#!/usr/bin/env python # -*- coding: utf-8 -*- # # Helper Methods # def getVocabularyTermCodeForVocabularyAndTermLabel(vocabularyCode, termLabel): vocabulary = vocabularyDefinitions[vocabularyCode] for term in vocabulary: if term[1] == termLabel: #print repr("TERM NOT FOUND IN VOCABULARY LIST: " + unicode(vocabularyCode) + " : '" + unicode(termLabel) + "'") return term[0] return None # "VOCABULARY_CODE" : { "TERM_CODE" : "OBJECT" } createdVocabularyTerms = { } def printCreatedTerms(): print "--- Created Vocabulary Terms Report" for vocabularyCode in createdVocabularyTerms: print "Vocabulary [" + vocabularyCode + "]" for vocabularyTermCode in createdVocabularyTerms[vocabularyCode]: print "Term [" + vocabularyTermCode + "] Label: [" + repr(createdVocabularyTerms[vocabularyCode][vocabularyTermCode].getLabel()) + "]" print "---" def getCreatedTerm(vocabularyCode, termCode): if vocabularyCode in createdVocabularyTerms: if termCode in createdVocabularyTerms[vocabularyCode]: return createdVocabularyTerms[vocabularyCode][termCode] return None def addCreatedTerm(vocabularyCode, termCode, object): if vocabularyCode not in createdVocabularyTerms: createdVocabularyTerms[vocabularyCode] = {} createdVocabularyTerms[vocabularyCode][termCode] = object def createVocabularyTerm(tr, vocabularyCode, termCode, termLabel): createdTerm = getCreatedTerm(vocabularyCode, termCode) if createdTerm is None: vocabulary = tr.getVocabularyForUpdate(vocabularyCode) for term in vocabulary.getTerms(): if term.getCode() == termCode: createdTerm = term if createdTerm is None: createdTerm = tr.createNewVocabularyTerm() createdTerm.setCode(termCode) createdTerm.setLabel(termLabel) createdTerm.setOrdinal(vocabulary.getTerms().size()) vocabulary.addTerm(createdTerm) addCreatedTerm(vocabularyCode, termCode, createdTerm) return createdTerm # # Vocabularies # vocabularyDefinitions = { "ALL_LAB_MEMBERS" : [ ["ANNA_DEPLAZES", "Anna Deplazes"], ["ANNE-CHRISTINE_BUTTY", "Anne-Christine Butty"], ["BRIAN_LUKE", "Brian Luke"], ["CAROLINE_ZBINDEN", "Caroline Zbinden"], ["CELINE_LAFOURCADE", "Celine Lafourcade"], ["CHRISTINE_RUPP", "Christine Rupp"], ["CLAUDINE_KRAFT", "Claudine Kraft"], ["EDYTA_SIERGIEJUK", "Edyta Siergiejuk"], ["FABIAN_HERZOG", "Fabian Herzog"], ["FABIAN_RUDOLF", "Fabian Rudolf"], ["FRANK_VAN_DROGEN", "Frank Van Drogen"], ["GERDA_JORRITSMA", "Gerda Jorritsma"], ["GWEN_RABUT", "Gw\xe9nael Rabut"], ["INGRID_STOFFEL-STUDER", "Ingrid Stoffel-Studer"], ["IRAM_ZAIDI", "Iram Zaidi"], ["IZABELA_SUMARA", "Izabela Sumara"], ["LIONEL_PINTARD", "Lionel Pintard"], ["MALIKAJAQUENOUD", "MalikaJaquenoud"], ["MARC_SOHRMANN", "Marc Sohrmann"], ["MARIE-LYN_HECHT", "Marie-Lyn Hecht"], ["MARIE-PIERRE_GULLI", "Marie-Pierre Gulli"], ["MATTHIAS_PETER", "Matthias Peter"], ["MICHAEL_OLMA", "Michael Olma"], ["MICHAEL_SCHNEIDER", "Michael Schneider"], ["MICHELE_KNAUS", "Michele Knaus"], ["MONIKA_GERSBACH", "Monika Gersbach"], ["NATHALIE_MEYER-SCHALLER", "Nathalie Meyer-Schaller"], ["NATHALIE_PERRINJAQUET", "Nathalie Perrinjaquet"], ["NICOLAS_DARD", "Nicolas Dard"], ["NICOLAS_PAGE", "Nicolas Page"], ["PATRICK_PEDRIOLI", "Patrick Pedrioli"], ["PHILIPPE_WIGET", "Philippe Wiget"], ["PIERRE_MAILLARD", "Pierre Maillard"], ["REINHARD_DECHANT", "Reinhard Dechant"], ["SANDER_SPRINGER", "Sander Springer"], ["SARAH_GLASER", "Sarah Glaser"], ["SARAH_MAERKI", "Sarah M\xe4rki"], ["SEBASTIAN_LEIDEL", "Sebastian Leidel"], ["SERGE_PELET", "Serge Pelet"], ["STEFAN_MUELLER", "Stefan M�ller"], ["TANIA_ROBERTS", "Tania Roberts"], ["THIMO_KURZ", "Thimo Kurz"], ["TOBIAS_BRAUN", "Tobias Braun"], ["VANESSA_REZGUI", "Vanessa Rezgui"], ["WOJCIECH_PIWKO", "Wojciech Piwko"], ["YUKIKO_SHIMADA", "Yukiko Shimada"], ["YVONNE_GLOOR", "Yvonne Gloor"], ["JOCHEN_BECK", "Jochen Beck"], ["MONIKA_KIJANSKA", "Monika Kijanska"], ["ANGIE_RAGHEB", "Angie Ragheb"], ["ANNE_PACQUELET", "Anne Pacquelet"], ["BJORN_HEGEMANN", "Bj\xf6rn Hegemann"], ["JANNY_TILMA", "Janny Tilma"], ["THIBAULT_COURTHEOUX", "Thibault Courtheoux"], ["SAMUEL_GILBERTO", "Samuel Gilberto"], ["REMY_BUSER", "Remy Buser"], ["RADOSLAV_ENCHEV", "Radoslav Enchev"], ["MICHAELA_HUBNER", "Michaela Hubner"], ["MIA_LI", "Mia Li"], ["JULIEN_MOUYSSET", "Julien Mouysset"] ], "LAB_MEMBERS_INITIALS" : [ ["AD", "AD"], ["ACB", "ACB"], ["BL", "BL"], ["CZ", "CZ"], ["CL", "CL"], ["CR", "CR"], ["CK", "CK"], ["ES", "ES"], ["FH", "FH"], ["FR", "FR"], ["FD", "FD"], ["GJ", "GJ"], ["GR", "GR"], ["ISS", "ISS"], ["IZ", "IZ"], ["IS", "IS"], ["LP", "LP"], ["MJ", "MJ"], ["MSO", "MSo"], ["MH", "MH"], ["MG", "MG"], ["MP", "MP"], ["MO", "MO"], ["MSC", "MSc"], ["MK", "MK"], ["MG", "MG"], ["NS", "NS"], ["NPE", "NPe"], ["ND", "ND"], ["NPA", "NPa"], ["PP", "PP"], ["PW", "PW"], ["PM", "PM"], ["RD", "RD"], ["SS", "SS"], ["SG", "SG"], ["SMA", "SMa"], ["SL", "SL"], ["SP", "SP"], ["SM", "SM"], ["TR", "TR"], ["TK", "TK"], ["TB", "TB"], ["VR", "VR"], ["WP", "WP"], ["YS", "YS"], ["YG", "YG"], ["JB", "JB"], ["MKI", "MKi"] ], "BLOCK" : [ ["1BSA_01TRITON-X100", "1% BSA; 0.1% Triton-X100"], ], "CLASS" : [ ["IGM", "IgM"], ["IGG1", "IgG1"], ["IGG2", "IgG2"] ], "COMPANY" : [ ["ABCAM", "abcam"], ["CELL_SIGNALING", "cell signaling"], ["STRATAGEN", "stratagene"], ["CLONTECH", "clontech"], ["UBI", "ubi"], ["SOUTHERN_BIOTECH", "southern biotech"], ["PIERCE", "pierce"], ["PHARMIGEN", "pharmingen"], ["MOLECULAR_PROBES", "molecular probes"], ["PHARMACIA", "pharmacia"], ["BIORAD", "biorad"], ["EUROGENETIC", "eurogentec"], ["HOMEMADE", "homemade"], ["BD_BIOSCIENCE", "BD bioscience"], ["OBTAINED_FROM", "obtained from "], ["ZYMED", "Zymed"], ["UNKNOWN", "Unknown"], ["SANTA_CRUZ", "Santa Cruz"], ["BIOLEGEND", "Biolegend"], ["BETHYL", "Bethyl"], ["UPSTATE", "Upstate"], ["ROCKLAND", "Rockland"], ["NOVUS_BIOLOGICALS", "Novus Biologicals"], ["CHEMICON_INTERNATIONAL", "Chemicon International"], ["SIGMA", "Sigma"], ["ALPHA_DIAGNOSTIC_INTERNATIONAL", "Alpha Diagnostic International"], ["MILLIPORE", "Millipore"], ["ACTIVE_MOTIF", "Active motif"], ["NEB", "NEB"], ["NEOMARKERS", "Neomarkers"], ["LUBIOSCIENCE", "LubioScience"], ["EBIOSCIENCE", "eBioscience"], ["INVITROGEN", "Invitrogen"], ["STRESSGEN", "Stressgen"], ["COVANCE", "Covance"], ["ENZO_LIFE_SCIENCES", "Enzo Life Sciences"], ["CALBIOCHEM", "Calbiochem"], ["ROCHE", "Roche"], ["CYTOSKELETON", "Cytoskeleton"], ["OPEN_BIOSYSTEMS", "Open Biosystems"], ["BD_TRANSDUCTION", "BD Transduction"], ["ATLAS_ANTIBODIES_AB", "Atlas Antibodies AB"], ["GENENTECH", "Genentech"], ["TRANSDUCTION_LABS", "Transduction Labs"], ["ANTIBODIES_INCORPORATED", "Antibodies Incorporated"], ["BABCO", "BAbCO"], ["ERICH_NIGG_LAB_BASEL", "Erich Nigg lab (Basel)"], ["FRANCIS_BARR", "Francis Barr"], ["AVIVA_SYSTEMS_BIOLOGY", "Aviva Systems Biology"], ["LUCERNACHEM", "LucernaChem"], ["LI-COR", "LI-COR"], ["ABGENT", "Abgent"], ["CHROMOTEK", "Chromotek"], ["ABNOVA", "Abnova"], ["UNKNOWN", "Unknown"], ["ABSEA", "Absea"], ["GE_HEALTHCARE", "GE Healthcare"], ["GRAMSCH_LABORATORIES", "Gramsch Laboratories"], ["ADIPOGEN", "Adipogen"], ["COSMO_BIO_CO", "Cosmo bio co."], ["BECKTON_DICKINSON", "Beckton Dickinson"], ["BIOTIUM", "Biotium"] ], "CONCENTRATION_FACS" : [ ["1_TO_10", "1 : 10"], ["1_TO_20", "1 : 20"], ["1_TO_30", "1 : 30"], ["1_TO_40", "1 : 40"], ["1_TO_50", "1 : 50"], ["1_TO_100", "1 : 100"], ["1_TO_200", "1 : 200"], ["1_TO_500", "1 : 500"], ["1_TO_1000", "1 : 1000"], ["1_TO_2000", "1 : 2000"], ["1_TO_3000", "1 : 3000"], ["NOT_TESTED", "not tested"], ["NOT_WORKING", "not working"] ], "CONCENTRATION_IP" : [ ["1UL", "1 �l"], ["5UL", "5 �l"], ["10UL", "10 �l"], ["15UL", "15 �l"], ["20UL", "20 �l"], ["NOT_TESTED", "not tested"], ["NOT_WORKING", "not working"] ], "CONCENTRATION_WESTERN" : [ ["1_TO_100", "1 : 100"], ["1_TO_500", "1 : 500"], ["1_TO_1000", "1 : 1000"], ["1_TO_2000", "1 : 2000"], ["1_TO_3000", "1 : 3000"], ["1_TO_5000", "1 : 5000"], ["1_TO_10000", "1 : 10000"], ["1_TO_20000", "1 : 20000"], ["1_TO_25000", "1 : 25000"], ["NOT_TESTED", "not tested"], ["NOT_WORKING", "not working"] ], "CURRENT_LAB_MEMBERS" : [ ["CAROLINE_ZBINDEN", "Caroline Zbinden"], ["FRANK_VAN_DROGEN", "Frank Van Drogen"], ["INGRID_STOFFEL-STUDER", "Ingrid Stoffel-Studer"], ["MATTHIAS_PETER", "Matthias Peter"], ["REINHARD_DECHANT", "Reinhard Dechant"], ["WOJCIECH_PIWKO", "Wojciech Piwko"], ["JOCHEN_BECK", "Jochen Beck"] ], "FIX" : [ ["1H-RT", "1h, RT"], ["PTEMF", "PTEMF"], ["PFA", "PFA"], ["MEOH", "MeOH"] ], "LABEL" : [ ["HRP", "hrp"], ["AP", "ap"], ["FITC", "fitc"], ["CY3", "Cy3"], ["ALEXA647", "Alexa 647"] ], "ANTIBODY_LOCATION" : [ ["SMALL_PETER_LAB", "Small Peter Lab"], ["BIG_PETER_LAB", "Big Peter Lab"], ["NEW_PETER_LAB", "New Peter Lab"], ["MINUS20_C-FLOOR", "-20C C-Floor"] ], "MONO-POLYCLONAL" : [ ["MONOCLONAL", "Monoclonal"], ["POLYCLONAL", "Polyclonal"], ["UNKNOWN", "Unknown"] ], "SOURCE" : [ ["MOUSE", "Mouse"], ["RABBIT", "Rabbit"], ["HAMSTER", "Hamster"], ["GOAT", "Goat"], ["RAT", "Rat"], ["CHICKEN", "Chicken"], ["SHEEP", "Sheep"], ["HUMAN", "Human"], ["GUINEA_PIG", "Guinea pig"], ["DONEKY", "Donkey"], ["UNKNOWN", "Unknown"] ], "CELL_LOCATION" : [ ["FRIDGE", "fridge"], ["FREEZER", "freezer"], ["REFCO", "refco"], ["TANK", "tank"] ], "SELECTION" : [ ["NEOMYCIN_G418", "Neomycin/G418"], ["HYGROMYCIN", "Hygromycin"], ["MPA", "MPA"], ["G418", "G418"], ["PUROMYCIN", "puromycin"], ["BLASTICIDIN", "Blasticidin"], ["ZEOCIN", "Zeocin"] ], "CO2" : [ ["5", "5"], ["7.5", "7.5"] ], "GROWTH_TEMPERATURE" : [ ["37", "37"], ["28", "28"], ["34", "34"] ], "MEDIUM" : [ ["RPMI1640", "RPMI 1640"], ["ISCOVES", "Iscoves"], ["DMEM", "DMEM"], ["LB", "LB"], ["DMEM_NUTRIENT", "DMEM nutrient mixture F-12 HAM [D8437]"] ], "CELL_OBTAINED_FROM" : [ ["FREIBURG", "Freiburg"], ["ATCC", "ATCC"], ["DANIEL_GERLICH", "Daniel Gerlich"], ["ERICH_NIGG", "Erich Nigg"], ["KREK", "Krek"], ["TONY_HEYMAN", "Tony Heyman"], ["THOMAS-WILD_ULRIKE-KUTAY", "Thomas Wild/Ulrike Kutay"], ["JAN_MICHAEL_PETERS", "Jan-Michael Peters"], ["M_BRANDEIS", "M Brandeis"], ["ARI_HELENIUS", "Ari Helenius"], ["ROMEO_RICCI", "Romeo Ricci"] ], "CELL_SPECIES" : [ ["HUMAN", "human"], ["MOUSE", "mouse"], ["RAT", "rat"], ["CHINESE_HAMSTER", "chines hamster"], ["HYBRIDOMA", "hybridoma (human & mouse)"] ], "CONC_UNITS" : [ ["MICROG_MICROL", "�g/�l"], ["MG_ML", "mgl/ml"], ["UG_ML", "ug/ml"] ], "STRAIN_SOURCE" : [ ["F_CHANG", "F. Chang"], ["J_CHANT", "J. Chant"], ["R_DESHAIES", "R. Deshaies"], ["E_ELION", "E. Elion"], ["P_HIETER", "P. Hieter"], ["I_HERSKOWITZ", "I. Herskowitz"], ["A_NEIMAN", "A. Neiman"], ["P_SORGER", "P. Sorger"], ["T_STEARNS", "T. Stearns"], ["MARC_BONDEL", "Marc Bondel"], ["G_SUMARA", "G. Sumara"], ["MICHAEL_ALTMANN", "Michael Altmann"], ["HETEROZYGOUS_DIPLOID_COLLECTION", "Heterozygous diploid collection"], ["ANNE-CHRISTINE_BUTTY", "Anne-Christine Butty"], ["ANNE_PAQUELET", "Anne Paquelet"], ["YAGMUR-TURGAY_KUTAY-GROUP", "Yagmur Turgay - Kutay group"], ["BARBAR_CATARIN", "Barbar Catarin"], ["FRANK_VAN-DROGEN", "Frank van Drogen"], ["HEMMO_MEYER", "Hemmo Meyer"], ["JEAN-MARC_GALLAND", "Jean-Marc Galland"], ["JEFF_PARVIN", "Jeff Parvin"], ["MARIE-PIERRE_GULLI", "Marie-Pierre Gulli"], ["MIKIKO_TAKAHASHI", "Mikiko Takahashi"], ["SANDRA_HENCHOZ", "Sandra Henchoz"], ["MALIKA_JAQUENOUD", "Malika Jaquenoud"], ["GERDA_JORRITSMA", "Gerda Jorritsma"], ["CELINE_LAFOURCADE", "Céline Lafourcade"], ["CELINE_LONGARETTI", "Céline Longaretti"], ["BRIAN_LUKE", "Brian Luke"], ["GUY_NIEDERHAUSER", "Guy Niederhäuser"], ["NICOLAS_PAGE", "Nicolas Pag�"], ["NATHALIE_PERRINJAQUET", "Nathalie Perrinjaquet"], ["MATTHIAS_PETER", "Matthias Peter"], ["AUDREY_PETIT", "Audrey Petit"], ["LIONEL_PINTARD", "Lionel Pintard"], ["YUKIKO_SHIMADA", "Yukiko Shimada"], ["PHILIPPE_WIGET", "Philippe Wiget"], ["VOLKER_STUCKE", "Volker Stucke"], ["KATRIN_PETER", "Katrin Peter"], ["MARC_BLONDEL", "marc blondel"], ["M_FUNK", "M. Funk"], ["ATTILA_BECSKEI", "Attila Becskei"], ["GWENAEL_RABUT", "Gwenael Rabut"], ["PHILIP_JERMANN", "Philip Jermann"], ["P_PRYCIAK", "P.Pryciak"], ["LINDA_HICKE", "Linda Hicke"], ["RZPD", "RZPD"], ["OPENBIO", "OpenBio"], ["F_POSAS", "F. Posas"], ["HAPLOID_COLLECTION", "Haploid collection"], ["MIRIAM_BORTFELD", "Miriam Bortfeld"], ["EUROSCARF", "Euroscarf"], ["TS_COLLECTION", "ts collection"], ["CONZELMANN_LAB", "Conzelmann lab"], ["SEBASTIAN_LEIDEL", "Sebastian Leidel"], ["ANNA_DEPLAZES", "Anna Deplazes"], ["BIBOU", "Bibou"], ["MARC_SOHRMANN", "Marc sohrmann"] ], "SELECTION_YEAST" : [ ["NONE", "None"], ["URA", "Ura"], ["LEU", "Leu"], ["TRP", "Trp"], ["HIS", "His"], ["VIABILITY", "Viability"], ["NAT", "nat"], ["KAN", "kan"], ["KAN_NAT", "kan + nat"], ["HIS_KAN", "HIS + kan"], ["HIS_KAN_NAT", "HIS + kan + nat"], ["HIS", "HIS"], ["LEU_NAT", "leu + nat"], ["ADE2", "ade2"] ], "DERIVATION" : [ ["GAMMA_INTEG", "gamma integ"], ["DELTA_INTEG", "� integ"], ["5FAO_LOOPOUT", "5-FAO loopout"], ["PLASMID_SHUFFLE", "plasmid shuffle"], ["TETRAD", "tetrad"], ["LOOP-IN_LOOP-OUT", "loop-in/loop-out"], ["GALPHO", "GalpHO mating type switch"], ["DELETION", "Deletion"], ["INTEGRATION", "Integration"] ], "STRAIN_BACKGROUND" : [ ["W303", "W303"], ["K699", "K699"], ["K700", "K700"], ["S288C", "S288C"], ["1278", "*1278*"], ["EG123", "EG123"], ["DF5", "DF5"], ["SIGMA", "Sigma"], ["UNKNOWN", "Don't know"], ["BY7092", "BY7092"], ["BY5565", "BY5565"], ["BY4741", "BY4741"] ], "CIR" : [ ["CIR_PLUS", "cir+"], ["CIR_DEG", "cir�"], ], "GAL" : [ ["PLUS", "Plus"], ["PLUS_PLUS", "Plus/Plus"], ["GAL1", "gal1"], ["GAL1_GAL1", "gal1/gal1"], ["GAL2", "gal2"], ["GAL2_GAL2", "gal2/gal2"], ], "MAT" : [ ["AT", "@"], ["A", "a"], ["ALPHA", "alpha"], ["DIPLOID", "diploid"], ["UNKNOWN", "unknown"] ], "OLIGO_ORGANISM" : [ ["BMV", "BMV"], ["HUMAN", "human"], ["MOUSE", "mouse"], ["RAT", "rat"], ["XENOPUS", "xenopus"], ["DROSOPHILA", "drosophila"], ["YEAST", "yeast"], ["ECOLI", "E.coli"], ["SYNTHETIC", "synthetic"], ["HIV1", "HIV-1"], ["CELEGANS", "C.elegans"], ["MYCOPLASMA", "mycoplasma"] ], "OLIGO_GRADE" : [ ["DESALTED", "desalted"], ["HPLC", "hplc"], ["PURITY", "purity"], ["UNKNOWN", "?"] ], "PRIMER_POSITION" : [ ["FORWARD", "forward"], ["REVERSE", "reverse"] ], "OLIGO_COMPANY" : [ ["MWG", "MWG"], ["BIG", "BIG"], ["PHARMACIA", "Pharmacia"], ["IGLOI", "Igloi"], ["INVITROGEN", "invitrogen"], ["MICROSYNTH", "microsynth"] ], "OLIGO_USAGE" : [ ["PCR", "pcr"], ["SEQUENCING", "sequencing"], ["HYBRIDIZE", "hybridize"], ["MUTAGENESIS", "mutagenesis"], ["RT-PCR", "Real-Time PCR"] ], "RESTRICTION" : [ ["AATII", "AatII"], ["ACCI", "AccI"], ["ACII", "AciI"], ["AFLII", "AflII"], ["AFLIII", "AflIII"], ["AGEI", "AgeI"], ["ALUI", "AluI"], ["ALWI", "AlwI"], ["ALWNI", "AlwNI"], ["APAI", "ApaI"], ["APALI", "ApaLI"], ["APOI", "ApoI"], ["ASCI", "AscI"], ["ASEI", "AseI"], ["AVAI", "AvaI"], ["AVAII", "AvaII"], ["AVRII", "AvrII"], ["BAMHI", "BamHI"], ["BANI", "BanI"], ["BANII", "BanII"], ["BBSI", "BbsI"], ["BBVI", "BbvI"], ["BCGI-1", "BcgI-1"], ["BCGI-2", "BcgI-2"], ["BCLI", "BclI"], ["BFAI", "BfaI"], ["BGLI", "BglI"], ["BGLII", "BglII"], ["BLPI", "BlpI"], ["BPMI", "BpmI"], ["BSAAI", "BsaAI"], ["BSABI", "BsaBI"], ["BSAHI", "BsaHI"], ["BSAI", "BsaI"], ["BSAJI", "BsaJI"], ["BSAWI", "BsaWI"], ["BSERI", "BseRI"], ["BSGI", "BsgI"], ["BSIEI", "BsiEI"], ["BSIHKAI", "BsiHKAI"], ["BSIWI", "BsiWI"], ["BSLI", "BslI"], ["BSMAI", "BsmAI"], ["BSMBI", "BsmBI"], ["BSMFI", "BsmFI"], ["BSMI", "BsmI"], ["BSOFI", "BsoFI"], ["BSP1286I", "Bsp1286I"], ["BSPEI", "BspEI"], ["BSPHI", "BspHI"], ["BSPMI", "BspMI"], ["BSRBI", "BsrBI"], ["BSRDI", "BsrDI"], ["BSRFI", "BsrFI"], ["BSRGI", "BsrGI"], ["BSRI", "BsrI"], ["BSSHII", "BssHII"], ["BST1107I", "Bst1107I"], ["BSTBI", "BstBI"], ["BSTEII", "BstEII"], ["BSTNI", "BstNI"], ["BSTUI", "BstUI"], ["BSTXI", "BstXI"], ["BSTYI", "BstYI"], ["BSU36I", "Bsu36I"], ["CAC8I", "Cac8I"], ["CLAI", "ClaI"], ["CVIJI", "CviJI"], ["DDEI", "DdeI"], ["DPNI", "DpnI"], ["DRAI", "DraI"], ["DRAIII", "DraIII"], ["DRDI", "DrdI"], ["DSAI", "DsaI"], ["EAEI", "EaeI"], ["EAGI", "EagI"], ["EAM1105I", "Eam1105I"], ["EARI", "EarI"], ["ECO47III", "Eco47III"], ["ECO57I", "Eco57I"], ["ECONI", "EcoNI"], ["ECOO109I", "EcoO109I"], ["ECORI", "EcoRI"], ["ECORV", "EcoRV"], ["FOKI", "FokI"], ["FSEI", "FseI"], ["FSPI", "FspI"], ["HAEII", "HaeII"], ["HAEIII", "HaeIII"], ["HGAI", "HgaI"], ["HHAI", "HhaI"], ["HINCII", "HincII"], ["HINDIII", "HindIII"], ["HINFI", "HinfI"], ["HPAI", "HpaI"], ["HPAII", "HpaII"], ["HPHI", "HphI"], ["KPNI", "KpnI"], ["MAEII", "MaeII"], ["MAEIII", "MaeIII"], ["MBOI", "MboI"], ["MBOII", "MboII"], ["MLUI", "MluI"], ["MNLI", "MnlI"], ["MSCI", "MscI"], ["MSEI", "MseI"], ["MSLI", "MslI"], ["MSPA1I", "MspA1I"], ["MUNI", "MunI"], ["MWOI", "MwoI"], ["NAEI", "NaeI"], ["NARI", "NarI"], ["NCII", "NciI"], ["NCOI", "NcoI"], ["NDEI", "NdeI"], ["NHEI", "NheI"], ["NLAIII", "NlaIII"], ["NLAIV", "NlaIV"], ["NOTI", "NotI"], ["NRUI", "NruI"], ["NSII", "NsiI"], ["NSPI", "NspI"], ["PACI", "PacI"], ["PFLMI", "PflMI"], ["PLEI", "PleI"], ["PMEI", "PmeI"], ["PMLI", "PmlI"], ["PPUMI", "PpuMI"], ["PSHAI", "PshAI"], ["PSP1406I", "Psp1406I"], ["PSTI", "PstI"], ["PVUI", "PvuI"], ["PVUII", "PvuII"], ["RSAI", "RsaI"], ["RSRII", "RsrII"], ["SACI", "SacI"], ["SACII", "SacII"], ["SALI", "SalI"], ["SAPI", "SapI"], ["SAU96I", "Sau96I"], ["SCAI", "ScaI"], ["SCRFI", "ScrFI"], ["SEXAI", "SexAI"], ["SFANI", "SfaNI"], ["SFCI", "SfcI"], ["SFII", "SfiI"], ["SGFI", "SgfI"], ["SGRAI", "SgrAI"], ["SMAI", "SmaI"], ["SNABI", "SnaBI"], ["SPEI", "SpeI"], ["SPHI", "SphI"], ["SRFI", "SrfI"], ["SSE8387I", "Sse8387I"], ["SSPI", "SspI"], ["STUI", "StuI"], ["STYI", "StyI"], ["SWAI", "SwaI"], ["TAQI", "TaqI"], ["TFII", "TfiI"], ["TSP45I", "Tsp45I"], ["TSP509I", "Tsp509I"], ["TTH111I", "Tth111I"], ["XBAI", "XbaI"], ["XCMI", "XcmI"], ["XHOI", "XhoI"], ["XMNI", "XmnI"], ["SACI_NHEI", "sacI NheI"], ["XMAI", "XmaI"], ["BAMHI", "BamHI"], ["CLAI", "ClaI"], ["PACI", "PacI"], ["NOTI", "NotI"], ["SALI", "SalI"], ["XHOI", "XhoI"], ["NONE", "none"] ], "BACKBONE" : [ ["PCDNA3", "pCDNA3"], ["PABES-NEO2000", "pABES-neo 2000"], ["PUC19", "pUC 19"], ["PMX-1", "pMX-1"], ["PRMHA-3", "pRmHa-3"] ], "BACTERIAL_HOST" : [ ["DH10B", "DH10B"], ["JM110", "JM110"], ["BL21", "BL21"], ["DH5A", "DH5a"], ["PB3", "PB3"], ["DB31", "DB3.1"], ["CCDB_SURVIVAL", "ccdB survival"] ], "BIOSAFETY_LEVEL" : [ ["S1", "S1"], ["S2", "S2"], ["S3", "S3"] ], "SELECTION_IN_BACTERIA" : [ ["AMPICILLIN", "Ampicillin"], ["KANAMYCIN", "Kanamycin"], ["SPECTINOMCIN", "Spectinomcin"], ["UNKNOWN", "Unknown"] ], "SELECTION_IN_EUKARYOTES" : [ ["G418_NEO", "G418/neo"], ["MPA", "MPA"], ["HYGROMYCIN", "Hygromycin"] ], "SOURCE_OF_REPLICON" : [ ["CMV", "CMV"] ], "PLASMID_ORGANISM" : [ ["HUMAN", "human"], ["MOUSE", "mouse"], ["RAT", "rat"], ["XENOPUS", "xenopus"], ["DROSOPHILA", "drosophila"], ["YEAST", "yeast"], ["ECOLI", "E.coli"], ["SYNTHETIC", "synthetic"] ], "PROMOTER" : [ ["ENDOGENOUS", "endogenous"], ["GAL1", "gal1"], ["GALL", "galL"], ["GALS", "galS"], ["TET", "tet"], ["ADH", "adh"], ["CYC", "cyc"], ["GPD", "gpd"], ["DASH", "\"-\""], ["CMV", "cmv"], ["SV40", "SV40"], ["TET_ON", "tet on"], ["TET_OFF", "tet off"], ["RIM1", "rim1"] ], "EXON_OR_THREE_PRIME" : [ ["EXON", "exon"], ["3P", "3'"], ["5P", "5'"] ], "SIRNA_SPECIES" : [ ["HUMAN", "Human"], ["MOUSE", "Mouse'"], ], "SIRNA_COMPANY" : [ ["AMBION", "Ambion"], ["DHARMACON", "Dharmacon'"], ["INVITORGEN", "Invitrogen'"], ["MICROSYNTH", "Microsynth'"], ["QIAGEN", "Qiagen'"], ["GIFT", "Gift'"] ], "SIRNA_FREEZER_LOCATION" : [ ["BIGLABFREEZER", "BigLab freezer"], ["SMALLLAB_BIGFREEZER", "SmallLab Big freezer'"], ["FREEZER_G17", "Freezer G17'"], ["G93-FRANK", "G9.3--Frank'"], ["FREEZER-G17_BOX_NATHALIE", "Freezer G17 Box Nathalie'"], ["BOX-THIBAULT-BIGFREEZER-SMALLLAB", "Box thibault Big freezer small lab'"], ["BOX-NATHALIE", "Box Nathalie'"] ], "TRANSFECTION_AGENT" : [ ["FUGENE", "Fugene"], ["LIPOFECTAMINE", "Lipofectamine'"], ["OLIGOFECTAMINE", "Oligofectamine'"], ["RNAIMAX", "RNAimax'"] ], "FREEZER" : [ ["G9_FRIDGE-1", "G9 Fridge 1"], ["G9_FRIDGE-2", "G9 Fridge 2"], ["G9_FREEZER-A", "-20C Small Peter Lab"], ["G9_FREEZER-B", "G9 Freezer B"], ["G9_FREEZER-C", "G9 Freezer C"], ["G10_FREEZER-D", "G10 Freezer D"], ["G10_FREEZER-E", "G10 Freezer E"], ["G10_FREEZER-F", "G10 Freezer F"], ["G10_FREEZER-G", "G10 Freezer G"], ["G10_FREEZER-H", "G10 Freezer H"], ["G10_FREEZER-I", "G10 Freezer I"], ["G10_FRIDGE-3", "+4C Big Peter Lab"], ["G10_FRIDGE-4", "G10 Fridge 4"], ["G10_FRIDGE-5", "G10 Fridge 5"], ["G10_FRIDGE-6", "G10 Fridge 6"], ["G10_FRIDGE-7", "G10 Fridge 7"], ["G11_FRIDGE-8", "G10 Fridge 8"], ["G14_FREEZER-J", "G14 Freezer J"], ["G14_FREEZER-K", "G14 Freezer K"], ["G14_FREEZER-L", "G14 Freezer L"], ["G14_FREEZER-M", "G14 Freezer M"], ["G14_FRIDGE-9", "G14 Fridge 9"], ["G14_FRIDGE-10", "G14 Fridge 10"], ["G17_FRIDGE-11", "G17 Fridge 11"], ["G17_FRIDGE-12", "G17 Fridge 12"], ["G17_FREEZER-N", "G17 Freezer N"], ["USER_BENCH-20", "Bench -20�C"], ["USER_BENCH-80", "Bench -80�C"], ["USER_BENCH-RT", "Bench RT"], ["USER_BENCH", "Bench"] ], "STORAGE_BOX_SIZE" : [ ["9X9", "9 x 9 box"], ["8X8", "8 x 8 box"], ["5X5", "5 x 5 box"], ["10X10", "10 x 10 box"], ["10X5", "10 x 5 box"], ["10X12", "10 x 12 box"] ], }