content: /*************************************************************************
  *                                                                        *
  *  This file is part of the 20n/act project.                             *
  *  20n/act enables DNA prediction for synthetic biology/bioengineering.  *
  *  Copyright (C) 2017 20n Labs, Inc.                                     *
  *                                                                        *
  *  Please direct all queries to act@20n.com.                             *
  *                                                                        *
  *  This program is free software: you can redistribute it and/or modify  *
  *  it under the terms of the GNU General Public License as published by  *
  *  the Free Software Foundation, either version 3 of the License, or     *
  *  (at your option) any later version.                                   *
  *                                                                        *
  *  This program is distributed in the hope that it will be useful,       *
  *  but WITHOUT ANY WARRANTY; without even the implied warranty of        *
  *  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the         *
  *  GNU General Public License for more details.                          *
  *                                                                        *
  *  You should have received a copy of the GNU General Public License     *
  *  along with this program.  If not, see <http://www.gnu.org/licenses/>. *
  *                                                                        *
  *************************************************************************/
  
  package act.shared;
  
  public class GenePubmedCaseStudy {
    // We did two case studies on the words in Gene and Pubmed:
    // 1. ChangWords: Words from the papers/gene comments that we needed to infer genes for the chang paper.
    //     See the post http://pathway-synthesis.tumblr.com/post/19209966057/looking-ahead-path-edges-to-gene-names
    // 2a. GeneEntries25Words: Words that we pulled out of 25 random gene entries (153 words)
    // 2b. PubmedEntries25Words: Words pulled out of 25 random pubmed entries (391 words)
    //
    // All these were filtered through the ~saurabhs/Downloads/pathway\ synthesis/organisms/hunspell-1.3.2/filter.sh script
    // That script runs a spell check using en_US.dic and output words that are misspelled (i.e., bio words)
    // That script is also responsible for checking whether those words are organism names. The remaining are potential chemical names
  
    public static String[] ChangWords = new String[] {
      "0g",
      "1g",
      "3R",
      "AF321779",
      "ATCC",
      "BCD",
      "BDH",
      "BUT1",
      "BUT2",
      "BYDH",
      "Butanol",
      "C2",
      "C4",
      "Clostridium",
      "CoA",
      "Coenzyme",
      "DC3000",
      "DSM",
      "Genebank",
      "H16",
      "HBD",
      "HPLC",
      "Intracellular",
      "Ki",
      "NADH",
      "NADP",
      "NADPH",
      "PHB",
      "PMID",
      "PUBMED",
      "PhaA",
      "PhaB",
      "PhaC",
      "Pseudomonas",
      "Ralstonia",
      "Rhizobia",
      "Streptomyces",
      "THL",
      "YP",
      "acetoacetyl",
      "acetobutylicum",
      "acetyacetyl",
      "acetyl",
      "acetyltransferase",
      "acidogenic",
      "ack",
      "acyl",
      "adhE2",
      "adhe",
      "adhe1",
      "aldehyde",
      "amino",
      "bcd",
      "biosynthesis",
      "biosynthetic",
      "bp",
      "butanol",
      "butanologenic",
      "butyraldehyde",
      "butyrate",
      "butyric",
      "butyryl",
      "ccr",
      "ccrA",
      "cfa8",
      "chromatography",
      "coenzyme",
      "coli",
      "collinus",
      "complementation",
      "coronafacic",
      "crotonoyl",
      "crotonyl",
      "crt",
      "dehydratase",
      "dehydrogenase",
      "dehydrogenases",
      "dodecyl",
      "electrophoretic",
      "enoyl",
      "etfA",
      "etfB",
      "eutropha",
      "hbd",
      "heterologous",
      "hydroxy",
      "hydroxybutanoyl",
      "hydroxybutyryl",
      "hyperproducing",
      "isologs",
      "isopalmitoyl",
      "kDa",
      "ketothiolase",
      "kinase",
      "lookup",
      "mM",
      "mannitol",
      "microM",
      "mol",
      "muM",
      "operon",
      "overexpress",
      "overexpressing",
      "oxidoreductase",
      "palmitoyl",
      "phaA",
      "phaB",
      "phaB1",
      "phaB2",
      "phaB3",
      "phosphotransbutyrylase",
      "polyacrylamide",
      "polyhydroxyalkanoate",
      "polyhydroxybutyrate",
      "pregrown",
      "ptb",
      "pv",
      "recombinant",
      "reductase",
      "reductases",
      "serendipitously",
      "solventogenic",
      "spectrophotometric",
      "str",
      "subunits",
      "synthase",
      "synthases",
      "syringae",
      "tac",
      "thiL",
      "thioesters",
      "thiolase",
      "thl",
      "titer",
      "tyrobutyricum",
      "phaB1",
      "phaB2",
      "phaB3",
      };
  
    public static String[] GeneEntries25Words = new String[] {
      "AA049537",
      "APEC",
      "BW2952",
      "BX571856",
      "CoA",
      "EC4115",
      "EDL933",
      "EKO11",
      "Fpr",
      "H2",
      "H7",
      "Hpr",
      "IIA",
      "JH1",
      "KEGG",
      "KO11FL",
      "MG1655",
      "MRSA252",
      "MSSA476",
      "Mu3",
      "NAD",
      "NADP",
      "NCTC",
      "NTR",
      "O1",
      "O103",
      "O157",
      "O2R",
      "Ortholog",
      "PFAM",
      "Pta",
      "R6K",
      "SAB1560c",
      "SAHV",
      "SAOUHSC",
      "SAR2008",
      "SAS1659",
      "SAS1839",
      "SE11",
      "SSON",
      "SaurJH1",
      "TIGRFAM",
      "TrbB",
      "UDP",
      "UDPdiphospho",
      "UTI89",
      "Z3922",
      "accA",
      "acetyl",
      "acetylglucosamine",
      "acetylglucosaminyl",
      "acetylglucosaminyltransferase",
      "acetylmuramyl",
      "aconitate",
      "acyl",
      "acylglycerophosphoethanolamine",
      "acyltransferase",
      "adenosyl",
      "adenosylmethionine",
      "aminopropyl",
      "arcAB",
      "aureus",
      "auxilary",
      "b3947",
      "bifunctional",
      "biosynthesis",
      "carboxylase",
      "carboxytransferase",
      "catabolism",
      "chorismate",
      "citB",
      "citrate",
      "coli",
      "deaminase",
      "decarboxylase",
      "dehydratase",
      "dehydrogenase",
      "dehydropantoate",
      "deoxyribose",
      "deoxyuridine",
      "dihydroxy",
      "ethanolamine",
      "eutD",
      "fdoG",
      "ferredoxin",
      "formate",
      "fpr",
      "frameshift",
      "glpD",
      "guaB",
      "hemC",
      "homocysteine",
      "homodimeric",
      "hydratase",
      "hydroxymethylbilane",
      "hydroxymethyltransferase",
      "inositol",
      "isocitrate",
      "ligase",
      "lyase",
      "malate",
      "malic",
      "menC",
      "methionine",
      "methylenetetrahydrofolate",
      "methyltetrahydrofolate",
      "methyltransferase",
      "monophosphate",
      "murG",
      "muramoylpentapeptide",
      "oxobutanoate",
      "p1658",
      "panB",
      "pentapeptide",
      "peptidoglycan",
      "phospholipid",
      "phosphorylase",
      "phosphorylytic",
      "phosphotransacetylase",
      "phosphotransferase",
      "porphobilinogen",
      "porphyrin",
      "prephenate",
      "ptsA",
      "ptsP",
      "putrescine",
      "pyrophosphoryl",
      "pyruvate",
      "reductase",
      "ribose",
      "sab",
      "sao",
      "sn",
      "speD",
      "spermidine",
      "ssn",
      "str",
      "subsp",
      "substr",
      "subtilis",
      "subunit",
      "succinylbenzoyl",
      "synthase",
      "synthetase",
      "tetrahydrofolate",
      "transcriptional",
      "transferase",
      "transposase",
      "ubiquinol",
      "ubiquinone",
      "udp",
      "undecaprenol",
      "uridine"
    };
  
    public static String[] PubmedEntries25Words = new String[] {
      "2A",
      "30a",
      "3H",
      "4E6",
      "A4",
      "ACAM2010",
      "APEC",
      "Acad",
      "Adenosylmethionine",
      "B1",
      "Bacteriol",
      "Biofilm",
      "C5",
      "CFA",
      "CFU",
      "CN",
      "Ca2",
      "Caenorhabditis",
      "Calsequestrin",
      "Complementation",
      "Conjugative",
      "CtsR",
      "Cys",
      "Disuccinimidyl",
      "EAST1",
      "EGF",
      "EGFR",
      "EHEC",
      "EHECs",
      "EI",
      "ELISPOT",
      "EMRSA",
      "ETEC",
      "Ec",
      "Enterobacter",
      "Enterobacteriaceae",
      "ExPEC",
      "FGF",
      "FGFR",
      "GLB",
      "Genomic",
      "Gln",
      "Globins",
      "Glutamyl",
      "H28",
      "H7",
      "HPr",
      "Hederstedt",
      "HemA",
      "Histidine",
      "Huynh",
      "IEs",
      "IFNGR1",
      "IIA",
      "IgA",
      "IgG",
      "Immunoglobulin",
      "IncF",
      "IncX1",
      "JAK",
      "JAKs",
      "K1",
      "K12",
      "Kafala",
      "Kd",
      "Lactobacillus",
      "Leu17",
      "Lymphoblastoid",
      "Lys",
      "Lys16",
      "MC4100",
      "MG1655",
      "MICs",
      "MRSA",
      "MRSA252",
      "MS2027",
      "MSSA476",
      "Mbp",
      "Microbiol",
      "Mu3",
      "Mu50",
      "MuLac",
      "Multistep",
      "N315",
      "NAD",
      "NH2",
      "NPr",
      "NaCNBH3",
      "Ntr",
      "O1",
      "O103",
      "O111",
      "O152",
      "O157",
      "O2",
      "O26",
      "ORF1",
      "ORF2",
      "PCR",
      "PKA",
      "PP1",
      "PP2A",
      "PRIP",
      "PcrA",
      "Petricek",
      "Phosphoryl",
      "Phosphorylation",
      "Plasmid",
      "Proc",
      "RNAIII",
      "RTKs",
      "Recombinantly",
      "Recsei",
      "RepD",
      "RepFII",
      "Rutberg",
      "SAR2632",
      "SCC",
      "SCCmec",
      "SDS",
      "SE11",
      "SLD1a",
      "SNP",
      "SNPs",
      "STATs",
      "Sa",
      "Sasarman",
      "Schrder",
      "Selenate",
      "Shiga",
      "Shigella",
      "SpLE3",
      "Subunit",
      "T3SS",
      "T4S",
      "Tn5",
      "Typhimurium",
      "Tyr",
      "UPEC",
      "UTI",
      "Uropathogenic",
      "VSSA",
      "Xa",
      "acceptor",
      "acetylglucosamine",
      "adenosylmethionine",
      "agr",
      "alanyl",
      "amination",
      "amino",
      "aminoglycosides",
      "aminolaevuline",
      "aminolevulinic",
      "aminotransferase",
      "ammonium",
      "amyloid",
      "anhydromannitol",
      "antithrombin",
      "arcA",
      "aroC",
      "aureus",
      "autotransporters",
      "autoxidation",
      "biofilm",
      "biomarkers",
      "biosynthesis",
      "biosynthetic",
      "bp",
      "calsequestrin",
      "carboxymethylation",
      "catalytically",
      "chromatography",
      "cofactor",
      "coli",
      "colonisation",
      "commensal",
      "commensality",
      "complementation",
      "conformational",
      "conjugative",
      "cooperativity",
      "crtM",
      "culturable",
      "cyanoborohydride",
      "cytoglobin",
      "cytokines",
      "daptomycin",
      "deaminase",
      "decarboxylase",
      "dehydratase",
      "di",
      "dichroism",
      "dihydroxy",
      "diplay",
      "dodecyl",
      "downstreatm",
      "effector",
      "electrophoresis",
      "elegans",
      "energetics",
      "enteric",
      "enterica",
      "enteroaggregative",
      "enterocyte",
      "enterohemorrhagic",
      "enterotoxigenic",
      "enterotoxin",
      "epigenetic",
      "epigenetics",
      "equimolar",
      "extracellular",
      "extraintestinal",
      "fibroblast",
      "fimbria",
      "fimbriae",
      "fluorometry",
      "forskolin",
      "fusidic",
      "genomic",
      "genomics",
      "genotyping",
      "globin",
      "globins",
      "glucosamine",
      "glucuronic",
      "glutamate",
      "glutamyl",
      "graR",
      "graRn",
      "graSR",
      "helicase",
      "hemA",
      "hemAXCDBL",
      "hemB",
      "hemC",
      "hemCDBL",
      "hemD",
      "hemL",
      "hemX",
      "histidine",
      "histidyl",
      "hydrophobicity",
      "hydroxymethylbilane",
      "iduronic",
      "immunogenic",
      "immunogenicity",
      "immunoprecipitate",
      "integron",
      "isoproterenol",
      "kDa",
      "kb",
      "kilodalton",
      "kinase",
      "kinases",
      "lactam",
      "lambdoid",
      "ligand",
      "ligands",
      "linoleic",
      "lymphoblastoid",
      "mM",
      "mV",
      "mec",
      "menC",
      "menD",
      "menE",
      "menF",
      "menFDHBCE",
      "menaquinone",
      "menaquinones",
      "methicillin",
      "microM",
      "microarrays",
      "mol",
      "multilocus",
      "murine",
      "mutagenesis",
      "mutualist",
      "nathphoic",
      "neuroglobin",
      "nosocomial",
      "nucleotide",
      "octasaccharide",
      "oligomers",
      "oligonucleotide",
      "oligopeptide",
      "oligosaccharide",
      "ompC",
      "ompF",
      "operon",
      "ortholog",
      "overexpressed",
      "overexpression",
      "oxacillin",
      "pAPEC",
      "pC221",
      "pJCB12",
      "pMAS2027",
      "paralogue",
      "paralogues",
      "pathogenesis",
      "pathogenome",
      "pentasaccharide",
      "peptide",
      "peptidoglycan",
      "periurethral",
      "phenotypes",
      "phenotypic",
      "phosphatase",
      "phosphatases",
      "phospho",
      "phosphoenolpyruvate",
      "phospholipase",
      "phosphoryl",
      "phosphorylate",
      "phosphorylated",
      "phosphorylates",
      "phosphorylation",
      "phosphotransferase",
      "phosphotyrosine",
      "phylogenetic",
      "phylogenomic",
      "placMu50",
      "plasmid",
      "plasmids",
      "polyacrylamide",
      "polymerase",
      "porphobilinogen",
      "preamyloid",
      "processivity",
      "prophage",
      "prophages",
      "protease",
      "proteolytic",
      "proteomics",
      "ptsP",
      "pyruvoyl",
      "qRT",
      "quaternary",
      "reactivity",
      "recombinant",
      "recombinational",
      "redox",
      "reductase",
      "regulons",
      "replicon",
      "resequencing",
      "reticulum",
      "rpoN",
      "sarA",
      "sarcoplasmic",
      "sasF",
      "selenate",
      "semialdehyde",
      "serine",
      "serotype",
      "serotypes",
      "serovar",
      "sigB",
      "signalling",
      "stabilisation",
      "staphyloxanthin",
      "subcellular",
      "suberate",
      "subtilis",
      "subunit",
      "subunits",
      "sulfated",
      "sulfonamides",
      "synthase",
      "tRNA",
      "tetrasaccharide",
      "threonine",
      "transcriptional",
      "transesterification",
      "translational",
      "translocation",
      "transposon",
      "trimethoprim",
      "typhimurium",
      "tyrosine",
      "uropathogenic",
      "uroporphyrinogen",
      "vancomycin",
      "vitro",
      "vivo",
      "vraE",
      "zoonotic",
      "C",
    };
  }
  