonym: "epsilon-myristoyllysine" []
related_synonym: "KMY" []
related_synonym: "N(zeta)-myristoyllysine" []
related_synonym: "N6-(1-oxotetradecyl)-L-lysine" []
related_synonym: "N6-myristoyl-L-lysine" []
exact_synonym: "myristoyllysine" []
is_a: PAR:0560 ! myristoylated residue

[Term]
id: PAR:0157
name: methylated residue
def: "residue modification." [pubmed:11125103 "primary-reference"]
is_a: PAR:0120 ! post translation modification

[Term]
id: PAR:0158
name: n-methyl-alanine
def: "residue modification." [pubmed:11125103 "primary-reference", resid:AA0061 "identity"]
related_synonym: "(S)-2-methylaminopropanoic acid" []
related_synonym: "[A:meth_n]" []
related_synonym: "AMT" []
related_synonym: "N-methyl-L-alanine" []
related_synonym: "N-methylalanine" []
exact_synonym: "methylalanine" []
is_a: PAR:0562 ! methylated alanine

[Term]
id: PAR:0159
name: n,n,n-trimethyl-alanine
def: "residue modification." [pubmed:11125103 "primary-reference", resid:AA0062 "identity"]
related_synonym: "(S)-1-carboxy-N,N,N-trimethylethanaminium" []
related_synonym: "(S)-2-(trimethylammonio)propanoic acid" []
related_synonym: "[A:meth_n3]" []
related_synonym: "AM3" []
related_synonym: "N,N,N-trimethyl-L-alanine" []
exact_synonym: "trimethylalanine" []
is_a: PAR:0562 ! methylated alanine

[Term]
id: PAR:0160
name: omega-n,omega-n-dimethyl-arginine
def: "residue modification." [pubmed:11125103 "primary-reference", resid:AA0068 "identity"]
related_synonym: "(S)-2-amino-5-[((dimethylamino)iminomethyl)amino]pentanoic acid" []
related_synonym: "[R:meth_n7]" []
related_synonym: "asymmetric dimethylarginine" []
related_synonym: "NG,NG-dimethylarginine" []
related_synonym: "omega-N,omega-N-dimethyl-L-arginine" []
related_synonym: "RM2" []
exact_synonym: "dimethylarginine" []
is_a: PAR:0563 ! methylated arginine

[Term]
id: PAR:0161
name: beta-methylthioaspartic acid
def: "residue modification." [pubmed:11125103 "primary-reference", resid:AA0232 "identity"]
related_synonym: "(2R,3Xi)-2-amino-3-methylsulfanylbutanedioic acid" []
related_synonym: "3-carboxy-S-methyl-cysteine" []
related_synonym: "3-methylthio-aspartic acid" []
related_synonym: "[D:meth_b]" []
related_synonym: "beta-methylthio-aspartic acid" []
related_synonym: "DM2" []
related_synonym: "L-beta-methylthioaspartic acid" []
exact_synonym: "methylthioaspartate" []
is_a: PAR:0157 ! methylated residue

[Term]
id: PAR:0162
name: n5-methyl-glutamine
def: "residue modification." [pubmed:11125103 "primary-reference", resid:AA0071 "identity"]
related_synonym: "(S)-2-amino-N5-methylpentanediamic acid" []
related_synonym: "[Q:meth_n5]" []
related_synonym: "gamma-methylglutamine" []
related_synonym: "N(delta)-methylglutamine" []
related_synonym: "N-methylglutamine" []
related_synonym: "N5-methyl-L-glutamine" []
related_synonym: "QM5" []
exact_synonym: "methylglutamine" []
is_a: PAR:0157 ! methylated residue

[Term]
id: PAR:0163
name: glutamic acid 5-methyl ester
def: "residue modification." [pubmed:11125103 "primary-reference", resid:AA0072 "identity"]
related_synonym: "(S)-2-aminopentanedioic acid 5-methyl ester" []
related_synonym: "5-methyl-L-glutamate" []
related_synonym: "[E:meth_o5]" []
related_synonym: "EM5" []
related_synonym: "glutamic acid gamma-methyl ester" []
related_synonym: "L-glutamic acid 5-methyl ester" []
exact_synonym: "glutamatemethylester" []
is_a: PAR:0157 ! methylated residue

[Term]
id: PAR:0164
name: 3'-methyl-histidine
def: "residue modification." [pubmed:11125103 "primary-reference", resid:AA0073 "identity"]
related_synonym: "(S)-2-amino-3-(3-methyl-3H-imidazol-4-yl)propanoic acid" []
related_synonym: "1-methylhistidine [misnomer]" []
related_synonym: "3'-methyl-L-histidine" []
related_synonym: "[H:meth_n4]" []
related_synonym: "MHS" []
related_synonym: "N(delta)-methylhistidine" []
related_synonym: "pi-methylhistidine" []
related_synonym: "pros-methylhistidine" []
exact_synonym: "methylhistidine" []
is_a: PAR:0157 ! methylated residue

[Term]
id: PAR:0165
name: n6-methyl-lysine
def: "residue modification." [pubmed:11125103 "primary-reference"]
related_synonym: "(S)-2-amino-6-methylaminohexanoic acid" []
related_synonym: "[K:meth_1]" []
related_synonym: "epsilon-methyllysine" []
related_synonym: "MLZ" []
related_synonym: "N(zeta)-methyllysine" []
related_synonym: "N6-methyl-L-lysine" []
exact_synonym: "methyllysine" []
is_a: PAR:0548 ! methylated-lysine

[Term]
id: PAR:0166
name: n6,n6-dimethyl-lysine
def: "residue modification." [pubmed:11125103 "primary-reference", resid:AA0075 "identity"]
related_synonym: "(S)-2-amino-6-dimethylaminohexanoic acid" []
related_synonym: "[K:meth_2]" []
related_synonym: "epsilon-dimethyllysine" []
related_synonym: "lysine derivative Lys(y)" []
related_synonym: "MLY" []
related_synonym: "N(zeta)-dimethyllysine" []
related_synonym: "N6,N6-dimethyl-L-lysine" []
exact_synonym: "dimethyllysine" []
is_a: PAR:0548 ! methylated-lysine

[Term]
id: PAR:0167
name: n6,n6,n6-trimethyl-lysine
def: "residue modification." [pubmed:11125103 "primary-reference", resid:AA0074 "identity"]
related_synonym: "(S)-2-amino-6-(trimethylammonio)hexanoic acid" []
related_synonym: "(S)-5-amino-5-carboxy-N,N,N-trimethylpentanaminium" []
related_synonym: "[K:meth_3]" []
related_synonym: "epsilon-trimethyllysine" []
related_synonym: "M3L" []
related_synonym: "N(zeta)-trimethyllysine" []
related_synonym: "N6,N6,N6-trimethyl-L-lysine" []
exact_synonym: "trimethyllysine" []
is_a: PAR:0548 ! methylated-lysine

[Term]
id: PAR:0168
name: n-methyl-methionine
def: "residue modification." [pubmed:11125103 "primary-reference", resid:AA0064 "identity"]
related_synonym: "(S)-2-methylamino-4-(methylsulfanyl)butanoic acid" []
related_synonym: "2-methylamino-4-(methylthio)butanoic acid" []
related_synonym: "[M:meth]" []
related_synonym: "MMT" []
related_synonym: "N-methyl-L-methionine" []
related_synonym: "N-methylmethionine" []
exact_synonym: "methylmethionine" []
is_a: PAR:0157 ! methylated residue

[Term]
id: PAR:0169
name: n-methyl-phenylalanine
def: "residue modification." [pubmed:14755292 "primary-reference"]
related_synonym: "(S)-2-methylamino-3-phenylpropanoic acid" []
related_synonym: "[F:meth]" []
related_synonym: "FMT" []
related_synonym: "N-methyl-L-phenylalanine" []
related_synonym: "N-methylphenylalanine" []
exact_synonym: "methylphenylalanine" []
is_a: PAR:0157 ! methylated residue

[Term]
id: PAR:0170
name: phosphorylated residue
def: "residue modification." [pubmed:11125103 "primary-reference"]
exact_synonym: "phosphorylated" []
is_a: PAR:0120 ! post translation modification

[Term]
id: PAR:0171
name: omega-n-phospho-arginine
def: "residue modification." [pubmed:11125103 "primary-reference", resid:AA0222 "identity"]
related_synonym: "(S)-2-amino-5-[imino(phosphonoamino)methyl]aminopentanoic acid" []
related_synonym: "[R:po]" []
related_synonym: "alpha-amino-delta-phosphonoguanidinovaleric acid" []
related_synonym: "N5-[imino(phosphonoamino)methyl]-L-ornithine" []
related_synonym: "omega-N-phospho-L-arginine" []
related_synonym: "RPO" []
exact_synonym: "phosphoarginine" []
is_a: PAR:0170 ! phosphorylated residue

[Term]
id: PAR:0172
name: aspartic 4-phosphoric anhydride
def: "residue modification." [pubmed:11125103 "primary-reference", resid:AA0033 "identity"]
related_synonym: "(S)-2-aminobutanedioic 4-phosphoric anhydride" []
related_synonym: "[D:po]" []
related_synonym: "beta-aspartyl phosphate" []
related_synonym: "DPO" []
related_synonym: "L-aspartic 4-phosphoric anhydride" []
related_synonym: "phosphoaspartic acid" []
exact_synonym: "phosphoaspartic acid" []
is_a: PAR:0170 ! phosphorylated residue

[Term]
id: PAR:0173
name: s-phospho-cysteine
def: "residue modification." [pubmed:11125103 "primary-reference", resid:AA0034 "identity"]
related_synonym: "(R)-2-amino-3-(phosphonosulfanyl)propanoic acid" []
related_synonym: "[C:po]" []
related_synonym: "CPO" []
related_synonym: "cysteine phosphate thioester" []
related_synonym: "S-phospho-L-cysteine" []
related_synonym: "S-phosphonocysteine" []
related_synonym: "S3-phosphocysteine" []
exact_synonym: "phosphocysteine" []
is_a: PAR:0170 ! phosphorylated residue

[Term]
id: PAR:0174
name: 1'-phospho-histidine
def: "residue modification." [pubmed:11125103 "primary-reference", resid:AA0035 "identity"]
related_synonym: "(S)-2-amino-3-(1-phosphono-1H-imidazol-4-yl)propanoic acid" []
related_synonym: "1'-phospho-L-histidine" []
related_synonym: "[H:po_e]" []
related_synonym: "histidine-3-phosphate [misnomer]" []
related_synonym: "histidine-N(epsilon)-phosphate" []
related_synonym: "histidine-N1'-phosphate" []
related_synonym: "HPE" []
related_synonym: "tau-phosphohistidine" []
related_synonym: "tele-phosphohistidine" []
exact_synonym: "1-phosphohistidine" []
is_a: PAR:0555 ! phospho-histidine

[Term]
id: PAR:0175
name: 3'-phospho-histidine
def: "residue modification." [pubmed:11125103 "primary-reference", resid:AA0036 "identity"]
related_synonym: "(S)-2-amino-3-(3-phosphono-3H-imidazol-4-yl)propanoic acid" []
related_synonym: "[H:po_d]" []
related_synonym: "histidine-1-phosphate [misnomer]" []
related_synonym: "histidine-N(delta)-phosphate" []
related_synonym: "histidine-N3'-phosphate" []
related_synonym: "HPD" []
related_synonym: "pi-phosphohistidine" []
related_synonym: "pros-phosphohistidine" []
exact_synonym: "3-phosphohistidine" []
is_a: PAR:0555 ! phospho-histidine

[Term]
id: PAR:0176
name: o-phospho-serine
def: "residue modification." [pubmed:11125103 "primary-reference", resid:AA0037 "identity"]
related_synonym: "(S)-2-amino-3-(phosphonooxy)propanoic acid" []
related_synonym: "2-amino-3-hydroxypropanoic acid 3-phosphate" []
related_synonym: "2-amino-3-hydroxypropanoic acid 3-phosphate;O-phosphonoserine;O3-phosphoserine" []
related_synonym: "[S:po]" []
related_synonym: "O-phospho-L-serine" []
related_synonym: "O-phosphonoserine" []
related_synonym: "O3-phosphoserine" []
related_synonym: "serine phosphate ester" []
related_synonym: "SPO" []
exact_synonym: "phosphoserine" []
is_a: PAR:0170 ! phosphorylated residue

[Term]
id: PAR:0177
name: o-phospho-threonine
def: "residue modification." [pubmed:11125103 "primary-reference", resid:AA0038 "identity"]
related_synonym: "(2S,3R)-2-amino-3-phosphonooxybutanoic acid" []
related_synonym: "2-amino-3-hydroxybutanoic acid 3-phosphate" []
related_synonym: "[T:po]" []
related_synonym: "O-phospho-L-threonine" []
related_synonym: "O3-phosphothreonine" []
related_synonym: "threonine phosphate ester" []
related_synonym: "TPO" []
exact_synonym: "phosphothreonine" []
is_a: PAR:0170 ! phosphorylated residue

[Term]
id: PAR:0178
name: o4'-phospho-tyrosine
def: "residue modification." [pubmed:11125103 "primary-reference", resid:AA0039 "identity"]
related_synonym: "(S)-2-amino-3-(4-phosphonooxyphenyl)propanoic acid" []
related_synonym: "2-amino-3-(4-hydroxyphenyl)propanoic acid 4'-phosphate" []
related_synonym: "[Y:po]" []
related_synonym: "O4'-phospho-L-tyrosine" []
related_synonym: "O4-phosphotyrosine" []
related_synonym: "tyrosine phosphate" []
related_synonym: "YPO" []
exact_synonym: "phosphotyrosine" []
is_a: PAR:0170 ! phosphorylated residue

[Term]
id: PAR:0179
name: other modification
def: "residue modification." [pubmed:11125103 "primary-reference"]
is_a: PAR:0120 ! post translation modification

[Term]
id: PAR:0180
name: selenocysteine
def: "residue modification." [pubmed:11125103 "primary-reference", resid:AA0022 "identity"]
related_synonym: "3-selenylalanine" []
related_synonym: "[C:sel]" []
related_synonym: "CSE" []
related_synonym: "L-selenocysteine" []
related_synonym: "selenium cysteine" []
is_a: PAR:0179 ! other modification

[Term]
id: PAR:0181
name: selenomethionine
def: "residue modification." [pubmed:11125103 "primary-reference"]
related_synonym: "[M:sel]" []
related_synonym: "L-selenomethionine" []
related_synonym: "MSE" []
is_a: PAR:0179 ! other modification

[Term]
id: PAR:0182
name: 3-oxoalanine
def: "residue modification." [pubmed:11125103 "primary-reference", resid:AA0185 "identity"]
related_synonym: "(S)-2-amino-3-oxopropanoic acid" []
related_synonym: "2-amino-3-oxopropionic acid" []
related_synonym: "[S:oxal]" []
related_synonym: "L-3-oxoalanine" []
related_synonym: "L-alpha-formylglycine" []
related_synonym: "L-amino-malonic acid semialdehyde" []
related_synonym: "L-aminomalonaldehydic acid" []
related_synonym: "L-serinesemialdehyde [misnomer]" []
related_synonym: "SOX" []
exact_synonym: "oxoalanine" []
is_a: PAR:0179 ! other modification

[Term]
id: PAR:0183
name: 2-pyrrolidone-5-carboxylic acid
def: "residue modification." [pubmed:11125103 "primary-reference", resid:AA0031 "identity"]
related_synonym: "(S)-5-oxo-2-pyrrolidinecarboxylic acid" []
related_synonym: "2-oxopyrrolidine-5-carboxylic acid" []
related_synonym: "5-oxoproline" []
related_synonym: "5-oxopyrrolidine-2-carboxylic acid" []
related_synonym: "[E:pyro]" []
related_synonym: "PCA" []
related_synonym: "pyroglutamic acid" []
exact_synonym: "pyroglutamic acid" []
is_a: PAR:0179 ! other modification

[Term]
id: PAR:0184
name: glutamyl 5-glycerylphosphorylethanolamine
def: "residue modification." [pubmed:11125103 "primary-reference", resid:AA0170 "identity"]
related_synonym: "(S)-2-amino-5-[2-([([2,3-dihydroxypropyl]oxy)(hydroxy)phosphoryl]oxy)ethyl]amino-5-oxopentanoic acid" []
related_synonym: "[E:gpe]" []
related_synonym: "EGE" []
related_synonym: "L-glutamyl 5-glycerophosphoethanolamine" []
related_synonym: "L-glutamyl 5-glycerophosphorylethanolamine" []
related_synonym: "L-glutamyl 5-glycerylphosphorylethanolamine" []
exact_synonym: "glycerylpo4etohamine" []
is_a: PAR:0179 ! other modification

[Term]
id: PAR:0185
name: 2'-[3-carboxamido-3-(trimethylammonio)propyl]-histidine
def: "residue modification." [pubmed:11125103 "primary-reference", resid:AA0040 "identity"]
related_synonym: "2'-[3-carboxamido-3-(trimethylammonio)propyl]-L-histidine" []
related_synonym: "2-[(Xi)-3-carboxamido-3-(trimethylammonio)propyl]-4-((S)-2-amino-2-carboxyethyl)-1H-imidazole" []
related_synonym: "2-[3-carboxamido-3-(trimethylammonio)propyl]histidine" []
related_synonym: "2-amino-3-[[2-(3-amino-3-carbamoyl-prop-1-enyl)-1,1,3-trimethyl-2,3-dihydroimidazol-5-yl]]propanoic acid" []
related_synonym: "2-amino-4-[[5-(2-amino-2-carboxylato-ethyl)-1,1,3-trimethyl-2,3-dihydroimidazol-2-yl]]but-3-enamide" []
related_synonym: "[H:diph]" []
related_synonym: "alpha-(aminocarbonyl)-4-(2-amino-2-carboxyethyl)-N,N,N-trimethyl-1H-imidazole-2-propanaminium" []
related_synonym: "diphthamide" []
related_synonym: "HDP" []
exact_synonym: "diphthamide" []
is_a: PAR:0179 ! other modification

[Term]
id: PAR:0186
name: n6-biotinyl-lysine
def: "residue modification." [pubmed:11125103 "primary-reference", resid:AA0117 "identity"]
related_synonym: "(3aS-(3aalpha,4beta,6aalpha))-N6-(5-(hexahydro-2-oxo-1H-thieno(3,4-d)imidazol-4-yl)-1-oxopentyl)-L-lysine" []
related_synonym: "(S)-2-amino-6-[5-((3aS,4S,6aR)-hexahydro-2-oxo-1H-thieno[3,4-d]imidazol-4-yl)-1-oxopentyl]aminohexanoic acid" []
related_synonym: "[K:biotin]" []
related_synonym: "biocytin" []
related_synonym: "epsilon-N-biotinyllysine" []
related_synonym: "KBT" []
related_synonym: "N6-[5-((3aS,4S,6aR)-hexahydro-2-oxo-1H-thieno[3,4-d]imidazol-4-yl)-1-oxopentyl]-L-lysine" []
related_synonym: "N6-biotinyl-L-lysine" []
related_synonym: "N6-biotinyllysine" []
exact_synonym: "biotinyllysine" []
is_a: PAR:0179 ! other modification

[Term]
id: PAR:0187
name: n6-(4-amino-2-hydroxybutyl)-lysine
def: "residue modification." [pubmed:11125103 "primary-reference", resid:AA0116 "identity"]
related_synonym: "(S,R)-2-amino-6-(4-amino-2-hydroxybutylamino)hexanoic acid" []
related_synonym: "[K:hypu]" []
related_synonym: "hypusine" []
related_synonym: "KHY" []
related_synonym: "N6-(4-amino-2-hydroxybutyl)-L-lysine" []
exact_synonym: "hypusine" []
is_a: PAR:0179 ! other modification

[Term]
id: PAR:0188
name: n6-retinal-lysine
def: "residue modification." [pubmed:11125103 "primary-reference", resid:AA0120 "identity"]
related_synonym: "(S)-2-amino-6-[(2E,4E,6E,8E)-3,7-dimethyl-9-(2,6,6-trimethylcyclohex-1-en-1-yl)-2,4,6,8-nonatetraenylidene]aminohexanoic acid" []
related_synonym: "[K:retin]" []
related_synonym: "KRT" []
related_synonym: "N6-retinal-L-lysine" []
related_synonym: "N6-retinyl-lysine" []
related_synonym: "N6-retinylidene-L-lysine" []
exact_synonym: "retinallysine" []
is_a: PAR:0179 ! other modification

[Term]
id: PAR:0189
name: ubiquitinated lysine
def: "Residue modification due to a cross-link between a lysine and a glycine from the ubiquitine protein." [pubmed:11125103 "primary-reference", resid:AA0125 "identity"]
related_synonym: "[K:ub]" []
related_synonym: "KUB" []
related_synonym: "N6-glycyl-L-lysine" []
related_synonym: "N6-glycyllysine" []
is_a: PAR:0179 ! other modification

[Term]
id: PAR:0190
name: interaction type
def: "Connection between molecule." [pubmed:14755292 "primary-reference"]
relationship: part_of PAR:1004 ! PROTEIN AFFINITY REAGENT CV

[Term]
id: PAR:0192
name: acetylation reaction
def: "Reaction, that can affect K,C,A,D,E,Q,G,I,K,M,P,S,T,Y,V residues." [go:GO\:0006473 "identity", pubmed:14755292 "primary-reference", resid:AA0041 "see-also", resid:AA0042 "see-also", resid:AA0043 "see-also", resid:AA0044 "see-also", resid:AA0045 "see-also", resid:AA0046 "see-also", resid:AA0047 "see-also", resid:AA0048 "see-also", resid:AA0049 "see-also", resid:AA0050 "see-also", resid:AA0051 "see-also", resid:AA0052 "see-also", resid:AA0053 "see-also", resid:AA0054 "see-also", resid:AA0055 "see-also", resid:AA0056 "see-also"]
exact_synonym: "acetylation" []
is_a: PAR:0414 ! enzymatic reaction

[Term]
id: PAR:0193
name: amidation reaction
def: "Irreversible reaction that can affect A,R,N,D,C,Q,E,G,H,I,L,K,M,F,P,S,T,W,Y or V residues." [go:GO\:0001519 "identity", pubmed:14755292 "primary-reference", resid:AA0081 "see-also", resid:AA0082 "see-also", resid:AA0083 "see-also", resid:AA0084 "see-also", resid:AA0085 "see-also", resid:AA0086 "see-also", resid:AA0087 "see-also", resid:AA0088 "see-also", resid:AA0089 "see-also", resid:AA0090 "see-also", resid:AA0091 "see-also", resid:AA0092 "see-also", resid:AA0093 "see-also", resid:AA0094 "see-also", resid:AA0095 "see-also", resid:AA0096 "see-also", resid:AA0097 "see-also", resid:AA0098 "see-also", resid:AA0099 "see-also", resid:AA0100 "see-also"]
exact_synonym: "amidation" []
is_a: PAR:0414 ! enzymatic reaction

[Term]
id: PAR:0194
name: cleavage reaction
def: "Covalent bond breakage in a molecule leading to the formation of smaller molecules." [pubmed:14755292 "primary-reference"]
exact_synonym: "cleavage" []
is_a: PAR:0414 ! enzymatic reaction

[Term]
id: PAR:0195
name: covalent binding
def: "Interaction leading to the formation of covalent bond within an autocatalytic molecule or between partners." [pubmed:14755292 "primary-reference"]
is_a: PAR:0407 ! direct interaction

[Term]
id: PAR:0197
name: deacetylation reaction
def: "N6-acetyl-L-lysine or S-acetyl-L-cysteine are cleaved and return K or C residues." [go:GO\:0006476 "identity", pubmed:14755292 "primary-reference", resid:AA0055 "see-also", resid:AA0056 "see-also"]
exact_synonym: "deacetylation" []
is_a: PAR:0414 ! enzymatic reaction

[Term]
id: PAR:0198
name: defarnesylation reaction
def: "S-farnesyl-L-cysteined is cleaved and returns a C residue." [pubmed:14755292 "primary-reference", resid:AA0102 "identity"]
exact_synonym: "defarnesylation" []
is_a: PAR:0212 ! lipid cleavage

[Term]
id: PAR:0199
name: deformylation reaction
def: "N6-formyl-L-lysine is cleaved and returns a K residue." [pubmed:14755292 "primary-reference", resid:AA0211 "identity"]
exact_synonym: "deformylation" []
is_a: PAR:0414 ! enzymatic reaction

[Term]
id: PAR:0200
name: degeranylation reaction
def: "S-geranylgeranyl-L-cysteine is cleaved and returns a C residue." [pubmed:14755292 "primary-reference", resid:AA0104 "identity"]
exact_synonym: "degeranylation" []
is_a: PAR:0212 ! lipid cleavage

[Term]
id: PAR:0201
name: demyristoylation reaction
def: "N6-myristoyl-L-lysine is cleaved and returns a K residue." [pubmed:14755292 "primary-reference", resid:AA0078 "identity"]
exact_synonym: "demyristoylation" []
is_a: PAR:0212 ! lipid cleavage

[Term]
id: PAR:0202
name: depalmitoylation reaction
def: "S-palmitoyl-L-cysteine, N6-palmitoyl-L-lysine, O-palmitoyl-L-threonine or O-palmitoyl-L-serine are cleaved and return C,K,T or S residues." [pubmed:14755292 "primary-reference", resid:AA0060 "see-also", resid:AA0077 "see-also", resid:AA0106 "see-also"]
exact_synonym: "depalmitoylation" []
is_a: PAR:0212 ! lipid cleavage

[Term]
id: PAR:0203
name: dephosphorylation reaction
def: "Phosphoresidues are cleaved and return D,C,H,S,T,Y or R residues." [go:GO\:0016311 "identity", pubmed:14755292 "primary-reference", resid:AA0033 "see-also", resid:AA0034 "see-also", resid:AA0035 "see-also", resid:AA0036 "see-also", resid:AA0037 "see-also", resid:AA0038 "see-also", resid:AA0039 "see-also", resid:AA0222 "see-also"]
exact_synonym: "dephosphorylation" []
is_a: PAR:0414 ! enzymatic reaction

[Term]
id: PAR:0204
name: deubiquitination reaction
def: "Cleavage of the G-K bond and release of ubiquitin or ubiquitin like proteins." [go:GO\:0016579 "identity", pubmed:11583613 "primary-reference", resid:AA0125 "identity"]
exact_synonym: "deubiquitination" []
is_a: PAR:0414 ! enzymatic reaction

[Term]
id: PAR:0206
name: farnesylation reaction
def: "Reversible reaction that can affect C residue." [go:GO\:0018347 "identity", pubmed:14755292 "primary-reference", resid:AA0102 "identity"]
exact_synonym: "farnesylation" []
is_a: PAR:0211 ! lipid addition

[Term]
id: PAR:0207
name: formylation reaction
def: "Reaction that can affect K or G residues." [go:GO\:0018256 "identity", pubmed:14755292 "primary-reference", resid:AA0057 "see-also", resid:AA0211 "see-also"]
exact_synonym: "formylation" []
is_a: PAR:0414 ! enzymatic reaction

[Term]
id: PAR:0209
name: geranylgeranylation reaction
def: "Reversible reaction that can affect C residue." [go:GO\:0018348 "identity", pubmed:14755292 "primary-reference", resid:AA0104 "identity"]
exact_synonym: "geranylgeranylation" []
is_a: PAR:0211 ! lipid addition

[Term]
id: PAR:0210
name: hydroxylation reaction
def: "Irreversible reaction that can affect K,P,Y or R residues." [go:GO\:0018126 "identity", pubmed:14755292 "primary-reference", resid:AA0028 "see-also", resid:AA0029 "see-also", resid:AA0030 "see-also", resid:AA0146 "see-also", resid:AA0215 "see-also"]
exact_synonym: "hydroxylation" []
is_a: PAR:0414 ! enzymatic reaction

[Term]
id: PAR:0211
name: lipid addition
def: "Covalent or non covalent binding of lipid group on a protein residue." [go:GO\:0006497 "identity", pubmed:14755292 "primary-reference"]
is_a: PAR:0414 ! enzymatic reaction

[Term]
id: PAR:0212
name: lipid cleavage
def: "Cleavage of a lipid group covalently bound to a protein residue." [pubmed:14755292 "primary-reference"]
is_a: PAR:0194 ! cleavage reaction

[Term]
id: PAR:0213
name: methylation reaction
def: "The covalent attachment of a methyl residue to one or more monomeric units in a polypeptide, polynucleotide, polysaccharide, or other biological polymer. Irreversible reaction that can affect A,G,M,F,P,C,R,N,Q,E,H,or K residues." [go:GO\:0043414 "identity", pubmed:14755292 "primary-reference", resid:AA0061 "see-also", resid:AA0062 "see-also", resid:AA0063 "see-also", resid:AA0064 "see-also", resid:AA0065 "see-also", resid:AA0066 "see-also", resid:AA0067 "see-also", resid:AA0068 "see-also", resid:AA0069 "see-also", resid:AA0070 "see-also", resid:AA0071 "see-also", resid:AA0072 "see-also", resid:AA0073 "see-also", resid:AA0074 "see-also", resid:AA0075 "see-also", resid:AA0076 "see-also", resid:AA0234 "see-also", resid:AA0272 "see-also"]
exact_synonym: "methylation" []
is_a: PAR:0414 ! enzymatic reaction

[Term]
id: PAR:0214
name: myristoylation reaction
def: "Reaction that can affect K or G residues." [go:GO\:0018319 "identity", pubmed:14755292 "primary-reference", resid:AA0059 "see-also", resid:AA0078 "see-also"]
exact_synonym: "myristoylation" []
is_a: PAR:0211 ! lipid addition

[Term]
id: PAR:0216
name: palmitoylation reaction
def: "Reversible reaction that can affect C,K,T or S residues." [go:GO\:0018318 "identity", pubmed:14755292 "primary-reference", resid:AA0060 "see-also", resid:AA0077 "see-also", resid:AA0079 "see-also", resid:AA0080 "see-also", resid:AA0106 "see-also"]
exact_synonym: "palmitoylation" []
is_a: PAR:0211 ! lipid addition

[Term]
id: PAR:0217
name: phosphorylation reaction
def: "Reversible reaction that can affect D,C,H,S,T,Y,R residues." [go:GO\:0016310 "identity", pubmed:14755292 "primary-reference", resid:AA0033 "see-also", resid:AA0034 "see-also", resid:AA0035 "see-also", resid:AA0036 "see-also", resid:AA0037 "see-also", resid:AA0038 "see-also", resid:AA0039 "see-also", resid:AA0222 "see-also"]
exact_synonym: "phosphorylation" []
is_a: PAR:0414 ! enzymatic reaction

[Term]
id: PAR:0218
name: physical interaction
def: "Interaction among molecules that can be direct or indirect." [pubmed:14755292 "primary-reference"]
related_synonym: "aggregation" []
is_a: PAR:0190 ! interaction type

[Term]
id: PAR: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:GO\:0016567 "identity", pubmed:11583613 "primary-reference", resid:AA0125 "identity"]
exact_synonym: "ubiquitination" []
is_a: PAR:0414 ! enzymatic reaction

[Term]
id: PAR: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 enriched by immunoprecipitation with a specific antibody. After reversal of the cross-links, the enriched DNA is amplified and labeled with a fluorescent dye (Cy5) by using a ligation-mediatedpolymerase chain reaction (LM-PCR). In parallel a sample of DNA that is not enriched by immunoprecipitation is subjected to LM-PCR in the presence of a different fluorophore (Cy3), and both immunoprecipitation (IP)-enriched and unenriched pools of labeled DNA were hybridized to a single DNA microarray containing a set of intergenic sequences. The ratio of the Cy5 to Cy3 fluorescence intensities measured at each DNA element in the microarray provided a measure of the extent of binding of the transcription factor to the corresponding genomic locus." [pubmed:11125145 "primary-reference", pubmed:11206552 "method reference"]
exact_synonym: "chip-chip" []
is_a: PAR:0008 ! array technology
is_a: PAR:0402 ! chromatin immunoprecipitation assays

[Term]
id: PAR: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 groups, and can then be eluted by increasing the concentration of sodium chloride or another salt in the eluting buffer by competition of sodium ions with positively charged groups on the protein for binding to the column. Protein that have a low density of net positive charge will tend to emerge first, followed by those having a higher charge density. Positively charged complexes or proteins (cationic proteins) can be separated on negatively charged carboxymethyl-cellulose (CM-cellulose) columns. Conversely, negatively charged complexes or proteins (anionic proteins) can be separated by chromatography on positively charged diethylaminoethyl-cellulose (DEAE-cellulose) columns." [pubmed:14755292 "primary-reference"]
related_synonym: "IEC" []
exact_synonym: "ion exchange chrom" []
is_a: PAR:0091 ! chromatography technology

[Term]
id: PAR: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 ligand in the matrix. The more hydrophobic the matrix on each ligand, the greater is the tendency of the column to retain hydrophobic moieties. Thus hydrophilic compounds elute more quickly than do hydrophobic compounds." [pubmed:14755292 "primary-reference"]
exact_synonym: "reverse phase chrom" []
is_a: PAR:0091 ! chromatography technology

[Term]
id: PAR:0233
name: protein dna complex
def: "A stable set of interacting protein and DNA that can be copurified and operate as a functional unit." [pubmed:14755292 "primary-reference"]
is_a: PAR:0314 ! complex

[Term]
id: PAR:0234
name: 131i radiolabel
def: "Molecule labelled with 131 radio isotope of iodine atoms." [pubmed:14755292 "primary-reference"]
related_synonym: "131I" []
related_synonym: "I131" []
is_a: PAR:0517 ! radiolabel

[Term]
id: PAR:0235
name: 14c radiolabel
def: "Molecule labelled with the radio isotope 14 of carbon atoms." [pubmed:14755292 "primary-reference"]
related_synonym: "14C" []
related_synonym: "C14" []
is_a: PAR:0517 ! radiolabel

[Term]
id: PAR:0236
name: 32p radiolabel
def: "Molecule labelled with the radio isotope 32 of phosphorus atoms." [pubmed:14755292 "primary-reference"]
related_synonym: "32P" []
related_synonym: "P32" []
is_a: PAR:0517 ! radiolabel

[Term]
id: PAR:0237
name: 33p radiolabel
def: "Molecule labelled with the radio isotope 33 of phosphorus atoms." [pubmed:14755292 "primary-reference"]
related_synonym: "33P" []
related_synonym: "P33" []
is_a: PAR:0517 ! radiolabel

[Term]
id: PAR:0238
name: 3h radiolabel
def: "Molecules labelled with isotope 3 of hydrogen atoms." [pubmed:14755292 "primary-reference"]
related_synonym: "3H" []
related_synonym: "H3" []
related_synonym: "tritium" []
is_a: PAR:0517 ! radiolabel

[Term]
id: PAR:0239
name: biotin tag
def: "Biotin, a 244 Dalton vitamin found in tissue and blood, binds with high affinity to avidin and streptavidin protein. Since biotin is a relatively small molecule, it can be conjugated to many proteins or nucleic acids without significantly altering their biological activity. Biotinylation reagents are available for targeting a variety of specific functional groups, including primary amines, sulfhydryls, carboxyls and carbohydrates that lead to nucleotides or amino acid biotinilation." [pubmed:14755292 "primary-reference"]
is_a: PAR:0507 ! tag

[Term]
id: PAR:0240
name: fusion protein
def: "The protein under study is expressed as a fusion with a labelling protein, having either fluorescence properties or an enzymatic activity that facilitates its purification, identification, localisation or quantification." [pubmed:14755292 "primary-reference"]
is_a: PAR:0507 ! tag

[Term]
id: PAR:0241
name: horseradish peroxidase tag
def: "Protein is fused to horseradish peroxidase, and the measure of this enzyme activity can be taken as indicative of presence of protein." [pubmed:14755292 "primary-reference"]
exact_synonym: "hrp tag" []
is_a: PAR:0365 ! enzyme tag

[Term]
id: PAR:0243
name: isoform parent sequence reference
def: "Reference to the master sequence from which this isoform has been derived." [pubmed:14755292 "primary-reference"]
exact_synonym: "isoform-parent" []
is_a: PAR:0353 ! cross-reference type

[Term]
id: PAR:0244
name: reactome complex
def: "Collection of functional complexes within Reactome - a knowledgebase of biological processes." [pubmed:14755292 "primary-reference"]
xref_analog: id-validation-regexp:\"REACT_[0-9\]\{1\,4}\\.[0-9\]\{1\,3}|[0-9\]\" "ANNOTATION"
xref_analog: search-url: http\://www.reactome.org/cgi-bin/eventbrowser?ID=$\{ac} "ANNOTATION"
xref_analog: url:http\://www.reactome.org/ "ANNOTATION"
is_a: PAR:0467 ! reactome

[Term]
id: PAR:0245
name: reactome protein
def: "Collection of protein within the Reactome database - a knowledgebase of biological processes." [pubmed:14755292 "primary-reference"]
xref_analog: id-validation-regexp:\"REACT_[0-9\]\{1\,4}\\.[0-9\]\{1\,3}|[OPQ\][0-9\][A-Z0-9\]\{3}[0-9\]|[OPQ\][0-9\][A-Z0-9\]\{3}[0-9\]-[0-9\]+|[A-Z\]\{3}[0-9\]\{5}|[OPQ\][0-9\][A-Z0-9\]\{3}[0-9\]-PRO_[0-9\]\{10}\" "ANNOTATION"
xref_analog: search-url: http\://www.reactome.org/cgi-bin/search?SUBMIT=1&QUERY_CLASS=DatabaseIdentifier&QUERY=SWALL\:$\{ac} "ANNOTATION"
xref_analog: url:http\://www.reactome.org/ "ANNOTATION"
is_a: PAR:0467 ! reactome

[Term]
id: PAR:0246
name: cabri
def: "CABRI cell lines catalogue available at." [pubmed:14755292 "primary-reference"]
xref_analog: id-validation-regexp:\"[0-9\]+|ACC\\s[A-Z0-9\]+|ECACC\\s[A-Z0-9\]+|LMBP\\s[A-Z0-9\]+|ICLC\\s[A-Z0-9\]+|CIP-[0-9\]+\" "ANNOTATION"
xref_analog: search-url: http\://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?[libs%3d\{dsmz_mutz%20ecacc_cell%20iclc%20CABI_BACT%20CIP_BACT%20CABI_YEAST%20DSMZ_PLANT_CELL}-id\:$\{ac}\]+-e "ANNOTATION"
xref_analog: url:http\://www.cabri.org/ "ANNOTATION"
is_a: PAR:0473 ! participant database

[Term]
id: PAR:0247
name: newt
def: "New EBI Web Taxonomy." [pubmed:14755292 "primary-reference"]
xref_analog: id-validation-regexp:\"[0-9\]+\" "ANNOTATION"
xref_analog: search-url: http\://www.ebi.ac.uk/newt/display?search=$\{ac} "ANNOTATION"
xref_analog: url:http\://www.ebi.ac.uk/newt "ANNOTATION"
is_a: PAR:0473 ! participant database

[Term]
id: PAR:0248
name: resid
def: "The RESID Database of Protein Modifications is a comprehensive collection of annotations and structures for protein modifications including amino-terminal, carboxyl-terminal and peptide chain cross-link post-translational modifications." [pubmed:14755292 "primary-reference"]
xref_analog: id-validation-regexp:\"AA[0-9\]\{4}\" "ANNOTATION"
xref_analog: search-url: http\://srs.ebi.ac.uk/cgi-bin/wgetz?[resid-id\:$\{ac}\]+-e "ANNOTATION"
xref_analog: url:http\://www.ebi.ac.uk/RESID/index.html "ANNOTATION"
is_a: PAR:0447 ! feature database
is_a: PAR:0473 ! participant database

[Term]
id: PAR:0249
name: huge
def: "A Database of Human Unidentified Gene-Encoded Large Proteins Analyzed by Kazusa Human cDNA Project." [pubmed:14755292 "primary-reference"]
xref_analog: id-validation-regexp:\"KIAA[0-9\]\{4}[A-Z\]\{0\,1}\" "ANNOTATION"
xref_analog: search-url: http\://www.kazusa.or.jp/huge/gfpage/$\{ac} "ANNOTATION"
xref_analog: url:http\://www.kazusa.or.jp/huge/ "ANNOTATION"
is_a: PAR:0683 ! sequence database

[Term]
id: PAR:0251
name: gene product
def: "Reference of a protein object pointing to its genomic or nucleic acid sequence." [pubmed:14755292 "primary-reference"]
is_a: PAR:0353 ! cross-reference type

[Term]
id: PAR:0252
name: biological feature
def: "Property of a subsequence that may interfere with the binding of a molecule and are supported by experimental evidences." [pubmed:14755292 "primary-reference"]
is_a: PAR:0116 ! feature type

[Term]
id: PAR:0253
name: isotope label
def: "One of several nuclides having the same number of protons in their nuclei and hence having the same atomic number, but differing in the number of neutrons and therefore, in the mass number." [pubmed:14755292 "primary-reference"]
is_a: PAR:0505 ! experimental feature

[Term]
id: PAR:0276
name: blue native page
def: "Blue native PAGE (BN-PAGE) permits a high-resolution separation of multi-protein complexes under native conditions. Blue native (BN)-PAGE is a charge shift method, in which the electrophoretic mobility of a complex is determined by the negative charge of the bound Coomassie dye and the size and shape of the complex. Coomassie does not act as a detergent and preserves the structure of complexes. Importantly, the resolution of BN-PAGE is much higher than that of other methods such as gel filtration or sucrose-gradient ultracentrifugation. Combined with other pre-purifications or dialysis steps this method permits the analysis of multi-protein complexes of whole cellular lysates by BN-PAGE." [pubmed:14665681 "primary-reference"]
exact_synonym: "bn-page" []
is_a: PAR:0404 ! comigration in non denaturing gel electrophoresis

[Term]
id: PAR:0300
name: alias type
def: "Descriptor of type of nomenclature used to describe interactor." [pubmed:14755292 "primary-reference"]
related_synonym: "CvAliasType" []
relationship: part_of PAR:1004 ! PROTEIN AFFINITY REAGENT CV

[Term]
id: PAR:0301
name: gene name
def: "Gene name." [pubmed:14755292 "primary-reference"]
related_synonym: "gene" []
is_a: PAR:0300 ! alias type

[Term]
id: PAR:0302
name: gene name synonym
def: "Gene name synonym." [pubmed:14755292 "primary-reference"]
is_a: PAR:0300 ! alias type

[Term]
id: PAR:0303
name: gene ontology synonym
def: "Synonym as used in Gene Ontology." [pubmed:14755292 "primary-reference"]
exact_synonym: "go synonym" []
is_a: PAR:0300 ! alias type

[Term]
id: PAR:0304
name: isoform synonym
def: "Isoform synonym." [pubmed:14755292 "primary-reference"]
is_a: PAR:0300 ! alias type

[Term]
id: PAR:0305
name: ordered locus name
def: "A name used to represent an ORF in a completely sequenced genome or chromosome. It is generally based on a prefix representing the organism and a number which usually represents the sequential ordering of genes on the chromosome. Depending on the genome sequencing center, numbers are attributed only to protein-coding genes, or also to pseudogenes, or also to tRNAs and other features." [pubmed:14755292 "primary-reference"]
related_synonym: "CDS number" []
related_synonym: "ONL" []
related_synonym: "Ordered locus name" []
related_synonym: "ORF number" []
related_synonym: "systematic gene number" []
exact_synonym: "locus name" []
xref_analog: comment:For instance HI0934\, Rv3245c\, At5g34500\, YER456W. "ANNOTATION"
is_a: PAR:0300 ! alias type

[Term]
id: PAR:0306
name: open reading frame name
def: "A name temporarily attributed by a sequencing project to an open reading frame. This name is generally based on a cosmid numbering system." [pubmed:14755292 "primary-reference"]
exact_synonym: "orf name" []
xref_analog: comment:For instance MtCY277.28c\, SYGP-ORF50\, SpBC2F12.04\, C06E1.1\, CG10954. Also called Sequencing names or Contig names or Temporary ORFNames. "ANNOTATION"
is_a: PAR:0300 ! alias type

[Term]
id: PAR:0313
name: interactor type
def: "Molecular species involved in the interaction." [pubmed:14755292 "primary-reference"]
related_synonym: "participant type" []
relationship: part_of PAR:1004 ! PROTEIN AFFINITY REAGENT CV

[Term]
id: PAR:0314
name: complex
def: "Set of interacting molecules that can be copurified. This term and its children should be use only at PARTICIPANT level." [pubmed:14755292 "primary-reference"]
is_a: PAR:0313 ! interactor type

[Term]
id: PAR:0315
name: protein complex
def: "A stable set of interacting proteins that can be copurified and operate as a functional unit." [pubmed:14755292 "primary-reference"]
is_a: PAR:0314 ! complex

[Term]
id: PAR:0316
name: ribonucleoprotein complex
def: "A macromolecular complex containing both protein and RNA molecules." [go:GO\:0030529 "identity", pubmed:14755292 "primary-reference"]
related_synonym: "protein rna complex" []
exact_synonym: "ribonucleoprot compl" []
is_a: PAR:0314 ! complex

[Term]
id: PAR:0318
name: nucleic acid
def: "Linear polymers of nucleotides, linked by 3',5' phosphodiester linkages." [pubmed:14755292 "primary-reference", so:SO\:0000348 "identity"]
is_a: PAR:0383 ! biopolymer

[Term]
id: PAR:0319
name: deoxyribonucleic acid
def: "Polymer formed by the deoxyribose sugar group, and the nucleotides bases adenine, guanine, thymine and cytosine." [pubmed:14755292 "primary-reference", so:SO\:0000352 "identity"]
related_synonym: "deoxyribonucleic acid" []
related_synonym: "DNA" []
exact_synonym: "dna" []
is_a: PAR:0318 ! nucleic acid

[Term]
id: PAR:0320
name: ribonucleic acid
def: "Polymer formed by ribose sugar group, and the bases of the nucleotides adenine, guanine, uracil and cytosine." [pubmed:14755292 "primary-reference", so:SO\:0000356 "identity"]
related_synonym: "RNA" []
exact_synonym: "rna" []
is_a: PAR:0318 ! nucleic acid

[Term]
id: PAR:0321
name: catalytic rna
def: "Species of RNA that catalyses cleavage or trans-esterification of the phosphodiester link." [pubmed:14755292 "primary-reference"]
related_synonym: "catalytic ribonucleic acid" []
related_synonym: "catalytic RNA" []
exact_synonym: "crna" []
is_a: PAR:0320 ! ribonucleic acid

[Term]
id: PAR:0322
name: guide rna
def: "Small RNA molecules that hybridize to specific mRNAs and direct their RNA editing." [pubmed:14755292 "primary-reference"]
related_synonym: "guide RNA" []
exact_synonym: "grna" []
is_a: PAR:0320 ! ribonucleic acid

[Term]
id: PAR:0323
name: heterogeneous nuclear rna
def: "A heterogeneous mixture of RNA molecules with a rapid turnover rate that occurs in cell nuclei during protein synthesis; it is the form of RNA synthesized in eukaryotes by RNA polymerase II, which is translated into protein." [pubmed:14755292 "primary-reference"]
related_synonym: "heterogeneous nuclear ribonucleic acid" []
related_synonym: "heterogeneous nuclear RNA" []
exact_synonym: "hnrna" []
is_a: PAR:0320 ! ribonucleic acid

[Term]
id: PAR:0324
name: messenger rna
def: "Single-stranded RNA molecule that specifies the amino acid sequence of one or more polypeptide chains." [pubmed:14755292 "primary-reference"]
related_synonym: "mRNA" []
exact_synonym: "mrna" []
is_a: PAR:0320 ! ribonucleic acid

[Term]
id: PAR:0325
name: transfer rna
def: "The low molecular weight RNAs that specifically bind amino acids by aminoacetylation to form aminoacyl tRNA and which possess a special nucleotide triplet, the anticodon." [pubmed:14755292 "primary-reference"]
related_synonym: "transfer ribonucleic acid" []
related_synonym: "transfer RNA" []
related_synonym: "tRNA" []
exact_synonym: "trna" []
is_a: PAR:0320 ! ribonucleic acid

[Term]
id: PAR:0326
name: protein
def: "A linear polymer of amino acids joined by peptide bonds in a specific sequence." [pubmed:14755292 "primary-reference", so:SO\:0000358 "identity"]
is_a: PAR:0383 ! biopolymer

[Term]
id: PAR:0327
name: peptide
def: "Chains of amino acids joined by peptide bonds. Distinction between peptides, oligopeptides and polypeptides is arbitrarily by length; a polypeptide is perhaps more than 15 residues." [pubmed:14755292 "primary-reference"]
related_synonym: "oligopeptide" []
related_synonym: "polypeptide" []
is_a: PAR:0383 ! biopolymer

[Term]
id: PAR:0328
name: small molecule
def: "Molecule not part of or directly encoded by the genome, encompasses any constitutionally or isotopically distinct atom, molecule, ion, ion pair, radical, radical ion, complex, conformer, etc., identifiable as a separately distinguishable entity." [pubmed:14755292 "primary-reference"]
is_a: PAR:0313 ! interactor type

[Term]
id: PAR:0329
name: unknown participant
def: "Any type of molecule, including complexes, that may be observed but not identified. This term should be use only at PARTICIPANT level." [pubmed:14755292 "primary-reference"]
is_a: PAR:0313 ! interactor type

[Term]
id: PAR:0333
name: feature range status
def: "Describes sequence positions resolution of a given participant feature. In PSI schema this CV is associated with the start and end position of a feature range." [pubmed:14755292 "primary-reference"]
related_synonym: "CvFuzzyType" []
related_synonym: "endStatus" []
related_synonym: "startStatus" []
relationship: part_of PAR:1004 ! PROTEIN AFFINITY REAGENT CV

[Term]
id: PAR:0334
name: c terminal position
def: "Term describing the last amino acid of a peptide chain." [pubmed:14755292 "primary-reference"]
related_synonym: "c-term" []
related_synonym: "c-terminal" []
related_synonym: "c-terminus" []
related_synonym: "carboxy-terminus" []
exact_synonym: "c terminal" []
xref_analog: comment:Displayed as 'c'. "ANNOTATION"
is_a: PAR:0333 ! feature range status

[Term]
id: PAR:0335
name: certain sequence position
def: "Position within the sequence clearly defined." [pubmed:14755292 "primary-reference"]
exact_synonym: "certain" []
is_a: PAR:0333 ! feature range status

[Term]
id: PAR:0336
name: greater than
def: "Partially determined sequence position known to be in a location higher than a given position." [pubmed:14755292 "primary-reference"]
xref_analog: comment:Displayed as '>'. "ANNOTATION"
is_a: PAR:0333 ! feature range status

[Term]
id: PAR:0337
name: less than
def: "Partially determined sequence position known to be in a position lower than a given position." [pubmed:14755292 "primary-reference"]
xref_analog: comment:Displayed as '<'. "ANNOTATION"
is_a: PAR:0333 ! feature range status

[Term]
id: PAR:0338
name: range
def: "Describes a sequence position known to be in a certain range, where the exact position is unclear." [pubmed:14755292 "primary-reference"]
xref_analog: comment:For instance when an amino acid modification is known to be in the region from 5 to 7. Displayed as '..'. "ANNOTATION"
is_a: PAR:0333 ! feature range status

[Term]
id: PAR:0339
name: undetermined sequence position
def: "Term describing a completely unknown or unspecified sequence position." [pubmed:14755292 "primary-reference"]
exact_synonym: "undetermined" []
xref_analog: comment:Displayed as '?'. "ANNOTATION"
is_a: PAR:0333 ! feature range status

[Term]
id: PAR:0340
name: n terminal position
def: "Term describing the first amino acid of a peptide chain." [pubmed:14755292 "primary-reference"]
related_synonym: "amino-terminus" []
related_synonym: "n-term" []
related_synonym: "n-terminal" []
related_synonym: "n-terminus" []
exact_synonym: "n terminal " []
xref_analog: comment:Displayed as 'n'. "ANNOTATION"
is_a: PAR:0333 ! feature range status

[Term]
id: PAR:0341
name: ragged n terminus
def: "Mixture of protein forms where N-terminus has been progressively truncated." [pubmed:14755292 "primary-reference"]
is_a: PAR:0340 ! n terminal position

[Term]
id: PAR:0345
name: author assigned name
def: "Name assigned to a molecule by the authors within a paper that may differ from the reference database." [pubmed:14755292 "primary-reference"]
is_a: PAR:0300 ! alias type

[Term]
id: PAR:0346
name: experimental preparation
def: "Set of terms to describe the participant experimental treatment and status. This term group in fact 4 orthologues short controlled vocabularies delivery method, expression level, molecular source, and sample process. Each participant can then be annotated with a maximum of 4 terms selected from each short list." [pubmed:14755292 "primary-reference"]
exact_synonym: "experimental prep" []
relationship: part_of PAR:1004 ! PROTEIN AFFINITY REAGENT CV

[Term]
id: PAR:0350
name: purity state
def: "Molecule has undergone one or more purification steps to isolate it from the cellular environment. The purity corresponds to a quantitative assessment of the homogeneity or uniformity of a mixture. It refers to the degree of being free of contaminants or heterogeneous components." [pubmed:14755292 "primary-reference"]
is_a: PAR:1014 ! molecular state

[Term]
id: PAR:0351
name: homogeneous
def: "The author states a molecule is completely pure, i.e. no other molecular species are present." [pubmed:14755292 "primary-reference"]
related_synonym: "pure" []
is_a: PAR:0350 ! purity state

[Term]
id: PAR:0352
name: partially purified
def: "The author states a molecule is only partially purified, i.e. other molecular species are also known to be present." [pubmed:14755292 "primary-reference"]
is_a: PAR:0350 ! purity state

[Term]
id: PAR:0353
name: cross-reference type
def: "Qualifier to describe the type of information a cross-reference is pointing to." [pubmed:14755292 "primary-reference"]
related_synonym: "CvXrefQualifier" []
related_synonym: "refType" []
exact_synonym: "xref type" []
relationship: part_of PAR:1004 ! PROTEIN AFFINITY REAGENT CV

[Term]
id: PAR:0354
name: gene ontology term for cellular component
def: "Cross reference pointing to a Gene Ontology -'cellular component' term." [pubmed:14681407 "primary-reference"]
related_synonym: "go component term" []
exact_synonym: "component" []
is_a: PAR:1324 ! gene ontology term

[Term]
id: PAR:0355
name: gene ontology term for cellular function
def: "Cross reference pointing to a Gene Ontology -'cellular function' term." [pubmed:14681407 "primary-reference"]
related_synonym: "go function term" []
exact_synonym: "function" []
is_a: PAR:1324 ! gene ontology term

[Term]
id: PAR:0356
name: identical object
def: "Reference to the corresponding object in another database. Correspondence may be complete or partial." [pubmed:14755292 "primary-reference"]
exact_synonym: "identity" []
xref_analog: comment:For instance this qualifier\, in an interaction entry\, can be associated to a cross reference to the same interaction in an other database. "ANNOTATION"
is_a: PAR:0353 ! cross-reference type

[Term]
id: PAR:0357
name: method reference
def: "Reference to a related paper which more fully describes either the experimental method or one or more of the interactors used within the experiment." [pubmed:14755292 "primary-reference"]
is_a: PAR:0353 ! cross-reference type

[Term]
id: PAR:0358
name: primary reference
def: "Used to indicate the PMID from which the experimental data is extracted." [pubmed:14755292 "primary-reference"]
is_a: PAR:0353 ! cross-reference type

[Term]
id: PAR:0359
name: gene ontology term for cellular process
def: "Cross reference pointing to a Gene Ontology -'cellular process' term." [pubmed:14681407 "primary-reference"]
related_synonym: "go process term" []
exact_synonym: "process" []
is_a: PAR:1324 ! gene ontology term

[Term]
id: PAR:0360
name: secondary accession number
def: "Reference to the corresponding object in another database (like identity xref qualifier) but the identifier used in the external database is a secondary identifier or former accesion numbers" [pubmed:14755292 "primary-reference"]
exact_synonym: "secondary-ac" []
is_a: PAR:0353 ! cross-reference type

[Term]
id: PAR:0361
name: see-also
def: "Related object within the same database or pointing to external database." [pubmed:14755292 "primary-reference"]
is_a: PAR:0353 ! cross-reference type

[Term]
id: PAR:0365
name: enzyme tag
def: "Molecule under study is fused to an enzyme, for example alkaline phosphatase, and measure of enzyme activity can be taken as indicative of presence of protein." [pubmed:10935637 "primary-reference"]
is_a: PAR:0240 ! fusion protein

[Term]
id: PAR:0366
name: alkaline phosphatase tag
def: "Protein is fused to alkaline phosphatase, and the measure of this enzyme activity can be taken as indicative of presence of protein." [pubmed:10935637 "primary-reference"]
exact_synonym: "alk phosphatase tag" []
is_a: PAR:0365 ! enzyme tag

[Term]
id: PAR:0367
name: green fluorescent protein tag
def: "The green fluorescent protein of the bioluminescent jellyfish Aequorea victoria can be fused to individual proteins which then acquire fluorescence excitation and emission spectra virtually identical to those of the native." [pubmed:7491768 "primary-reference"]
related_synonym: "GFP" []
related_synonym: "green fluorescent protein" []
exact_synonym: "gfp tag" []
is_a: PAR:0687 ! fluorescent protein tag

[Term]
id: PAR:0368
name: yellow fluorescent protein tag
def: "Yellow fluorescent protein from Vibrio fischeri can be fused to individual proteins which then acquire fluorescence excitation and emission spectra virtually identical to those of the native." [pubmed:10929120 "primary-reference"]
related_synonym: "yellow fluorescent protein" []
related_synonym: "YFP" []
exact_synonym: "yfp tag" []
is_a: PAR:0687 ! fluorescent protein tag

[Term]
id: PAR:0371
name: 35s radiolabel
def: "Molecule labelled with 35 radio isotope of sulfur. Proteins are often metabolically labelled, usually be growth in 35S labelled culture medium." [pubmed:14755292 "primary-reference"]
related_synonym: "35S" []
related_synonym: "S35" []
related_synonym: "s35 radiolabelled" []
is_a: PAR:0517 ! radiolabel

[Term]
id: PAR:0373
name: dye label
def: "Dye coupled to a molecule allowing its identification isolation and monitoring." [pubmed:14577292 "primary-reference"]
exact_synonym: "dye labelled" []
is_a: PAR:0505 ! experimental feature

[Term]
id: PAR:0374
name: cyanine label
def: "The organic cyanine dyes emit in the red range (>550 nm), offer a number of advantages. Their emission range is such that background fluorescence is often reduced. In addition these molecules can be linked directly to specific locations in synthetically produced nucleic acids." [pubmed:14577292 "primary-reference"]
is_a: PAR:0373 ! dye label
is_a: PAR:0857 ! fluorescent dye label

[Term]
id: PAR:0375
name: cy3 label
def: "The organic cyanine Cy3 emits maximally at 570 nm." [pubmed:14577292 "primary-reference"]
is_a: PAR:0374 ! cyanine label

[Term]
id: PAR:0376
name: cy5 label
def: "The organic cyanine Cy5 emits maximally at 670 nm." [pubmed:14577292 "primary-reference"]
is_a: PAR:0374 ! cyanine label

[Term]
id: PAR:0377
name: fluorescein isothiocyanate label
def: "Fluorescein isothiocyanate is a yellow-green coloured low molecular weight dye which couples to proteins via reaction with primary amine groups at high pH. FITC is excitable at 488nm, close to its absorption maximum at 494nm, and produces maximum fluorescence emission around 520nm." [pubmed:14577292 "primary-reference"]
related_synonym: "FITC labelled" []
related_synonym: "fluorescein isothiocyanate labbeled" []
exact_synonym: "fitc labelled" []
is_a: PAR:0373 ! dye label
is_a: PAR:0857 ! fluorescent dye label

[Term]
id: PAR:0378
name: rare isotope label
def: "Molecule can be labelled including rare isotopes among its constituent atoms that can be used to identify, localize or quantify the full molecule." [pubmed:14577292 "primary-reference"]
exact_synonym: "rare isotope label" []
is_a: PAR:0253 ! isotope label

[Term]
id: PAR:0379
name: 13c label
def: "Molecules labelled with isotope 13 of carbon atoms." [pubmed:14577292 "primary-reference"]
related_synonym: "13C" []
related_synonym: "C13" []
is_a: PAR:0378 ! rare isotope label

[Term]
id: PAR:0380
name: 15n label
def: "Molecules labelled with isotope 15 of nytrogen atoms." [pubmed:14577292 "primary-reference"]
related_synonym: "15N" []
related_synonym: "N15" []
is_a: PAR:0378 ! rare isotope label

[Term]
id: PAR:0381
name: 2h label
def: "Molecules labelled with isotope 2 of hydrogen atoms." [pubmed:14577292 "primary-reference"]
related_synonym: "2H2" []
related_synonym: "D2" []
related_synonym: "deuterium" []
is_a: PAR:0378 ! rare isotope label

[Term]
id: PAR:0382
name: mutation increasing interaction
def: "Residue of a protein whose identity mutation or deletion increases significantly interaction strength." [pubmed:14755292 "primary-reference"]
exact_synonym: "mutation increasing" []
is_a: PAR:0118 ! mutation

[Term]
id: PAR:0383
name: biopolymer
def: "Molecule consisting of a specific sequence of amino acidic or nucleotidic monomers strung together through chemical bonds." [pubmed:14577292 "primary-reference"]
is_a: PAR:0313 ! interactor type

[Term]
id: PAR:0384
name: alexa label
def: "All Alexa dyes are fluorescent iodoacetamide dyes that can be conjugated with the primary amines of biomolecules. All Alexa dyes and their conjugates are more fluorescent and more photostable than the commonly used dyes. The numbers in the Alexa names indicate the approximate excitation wavelength maximum in nm)." [pubmed:10449539 "primary-reference"]
is_a: PAR:0373 ! dye label
is_a: PAR:0857 ! fluorescent dye label

[Term]
id: PAR:0385
name: alexa 350 label
def: "Alexa fluorescent dye analogue to AMCA (7-amino-4-methylcoumarin-3-acetic acid) with an approximate excitation wavelength maximum of 350 nm." [pubmed:10449539 "primary-reference"]
is_a: PAR:0384 ! alexa label

[Term]
id: PAR:0386
name: alexa 430 label
def: "Alexa fluorescent dye analogue to Lucifer Yellow with an approximate excitation wavelength maximum of 430 nm." [pubmed:10449539 "primary-reference"]
is_a: PAR:0384 ! alexa label

[Term]
id: PAR:0387
name: alexa 488 label
def: "Alexa fluorescent dye analogue to Oregon Green 488 with an approximate excitation wavelength maximum of 488 nm." [pubmed:10449539 "primary-reference"]
is_a: PAR:0384 ! alexa label

[Term]
id: PAR:0388
name: alexa 532 label
def: "Alexa fluorescent dye analogue to Rhodamine 6G with an approximate excitation wavelength maximum of 532nm." [pubmed:10449539 "primary-reference"]
is_a: PAR:0384 ! alexa label

[Term]
id: PAR:0389
name: alexa 546 label
def: "Alexa fluorescent dye analogue to Cy3 with an approximate excitation wavelength maximum of 546nm." [pubmed:10449539 "primary-reference"]
is_a: PAR:0384 ! alexa label

[Term]
id: PAR:0390
name: alexa 568 label
def: "Alexa fluorescent dye analogue to Rhodamine Red-X with an approximate excitation wavelength maximum of 568nm." [pubmed:10449539 "primary-reference"]
is_a: PAR:0384 ! alexa label

[Term]
id: PAR:0391
name: alexa 594 label
def: "Alexa fluorescent dye analogue to Texas Red-X with an approximate excitation wavelength maximum of 594nm." [pubmed:10449539 "primary-reference"]
is_a: PAR:0384 ! alexa label

[Term]
id: PAR:0396
name: predetermined participant
def: "Molecule whose sequence identity is not checked and has been assumed from external or previous experimental evidence(s)." [pubmed:14755292 "primary-reference"]
exact_synonym: "predetermined" []
is_a: PAR:0661 ! experimental participant identification

[Term]
id: PAR:0401
name: biochemical
def: "The application of chemical principles and methods to biological experiments." [pubmed:14755292 "primary-reference"]
is_a: PAR:0001 ! interaction detection method

[Term]
id: PAR:0402
name: chromatin immunoprecipitation assays
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 proteins to DNA. An antibody against a protein suspected of binding a given cis-element is then used to immunoprecipitate chromatin fragments. Polymerase chain reaction analysis of the immunoprecipitate with primers flanking the cis-element reveals whether a specific DNA sequence is recovered in an immune-specific manner and therefore whether the protein contacted the site in living cells." [pubmed:12054902 "primary-reference"]
exact_synonym: "ch-ip" []
is_a: PAR:0401 ! biochemical

[Term]
id: PAR: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." [pubmed:14755292 "primary-reference"]
is_a: PAR:0190 ! interaction type

[Term]
id: PAR:0404
name: comigration in non denaturing gel electrophoresis
def: "comigration by non denaturing gel electrophoresis." [pubmed:14755292 "primary-reference"]
exact_synonym: "comig non denat gel" []
is_a: PAR:0807 ! comigration in gel electrophoresis

[Term]
id: PAR: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." [pubmed:14755292 "primary-reference"]
is_a: PAR:0401 ! biochemical

[Term]
id: PAR:0407
name: direct interaction
def: "Interaction that is proven to involve only its interactors." [pubmed:14755292 "primary-reference"]
is_a: PAR:0218 ! physical interaction

[Term]
id: PAR:0408
name: disulfide bond
def: "Covalent bond mediated by 2 sulfur atoms." [pubmed:14755292 "primary-reference"]
is_a: PAR:0195 ! covalent binding

[Term]
id: PAR: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 interacting partner and then is submitted to the same partial digestion. The two samples are then analyzed in parallel by electrophoresis on a denaturing acrylamide gel. After autoradiography the identification of the bands that correspond to fragments missing from the lane loaded with the second sample reveals the region of the nucleic acid that is protected from nuclease digestion upon binding." [pubmed:14755292 "primary-reference"]
is_a: PAR:0417 ! footprinting

[Term]
id: PAR: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 opportunity to obtain 3D information on structural cellular arrangements with a high resolution." [pubmed:12160704 "primary-reference"]
exact_synonym: "sem" []
is_a: PAR:0040 ! electron microscopy

[Term]
id: PAR: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 washing and a secondary antibody conjugated to an enzyme (e.g. horseradish peroxidase) is added. Following a washing step to remove unbound secondary ligand, the extent to which a chromogenic substrate (e.g. 3,3', 5,5' tetramethyl benzidine chromogen [TMB]) is converted to a soluble coloured product by the conjugated enzyme in a given time is determined by spectrophotometry using a standard microplate absorbance reader. A similar type of approach can be utilized to detect enzymatic activities. The substrate, attached to a solid phase is incubated in the presence of the enzyme and the enzymatic modification is monitored by an antibody that is specific for the modified substrate (for instance a phosphorylated protein)." [pubmed:14755292 "primary-reference"]
related_synonym: "ELISA" []
exact_synonym: "elisa" []
is_a: PAR:0401 ! biochemical
is_a: PAR:0421 ! identification by antibody

[Term]
id: PAR:0412
name: EM 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 larger complex including the antibody. By this approach, at least one protein of the complex is directly identified." [pubmed:12169687 "primary-reference"]
exact_synonym: "emsa supershift" []
is_a: PAR:0413 ! electrophoretic mobility shift assay

[Term]
id: PAR: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 with a purified protein (or a protein mixture). After the electrophoresis run and autoradiography by comparing the nucleic acid migration in the two lanes the retardation of the nucleic acid due to its interaction with a protein can be easily observed." [pubmed:12169687 "primary-reference"]
related_synonym: "band shift" []
related_synonym: "Gel retardation assay" []
exact_synonym: "emsa" []
is_a: PAR:1320 ! electrophoresis

[Term]
id: PAR:0414
name: enzymatic reaction
def: "terms aiming to represent biochemical reactions referring to their resulting product modifications." [pubmed:14755292 "primary-reference"]
related_synonym: "Biochemical reaction" []
is_a: PAR:0407 ! direct interaction

[Term]
id: PAR: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 sample, but the image is based on the second light source -- the light emanating from the fluorescent species -- rather than from the light originally used to illuminate, and excite, the sample." [pubmed:14755292 "primary-reference"]
exact_synonym: "fluorescence imaging" []
is_a: PAR:0428 ! imaging techniques

[Term]
id: PAR:0417
name: footprinting
def: "footprinting analysis is used to identify regions of molecules directly involved in binding other macromolecules and therefore protected from the effects of degradative enzymes." [pubmed:14755292 "primary-reference"]
is_a: PAR:0401 ! biochemical

[Term]
id: PAR:0421
name: identification by antibody
def: "antibody mediated identification." [pubmed:14755292 "primary-reference"]
exact_synonym: "antibody detection" []
is_a: PAR:0661 ! experimental participant identification

[Term]
id: PAR:0422
name: immunostaining
def: "Method using an antibody coupled with some colouring agent to detect a specific protein within a cell or tissue sample. In some cases the primary antibody is directly linked to a colouring agent, more often the primary antibody is targeted by a secondary antibody, targeting the primary antibody." [pubmed:14755292 "primary-reference"]
is_a: PAR:0401 ! biochemical
is_a: PAR:0421 ! identification by antibody

[Term]
id: PAR:0425
name: kinase scintillation proximity assay
def: "Relies on the radiolabelling of a peptide substrate immobilized on a scintillant coated SPA-bead. The kinase transfers a phosphate isotope from the nucleotide to the substrate." [pubmed:14755292 "primary-reference"]
exact_synonym: "kinase spa" []
is_a: PAR:0099 ! scintillation proximity assay

[Term]
id: PAR:0426
name: light microscopy
def: "Light visible microscopy uses environmental light to illuminate the sample and produce a magnified image of the sample." [pubmed:14755292 "primary-reference"]
is_a: PAR:0428 ! imaging techniques

[Term]
id: PAR:0427
name: mass spectrometry
def: "mass spectrometry." [pubmed:14755292 "primary-reference"]
is_a: PAR:0661 ! experimental participant identification

[Term]
id: PAR:0428
name: imaging techniques
def: "Methods that provide images of molecules at various resolution depending on the technology used." [pubmed:14755292 "primary-reference"]
related_synonym: "microscopy" []
is_a: PAR:0001 ! interaction detection method
is_a: PAR:0661 ! experimental participant identification

[Term]
id: PAR:0429
name: necessary binding site
def: "A sequence range within a protein identified as being absolutely required for an interaction." [pubmed:14755292 "primary-reference"]
exact_synonym: "required to bind" []
is_a: PAR:0117 ! binding site

[Term]
id: PAR:0430
name: nucleic acid uv cross-linking assay
def: "Radiolabelled nucleic acids with a known sequence are incubated with purified proteins or reproducible protein mixture (HPLC eluate fractions) and then irradiated with UV. The complex are treated with an enzyme to remove the unbound nucleic acid (Rnase A or Dnase I for example), washed and then analyzed by electrophoresis. The eventual complexes are identified by autoradiography. The proteins involved in the complex can be recognized by specific antibodies or by retrieving the original protein mixture and carrying further analysis on it. The affinity of the binding can be estimated by adding a non-labelled nucleic acid as competitor before the UV irradiation." [pubmed:14755292 "primary-reference"]
exact_synonym: "nucl ac uv crosslink" []
is_a: PAR:0030 ! cross-linking study

[Term]
id: PAR:0433
name: partial identification of protein sequence
def: "partial protein sequence identification." [pubmed:14755292 "primary-reference"]
exact_synonym: "partial id prot seq" []
is_a: PAR:0093 ! protein sequence identification

[Term]
id: PAR:0436
name: protein footprinting
def: "Protein footprinting is a technique for identifying structural changes modulated by protein-ligand binding, and mapping protein-ligand interfaces This technique involves attaching cutting reagents randomly to amino acid residue (e.g. lysine or cysteine) on the proteins surface and then using this lysine-labelled protein to cleave polypeptide backbone of the other protein at exposed residues adjacent to its binding site." [pubmed:14600024 "primary-reference", pubmed:14967031 "method reference", pubmed:14987073 "method reference"]
is_a: PAR:0659 ! experimental feature detection

[Term]
id: PAR:0440
name: saturation binding
def: "Saturation binding experiments measure specific ligand binding at equilibrium at various concentrations of the ligand. Analysis of these data can determine receptor number and affinity." [pubmed:14755292 "primary-reference"]
is_a: PAR:0401 ! biochemical

[Term]
id: PAR:0442
name: sufficient binding site
def: "Binding will occur when this sequence range is present within a protein." [pubmed:14755292 "primary-reference"]
exact_synonym: "sufficient to bind" []
is_a: PAR:0117 ! binding site

[Term]
id: PAR:0444
name: database citation
def: "Database citation list names of databases commonly used to cross reference interaction data." [pubmed:14755292 "primary-reference"]
relationship: part_of PAR:1004 ! PROTEIN AFFINITY REAGENT CV

[Term]
id: PAR:0445
name: literature database
def: "literature reference" [pubmed:14755292 "primary-reference"]
exact_synonym: "experiment xref" []
is_a: PAR:0444 ! database citation

[Term]
id: PAR:0446
name: pubmed
def: "PubMed is designed to provide access to citations from biomedical literature." [pubmed:14755292 "primary-reference"]
xref_analog: id-validation-regexp:\"[0-9\]+\" "ANNOTATION"
xref_analog: search-url: http\://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=$\{ac}&dopt=Abstract "ANNOTATION"
xref_analog: url:http\://www.ncbi.nlm.nih.gov/entrez/query.fcgi "ANNOTATION"
is_a: PAR:0445 ! literature database

[Term]
id: PAR:0447
name: feature database
def: "feature database." [pubmed:14755292 "primary-reference"]
exact_synonym: "feature xref" []
is_a: PAR:0444 ! database citation

[Term]
id: PAR:0448
name: gene ontology
def: "The objective of Gene Ontology (GO) is to provide controlled vocabularies for the description of the molecular function, biological process and cellular component of gene products." [pubmed:14755292 "primary-reference"]
exact_synonym: "go" []
xref_analog: id-validation-regexp:\"GO\:[0-9\]\{7}\" "ANNOTATION"
xref_analog: url:http\://www.ebi.ac.uk/GO "ANNOTATION"
is_a: PAR:0447 ! feature database
is_a: PAR:0461 ! interaction database

[Term]
id: PAR:0449
name: interpro
def: "InterPro combines a number of databases (referred to as member databases) that use different methodologies and a varying degree of biological information on well-characterised proteins to derive protein signatures." [pubmed:1252001 "primary-reference"]
related_synonym: "InterPro" []
xref_analog: id-validation-regexp:\"IPR[0-9\]\{6}\" "ANNOTATION"
xref_analog: search-url: http\://www.ebi.ac.uk/interpro/DisplayIproEntry?ac=$\{ac} "ANNOTATION"
xref_analog: url:http\://www.ebi.ac.uk/interpro/ "ANNOTATION"
is_a: PAR:0447 ! feature database

[Term]
id: PAR:0450
name: cdd
def: "The Conserved Domain Database may be used to identify the conserved domains present in a protein sequence." [pubmed:14755292 "primary-reference"]
related_synonym: "CDD" []
xref_analog: id-validation-regexp:\"[0-9\]+\" "ANNOTATION"
xref_analog: url:http\://www.ncbi.nlm.nih.gov/Structure/cdd/cdd.shtml "ANNOTATION"
is_a: PAR:0447 ! feature database

[Term]
id: PAR:0451
name: pfam
def: "Pfam is a large collection of multiple sequence alignments and hidden Markov models covering many common protein domains." [pubmed:14755292 "primary-reference"]
related_synonym: "Pfam" []
xref_analog: id-validation-regexp:\"PF[0-9\]\{5}\" "ANNOTATION"
xref_analog: url:http\://www.sanger.ac.uk/Software/Pfam "ANNOTATION"
is_a: PAR:0449 ! interpro

[Term]
id: PAR:0452
name: pirsf
def: "PIRSF is a classification system based on evolutionary relationship of whole proteins." [pubmed:14755292 "primary-reference"]
related_synonym: "PIRSF" []
xref_analog: id-validation-regexp:\"PIRSF[0-9\]\{5}\" "ANNOTATION"
xref_analog: url:http\://pir.georgetown.edu/iproclass/ "ANNOTATION"
is_a: PAR:0449 ! interpro

[Term]
id: PAR:0453
name: prints
def: "PRINTS is a compendium of protein fingerprints. A fingerprint is a group of conserved motifs used to characterise a protein family." [pubmed:14755292 "primary-reference"]
related_synonym: "PRINTS" []
xref_analog: id-validation-regexp:\"PR[0-9\]\{6}\" "ANNOTATION"
xref_analog: url:http\://umber.sbs.man.ac.uk/dbbrowser/PRINTS/ "ANNOTATION"
is_a: PAR:0449 ! interpro

[Term]
id: PAR:0454
name: prodom
def: "The ProDom protein domain database consists of an automatic compilation of homologous domains." [pubmed:14755292 "primary-reference"]
related_synonym: "ProDom" []
xref_analog: id-validation-regexp:\"PD[0-9\]\{6}\" "ANNOTATION"
xref_analog: url:http\://protein.toulouse.inra.fr/prodom.html "ANNOTATION"
is_a: PAR:0449 ! interpro

[Term]
id: PAR:0455
name: prosite
def: "PROSITE is a database of protein families and domains. It consists of biologically significant sites, patterns and profiles." [pubmed:14755292 "primary-reference"]
related_synonym: "Prosite" []
xref_analog: id-validation-regexp:\"PS[0-9\]\{5}\" "ANNOTATION"
xref_analog: url:http\://us.expasy.org/prosite/ "ANNOTATION"
is_a: PAR:0449 ! interpro

[Term]
id: PAR:0456
name: scop superfamily
def: "SUPERFAMILY is a library of profile hidden Markov models that represent all proteins of known structure. The library is based on the SCOP classification of proteins: each model corresponds to a SCOP domain." [pubmed:14755292 "primary-reference"]
related_synonym: "SCOP superfamily" []
xref_analog: id-validation-regexp:\"[0-9\]+\" "ANNOTATION"
xref_analog: url:http\://supfam.mrc-lmb.cam.ac.uk/SUPERFAMILY/ "ANNOTATION"
is_a: PAR:0449 ! interpro

[Term]
id: PAR:0457
name: smart
def: "SMART (a Simple Modular Architecture Research Tool) allows the identification and annotation of genetically mobile domains and the analysis of domain architectures." [pubmed:14755292 "primary-reference"]
related_synonym: "SMART" []
xref_analog: id-validation-regexp:\"SM[0-9\]\{5}\" "ANNOTATION"
xref_analog: url:http\://smart.embl-heidelberg.de/ "ANNOTATION"
is_a: PAR:0449 ! interpro

[Term]
id: PAR:0458
name: tigrfams
def: "TIGRFAMs is a collection of protein families, featuring curated multiple sequence alignments, Hidden Markov Models (HMMs) and annotation." [pubmed:14755292 "primary-reference"]
related_synonym: "TIGRFAMs" []
xref_analog: id-validation-regexp:\"TIGR[0-9\]+\" "ANNOTATION"
xref_analog: url:http\://www.tigr.org/TIGRFAMs "ANNOTATION"
is_a: PAR:0449 ! interpro

[Term]
id: PAR:0459
name: mmdb
def: "MMDB (Molecular Modeling DataBase), is a subset of three-dimensional structures obtained from the Protein Data Bank." [pubmed:14755292 "primary-reference"]
related_synonym: "MMDB" []
xref_analog: id-validation-regexp:\"[0-9\]+\" "ANNOTATION"
xref_analog: url:http\://www.ncbi.nlm.nih.gov/Structure "ANNOTATION"
is_a: PAR:0447 ! feature database
is_a: PAR:0461 ! interaction database

[Term]
id: PAR:0460
name: rcsb pdb
def: "The RCSB PDB provides a variety of tools and resources for studying the structures of biological macromolecules and their relationships to sequence, function, and disease." [pubmed:14634627 "primary-reference"]
related_synonym: "PDB" []
xref_analog: id-validation-regexp:\"[0-9\][a-zA-Z0-9\]\{3}\" "ANNOTATION"
xref_analog: search-url: http\://www.pdb.org/pdb/explore/explore.do?structureId=$\{ac} "ANNOTATION"
xref_analog: url:http\://www.pdb.org/ "ANNOTATION"
is_a: PAR:0805 ! wwpdb

[Term]
id: PAR:0461
name: interaction database
def: "interaction database." [pubmed:14755292 "primary-reference"]
exact_synonym: "interaction xref" []
is_a: PAR:0444 ! database citation

[Term]
id: PAR:0462
name: bind
def: "The Biomolecular Interaction Network Database (BIND) is a collection of records documenting molecular interactions." [pubmed:14755292 "primary-reference"]
related_synonym: "BIND" []
xref_analog: id-validation-regexp:\"[0-9\]+\" "ANNOTATION"
xref_analog: url:http\://www.blueprint.org/bind "ANNOTATION"
is_a: PAR:0461 ! interaction database
is_a: PAR:0489 ! source database

[Term]
id: PAR:0463
name: grid
def: "The General Repository for Interaction Datasets (GRID) is a database of genetic and physical interactions." [pubmed:14755292 "primary-reference"]
related_synonym: "GRID" []
xref_analog: url:http\://biodata.mshri.on.ca/grid "ANNOTATION"
is_a: PAR:0461 ! interaction database
is_a: PAR:0489 ! source database

[Term]
id: PAR:0464
name: cygd
def: "The MIPS Comprehensive Yeast Genome Database (CYGD) aims to present information on the molecular structure and functional network of the entirely sequenced, well-studied model eukaryote, the budding yeast Saccharomyces cerevisiae. In addition the data of various projects on related yeasts are used for comparative analysis." [pubmed:14755292 "primary-reference"]
related_synonym: "CYGD" []
related_synonym: "CYGD (MIPS)" []
related_synonym: "MIPS" []
related_synonym: "MPact" []
xref_analog: id-validation-regexp:\"[0-9\]+\" "ANNOTATION"
xref_analog: url:http\://mips.gsf.de/genre/proj/mpact "ANNOTATION"
xref_analog: url:http\://mips.gsf.de/proj/yeast/CYGD "ANNOTATION"
is_a: PAR:0461 ! interaction database
is_a: PAR:0489 ! source database
is_a: PAR:0683 ! sequence database

[Term]
id: PAR:0465
name: dip
def: "The database of interacting protein (DIP) database stores experimentally determined interactions between proteins. It combines information from a variety of sources to create a single, consistent set of protein-protein interactions." [pubmed:14755292 "primary-reference"]
related_synonym: "DIP" []
xref_analog: id-validation-regexp:\"DIP[0-9\]+[NE\]\" "ANNOTATION"
xref_analog: url:http\://dip.doe-mbi.ucla.edu/ "ANNOTATION"
is_a: PAR:0461 ! interaction database
is_a: PAR:0489 ! source database

[Term]
id: PAR:0466
name: ecocyc
def: " EcoCyc is a bioinformatics database that describes the genome and the biochemical machinery of E. coli K12 MG1655." [pubmed:14755292 "primary-reference"]
related_synonym: "EcoCyc" []
xref_analog: url:http\://ecocyc.org/ "ANNOTATION"
is_a: PAR:0461 ! interaction database

[Term]
id: PAR:0467
name: reactome
def: "The Reactome project is a collaboration among Cold Spring Harbor Laboratory, The European Bioinformatics Institute, and The Gene Ontology Consortium to develop a curated resource of core pathways and reactions in human biology." [pubmed:14755292 "primary-reference"]
related_synonym: "Genome Knowledge Base" []
related_synonym: "GKB" []
related_synonym: "Reactome" []
xref_analog: url:http\://www.reactome.org/ "ANNOTATION"
is_a: PAR:0461 ! interaction database

[Term]
id: PAR:0468
name: hprd
def: "The Human Protein Reference Database represents a centralized platform to visually depict and integrate information pertaining to domain architecture, post-translational modifications, interaction networks and disease association for each protein in the human proteome." [pubmed:14755292 "primary-reference"]
related_synonym: "HPRD" []
xref_analog: url:http\://www.hprd.org/ "ANNOTATION"
is_a: PAR:0461 ! interaction database

[Term]
id: PAR:0469
name: intact
def: "INTerAction datanase (IntAct) provides an open source database and toolkit for the storage, presentation and analysis of protein interactions." [pubmed:14681455 "primary-reference"]
related_synonym: "IntAct" []
xref_analog: id-validation-regexp:\"EBI-[0-9\]+|IA\:[0-9\]+\" "ANNOTATION"
xref_analog: search-url: http\://www.ebi.ac.uk/intact/search/do/hvWelcome?searchString=$\{ac} "ANNOTATION"
xref_analog: url:http\://www.ebi.ac.uk/intact "ANNOTATION"
is_a: PAR:0461 ! interaction database
is_a: PAR:0489 ! source database

[Term]
id: PAR:0470
name: kegg
def: " KEGG (Kyoto Encyclopedia of Genes and Genomes) is a knowledge base for systematic analysis of gene functions, linking genomic information with higher order functional information and also supplies information about chemical compounds, enzyme molecules and enzymatic reactions." [pubmed:14755292 "primary-reference"]
related_synonym: "KEGG" []
xref_analog: id-validation-regexp:\"[a-zA-Z\]+\:[a-zA-Z\]+[0-9\]+\" "ANNOTATION"
xref_analog: url:http\://www.genome.ad.jp/kegg/ "ANNOTATION"
is_a: PAR:0461 ! interaction database
is_a: PAR:0473 ! participant database

[Term]
id: PAR:0471
name: mint
def: "The Moleculer INTeraction database (MINT) is a relational database designed to store interactions between biological molecules." [pubmed:14755292 "primary-reference"]
related_synonym: "MINT" []
xref_analog: id-validation-regexp:\"MINT_[0-9\]+\" "ANNOTATION"
xref_analog: url:http\://mint.bio.uniroma2.it/mint/ "ANNOTATION"
is_a: PAR:0461 ! interaction database
is_a: PAR:0489 ! source database

[Term]
id: PAR:0472
name: msd pdb
def: "The Macromolecular Structure Database (MSD) - the European project for the collection, management and distribution of data about macromolecular structures, derived in part from the Protein Data Bank (PDB)." [pubmed:16381867 "primary-reference"]
related_synonym: "e-MSD" []
related_synonym: "PQS" []
xref_analog: id-validation-regexp:\"[0-9\][a-zA-Z0-9\]\{3}\" "ANNOTATION"
xref_analog: search-url: http\://www.ebi.ac.uk/msd-srv/atlas?id=$\{ac} "ANNOTATION"
xref_analog: url:http\://www.ebi.ac.uk/msd/ "ANNOTATION"
is_a: PAR:0805 ! wwpdb

[Term]
id: PAR:0473
name: participant database
def: "participant database." [pubmed:14755292 "primary-reference"]
exact_synonym: "participant xref" []
is_a: PAR:0444 ! database citation

[Term]
id: PAR:0474
name: chebi
def: "A definitive, freely available database of Chemical compounds of Biological Interest (ChEBI)." [pubmed:14755292 "primary-reference"]
related_synonym: "ChEBI" []
xref_analog: id-validation-regexp:\"CHEBI\:[0-9\]+\" "ANNOTATION"
xref_analog: url:http\://www.ebi.ac.uk/chebi/ "ANNOTATION"
is_a: PAR:0473 ! participant database

[Term]
id: PAR:0475
name: ddbj/embl/genbank
def: "DDBJ/EMBL/GenBank Nucleotide Sequence Database Collaboration exchange new and updated data on a daily basis to achieve optimal synchronisation." [pubmed:14755292 "primary-reference"]
related_synonym: "DDBJ" []
related_synonym: "DDBJ/EMBL/GenBank" []
related_synonym: "EMBL" []
related_synonym: "GenBank" []
xref_analog: id-validation-regexp:\"[A-Z\][0-9\]\{5}|[A-Z\][0-9\]\{5}/.[0-9\]+|[A-Z\]\{2}[0-9\]\{6}|[A-Z\]\{2}[0-9\]\{6}/.[0-9\]+|[A-Z\]\{4}[0-9\]\{8}|[A-Z\]\{4}[0-9\]\{8}/.[0-9\]+\" "ANNOTATION"
xref_analog: search-url: http\://www.ebi.ac.uk/cgi-bin/dbfetch?db=EMBLSVA&id=$\{ac} "ANNOTATION"
xref_analog: url:http\://www.ebi.ac.uk/embl/Contact/collaboration "ANNOTATION"
is_a: PAR:0683 ! sequence database

[Term]
id: PAR:0476
name: ensembl
def: " Ensembl is a joint project between the EMBL-EBI and the Wellcome Trust Sanger Institute that aims at developing a system that maintains automatic annotation of large eukaryotic genomes." [pubmed:15078858 "primary-reference"]
related_synonym: "Ensembl" []
xref_analog: id-validation-regexp:\"ENS[A-Z\]+[0-9\]\{11}\" "ANNOTATION"
xref_analog: url:http\://www.ebi.ac.uk/ensembl "ANNOTATION"
is_a: PAR:0683 ! sequence database

[Term]
id: PAR:0477
name: entrez gene/locuslink
def: "LocusLink provides a single query interface to curated sequence and descriptive information about genetic loci." [pubmed:14755292 "primary-reference"]
related_synonym: "Entrez gene/locuslink" []
exact_synonym: "entrezgene/locuslink" []
xref_analog: id-validation-regexp:\"[0-9\]+|[A-Z\]\{1\,2}_[0-9\]+|[A-Z\]\{1\,2}_[A-Z\]\{1\,4}[0-9\]+\" "ANNOTATION"
xref_analog: url:http\://www.ncbi.nlm.nih.gov/LocusLink/ "ANNOTATION"
is_a: PAR:0683 ! sequence database

[Term]
id: PAR:0478
name: flybase
def: "FlyBase is a comprehensive database for information on the genetics and molecular biology of Drosophila." [pubmed:14755292 "primary-reference"]
related_synonym: "FlyBase" []
xref_analog: id-validation-regexp:\"FBgn[0-9\]\{7}\" "ANNOTATION"
xref_analog: search-url: http\://flybase.net/cgi-bin/fbannq.html?acc=$\{ac} "ANNOTATION"
xref_analog: url:http\://fbserver.gen.cam.ac.uk\:7081/ "ANNOTATION"
is_a: PAR:0683 ! sequence database

[Term]
id: PAR:0479
name: mgd/mgi
def: "Mouse Genome Informatics (MGI) provides integrated access to data on the genetics, genomics, and biology of the laboratory mouse." [pubmed:14755292 "primary-reference"]
related_synonym: "MGD/MGI" []
xref_analog: id-validation-regexp:\"MGI\:[0-9\]+\" "ANNOTATION"
xref_analog: url:http\://www.informatics.jax.org/ "ANNOTATION"
is_a: PAR:0683 ! sequence database

[Term]
id: PAR:0480
name: omim
def: "Online Mendelian Inheritance in Man (OMIM) is a catalogue of human genes and genetic disorders, with links to literature references, sequence records, maps, and related databases." [pubmed:14755292 "primary-reference"]
related_synonym: "OMIM" []
xref_analog: id-validation-regexp:\"[0-9\]+\" "ANNOTATION"
xref_analog: search-url: http\://www.ncbi.nlm.nih.gov/entrez/dispomim.cgi?id=$\{ac} "ANNOTATION"
xref_analog: url:http\://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=OMIM "ANNOTATION"
is_a: PAR:0683 ! sequence database

[Term]
id: PAR:0481
name: refseq
def: "The Reference Sequence (RefSeq) collection aims to provide a comprehensive, integrated, non-redundant set of sequences, including genomic DNA, transcript (RNA), and protein products, for a number of organisms." [pubmed:14755292 "primary-reference"]
related_synonym: "Refseq" []
xref_analog: id-validation-regexp:\"[XNZ\][A-Z\]_[0-9\]+|[0-9\]+\" "ANNOTATION"
xref_analog: url:http\://www.ncbi.nlm.nih.gov/RefSeq/ "ANNOTATION"
is_a: PAR:0683 ! sequence database

[Term]
id: PAR:0482
name: rfam
def: "Rfam is a large collection of multiple sequence alignments and covariance models covering many common non-coding RNA families." [pubmed:14755292 "primary-reference"]
related_synonym: "rfam" []
xref_analog: id-validation-regexp:\"RF[0-9\]\{5}\" "ANNOTATION"
xref_analog: url:http\://www.sanger.ac.uk/Software/Rfam/ "ANNOTATION"
is_a: PAR:0683 ! sequence database

[Term]
id: PAR:0483
name: rgd
def: "The Rat Genome Database (RGD) curates and integrates rat genetic and genomic data." [pubmed:14755292 "primary-reference"]
related_synonym: "RGD" []
xref_analog: id-validation-regexp:\"[0-9\]+\" "ANNOTATION"
xref_analog: url:http\://rgd.mcw.edu/ "ANNOTATION"
is_a: PAR:0683 ! sequence database

[Term]
id: PAR:0484
name: sgd
def: "SGD is a scientific database of the molecular biology and genetics of the yeast Saccharomyces cerevisiae." [pubmed:14755292 "primary-reference"]
related_synonym: "SGD" []
xref_analog: id-validation-regexp:\"S[0-9\]\{9}\" "ANNOTATION"
xref_analog: search-url: http\://genome-www4.stanford.edu/cgi-bin/SGD/locus.pl?locus=$\{ac} "ANNOTATION"
xref_analog: url:http\://www.yeastgenome.org/ "ANNOTATION"
is_a: PAR:0683 ! sequence database

[Term]
id: PAR:0485
name: uniparc
def: "UniProt Archive (UniParc) is part of UniProt project. It is a non-redundant archive of protein sequences derived from many sources." [pubmed:14681372 "primary-reference"]
related_synonym: "UniParc" []
xref_analog: id-validation-regexp:\"UPI[A-F0-9\]\{10}\" "ANNOTATION"
xref_analog: search-url: http\://www.ebi.uniprot.org/entry/$\{ac} "ANNOTATION"
xref_analog: url:http\://www.ebi.ac.uk/uniparc/ "ANNOTATION"
is_a: PAR:0683 ! sequence database

[Term]
id: PAR:0486
name: uniprot knowledge base
def: "UniProt (Universal Protein Resource) is the world's most comprehensive catalogue of information on proteins. It is a central repository of protein sequence and function created by joining the information contained in Swiss-Prot, TrEMBL, and PIR." [pubmed:14681372 "primary-reference"]
related_synonym: "UniProt" []
exact_synonym: "uniprotkb" []
xref_analog: id-validation-regexp:\"[OPQ\][0-9\][A-Z0-9\]\{3}[0-9\]|[OPQ\][0-9\][A-Z0-9\]\{3}[0-9\]-[0-9\]+|[A-Z\]\{3}[0-9\]\{5}|[OPQ\][0-9\][A-Z0-9\]\{3}[0-9\]-PRO_[0-9\]\{10}\" "ANNOTATION"
xref_analog: search-url: http\://www.ebi.uniprot.org/entry/$\{ac} "ANNOTATION"
xref_analog: url:http\://www.expasy.uniprot.org/ "ANNOTATION"
is_a: PAR:0683 ! sequence database

[Term]
id: PAR:0487
name: wormbase
def: "WormBase is the central worm database that houses the gene reports, locus reports, translation reports, expression pattern data and genome browser." [pubmed:14755292 "primary-reference"]
related_synonym: "WormBase" []
xref_analog: id-validation-regexp:\"WBGene[0-9\]\{8}\" "ANNOTATION"
xref_analog: url:http\://www.wormbase.org/ "ANNOTATION"
is_a: PAR:0683 ! sequence database

[Term]
id: PAR:0488
name: psi-mi
def: "Controlled vocabularies developed by HUPO Proteomic standard initiative for Molecular Interaction" [pubmed:14755292 "primary-reference"]
related_synonym: "PSI-MI" []
xref_analog: id-validation-regexp:\"MI\:[0-9\]\{4}\" "ANNOTATION"
xref_analog: search-url: http\://www.ebi.ac.uk/ontology-lookup/?termId=$\{ac} "ANNOTATION"
is_a: PAR:0444 ! database citation

[Term]
id: PAR:0489
name: source database
def: "Database that orignally provided the interaction record for exchange purposes." [pubmed:14755292 "primary-reference"]
is_a: PAR:0444 ! database citation

[Term]
id: PAR:0495
name: experimental role
def: "Role played by the participant within the experiment." [pubmed:14755292 "primary-reference"]
relationship: part_of PAR:1004 ! PROTEIN AFFINITY REAGENT CV

[Term]
id: PAR:0496
name: bait
def: "Molecule experimentally treated to capture its interacting partners." [pubmed:14755292 "primary-reference"]
is_a: PAR:0495 ! experimental role

[Term]
id: PAR:0497
name: neutral component
def: "Molecule role in an experimental setting that does not have an embedded asymmetry." [pubmed:14755292 "primary-reference"]
is_a: PAR:0495 ! experimental role

[Term]
id: PAR:0498
name: prey
def: "Molecule experimentally identified as being captured by a given bait." [pubmed:14755292 "primary-reference"]
is_a: PAR:0495 ! experimental role

[Term]
id: PAR:0499
name: unspecified role
def: "Role not specified or not applicable to the data." [pubmed:14755292 "primary-reference"]
is_a: PAR:0500 ! biological role

[Term]
id: PAR:0500
name: biological role
def: "Description of molecules polarity on a directional interaction." [pubmed:14755292 "primary-reference"]
relationship: part_of PAR:1004 ! PROTEIN AFFINITY REAGENT CV

[Term]
id: PAR:0505
name: experimental feature
def: "The form of a molecule that was actually used to experimentally demonstrate the interaction, that may differ from the sequence described by the identifying accession number." [pubmed:14755292 "primary-reference"]
is_a: PAR:0116 ! feature type

[Term]
id: PAR:0507
name: tag
def: "Small molecules, peptides or full proteins that can be used as label as they confer some property that facilitates identification purification and monitoring to the labelled molecule." [pubmed:14755292 "primary-reference"]
is_a: PAR:0505 ! experimental feature

[Term]
id: PAR:0510
name: homogeneous time resolved fluorescence
def: "Methods based on the exceptionally long fluorescence lifetime characteristics of certain fluorophores, which allows the elimination of the effects of background fluorescence. Uses nonradiative energy transfer or quenching between fluorescent lanthanide chelates and different acceptors to measure reaction rates." [pubmed:14987100 "primary-reference"]
related_synonym: "homogeneous time-resolved fluorescence" []
exact_synonym: "htrf" []
is_a: PAR:0051 ! fluorescence technology

[Term]
id: PAR: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." [pubmed:14755292 "primary-reference"]
related_synonym: "radiolabeled" []
exact_synonym: "radiolabelled" []
is_a: PAR:0253 ! isotope label

[Term]
id: PAR: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." [pubmed:14755292 "primary-reference"]
related_synonym: "DYKDDDDKV epitope tag" []
related_synonym: "FLAG" []
related_synonym: "FLAG-tagged" []
is_a: PAR:0507 ! tag

[Term]
id: PAR:0519
name: glutathione s tranferase tag
def: "The protein is expressed and purified as a fusion to the glutathione S-tranferase protein." [pubmed:14755292 "primary-reference"]
related_synonym: "glutathione S-tranferase tag" []
exact_synonym: "gst tag" []
is_a: PAR:0365 ! enzyme tag

[Term]
id: PAR: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." [pubmed:14755292 "primary-reference"]
related_synonym: "YPYDVPDYA epitope tag" []
is_a: PAR:0507 ! tag

[Term]
id: PAR: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." [pubmed:14755292 "primary-reference"]
related_synonym: "6-His-tag" []
related_synonym: "Hexa-His-tag" []
related_synonym: "Histidine-tag" []
is_a: PAR:0507 ! tag

[Term]
id: PAR: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." [pubmed:14755292 "primary-reference"]
related_synonym: "EUKLISEED epitope tag" []
is_a: PAR:0507 ! tag

[Term]
id: PAR:0523
name: t7 tag
def: "The protein of interest is expressed as a fusion to the peptide MASMTGGQQMG for which antibodies are commercially available." [pubmed:14755292 "primary-reference"]
related_synonym: "MASMTGGQQMG epitope tag" []
is_a: PAR:0507 ! tag

[Term]
id: PAR: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 protein at, or close to, its natural level. The fusion protein and associated components are recovered from cell extracts by affinity selection on an IgG matrix. After washing, the TEV protease is added to release the bound material. The eluate is incubated with calmodulin-coated beads in the presence of calcium. This second affinity step is required to remove the TEV protease as well as traces of contaminants remaining after the first affinity selection. After washing, the bound material is released with EGTA. This tag allows two steps purification steps ensuring a highly selective purification of the tapped protein (first round of selection on the protein A, a high affinity tag) under mild condition (non denaturant pH or conditions required to remove the tag)." [pubmed:14755292 "primary-reference"]
related_synonym: "CBP-ProtA tagged" []
exact_synonym: "tap tagged" []
is_a: PAR:0677 ! tandem tag

[Term]
id: PAR:0525
name: v5 tag
def: "The protein of interest is expressed as a fusion to the peptide GKPIPNPLLGLDST for which antibodies are commercially available." [pubmed:14755292 "primary-reference"]
related_synonym: "GKPIPNPLLGLDST epitope tag" []
is_a: PAR:0507 ! tag

[Term]
id: PAR:0526
name: n-acetyl-lysine
def: "residue modification." [pubmed:14755292 "primary-reference", resid:AA0048 "see-also", resid:AA0055 "see-also"]
exact_synonym: "acetyllysine" []
is_a: PAR:0121 ! acetylated residue

[Term]
id: PAR:0527
name: adp ribosylated residue
def: "residue modification." [pubmed:14755292 "primary-reference"]
exact_synonym: "adp-ribosylated" []
is_a: PAR:0120 ! post translation modification

[Term]
id: PAR:0528
name: omega-n-(adp-ribosyl)-arginine
def: "residue modification." [pubmed:14755292 "primary-reference", resid:AA0168 "identity"]
related_synonym: "(S)-2-amino-5-([imino([adenosine 5'-(trihydrogen diphosphate) 5'->5'-ester with alpha-D-ribofuranosyl]amino)methyl]amino)pentanoic acid" []
related_synonym: "N(omega)-[alpha-D-ribofuranoside 5'->5'-ester with adenosine 5'-(trihydrogen diphosphate)]-L-arginine" []
related_synonym: "N(omega)-alpha-D-ribofuranosyl-L-arginine 5'->5'-ester with adenosine 5'-(trihydrogen diphosphate)" []
related_synonym: "omega-N-(ADP-ribosyl)-L-arginine" []
exact_synonym: "adp-ribosylarginine" []
is_a: PAR:0527 ! adp ribosylated residue

[Term]
id: PAR:0529
name: s-(adp-ribosyl)-cysteine
def: "residue modification." [pubmed:14755292 "primary-reference", resid:AA0169 "identity"]
related_synonym: "(R)-2-amino-3-([adenosine 5'-(trihydrogen diphosphate) 5'->5'-ester with alpha-D-ribofuranosyl]sulfanyl)propanoic acid" []
related_synonym: "S-(ADP-ribosyl)-L-cysteine" []
related_synonym: "S-alpha-D-ribofuranosyl-L-cysteine 5'->5'-ester with adenosine 5'-(trihydrogen diphosphate)" []
related_synonym: "S-L-cysteine alpha-D-ribofuranoside 5'->5'-ester with adenosine 5'-(trihydrogen diphosphate)" []
exact_synonym: "adp-ribosylcysteine" []
is_a: PAR:0527 ! adp ribosylated residue

[Term]
id: PAR:0530
name: glutamyl-5-poly(adp-ribose)
def: "residue modification." [pubmed:14755292 "primary-reference", resid:AA0295 "identity"]
related_synonym: "(S)-2-amino-5-poly[2'-adenosine 5'-(trihydrogen diphosphate) 5'->5'-ester with 1alpha-D-ribofuranosyl]oxy-5-oxopentanoic acid" []
related_synonym: "L-glutamyl-5-poly(ADP-ribose)" []
related_synonym: "L-isoglutamyl-poly(ADP-ribose)" []
exact_synonym: "adp-ribosylglutamate" []
is_a: PAR:0527 ! adp ribosylated residue

[Term]
id: PAR:0531
name: o-(adp-ribosyl)-serine
def: "residue modification." [pubmed:14755292 "primary-reference", resid:AA0237 "identity"]
related_synonym: "(S)-2-amino-3-([adenosine 5'-(trihydrogen diphosphate) 5'->5'-ester with alpha-D-ribofuranosyl]oxy)-propanoic acid Formula" []
related_synonym: "O-(ADP-ribosyl)-L-serine" []
related_synonym: "O3-(ADP-ribosyl)-L-serine" []
related_synonym: "O3-[alpha-D-ribofuranoside 5'->5'-ester with adenosine 5'-(trihydrogen diphosphate)]-L-serine" []
related_synonym: "O3-alpha-D-ribofuranosyl-L-serine 5'->5'-ester with adenosine 5'-(trihydrogen diphosphate)" []
exact_synonym: "adp-ribosylserine" []
is_a: PAR:0527 ! adp ribosylated residue

[Term]
id: PAR:0532
name: n4-(adp-ribosyl)-asparagine
def: "residue modification." [pubmed:14755292 "primary-reference", resid:AA0231 "identity"]
related_synonym: "(S)-2-amino-4-([adenosine 5'-(trihydrogen diphosphate) 5'->5'-ester with alpha-D-ribofuranosyl]amino)-4-oxobutanoic acid" []
related_synonym: "N4-(ADP-ribosyl)-L-asparagine" []
related_synonym: "N4-[alpha-D-ribofuranoside 5'->5'-ester with adenosine 5'-(trihydrogen diphosphate)]-L-asparagine" []
related_synonym: "N4-alpha-D-ribofuranosyl-L-asparagine 5'->5'-ester with adenosine 5'-(trihydrogen diphosphate)" []
exact_synonym: "adpribosylasparagine" []
is_a: PAR:0527 ! adp ribosylated residue

[Term]
id: PAR:0533
name: glycosylated residue
def: "residue modification." [pubmed:14755292 "primary-reference"]
is_a: PAR:0120 ! post translation modification

[Term]
id: PAR:0534
name: glycosyl-cysteine
def: "residue modification." [pubmed:14755292 "primary-reference", resid:AA0122 "identity"]
related_synonym: "S-glycosyl-L-cysteine" []
is_a: PAR:0533 ! glycosylated residue

[Term]
id: PAR:0535
name: glycosyl-serine
def: "residue modification." [pubmed:14755292 "primary-reference", resid:AA0154 "identity"]
related_synonym: "O-glycosyl-L-serine" []
related_synonym: "O3-glycosyl-L-serine" []
is_a: PAR:0533 ! glycosylated residue

[Term]
id: PAR:0536
name: glycosyl-threonine
def: "residue modification." [pubmed:14755292 "primary-reference", resid:AA0155 "identity"]
related_synonym: "O-glycosyl-L-threonine" []
related_synonym: "O3-glycosyl-L-threonine" []
is_a: PAR:0533 ! glycosylated residue

[Term]
id: PAR:0537
name: omega-n-glycosyl-arginine
def: "residue modification." [pubmed:14755292 "primary-reference", resid:AA0327 "identity"]
related_synonym: "omega-N-glycosyl-L-arginine" []
exact_synonym: "glycosylarginine" []
is_a: PAR:0533 ! glycosylated residue

[Term]
id: PAR:0538
name: n4-glycosyl-asparagine
def: "residue modification." [pubmed:14755292 "primary-reference", resid:AA0151 "identity"]
related_synonym: "N4-glycosyl-L-asparagine" []
exact_synonym: "glycosylasparagine" []
is_a: PAR:0533 ! glycosylated residue

[Term]
id: PAR:0539
name: gpi-anchor amidated residue
def: "residue modification." [pubmed:14755292 "primary-reference"]
is_a: PAR:0150 ! lipid modification

[Term]
id: PAR:0540
name: gpi-anchor alanine
def: "residue modification." [pubmed:14755292 "primary-reference", resid:AA0163 "identity"]
related_synonym: "N-alanyl-glycosylphosphatidylinositolethanolamine" []
exact_synonym: "gpi-alanine" []
is_a: PAR:0539 ! gpi-anchor amidated residue

[Term]
id: PAR:0541
name: gpi-anchor asparagine
def: "residue modification." [pubmed:14755292 "primary-reference", resid:AA0158 "identity"]
related_synonym: "N-asparaginyl-glycosylphosphatidylinositolethanolamine" []
exact_synonym: "gpi-asparagine" []
is_a: PAR:0539 ! gpi-anchor amidated residue

[Term]
id: PAR:0542
name: gpi-anchor aspartate
def: "residue modification." [pubmed:14755292 "primary-reference", resid:AA0159 "identity"]
related_synonym: "N-aspartyl-glycosylphosphatidylinositolethanolamine" []
exact_synonym: "gpi-aspartate" []
is_a: PAR:0539 ! gpi-anchor amidated residue

[Term]
id: PAR:0543
name: gpi-anchor cysteine
def: "residue modification." [pubmed:14755292 "primary-reference", resid:AA0160 "identity"]
related_synonym: "N-cysteinyl-glycosylphosphatidylinositolethanolamine" []
exact_synonym: "gpi-cysteine" []
is_a: PAR:0539 ! gpi-anchor amidated residue

[Term]
id: PAR:0544
name: gpi-anchor glycine
def: "residue modification." [pubmed:14755292 "primary-reference", resid:AA0161 "identity"]
related_synonym: "N-glycyl-glycosylphosphatidylinositolethanolamine" []
exact_synonym: "gpi-glycine" []
is_a: PAR:0539 ! gpi-anchor amidated residue

[Term]
id: PAR:0545
name: gpi-anchor serine
def: "residue modification." [pubmed:14755292 "primary-reference", resid:AA0162 "identity"]
related_synonym: "N-seryl-glycosylphosphatidylinositolethanolamine" []
exact_synonym: "gpi-serine" []
is_a: PAR:0539 ! gpi-anchor amidated residue

[Term]
id: PAR:0546
name: gpi-anchor threonine
def: "residue modification." [pubmed:14755292 "primary-reference", resid:AA0164 "identity"]
related_synonym: "N-threonyl-glycosylphosphatidylinositolethanolamine" []
exact_synonym: "gpi-threonine" []
is_a: PAR:0539 ! gpi-anchor amidated residue

[Term]
id: PAR:0547
name: s-prenyl-cysteine
def: "residue modification." [pubmed:14755292 "primary-reference"]
exact_synonym: "prenylcysteine" []
is_a: PAR:0150 ! lipid modification

[Term]
id: PAR:0548
name: methylated-lysine
def: "residue modification." [pubmed:14755292 "primary-reference", resid:AA0074 "see-also", resid:AA0075 "see-also", resid:AA0076 "see-also"]
exact_synonym: "methylatedlysine" []
is_a: PAR:0157 ! methylated residue

[Term]
id: PAR:0549
name: alkylated cysteine
def: "Artificial residue modification enabling studies of cysteine binding status." [pubmed:15325307 "primary-reference"]
is_a: PAR:0179 ! other modification

[Term]
id: PAR:0550
name: gamma-carboxyglutamic acid
def: "residue modification." [pubmed:14755292 "primary-reference", resid:AA0032 "identity"]
related_synonym: "(S)-3-amino-1,1,3-propanetricarboxylic acid" []
related_synonym: "1-carboxyglutamic acid [misnomer]" []
related_synonym: "4-carboxyglutamic acid" []
related_synonym: "L-gamma-carboxyglutamic acid" []
exact_synonym: "carboxyglutamic acid" []
is_a: PAR:0179 ! other modification

[Term]
id: PAR:0551
name: nitro-tyrosine
def: "residue modification." [pubmed:15657065 "primary-reference", pubmed:9636206 "method reference"]
related_synonym: "nitrated tyrosine" []
is_a: PAR:0179 ! other modification

[Term]
id: PAR:0552
name: s-nitrosyl-cysteine
def: "residue modification." [pubmed:14755292 "primary-reference", resid:AA0230 "identity"]
related_synonym: "(R)-2-amino-3-nitrososulfanyl-propanoic acid" []
related_synonym: "L-cysteine nitrite ester" []
related_synonym: "S-nitrosocysteine" []
related_synonym: "S-nitrosyl-L-cysteine" []
exact_synonym: "nitrosylcysteine" []
is_a: PAR:0179 ! other modification

[Term]
id: PAR:0553
name: o4'-sulfo-tyrosine
def: "residue modification." [pubmed:14755292 "primary-reference", resid:AA0172 "identity"]
related_synonym: "(S)-2-amino-3-(4-sulfooxyphenyl)propanoic acid" []
related_synonym: "2-amino-3-(4-hydroxyphenyl)propanoic acid 4'-sulfate" []
related_synonym: "O4'-sulfo-L-tyrosine" []
related_synonym: "O4-sulfotyrosine" []
related_synonym: "tyrosine sulfate" []
exact_synonym: "sulfotyrosine" []
is_a: PAR:0179 ! other modification

[Term]
id: PAR:0554
name: sumoylated lysine
def: "Residue modification due to a cross-link between a lysine and a glycine from the sumo (Small Ubiquitin-related MOdifier) protein." [pubmed:12612601 "primary-reference", resid:AA0125 "identity"]
related_synonym: "(S)-2-amino-6-[(aminoacetyl)amino]hexanoic acid" []
related_synonym: "N6-glycyl-L-lysine" []
related_synonym: "N6-glycyllysine" []
is_a: PAR:0179 ! other modification

[Term]
id: PAR:0555
name: phospho-histidine
def: "residue modification." [pubmed:14755292 "primary-reference", resid:AA0035 "see-also", resid:AA0036 "see-also"]
exact_synonym: "phosphoshistidine" []
is_a: PAR:0170 ! phosphorylated residue

[Term]
id: PAR:0556
name: transglutamination reaction
def: "Gln-Lys cross-link catalyzed by a transglutaminase." [pubmed:14755292 "primary-reference", resid:AA0124 "identity"]
exact_synonym: "transglutamination" []
is_a: PAR:0195 ! covalent binding

[Term]
id: PAR:0557
name: adp ribosylation reaction
def: "Reaction that can affect Arg, Cys, Glu, Arg and Asn residues." [go:GO\:0006471 "identity", pubmed:14755292 "primary-reference", resid:AA0168 "see-also", resid:AA0169 "see-also", resid:AA0231 "see-also", resid:AA0237 "see-also", resid:AA0295 "see-also"]
exact_synonym: "adp ribosylation" []
is_a: PAR:0414 ! enzymatic reaction

[Term]
id: PAR:0558
name: deglycosylation reaction
def: "Reaction catalyzed by PNGase, a deglycosylating enzyme that promotes the hydrolysis of the beta-aspartylglycosylamine bond of aspargine-linked glycopeptides and glycoproteins." [go:GO\:0006517 "identity", pubmed:15670854 "primary-reference"]
exact_synonym: "deglycosylation" []
is_a: PAR:0414 ! enzymatic reaction

[Term]
id: PAR:0559
name: glycosylation reaction
def: "The covalent attachment of a glycosyl residue to one or more monomeric units in a polypeptide, polynucleotide, polysaccharide, or other biological polymer. Reaction that can affect Ser, Thr, Cys, Arg, and Asn residues. This reaction is known to be reversible in the case of Asn substrate." [go:GO\:0043413 "identity", pubmed:14755292 "primary-reference", resid:AA0122 "see-also", resid:AA0151 "see-also", resid:AA0154 "see-also", resid:AA0155 "see-also", resid:AA0327 "see-also"]
exact_synonym: "glycosylation" []
is_a: PAR:0414 ! enzymatic reaction

[Term]
id: PAR:0560
name: myristoylated residue
def: "residue modification." [pubmed:14755292 "primary-reference"]
exact_synonym: "myristoylated aa" []
is_a: PAR:0150 ! lipid modification

[Term]
id: PAR:0561
name: palmitoylated residue
def: "residue modification." [pubmed:14755292 "primary-reference"]
exact_synonym: "palmitoylated aa" []
is_a: PAR:0150 ! lipid modification

[Term]
id: PAR:0562
name: methylated alanine
def: "residue modification." [pubmed:14755292 "primary-reference", resid:AA0061 "see-also", resid:AA0062 "see-also"]
is_a: PAR:0157 ! methylated residue

[Term]
id: PAR:0563
name: methylated arginine
def: "residue modification." [pubmed:14755292 "primary-reference", resid:AA0068 "see-also", resid:AA0069 "see-also"]
is_a: PAR:0157 ! methylated residue

[Term]
id: PAR:0564
name: omega-n-methyl-arginine
def: "residue modification." [pubmed:14755292 "primary-reference", resid:AA0069 "identity"]
related_synonym: "(S)-2-amino-5-[(imino(methylamino)methyl)amino]pentanoic acid" []
related_synonym: "NG-methylarginine;" []
related_synonym: "omega-N-methyl-L-arginine" []
exact_synonym: "methylarginine" []
is_a: PAR:0563 ! methylated arginine

[Term]
id: PAR:0565
name: neddylated lysine
def: "Residue modification due to a cross-link between a lysine and a glycine from the Nedd8 protein family." [pubmed:111 "primary-reference"]
is_a: PAR:0179 ! other modification

[Term]
id: PAR: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:GO\:0016925 "identity", pubmed:15985640 "primary-reference"]
exact_synonym: "sumoylation" []
is_a: PAR:0414 ! enzymatic reaction

[Term]
id: PAR: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:GO\:0045116 "identity", pubmed:16127432 "primary-reference"]
exact_synonym: "neddylation" []
is_a: PAR:0414 ! enzymatic reaction

[Term]
id: PAR:0568
name: desumoylation reaction
def: "Cleavage of the G-K bond and release of the SUMO ubiquitin like proteins." [go:GO\:0016926 "identity", pubmed:15985640 "primary-reference"]
exact_synonym: "desumoylation" []
is_a: PAR:0414 ! enzymatic reaction

[Term]
id: PAR: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:GO\:0000338 "identity", pubmed:16127432 "primary-reference"]
exact_synonym: "deneddylation" []
is_a: PAR:0414 ! enzymatic reaction

[Term]
id: PAR:0570
name: protein cleavage
def: "Covalent modification of a polypeptide occuring during its maturation or its proteolytic degradation." [pubmed:14744292 "primary-reference"]
is_a: PAR:0194 ! cleavage reaction

[Term]
id: PAR: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:GO\:0006379 "identity", pubmed:14681407 "primary-reference"]
is_a: PAR:0194 ! cleavage reaction

[Term]
id: PAR:0572
name: dna cleavage
def: "Covalent bond breakage of a DNA molecule leading to the formation of smaller fragements." [pubmed:14755292 "primary-reference"]
is_a: PAR:0194 ! cleavage reaction

[Term]
id: PAR:0573
name: mutation disrupting interaction
def: "Residue of a protein whose identity mutation or deletion totally disrupt an interaction." [pubmed:14755292 "primary-reference"]
exact_synonym: "mutation disrupting" []
is_a: PAR:0119 ! mutation decreasing interaction

[Term]
id: PAR:0574
name: digital object identifier
def: "Identifier of a publication prior it pubmed indexing." [pubmed:14755292 "primary-reference"]
exact_synonym: "doi" []
xref_analog: id-validation-regexp:\"doi\:[0-9\]+\\.[0-9\]+\" "ANNOTATION"
is_a: PAR:0445 ! literature database

[Term]
id: PAR: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." [pubmed:14755292 "primary-reference"]
related_synonym: "AfCS" []
exact_synonym: "afcs" []
xref_analog: id-validation-regexp:\"[0-9\]+\" "ANNOTATION"
xref_analog: search-url: http\://www.signaling-gateway.org/data/Y2H/cgi-bin/y2h_int.cgi?id=$\{ac} "ANNOTATION"
xref_analog: url:http\://www.signaling-gateway.org "ANNOTATION"
is_a: PAR:0461 ! interaction database
is_a: PAR:0489 ! source database

[Term]
id: PAR: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." [pubmed:14755292 "primary-reference"]
related_synonym: "maltose binding protein tag" []
exact_synonym: "mbp tag" []
is_a: PAR:0240 ! fusion protein

[Term]
id: PAR:0585
name: intenz
def: "IntEnz is the name for the Integrated relational Enzyme database and is the official version of the Enzyme Nomenclature. The Enzyme Nomenclature comprises recommendations of the Nomenclature Committee of the International Union of Bio chemistry and Molecular Biology (NC-IUBMB) on the nomenclature and classification of enzyme-catalysed reactions. IntEnz is supported by NC-IUBMB and contains enzyme data curated and approved by this committee. The database IntEnz is available at." [pubmed:14681451 "primary-reference"]
xref_analog: id-validation-regexp:\"[0-6\]\{1}\\.(\\d+|-)\\.(\\d+|-)\\.(\\d+|-)\" "ANNOTATION"
xref_analog: search-url: http\://www.ebi.ac.uk/intenz/query?cmd=Search&q=$\{ac}&t=exact&fields=ec "ANNOTATION"
xref_analog: url:http\://www.ebi.ac.uk/intenz "ANNOTATION"
is_a: PAR:0461 ! interaction database

[Term]
id: PAR:0590
name: attribute name
def: "Collection of topic describing the free text stored as an attribute value." [pubmed:14755292 "primary-reference"]
related_synonym: "CvTopic" []
relationship: part_of PAR:1004 ! PROTEIN AFFINITY REAGENT CV

[Term]
id: PAR:0592
name: ipfam
def: "Web resource that allows the investigation of protein interactions in the Protein Data Bank structures at the level of Pfam domains and amino acid residues. iPfam is available on the Web for browsing at." [pubmed:15353450 "primary-reference"]
xref_analog: url:http\://www.sanger.ac.uk/Software/Pfam/iPfam/ "ANNOTATION"
is_a: PAR:0447 ! feature database

[Term]
id: PAR:0593
name: translocation
def: "Xref pointing to a GO process term describing the start and end location of a migrating molecule, for instance see GO:0006611, 'protein-nucleus export'." [pubmed:14681407 "primary-reference"]
is_a: PAR:0353 ! cross-reference type

[Term]
id: PAR:0594
name: translocation start
def: "Xref pointing to a GO compartment term describing the start location of a migrating molecule." [pubmed:14681407 "primary-reference"]
is_a: PAR:0593 ! translocation

[Term]
id: PAR:0595
name: translocation end
def: "Xref pointing to a GO compartment term describing the end location of a migrating molecule." [pubmed:14755292 "primary-reference"]
is_a: PAR:0593 ! translocation

[Term]
id: PAR:0597
name: feature description
def: "The feature text description may include information about the feature detection method." [pubmed:14755292 "primary-reference"]
is_a: PAR:0668 ! feature attribute name

[Term]
id: PAR:0599
name: figure legend
def: "Text pointing to a specific paper figure legend where the experimental evidences for an interaction are shown." [pubmed:14755292 "primary-reference"]
is_a: PAR:0664 ! interaction attribute name
is_a: PAR:0665 ! experiment attibute name

[Term]
id: PAR: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." [pubmed:15892872 "primary-reference"]
exact_synonym: "so" []
xref_analog: id-validation-regexp:\"SO\:[0-9\]\{7}\" "ANNOTATION"
is_a: PAR:0447 ! feature database
is_a: PAR:0473 ! participant database

[Term]
id: PAR:0602
name: chemical footprinting
def: "Sites of sequence-specific DNA-protein interaction are identified by altered reactivity of a chemical probe to DNA bound by a protein compared to the same nucleotide sequence in naked DNA. Nucleotides in close contact with the binding protein are protected from modification or cleavage by the probe. In certain case DNA-protein interactions can be indicated by enhanced modification or cleavage by the probe at particular nucleotides. When these probes are administrated to intact cells, the pattern of protection from the probes identifies the location of DNA-protein interactions in vivo." [pubmed:8238889 "primary-reference"]
exact_synonym: "chemical footprint" []
is_a: PAR:0409 ! dna footprinting

[Term]
id: PAR: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 detected by DMS footprinting. However as DMS diffuses across membrane it can also be used for in vivo footprinting. The experiment involves the treatment with DMS of two DNA samples with identical sequence, one protein bound and the other naked. The two samples are treated with piperidine to induce chemical cleavage of the DMS modified guanine residues followed by digestion with restriction enzymes. Once labelled the samples are run in parallel on a gel to visualize the pattern of nested fragments sharing a common end generated by restriction enzyme(or PCR primer extension) and a variable end guanine dependent. The missing bands of the protein bound sample correspond to the guanine residues protected from modification by an interaction." [pubmed:8238889 "primary-reference"]
exact_synonym: "dms footprinting" []
is_a: PAR:0602 ! chemical footprinting

[Term]
id: PAR: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 electrophoresis allows detection of interaction between transcription factor and the DNA sequence under their control." [pubmed:8238889 "primary-reference"]
exact_synonym: "k-mn-04 footprinting" []
is_a: PAR:0602 ! chemical footprinting

[Term]
id: PAR:0605
name: enzymatic footprinting
def: "Sites of sequence-specific DNA-protein interaction are identified by altered reactivity of an enzymatic probe to DNA bound by a protein compared to the same nucleotide sequence in naked DNA. Nucleotides in close contact with the binding protein are protected from cleavage by the enzyme. When these enzymes are administrated to intact cells, the pattern of protection from the probes identifies the location of DNA-protein interactions in vivo." [pubmed:8238889 "primary-reference"]
exact_synonym: "enzymatic footprint" []
is_a: PAR:0409 ! dna footprinting

[Term]
id: PAR: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 treating intact cells with permeabilising drugs. In this latter case DNase I in vivo footprinting allow studies of the chromatin structure in genomic DNA." [pubmed:8238889 "primary-reference"]
exact_synonym: "dnase 1 footprinting" []
is_a: PAR:0605 ! enzymatic footprinting

[Term]
id: PAR: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 least seven protein subunits to form a snRNP (small nuclear ribonucleoprotein). These snRNPs form the core of the spliceosome." [pubmed:14755292 "primary-reference"]
related_synonym: "snRNA" []
exact_synonym: "snrna" []
is_a: PAR:0320 ! ribonucleic acid

[Term]
id: PAR: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." [pubmed:14755292 "primary-reference"]
related_synonym: "rRNA" []
exact_synonym: "rrna" []
is_a: PAR:0320 ! ribonucleic acid

[Term]
id: PAR: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 two types of modified nucleotides, (2'-O-methylated nucleotides and pseudouridine), and mediating endonucleolytic cleavages of pre-rRNA." [pubmed:14755292 "primary-reference"]
related_synonym: "snoRNA" []
exact_synonym: "snorna" []
is_a: PAR:0320 ! ribonucleic acid

[Term]
id: PAR: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." [pubmed:10542148 "primary-reference"]
related_synonym: "dicer RNA" []
related_synonym: "micro RNA" []
related_synonym: "siRNA" []
exact_synonym: "sirna" []
is_a: PAR:0320 ! ribonucleic acid

[Term]
id: PAR:0611
name: signal recognition particle rna
def: "Small (300 nucleotides) stable RNAs transcribed by RNA pol III that are part of the signal-recognition particle (SRP). This particle comprises one RNA and six proteins bound to the RNA. SRP function is to assist secretory proteins sorting in the endoplasmic reticulum (ER). SRP is a cytosolic particle that transiently binds to the ER signal sequence of a nascent protein, to the large ribosomal unit, and to the SRP receptor in the ER membrane." [pubmed:14755292 "primary-reference"]
related_synonym: "srpRNA" []
exact_synonym: "srprna" []
is_a: PAR:0320 ! ribonucleic acid

[Term]
id: PAR:0612
name: comment
def: "Comment for public view. This attribute can be associated to interaction, experiment, Cv term, an organism and any participant." [pubmed:14755292 "primary-reference"]
is_a: PAR:0664 ! interaction attribute name
is_a: PAR:0665 ! experiment attibute name
is_a: PAR:0666 ! participant attribute name
is_a: PAR:0668 ! feature attribute name
is_a: PAR:0669 ! organism attribute name

[Term]
id: PAR:0616
name: example
def: "Example generally associated to Cv terms. Test." [pubmed:14755292 "primary-reference"]
is_a: PAR:0300 ! alias type

[Term]
id: PAR:0627
name: experiment modification
def: "Modifications of the standard experimental method described in the CV." [pubmed:14755292 "primary-reference"]
exact_synonym: "exp-modification" []
is_a: PAR:0665 ! experiment attibute name

[Term]
id: PAR:0634
name: contact email
def: "E-mail address to contact the author/organisation which has produced the data. This attribute is generally associated to an experiment." [pubmed:14755292 "primary-reference"]
is_a: PAR:0665 ! experiment attibute name

[Term]
id: PAR:0635
name: contact comment
def: "Free text notes on how to contact the author organisation which has produced the data This attribute is generally associated to an experiment." [pubmed:14755292 "primary-reference"]
is_a: PAR:0665 ! experiment attibute name

[Term]
id: PAR:0636
name: author-list
def: "List of authors associated to a publication. This attribute is generally associated to an experiment." [pubmed:123456789 "primary-reference", pubmed:14755292 "primary-reference"]
is_a: PAR:0665 ! experiment attibute name

[Term]
id: PAR:0637
name: immunoglobulin isoform
def: "The isoform, e.g. IgG, of an immunoglobulin." [pubmed:14755292 "primary-reference"]
related_synonym: "isotype" []
exact_synonym: "antibody isoform" []
is_a: PAR:0666 ! participant attribute name

[Term]
id: PAR:0639
name: resulting ptm
def: "Post translational modification occurs subsequently to an interaction." [pubmed:14755292 "primary-reference"]
is_a: PAR:0668 ! feature attribute name

[Term]
id: PAR:0640
name: parameter type
def: "Parameter for enzymatic or binding kinetic studies." [pubmed:14755292 "primary-reference"]
relationship: part_of PAR:1004 ! PROTEIN AFFINITY REAGENT CV

[Term]
id: PAR:0641
name: ic50
def: "Molar concentration of an antagonist which produces 50% of the maximum possible inhibitory response for that antagonist. Note this measure depends on the specific antagonist used and upon experimental conditions, notably temperature, pH and solution composition (e.g., salts, chelating agents and others). Thus the ic50 is a relative measure and its values can be compared only when sharing the same experimental setting. Unit Molar." [pubmed:14755292 "primary-reference"]
related_synonym: "IC50" []
is_a: PAR:0640 ! parameter type

[Term]
id: PAR:0642
name: ec50
def: "Molar concentration of an agonist which produces 50% of the maximum possible response for that agonist. Note this measure depends on the specific agonist used and upon experimental conditions, notably temperature, pH and solution composition (e.g., salts, chelating agents and others). Thus the ec50 is a relative measure and its values can be compared only when sharing the same experimental setting. Unit Molar." [pubmed:14755292 "primary-reference"]
related_synonym: "EC50" []
is_a: PAR:0640 ! parameter type

[Term]
id: PAR:0643
name: ki
def: "Equilibrium constant for dissociation of an inhibitor. Unit Molar." [pubmed:14755292 "primary-reference"]
related_synonym: "Ki" []
is_a: PAR:0640 ! parameter type

[Term]
id: PAR:0644
name: km
def: "Michaelis-Menten constant: concentration of substrate at which the reaction rate is equal to half the maximal rate (i.e. Km={s} when Vo=1/2Vmax). Unit Molar." [pubmed:14755292 "primary-reference"]
related_synonym: "Km" []
is_a: PAR:0640 ! parameter type

[Term]
id: PAR:0645
name: kcat
def: "The number of substrate molecules converted to product in a given unit of time, on a single enzyme molecule when the enzyme is saturated with substrate. Unit per second, or s-1." [pubmed:14755292 "primary-reference"]
related_synonym: "turnover number" []
is_a: PAR:0640 ! parameter type

[Term]
id: PAR:0646
name: Kd
def: "The equilibrium dissociation constant of a receptor/ligand or proteinA/proteinB complex. Unit Molar (generally M-1)." [pubmed:14755292 "primary-reference"]
related_synonym: "Kd" []
is_a: PAR:0640 ! parameter type

[Term]
id: PAR:0647
name: parameter unit
def: "Controlled vocabulary for kinetic constant units. See als" [pubmed:14755292 "primary-reference"]
xref_analog: url:http\://www.ebi.ac.uk/ontology-lookup/browse.do?ontName=UO "ANNOTATION"
relationship: part_of PAR:1004 ! PROTEIN AFFINITY REAGENT CV

[Term]
id: PAR:0648
name: molar
def: "Molarity is the number of moles of solute dissolved in one liter of solution. The units, therefore are moles per liter, specifically it's moles of solute per liter of solution. These units are abbreviated as M and it means moles per liter (not just moles)." [pubmed:14755292 "primary-reference"]
related_synonym: "M" []
is_a: PAR:0647 ! parameter unit

[Term]
id: PAR:0649
name: second
def: "The second is the duration of 9 192 631 770 periods of the radiation corresponding to the transition between the two hyperfine levels of the ground state of the cesium-133 atom. The second was originally defined as 1/86 400 mean solar day until astronomers discovered that the mean solar day is actually not constant." [pubmed:14755292 "primary-reference"]
related_synonym: "s" []
related_synonym: "sec" []
is_a: PAR:0647 ! parameter unit

[Term]
id: PAR:0656
name: identified peptide
def: "Peptide whose sequence is experimentally identified and can lead to a full protein identification." [pubmed:14755292 "primary-reference"]
is_a: PAR:0505 ! experimental feature

[Term]
id: PAR:0657
name: systematic evolution of ligands by exponential enrichment
def: "RNA and cDNA constructs with variable central sequences and a constant flanking region are collected in a complex library. The library is then screened to select either specific binding partners of a bait molecule (generally a protein) or particular enzymatic activities of the nucleic acid molecules themselves. The selected nucleic acids are amplified using the constant flanking regions to increase their abundance. Cycles of selection-amplification can be repeated to increase the specificity of the targets that, at the end, are individually identified by sequencing." [pubmed:11539574 "primary-reference"]
related_synonym: "in vitro evolution of nucleic acids" []
exact_synonym: "selex" []
is_a: PAR:0401 ! biochemical

[Term]
id: PAR:0658
name: multidimensional protein identification technology
def: "MudPIT is a method for rapid and large-scale protein identification by multidimensional liquid chromatography associated with tandem mass spectrometry. The chromatography step consists of strong cation exchange material back-to-back with reversed phase material inside fused silica capillaries. The peptides bound to the cation-exchange resin are freed by the gradually increasing salt concentration of the buffer and are subsequently retained by the reversed phase resin. Increasing buffers hydrophobicity progressively elute peptides from the reversed phase packing directly into the mass spectrometer. Typically this mass spectrometer will be a tandem electrospray, so peptides undergo ionization in the liquid phase, are separated in a primary mass spectrometer, analysed in the second mass spectrometer and identified." [pubmed:11231557 "primary-reference"]
exact_synonym: "mudpit" []
is_a: PAR:0093 ! protein sequence identification
is_a: PAR:0427 ! mass spectrometry
is_a: PAR:0815 ! confirmation by molecular weight

[Term]
id: PAR:0659
name: experimental feature detection
def: "experimental feature detection." [pubmed:14755292 "primary-reference"]
exact_synonym: "exp feature detect" []
is_a: PAR:0003 ! feature detection method

[Term]
id: PAR:0660
name: feature prediction
def: "Feature detection based on computational analysis." [pubmed:14755292 "primary-reference"]
is_a: PAR:0003 ! feature detection method

[Term]
id: PAR:0661
name: experimental participant identification
def: "experimental participant identification." [pubmed:14755292 "primary-reference"]
exact_synonym: "experimental particp" []
is_a: PAR:0002 ! participant identification method

[Term]
id: PAR:0662
name: imex primary
def: "Interaction identifier of a database that created the record in the context of IMEx consortium." [pubmed:14755292 "primary-reference"]
xref_analog: url:http\://imex.sourceforge.net/ "ANNOTATION"
is_a: PAR:0353 ! cross-reference type

[Term]
id: PAR:0663
name: confocal microscopy
def: "A confocal is a standard epifluorescence microscope with improvement essentially coming from the rejection of out-of-focus light interference. Confocal imaging system achieves this by two strategies: a) by illuminating a single point of the specimen at any one time with a focused beam, so that illumination intensity drops off rapidly and b) by the use of blocking a pinhole aperture in a conjugate focal plane to the specimen so that light emitted away from the point in the specimen being illuminated is blocked from reaching the detector. Only the light from the single point illuminated of the specimen passing through the image pinhole is detected by a photodetector. Usually a computer is used to control the sequential scanning of the sample and to assemble the image for display onto a video screen." [pubmed:14755292 "primary-reference"]
is_a: PAR:0428 ! imaging techniques

[Term]
id: PAR:0664
name: interaction attribute name
def: "Attribute name of annotation associated to an interaction element." [pubmed:14755292 "primary-reference"]
exact_synonym: "interaction att name" []
is_a: PAR:0590 ! attribute name

[Term]
id: PAR:0665
name: experiment attibute name
def: "Attribute name of annotation associated to an experiment element." [pubmed:14755292 "primary-reference"]
exact_synonym: "experiment att name" []
is_a: PAR:0590 ! attribute name

[Term]
id: PAR:0666
name: participant attribute name
def: "Attribute name of annotation associated to a participant element." [pubmed:14755292 "primary-reference"]
exact_synonym: "participant att name" []
is_a: PAR:0590 ! attribute name

[Term]
id: PAR:0668
name: feature attribute name
def: "Attribute name of annotation associated to a feature element." [pubmed:14755292 "primary-reference"]
exact_synonym: "feature att name" []
is_a: PAR:0590 ! attribute name

[Term]
id: PAR:0669
name: organism attribute name
def: "Attribute name of annotation associated to an organism element." [pubmed:14755292 "primary-reference"]
exact_synonym: "organism att name" []
is_a: PAR:0590 ! attribute name

[Term]
id: PAR:0670
name: imex
def: "International Molecular Interaction Exchange." [pubmed:14755292 "primary-reference"]
related_synonym: "IMEx" []
is_a: PAR:0461 ! interaction database

[Term]
id: PAR:0673
name: complex synonym
def: "Alternative names to describe a complex." [pubmed:14755292 "primary-reference"]
is_a: PAR:0300 ! alias type

[Term]
id: PAR:0674
name: peptide parent sequence reference
def: "Describe cross link pointing to a peptide parent sequence." [pubmed:14755292 "primary-reference"]
exact_synonym: "peptide-parent" []
is_a: PAR:0353 ! cross-reference type

[Term]
id: PAR:0675
name: international protein index
def: "IPI provides a top level guide to the main databases that describe the proteomes of higher eukaryotic organisms. IPI effectively maintains a database of cross references between the primary data sources, provides minimally redundant yet maximally complete sets of proteins for featured species (one sequence per transcript) and maintains stable identifiers (with incremental versioning) to allow the tracking of sequences in IPI between IPI releases. IPI is updated monthly in accordance with the latest data released by the primary data sources." [pubmed:15221759 "primary-reference"]
exact_synonym: "ipi" []
xref_analog: id-validation-regexp:\"IPI[0-9\]+.[0-9\]+|IPI[0-9\]+\" "ANNOTATION"
is_a: PAR:0683 ! sequence database

[Term]
id: PAR:0677
name: tandem tag
def: "A tandem tag consists of the concatenation of simple distinct tags that is engineered to be cloned as a unique element onto a sequence of interest. Note that when a protein is fused to many simple tags that are inserted individually and possibly in different sequence positions these should be reported as independent features." [pubmed:14755292 "primary-reference"]
is_a: PAR:0507 ! tag

[Term]
id: PAR:0678
name: antibody array
def: "A microarray consisting of antibodies spotted on a solid support in appropriate orientation is incubated with a biological sample (or antigen). Some proteins are captured by the antibodies in the array. Protein of  forming complexes on the array are identified according to their prior labelling (tag, ELISA, biotin and others)." [pubmed:12454649 "primary-reference"]
related_synonym: "antigen capture assay" []
related_synonym: "sandwich immunoassay" []
is_a: PAR:0008 ! array technology

[Term]
id: PAR:0679
name: poly adenine
def: "A sequence of adenine nucleotides that is added to the 3' end of some primary transcript messenger RNA molecules in eukaryotes during post-transcriptional processing. The added tail is believed to confer stability to the molecule." [pubmed:14755292 "primary-reference"]
related_synonym: "poly A" []
exact_synonym: "poly a" []
is_a: PAR:0320 ! ribonucleic acid

[Term]
id: PAR:0680
name: single stranded deoxyribonucleic acid
def: "DNA that consists of only one chain of nucleotides rather than the two base pairing strands found in DNA in the double helix form." [pubmed:14755292 "primary-reference"]
related_synonym: "ss DNA" []
exact_synonym: "ss dna" []
is_a: PAR:0319 ! deoxyribonucleic acid

[Term]
id: PAR:0681
name: double stranded deoxyribonucleic acid
def: "DNA that consists of two base pairing strands. The 2 nucleotide chains are held together by hydrogen bonds between base pairs of nucleotides." [pubmed:14755292 "primary-reference"]
related_synonym: "ds DNA" []
exact_synonym: "ds dna" []
is_a: PAR:0319 ! deoxyribonucleic acid

[Term]
id: PAR:0683
name: sequence database
def: "Database collecting nucleic or amino acid sequences mainly derived from genomic sequence." [pubmed:14755292 "primary-reference"]
is_a: PAR:0473 ! participant database

[Term]
id: PAR:0685
name: source reference
def: "Reference pointing to the originating database in which an interaction, or other curated information, was first described." [pubmed:14755292 "primary-reference"]
is_a: PAR:0353 ! cross-reference type

[Term]
id: PAR:0687
name: fluorescent protein tag
def: "Protein having well characterized fluorescence excitation and emission spectra used as fusion with a protein under study to facilitate its  localisation or identification." [pubmed:14755292 "primary-reference"]
exact_synonym: "fluorescent prot tag" []
is_a: PAR:0240 ! fusion protein

[Term]
id: PAR:0688
name: dna binding domain tag
def: "Part of a transcription factor responsible for the binding of gene regulatory region prior to their transcription. Such tags are generally used in two hybrid experiments where they are fused to a bait polypeptide tested for its ability to interact with a prey fused to an activation domain tag. " [pubmed:14755292 "primary-reference"]
exact_synonym: "dna binding domain" []
is_a: PAR:0240 ! fusion protein

[Term]
id: PAR:0689
name: activation domain tag
def: "Part of a transcription factor responsible for the activation of DNA transcription. Such tags are generally used in two hybrid experiments where they are fused to a prey polypeptide tested for its ability to interact with a bait fused to a DNA binding domain tag. " [pubmed:14755292 "primary-reference"]
exact_synonym: "activation domain" []
is_a: PAR:0240 ! fusion protein

[Term]
id: PAR:0690
name: gal4 activation domain
def: "Part of the yeast transcription factor GAL4 (amino acids 766-881) specifically responsible for DNA transcription activation." [pubmed:14755292 "primary-reference"]
exact_synonym: "gal4 ad" []
is_a: PAR:0689 ! activation domain tag

[Term]
id: PAR:0691
name: vp16 activation domain
def: "Full viral protein vp16 exclusively responsible for preferential transcriptional activation of viral genes. Activation requires the formation of a complex with the host cell transcription factor." [pubmed:14755292 "primary-reference"]
exact_synonym: "vp16 ad" []
is_a: PAR:0689 ! activation domain tag

[Term]
id: PAR:0692
name: b42 activation domain
def: "B42 is an acidic sequence of 89 residues  derived from Escherichia coli acting as weak transcription activation domain. When use in two hybrid experiments, the weakness of B42 as activator increases the sensitivity of the interaction detection." [pubmed:14613974 "primary-reference"]
exact_synonym: "b42 ad" []
is_a: PAR:0689 ! activation domain tag

[Term]
id: PAR:0693
name: gal4 dna binding domain
def: "Part of the yeast transcription factor GAL4 (amino acids 11-38) specifically responsible for DNA binding of a 17 base-pair long sequence in the upstream activating sequence of galactose-induced genes.\n" [pubmed:14755292 "primary-reference"]
exact_synonym: "gal4 dna bd" []
is_a: PAR:0688 ! dna binding domain tag

[Term]
id: PAR:0694
name: lexa dna binding domain
def: "Amino terminal (1-220) part of the Escherichia coli lexA repressor, binding to 16 base pair palindromic DNA sequences. " [pubmed:14755292 "primary-reference"]
exact_synonym: "lexa dna bd" []
is_a: PAR:0688 ! dna binding domain tag

[Term]
id: PAR:0695
name: sandwich immunoassay
def: "Antibody array where proteins retained by the arrayed antibodies are identified using a detector antibody. The detector antibody is either modified with a directly detectable label (enzyme, fluorescent molecule, isotope, etc.), or it is biotinylated for detection after subsequent probing with labeled streptavidin." [pubmed:12454649 "primary-reference"]
is_a: PAR:0678 ! antibody array

[Term]
id: PAR:0701
name: dna strand elongation
def: "The process by which a DNA strand is synthesized from template DNA by the action of polymerases, which add nucleotides to the 3' end of the nascent DNA strand." [go:GO\:0006271 "identity", pubmed:14755292 "primary-reference"]
related_synonym: "DNA replication elongation " []
exact_synonym: "elongation" []
is_a: PAR:0414 ! enzymatic reaction

[Term]
id: PAR:0702
name: panther
def: "The PANTHER (Protein ANalysis THrough Evolutionary Relationships) Classification System is a unique resource that classifies genes by their functions using published scientific experimental evidence and evolutionary relationships to predict function even in the absence of direct experimental evidence.\nwww.pantherdb.org/ " [pubmed:14755292 "primary-reference"]
related_synonym: "PANTHER" []
is_a: PAR:0449 ! interpro

[Term]
id: PAR:0703
name: gene3d
def: "The Gene3D database provides a combined structural, functional and evolutionary view of the protein world. It is focused on providing structural annotation for protein sequences without structural representatives--including the complete proteome sets of over 240 different species." [pubmed:14755292 "primary-reference"]
related_synonym: "Gene3D" []
xref_analog: url:http\://cathwww.biochem.ucl.ac.uk\:8080/Gene3D/ "ANNOTATION"
is_a: PAR:0449 ! interpro

[Term]
id: PAR:0705
name: anti tag western blot
def: "Western blot assay performed when specific antibodies for the protein of interest are not available. Therefore the protein is expressed as a hybrid protein fused to a tag for which efficient antibodies are available.The antibody may be either monoclonal or polyclonal." [pubmed:14755292 "primary-reference"]
exact_synonym: "anti tag western" []
is_a: PAR:0113 ! western blot
is_a: PAR:0866 ! tag visualisation

[Term]
id: PAR:0707
name: anti tag immunostaining
def: "Immunostaining assay performed when specific antibodies for the protein of interest are not available. Therefore the  protein is expressed as a hybrid protein fused to a tag peptide/protein for which efficient antibodies are available. The anti tag antibody may be either monoclonal or polyclonal." [pubmed:14755292 "primary-reference"]
exact_synonym: "anti tag immunost" []
is_a: PAR:0422 ! immunostaining

[Term]
id: PAR:0708
name: monoclonal antibody immunostaining
def: "A monospecific antibody for the protein of interest is available, this is used to detect a specific protein within a cell or tissue sample." [pubmed:14755292 "primary-reference"]
exact_synonym: "monoclonal immunost" []
is_a: PAR:0422 ! immunostaining

[Term]
id: PAR:0709
name: polyclonal antibody immunostaining
def: "Immunostaining assay carried out using a mixture of different antibodies that represent the immune response, normally in an experimental animal, to the protein of interest. These antibodies are used to detect the protein within a cell or tissue sample." [pubmed:14755292 "primary-reference"]
exact_synonym: "polyclonal immunost" []
is_a: PAR:0422 ! immunostaining

[Term]
id: PAR:0730
name: pubchem
def: "PubChem provides information on the biological activities of small molecules." [pubmed:16381840 "primary-reference"]
related_synonym: "PubChem" []
xref_analog: url:http\://pubchem.ncbi.nlm.nih.gov/ "ANNOTATION"
is_a: PAR:0473 ! participant database

[Term]
id: PAR:0731
name: 3d repertoire
def: "The aim of 3D Repertoire is to determine the structures of all amenable complexes in a cell at medium or high resolution,  which will later serve to integrate in toponomic and dynamic analyses of protein complexes in a cell. Complex models, EM pictures, expression and purification protocols obtained in the project will be collected in a database connected to the PDB repository." [pubmed:14755292 "primary-reference"]
related_synonym: "3D Repertoire" []
is_a: PAR:0489 ! source database

[Term]
id: PAR:0732
name: red fluorescent protein tag
def: "The red fluorescent protein derived from Discosoma reef coral can be fused to individual proteins which then acquire fluorescence excitation and emission spectra virtually identical to those of the native." [pubmed:14755292 "primary-reference"]
related_synonym: "red fluorescent protein" []
related_synonym: "RFP" []
exact_synonym: "rfp tag" []
is_a: PAR:0687 ! fluorescent protein tag

[Term]
id: PAR:0733
name: cyan fluorescent protein tag
def: "The cyan fluorescent protein derived from Anthozoa reef coral can be fused to individual proteins which then acquire fluorescence excitation and emission spectra virtually identical to those of the native." [pubmed:14755292 "primary-reference"]
related_synonym: "CFP" []
related_synonym: "cyan fluorescent protein" []
exact_synonym: "cfp tag" []
is_a: PAR:0687 ! fluorescent protein tag

[Term]
id: PAR:0734
name: enhanced green fluorescent protein tag
def: "Variation of the green fluorescent protein derived from the bioluminescent jellyfish Aequorea victoria, can be fused to individual proteins which then acquire fluorescence excitation and emission spectra virtually identical to those of the native. " [pubmed:14755292 "primary-reference"]
related_synonym: "EGFP" []
related_synonym: "enhanced green fluorescent protein" []
exact_synonym: "egfp tag" []
is_a: PAR:0367 ! green fluorescent protein tag

[Term]
id: PAR:0735
name: transactivating tag
def: "Tag derived from the transactivating (Tat) protein of human immunodeficiency virus 1 (HIV-1) that can enter cells efficiently when added exogenously in tissue culture. The Tat tag can carry other molecules into cells, by fusion of Tat peptides (residues 1-72 or 37-72,) to any molecule under study. Tat-mediated uptake may allow the delivery of macromolecules previously thought to be impermeable to living cells. " [pubmed:8290579 "primary-reference"]
related_synonym: "Tat tag" []
exact_synonym: "tat tag" []
is_a: PAR:0740 ! cell penetrating peptide tag

[Term]
id: PAR:0737
name: peptide sequence database
def: "database storing sequences detected by peptide identification methods. " [pubmed:14755292 "primary-reference"]
exact_synonym: "pep seq db" []
is_a: PAR:0683 ! sequence database

[Term]
id: PAR:0738
name: pride
def: "PRIDE is a public repository of protein and peptide identifications for the proteomics community." [pubmed:16381953 "primary-reference"]
xref_analog: url:http\://www.ebi.ac.uk/pride/ "ANNOTATION"
is_a: PAR:0737 ! peptide sequence database

[Term]
id: PAR:0739
name: penetrating tag
def: "Membrane shuttling peptide derived from the Drosophila homeobox protein Antennapedia: RQIKIWFQNRRMKWKK" [pubmed:16574060 "primary-reference"]
is_a: PAR:0740 ! cell penetrating peptide tag

[Term]
id: PAR:0740
name: cell penetrating peptide tag
def: "The peptides named CPPs vary greatly in size, amino acid sequence, and charge, but share the common feature that they have the ability to rapidly translocate the plasma membrane and enable delivery to the cytoplasm or nucleus." [pubmed:16574060 "primary-reference"]
related_synonym: "cell-penetrating peptides" []
related_synonym: "CPPs" []
related_synonym: "membrane translocating sequences" []
related_synonym: "MTS" []
related_synonym: "protein transduction domains" []
related_synonym: "PTDs" []
related_synonym: "Trojan peptides" []
is_a: PAR:0507 ! tag

[Term]
id: PAR:0741
name: peptide atlas
def: "PeptideAtlas addresses these needs by identifying peptides by tandem mass spectrometry (MS/MS), statistically validating those identifications and then mapping identified sequences to the genomes of eukaryotic organisms." [pubmed:15642101 "primary-reference", pubmed:16381952 "method reference"]
related_synonym: "PeptideAtlas" []
xref_analog: url:http\://www.peptideatlas.org/ "ANNOTATION"
is_a: PAR:0737 ! peptide sequence database

[Term]
id: PAR:0742
name: gpm
def: "Global Proteome Machine aim to improve the quality of analysis, make the results portable and to provide a common platform for testing and validating proteomics results." [pubmed:15595733 "primary-reference"]
related_synonym: "Global Proteome Machine" []
xref_analog: url:http\://www.thegpm.org "ANNOTATION"
is_a: PAR:0737 ! peptide sequence database

[Term]
id: PAR: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 joined the wwPDB in 2006. The mission of the wwPDB is to maintain a single Protein Data Bank Archive of macromolecular structural data that is freely and publicly available to the global community." [pubmed:14634627 "primary-reference"]
related_synonym: "wwPDB" []
xref_analog: id-validation-regexp:\"[0-9\][a-zA-Z0-9\]\{3}\" "ANNOTATION"
xref_analog: url:http\://www.wwpdb.org/ "ANNOTATION"
is_a: PAR:0447 ! feature database
is_a: PAR:0461 ! interaction database
is_a: PAR:0489 ! source database

[Term]
id: PAR: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 the Research Collaboration for Structural Bioinformatics(RCSB) and the MSD in the European Bioinformatics Institute(MSD-EBI) in EU. All three organizations serve as deposition, data processing and distribution sites." [pubmed:12099029 "primary-reference"]
related_synonym: "PDBj" []
xref_analog: id-validation-regexp:\"[0-9\][a-zA-Z0-9\]\{3}\" "ANNOTATION"
xref_analog: search-url: http\://pdbjs3.protein.osaka-u.ac.jp/xPSSS/DetailServlet?PDBID=$\{ac}&PAGEID=Summary "ANNOTATION"
xref_analog: url:http\://www.pdbj.org/ "ANNOTATION"
is_a: PAR:0805 ! wwpdb

[Term]
id: PAR: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." [pubmed:14755292 "primary-reference"]
exact_synonym: "comigration in gel" []
is_a: PAR:1320 ! electrophoresis

[Term]
id: PAR: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." [pubmed:14755292 "primary-reference", pubmed:16732283 "method reference"]
exact_synonym: "comigration in sds" []
is_a: PAR:0807 ! comigration in gel electrophoresis

[Term]
id: PAR: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 fluorescent protein (YFP) when they are brought together by interactions between proteins fused to each fragment." [pubmed:11983170 "primary-reference"]
exact_synonym: "bifc" []
is_a: PAR:0051 ! fluorescence technology

[Term]
id: PAR: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." [pubmed:14755292 "primary-reference"]
exact_synonym: "substitut analysis" []
is_a: PAR:0074 ! mutation analysis

[Term]
id: PAR: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." [pubmed:14755292 "primary-reference"]
is_a: PAR:0074 ! mutation analysis

[Term]
id: PAR: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." [pubmed:14755292 "primary-reference"]
exact_synonym: "cam  tag" []
is_a: PAR:0240 ! fusion protein

[Term]
id: PAR: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 the detection of specific proteins to the analysis of DNA sequences. Proximity probes containing oligonucleotide extensions are designed to bind pairwise to target proteins and to form amplifiable tag sequences by ligation when brought in proximity." [pubmed:15155907 "primary-reference"]
related_synonym: "pELISA" []
exact_synonym: "p elisa" []
is_a: PAR:0401 ! biochemical
is_a: PAR:0421 ! identification by antibody

[Term]
id: PAR: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 immunoblotting with antibodies against the tag (e.g., Protein A, GFP, and 6xHis)." [pubmed:16615907 "primary-reference"]
related_synonym: "pal" []
exact_synonym: "protease access" []
is_a: PAR:0417 ! footprinting

[Term]
id: PAR:0815
name: confirmation by molecular weight
def: "Molecule whose sequence identity is derived from their molecular weight" [pubmed:14755292 "primary-reference"]
exact_synonym: "weight identificat" []
is_a: PAR:0396 ! predetermined participant

[Term]
id: PAR: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." [pubmed:14755292 "primary-reference"]
exact_synonym: "weight by staining" []
is_a: PAR:0815 ! confirmation by molecular weight

[Term]
id: PAR: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." [pubmed:14755292 "primary-reference"]
exact_synonym: "weight silver stain" []
is_a: PAR:0816 ! molecular weight estimation by staining

[Term]
id: PAR: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." [pubmed:14755292 "primary-reference"]
exact_synonym: "weight by comassie" []
is_a: PAR:0816 ! molecular weight estimation by staining

[Term]
id: PAR: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." [pubmed:14755292 "primary-reference"]
exact_synonym: "weight by bromide" []
is_a: PAR:0816 ! molecular weight estimation by staining

[Term]
id: PAR: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." [pubmed:14755292 "primary-reference"]
related_synonym: "safe DNA gel stain" []
exact_synonym: "weight by sybr" []
is_a: PAR:0816 ! molecular weight estimation by staining

[Term]
id: PAR: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." [pubmed:14755292 "primary-reference"]
exact_synonym: "weight autoradiogra" []
is_a: PAR:0815 ! confirmation by molecular weight

[Term]
id: PAR: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." [pubmed:14755292 "primary-reference"]
exact_synonym: "weight by hoechst" []
is_a: PAR:0816 ! molecular weight estimation by staining

[Term]
id: PAR:0823
name: predetermined feature
def: "Feature detection not verified in the context of an experiment but assumed from external or previous experimental evidence(s)." [pubmed:14755292 "primary-reference"]
exact_synonym: "predetermined featur" []
is_a: PAR:0093 ! protein sequence identification
is_a: PAR:0427 ! mass spectrometry
is_a: PAR:0659 ! experimental feature detection

[Term]
id: PAR:0824
name: x ray powder diffraction
def: "Analysis of a diffraction pattern generated by an isotropic sample composed of many randomly oriented crystals. " [pubmed:14755292 "primary-reference"]
related_synonym: "X-ray" []
related_synonym: "x-ray powder diffraction" []
exact_synonym: "x ray powder diffrac" []
is_a: PAR:0114 ! x ray crystallography

[Term]
id: PAR:0825
name: x ray fiber diffraction
def: "Analysis  of diffraction pattern of a partially ordered sample composed of fibers oriented parallel to each other." [pubmed:14755292 "primary-reference"]
related_synonym: "X-ray" []
related_synonym: "x-ray fiber diffraction" []
exact_synonym: "x ray fiber diffrac" []
is_a: PAR:0114 ! x ray crystallography

[Term]
id: PAR: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. " [pubmed:14755292 "primary-reference"]
exact_synonym: "saxs" []
is_a: PAR:0067 ! light scattering

[Term]
id: PAR: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 biomedical research. In terms of the latter, the National Center for X-ray Tomography (NCXT) is one of the principle developers of this technology, in particular for imaging whole, hydrated cells." [pubmed:14755292 "primary-reference"]
related_synonym: "x-ray tomography" []
is_a: PAR:0428 ! imaging techniques

[Term]
id: PAR:0829
name: multiple parent reference
def: "This qualifier is used  for hybrid or composite molecules with more than one crossreference to parent molecules." [pubmed:14755292 "primary-reference"]
exact_synonym: "multiple parent" []
is_a: PAR:0353 ! cross-reference type

[Term]
id: PAR:0830
name: tissue list
def: "List of tissue used as  topic in UniProt RC line." [pubmed:14755292 "primary-reference"]
xref_analog: id-validation-regexp:\"[0-9\]+|ACC\\s[A-Z0-9\]+|ECACC\\s[A-Z0-9\]+|LMBP\\s[A-Z0-9\]+|ICLC\\s[A-Z0-9\]+|CIP-[0-9\]+\" "ANNOTATION"
xref_analog: search-url: http\://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?[libs%3d\{dsmz_mutz%20ecacc_cell%20iclc%20CABI_BACT%20CIP_BACT%20CABI_YEAST%20DSMZ_PLANT_CELL}-id\:$\{ac}\]+-e "ANNOTATION"
xref_analog: url:http\://www.expasy.org/cgi-bin/lists?tisslist.txt "ANNOTATION"
is_a: PAR:0473 ! participant database

[Term]
id: PAR:0831
name: cell ontology
def: "Ontology of cell types." [pubmed:16381901 "primary-reference"]
xref_analog: id-validation-regexp:\"[0-9\]+|ACC\\s[A-Z0-9\]+|ECACC\\s[A-Z0-9\]+|LMBP\\s[A-Z0-9\]+|ICLC\\s[A-Z0-9\]+|CIP-[0-9\]+\" "ANNOTATION"
xref_analog: search-url: http\://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?[libs%3d\{dsmz_mutz%20ecacc_cell%20iclc%20CABI_BACT%20CIP_BACT%20CABI_YEAST%20DSMZ_PLANT_CELL}-id\:$\{ac}\]+-e "ANNOTATION"
xref_analog: url:http\://obo.sourceforge.net/cgi-bin/detail.cgi?cell "ANNOTATION"
is_a: PAR:0473 ! participant database

[Term]
id: PAR: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" [resid:AA0025 "identity"]
related_synonym: "Half of a disulfide bridge" []
is_a: PAR:0179 ! other modification

[Term]
id: PAR:0833
name: autoradiography
def: "Experimental method by which radiolabel is detected by exposure to a photographic emulsion forming a pattern on the film." [pubmed:14755292 "primary-reference"]
is_a: PAR:0078 ! nucleotide sequence identification

[Term]
id: PAR:0834
name: ka
def: "Association rate constant or rate of complex formation. Unit MOLE per SECOND (M-1 s-1)" [pubmed:14755292 "primary-reference"]
exact_synonym: "kon" []
is_a: PAR:0640 ! parameter type

[Term]
id: PAR:0835
name: kd
def: "Dissociation rate constant measuring the stability of a complex. Unit SECOND (s-1)" [pubmed:14755292 "primary-reference"]
exact_synonym: "koff" []
is_a: PAR:0640 ! parameter type

[Term]
id: PAR:0836
name: temperature of interaction
def: "Temperature at which interaction was determined. The unit is KELVIN (K)." [pubmed:14755292 "primary-reference"]
related_synonym: "t interaction" []
related_synonym: "Tint" []
is_a: PAR:0640 ! parameter type

[Term]
id: PAR:0837
name: pH of interaction
def: "pH at which interaction was determined." [pubmed:14755292 "primary-reference"]
related_synonym: "pHint" []
is_a: PAR:0640 ! parameter type

[Term]
id: PAR: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)." [pubmed:14755292 "primary-reference"]
related_synonym: "K" []
is_a: PAR:0647 ! parameter unit

[Term]
id: PAR:0839
name: mole per second
def: "Per mole per second, unit for association rate constant" [pubmed:14755292 "primary-reference"]
related_synonym: "M-1s-1" []
is_a: PAR:0647 ! parameter unit

[Term]
id: PAR:0844
name: phosphotransfer reaction
def: "Reaction where a phosphate is transferred between two proteins of a phosphorelay system. " [pubmed:14755292 "primary-reference", pubmed:16712436 "method reference"]
exact_synonym: "phosphotransfer" []
is_a: PAR:0414 ! enzymatic reaction

[Term]
id: PAR:0845
name: spin label
def: "Paramagnetic fragment, most often a cyclic nitroxide derivative, covalently attached to a molecule of interest." [pubmed:10966640 "primary-reference"]
is_a: PAR:0505 ! experimental feature

[Term]
id: PAR: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." [pubmed:10966640 "primary-reference"]
is_a: PAR:0845 ! spin label

[Term]
id: PAR: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." [pubmed:14755292 "primary-reference"]
related_synonym: "5-dimethylaminonaphthalene-1-sulfonyl tag" []
is_a: PAR:0507 ! tag

[Term]
id: PAR:0848
name: 125i radiolabel
def: "Molecule labelled with 125 radio isotope of iodine atoms." [pubmed:14755292 "primary-reference"]
related_synonym: "125I" []
related_synonym: "I125" []
is_a: PAR:0517 ! radiolabel

[Term]
id: PAR: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 structural data for a particular organism or group of organisms. Searches of the NCBI taxonomy may be made on the basis of whole or partial organism names, and direct links to organisms commonly used in biological research are also provided. The Taxonomy Browser can also be used to display the number of nucleic acid sequences, protein sequences, and protein structures available for organisms included in the branch. From the data display for a particular organism, one can retrieve and download the sequence data for that organism, or protein 3D structure data if available." [pubmed:10592169 "primary-reference"]
xref_analog: id-validation-regexp:\"[0-9\]+\" "ANNOTATION"
xref_analog: 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 "ANNOTATION"
xref_analog: url:http\://www.ncbi.nlm.nih.gov/Taxonomy/ "ANNOTATION"
is_a: PAR:0473 ! participant database

[Term]
id: PAR: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." [pubmed:17372197 "primary-reference"]
related_synonym: "ENCODE" []
related_synonym: "Encyclopedia Of DNA Elements" []
xref_analog: url:http\://www.genome.gov/10005107 "ANNOTATION"
is_a: PAR:0683 ! sequence database

[Term]
id: PAR:0851
name: protein genbank identifier
def: "GenBank Identifier or GI numbers for proteins." [pubmed:17170002 "primary-reference"]
related_synonym: "GenBank Protein GI" []
related_synonym: "genbank protein gi" []
exact_synonym: "genbank_protein_gi" []
xref_analog: id-validation-regexp:\"[0-9\]+\" "ANNOTATION"
xref_analog: search-url: http\://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=protein&cmd=Retrieve&dopt=Graphics&list_uids=$\{ac} "ANNOTATION"
is_a: PAR:0860 ! genbank indentifier

[Term]
id: PAR:0852
name: nucleotide genbank identifier
def: "GenBank Identifier or GI numbers for nucleotide." [pubmed:17170002 "primary-reference"]
related_synonym: "genbank nucleotide" []
related_synonym: "GenBank Nucleotide" []
exact_synonym: "genbank_nucleotide_gi" []
xref_analog: id-validation-regexp:\"[0-9\]+\" "ANNOTATION"
xref_analog: search-url: http\://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=nucleotide&cmd=Retrieve&dopt=Graphics&list_uids=$ "ANNOTATION"
is_a: PAR:0860 ! genbank indentifier

[Term]
id: PAR:0853
name: dna overhang
def: "An overhang is a stretch of unpaired nucleotides in the end of a DNA molecule. These unpaired nucleotides can be in either strand, creating either 3' or 5' overhangs.\nLonger overhangs are called cohessive ends or sticky ends. They are most\noften created by restriction endonucleases when they cut DNA. Very often\nthey cut the two DNA strands four base pairs from each other, creating a\nfour-base 3' overhang in the other molecule and a complementary 5' overhang\nin the other. These ends are called cohessive since they are easily joined\nback together by a ligase" [pubmed:14755292 "primary-reference"]
related_synonym: "cohessive ends" []
related_synonym: "sticky ends" []
is_a: PAR:0505 ! experimental feature

[Term]
id: PAR:0854
name: 3 prime overhang
def: "An overhang is a stretch of unpaired nucleotides in the end of a 3' strand of a DNA molecule." [pubmed:14755292 "primary-reference"]
related_synonym: "3 prime sticky end" []
is_a: PAR:0853 ! dna overhang

[Term]
id: PAR:0855
name: 5 prime overhang
def: "An overhang is a stretch of unpaired nucleotides in the end of a 5' strand of a DNA molecule." [pubmed:14755292 "primary-reference"]
related_synonym: "5 prime sticky end" []
is_a: PAR:0853 ! dna overhang

[Term]
id: PAR:0856
name: fluorophore
def: "A fluorophore is a component of a molecule which causes a molecule to be fluorescent. It is a functional group in a molecule which will absorb energy of a specific wavelength and re-emit energy at a different (but equally specific) wavelength. The amount and wavelength of the emitted energy depend on both the fluorophore and the chemical environment of the fluorophore." [pubmed:14755292 "primary-reference"]
is_a: PAR:0505 ! experimental feature

[Term]
id: PAR:0857
name: fluorescent dye label
def: "Dye label containing a  fluorophore  which  absorb energy of a specific wavelength and re-emit energy at a different (but equally specific) wavelength. " [pubmed:14755292 "primary-reference"]
is_a: PAR:0856 ! fluorophore

[Term]
id: PAR:0859
name: intermolecular force
def: "An optical tweezer is a scientific instrument that uses a focused laser beam to provide an attractive or repulsive force, depending on the index mismatch (typically on the order of piconewtons) to physically hold and move microscopic dielectric objects (i.e.highly resistants to the flow of an electric current). This instrument allow to measure the forces generated between interacting molecules - either at the level of just single interacting pair of molecules or at the level of larger molecular assemblies. " [pubmed:17023539 "primary-reference", pubmed:17081984 "method reference"]
related_synonym: "force measurement" []
related_synonym: "molecular force measurement" []
related_synonym: "optical tweezer" []
related_synonym: "single molecule force measurement" []
related_synonym: "surface adhesion force measurement" []
is_a: PAR:0013 ! biophysical

[Term]
id: PAR:0860
name: genbank indentifier
def: " edit" [pubmed:15078858 "primary-reference"]
xref_analog: id-validation-regexp:\"ENS[A-Z\]+[0-9\]\{11}\" "ANNOTATION"
is_a: PAR:0683 ! sequence database

[Term]
id: PAR:0861
name: protein a tag
def: "The protein A is a bacterial cell wall  isolated from Staphylococcus aureus that  binds to mammalian IgGs mainly through Fc regions. The protein A can be use to retaint antibodies or as fusion tag of a protein under analysis." [pubmed:14755292 "primary-reference"]
related_synonym: "protein A" []
is_a: PAR:0240 ! fusion protein

[Term]
id: PAR:0862
name: zz tag
def: "The ZZ tag is a tag made out of two tandem repeats of the Protein A IgG binding domain. " [pubmed:11694505 "primary-reference"]
related_synonym: "ZZ tag" []
is_a: PAR:0861 ! protein a tag

[Term]
id: PAR:0863
name: thiol reactive lanthanide label
def: "Thiol-reactive lanthanide complexes have been synthesized that are luminescent when bound to terbium and/or europium. The Tb3+-DTPA-cs124-EMCH complexes consist of a diethylenetriaminepentaacetate (DTPA) chelate covalently joined through one amide bond to a chromophore, carbostyril 124, and via a second amide bond to a maleimide, bromoacetamide, or pyridyldithio moiety. This label can be Site-specific attachted to both proteins and DNA." [pubmed:10077482 "primary-reference"]
related_synonym: "Tb3+-DTPA-cs124-EMCH" []
is_a: PAR:0505 ! experimental feature

[Term]
id: PAR:0864
name: brenda
def: "A structured controlled vocabulary for the source of an enzyme. It comprises terms for tissues, cell lines, cell types and cell cultures from uni- and multicellular organisms." [pubmed:14755292 "primary-reference"]
xref_analog: id-validation-regexp:\"[0-9\]+|ACC\\s[A-Z0-9\]+|ECACC\\s[A-Z0-9\]+|LMBP\\s[A-Z0-9\]+|ICLC\\s[A-Z0-9\]+|CIP-[0-9\]+\" "ANNOTATION"
xref_analog: search-url: http\://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?[libs%3d\{dsmz_mutz%20ecacc_cell%20iclc%20CABI_BACT%20CIP_BACT%20CABI_YEAST%20DSMZ_PLANT_CELL}-id\:$\{ac}\]+-e "ANNOTATION"
xref_analog: url:http\://www.brenda.uni-koeln.de/ "ANNOTATION"
is_a: PAR:0473 ! participant database

[Term]
id: PAR:0866
name: tag visualisation
def: "Molecule whose sequence identity is not checked after the interaction but its presence is detected through its tag." [pubmed:14755292 "primary-reference"]
is_a: PAR:0396 ! predetermined participant

[Term]
id: PAR:0867
name: tag visualisation by fluorescence
def: "Molecule whose sequence identity is not checked after the interaction but its presence is detected through a flouroscent tag." [pubmed:14755292 "primary-reference"]
exact_synonym: "tag fluorescence" []
is_a: PAR:0866 ! tag visualisation

[Term]
id: PAR:0868
name: author identifier
def: "author published identifier" [pubmed:14755292 "primary-reference"]
is_a: PAR:0353 ! cross-reference type

[Term]
id: PAR:0869
name: originally assigned identifier
def: "Identifier assigned when the record was created." [pubmed:14755292 "primary-reference"]
is_a: PAR:0353 ! cross-reference type

[Term]
id: PAR:0871
name: demethylation reaction
def: "The cleavage of a methyl residue from a polypeptide." [go:GO\:0006482 "identity", pubmed:17277772 "primary-reference"]
exact_synonym: "demethylation" []
is_a: PAR:0414 ! enzymatic reaction

[Term]
id: PAR:0872
name: atomic force microscopy
def: "The atomic force microscope (AFM) is a very high-resolution type of scanning probe microscope, with demonstrated resolution of fractions of a nanometer, more than 1000 times better than the optical diffraction limit. The AFM was invented by Binnig, Quate and Gerber in 1986, and is one of the foremost tools for imaging, measuring and manipulating matter at the nanoscale.The term 'microscope' in the name is actually a misnomer because it implies looking, while in fact the information is gathered by feeling out the surface with a mechanical feeler." [pubmed:17502105 "primary-reference"]
related_synonym: "AFM" []
exact_synonym: "atomic force microsc" []
xref_analog: url:http\://en.wikipedia.org/wiki/Atomic_force_microscope "ANNOTATION"
is_a: PAR:0428 ! imaging techniques

[Term]
id: PAR:0875
name: dataset
def: "Targeted curation dataset grouping experiments by topic or dataset origin." [pubmed:14755292 "primary-reference"]
is_a: PAR:0665 ! experiment attibute name

[Term]
id: PAR:0878
name: author submitted
def: "Data directly submitted by the authors to a database prior publication." [pubmed:14755292 "primary-reference"]
is_a: PAR:0665 ! experiment attibute name

[Term]
id: PAR:0881
name: nucleoside triphosphatase reaction
def: "Catalysis of the hydrolisis of a  nucleoside triphosphate into a nucleoside diphosphate plus phosphate." [go:GO\:0017111 "identity"]
exact_synonym: "triphosphatase react" []
is_a: PAR:0414 ! enzymatic reaction

[Term]
id: PAR:0882
name: atpase reaction
def: "Catalysis of the hydrolisis of ATP+ H2O = ADP + phosphate." [go:GO\:0017111 "identity"]
is_a: PAR:0881 ! nucleoside triphosphatase reaction

[Term]
id: PAR:0883
name: gtpase reaction
def: "Catalysis of the hydrolisis of GTP+ H2O = GDP + phosphate." [go:GO\:0017111 "identity"]
is_a: PAR:0881 ! nucleoside triphosphatase reaction

[Term]
id: PAR:0884
name: vsv tag
def: "Epitope tag derived from vesicular stomatitis virus (VSV) glycoprotein. The tag sequence is YTDIEMNRLGK and many antibodies against it are commercially available." [pubmed:14755292 "primary-reference"]
related_synonym: "vesicular stomatitis virus tag" []
is_a: PAR:0507 ! tag

[Term]
id: PAR:0885
name: journal
def: "Name and details of a journal from which paper has been taken." [pubmed:14755292 "primary-reference"]
is_a: PAR:0665 ! experiment attibute name

[Term]
id: PAR:0886
name: publication year
def: "Year of publication of a paper." [pubmed:14755292 "primary-reference"]
is_a: PAR:0665 ! experiment attibute name

[Term]
id: PAR:1002
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." [pubmed:14755292 "primary-reference"]
is_a: PAR:1168 ! native/denatured state

[Term]
id: PAR:1003
name: tertiary structure
def: "This feature type corresponds to the tertiary (3D) structure of part of a protein. Thus it is used when the 3D structure has been determined for only a part of a protein." [pubmed:14755292 "primary-reference"]
is_a: PAR:0252 ! biological feature

[Term]
id: PAR:1004
name: PROTEIN AFFINITY REAGENT CV
def: "This is the draft protein affinity reagent CV" [pubmed:14755292 "primary-reference"]
exact_synonym: "psi-par" []

[Term]
id: PAR:1005
name: native
def: "State of the protein without interference i.e. the natural form." [pubmed:14755292 "primary-reference"]
is_a: PAR:1168 ! native/denatured state

[Term]
id: PAR:1006
name: aggregated
def: "The state of being in a coherent, stable cluster with other members of a set of proteins, usually all the same." [pubmed:14755292 "primary-reference"]
is_a: PAR:1067 ! aggregation state

[Term]
id: PAR:1007
name: refolded
def: "Describes state of the protein after having been denatured and allowed to fold again. This folded state may or may not be the native state." [pubmed:14755292 "primary-reference"]
is_a: PAR:1139 ! folding state

[Term]
id: PAR:1008
name: antibody-producing hybridoma
def: "Antibody-producing hybridomas are cells that have been engineered to It proliferate and produce a continuous supply of a specific monoclonal antibody. They are produced in the laboratory from the fusion of an antibody-producing lymphocyte and a nonantibody-producing cancer cell, usually a myeloma or lymphoma." [pubmed:14755292 "primary-reference"]
exact_synonym: "Ab-produci hybridoma" []
is_a: PAR:1147 ! composite interactor

[Term]
id: PAR:1009
name: intact antibody
def: "An intact antibody corresponds to a whole unmodified immunoglobulin." [pubmed:14755292 "primary-reference"]
related_synonym: "Ab" []
is_a: PAR:1279 ! antibody

[Term]
id: PAR:1010
name: purity statement
def: "Purity statement for a molecule e.g. \"Affinity purified using the PrEST-antigen as affinity ligand.\". The purity corresponds to a quantitative assessment of the homogeneity or uniformity of a mixture. It refers to the degree of being free of contaminants or heterogeneous components." [pubmed:14755292 "primary-reference"]
is_a: PAR:0666 ! participant attribute name

[Term]
id: PAR:1011
name: shipping information
def: "Shipping information of a molecule e.g. \"Shipped at ambient temperature.\"." [pubmed:14755292 "primary-reference"]
is_a: PAR:0666 ! participant attribute name

[Term]
id: PAR:1012
name: storage instructions
def: "Storage instructions for commercial biomolecule e.g. \"Aliquot and store at -20C. Avoid repeated freezing and thawing.\"." [pubmed:14755292 "primary-reference"]
is_a: PAR:0666 ! participant attribute name

[Term]
id: PAR:1013
name: supplied form
def: "Form of a biomolecule e.g. \"Supplied in 10 mM phosphate buffer (pH 7.2), 150 mM NaCl, 50 % glycerol.\"." [pubmed:14755292 "primary-reference"]
is_a: PAR:0666 ! participant attribute name

[Term]
id: PAR:1014
name: molecular state
def: "Statement about the stable state of a molecule e.g. a protein." [pubmed:14755292 "primary-reference"]
is_a: PAR:0346 ! experimental preparation

[Term]
id: PAR:1016
name: protein sequencing
def: "The determination of primary structure (or sequence) of an unbranched biopolymer such as DNA or proteins." [pubmed:14755292 "primary-reference"]
related_synonym: "peptide sequencing" []
related_synonym: "sequencing" []
is_a: PAR:1314 ! molecule characterisation

[Term]
id: PAR:1017
name: HPLC retention time
def: "The retention time is the characteristic time it takes for a particular analyte to pass through a chromatograpy system (from the column inlet to the detector) under set conditions." [pubmed:14755292 "primary-reference"]
is_a: PAR:0640 ! parameter type

[Term]
id: PAR:1022
name: screening rounds
def: "The number of screening rounds used in the selection experiment." [pubmed:14755292 "primary-reference"]
is_a: PAR:1178 ! molecule library attribute

[Term]
id: PAR:1026
name: tissue culture
def: "Name, reference or description of a tissue culture used in the experiment. A permanently established tissue cell culture that will proliferate indefinately provided that it has the appropriate medium and space." [pubmed:14755292 "primary-reference"]
is_a: PAR:1124 ! experimental material attribute

[Term]
id: PAR:1027
name: immunohisto/cytofluorescence
def: "IMM	CYT/HIS	DETEC	Immunohisto/cytofluorescence" [pubmed:123456789 "primary-reference"]
is_a: PAR:0013 ! biophysical

[Term]
id: PAR:1028
name: provider
def: "The provider of the molecule. This is typically a commercial company, but can also be an academic lab or other source." [pubmed:14755292 "primary-reference"]
exact_synonym: "supplier" []
is_a: PAR:0666 ! participant attribute name

[Term]
id: PAR:1029
name: antibody fragment
def: "An antibody fragment is a part of an immunoglobulin molecule or an association of parts of immunoglobulin molecules in a new stable complex." [pubmed:14755292 "primary-reference"]
is_a: PAR:1279 ! antibody

[Term]
id: PAR:1031
name: Fab
def: "A Fab fragment is a part of an immunoglobulin antibody that consists of both a light chain and part of a heavy chain. By comparison, natural antibodies consist of two heavy and two light chains. An FAB (fragment antibody) offers the advantages of smaller size and lower cross-reactivity compared to the complete antibody." [pubmed:14755292 "primary-reference"]
is_a: PAR:1029 ! antibody fragment

[Term]
id: PAR:1032
name: Fab2
def: "A Fab2 is a genetically engineered antibody derivate consisting in two Fab fragments joined together by a flexible peptide linker." [pubmed:14755292 "primary-reference"]
is_a: PAR:1029 ! antibody fragment

[Term]
id: PAR:1033
name: Fv
def: "A Fv is a genetically engineered antibody derivate consisting of both the variable heavy chain (VH) and the light chain (VL) of an immunoglobulin." [pubmed:14755292 "primary-reference"]
is_a: PAR:1029 ! antibody fragment

[Term]
id: PAR:1034
name: molecule library
def: "Name, reference or description of a molecule library containing for example cDNA clones or chemical compounds." [pubmed:14755292 "primary-reference"]
is_a: PAR:1178 ! molecule library attribute

[Term]
id: PAR:1037
name: insert position
def: "The position of insert of a specific gene into the expression vector." [pubmed:14755292 "primary-reference"]
is_a: PAR:1059 ! cDNA expression material attribute

[Term]
id: PAR:1038
name: experimental kit
def: "Name, reference or description of an experimental kit This is a set of tools, supplies, instructions, etc. that have been designed for a specific purpose" [pubmed:14755292 "primary-reference"]
is_a: PAR:1055 ! equipment

[Term]
id: PAR:1039
name: immunoluminescent assay
def: "IMM	LUM	ASS	immunoluminescent assay" [pubmed:123456789 "primary-reference"]
is_a: PAR:0013 ! biophysical

[Term]
id: PAR:1040
name: fluorescence intensity distribution analysis [fida]
def: "KW1	FLUO	ASS	fluorescence intensity distribution analysis [FIDA]" [pubmed:123456789 "primary-reference"]
is_a: PAR:0051 ! fluorescence technology

[Term]
id: PAR:1041
name: fluorescent immunoassay
def: "IMM	FLUO	ASS	Fluorescent immunoassay" [pubmed:123456789 "primary-reference"]
is_a: PAR:0051 ! fluorescence technology

[Term]
id: PAR:1042
name: elisa double sandwich assay
def: "IMM	ENZ	ASS	ELISA double sandwich assay" [pubmed:123456789 "primary-reference"]
is_a: PAR:0411 ! enzyme linked immunosorbent assay

[Term]
id: PAR:1043
name: elisa indirect
def: "IMM	ENZ	ASS	ELISA Indirect" [pubmed:123456789 "primary-reference"]
is_a: PAR:0411 ! enzyme linked immunosorbent assay

[Term]
id: PAR:1044
name: eia enzyme immunoassay
def: "IMM	ENZ	ASS	EIA enzyme immunoassay" [pubmed:123456789 "primary-reference"]
is_a: PAR:0411 ! enzyme linked immunosorbent assay

[Term]
id: PAR:1045
name: emit enzyme multiplied immunoassay technique
def: "IMM	ENZ	ASS	EMIT Enzyme Multiplied Immunoassay Technique" [pubmed:123456789 "primary-reference"]
is_a: PAR:0411 ! enzyme linked immunosorbent assay

[Term]
id: PAR:1046
name: protein expression
def: "Protein expression methods," [pubmed:123456789 "primary-reference"]
is_a: PAR:1328 ! molecule production method

[Term]
id: PAR:1047
name: equilibrium assay
def: "KW1	KW2	ASS	Equilibrium assay" [pubmed:123456789 "primary-reference"]
is_a: PAR:0401 ! biochemical

[Term]
id: PAR:1048
name: cell cloning
def: "Cloning." [pubmed:123456789 "primary-reference"]
is_a: PAR:1328 ! molecule production method

[Term]
id: PAR:1050
name: affibody
def: "Affibodies are engineered binding proteins forwhich the three-helix bundle Z domain derived from Staphylococcus aureus protein A (SPA), is used as a scaffold." [pubmed:14755292 "primary-reference"]
is_a: PAR:1100 ! engineered protein scaffold

[Term]
id: PAR:1051
name: monoclonal antibody
def: "A monoclonal antibody is an antibody produced by a clone or genetically homogenous fast-growing cells i.e., hybridoma. Hybridoma cells are cloned to establish cell lines producing a specific antibody that is chemically and immunologically homogeneous." [pubmed:14755292 "primary-reference"]
exact_synonym: "mAb" []
is_a: PAR:1009 ! intact antibody

[Term]
id: PAR:1052
name: zinc finger
def: "Zinc finger (Znf) domains are relatively small protein motifs that bind one or more zinc atoms, and which usually contain multiple finger-like protrusions that make tandem contacts with their target molecule. They are used in the design of protein scaffolds." [pubmed:14755292 "primary-reference"]
exact_synonym: "zinc finger" []
is_a: PAR:1100 ! engineered protein scaffold

[Term]
id: PAR:1053
name: lipocalin
def: "Some proteins of the lipocallin family present a beta-barrel structure similar to the one which was first identified in the retinol-binding protein (RBP) and which provides them with interesting biinding properties. They are used in the design of protein scaffolds." [pubmed:14755292 "primary-reference"]
related_synonym: "anticalin" []
is_a: PAR:1100 ! engineered protein scaffold

[Term]
id: PAR:1054
name: sensitivity determination
def: "Determination the sensitivity of an assay for the detection of one or more biomolecules." [pubmed:14755292 "primary-reference"]
related_synonym: "detection limit determination" []
exact_synonym: "sensitivity determin" []
is_a: PAR:1314 ! molecule characterisation

[Term]
id: PAR:1055
name: equipment
def: "Name, reference or description of experimental equipment. A piece of equipment is an item, often an electrical instrument, which is designed to carry out a specific function or set of functions, ." [pubmed:14755292 "primary-reference"]
is_a: PAR:0665 ! experiment attibute name

[Term]
id: PAR:1056
name: cDNA expression
def: "The process in which the inheritable information in a gene, such as the DNA sequence, is made into a functional gene product, such as protein or RNA." [pubmed:14755292 "primary-reference"]
related_synonym: "cdna cloning" []
is_a: PAR:1328 ! molecule production method

[Term]
id: PAR:1057
name: single chain Fv
def: "A single chain Fv is a genetically engineered antibody derivate consisting of both the variable heavy chain (VH) and the light chain (VL) of an immunoglobulin. These entities are joined together by a flexible peptide linker." [pubmed:14755292 "primary-reference"]
related_synonym: "scFv" []
is_a: PAR:1029 ! antibody fragment

[Term]
id: PAR:1059
name: cDNA expression material attribute
def: "Attribute name of annotation associated to an expression vector." [pubmed:14755292 "primary-reference"]
exact_synonym: "cDNA vector attribute" []
is_a: PAR:1124 ! experimental material attribute

[Term]
id: PAR:1060
name: software
def: "Name, reference or description of software used in the experiment. A software is a set of coded instructions, which a computer follows in processing data, performing an operation, or solving a logical problem, upon execution of the program." [pubmed:14755292 "primary-reference"]
is_a: PAR:0665 ! experiment attibute name

[Term]
id: PAR:1061
name: culture medium
def: "Name, reference or description of a cell culture medium. A culture medium is a liquid or gel designed to support the growth of microorganisms, such as bacteria or yeast, or cells derived from plants or animals. The most common growth media for microorganisms are nutrient broths and agar plates." [pubmed:14755292 "primary-reference"]
is_a: PAR:1124 ! experimental material attribute

[Term]
id: PAR:1062
name: Fab3
def: "A Fab3 is a genetically engineered antibody derivate consisting in three Fab fragments joined together by a flexible peptide linker." [pubmed:14755292 "primary-reference"]
is_a: PAR:1029 ! antibody fragment

[Term]
id: PAR:1063
name: minibody
def: "A minibody is a genetically engineered antibody derivate consisting in the VL and VH domains of a native antibody fused to the hinge region and CH3 domain of the immunoglobulin molecule." [pubmed:14755292 "primary-reference"]
is_a: PAR:1029 ! antibody fragment

[Term]
id: PAR:1064
name: secondary structure
def: "The secondary structure is the general three-dimensional form of local segments of biopolymers such as proteins and nucleic acids. Regular hydrogen-bond interactions within contiguous stretches of polymer chain give rise to alpha helices, beta strands (which align to form beta sheets) or other types of coils. This is the first folding level of protein polymer chain conformation." [pubmed:14755292 "primary-reference"]
is_a: PAR:0252 ! biological feature

[Term]
id: PAR:1065
name: virus
def: "A sub-microscopic infectious agent that is unable to grow or reproduce outside a host cell. Each viral particle, or virion, consists of genetic material, DNA or RNA, within a protective protein coat called a capsid. Viruses infect cellular life forms and are grouped into animal, plant and bacterial types, according to the type of host infected." [pubmed:14755292 "primary-reference"]
is_a: PAR:1147 ! composite interactor

[Term]
id: PAR:1066
name: BisScFv
def: "A BiScFv is a genetically engineered antibody derivate consisting in the two ScFv joined together by a flexible peptide linker." [pubmed:14755292 "primary-reference"]
is_a: PAR:1029 ! antibody fragment

[Term]
id: PAR:1067
name: aggregation state
def: "Statement regarding the relationship of the protein to others of the same type in solutions." [pubmed:14755292 "primary-reference"]
is_a: PAR:1014 ! molecular state

[Term]
id: PAR:1068
name: cv term
def: "Cross reference pointing to a cv term." [pubmed:14755292 "primary-reference"]
related_synonym: "ontology term" []
is_a: PAR:0353 ! cross-reference type

[Term]
id: PAR:1069
name: diabody
def: "A diabody is a genetically engineered antibody derivate consisting in two minibodies joined together in a dimer which can be either monvalent or divalent." [pubmed:14755292 "primary-reference"]
is_a: PAR:1029 ! antibody fragment

[Term]
id: PAR:1070
name: in vitro expression system
def: "Name, reference or description of an in vitro expression system. In vitro expression encompasses two general strategies. The first is to use isolated RNA synthesized in vivo or in vitro as a template for the translation reaction (e.g., using Promegas Rabbit Reticulocyte Lysate(a,b,c) (Cat.no L4151) or Wheat Germ Extract (Cat.no L4380) Systems). The second is to use a coupled transcription/translation system in which DNA is used as a template (e.g., Promegas TNT (a,b,c,d,e) and E. coli S30 Extract(a,b) Systems). This DNA may be either a gene cloned into a plasmid vector (cDNA) or a PCR(f)-generated template." [pubmed:14755292 "primary-reference"]
exact_synonym: "expr. system name" []
xref_analog: url:http\://www.promega.com/guides/ive_guide/ivex_gde.pdf "ANNOTATION"
is_a: PAR:1059 ! cDNA expression material attribute

[Term]
id: PAR:1071
name: biosapiens annotations term
def: "Cross reference pointing to a \"Biosapiens Annotations\" (BS) CV term." [pubmed:14755292 "primary-reference"]
exact_synonym: "BS term" []
is_a: PAR:1068 ! cv term

[Term]
id: PAR:1072
name: polymerase chain reaction
def: "NUC	ENZ	SYNT	Polymerase Chain Reaction (PCR)" [pubmed:123456789 "primary-reference"]
related_synonym: "pcr" []
exact_synonym: "PCR" []
is_a: PAR:0001 ! interaction detection method

[Term]
id: PAR:1073
name: rt-pcr
def: "NUC	ENZ	SYNT	RT-PCR" [pubmed:123456789 "primary-reference"]
is_a: PAR:1072 ! polymerase chain reaction

[Term]
id: PAR:1074
name: solution phase peptide synthesis
def: "AA	CHEM	SYNT	Solution phase peptide synthesis" [pubmed:123456789 "primary-reference"]
is_a: PAR:0083 ! peptide synthesis

[Term]
id: PAR:1075
name: chemical synthesis
def: "The purposeful execution of chemical reactions in order to build one or more complex substances or compounds from simpler elements or compounds." [pubmed:123456789 "primary-reference"]
is_a: PAR:1328 ! molecule production method

[Term]
id: PAR:1076
name: fmoc-spps
def: "9H-(f)luoren-9-yl(m)eth(o)xy(c)arbonyl solid-phase peptide synthesis (fmoc-spps) is a method for peptide synthesis." [pubmed:123456789 "primary-reference"]
is_a: PAR:0083 ! peptide synthesis

[Term]
id: PAR:1077
name: boc-spps
def: "(B)ut(o)xy(c)arbonyl Solid-phase peptide synthesis (boc-spps) is a method for peptide synthesis." [pubmed:123456789 "primary-reference"]
is_a: PAR:0083 ! peptide synthesis

[Term]
id: PAR:1078
name: animal immunization
def: "Immunisation is the process by which an individual's immune system is triggered by an immunogen; especially the treatment of an animal with the purpose of making it produce antibodies." [pubmed:123456789 "primary-reference"]
relationship: part_of PAR:1106 ! antibody production method

[Term]
id: PAR:1079
name: solid phase peptide synthesis (spps)
def: "AA	CHEM	SYNT	Solid Phase Peptide Synthesis (SPPS)" [pubmed:123456789 "primary-reference"]
is_a: PAR:0083 ! peptide synthesis

[Term]
id: PAR:1080
name: in vitro transcription
def: "NUC	ENZ	SYNT	In vitro transcription	inferred from in vitro transcription reconstitution assay	ECO:0000150" [pubmed:123456789 "primary-reference"]
is_a: PAR:1046 ! protein expression

[Term]
id: PAR:1081
name: error-prone polymerase chain reaction
def: "NUC	ENZ	SYNT	Error-prone polymerase chain reaction" [pubmed:123456789 "primary-reference"]
is_a: PAR:1072 ! polymerase chain reaction

[Term]
id: PAR:1084
name: expression vector map
def: "Reference, e.g. an URL, to an expression vector map. An expression vector map is a schematic drawing of the layout of the expression vector and its components such as promoter and enzyme restriction sites." [pubmed:14755292 "primary-reference"]
exact_synonym: "cDNA vector map url" []
is_a: PAR:1059 ! cDNA expression material attribute

[Term]
id: PAR:1085
name: criterion
def: "A criterion, such as a cut-off for assay readouts, used for defining the interation as positive or negative, e.g. binding between 2 molecules does or does not occur." [pubmed:14755292 "primary-reference"]
exact_synonym: "criterion" []
is_a: PAR:0664 ! interaction attribute name

[Term]
id: PAR:1086
name: triabody
def: "A triabody is a genetically engineered antibody derivate consisting in thee minibodies joined together in a trimer which can be from monovalent to trivalent." [pubmed:14755292 "primary-reference"]
is_a: PAR:1029 ! antibody fragment

[Term]
id: PAR:1088
name: tetrabody
def: "A tetrabody is a genetically engineered antibody derivate consisting in four minibodies joined together in a quadrimer which can be from monovalent to quadrivalent." [pubmed:14755292 "primary-reference"]
is_a: PAR:1029 ! antibody fragment

[Term]
id: PAR:1089
name: expression vector sequence
def: "The primary sequence of an expression vector." [pubmed:14755292 "primary-reference"]
related_synonym: "cdna cloning vector sequence" []
exact_synonym: "cDNA vector sequence" []
is_a: PAR:1059 ! cDNA expression material attribute

[Term]
id: PAR:1090
name: ScFv-Fc
def: "A scFv-Fc is a genetically engineered antibody derivate consisting in a fusion molecule between an scFv fragment and an Fc region from an antibody." [pubmed:14755292 "primary-reference"]
is_a: PAR:1029 ! antibody fragment

[Term]
id: PAR:1093
name: competitor
def: "Substance that is competing in a binding assay." [pubmed:14755292 "primary-reference"]
is_a: PAR:0495 ! experimental role

[Term]
id: PAR:1094
name: liquid-liquid extraction
def: "Method to separate compounds based on their relative solubilities in two different immiscible liquids, usually water and an organic solvent. It is an extraction of a substance from one liquid phase into another liquid phase." [pubmed:123456789 "primary-reference"]
related_synonym: "partitioning" []
exact_synonym: "solvent extraction" []
is_a: PAR:1328 ! molecule production method

[Term]
id: PAR:1096
name: molecule description
def: "Free-text description of a molecule. This can for example be a summary of the identity and properties of the molecule." [pubmed:14755292 "primary-reference"]
is_a: PAR:0666 ! participant attribute name

[Term]
id: PAR:1097
name: normalised readout
def: "The normalised value of a numeric experimental readout. The specific type of readout is defined by the associated experimental method, for example an absorbance value from an ELISA." [pubmed:14755292 "primary-reference"]
is_a: PAR:1148 ! readout

[Term]
id: PAR:1099
name: ankyrin repeat
def: "Ankyrin Repeats are tandem modules of about 33 amino acids. The conserved domain structure has been described as side-by-side anti-parallel alpha helices connected by intervening beta hairpin motifs or as beta, alpha, alpha, beta secondary structures or as an L-shaped beta-hairpin and two alpha-helices. The repeats associate to form a higher order structure. Despite sequence variation, the domain core maintains a stable surface of contact residues to mediate protein-protein interactions. The Ankyrin cytoskeletal protein is composed almost entirely of these repeats." [pubmed:14755292 "primary-reference"]
related_synonym: "ankyrin scaffold" []
exact_synonym: "DARPin" []
is_a: PAR:1100 ! engineered protein scaffold

[Term]
id: PAR:1100
name: engineered protein scaffold
def: "An engineered protein scaffold is an amino acid sequence based on a protein framework chosen for its specific biophysical properties." [pubmed:14755292 "primary-reference"]
exact_synonym: "protein scaffold" []
is_a: PAR:0326 ! protein

[Term]
id: PAR:1101
name: preceding interaction
def: "A reference to the preceeding interaction in an experimental workflow." [pubmed:14755292 "primary-reference"]
is_a: PAR:0353 ! cross-reference type

[Term]
id: PAR:1102
name: armadillo repeat
def: "Armadillo repeat proteins are abundant eukaryotic proteins involved in several cellular processes, including signaling, transport, and cytoskeletal regulation. These sequences constitute the starting point for the generation of designed armadillo repeat protein libraries for the selection of peptide binders, exploiting their modular structure and their conserved binding mode." [pubmed:14755292 "primary-reference"]
is_a: PAR:1100 ! engineered protein scaffold

[Term]
id: PAR:1103
name: leucine-rich repeat
def: "Leucin rich repeats are right-handed beta-alpha superhelix used in the design of protein scaffolds." [pubmed:14755292 "primary-reference"]
exact_synonym: "leucine-rich repeat" []
is_a: PAR:1100 ! engineered protein scaffold

[Term]
id: PAR:1104
name: extracellular domain
def: "The part of a membrane protein that is located outside of the cellmembrane." [pubmed:14755292 "primary-reference"]
is_a: PAR:0252 ! biological feature

[Term]
id: PAR:1105
name: hybridoma generation
def: "A hybridoma producing monoclonal antibodies is generated by removing B-cells from an immunised animal and fusing these with myeloma tumor cells that can grow indefinitely in culture (myeloma is a B-cell cancer). This fusion is performed by making the cell membranes more permeable. Hybridoma have to be selected and subsequently cloned by limiting dilution." [pubmed:14755292 "primary-reference"]
related_synonym: "hybridization" []
relationship: part_of PAR:1106 ! antibody production method

[Term]
id: PAR:1106
name: antibody production method
def: "An experimental method used to produce an antibody." [pubmed:123456789 "primary-reference"]
is_a: PAR:1328 ! molecule production method

[Term]
id: PAR:1107
name: kinetics determination
def: "The determination of the kinetics of the molecule." [pubmed:14755292 "primary-reference"]
related_synonym: "kinetics scope" []
is_a: PAR:1314 ! molecule characterisation

[Term]
id: PAR:1108
name: tissue
def: "Name, reference or description of a tissue used in the experiment. A tissue is a group of cells organized into a structural and functional unit; the component cells may be alike (simple tissue) or varied (complex tissue)." [pubmed:14755292 "primary-reference"]
is_a: PAR:1124 ! experimental material attribute

[Term]
id: PAR:1109
name: molecular weight
def: "The molecular weight is the he sum of the relative atomic masses of the constituent atoms of a molecule. It may be only available as an experimentally acquired estimate. The unit is Dalton." [pubmed:14755292 "primary-reference"]
related_synonym: "mass" []
related_synonym: "mw" []
is_a: PAR:0640 ! parameter type

[Term]
id: PAR:1110
name: time of exposure
def: "The time of exposure is the length of time that molecules have to interact e.g a capture reagent and a targeted protein." [pubmed:14755292 "primary-reference"]
is_a: PAR:0640 ! parameter type

[Term]
id: PAR:1111
name: production yield
def: "The amount of product obtained from the production of a biomolecule e.g. in mg of protein per litre of cell culture or the mass of the product obtained in mg." [pubmed:14755292 "primary-reference"]
is_a: PAR:0640 ! parameter type

[Term]
id: PAR:1112
name: complex biological mixture
def: "A biological mixture extracted from an animal or plant." [pubmed:14755292 "primary-reference"]
exact_synonym: "biological mixture" []
is_a: PAR:1147 ! composite interactor

[Term]
id: PAR:1113
name: concentration
def: "Concentration is the measure of how much dissolved substance is contained per unit of solvent volume." [pubmed:14755292 "primary-reference"]
is_a: PAR:0640 ! parameter type

[Term]
id: PAR:1114
name: price
def: "The amount of money for which a product is sold." [pubmed:14755292 "primary-reference"]
related_synonym: "cost" []
is_a: PAR:0640 ! parameter type

[Term]
id: PAR:1115
name: volume
def: "The volume of a solid object is the three-dimensional concept of how much space it occupies." [pubmed:14755292 "primary-reference"]
related_synonym: "V" []
is_a: PAR:0640 ! parameter type

[Term]
id: PAR:1116
name: solubility
def: "Solubility refers to the ability for a given substance to dissolve in a solvent. It is measured in terms of the maximum amount of solute dissolved in a solvent at equilibrium." [pubmed:14755292 "primary-reference"]
is_a: PAR:0640 ! parameter type

[Term]
id: PAR:1117
name: protein affinity reagent
def: "A molecule designed to bind to a protein target." [pubmed:14755292 "primary-reference"]
related_synonym: "par" []
exact_synonym: "affinity reagent" []
is_a: PAR:0500 ! biological role

[Term]
id: PAR:1118
name: experimental control
def: "A molecule being used as an experimental control plays the role of eliminating alternate explanations of experimental results. In a controlled experiment, two virtually identical experiments are conducted. In one of them, the molecule being tested for effect, e.g a candidate drug is used and in the other experiment this is compared to the effect of an alternative substance e.g. placebo." [pubmed:14755292 "primary-reference"]
is_a: PAR:0495 ! experimental role

[Term]
id: PAR:1119
name: negative control
def: "A negative control is known or predicted to give a negative result e.g. molecule A does not bind to molecule B. In a quantitative assay the negative control is often used to define the base-line result, or \"background\", obtained when a test does not produce a measurable positive result. This is subtracted from the test sample results." [pubmed:14755292 "primary-reference"]
is_a: PAR:1118 ! experimental control

[Term]
id: PAR:1120
name: protein affinity reagent target
def: "The target of the protein affinity reagent i.e. typically a protein." [pubmed:14755292 "primary-reference"]
exact_synonym: "par target" []
is_a: PAR:0500 ! biological role

[Term]
id: PAR:1121
name: PSI-PAR term for experimental scope
def: "Cross reference pointing to a term in the experimental scope CV subtype." [pubmed:14681407 "primary-reference"]
exact_synonym: "exp scope" []
is_a: PAR:1068 ! cv term

[Term]
id: PAR:1122
name: protocol reference
def: "Reference of a experiment pointing to a protocol that has been applied. A protocol is the formal plan of an experiment or research activity, including the objective, rationale, design, materials and methods for the conduct of the study; intervention description, and method of data analysis." [pubmed:14755292 "primary-reference"]
is_a: PAR:0353 ! cross-reference type

[Term]
id: PAR:1123
name: molecule library source
def: "The source of the library for example the organism, strain or cell type of a cDNA library." [pubmed:14755292 "primary-reference"]
is_a: PAR:1178 ! molecule library attribute

[Term]
id: PAR:1124
name: experimental material attribute
def: "Attribute name of annotation associated to an experimental material. A material is the specific biological (or chemical) components with which a particular experiment is performed." [pubmed:14755292 "primary-reference"]
is_a: PAR:0665 ! experiment attibute name

[Term]
id: PAR:1125
name: starting material
def: "Biological material used as a starting material in the production of a molecule." [pubmed:14755292 "primary-reference"]
is_a: PAR:0495 ! experimental role

[Term]
id: PAR:1126
name: intermediate product
def: "An intermediate generated in the process of a molecule production." [pubmed:14755292 "primary-reference"]
is_a: PAR:0495 ! experimental role

[Term]
id: PAR:1127
name: expression analysis
def: "The determination of gene or protein expression." [pubmed:14755292 "primary-reference"]
is_a: PAR:1314 ! molecule characterisation

[Term]
id: PAR:1128
name: cross-reactivity assessment
def: "Determination of the molecular entities (wanted an unwanted) bound by a molecule." [pubmed:14755292 "primary-reference"]
exact_synonym: "specificity assessment" []
is_a: PAR:1132 ! binding assessment

[Term]
id: PAR:1129
name: binding site determination
def: "Determination of the region of a molecule B which is bound (or recognized) by a molecule A." [pubmed:14755292 "primary-reference"]
exact_synonym: "binding site determination" []
is_a: PAR:1132 ! binding assessment

[Term]
id: PAR:1130
name: solubility assessment
def: "Analysis of the ability of a molecule to stay in solution under defined experimental conditions" [pubmed:14755292 "primary-reference"]
exact_synonym: "solubility assessment" []
is_a: PAR:1314 ! molecule characterisation

[Term]
id: PAR:1131
name: purity assessment
def: "The analysis of the molecular species present in a given sample in order to assess the level of purity." [pubmed:14755292 "primary-reference"]
exact_synonym: "purity assessment" []
is_a: PAR:1314 ! molecule characterisation

[Term]
id: PAR:1132
name: binding assessment
def: "Determination of the binding characteristics of a molecule with it target molecule, e.g. the affinity of an antibody to a protein." [pubmed:14755292 "primary-reference"]
exact_synonym: "binding assessment" []
is_a: PAR:1314 ! molecule characterisation

[Term]
id: PAR:1133
name: kinetics assessment
def: "Determination of binding complex association and dissociation rates by measurement of the kinetics constants kon (or ka)  (in M-1.min-1) and koff (kd) (in min-1)" [pubmed:14755292 "primary-reference"]
exact_synonym: "kinetics assessment" []
is_a: PAR:1132 ! binding assessment

[Term]
id: PAR:1134
name: affinity determination
def: "Determination of the strenght with which a molecule A binds a molecule B, by measurement, at equilibrium, of the association (or affinity) constant KA (in M-1) or dissociation constant KD (in M)." [pubmed:14755292 "primary-reference"]
exact_synonym: "affinity determination" []
is_a: PAR:1132 ! binding assessment

[Term]
id: PAR:1135
name: stability assement
def: "Analysis of the ability of a molecule to keep its intrinsic structure unchanged under defined physicochemical conditions." [pubmed:14755292 "primary-reference"]
exact_synonym: "stability assessment" []
is_a: PAR:1314 ! molecule characterisation

[Term]
id: PAR:1136
name: elisa sandwich assay
def: "IMM	ENZ	ASS	ELISA sandwich assay" [pubmed:123456789 "primary-reference"]
is_a: PAR:0411 ! enzyme linked immunosorbent assay

[Term]
id: PAR:1137
name: mAb harvesting from hybridoma
def: "The growing of a hybridoma culture and the isolation of mAbs from the hybridoma." [pubmed:14755292 "primary-reference"]
exact_synonym: "mAb harvesting" []
relationship: part_of PAR:1106 ! antibody production method

[Term]
id: PAR:1138
name: expression level analysis
def: "The determination of gene or protein expression level." [pubmed:14755292 "primary-reference"]
is_a: PAR:1127 ! expression analysis

[Term]
id: PAR:1139
name: folding state
def: "Statement about the conformation of a protein." [pubmed:14755292 "primary-reference"]
is_a: PAR:1014 ! molecular state

[Term]
id: PAR:1140
name: unfolded
def: "Protein state which displays no structural conformations." [pubmed:14755292 "primary-reference"]
is_a: PAR:1139 ! folding state

[Term]
id: PAR:1141
name: molecule library size
def: "The number of individual members in a molecule library." [pubmed:14755292 "primary-reference"]
exact_synonym: "library complexity" []
is_a: PAR:1178 ! molecule library attribute

[Term]
id: PAR:1142
name: microarray attribute
def: "Attribute name of annotation associated to a microarray." [pubmed:14755292 "primary-reference"]
is_a: PAR:1124 ! experimental material attribute

[Term]
id: PAR:1143
name: arraying method
def: "The method used to immobilise samples on the array." [pubmed:14755292 "primary-reference"]
related_synonym: "spotting method" []
is_a: PAR:1142 ! microarray attribute

[Term]
id: PAR:1144
name: positive control
def: "A positive control is known or anticipated from previous experience to give a positive result e.g. binding to a certain protein." [pubmed:14755292 "primary-reference"]
is_a: PAR:1118 ! experimental control

[Term]
id: PAR:1145
name: microarray support
def: "The solid phase of the microarray e.g. a glass slide." [pubmed:14755292 "primary-reference"]
related_synonym: "matrix" []
related_synonym: "solid phase" []
is_a: PAR:1142 ! microarray attribute

[Term]
id: PAR:1146
name: expression distribution analysis
def: "The determination of gene or protein expression level." [pubmed:14755292 "primary-reference"]
is_a: PAR:1127 ! expression analysis

[Term]
id: PAR:1147
name: composite interactor
def: "A composite interactor." [pubmed:14755292 "primary-reference"]
is_a: PAR:0313 ! interactor type

[Term]
id: PAR:1148
name: readout
def: "A numeric experimental readout. The specific type of readout, e.g. an ELISA score, is defined by the associated experiment." [pubmed:14755292 "primary-reference"]
related_synonym: "score" []
is_a: PAR:0640 ! parameter type

[Term]
id: PAR:1149
name: serum array
def: "Array spotted with serum samples." [pubmed:14755292 "primary-reference"]
is_a: PAR:1288 ! reverse phase array

[Term]
id: PAR:1150
name: PSI-PAR
def: "Controlled vocabularies developed by HUPO Proteomic standard initiative for Protein Affinity Reagents." [pubmed:14755292 "primary-reference"]
xref_analog: id-validation-regexp:\"PAR\:[0-9\]\{4}\" "ANNOTATION"
xref_analog: search-url: http\://www.ebi.ac.uk/ontology-lookup/?termId=$\{ac} "ANNOTATION"
is_a: PAR:0444 ! database citation

[Term]
id: PAR:1151
name: microarray
def: "Name, reference or description of a microarray. A collection of microscopic samples, such as genes, proteins and tissues, arrayed on a solid surface e.g. by covalent attachment to a chemical matrix. Microarrays allows for the simultaneous analysis of many samples facilitating quick and efficient generation of experimental data." [pubmed:14755292 "primary-reference"]
is_a: PAR:1142 ! microarray attribute

[Term]
id: PAR:1152
name: molecule modification
def: "The chemical or enzymatic modification of a molecule." [pubmed:14755292 "primary-reference"]
is_a: PAR:1316 ! experimental scope

[Term]
id: PAR:1153
name: synovial fluid
def: "Synovial fluid is a thick, stringy fluid found in the cavities of synovial joints. Synovial fluid reduces friction between the articular cartilage and other tissues in joints to lubricate and cushion them during movement." [pubmed:14755292 "primary-reference"]
is_a: PAR:1112 ! complex biological mixture

[Term]
id: PAR:1154
name: generation product
def: "The key product generated in a molecule production experiment e.g. a protein expressed by cDNA cloning." [pubmed:14755292 "primary-reference"]
is_a: PAR:0495 ! experimental role

[Term]
id: PAR:1155
name: cell lysate
def: "A solution containing the contents of lysed cells. Lysis refers to the death of a cell by breaking of the cellular membrane, often by viral or osmotic mechanisms." [pubmed:14755292 "primary-reference"]
is_a: PAR:1112 ! complex biological mixture

[Term]
id: PAR:1156
name: growth medium
def: "A growth medium or culture medium is a liquid or gel designed to support the growth of microorganisms, such as bacteria or yeast, or cells derived from plants or animals. The most common growth media for microorganisms are nutrient broths and agar plates." [pubmed:14755292 "primary-reference"]
is_a: PAR:1147 ! composite interactor

[Term]
id: PAR:1158
name: serum
def: "The clear yellowish fluid obtained upon separating whole blood into its solid and liquid components after it has been allowed to clot. Blood serum from the tissues of immunized animals, contains antibodies to one or more specific disease antigens, and when injected into humans or other animals, it can transfer immunity to those diseases." [pubmed:14755292 "primary-reference"]
is_a: PAR:1112 ! complex biological mixture

[Term]
id: PAR:1160
name: results comment
def: "Comment on results for public view, for example a clarification, highlighting or summary of the results." [pubmed:14755292 "primary-reference"]
is_a: PAR:0664 ! interaction attribute name

[Term]
id: PAR:1162
name: hybridoma
def: "Name, reference or description of a hybridoma. Hybridomas are cells that have been engineered to It proliferate and produce a continuous supply of a specific monoclonal antibody. They are produced in the laboratory from the fusion of an antibody-producing lymphocyte and a nonantibody-producing cancer cell, usually a myeloma or lymphoma." [pubmed:14755292 "primary-reference"]
is_a: PAR:1124 ! experimental material attribute

[Term]
id: PAR:1163
name: cell-display
def: "KW1	LIB	SCREEN	Cell-display" [pubmed:123456789 "primary-reference"]
is_a: PAR:0034 ! display technology

[Term]
id: PAR:1164
name: cell subcloning  by limited dilution
def: "KW1	CELL	SELEC	cell subcloning  by limited dilution" [pubmed:123456789 "primary-reference"]
is_a: PAR:1048 ! cell cloning

[Term]
id: PAR:1165
name: continuous cell subcloning
def: "KW1	CELL	SELEC	continuous cell subcloning" [pubmed:123456789 "primary-reference"]
is_a: PAR:1048 ! cell cloning

[Term]
id: PAR:1167
name: dna chain termination sequencing method (sanger)
def: "NUC	CHEM	SEQ	DNA Chain termination sequencing method (Sanger)	Sanger sequencing 	FIX:0000877" [pubmed:123456789 "primary-reference"]
is_a: PAR:0078 ! nucleotide sequence identification

[Term]
id: PAR:1168
name: native/denatured state
def: "Statement about the native/denatured conformation of the protein." [pubmed:14755292 "primary-reference"]
is_a: PAR:1014 ! molecular state

[Term]
id: PAR:1169
name: lysate array
def: "Array spotted with cell lysates. Are typically used to investigate protein expression in cells or cell lines." [pubmed:14755292 "primary-reference"]
is_a: PAR:1288 ! reverse phase array

[Term]
id: PAR:1170
name: tissue array
def: "A collection of tissues are spot on a surface and can be screened using common probes, such as DNA, RNA, peptide, protein and antibodies. Tissue arrays permit a rapid and large-scale molecular analysis of various tissue specimens in parallel and the determination of the tissue specificity of the probe." [pubmed:14755292 "primary-reference"]
related_synonym: "tissue microarray" []
related_synonym: "tissue-chips" []
is_a: PAR:0678 ! antibody array

[Term]
id: PAR:1171
name: folded
def: "A state in which a protein has adopted a structured, stable and ordered conformation." [pubmed:14755292 "primary-reference"]
is_a: PAR:1139 ! folding state

[Term]
id: PAR:1172
name: protocol
def: "Free text protocol or alternatively the name of reference (e.g. url) of a protocol in arbitrary format. A protocol is the formal plan of an experiment or research activity, including the objective, rationale, design, materials and methods for the conduct of the study; intervention description, and method of data analysis." [pubmed:14755292 "primary-reference"]
is_a: PAR:0665 ! experiment attibute name

[Term]
id: PAR:1173
name: plasma array
def: "Array spotted with plasma samples." [pubmed:14755292 "primary-reference"]
is_a: PAR:1288 ! reverse phase array

[Term]
id: PAR:1176
name: unknown method
def: "The method is not known." [pubmed:14755292 "primary-reference"]
is_a: PAR:0001 ! interaction detection method
is_a: PAR:0002 ! participant identification method

[Term]
id: PAR:1177
name: expression construct sequence
def: "The primary sequence of a cDNA construct." [pubmed:14755292 "primary-reference"]
is_a: PAR:1059 ! cDNA expression material attribute

[Term]
id: PAR:1178
name: molecule library attribute
def: "Attribute name of annotation associated to molecul library such as a collection of small molecules or cDNA clones." [pubmed:14755292 "primary-reference"]
is_a: PAR:1124 ! experimental material attribute

[Term]
id: PAR:1179
name: non-aggregated
def: "Not part of any cluster of the same protein." [pubmed:14755292 "primary-reference"]
is_a: PAR:1067 ! aggregation state

[Term]
id: PAR:1180
name: maxam-gilbert  dna sequencing
def: "NUC	CHEM	SEQ	Maxam-Gilbert  DNA sequencing	Maxam-Gilbert sequencing	FIX:0000875" [pubmed:123456789 "primary-reference"]
is_a: PAR:0056 ! full identification by sequencing

[Term]
id: PAR:1181
name: immunologic adjuvant
def: "In immunology, an adjuvant is an agent that may stimulate the immune system and increase the response to a vaccine, without having any specific antigenic effect in itself. Known adjuvants include oils, aluminum salts and virosomes." [pubmed:14755292 "primary-reference"]
is_a: PAR:1184 ! secondary reagent

[Term]
id: PAR:1184
name: secondary reagent
def: "A reagent is a chemical that has general laboratory application and that is not labelled or otherwise intended for a specific experiment. General purpose reagents include antibody second reagents, detection reagents, cytological preservatives, fixatives and adhesives, tissue processing reagents, isotonic solutions, and pH buffers." [pubmed:123456789 "primary-reference"]
is_a: PAR:0495 ! experimental role

[Term]
id: PAR:1186
name: secondary protein affinity reagent
def: "A secondary antibody is an antibody that binds to primary antibodies or antibody fragments. They are typically labeled with probes that make them useful for detection, purification or cell sorting applications. Secondary antibodies may be polyclonal or monoclonal, and are available with specificity for whole Ig molecules or antibody fragments such as the Fc or Fab regions. Specific secondary antibodies are usually chosen to work in specific laboratory applications. They are selected according to the source of the primary antibody, the class of the primary antibody (e.g., IgG or IgM), and the kind of label which is preferred." [pubmed:14755292 "primary-reference"]
related_synonym: "detection antibody" []
exact_synonym: "secondary PAR" []
is_a: PAR:1184 ! secondary reagent

[Term]
id: PAR:1188
name: dna chemical sequencing
def: "NUC	CHEM	SEQ	DNA Chemical sequencing	DNA sequencing	FIX:0000873" [pubmed:123456789 "primary-reference"]
is_a: PAR:0056 ! full identification by sequencing

[Term]
id: PAR:1189
name: detection limit
def: "The lowest substance quantity or signal strength that can be distinguished from the absence of that substance or signal." [pubmed:14755292 "primary-reference"]
is_a: PAR:0640 ! parameter type

[Term]
id: PAR:1190
name: immunogen
def: "Substance that, when injected or absorbed into animal tissues, stimulates an immune response typically the production of antibodies. Immunogens, or antigens, are usually proteins or polysaccharides." [pubmed:14755292 "primary-reference"]
related_synonym: "antigen" []
is_a: PAR:0495 ! experimental role

[Term]
id: PAR:1191
name: c-terminal amino acid analysis
def: "AA	CHEM	SEQ	 C-terminal amino acid analysis	C-terminal sequencing 	FIX:0000718" [pubmed:123456789 "primary-reference"]
is_a: PAR:0433 ! partial identification of protein sequence

[Term]
id: PAR:1192
name: nucleic acid fragment
def: "subpart of a longer nucleic acid" [pubmed:14755292 "primary-reference"]
relationship: part_of PAR:0318 ! nucleic acid

[Term]
id: PAR:1197
name: molecular weight determination
def: "Determination of the molecular weight (in g.mol-1 or Dalton (Da))." [pubmed:14755292 "primary-reference"]
related_synonym: "mass determination" []
exact_synonym: "MW determination" []
is_a: PAR:1314 ! molecule characterisation

[Term]
id: PAR:1207
name: expression vector
def: "Name, reference or description of a expression vector. An expression vector is generally a plasmid and is introduced into a target cell, which cellular transcription and translation machinery is used for the expression of a specific gene." [pubmed:14755292 "primary-reference"]
related_synonym: "cdna cloning vector" []
is_a: PAR:1059 ! cDNA expression material attribute

[Term]
id: PAR:1218
name: agarose gel electrophoresis
def: "KW1	ELECT	SEP	agarose gel electrophoresis	agarose gel electrophoresis	sep:00171" [pubmed:123456789 "primary-reference"]
is_a: PAR:1320 ! electrophoresis

[Term]
id: PAR:1220
name: electrochemiluminescence
def: "KW1	KW2	DETEC	electrochemiluminescence	electrogenerated chemiluminescence	REX:0000295" [pubmed:123456789 "primary-reference"]
is_a: PAR:0013 ! biophysical

[Term]
id: PAR:1221
name: fluorescence quenching
def: "KW1	KW2	DETEC	fluorescence quenching" [pubmed:123456789 "primary-reference"]
is_a: PAR:0051 ! fluorescence technology

[Term]
id: PAR:1222
name: proteolytic digestion
def: "AA	ENZ	HYDROL	proteolytic digestion	Enzyme digestion	PRIDE:0000024" [pubmed:123456789 "primary-reference"]
is_a: PAR:1328 ! molecule production method

[Term]
id: PAR:1225
name: enzyme chemiluminescence (ecl)
def: "KW1	ENZ	DETEC	enzyme chemiluminescence (ECL)" [pubmed:123456789 "primary-reference"]
is_a: PAR:0411 ! enzyme linked immunosorbent assay

[Term]
id: PAR:1230
name: raw data
def: "A reference, e.g. a url, to raw data for example a gel image or HPLC chromatogram. Raw data corresponds to the data which was directly acquired during the course of an experiment." [pubmed:14755292 "primary-reference"]
is_a: PAR:0664 ! interaction attribute name

[Term]
id: PAR:1233
name: parent gene
def: "A reference to the gene encoding the specific protein or peptide." [pubmed:14755292 "primary-reference"]
is_a: PAR:0353 ! cross-reference type

[Term]
id: PAR:1247
name: polyclonal antibody
def: "A polyclonal antibody is a heterogeneous antibody derived from a host organism, typically produced by immunization of a suitable mammal with an antigen which induces B-lymphocytes to produce IgG immunoglobulins specific for the antigen. The resulting collection of antibodies has specificity for different epitopes of the antigen." [pubmed:14755292 "primary-reference"]
exact_synonym: "pAb" []
is_a: PAR:1009 ! intact antibody

[Term]
id: PAR:1250
name: aptamer
def: "Nucliec acid aptamers are double-stranded DNA or single-stranded RNA oligonucleotide sequences which were selected from random pools because of their capacity to recognize target molecules. Fundamentally distinct from antibodies, aptamers mimic their properties." [pubmed:14755292 "primary-reference"]
is_a: PAR:0680 ! single stranded deoxyribonucleic acid

[Term]
id: PAR:1252
name: ss rna
def: "single stand RNS" [pubmed:14755292 "primary-reference"]
exact_synonym: "ss rna" []
is_a: PAR:0320 ! ribonucleic acid

[Term]
id: PAR:1263
name: handling instructions
def: "Handling instructions for a biomolecule (e.g. \"The antibody solution should be gently mixed before use\")." [pubmed:14755292 "primary-reference"]
is_a: PAR:0666 ! participant attribute name

[Term]
id: PAR:1264
name: stability info
def: "A statement about the stability of the molecule under certain conditions, including for example pH, temperature and detergent. The stability corresponds to the quality of being free from change or variation over time or not taking part readily in chemical change." [pubmed:14755292 "primary-reference"]
is_a: PAR:0666 ! participant attribute name

[Term]
id: PAR:1275
name: purity
def: "The purity corresponds to a quantitative assessment of the homogeneity or uniformity of a mixture. It refers to the degree of being free of contaminants or heterogeneous components." [pubmed:14755292 "primary-reference"]
is_a: PAR:0640 ! parameter type

[Term]
id: PAR:1278
name: solubility info
def: "A statement about the solubility of the molecule under certain conditions, including for example pH, temperature and detergent." [pubmed:14755292 "primary-reference"]
is_a: PAR:0666 ! participant attribute name

[Term]
id: PAR:1279
name: antibody
def: "An antibody is any of the structurally related proteins that function as immunoglobulins. They are divided into five classes (IGA, IGD, IGE, IGG, IGM) on the basis of structure and biological activity." [pubmed:14755292 "primary-reference"]
related_synonym: "immunoglobulin" []
is_a: PAR:0326 ! protein

[Term]
id: PAR:1281
name: recombinant protein expression
def: "AA	REC	SYNT	recombinant protein expression	inferred from protein expression	ECO:0000010" [pubmed:123456789 "primary-reference"]
is_a: PAR:1046 ! protein expression

[Term]
id: PAR:1288
name: reverse phase array
def: "In reverse phase array, the target sample is spotTED onto the array." [pubmed:15671044 "primary-reference"]
is_a: PAR:0678 ! antibody array

[Term]
id: PAR:1296
name: exact binding site
def: "The subsequence of a protein that is involved the binding of another molecule. The binding site can be linear or conformational i.e. structurally proximal residues that might be discontinous in the primary sequence." [pubmed:14755292 "primary-reference"]
related_synonym: "epitope" []
related_synonym: "paratope" []
is_a: PAR:0117 ! binding site

[Term]
id: PAR:1308
name: quantification
def: "Measurement of the amount of a particular molecule or group of molecules present in a given sample." [pubmed:14755292 "primary-reference"]
exact_synonym: "quantification" []
is_a: PAR:1314 ! molecule characterisation

[Term]
id: PAR:1309
name: library screening
def: "The iterative process for the selection of entities based on particular characteristics from a broad population, for example the affinity of a reagent for a target protein." [pubmed:14755292 "primary-reference"]
related_synonym: "library panning" []
related_synonym: "library selection" []
is_a: PAR:1328 ! molecule production method

[Term]
id: PAR:1313
name: smiles string
def: "The SMILES (simplified molecular input line entry specification) string is an alphanumerical representation of chemical structure (http://en.wikipedia.org/wiki/SMILES)." [pubmed:14755292 "primary-reference"]
is_a: PAR:0666 ! participant attribute name

[Term]
id: PAR:1314
name: molecule characterisation
def: "The determination of structural and biophysical properties of molecular entities." [pubmed:14755292 "primary-reference"]
related_synonym: "molecule quality control" []
is_a: PAR:1316 ! experimental scope

[Term]
id: PAR:1316
name: experimental scope
def: "The scope or purpose of an experiment." [pubmed:14755292 "primary-reference"]
relationship: part_of PAR:1004 ! PROTEIN AFFINITY REAGENT CV

[Term]
id: PAR:1317
name: molecule production
def: "An experimental process that is applied in the production of a molecule. This includes purification steps necessary to obtain the molecule in a form that can be used." [pubmed:14755292 "primary-reference"]
related_synonym: "production" []
is_a: PAR:1316 ! experimental scope

[Term]
id: PAR:1320
name: electrophoresis
def: "electrophoresis" [pubmed:123456789 "primary-reference"]
is_a: PAR:0001 ! interaction detection method

[Term]
id: PAR:1323
name: biosapiens annotations term for secondary structure
def: "Cross reference pointing to a \"Biosapiens Annotations\" (BS) CV term in the \"secondary structure\" branch (BS:00003)." [pubmed:14755292 "primary-reference"]
exact_synonym: "bs sec. struct. term" []
is_a: PAR:1071 ! biosapiens annotations term

[Term]
id: PAR:1324
name: gene ontology term
def: "Cross reference pointing to a Gene Ontology CV term." [pubmed:14681407 "primary-reference"]
is_a: PAR:1068 ! cv term

[Term]
id: PAR:1326
name: biosapiens annotations cv
def: "Controlled vocabulary for Biosapiens Annotations (BS) (http://www.ebi.ac.uk/ontology-lookup/browse.do?ontName=BS)." [pubmed:14755292 "primary-reference"]
exact_synonym: "bs" []
xref_analog: id-validation-regexp:\"MI\:[0-9\]\{4}\" "ANNOTATION"
xref_analog: search-url: http\://www.ebi.ac.uk/ontology-lookup/?termId=$\{ac} "ANNOTATION"
is_a: PAR:0447 ! feature database

[Term]
id: PAR:1328
name: molecule production method
def: "This is an experimental method that is used to produce a molecule." [pubmed:123456789 "primary-reference"]
relationship: part_of PAR:1004 ! PROTEIN AFFINITY REAGENT CV

[Typedef]
id: part_of
name: part of
is_transitive: true