[Sbfc-svn] SF.net SVN: sbfc:[676] trunk

[<nik...@us...>]

Revision: 676
          http://sourceforge.net/p/sbfc/code/676
Author:   niko-rodrigue
Date:     2016-07-19 14:37:14 +0000 (Tue, 19 Jul 2016)
Log Message:
-----------
switch to java 1.7 + cleaned the old jsbml jar file + added a class to be able to load and query an OBO file + added the MI obo file

Modified Paths:
--------------
    trunk/build.xml
    trunk/lib/sbfc-1.3.7.jar

Added Paths:
-----------
    trunk/src/org/sbfc/ontology/
    trunk/src/org/sbfc/ontology/OboOntology.java
    trunk/src/org/sbfc/ontology/mi.obo

Removed Paths:
-------------
    trunk/lib/jsbml-1.2-SNAPSHOT-20160317-with-dependencies.jar

Modified: trunk/build.xml
===================================================================
--- trunk/build.xml	2016-07-19 06:52:59 UTC (rev 675)
+++ trunk/build.xml	2016-07-19 14:37:14 UTC (rev 676)
@@ -200,8 +200,8 @@
            debug="${debug}"
            optimize="${optimize}"
            verbose="${verbose}"
-           source="1.6"
-           target="1.6"
+           source="1.7"
+           target="1.7"
            classpathref="sbfc.classpath">
 		</javac>
 	</target>

Deleted: trunk/lib/jsbml-1.2-SNAPSHOT-20160317-with-dependencies.jar
===================================================================
(Binary files differ)

Modified: trunk/lib/sbfc-1.3.7.jar
===================================================================
(Binary files differ)

Added: trunk/src/org/sbfc/ontology/OboOntology.java
===================================================================
--- trunk/src/org/sbfc/ontology/OboOntology.java	                        (rev 0)
+++ trunk/src/org/sbfc/ontology/OboOntology.java	2016-07-19 14:37:14 UTC (rev 676)
@@ -0,0 +1,192 @@
+/*
+ * ----------------------------------------------------------------------------
+ * This file is part of JSBML. Please visit <http://sbml.org/Software/JSBML>
+ * for the latest version of JSBML and more information about SBML.
+ *
+ * Copyright (C) 2009-2016 jointly by the following organizations:
+ * 1. The University of Tuebingen, Germany
+ * 2. EMBL European Bioinformatics Institute (EBML-EBI), Hinxton, UK
+ * 3. The California Institute of Technology, Pasadena, CA, USA
+ * 4. The University of California, San Diego, La Jolla, CA, USA
+ * 5. The Babraham Institute, Cambridge, UK
+ * 6. Boston University, Boston, MA, USA
+ * 
+ * This library is free software; you can redistribute it and/or modify it
+ * under the terms of the GNU Lesser General Public License as published by
+ * the Free Software Foundation. A copy of the license agreement is provided
+ * in the file named "LICENSE.txt" included with this software distribution
+ * and also available online as <http://sbml.org/Software/JSBML/License>.
+ * ----------------------------------------------------------------------------
+ */
+package org.sbfc.ontology;
+
+import java.io.BufferedReader;
+import java.io.FileReader;
+import java.io.InputStreamReader;
+import java.util.HashSet;
+import java.util.NoSuchElementException;
+import java.util.Set;
+
+import org.biojava.nbio.ontology.Ontology;
+import org.biojava.nbio.ontology.io.OboParser;
+import org.sbml.jsbml.ontology.Term;
+import org.sbml.jsbml.ontology.Triple;
+
+/**
+ * <p>
+ * Methods for interacting with an OBO Ontology  terms. This class
+ * uses the BioJava classes for working with ontologies and contains static
+ * classes to represent single {@link Term}s and {@link Triple}s of subject,
+ * predicate, and object, where each of these three entities is again an
+ * instance of {@link Term}. The classes {@link Term} and {@link Triple}
+ * basically wrap the underlying functions from BioJava, but the original
+ * {@link Object}s can be accessed via dedicated get methods. Furthermore, the
+ * {@link Ontology} from BioJava, which is used in this class, can be obtained
+ * using the method {@link #getOntology()}.
+ * 
+ * @author Nicolas Rodriguez
+ */
+public class OboOntology {
+
+  
+  /**
+   * Ontology file
+   */
+  private Ontology ontology;
+
+  /**
+   * Used to store converted BioJava terms
+   */
+  private Set<Term> terms;
+
+  /**
+   * 
+   * @param ontologyPath path to the ontology file
+   */
+  public OboOntology(String ontologyPath) 
+  {
+    OboParser parser = new OboParser(); // TODO - have a constructor to be able to pass a file or inputStream.
+    
+    try {
+      //InputStream is = OboOntology.class.getResourceAsStream(ontologyPath);
+      FileReader is = new FileReader(ontologyPath);
+      
+      ontology = parser.parseOBO(new BufferedReader(is), "OBO Ontology", "Ontology"); // new InputStreamReader(is)
+      // convert between BioJava's Terms and our Terms.
+      terms = new HashSet<Term>();
+    } catch (Throwable e) {
+      e.printStackTrace();
+    }
+
+  }
+
+  /**
+   * Checks the format of the given string.
+   * 
+   * @param ontologyTermId an ontology term id
+   * @return {@code true} if the given String is not null and not empty.
+   */
+  public boolean checkTerm(String ontologyTermId) {
+    return (ontologyTermId != null) && (ontologyTermId.trim().length() > 0);
+  }
+
+  /**
+   * Grants access to the underlying {@link Ontology} form BioJava.
+   * 
+   * @return the underlying {@link Ontology} form BioJava.
+   */
+  public Ontology getOntology() {
+    return ontology;
+  }
+
+  /**
+   * Gets the OboOntology term with the id 'cboTerm'.
+   * 
+   * @jsbml.warning The methods will throw NoSuchElementException if the id is
+   *                not found or null.
+   * 
+   * @param cboTerm
+   *            the id of the OboOntology term to search for.
+   * @return the OboOntology term with the id 'cboTerm'.
+   * @throws NoSuchElementException
+   *             if the id is not found or null.
+   */
+  public Term getTerm(String cboTerm) {
+    return new Term(ontology.getTerm(cboTerm));
+  }
+
+  /**
+   * Return the set of terms of the OboOntology.
+   * 
+   * <p>
+   * This methods return only Term object and no Triple object that represent
+   * the relationship between terms. If you want to access the full set of
+   * {@link org.biojava.nbio.ontology.Term} containing also the
+   * {@link org.biojava.nbio.ontology.Triple}, use {@link OboOntology#getOntology()} to get
+   * the underlying biojava object.
+   * 
+   * @return the set of terms of the OboOntology.
+   */
+  public Set<Term> getTerms() {
+    if (terms.size() < ontology.getTerms().size()) {
+      for (org.biojava.nbio.ontology.Term term : ontology.getTerms()) {
+        if (term instanceof org.biojava.nbio.ontology.Term) {
+          terms.add(new Term(term));
+        }
+      }
+    }
+    return terms;
+  }
+
+  /**
+   * Returns a set of Triple which match the supplied subject, predicate and
+   * object.
+   * 
+   * <p>
+   * If any of the parameters of this method are null, they are treated as
+   * wildcard.
+   * 
+   * @param subject
+   *            the subject to search for, or {@code null}.
+   * @param predicate
+   *            the relationship to search for, or {@code null}.
+   * @param object
+   *            the object to search for, or {@code null}.
+   * @return a set of Triple which match the supplied subject, predicate and
+   *         object.
+   * 
+   * @see org.biojava.nbio.ontology.Ontology#getTriples(org.biojava.nbio.ontology.Term,
+   *      org.biojava.nbio.ontology.Term, org.biojava.nbio.ontology.Term)
+   */
+  public Set<Triple> getTriples(Term subject, Term predicate,
+    Term object) {
+    Set<Triple> triples = new HashSet<Triple>();
+    for (org.biojava.nbio.ontology.Triple triple : ontology.getTriples(
+      subject != null ? subject.getTerm() : null,
+        object != null ? object.getTerm() : null,
+          predicate != null ? predicate.getTerm() : null)) {
+      triples.add(new Triple(triple));
+    }
+    return triples;
+  }
+
+  /**
+   * Test main class
+   * 
+   * @param args program arguments
+   */
+  public static void main(String[] args) {
+    OboOntology ontology = new OboOntology("src/org/sbfc/ontology/mi.obo");
+    
+    int i = 0;
+    for (Term term : ontology.getTerms()) {
+      System.out.println(Term.printTerm(term));
+      i++;
+    }
+    System.out.println("\nThere is " + i + " terms in this ontology.");
+
+//    System.out.println("Get CellDeath by name = " + Term.printTerm(getTerm("CellDeath")));
+//    System.out.println("Get CellDeath by id  = " + Term.printTerm(getTerm("MI:1234567")));
+  }
+
+}

Added: trunk/src/org/sbfc/ontology/mi.obo
===================================================================
--- trunk/src/org/sbfc/ontology/mi.obo	                        (rev 0)
+++ trunk/src/org/sbfc/ontology/mi.obo	2016-07-19 14:37:14 UTC (rev 676)
@@ -0,0 +1,16021 @@
+format-version: 1.4
+date: 18:07:2016 10:23
+saved-by: rodrigue
+auto-generated-by: The OWL API (version 1.0-rc)
+id_space: oboInOwl http://www.geneontology.org/formats/oboInOwl#
+id_space: mi http://purl.obolibrary.org/obo/mi.owl#
+id_space: rdfs http://www.w3.org/2000/01/rdf-schema#
+id_space: owl http://www.w3.org/2002/07/owl#
+id_space: mi2 http://purl.obolibrary.org/obo/mi#
+id_space: obo http://purl.obolibrary.org/obo/
+id_space: rdf http://www.w3.org/1999/02/22-rdf-syntax-ns#
+id_space: xsd http://www.w3.org/2001/XMLSchema#
+remark: short labels are reported as PSI-MI-short synonyms that are created when a term is more than 20 characteres long.
+remark: The PSI MI schema defines short labels for controlled vocabulary terms
+remark: Each of the top level terms in this file is the root term of an independent controlled vocabulary
+remark: The last accession number used in this file is stored in a separate file,
+remark: The maintenance of this file is ensured by Sandra Orchard or...@eb... and Luisa Montecchi Palazzi lu...@eb...
+remark: publisher: This file is published by the PSI MI working group see http://psidev.info/MI
+remark: coverage: This file collect controlled vocabularies describing different aspects of molecular interactions.
+remark: mapping an element of the PSI Molecular Interaction XML schema.
+remark: psi-mi.lastac. It MUST be updated when this file is updated.
+remark: Notes:
+remark: formalized in a mapping file available at http://www.psidev.info/files/validator/xml/MI-CVMapping.xml.
+remark: The correct use of these vocabularies in the PSI Molecular Interaction XML schema is
+remark: CVversion: 2.5.5
+date: 20:06:2016 14:19
+saved-by: ppm
+hasOBOFormatVersion: 1.2
+default-namespace: PSI-MI
+auto-generated-by: OBO-Edit 2.3.1
+versionInfo: 2016-07-18
+
+
+
+[Typedef]
+id: contains
+name: contains
+namespace: mi2
+comment: The inverse relationship to "part of".
+is_transitive: true
+is_metadata_tag: false
+def: 'Entity A' contains 'Entity B' implies that 'Entity B' is a part of the structure of 'Entity A'.
+hasOBONamespace: PSI-MOD
+id2: contains
+
+[Typedef]
+id: derives_from
+name: derives from
+namespace: mi2
+is_transitive: true
+is_metadata_tag: false
+def: 'Entity A' derives_from 'Entity B' implies that 'Entity A' is chemically derived from 'Entity B'.
+hasOBONamespace: PSI-MOD
+id2: derives_from
+
+[Typedef]
+id: has_functional_parent
+name: has functional parent
+namespace: mi2
+comment: This relationship indicates that the formula and mass of the child are not inherited from the mass of the parent.
+is_transitive: true
+is_metadata_tag: false
+def: 'Entity A' has_functional_parent 'Entity B' implies that 'Entity B' has at least one chacteristic group from which 'Entity A' can be derived by functional modification.
+hasOBONamespace: PSI-MOD
+id2: has_functional_parent
+
+[Typedef]
+id: part_of
+name: part of
+namespace: mi2
+is_transitive: true
+is_metadata_tag: false
+def: 'Entity A' part_of 'Entity B' implies that 'Entity A' is a part of the structure of 'Entity B'.
+hasOBONamespace: PSI-MI
+id2: part_of
+
+
+
+[Term]
+id: MI:0000
+name: molecular interaction
+namespace: obo
+def: Controlled vocabularies originally created for protein protein interactions, extended to other molecules interactions.
+hasExactSynonym: mi
+hasOBONamespace: PSI-MI
+id2: MI:0000
+
+[Term]
+id: MI:0001
+name: interaction detection method
+namespace: obo
+relationship: part_of MI_0000
+
+hasExactSynonym: interaction detect
+def: Method to determine the interaction.
+hasOBONamespace: PSI-MI
+id2: MI:0001
+
+[Term]
+id: MI:0002
+name: participant identification method
+namespace: obo
+relationship: part_of MI_0000
+
+def: Method to determine the molecules involved in the interaction.
+hasExactSynonym: participant detection
+hasExactSynonym: participant ident
+hasOBONamespace: PSI-MI
+id2: MI:0002
+
+[Term]
+id: MI:0003
+name: feature detection method
+namespace: obo
+relationship: part_of MI_0000
+
+def: Method to determine the features of the proteins involved in the interaction.
+hasExactSynonym: feature detection
+hasOBONamespace: PSI-MI
+id2: MI:0003
+
+[Term]
+id: MI:0004
+name: affinity chromatography technology
+namespace: obo
+is_a: MI_0091
+is_a: MI_0400
+hasExactSynonym: Affinity purification
+hasExactSynonym: affinity chrom
+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.
+hasOBONamespace: PSI-MI
+id2: MI:0004
+
+[Term]
+id: MI:0005
+name: alanine scanning
+namespace: obo
+is_a: MI_0810
+def: This approach is used to identify the residues that are involved in an interaction. Several variants of the native protein are prepared by sequentially  mutating each residue of interest to an alanine. The mutated proteins are expressed and probed in the binding assay.
+hasOBONamespace: PSI-MI
+id2: MI:0005
+
+[Term]
+id: MI:0006
+name: anti bait coimmunoprecipitation
+namespace: obo
+is_a: MI_0019
+def: A specific antibody for the molecule of interest (bait) is available, this is used to generate a high affinity resin to capture the endogenous bait present in a sample.
+hasExactSynonym: anti bait coip
+hasOBONamespace: PSI-MI
+id2: MI:0006
+
+[Term]
+id: MI:0007
+name: anti tag coimmunoprecipitation
+namespace: obo
+is_a: MI_0019
+hasExactSynonym: anti tag coip
+def: A specific antibody for the molecule of interest is not available, therefore the bait protein is expressed as a hybrid protein fused to a tag peptide/protein for which efficient and specific antibodies or a specific ligand are available.
+hasOBONamespace: PSI-MI
+id2: MI:0007
+
+[Term]
+id: MI:0008
+name: array technology
+namespace: obo
+is_a: MI_0400
+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.
+hasOBONamespace: PSI-MI
+id2: MI:0008
+
+[Term]
+id: MI:0009
+name: bacterial display
+namespace: obo
+is_a: MI_0054
+is_a: MI_0034
+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.
+hasOBONamespace: PSI-MI
+id2: MI:0009
+
+[Term]
+id: MI:0010
+name: beta galactosidase complementation
+namespace: obo
+is_a: MI_0090
+def: Beta-galactosidase activity can be used to monitor the interaction of chimeric proteins. Pairs of inactive beta gal deletion mutants are capable of complementing to restore activity when fused to interacting protein partners. Critical to the success of this system is the choice of two poorly complementing mutant moieties, since strongly complementing mutants spontaneously assemble and produce functional beta-gal activity detectable in absence of any fused protein fragment.
+hasExactSynonym: beta galactosidase
+hasOBONamespace: PSI-MI
+id2: MI:0010
+
+[Term]
+id: MI:0011
+name: beta lactamase complementation
+namespace: obo
+is_a: MI_0090
+def: This strategy is based on a protein fragment complementation assay (PCA) of the enzyme TEM-1 beta-lactamase. The approach includes a simple colorimetric in vitro assays using the cephalosporin nitrocefin and assays in intact cells using the fluorescent substrate CCF2/AM. The combination of in vitro colorimetric and in vivo fluorescence assays of beta-lactamase in mammalian cells permits a variety of sensitive and high-throughput large-scale applications.
+hasExactSynonym: beta lactamase
+hasOBONamespace: PSI-MI
+id2: MI:0011
+
+[Term]
+id: MI:0012
+name: bioluminescence resonance energy transfer
+namespace: obo
+is_a: MI_0051
+hasExactSynonym: BRET
+hasExactSynonym: bret
+hasExactSynonym: LRET
+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).
+hasOBONamespace: PSI-MI
+id2: MI:0012
+
+[Term]
+id: MI:0013
+name: biophysical
+namespace: obo
+is_a: MI_0045
+def: The application of physical principles and methods to biological experiments.
+hasOBONamespace: PSI-MI
+id2: MI:0013
+
+[Term]
+id: MI:0014
+name: adenylate cyclase complementation
+namespace: obo
+is_a: MI_0090
+hasExactSynonym: bacterial two-hybrid
+hasExactSynonym: adenylate cyclase
+def: Adenylate cyclase is encoded by the cyaA gene and contains a catalytic domain which can be proteolytically cleaved into two complementary fragments, T25 and T18, which remain associated in the presence of calmodulin in a fully active ternary complex. In the absence of calmodulin, the mixture of the two fragments does not exhibit detectable activity, suggesting that the two fragments do not associate. When expressed in an adenylate cyclase-deficient E. coli strain (E. coli lacks calmodulin or calmodulin-related proteins), the T25 and T18 fragments fused to putative interacting proteins are brought into close association which result in cAMP synthesis. The level of reconstructed adenylate cyclase can be estimated by monitoring the expression of a cAMP dependent reporter gene. The T25 tagged protein is generally regarded as the bait, the T18 as the prey.
+hasOBONamespace: PSI-MI
+id2: MI:0014
+
+[Term]
+id: MI:0016
+name: circular dichroism
+namespace: obo
+is_a: MI_0013
+hasExactSynonym: CD
+hasExactSynonym: cd
+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.
+hasOBONamespace: PSI-MI
+id2: MI:0016
+
+[Term]
+id: MI:0017
+name: classical fluorescence spectroscopy
+namespace: obo
+is_a: MI_0051
+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.
+hasExactSynonym: fluorescence spectr
+hasOBONamespace: PSI-MI
+id2: MI:0017
+
+[Term]
+id: MI:0018
+name: two hybrid
+namespace: obo
+is_a: MI_0232
+hasExactSynonym: Gal4 transcription regeneration
+hasExactSynonym: 2-hybrid
+hasExactSynonym: 2H
+hasExactSynonym: 2h
+hasExactSynonym: classical two hybrid
+hasExactSynonym: yeast two hybrid
+hasExactSynonym: 2 hybrid
+hasExactSynonym: two-hybrid
+hasExactSynonym: Y2H
+def: The classical two-hybrid system is a method that uses transcriptional activity as a measure of protein-protein interaction. It relies on the modular nature of many site-specific transcriptional activators (GAL 4) , which consist of a DNA-binding domain and a transcriptional activation domain. The DNA-binding domain serves to target the activator to the specific genes that will be expressed, and the activation domain contacts other proteins of the transcriptional machinery to enable transcription to occur. The two-hybrid system is based on the observation that the two domains of the activator need to be non-covalently brought together by the interaction of any two proteins. The application of this system requires the expression of two hybrid. Generally this assay is performed in yeast cell, but it can also be carried out in other organism. The bait protein is fused to the DNA binding molecule, the prey to the transcriptional activator.
+hasOBONamespace: PSI-MI
+hasRelatedSynonym: Y-2H
+id2: MI:0018
+
+[Term]
+id: MI:0019
+name: coimmunoprecipitation
+namespace: obo
+is_a: MI_0004
+hasExactSynonym: CoIp
+hasExactSynonym: Co-IP
+hasExactSynonym: co-immunoprecipitation
+hasExactSynonym: coip
+hasExactSynonym: immunoprecipitation
+def: In this approach an antibody, specific for the molecule of interest (bait) or any tag expressed within a fusion protein, is used to separate the bait from a molecular mixture or a cell lysate and to capture its ligand simultaneously. The partners that bind to the bait molecule retained by the resin can then be eluted and identified. The antibody may be free or bound to a matrix during this process.
+hasOBONamespace: PSI-MI
+id2: MI:0019
+
+[Term]
+id: MI:0020
+name: transmission electron microscopy
+namespace: obo
+is_a: MI_0040
+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.
+hasExactSynonym: tem
+hasOBONamespace: PSI-MI
+id2: MI:0020
+
+[Term]
+id: MI:0021
+name: colocalization by fluorescent probes cloning
+namespace: obo
+is_obsolete: true
+def: Two proteins can be localised to cell compartments, in the same experiment, if they are expressed as chimeric proteins fused to distinct proteins fluorescing at different wavelengths (Green Fluorescent Protein and Red Fluorescent Protein for example). Using a confocal microscope the two proteins can be visualized in living cells and it can be determined whether they have the same subcellular location. Fluorescence microscopy of cells expressing a GFP fusion protein can also demonstrate dynamic processes such as its translocation from one subcellular compartment to another. OBSOLETE: use imaging technique (MI:0428) and specific probe as feature of each interacting protein.
+hasExactSynonym: coloc fluoresc probe
+hasOBONamespace: PSI-MI
+id2: MI:0021
+
+[Term]
+id: MI:0022
+name: colocalization by immunostaining
+namespace: obo
+is_obsolete: true
+def: The subcellular location of a protein can be demonstrated by treating cells fixed on a microscope slide with an antibody specific for the protein of interest. A secondary antibody conjugated with a reactive enzyme (e.g. horseradish peroxidase) is then added. Following a washing step to remove the unbound secondary ligand, a chromogenic substrate (e.g. 3,3', 5,5' tetramethyl benzidine chromogen [TMB]) is converted to a soluble coloured product by the conjugated enzyme and can then be visualised by standard microscopic techniques. OBSOLETE since combination of Interaction Detection Method and Interaction Type.Consider using the Interaction Detection Method imaging techniques (MI:0428) coupled with Interaction Type colocalisation (MI:0403) and Participant detection immunostaining (MI:0422) instead.
+hasExactSynonym: coloc immunostaining
+hasExactSynonym: Immunostaining
+hasExactSynonym: Immunofluorescence Staining
+hasOBONamespace: PSI-MI
+id2: MI:0022
+
+[Term]
+id: MI:0023
+name: colocalization/visualisation technologies
+namespace: obo
+is_obsolete: true
+def: Techniques enabling the identification of the subcellular localisation of a protein or complex. Two different proteins show a similar distribution in the cell are said to co-localise. Obsolete since combination of Interaction Detection Method and Interaction Type. OBSOLETE. Consider using imaging techniques (MI:0428) as interaction detection method coupled with colocalisation (MI:0401) as interaction type and predetermined (MI:0396) as participant detection.
+hasExactSynonym: coloc visual technol
+hasOBONamespace: PSI-MI
+id2: MI:0023
+
+[Term]
+id: MI:0024
+name: confirmational text mining
+namespace: obo
+is_a: MI_0110
+hasExactSynonym: conformational tm
+def: Text mining is used to support interactions which have been determined by other methods.
+hasOBONamespace: PSI-MI
+id2: MI:0024
+
+[Term]
+id: MI:0025
+name: copurification
+namespace: obo
+is_obsolete: true
+def: Approaches designed to separate cell components on the basis of their physicochemical properties. The observation that two or more proteins copurify in one or several conditions is taken as an indication that they form a molecular complex. OBSOLETE since too non-specific. Consider use of cosedimentation (MI:0027) or comigration in non denaturing gel electrophoresis (MI:0404) or affinity chromatography technologies (MI:0004) or molecular sieving (MI:0071) or for unspecific cases biochemical (MI:0401).
+hasOBONamespace: PSI-MI
+id2: MI:0025
+
+[Term]
+id: MI:0026
+name: correlated mutations
+namespace: obo
+is_a: MI_0660
+is_a: MI_0101
+def: Pairs of multiple alignments of orthologous sequences are used to identify potential interacting partners as proteins that show covariation of their residue identities between different species. Proteins displaying inter-protein correlated mutations during evolution are likely to be interacting proteins due to co-adapted evolution of their protein interacting interfaces.
+hasOBONamespace: PSI-MI
+id2: MI:0026
+
+[Term]
+id: MI:0027
+name: cosedimentation
+namespace: obo
+is_a: MI_0401
+def: Separation of a mixture of molecules under the influence of a force such as artificial gravity. Molecules sedimenting together are assumed to interact.
+hasOBONamespace: PSI-MI
+id2: MI:0027
+
+[Term]
+id: MI:0028
+name: cosedimentation in solution
+namespace: obo
+is_a: MI_0027
+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.
+hasExactSynonym: solution sedimentati
+hasOBONamespace: PSI-MI
+id2: MI:0028
+
+[Term]
+id: MI:0029
+name: cosedimentation through density gradient
+namespace: obo
+is_a: MI_0027
+hasExactSynonym: density sedimentatio
+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.
+hasOBONamespace: PSI-MI
+id2: MI:0029
+
+[Term]
+id: MI:0030
+name: cross-linking study
+namespace: obo
+is_a: MI_0401
+def: Analysis of complexes obtained by input of energy or chemical treatments, or by introducing cysteines followed by oxidation to promote the formation of covalent bonds among molecules in close proximity.
+hasExactSynonym: crosslink
+hasOBONamespace: PSI-MI
+id2: MI:0030
+
+[Term]
+id: MI:0031
+name: protein cross-linking with a bifunctional reagent
+namespace: obo
+is_a: MI_0030
+hasExactSynonym: Label transfer techniques
+hasExactSynonym: Photoaffinity labelling
+hasExactSynonym: bifunctional agent crosslink
+def: Cross-linking agents induce the formation of covalent bonds among proteins that are neighbours. The cross-linker may be a bifunctional molecule having two reactive ends linked by a spacer, often containing a disulfide bond.  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.
+hasOBONamespace: PSI-MI
+id2: MI:0031
+
+[Term]
+id: MI:0032
+name: de novo protein sequencing by mass spectrometry
+namespace: obo
+is_a: MI_0427
+is_a: MI_0093
+is_a: MI_0659
+def: The strategy to determine the complete amino acid sequence of a protein by mass spectrometry relies on the generation of a nested set of fragments differing by one amino acid. This reveals the identity of the residue that has been removed at 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.
+hasExactSynonym: de novo protein sequence
+hasOBONamespace: PSI-MI
+hasRelatedSynonym: MS/MS
+id2: MI:0032
+
+[Term]
+id: MI:0033
+name: deletion analysis
+namespace: obo
+is_a: MI_0074
+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.
+hasOBONamespace: PSI-MI
+id2: MI:0033
+
+[Term]
+id: MI:0034
+name: display technology
+namespace: obo
+is_a: MI_0400
+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.
+hasOBONamespace: PSI-MI
+id2: MI:0034
+
+[Term]
+id: MI:0035
+name: docking
+namespace: obo
+is_a: MI_0577
+is_a: MI_0105
+def: Predicts the structure of a molecular complex from the unbound structures of its components. The initial approach in the majority of docking procedures is based largely on the 'rigid-body' assumption, whereby the proteins are treated as solid objects. Initial scoring of a complex is based on geometric fit or surface complementarity. This generally requires some knowledge of the binding site to limit the number of solutions.
+hasOBONamespace: PSI-MI
+id2: MI:0035
+
+[Term]
+id: MI:0036
+name: domain fusion
+namespace: obo
+is_a: MI_0058
+is_a: MI_0101
+def: The rosetta stone, or domain fusion procedure, is based on the assumption that proteins whose homologues in other organisms happen to be fused into a single protein chain are likely to interact or to be functionally related.
+hasExactSynonym: Rosetta Stone
+hasOBONamespace: PSI-MI
+id2: MI:0036
+
+[Term]
+id: MI:0037
+name: domain profile pairs
+namespace: obo
+is_a: MI_0660
+is_a: MI_0046
+is_a: MI_0101
+def: This approach uses a protein interaction network of a given organism to infer interaction in another organism using information about the interacting region. The regions or domains involved in interactions are clustered if they share sequence similarity and have common interacting partners. The resulting domain profiles are then used to screen the proteome of another organism and domain-domain interactions are inferred. Ultimately, an inferred protein interaction map is built in this second organism.
+hasOBONamespace: PSI-MI
+id2: MI:0037
+
+[Term]
+id: MI:0038
+name: dynamic light scattering
+namespace: obo
+is_a: MI_0067
+hasExactSynonym: dls
+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.
+hasOBONamespace: PSI-MI
+id2: MI:0038
+
+[Term]
+id: MI:0039
+name: edman degradation
+namespace: obo
+is_a: MI_0433
+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.
+hasOBONamespace: PSI-MI
+id2: MI:0039
+
+[Term]
+id: MI:0040
+name: electron microscopy
+namespace: obo
+is_a: MI_0428
+hasExactSynonym: Electron crystallography
+hasExactSynonym: Electron cryomicroscopy
+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.
+hasOBONamespace: PSI-MI
+id2: MI:0040
+
+[Term]
+id: MI:0041
+name: electron nuclear double resonance
+namespace: obo
+is_a: MI_0043
+hasExactSynonym: endor
+hasExactSynonym: ENDOR
+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.
+hasOBONamespace: PSI-MI
+id2: MI:0041
+
+[Term]
+id: MI:0042
+name: electron paramagnetic resonance
+namespace: obo
+is_a: MI_0043
+hasExactSynonym: ESR
+hasExactSynonym: EPR
+hasExactSynonym: epr
+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.
+hasOBONamespace: PSI-MI
+id2: MI:0042
+
+[Term]
+id: MI:0043
+name: electron resonance
+namespace: obo
+is_a: MI_0013
+is_a: MI_0659
+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.
+hasOBONamespace: PSI-MI
+id2: MI:0043
+
+[Term]
+id: MI:0045
+name: experimental interaction detection
+namespace: obo
+is_a: MI_0001
+hasExactSynonym: experimental interac
+def: Methods based on laboratory experiments to determine an interaction.
+hasOBONamespace: PSI-MI
+id2: MI:0045
+
+[Term]
+id: MI:0046
+name: experimental knowledge based
+namespace: obo
+is_a: MI_0063
+def: Predictive algorithms that rely on the information obtained by experimental results.
+hasExactSynonym: experimental info
+hasOBONamespace: PSI-MI
+id2: MI:0046
+
+[Term]
+id: MI:0047
+name: far western blotting
+namespace: obo
+is_a: MI_0892
+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.
+hasExactSynonym: Affinity blotting
+hasOBONamespace: PSI-MI
+id2: MI:0047
+
+[Term]
+id: MI:0048
+name: filamentous phage display
+namespace: obo
+is_a: MI_0084
+hasExactSynonym: filamentous phage
+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.
+hasOBONamespace: PSI-MI
+id2: MI:0048
+
+[Term]
+id: MI:0049
+name: filter binding
+namespace: obo
+is_a: MI_0892
+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.
+hasExactSynonym: Filter overlay assay
+hasRelatedSynonym: dot blot
+hasOBONamespace: PSI-MI
+id2: MI:0049
+
+[Term]
+id: MI:0050
+name: flag tag coimmunoprecipitation
+namespace: obo
+is_obsolete: true
+hasExactSynonym: flag tag coip
+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. OBSOLETE redundant term. Map to feature type: flag-tagged (MI:0518) and Interaction detection method: anti tag coimmunoprecipitation (MI:0007).
+hasOBONamespace: PSI-MI
+id2: MI:0050
+
+[Term]
+id: MI:0051
+name: fluorescence technology
+namespace: obo
+is_a: MI_0013
+hasExactSynonym: fluorescence
+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.
+hasOBONamespace: PSI-MI
+id2: MI:0051
+
+[Term]
+id: MI:0052
+name: fluorescence correlation spectroscopy
+namespace: obo
+is_a: MI_0051
+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.
+hasExactSynonym: fcs
+hasExactSynonym: FCS
+hasRelatedSynonym: fluctuation correlation specctrometry
+hasOBONamespace: PSI-MI
+id2: MI:0052
+
+[Term]
+id: MI:0053
+name: fluorescence polarization spectroscopy
+namespace: obo
+is_a: MI_0051
+hasExactSynonym: FPS
+hasExactSynonym: fps
+hasExactSynonym: Fluorescence anisotropy
+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.
+hasOBONamespace: PSI-MI
+id2: MI:0053
+
+[Term]
+id: MI:0054
+name: fluorescence-activated cell sorting
+namespace: obo
+is_a: MI_0051
+hasExactSynonym: facs
+hasExactSynonym: Flow cytometry
+hasExactSynonym: FACS
+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.
+hasOBONamespace: PSI-MI
+id2: MI:0054
+
+[Term]
+id: MI:0055
+name: fluorescent resonance energy transfer
+namespace: obo
+is_a: MI_0051
+hasExactSynonym: RET
+hasExactSynonym: FRET
+hasExactSynonym: fret
+hasExactSynonym: FRET analysis
+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.
+hasOBONamespace: PSI-MI
+id2: MI:0055
+
+[Term]
+id: MI:0056
+name: full identification by DNA sequencing
+namespace: obo
+is_a: MI_0078
+is_a: MI_0659
+def: Sequencing occurs during the course of the experiment. DNA sequencing is the process of determining the nucleotide order of a given DNA fragment. Thus far, most DNA sequencing has been performed using the chain termination method developed by Frederick Sanger. This technique uses sequence-specific termination of a DNA synthesis reaction using modified nucleotide substrates. However, new sequencing technologies such as Pyrosequencing are generating the majority of data.
+hasExactSynonym: full dna sequence
+hasOBONamespace: PSI-MI
+id2: MI:0056
+
+[Term]
+id: MI:0057
+name: gene neighbourhood
+namespace: obo
+is_a: MI_0058
+def: Gene pairs that show a conserved topological neighbourhood in many prokaryotic genomes are considered by this approach to encode interacting or functionally related proteins. By measuring the physical distance of any given gene pair in different genomes, interacting partners are inferred.
+hasOBONamespace: PSI-MI
+id2: MI:0057
+
+[Term]
+id: MI:0058
+name: genome based prediction
+namespace: obo
+is_a: MI_0063
+hasExactSynonym: genome prediction
+def: Methods that require fully sequenced genomes either because they are based on the comparison of genome topology or on the identification of orthologous sequences in different genomes.
+hasOBONamespace: PSI-MI
+id2: MI:0058
+
+[Term]
+id: MI:0059
+name: gst pull down
+namespace: obo
+is_obsolete: true
+def: The bait protein is expressed and purified as a fusion to the glutathione S-tranferase protein. The bait protein is normally attached to a glutathione sepharose resin or alternatively to a support containing an anti-GST antibody. OBSOLETE redundant term. Map to feature type : gst-tagged (MI:0519) and Interaction detection method: pull down (MI:0096).
+hasOBONamespace: PSI-MI
+id2: MI:0059
+
+[Term]
+id: MI:0060
+name: ha tag coimmunoprecipitation
+namespace: obo
+is_obsolete: true
+hasExactSynonym: ha tag coip
+def: The protein of interest is expressed as a fusion to the peptide YPYDVPDYA (a fragment of the influenza hemaglutinin protein) for which antibodies are commercially available. OBSOLETE redundant term. Map to feature type : ha-tagged (MI:0520) and Interaction detection method: anti tag coimmunoprecipitation (MI:0007).
+hasOBONamespace: PSI-MI
+id2: MI:0060
+
+[Term]
+id: MI:0061
+name: his pull down
+namespace: obo
+is_obsolete: true
+def: The bait protein is expressed and purified fused to an amino or carboxyterminal tail containing a variable number of histidines. The bait protein is normally attached to a metal (usually nickel) resin. OBSOLETE redundant term. Map to feature type : his-tagged (MI:0521) and Interaction detection method: pull down (MI:0096).
+hasOBONamespace: PSI-MI
+id2: MI:0061
+
+[Term]
+id: MI:0062
+name: his tag coimmunoprecipitation
+namespace: obo
+is_obsolete: true
+hasExactSynonym: his tag coip
+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. OBSOLETE redundant term. Map to feature type: his-tagged (MI:0521) and Interaction detection method: anti tag coimmunoprecipitation (MI:0007).
+hasOBONamespace: PSI-MI
+id2: MI:0062
+
+[Term]
+id: MI:0063
+name: interaction prediction
+namespace: obo
+is_a: MI_0001
+def: Computational methods to predict an interaction.
+hasExactSynonym: predicted interac
+hasExactSynonym: in silico methods
+hasOBONamespace: PSI-MI
+id2: MI:0063
+
+[Term]
+id: MI:0064
+name: interologs mapping
+namespace: obo
+is_a: MI_0046
+is_a: MI_0101
+hasExactSynonym: Homology based interaction prediction
+def: Protein interactions, experimentally detected in an organism, are extended to a second organism assuming that homologue proteins, in different organisms, maintain their interaction properties.
+hasOBONamespace: PSI-MI
+id2: MI:0064
+
+[Term]
+id: MI:0065
+name: isothermal titration calorimetry
+namespace: obo
+is_a: MI_0013
+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.
+hasExactSynonym: ITC
+hasExactSynonym: itc
+hasOBONamespace: PSI-MI
+id2: MI:0065
+
+[Term]
+id: MI:0066
+name: lambda phage display
+namespace: obo
+is_a: MI_0084
+hasExactSynonym: lambda phage
+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.
+hasOBONamespace: PSI-MI
+id2: MI:0066
+
+[Term]
+id: MI:0067
+name: light scattering
+namespace: obo
+is_a: MI_0013
+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.
+hasOBONamespace: PSI-MI
+id2: MI:0067
+
+[Term]
+id: MI:0068
+name: mass detection of residue modification
+namespace: obo
+is_a: MI_0659
+hasExactSynonym: modified residue ms
+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.
+hasOBONamespace: PSI-MI
+id2: MI:0068
+
+[Term]
+id: MI:0069
+name: mass spectrometry studies of complexes
+namespace: obo
+is_a: MI_0943
+hasExactSynonym: ms of complexes
+def: Mass spectrometric approaches to the study of macromolecular 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.
+hasOBONamespace: PSI-MI
+id2: MI:0069
+
+[Term]
+id: MI:0070
+name: mobility shift
+namespace: obo
+is_a: MI_0659
+def: Protein modifications can be identified by gel electrophoresis since any change in the mass and/or the charge of the protein can alter its mobility in PAGE. Although this method does not allow the unequivocal identification of the type of 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.
+hasOBONamespace: PSI-MI
+id2: MI:0070
+
+[Term]
+id: MI:0071
+name: molecular sieving
+namespace: obo
+is_a: MI_0091
+is_a: MI_0013
+hasExactSynonym: Size Exclusion Chromatography
+hasExactSynonym: Gel Filtration
+hasExactSynonym: Sizing column
+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.
+hasOBONamespace: PSI-MI
+id2: MI:0071
+
+[Term]
+id: MI:0072
+name: monoclonal antibody western blot
+namespace: obo
+is_a: MI_0113
+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.
+hasExactSynonym: monoclonal western
+hasOBONamespace: PSI-MI
+id2: MI:0072
+
+[Term]
+id: MI:0073
+name: mrna display
+namespace: obo
+is_a: MI_0034
+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.
+hasOBONamespace: PSI-MI
+id2: MI:0073
+
+[Term]
+id: MI:0074
+name: mutation analysis
+namespace: obo
+is_a: MI_0659
+def: Mutant molecules are produced by random or directed techniques and assayed for their ability to support binding.
+hasOBONamespace: PSI-MI
+id2: MI:0074
+
+[Term]
+id: MI:0075
+name: myc tag coimmunoprecipitation
+namespace: obo
+is_obsolete: true
+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. OBSOLETE redundant term. Map to feature type: myc-tagged (MI:0522) and Interaction detection method: anti tag coimmunoprecipitation (MI:0007).
+hasExactSynonym: myc tag coip
+hasOBONamespace: PSI-MI
+id2: MI:0075
+
+[Term]
+id: MI:0076
+name: neural network on interface properties
+namespace: obo
+is_a: MI_0577
+def: Neural networks are trained on the properties of residues belonging to a cluster of residues that are neighbours in space on protein surface. The predictor permits the inference of the residues that are likely to be on an interaction interface.
+hasExactSynonym: interface predictor
+hasOBONamespace: PSI-MI
+id2: MI:0076
+
+[Term]
+id: MI:0077
+name: nuclear magnetic resonance
+namespace: obo
+is_a: MI_0013
+is_a: MI_0659
+def: Nuclear magnetic resonance (NMR) is an effect whereby magnetic nuclei in a magnetic field absorb and re-emit electromagnetic (EM) energy. Certain atomic nuclei, and in particular hydrogen, have a magnetic moment or spin; i.e., 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 interacting molecule. NMR provides information about interacting atoms thereby permitting to obtain information about macromolecular structure and molecular interactions.
+hasExactSynonym: nmr
+hasExactSynonym: NMR
+hasOBONamespace: PSI-MI
+id2: MI:0077
+
+[Term]
+id: MI:0078
+name: nucleotide sequence identification
+namespace: obo
+is_a: MI_0661
+hasExactSynonym: nucleotide sequence
+hasExactSynonym: sequence cloning
+def: Identification of a nucleotide sequence. Depending on the experimental design, nucleotide sequence can be determined before the interac...
 
[truncated message content]