From abe1c4974ce818a0b0b7802b71607da5107796bd Mon Sep 17 00:00:00 2001 From: hyginn Date: Mon, 25 Sep 2017 01:30:15 -0400 Subject: [PATCH] Obsolete --- ABC-create_refDB.R | 410 --------------------------------------------- 1 file changed, 410 deletions(-) delete mode 100644 ABC-create_refDB.R diff --git a/ABC-create_refDB.R b/ABC-create_refDB.R deleted file mode 100644 index ef56250..0000000 --- a/ABC-create_refDB.R +++ /dev/null @@ -1,410 +0,0 @@ -# create_refDB.R -# Create a reference protein database for Mbp1-like proteins -# -# Boris Steipe for BCH441 -# -# For the species, see: -# cf. http://steipe.biochemistry.utoronto.ca/abc/index.php/Reference_species_for_fungi -# -# For the schema, see dbInit() in .utilities.R -# -# ============================================================================== - -refDB <- dbInit() - - -# === protein table === - -refDB$protein <- - rbind(refDB$protein, - data.frame( - ID = dbAutoincrement(refDB$protein$ID, ns = "ref"), - name = "MBP1_ASPNI", - RefSeqID = "XP_660758", - UniProtID = "Q5B8H6", - taxonomy.ID = as.integer(162425), - sequence = dbSanitizeSequence(" -MAAVDFSNVYSATYSSVPVYEFKIGTDSVMRRRSDDWINATHILKVAGFDKPARTRILEREVQKGVHEKVQGGYGKYQGT -WIPLQEGRQLAERNNILDKLLPIFDYVAGDRSPPPAPKHTSAASKPRAPKINKRVVKEDVFSAVNHHRSMGPPSFHHEHY -DVNTGLDEDESIEQATLESSSMIADEDMISMSQNGPYSSRKRKRGINEVAAMSLSEQEHILYGDQLLDYFMTVGDAPEAT -RIPPPQPPANFQVDRPIDDSGNTALHWACAMGDLEIVKDLLRRGADMKALSIHEETPLVRAVLFTNNYEKRTFPALLDLL -LDTISFRDWFGATLFHHIAQTTKSKGKWKSSRYYCEVALEKLRTTFSPEEVDLLLSCQDSVGDTAVLVAARNGVFRLVDL -LLSRCPRAGDLVNKRGETASSIMQRAHLAERDIPPPPSSITMGNDHIDGEVGAPTSLEPQSVTLHHESSPATAQLLSQIG -AIMAEASRKLTSSYGAAKPSQKDSDDVANPEALYEQLEQDRQKIRRQYDALAAKEAAEESSDAQLGRYEQMRDNYESLLE -QIQRARLKERLASTPVPTQTAVIGSSSPEQDRLLTTFQLSRALCSEQKIRRAAVKELAQQRADAGVSTKFDVHRKLVALA -TGLKEEELDPMAAELAETLEFDRMNGKGVGPESPEADHKDSASLPFPGPVVSVDA"), - stringsAsFactors = FALSE)) - - - -refDB$protein <- - rbind(refDB$protein, - data.frame( - ID = dbAutoincrement(refDB$protein$ID, ns = "ref"), - name = "MBP1_BIPOR", - RefSeqID = "XP_007682304", - UniProtID = "W6ZM86", - taxonomy.ID = as.integer(101162), - sequence = dbSanitizeSequence(" -MPPAPDGKIYSATYSNVPVYECNVNGHHVMRRRADDWINATHILKVADYDKPARTRILEREVQKGVHEKVQGGYGKYQGT -WIPLEEGRGLAERNGVLDKMRAIFDYVPGDRSPPPAPKHATAASNRMKPPRQTAAAVAAAAVAAAAAAAAVANHNALMSN -SRSQASEDPYENSQRSQIYREDTPDNETVISESMLGDADLMDMSQYSADGNRKRKRGMDQMSLLDQQHQIWADQLLDYFM -LLDHEAAVSWPEPPPSINLDRPIDEKGHAAMHWAAAMGDVGVVKELIHRGARLDCLSNNLETPLMRAVMFTNNFDKETMP -SMVKIFQQTVHRTDWFGSTVFHHIAATTSSSNKYVCARWYLDCIINKLSETWIPEEVTRLLNAADQNGDTAIMIAARNGA -RKCVRSLLGRNVAVDIPNKKGETADDLIRELNQRRRMHGRTRQASSSPFAPAPEHRLNGHVPHFDGGPLMSVPVPSMAVR -ESVQYRSQTASHLMTKVAPTLLEKCEELATAYEAELQEKEAEFFDAERVVKRRQAELEAVRKQVAELQSMSKGLHIDLND -EEAERQQEDELRLLVEEAESLLEIEQKAELRRLCSSMPQQNSDSSPVDITEKMRLALLLHRAQLERRELVREVVGNLSVA -GMSEKQGTYKKLIAKALGEREEDVESMLPEILQELEEAETQERAEGLDGSPV"), - stringsAsFactors = FALSE)) - - - -refDB$protein <- - rbind(refDB$protein, - data.frame( - ID = dbAutoincrement(refDB$protein$ID, ns = "ref"), - name = "MBP1_NEUCR", - RefSeqID = "XP_955821", - UniProtID = "Q7RW59", - taxonomy.ID = as.integer(5141), - sequence = dbSanitizeSequence(" -MVKENVGGNPEPGIYSATYSGIPVWEYQFGVDLKEHVMRRRHDDWVNATHILKAAGFDKPARTRILEREVQKDTHEKIQG -GYGRYQGTWIPLEQAEALARRNNIYERLKPIFEFQPGNESPPPAPRHASKPKAPKVKPAVPTWGSKSAKNANPPQPGTFL -PPGRKGLPAQAPDYNDADTHMHDDDTPDNLTVASASYMAEDDRYDHSHFSTGHRKRKRDELIEDMTEQQHAVYGDELLDY -FLLSRNEQPAVRPDPPPNFKPDWPIDNERHTCLHWASAMGDVDVMRQLKKFGASLDAQNVRGETPFMRAVNFTNCFEKQT -FPQVMKELFSTIDCRDLSGCTVIHHAAVMKIGRVNSQSCSRYYLDIILNRLQETHHPEFVQQLLDAQDNDGNTAVHLAAM -RDARKCIRALLGRGASTDIPNKQGIRAEELIKELNASISKSRSNLPQRSSSPFAPDTQRHDAFHEAISESMVTSRKNSQP -NYSSDAANTVQNRITPLVLQKLKDLTATYDSEFKEKDDAEKEARRILNKTQSELKALTASIDDYNSRLDTDDVAAKTAAE -MATARHKVLAFVTHQNRISVQEAVKQELAALDRANAVTNGTSTKSKSSSPSKKPKLSPIPDQKDKPPKDENETESEAEHP -DPPAAQAHQQQPGPSSQDTEVEDQDREEEEDDYTHRLSLAAELRSILQEQRSAENDYVEARGMLGTGERIDKYKHLLMSC -LPPDEQENLEENLEEMIKLMEQEDESVTDLPAGAVGGGGGGNAADGSGGGGQPSNGRRESVLPALRGGNGDGEMSRRGSR -TAAAAAAQVDGEREINGRAGAERTERIQEIAAV"), - stringsAsFactors = FALSE)) - - - -refDB$protein <- - rbind(refDB$protein, - data.frame( - ID = dbAutoincrement(refDB$protein$ID, ns = "ref"), - name = "MBP1_SACCE", - RefSeqID = "NP_010227", - UniProtID = "P39678", - taxonomy.ID = as.integer(4932), - sequence = dbSanitizeSequence(" -MSNQIYSARYSGVDVYEFIHSTGSIMKRKKDDWVNATHILKAANFAKAKRTRILEKEVLKETHEKVQGGF -GKYQGTWVPLNIAKQLAEKFSVYDQLKPLFDFTQTDGSASPPPAPKHHHASKVDRKKAIRSASTSAIMET -KRNNKKAEENQFQSSKILGNPTAAPRKRGRPVGSTRGSRRKLGVNLQRSQSDMGFPRPAIPNSSISTTQL -PSIRSTMGPQSPTLGILEEERHDSRQQQPQQNNSAQFKEIDLEDGLSSDVEPSQQLQQVFNQNTGFVPQQ -QSSLIQTQQTESMATSVSSSPSLPTSPGDFADSNPFEERFPGGGTSPIISMIPRYPVTSRPQTSDINDKV -NKYLSKLVDYFISNEMKSNKSLPQVLLHPPPHSAPYIDAPIDPELHTAFHWACSMGNLPIAEALYEAGTS -IRSTNSQGQTPLMRSSLFHNSYTRRTFPRIFQLLHETVFDIDSQSQTVIHHIVKRKSTTPSAVYYLDVVL -SKIKDFSPQYRIELLLNTQDKNGDTALHIASKNGDVVFFNTLVKMGALTTISNKEGLTANEIMNQQYEQM -MIQNGTNQHVNSSNTDLNIHVNTNNIETKNDVNSMVIMSPVSPSDYITYPSQIATNISRNIPNVVNSMKQ -MASIYNDLHEQHDNEIKSLQKTLKSISKTKIQVSLKTLEVLKESSKDENGEAQTNDDFEILSRLQEQNTK -KLRKRLIRYKRLIKQKLEYRQTVLLNKLIEDETQATTNNTVEKDNNTLERLELAQELTMLQLQRKNKLSS -LVKKFEDNAKIHKYRRIIREGTEMNIEEVDSSLDVILQTLIANNNKNKGAEQIITISNANSHA"), - stringsAsFactors = FALSE)) - - -refDB$protein <- - rbind(refDB$protein, - data.frame( - ID = dbAutoincrement(refDB$protein$ID, ns = "ref"), - name = "MBP1_SCHPO", # actually the Res2 protein - RefSeqID = "NP_593032", - UniProtID = "P41412", - taxonomy.ID = as.integer(4896), - sequence = dbSanitizeSequence(" -MAPRSSAVHVAVYSGVEVYECFIKGVSVMRRRRDSWLNATQILKVADFDKPQRTRVLERQVQIGAHEKVQGGYGKYQGTW -VPFQRGVDLATKYKVDGIMSPILSLDIDEGKAIAPKKKQTKQKKPSVRGRRGRKPSSLSSSTLHSVNEKQPNSSISPTIE -SSMNKVNLPGAEEQVSATPLPASPNALLSPNDNTIKPVEELGMLEAPLDKYEESLLDFFLHPEEGRIPSFLYSPPPDFQV -NSVIDDDGHTSLHWACSMGHIEMIKLLLRANADIGVCNRLSQTPLMRSVIFTNNYDCQTFGQVLELLQSTIYAVDTNGQS -IFHHIVQSTSTPSKVAAAKYYLDCILEKLISIQPFENVVRLVNLQDSNGDTSLLIAARNGAMDCVNSLLSYNANPSIPNR -QRRTASEYLLEADKKPHSLLQSNSNASHSAFSFSGISPAIISPSCSSHAFVKAIPSISSKFSQLAEEYESQLREKEEDLI -RANRLKQDTLNEISRTYQELTFLQKNNPTYSQSMENLIREAQETYQQLSKRLLIWLEARQIFDLERSLKPHTSLSISFPS -DFLKKEDGLSLNNDFKKPACNNVTNSDEYEQLINKLTSLQASRKKDTLYIRKLYEELGIDDTVNSYRRLIAMSCGINPED -LSLEILDAVEEALTREK"), - stringsAsFactors = FALSE)) - - - -refDB$protein <- - rbind(refDB$protein, - data.frame( - ID = dbAutoincrement(refDB$protein$ID, ns = "ref"), - name = "MBP1_COPCI", - RefSeqID = "XP_001837394", - UniProtID = "A8NYC6", - taxonomy.ID = as.integer(5346), - sequence = dbSanitizeSequence(" -MPEAQIFKATYSGIPVYEMMCKGVAVMRRRSDSWLNATQILKVAGFDKPQRTRVLEREVQKGEHEKVQGGYGKYQGTWIP -LERGMQLAKQYNCEHLLRPIIEFTPAAKSPPLAPKHLVATAGNRPVRKPLTTDLSAAVINTRSTRKQVADGVGEESDHDT -HSLRGSEDGSMTPSPSEASSSSRTPSPIHSPGTYHSNGLDGPSSGGRNRYRQSNDRYDEDDDASRHNGMGDPRSYGDQIL -EYFISDTNQIPPILITPPPDFDPNMAIDDDGHTSLHWACAMGRIRIVKLLLSAGADIFKVNKAGQTALMRSVMFANNYDV -RKFPELYELLHRSTLNIDNSNRTVFHHVVDVAMSKGKTHAARYYMETILTRLADYPKELADVINFQDEDGETALTMAARC -RSKRLVKLLIDHGADPKINNHDGKNAEDYILEDERFRSSPAPSSRVAAMSYRNAQVAYPPPGAPSTYSFAPANHDRPPLH -YSAAAQKASTRCVNDMASMLDSLAASFDQELRDKERDMAQAQALLTNIQAEILESQRTVLQLRQQAEGLSQAKQRLADLE -NALQDKMGRRYRLGFEKWIKDEETREKVIRDAANGDLVLTPATTSYTVDEDGDSDSGSNGDKNKGKRKAQVQQEEVSDLV -ELYSNIPTDPEELRKQCEALREEVSQSRKRRKAMFDELVTFQAEAGTSGRMSDYRRLIAAGCGGLEPLEIDSVLGMLLET -LEAEDPSSTSATWSGSKGQQTG"), - stringsAsFactors = FALSE)) - - - -refDB$protein <- - rbind(refDB$protein, - data.frame( - ID = dbAutoincrement(refDB$protein$ID, ns = "ref"), - name = "MBP1_CRYNE", - RefSeqID = "XP_569090", - UniProtID = "Q5KMQ9", - taxonomy.ID = as.integer(5207), - sequence = dbSanitizeSequence(" -MGKKVIASGGDNGPNTIYKATYSGVPVYEMVCRDVAVMRRRSDAYLNATQILKVAGFDKPQRTRVLEREVQKGEHEKVQG -GYGKYQGTWIPIERGLALAKQYGVEDILRPIIDYVPTSVSPPPAPKHSVAPPSKARRDKEKETGRTKATPSRTGPTSAAA -LQAQAQLNRAKMHDSTPDADASFRSFEERVSLTPEDDSSSDTPSPVASVMTDQDMEVDKMGMHMSMPNVTLSQNMEELGA -GSRKRSAAMMMEDEDQFGQLRSIRGNSAVHTPHGTPRHLGIGMPPEPIGPEQYTDIILNYFVSETSQIPSILVSPPHDFD -PNAPIDDDGHTALHWACAMGRVRVVKLLLTAGASIFAGNNAEQTPLMRSVMFSNNYDMRKFPELYELLHRSTLNIDKQNR -TVFHHIANLALTKGKTHAAKYYMETILARLADYPQELADVINFQDEEGETALTIAARARSRRLVKALLDHGANPKIKNRD -SRSAEDYILEDERFRSSPVPAPNGGIGKASTSAAAEKPLFAPQLYFSEAARLCGGQALTDITSHMQSLARSFDAELQGKE -RDILQAKALLTNIHTEVTENGRSITAITNQAAPLEEKRRELEALQASLKTRVKDALKKGYIGWLEGELVREQRWENGELE -GNEEEKAAVQALRDVPTGGQEVVQAEEEKLRWEIEEKRKRRAMFVEKFVRAQTEAGTSEQIAKYRKLVSAGLGGVSTNEV -DELMNQLLEGLEEENDNQVYNTTAGESGPSSWVQ"), - stringsAsFactors = FALSE)) - - - -refDB$protein <- - rbind(refDB$protein, - data.frame( - ID = dbAutoincrement(refDB$protein$ID, ns = "ref"), - name = "MBP1_PUCGR", - RefSeqID = "XP_003327086", - UniProtID = "E3KED4", - taxonomy.ID = as.integer(5297), - sequence = dbSanitizeSequence(" -MAYGGSIQPLRPPSRESATLHLHQPDLTVTSPPLSLTHCPPCVYSHFTHTPTSLIVIQVSLHSLLDQETYHLLPSRSPPT -VSVRMGTTTIYKATYSGVPVLEMPCEGIAVMRRRSDSWLNATQILKVAGFDKPQRTRVLEREIQKGTHEKIQGGYGKYQG -TWVPLDRGIDLAKQYGVDHLLSALFNFQPSSNESPPLAPKHVTALSTRVKVSKVSAASAARAARAVVPSLPSTSGLGGRN -TNNSWSNFDSDNEPGLPPAASSRESNGNWATQSKLARSSNLARARANINNSHPEDLPVPAPDQLQASPLPSMQTADPEND -NSLTPSELSLPSRTPSPIEDLPLTVNTASSQSTRNKGKSRDLPDDEDLSRGQKRKYDTSLVEDTSYSDGADDQYINGNPS -NAASAKYAKLILDYFVSESSQIPNFLNDPPSDFDPNVVIDDDGHTALHWACAMGRIKIIKLLLTCGADIFRANNAGQTAL -MRAVMFTNNHDLRTFPELFESFSGSVINIDRTDRTVFHYVIDIALTKGKVPAARYYLETILSQLSEYPKELIDILNFQDE -DGETALTLAARCRSKKLVKILLDHGANPKTANRDGKSAEDYILEDDKFRALSPTPCSSGPIRQLDQNSPGGTSNRSDFVD -LVDPVPIDSNLIPQRSPNASPPHYSETGQRVTKQLLPEVTSMIELLATTFDTELQDKERDLDHAVGLLSNIEKEYLEGQR -KILNYERMLSDFGEKKLALGDLEKELNDKLGKRYRFGWEKYVRDEEERARRITEQRSKYLQELSIEDRKLLDSSNLRFAD -PSKQEVLMKLQADERENSDLLNLIRTNSTDVESECDLLRESVQKLSEERERLFKEFINLSSENTGGENEEDDGANHTSAN -TSRLNNYRKLISLGCGGIGLDEVDEVIESLNEGIDVNELNDNGFLTEQDEELGNHQNYHNIHTQGR"), - stringsAsFactors = FALSE)) - - - -refDB$protein <- - rbind(refDB$protein, - data.frame( - ID = dbAutoincrement(refDB$protein$ID, ns = "ref"), - name = "MBP1_USTMA", - RefSeqID = "XP_011392621", - UniProtID = "A0A0D1DP35", - taxonomy.ID = as.integer(5270), - sequence = dbSanitizeSequence(" -MSGDKTIFKATYSGVPVYECIINNVAVMRRRSDDWLNATQILKVVGLDKPQRTRVLEREIQKGIHEKVQGGYGKYQGTWI -PLDVAIELAERYNIQGLLQPITSYVPSAADSPPPAPKHTISTSNRSKKIIPADPGALGRSRRATSIETESEVIGAAPNNV -SEGSMSPSPSDISSSSRTPSPLPADRAHPLHANHALAGYNGRDANNHARYADIILDYFVTENTTVPSLLINPPPDFNPDM -SIDDDEHTALHWACAMGRIRVVKLLLSAGADIFRVNSNQQTALMRATMFSNNYDLRKFPELFELLHRSILNIDRNDRTVF -HHVVDLALSRGKPHAARYYMETMINRLADYGDQLADILNFQDDEGETPLTMAARARSKRLVRLLLEHGADPKIRNKEGKN -AEDYIIEDERFRSSPSRTGPAGIELGADGLPVLPTSSLHTSEAGQRTAGRAVTLMSNLLHSLADSYDSEINTAEKKLTQA -HGLLKQIQTEIEDSAKVAEALHHEAQGVDEERKRVDSLQLALKHAINKRARDDLERRWSEGKQAIKRARLQAGLEPGALS -TSNATNAPATGDQKSKDDAKSLIEALPAGTNVKTAIAELRKQLSQVQANKTELVDKFVARAREQGTGRTMAAYRRLIAAG -CGGIAPDEVDAVVGVLCELLQESHTGARAGAGGERDDRARDVAMMLKGAGAAALAANAGAP"), - stringsAsFactors = FALSE)) - - - -refDB$protein <- - rbind(refDB$protein, - data.frame( - ID = dbAutoincrement(refDB$protein$ID, ns = "ref"), - name = "MBP1_WALME", - RefSeqID = "XP_006957051", - UniProtID = "I4YGC0", - taxonomy.ID = as.integer(1708541), - sequence = dbSanitizeSequence(" -MSAPPIYKACYSGVPVYEFNCKNVAVMKRRSDSWMNATQILKVANFDKPQRTRILEREVQKGTHEKVQGGYGKYQGTWIP -MERSVELARQYRIELLLDPIINYLPGPQSPPLAPKHATNVGSRARKSTAPAAQTLPSTSKVFHPLSSTKHPAKLAAATNA -KAEISDGEDASIPSSPSFKSNSSRTPSPIRINARKRKLEDEATIPSSAIDGSISYEDIILDYFISESTQIPALLIHPPSD -FNPNMSIDDEGHTAMHWACAMGKVRVVKLLLSAGADIFRVNHSEQTALMRSVMFSNNYDIRKFPQLYELLHRSTLNLDKH -DRTVLHHIVDLALTKSKTHAARYYMECVLSKLANYPDELADVINFQDDEGESALTLAARARSKRLVKLLLEHGADSKLPN -KDGKTAEDYILEDERFRQSPLLNSNHLRLHPPDTSIYAPPAHLFNSETSQNIANTSMSSVANLLESLAQSYDKEITQKER -DYQQAQVILRNIKTDIVEAKSNIEKMTIDSSEFEHLKHKLRELEMKLEEHSNDVYNKGWEEYSRNVDDPAIDAPSDNVQE -ECASLRNKIKDLQEKRISSMQELIKRQKEVGTGKKMSEYRKLISVGCGIPTTEIDAVLEMLLESLESENANKKAALASGI -SGALSSTSSAPSQATTSAPTGVATPGAPVPASSEKAGLLPPAPVMQ"), - stringsAsFactors = FALSE)) - -# === taxonomy table === - -refDB$taxonomy <- - rbind(refDB$taxonomy, - data.frame( - ID = as.integer(c(162425, - 101162, - 5141, - 4932, - 4896, - 5346, - 5207, - 5297, - 5270, - 1708541)), - species = c("Aspergillus nidulans", - "Bipolaris oryzae", - "Neurospora crassa", - "Saccharomyces cerevisiae", - "Schizosaccharomyces pombe", - "Coprinopsis cinerea", - "Cryptococcus neoformans", - "Puccinia Graminis", - "Ustilago maydis", - "Wallemia mellicola"), - stringsAsFactors = FALSE)) - - -# === feature table === - -refDB$feature <- - rbind(refDB$feature, - data.frame( - ID = c("ref_ftr_1", - "ref_ftr_2", - "ref_ftr_3", - "ref_ftr_4", - "ref_ftr_5", - "ref_ftr_6", - "ref_ftr_7", - "ref_ftr_8"), - name = c("APSES fold", - "KilA-N", - "AT hook", - "low complexity", - "Ankyrin", - "Swi6 fold", - "coiled coil", - "McInerny 2011"), - type.ID = rep("ref_typ_1", 8), - description = c("DNA binding domain by similarity to structure", - "DNA binding domain by Pfam annotation", - "DNA interaction motif by SMART annotation", - "SEG annotation by SMART", - "Ankyrin domain by SMART annotation", - "Swi6 fold by similarity to structure", - "Coiled coil by SMART annotation", - "Yeast cell cycle review"), - sourceDB = c("PDB", - "Pfam", - "SMART", - "SMART", - "SMART", - "PDB", - "SMART", - "PubMed"), - accession = c("1BM8_A_1_99", - "PF04383", - NA, - NA, - "SM00248", - "1SW6_B", - NA, - NA), - stringsAsFactors = FALSE)) - -# === protein annotation table === - -# there are many! This, we don't code explicitly, but read from a textfile -# I have prepared. - -tmp <- read.table("referenceDomainAnnotations.txt", - header = TRUE, - sep = "\t", - comment.char = "#", - strip.white = TRUE, - stringsAsFactors = FALSE) - -# remove the notes column - that is in the text file, only for our reference, -# not part of the data model -tmp <- tmp[ , -(ncol(tmp))] - -# add table IDs -for (i in 1:nrow(tmp)) { - tmp[i, "ID"] <- dbAutoincrement(tmp$ID, ns = "ref", code = "fan") -} - -# add table to DB -refDB$proteinAnnotation <- - rbind(refDB$proteinAnnotation, - tmp) - - -# === system table === - -refDB$system <- - rbind(refDB$system, - data.frame( - ID = "ref_sys_1", - name = "G1/S SACCE", - notes = paste("Regulates transition from G1 to S phase", - "in the yeast cell cycle."), - stringsAsFactors = FALSE)) - - -# === component table === - -refDB$component <- - rbind(refDB$component, - data.frame( - ID = "ref_cmp_1", - protein.ID = "ref_pro_4", # MBP1_SACCE - system.ID = "ref_sys_1", # G1/S SACCE - status = "include", - notes = paste("Part of MBF complex."), - stringsAsFactors = FALSE)) - - -# === system annotation table === - -refDB$systemAnnotation <- - rbind(refDB$systemAnnotation, - data.frame( - ID = "ref_san_1", - system.ID = "ref_sys_1", # G1/S SACCE - feature.ID = "ref_ftr_8", # PubMed - stringsAsFactors = FALSE)) - - -# === component annotation table === - -refDB$componentAnnotation <- - rbind(refDB$componentAnnotation, - data.frame( - ID = "ref_can_1", - component.ID = "ref_cmp_1", # Mbp1 in G1/S SACCE - feature.ID = "ref_ftr_8", # PubMed - stringsAsFactors = FALSE)) - - -# === type table === - -refDB$type <- - rbind(refDB$type, - data.frame( - ID = "ref_typ_0", - name = "UNDEF", - description = "Undefined type", - stringsAsFactors = FALSE)) - - -# === save - -save(refDB, file = "data/refDB.RData") - -# [END]