;; From http://www.alzforum.org/res/com/ant/glossary.asp
;; massaged in emacs

(defparameter *alzforum-methods*
  '((("2DE")
     ("Dimensional Electrophoresis")
     "Two-dimensional gel electrophoresis (2-D gel electrophoresis) is
used for detecting and analyzing hundreds to thousands of
proteins with high resolution. The technology is a combination of
isoelectric focusing (IEF) and polyacrylamide gel
electrophoresis (PAGE).  Proteins are first separated on the
basis of their isoelectric point then on their molecular
weight. Following the separation the gels may be stained and
analyzed by image analysis, or detected by fluorescence or
autoradiography. Alternately, the proteins can be transferred
onto an immobilizing membrane and detected with specific reagents
such as antibodies")

    (("AC")
     ("Affinity Chromatography")
     "The isolation or purification of a protein by a separation
process that uses a highly specific bioligand that has been
immobilized on an inert matrix. The matrix is typically an
agarose-gel bead, which is stable and to which the ligand is
attached.  An elution buffer is used, initially to wash away
unbound proteins and then later at higher concentration or
different pH to release the isolated protein from the ligand"
     (("overview" "http://users.rcn.com/jkimball.ma.ultranet/BiologyPages/A/AffinityChrom.html")
      ("overview" "http://www.rpi.edu/dept/chem-eng/Biotech-Environ/CHROMO/chromintro.html"))
     )

    (("AM")
     ("Antibody MicroArrays" "Capture Arrays" "Protein Arrays")
     "A fluorescence-based analysis in which covalently immobilized
antibodies are used to capture fluorescent labeled antigens in
order to compare two different samples with one another."
     (("overview" "http://www.bbriefings.com/pdf/16/fdd031_t_Bdbio.pdf")
      ("protein arrays" "http://www.functionalgenomics.org.uk/sections/resources/protein_arrays.htm")
      ("FAQs" "http://www.bdbiosciences.ca/canada/clontech/technical_service/FAQ/tabmicroarrayfaq.php"))
     )

    (("CE")
     ("Capillary Electrophoresis")
     "The use of small capillaries for electrophoresis allows for
higher electromagnetic fields because the fine capillaries are
very efficient at dissipating the heat generated.  The use of
stronger fields means quicker resulta and very efficient
separations."
     (("overview" "http://www.chemsoc.org/chembytes/ezine/2000/altria_nov00.htm"))
     )

    (("CIE")
     ("Countercurrent Immunoelectrophoresis" "One-dimensional double electroimmunodiffusion" "Counterelectrophoresis")
     "A technique in which antibody and antigen are placed in separate wells in an
agar plate and driven toward each other by an applied electric
field, because the gel is buffered at a pH between the
isoelectric points of the antigen and antibody.  It is more
sensitive and faster than double immunodiffusion (DID) and is
particularly useful for antigens that diffuse slowly in the
gel.")

    (("CM")
     ("Confocal Microscopy")
     "The confocal microscope uses pinholes, or apertures, to exclude out-of-focus light from an image. 
Only light from the plane of focus is collected and stored as a digital image. This image is referred to as an \"optical section\". Many of these sections can be collected and reconstructed into a three dimensional object. Specimens are probed with fluorescent probes for viewing. (see IF)"
     ()
     (("see" "IF"))
     )

    (("Crossed IEP")
     ("Crossed immunoelectrophoresis")
     "Combination of protein electrophoresis (EP) and rocket immunoelectrophoresis; protein antigens 
are separated by agarose gel electrophoresis; then a strip containing the separated antigens is cut out and placed in a trough in a gel containing antiserum, 
and an electric field perpendicular to the trough is applied, producing a \"rocket\" precipitin pattern for each antigen. Also called Laurell's first technique"
     )

    (("DID" "IDD" "ID")
     ("Double immunodiffusion" "Immuno double diffusion" "Ouchterlony" "Immunodiffusion")
     "A technique designed to establish the
identity of unknown protein samples based on the interaction
between antibodies and antigens in solution. Anti-serum,
antigens, and/or an unkown substance are each placed into
separate wells and allowed to diffuse radially outward through an
agarose gel.  As the expanding rings come in contact with each
other, insoluble antigen/antibody complexes precipitate out of
solution forming readily recognizable patterns."
 
     (("overview" "http://translate.google.com/translate?hl=en&sl=fr&u=http://www.snv.jussieu.fr/bmedia/ATP/immu2.htm&prev=/search%3Fq%3Douchterlony%26hl%3Den%26lr%3D%26sa%3DG"))
     ("example" "http://www.qedbio.com/pdf/K20000%20Kit%20Insert.pdf"))

    (("EIA")
     ("Enzyme Immunoassay")
     "Same as RIA except that the ligand is labeled with an enzyme instead of  with a radioactive tag. Usually equivalent to ELISA."
     (("references" "http://jim.mscs.mu.edu/models/paper1_98/compmodel13.htm")))

    (("ELIFA" "ELFA")
     ("Enzyme-linked Immunofluorescent Assay")
     "A variety of EIA in which a flourescent compound is used to indicate the presence of the antigen.")

    (("ELISA")
     ("Enzyme-linked Immuno Sorbant Assay")
     "ELISA typically involves a two-stage incubated immuno reaction. First the target antigen 
binds with a solid phase antibody.  Non-bound materials are washed away and an enzyme-labeled antibody, called a conjugate, binds to form a 'sandwich' 
complex.  Finally the antigen-antibody is introduced to a substrate where a chromogen is used to give a color change indicating the presence of the antibody."
     (("general" "http://www.biology.arizona.edu/immunology/activities/elisa/main.html")))

    (("EMSA" "ESA" "Gel MSA")
     ("Electrophoretic Mobility Shift Assay"  "Electromobility Shift Assay" "Gel Mobility Shift Assay")
     "EMSA is used to detect the interaction of DNA binding proteins with their DNA recognition sequences, 
and has been extended to allow detection of RNA binding proteins. Purified proteins or crude cell extracts are incubated with a radiolabelled DNA or RNA 
probe.  The complexes are separated from the free probe by migration through a nondenaturing polyacrylamide gel, with the complexes migrating more 
slowly."  

     (("overview" "http://www.piercenet.com/Products/Browse.cfm?fldID=99A16E15-3470-4FD1-9A3C-0BBABBBE45F9")
      ("other shift assays" "http://fred.hmc.psu.edu/ds/retrieve/fred/meshdescriptor/D024202")
      ("more" "http://www.piercenet.com/Products/Browse.cfm?fldID=99A16E15-3470-4FD1-9A3C-0BBABBBE45F9")
      ("more" "http://www.protocol-online.org/prot/Molecular_Biology/DNA-Protein_Interactions/Band_Shift_Assay/")))

    (("EP")
     ("Electrophoresis")
     "EP is used to separate a complex mixture of proteins with respect to the presence or other characteristics of one 
or more proteins to which they bond.  The separation is through migration of the charged molecules across a support medium and in response to an electric
field.  The medium is typically a gel but may be paper, potato starch, cellulose acetate, agarose or polyacrylamide gel; the last two gels are the most commonly 
used media. Agarose is usually made into dilute gels for separating large macromolecules, proteins and protein complexes.  Polyacrylamide gels (see PAGE) are 
used at higher concentrations, to separate most proteins and small oligonucleotides.  Proteins of known molecular weight are often included in the initial mixture, to serve as calibrating markers."
     (("definition" "http://www.google.com/search?hl=en&lr=&oi=defmore&q=define:ELECTROPHORESIS")))

    (("FC" "FACS")
     ("Flow Cytometry" "Fluorescence Activated Cell Sorter")
     "FC is a method of quantifying components or structural features of cells by optical means, 
and often uses fluorescent labeling.  Cells in single-cell suspension are flowed rapidly single-file through a laser beam.  Each cell scatters some of the light, 
and labeled cells emit flourescent light excited by the laser.  Cell size and granularity can be measured from the scattered light, and flourescent intensities measure 
the quantities of particular cell components."
     (("overview" "http://www.bio.umass.edu/mcbfacs/intro.htm")
      ("theory" "http://biology.berkeley.edu/crl/flow_cytometry_basic.html")
      ("animation" "http://www.wehi.edu.au/cytometry/flowintrol.html")))

    (("FISH")
     ("Fluorescent In-Situ Hybridization")
     "The hybridization reaction identifies, or labels, target genomic sequences so their location and size can be 
studied. DNA or RNA sequences from appropriate, chromosome-specific probes are first labeled with reporter molecules, which are later identified through fluorescence 
microscopy. The labeled DNA or RNA probe is then hybridized to the metaphase chromosomes or interphase nuclei on a slide. After washing and signal amplification, 
the specimen is screened for the reporter molecules by fluorescence microscopy."
     (("overview" "http://www.bio.davidson.edu/Courses/Molbio/MolStudents/spring2003/Baxter/MolecularTool.html")
      ("principles" "http://www.pasteur.fr/recherche/unites/biophyadn/e-fish.html")
      ("details" "http://www.microscopyu.com/articles/fluorescence/insitu/brennerinsitu.html")))
    
    (("IB" "IEB")
     ("Immunoblotting" "Immunoelectroblotting")
     "A general term for Western blots, dot blots, slot blots, etc.  After a gel separation the immobilized proteins are transferred to a filter paper or blotting paper via a sandwich involving the gel, nitrocelulose paper/blotting paper, and filter paper, either by electrophoresis under a low current for 20-30 minutes or by capillary blotting from wet to dry filter paper. The three popular blotting methods are Southern Blot, for DNA cut with restriction enzymes and probed with radioactive DNA, Northern Blot, for RNA probed with radioactive RNA or DNA, and Western Blot, for proteins (antigens) probed with proteins (antibodies).  See Western blots (WB)."
     (("IEB and Western Blots" "http://www.uct.ac.za/depts/microbiology/western.html"))
     (("see" "WB")))

    (("IC")
     ("Immunocytochemistry")
     "The use of antibodies to detect proteins within cells.  Often the antibodies are bound with electron-opaque 
markers, so as to visualize the proteins under an electron microscope.  Typically the cells are embedded or frozen, then sectioned and labelled with antibodies 
and markers."
     (("overview" "http://www.hei.org/research/depts/aemi/iem.htm")
      ("details" "http://www.uiowa.edu/~cemrf/courses/cytochemistry/cytochemistry.htm")))

    (("IEP")
     ("Immuno-electrophoresis")
     "IEP is a method of determining the levels of three major immunoglobulins: immunoglobulin M (IgM), immunoglobulin G (IgG), 
and immunoglobulin A (IgA). It combines the techniques of electrophoresis and immunodiffusion. To run this test, a gel is prepared with alternating wells and slots cut into it. 
The antigen mixture (usually a serum sample) is placed in the wells and electrophoresis is performed to separate the proteins in the sample. Then an antibody or mixture of 
antibodies is added to the slots in the gel. The separated antigens and the antibodies migrate toward one another and form precipitin arcs at the region of optimal concentrations."  

     (("overview" "http://www.chclibrary.org/micromed/00052660.html")))

    (("IF")
     ("Immunofluorescence")
     "The use of a fluorescene conjugated antibody or secondary antibody to visualize an antigen when viewed under a microscope or flow 
cytometer.    For fluorescent microscopy, the specimen is fixed to a slide and then the flourescent labelled antibody (primary or secondary) is added and the mixture is incubated, rinsed and examined
with a fluorescent microscope using filters appropriate for excitation and emission of the particular fluorochrome, can also be used with confocal microscopy (see CM). For FAC, single cell 
suspensions are fixed in solution and then a fluorescent-labeled antibody is added. The mixture is inserted through a flow cell and each cell scatters some of the light, 
and labeled cells emit fluorescent light excited by the laser beam. Results are recorded as peaks and scatter lines corresponding to wavelenth (see FAC)."
     (("overview" "http://www.sigmaaldrich.com/Area_of_Interest/Life_Science/Antibody_Explorer/Procedures/Immunofluorescence.html")
      ("protocols" "http://www.molbio.princeton.edu/facility/flowcyt/IF1.html")))

    (("IFE")
     ("Immunofixation Electrophoresis")
     "IFE combines zone electrophoresis with immunoprecipitation. This technique may be used 
to identify and characterize serum proteins. In IFE, proteins of sample are first separated by electrophoresis on a support (agarose) according to their charge 
and after that the medium is overlaid with monospesific antisera reactive with specific protein - antigen. If the antigen is present a characteristic immunoprecipitin band will form." 

     (("overview" "http://www.techpath.gr/hellabio/ife.html")))

    (("IFE with Cellulose acetate")
     ()
     "IFE uses a cellulose acetate strip, impregnated with antiserum, over the gel after electrophoretic 
migration has taken place.  After diffusion of the antiserum from the strips to the gel and precipitation of antigen-antibody complexes, the precipitin bands are stained. "

     (("overview" "http://www.cladocera.uoguelph.ca/tools/cae/default.htm?http://www.cladocera.uoguelph.ca/tools/cae/page2.htm")))

    (("IHC")
     ("Immunohistochemistry")
     "IHC is the process of staining tissues with antibodies and developing the result with histologic labels such as enzymes 
or fluorochromes. The tissues are rapidly frozen or fixed and embedded [paraffin (P)], then sectioned, stained and examined under a light or fluorescent microscope. 
The antibodies are labeled with enzymes or fluorescent tags, either by directly conjugating the antibody or by using tagged secondary antibodies.  The enzymes labeled 
specimens are developed with a dye. It is possible to develop the specimens with more than one antibody by using different colored dyes or different fluorochromes having 
different wavelengths. See Immunofluorescence (IF)"
     (("overview" "http://www.chemicon.com/resource/ANT101/a2D.asp")
      ("gallery and links" "http://home.primus.com.au/royellis/immuno.html"))
     (("see" "IF")))
    
    ;;     (("IHC(F)" "IH(F)")
    ;;      ("Immunohistochemistry, Frozen sections")
    ;;      ""
    ;;      ()
    ;;      (("see" "IHC")))
    
    ;;     (("IHC(P)" "IH(P)")
    ;;      ("Immunohistochemistry, Paraffin sections")
    ;;      ""
    ;;      ()
    ;;      (("see" "IHC")))

    (("IP")
     ("Immunoprecipitation")
     "When an antibody has multiple binding sites, each specific to a separate epitope,  an antibody, 
antigen chain may form which grows to be heavy enough to precipitate out of the solution.  Applications of imunoprecipitation can be 
be for immunodiffusion (ID) and for Immunoblotting (IB)."  
     (("overview" "http://www.sigmaaldrich.com/Area_of_Interest/Life_Science/Antibody_Explorer/Procedures/Immunoprecipitation.html")
      ("principles" "http://pingu.salk.edu/users/sefton/Hyper_protocols/immunoprecip.html")))

    (("ISH" "ISHH")
     ("In-Situ Hybridization Histochemistry")
     "ISH allows cell-specific localization of RNA or DNA sequences in tissue sections or on a chromosome. 
Tissue sections are incubated overnight under the appropriate conditions with labeled nucleic acid probes that specifically 'hybridize' to the RNA or DNA of interest. 
The tissue sections are then washed under low salt and high temperature conditions to reduce the amount of non-specific hybridization. The sections are then either
apposed to x-ray film (in the case of radio-labeled probes), or immunohistochemically treated to detect hybridized probe and to quantify the amount of RNA in a particular section (see FISH)."

     (("overview and protocols" "http://intramural.nimh.nih.gov/lcmr/snge/Protocols/ISHH/ISHH.html")
      ("principles" "http://www.bio.davidson.edu/Courses/Molbio/MolStudents/spring2003/Baxter/MolecularTool.html"))
     (("see" "FISH")))

    (("MgB")
     ("Magnetic beads")  
     "Magnetic particles present one intriguing way of sorting cells. Antibodies specific for a particular cell of interest are covalently 
bound to magnetic particles. A mixture of cells in solution are mixed with the magnetic antibodies. The entire reaction mixture is exposed to a magnetic field, which retains 
the cells of interest. Removing the magnet frees the cells again."  
     (("example" "http://www.dynal.no/kunder/dynal/dynalpub401.nsf/$all/786DDD00C03AC92CC1256E200053D887")))

    (("MxA")
     ("Multiplex Arrays")
     "Capture antibodies are spotted on the well surface of either 96- or 384-well plates. Each arrayed antibody captures 
specific proteins present in both the calibrated standards and the unknown samples added to the plate. The bound proteins are then quantitated using a biotinylated detection 
antibody, followed by the addition of streptavidin-horseradish peroxidase (HRP) and lastly, a chemiluminescent substrate. The luminescent signal is measured using a CCD plate imager"
     (("example" "http://www.piercenet.com/drugdiscovery/searchlight2.cfm")))

    (("NIA")
     ("Nephelometric Immunoassay")
     "Uses a monospecific anti-IgG subclass specific antiserum and the human IgG subclass to be determined.  
The generated immune complexes are quantified by measuring the side-scattered laser-light shining through the solution.  "
     (("example" "http://www.researchd.com/rdikits/rdinepkt.htm")))

    (("PAGE")
     ("Polyacrylamide Gel Electrophoresis")
     "Separation of proteins by their relative migration across a polyacrylamide gel medium in an electric field.  PAGE and gel electrophoresis in general are used for: determination of molecular size, approximate weight and purity of proteins, determination of number and size of subunits, determination of carbohydrate content, and isolation and recovery of individual proteins from complex mixtures."
     (("PAGE and SDS-PAGE" "http://www.uct.ac.za/depts/microbiology/sdspage.html")))

    (("RIA")
     ("Radio Immunoassay")
     "In this highly sensitive test a radioactive isotope is bound to the antigen and the amount of antigen 
is quantified by a gamma-ray counter.  The antigen is initially bound to the walls of a test tube or microplate, serum is added  which binds to the 
antigen and the bound antibody is detected by adding a radiolabeled ligand.  The addition of various concentrations of unlabeled ligand and the measurement 
of the various ratios of bound labeled to free labeled ligand produces a calibration curve for determining the ligand concentration."

     (("description" "http://jim.mscs.mu.edu/models/paper1_98/compmodel10.htm")))

    (("RID" "SRID")
     ("Radial Immunodiffusion" "Single Radial Immunodiffusion")
     "Method for obtaining a precipitate between an antibody and its specific 
antigen by suspending one in a gel and letting the other migrate through it from a well.  Multiple wells are often used. See Immunodiffusion (ID)  
Note: sometimes Single Radial Immunodiffusion is used to mean Ouchterlony."
     )
    
    (("RIP")
     ("Radio-immunoprecipitation")
     "Sensitive assay using radiolabeled antigens to detect specific antibodies in serum. The antigens are allowed 
to react with the serum and then precipitated using a special reagent such as Protein A sepharose beads. The bound radiolabeled immunoprecipitate is then 
commonly analyzed by gel electrophoresis."
     (("description" "http://lsvl.la.asu.edu/resources/mamajis/rip/rip.html")))

    (("RIE")				; note RIE synonym added by alanr
     ("Rocket Immunoelectrophoresis" "Rocket IEP")
     "One-dimensional single electroimmunodiffusion; a technique in which antigen is placed in a 
row of wells in an agar plate containing antiserum and an electric field perpendicular to the line of wells is applied; this drives the antigen through the gel, forming a 
spike or \"rocket\" precipitin pattern trailing away from each well. The length of the rocket is proportional to the amount of antigen placed in the well. Called also 
Laurell's second technique.  See IEP."
     ()
     ("see" "IEP"))

    (("TMA")
     ("Tissue Microarray"  "Tissue Array" "Tissue Chips")
     "Like NIA, it is based on detection of fluid-phase antigen complexes, but TIA works by measuring the decrease 
in light transmission rather than the side scattering of the light.   See NIA."
     (("overview" "http://tissuearray.org/yale/tisarray.html")
      ("principles" "http://tmalab.jhmi.edu/DeMarzo_Fedor_TMA.html")
      ("FAQ" "http://www.biogenex.net/profile.php?pagename=csfaq_tissuemic"))
     ("see" "NIA"))

    (("TIA")
     ("Turbidimetric Immunoassay")
     "Like NIA, it is based on detection of fluid-phase antigen complexes, but TIA works by measuring the decrease 
in light transmission rather than the side scattering of the light.   See NIA."
     ()
     (("see" "NIA")))

    (("WB")
     ("Western Blot")
     "The common means for probing proteins with radioactive or enzymatically-tagged antibodies after they have been spatialy separated 
and immobilized, typically on an agarose or poly-acrylamide gel (see IEP), and transfered to a filter paper or blotting paper through electrophoresis or capillary blotting.  
The antibody probe is typically enzyme-conjugated by cross-linking to the enzyme, and is added to the paper in buffer and incubated for several hours.  Extra probe is 
washed away, and the filter paper is then soaked in a solution that is a substrate for the enzyme and results in an insoluble colored deposit."
     (("Blots in general" "http://www.uct.ac.za/depts/microbiology/western.html")
      ("overview" "http://lsvl.la.asu.edu/resources/mamajis/western/western.html"))
     (("see" "IEP")))

    (("ChIP") ; added by alanr from http://www.protocol-online.org/prot/Molecular_Biology/Protein/Immunoprecipitation/Chromatin_Immunoprecipitation__ChIP_Assay_/index.html
     ("Chromatin Immunoprecipitation")
     "The ChIP assay is the key biochemical method used to map the location of modified histones and other chromosomal proteins in the genome. The important feature of these experiments is the use of an antibody that recognises and binds to the protein of interest, not only in free solution, but also when assembled into chromatin. ChIP assay combines two straightforward steps - first, in vivo formaldehyde cross-linking of whole cells that freezes protein-protein and protein-DNA interactions, followed by immunoprecipitation of protein-DNA complexes with specific antibodies from sonicated extracts."
     (("protocols" "http://www.protocol-online.org/prot/Molecular_Biology/Protein/Immunoprecipitation/Chromatin_Immunoprecipitation__ChIP_Assay_/index.html")))

    (("EM")   ; added by alanr from http://www.unl.edu/CMRAcfem/em.htm
     ("Electron Microscopy")
     "Electron Microscopes(EMs) function exactly as their optical counterparts except that they use a focused beam of electrons instead of light to \"image\" the specimen and gain information as to its structure and composition.
The basic steps involved in all EMs:
1. A stream of electrons is formed (by the Electron Source) and accelerated toward the specimen using a positive electrical potential
2. This stream is confined and focused using metal apertures and magnetic lenses into a thin, focused, monochromatic beam.
3. This beam is focused onto the sample using a magnetic lens
4. Interactions occur inside the irradiated sample, affecting the electron beam:"
     (("overview" "http://www.unl.edu/CMRAcfem/em.htm")))
    (("Block") ; added by alanr
     ("Block")
     "Can Block some activity of the target"
     )
    (("Neut") ; added by alanr
     ()
     "Can neutralize the target")
  (("DB") ; alanr
   ("Dot Blot")
   "A technique for detecting, analyzing, and identifying proteins, similar to the Western blot technique but differing in that protein samples are not separated electrophoretically but are spotted through circular templates directly onto the membrane or paper substrate."
   (("definition" "http://www.ndif.org/Terms/dot_blot.html")))
  (("FA") ; alanr
   ("Functional Assay")
   )
  (("FM") ; alanr
   ("Fluorescence microscopy")
   "In fluorescence microscopy, a cell is stained with a dye and the dye is illuminated with filtered light at the absorbing wavelength; the light emitted from the dye is viewed through a filter that allows only the emitted wavelength to be seen. The dye glows brightly against a dark background because only the emitted wavelength is allowed to reach the eyepieces or camera port of the microscope.  Most microscopes are designed using epi-illumination. In epi-illumination excitation, light goes through the objective lens and illuminates the object. Light emitted from the specimen is collected by the same objective lens."
   (("overview" "http://dept.kent.edu/projects/cell/fluoro.htm")))
  (("IA") ; alanr
   ("Immunoassay")
   "An immunoassay is a biochemical test that measures the level of a substance in a biological liquid, typically serum or urine, using the reaction of an antibody or antibodies to its antigen."
   (("overview" "http://en.wikipedia.org/wiki/Immunoassay")))
  (("IM") ; immunoelectron microscopy ? alanrn
   ("Immunomicroscopy")
   ""
   )
  (("NB") ;alanr
   ("Northern Blot")
  "The northern blot is a technique used in molecular biology research to study gene expression. It takes its name from the similarity of the procedure to the Southern blot procedure, named for biologist Edwin Southern, used to study DNA, with the key difference that RNA, rather than DNA, is the substance being analyzed by electrophoresis and detection with a hybridization probe."
   (("overview" "http://en.wikipedia.org/wiki/Northern_blot")))
  (("SB") ;alanr
   ("Southern Blot")
   "A Southern blot is a method in molecular biology of enhancing the result of an agarose gel electrophoresis by marking specific DNA sequences. The method is named after its inventor, the British biologist Edwin Southern."
   (("overview" "http://en.wikipedia.org/wiki/Southern_blot")))
  (("ISP") ;alanr
   ("Immunosorptive purification")
   "The immunosorptive purification of biological substances, e.g. macromolecules such as proteins, is a method that has been known for a long time which allows the efficient isolation of such substances from complex biological materials like serum, urine or cell lysates (Eveleigh and Levy, J. Solid-phase Biochem. 2 (1977), 45-78; Cooper, \"Biochemische Arbeitsmethoden\", pp. 222-241 (1981), Walter de Gruyter, Berlin; Pharmacia Fine Chemicals, Affinity Chromatography: Principles and Methods (1983), pp 92-95; Wawrazynczak and Cumber, in: Immunochemical Protocols, M. M. Manson ed. Methods in Molecular Biology 10, chapter 32 (1992), Humana Press, Totowa, N.J. USA). The desorption of the substances bound to the immobilized antibodies is usually achieved with unspecific methods e.g. by adding buffers with a low (<2.5) or high (>10) pH value, chaotropic reagents such as urea or guanidine hydrochloride, organic solvents or detergents to the elution buffer. "
   (("definition" "http://www.freepatentsonline.com/6635420.html")))
  (("IS") ; alanr
   ("Immunosorbent Assay")
   "")
  (("IH") ; alanr
   ("Inhibition")
   "Inhibits activity")
  ))
  

  

(defun report-link-types ()
  (remove-duplicates
   (loop for (acronyms names definition links intra) in *alzforum-methods*
      append (mapcar 'car links))
   :test 'equal))

(defvar *method-name-to-uri* (make-hash-table :test 'equalp))

(define-ontology alzmethods (:base "reagent:" :includes (reagent-antibody-domain) )
  (annotation-property !dc:altName)
  (annotation-property !rdfs:seeAlso)
  (class !reagentApplication :partial)
  (loop for (abbreviations full description external-links internal-links) in *alzforum-methods*
     for uri = (make-uri (clean-uri "www.w3.org"  "/2001/sw/hcls/ontologies/reagent.owl" "http" (#"replaceAll"  (car abbreviations) "[() ]" "_")))
       do (loop for name in (append full abbreviations)
	       do (setf (gethash name *method-name-to-uri*) uri))
     collect (class 
		 uri
	       (and description (#"replaceAll" description "\\n" " "))  
	       :partial
	       (loop for name in (append abbreviations full)
 		  collect (annotation !dc:altName name))
	       (annotation !rdfs:label (or (car full) (car abbreviations)))
	       (loop for name in (append abbreviations full)
 		  collect (annotation !dc:altName name))
 	       (when external-links
 		 (loop for (name link)  in external-links
 		    collect (annotation !rdfs:seeAlso  link)))
	       !reagentApplication
	       ))
  (sub-class-of !elifa !eia)
  (sub-class-of !wb !iep)
  (sub-class-of !rip !ip)
  (sub-class-of !crossed_iep !iep)
  (sub-class-of !rie !iep)
  (sub-class-of !rip !iep)
  (sub-class-of !iep !ep)
  (sub-class-of !page !ep)
  (sub-class-of !emsa !ep)
  (sub-class-of !2de !ep)
  (sub-class-of !fish !ish)
  (sub-class-of !ife_with_cellulose_acetate !ife)
  (sub-class-of !wb !ib)
  (sub-class-of !sb !ib)
  (sub-class-of !db !ib)
  (sub-class-of !ce !ep)
  (sub-class-of !chip !ip)
  (sub-class-of !cie !iep)
  (sub-class-of !fc !if)
  (sub-class-of !block !fa)
  (sub-class-of !neut !fa)
  (sub-class-of !ih !fa)
  (sub-class-of !elisa !is)
  (object-property !appliedToSamplePreparation
    "relating a reagent to the kind of sample preparation that it is used with")
  (loop for (meth methname methabbrev) in (list (list !ihc "Immunohistochemistry" "IHC")
						(list !if "Immunofluorescence" "IF")
						(list !ic "Immunocytochemistry" "IC"))
       append
       (loop for (abbrev sampleclass samplename) in (list (list "s" !CellSmearSample "Cell Smears")
							  (list "c" !CellsSample "Cells")
							  (list "v" !VibratomeSectionsSample "Vibratome Sections")
							  (list "p" !ParaffinSectionsSample "Paraffin Sections")
							  (list "f" !FrozenSectionsSample "Frozen Sections"))
	  for uri = (make-uri nil (format nil "reagent:~a_~a"  (string-downcase methabbrev) abbrev))
	  do (setf (gethash (format nil "~a(~a)" methabbrev abbrev)  *method-name-to-uri*) uri)
	    collect
	    (class uri
	      :complete
	      (annotation !rdfs:label (format nil "~a(~a)"  methname samplename))
	      (intersection-of meth (restriction !appliedToSamplePreparation (some-values-from sampleclass)))
	      ))))

;; (loop for n in '("Block" "ChIP" "DB" "ELISA" "EM" "EMSA" "FA" "FC" "FM" "IA" "IB" "IC" "IC(C)" "IC(F)" "IC(P)" "IC(S)" "IC(V)" "ID" "IEP" "IF" "IF(C)" "IF(F)" "IF(P)" "IF(S)" "IF(V)" "IFE" "IH" "IH(C)" "IH(F)" "IH(P)" "IH(S)" "IH(V)" "IM" "IP" "IS" "ISP" "NB" "Neut" "RIA" "RID" "RIE" "SB" "WB")
;;       unless (gethash n *method-name-to-uri*)
;;       do (print n))

;;http://www.protocol-online.org/prot/Molecular_Biology/Protein/
;;http://www.biogenesis.co.uk/catalogue/catalogue.stm
;;http://www.chemicon.com/techsupp/terminology.asp
;;http://www.ebiotrade.com/adf/PMG/abb.htm