#!/usr/bin/perl -w # retmode=text for text data # rettype=(format) # see: # http://eutils.ncbi.nlm.nih.gov/corehtml/query/static/efetchseq_help.html # http://eutils.ncbi.nlm.nih.gov/corehtml/query/static/efetchlit_help.html # http://eutils.ncbi.nlm.nih.gov/corehtml/query/static/efetchtax_help.html # http://www.ncbi.nlm.nih.gov/books/NBK3837/ (Entrez Utils help book) # # for table of formats (retmode and rettype) for each db # http://www.ncbi.nlm.nih.gov/books/NBK25499/table/chapter4.chapter4_table1/?report=objectonly %sequenceformats = ("genbank" => "gbwithparts", # resolves CON entries "genpept" => "gp", "fasta" => "fasta", "dbest" => "est", "dbgss" => "gss", ); %featureformats = ("genbank" => "ft", ); %geneformats = (); # no text format, xml or asn.1 %snpformats = (); # all are text %taxformats = (); # use report=uilist,brief,docsum,xml %litformats = (); # text (html) non-journals also xml,asn.1 # to fill in: # examples (required for testing access and formats) # EDAM terms %knownformats = ( "gene" => "text", # ()=>(asn.1) ()=>xml gene_table=>text "snp" => "chr fasta flt rsr brief docset ssexemplar genxml uilist", "genome" => "", "seqannot" => "", "nucleotide" => "genbank fasta", # "nuccore" => "genbank fasta", # genbank:gb=>text also gb=>xml gbc=>xml ft=>text "nucest" => "genbank fasta", # genbank:gb=>text also gb=>xml gbc=>xml "nucgss" => "genbank fasta", # genbank:gb=>text also gb=>xml gbc=>xml "protein" => "genpept fasta", # ft=>text genpept:gp also gp=>xml gpc=>xml "popset" => "genbank fasta",# genbank:gb=>text also gb=>xml gbc=>xml "sra" => "text xml" # (full)=>(xml) "pmc" => "text xml", # ()=>(xml) medline=>text "pubmed" => "text", "journals" => "text", "omim" => "text", "structure" => "", "bioproject" => "", "genomeprj" => "", "biosample" => "text xml", # (full)=>(xml) (full)=>text "biosystems" => "xml", # (xml)=>(xml) "blastdbinfo" => "", "books" => "", # "cancerchromosomes" => "", "cdd" => "", "gap" => "", "dbvar" => "", "epigenomics" => "", # "gensat" => "", "gds" => "Text", # (summary)=>(text) "geo" => "", "geoprofiles" => "", "homologene" => "text fasta xml", # ()=>(asn.1) ()=>xml alignmentscores=>text fasta->text homologene->text "mesh" => "text", # (full)=>(text) "ncbisearch" => "", "nlmcatalog" => "text xml", # ()=>(text) ()=>xml "omia" => "", "probe" => "", "proteinclusters" => "", "pcassay" => "", "pccompound" => "", "pcsubstance" => "", "taxonomy" => "text xml", # ()=>xml uilist=>text uilist=>xml "toolkit" => "", "toolkitall" => "", "unigene" => "", "unists" => "", "gencoll" => "", "gcassembly" => "", "assembly" => "", "clone" => "", "gapplus" => "", "pubmedhealth" => "", ); %knowntypes = ( "gene" => "text", "snp" => "text", "popset" => "text", "genome" => "nucleotide", "seqannot" => "text", "nucleotide" => "nucleotide", "nuccore" => "nucleotide", "nucest" => "nucleotide", "nucgss" => "nucleotide", "protein" => "protein", "pmc" => "text", "pubmed" => "text", "journals" => "text", "omim" => "text", "sra" => "text", "structure" => "", "genomeprj" => "", "bioproject" => "", "biosample" => "", "biosystems" => "", "blastdbinfo" => "", "books" => "", # "cancerchromosomes" => "", "cdd" => "", "gap" => "", "dbvar" => "", "epigenomics" => "", # "gensat" => "", "gds" => "text", "geo" => "", "geoprofiles" => "", "homologene" => "text sequence", "mesh" => "text", "ncbisearch" => "", "nlmcatalog" => "", "omia" => "", "probe" => "", "proteinclusters" => "", "pcassay" => "", "pccompound" => "", "pcsubstance" => "", "taxonomy" => "", "toolkit" => "", "toolkitall" => "", "unigene" => "", "unists" => "", "gencoll" => "", "gcassembly" => "", "assembly" => "", "clone" => "", "gapplus" => "", "pubmedhealth" => "", ); %dblist = ( "gene" => "", "snp" => "", "popset" => "", "genome" => "", "seqannot" => "", "nucleotide" => "", "nuccore" => "", "nucest" => "", "nucgss" => "", "protein" => "", "pmc" => "", "pubmed" => "", "journals" => "", "omim" => "", "sra" => "", "structure" => "", "genomeprj" => "", "bioproject" => "", "biosample" => "", "biosystems" => "", "blastdbinfo" => "", "books" => "", "cdd" => "", "gap" => "", "dbvar" => "", "epigenomics" => "", "gds" => "", "geo" => "", "geoprofiles" => "", "homologene" => "", "mesh" => "", "ncbisearch" => "", "nlmcatalog" => "", "omia" => "", "probe" => "", "proteinclusters" => "", "pcassay" => "", "pccompound" => "", "pcsubstance" => "", "taxonomy" => "", "toolkit" => "", "toolkitall" => "", "unigene" => "", "unists" => "", "gencoll" => "", "gcassembly" => "", "assembly" => "", "clone" => "", "gapplus" => "", "pubmedhealth" => "", ); %examples = ( "assembly" => "GCA_000001735.1", "bioproject" => "171810", "biosample" => "839651", "biosystems" => "bsid82991", "books" => "NBK1918", "cdd" => "118125", # pfam09589 "clone" => "23875610", "dbvar" => "nsv810341", "epigenomics" => "4041", "gap" => "phs000262.v2.p1", "gds" => "GDS3610", # GEO datasets "gene" => "877798", # amiC PA3364 "genome" => "4", "geo" => "GSM401290", "geoprofiles" => "11403194", "homologene" => "31384", "mesh" => "68009923", "nlmcatalog" => "101587112", "nuccore" => "CP002688.1 NC_003075.7", # genbankid, refseqid "nucest" => "170179497", # FE739931.1 "nucgss" => "269911359", # GS815963.1 "nucleotide" => "45269", # X13776 same as nuccore? "omia" => "1920", "omim" => "108390", "pcassay" => "925", # pubchem bioassay "pccompound" => "358063", # pubchem compound "pcsubstance" => "78180210", # pubchem substance "pmc" => "PMC3029258", "popset" => "401672041", "probe" => "6103371", "protein" => "112986", # acc P12345 "proteinclusters" => "PRK15614", "pubmed" => "22908228", "snp" => "rs2834167", "sra" => "SRX042485", "structure" => "50791", "taxonomy" => "9606", "toolkit" => "245792", "unigene" => "Mm.15621", "unists" => "44811", "blastdbinfo" => "", "genomeprj" => "", # same as bioproject? "gapplus" => "", "gcassembly" => "", # same as assembly? "gencoll" => "", # genome perhaps? "journals" => "", "ncbisearch" => "", # search returns URLs? "pubmedhealth" => "", "seqannot" => "", "toolkitall" => "", # book or doc page links? ); open (SERVER, ">server.entrez.new") || die "Cannot open entrez.server.new"; print SERVER "# server.entrez 2011-10-05 14:07:00\n"; print SERVER " # database names listed by the Einfo utility # http://eutils.ncbi.nlm.nih.gov/entrez/eutils/einfo.fcgi? # database dbxyz details listed by # http://eutils.ncbi.nlm.nih.gov/entrez/eutils/einfo.fcgi?db=dbxyz "; if (-e "entrez.info") {system "rm entrez.info"} $status = system "wget -q -O entrez.info \"http://eutils.ncbi.nlm.nih.gov/entrez/eutils/einfo.fcgi?\""; @dbname = (); open (DBLIST, "entrez.info") || die "Unable to open 'entrez.info'"; while() { if(/([^<]+)<\/DbName>/) { push @dbname, $1; } } close DBLIST; foreach $db (@dbname) { $type = "Text"; $format = "Text"; if(defined($knowntypes{$db})) {$type = $knowntypes{$db};} else{print STDERR "Unknown type for '$db'\n"} if(defined($knownformats{$db})) {$format = $knownformats{$db}} else{print STDERR "Unknown format for '$db'\n"} print SERVER " DBNAME $db [ type: \"$type\" format: \"$format\" "; if (-e "entrez.$db") {system "rm entrez.$db"} $status = system "wget -q -O entrez.$db \"http://eutils.ncbi.nlm.nih.gov/entrez/eutils/einfo.fcgi?db=$db\""; open (DBINFO, "entrez.$db") || die "Unable to open 'entrez.$db'"; $isfield=0; $isintro = 1; %fullname = (); %fulldesc = (); @fields = (); while () { if(//) {$isfield = 1;$isintro = 0} if(/<\/Field>/) {$isfield = 0} if($isintro) { if(/([^<]+)<\/Description>/) { $dbdesc{$db} = $1; print SERVER " comment: \"$dbdesc{$db}\"\n"; } } if(!$isfield){next} if(/([^<]+)<\/Name>/) { $field = $1; push @fields, $field; } elsif(/([^<]+)<\/FullName>/) { $fullname{$field} = $1; $fullname{$field} =~ s/[\s\/]/_/g; $fullname{$field} =~ s/\'//g; } elsif(/([^<]+)<\/Description>/) { $fulldesc{$field} = $1; $fulldesc{$field} =~ s/\'/'/g; } } close DBINFO; foreach $fd (@fields) { print SERVER " field: \"$fd $fullname{$fd} ! $fulldesc{$fd}\"\n"; } print SERVER "]\n"; } close SERVER; foreach $d (sort(keys(%knowntypes))){ if(!defined($dbdesc{$d})) { print STDERR "Expected database '$d' not found\n"; } }