rnalib.constants module

rnalib.constants.CANONICAL_CHROMOSOMES = {'GRCh38': ['chr1', 'chr2', 'chr3', 'chr4', 'chr5', 'chr6', 'chr7', 'chr8', 'chr9', 'chr10', 'chr11', 'chr12', 'chr13', 'chr14', 'chr15', 'chr16', 'chr17', 'chr18', 'chr19', 'chr20', 'chr21', 'chr22', 'chrX', 'chrY', 'chrM'], 'GRCm38': ['chr1', 'chr2', 'chr3', 'chr4', 'chr5', 'chr6', 'chr7', 'chr8', 'chr9', 'chr10', 'chr11', 'chr12', 'chr13', 'chr14', 'chr15', 'chr16', 'chr17', 'chr18', 'chr19', 'chrX', 'chrY', 'chrMT'], 'dmel': ['2L', '2R', '3L', '3R', '4', 'X', 'Y'], 'mm39': ['chr1', 'chr2', 'chr3', 'chr4', 'chr5', 'chr6', 'chr7', 'chr8', 'chr9', 'chr10', 'chr11', 'chr12', 'chr13', 'chr14', 'chr15', 'chr16', 'chr17', 'chr18', 'chr19', 'chrX', 'chrY', 'chrMT']}: Convenience lists of canonical chromosome names

rnalib.constants.MAX_INT = 2147483647: maximum integer value, assuming 32-bit ints

rnalib.constants.FTYPE_TO_SO = {'3UTR': 'three_prime_UTR', '5UTR': 'five_prime_UTR', 'CDS': 'CDS', 'UTR3': 'three_prime_UTR', 'UTR5': 'five_prime_UTR', 'exon': 'exon', 'five_prime_UTR': 'five_prime_UTR', 'gene': 'gene', 'intron': 'intron', 'lnc_RNA': 'transcript', 'mRNA': 'transcript', 'miRNA': 'transcript', 'ncRNA': 'transcript', 'ncRNA_gene': 'gene', 'pre_miRNA': 'transcript', 'pseudogenic_transcript': 'transcript', 'rRNA': 'transcript', 'snRNA': 'transcript', 'snoRNA': 'transcript', 'tRNA': 'transcript', 'three_prime_UTR': 'three_prime_UTR', 'transcript': 'transcript'}: Maps valid sub-feature types (e.g., ‘exon’, ‘CDS’) types to SO terms (e.g., ‘3UTR’ -> ‘three_prime_UTR’)

rnalib.constants.GFF_FLAVOURS = {('chess', 'gff'): {'copied_fields': ['source', 'gene_type'], 'feat_tid': 'Parent', 'ftype_to_SO': {'3UTR': 'three_prime_UTR', '5UTR': 'five_prime_UTR', 'CDS': 'CDS', 'UTR3': 'three_prime_UTR', 'UTR5': 'five_prime_UTR', 'exon': 'exon', 'five_prime_UTR': 'five_prime_UTR', 'gene': 'gene', 'intron': 'intron', 'lnc_RNA': 'transcript', 'mRNA': 'transcript', 'miRNA': 'transcript', 'ncRNA': 'transcript', 'ncRNA_gene': 'gene', 'pre_miRNA': 'transcript', 'pseudogenic_transcript': 'transcript', 'rRNA': 'transcript', 'snRNA': 'transcript', 'snoRNA': 'transcript', 'tRNA': 'transcript', 'three_prime_UTR': 'three_prime_UTR', 'transcript': 'transcript'}, 'gene_name': 'gene_name', 'gid': None, 'tid': 'ID', 'tx_gid': 'Parent'}, ('chess', 'gtf'): {'copied_fields': ['source', 'gene_type'], 'feat_tid': 'transcript_id', 'ftype_to_SO': {'3UTR': 'three_prime_UTR', '5UTR': 'five_prime_UTR', 'CDS': 'CDS', 'UTR3': 'three_prime_UTR', 'UTR5': 'five_prime_UTR', 'exon': 'exon', 'five_prime_UTR': 'five_prime_UTR', 'gene': 'gene', 'intron': 'intron', 'lnc_RNA': 'transcript', 'mRNA': 'transcript', 'miRNA': 'transcript', 'ncRNA': 'transcript', 'ncRNA_gene': 'gene', 'pre_miRNA': 'transcript', 'pseudogenic_transcript': 'transcript', 'rRNA': 'transcript', 'snRNA': 'transcript', 'snoRNA': 'transcript', 'tRNA': 'transcript', 'three_prime_UTR': 'three_prime_UTR', 'transcript': 'transcript'}, 'gene_name': 'gene_name', 'gid': None, 'tid': 'transcript_id', 'tx_gid': 'gene_id'}, ('ensembl', 'gff'): {'copied_fields': ['source', 'gene_type'], 'feat_tid': 'Parent', 'ftype_to_SO': {'3UTR': 'three_prime_UTR', '5UTR': 'five_prime_UTR', 'CDS': 'CDS', 'UTR3': 'three_prime_UTR', 'UTR5': 'five_prime_UTR', 'exon': 'exon', 'five_prime_UTR': 'five_prime_UTR', 'gene': 'gene', 'intron': 'intron', 'lnc_RNA': 'transcript', 'mRNA': 'transcript', 'miRNA': 'transcript', 'ncRNA': 'transcript', 'ncRNA_gene': 'gene', 'pre_miRNA': 'transcript', 'pseudogene': 'gene', 'pseudogenic_transcript': 'transcript', 'rRNA': 'transcript', 'snRNA': 'transcript', 'snoRNA': 'transcript', 'tRNA': 'transcript', 'three_prime_UTR': 'three_prime_UTR', 'transcript': 'transcript'}, 'gene_name': 'Name', 'gid': 'ID', 'tid': 'ID', 'tx_gid': 'Parent'}, ('flybase', 'gtf'): {'copied_fields': ['source', 'gene_type'], 'feat_tid': 'transcript_id', 'ftype_to_SO': {'3UTR': 'three_prime_UTR', '5UTR': 'five_prime_UTR', 'CDS': 'CDS', 'UTR3': 'three_prime_UTR', 'UTR5': 'five_prime_UTR', 'exon': 'exon', 'five_prime_UTR': 'five_prime_UTR', 'gene': 'gene', 'intron': 'intron', 'lnc_RNA': 'transcript', 'mRNA': 'transcript', 'miRNA': 'transcript', 'ncRNA': 'transcript', 'ncRNA_gene': 'gene', 'pre_miRNA': 'transcript', 'pseudogene': 'transcript', 'pseudogenic_transcript': 'transcript', 'rRNA': 'transcript', 'snRNA': 'transcript', 'snoRNA': 'transcript', 'tRNA': 'transcript', 'three_prime_UTR': 'three_prime_UTR', 'transcript': 'transcript'}, 'gene_name': 'gene_symbol', 'gid': 'gene_id', 'tid': 'transcript_id', 'tx_gid': 'gene_id'}, ('gencode', 'gff'): {'copied_fields': ['source', 'gene_type'], 'feat_tid': 'Parent', 'ftype_to_SO': {'3UTR': 'three_prime_UTR', '5UTR': 'five_prime_UTR', 'CDS': 'CDS', 'UTR3': 'three_prime_UTR', 'UTR5': 'five_prime_UTR', 'exon': 'exon', 'five_prime_UTR': 'five_prime_UTR', 'gene': 'gene', 'intron': 'intron', 'lnc_RNA': 'transcript', 'mRNA': 'transcript', 'miRNA': 'transcript', 'ncRNA': 'transcript', 'ncRNA_gene': 'gene', 'pre_miRNA': 'transcript', 'pseudogenic_transcript': 'transcript', 'rRNA': 'transcript', 'snRNA': 'transcript', 'snoRNA': 'transcript', 'tRNA': 'transcript', 'three_prime_UTR': 'three_prime_UTR', 'transcript': 'transcript'}, 'gene_name': 'gene_name', 'gid': 'ID', 'tid': 'ID', 'tx_gid': 'Parent'}, ('gencode', 'gtf'): {'copied_fields': ['source', 'gene_type'], 'feat_tid': 'transcript_id', 'ftype_to_SO': {'3UTR': 'three_prime_UTR', '5UTR': 'five_prime_UTR', 'CDS': 'CDS', 'UTR3': 'three_prime_UTR', 'UTR5': 'five_prime_UTR', 'exon': 'exon', 'five_prime_UTR': 'five_prime_UTR', 'gene': 'gene', 'intron': 'intron', 'lnc_RNA': 'transcript', 'mRNA': 'transcript', 'miRNA': 'transcript', 'ncRNA': 'transcript', 'ncRNA_gene': 'gene', 'pre_miRNA': 'transcript', 'pseudogenic_transcript': 'transcript', 'rRNA': 'transcript', 'snRNA': 'transcript', 'snoRNA': 'transcript', 'tRNA': 'transcript', 'three_prime_UTR': 'three_prime_UTR', 'transcript': 'transcript'}, 'gene_name': 'gene_name', 'gid': 'gene_id', 'tid': 'transcript_id', 'tx_gid': 'gene_id'}, ('generic', 'gff'): {'copied_fields': [], 'feat_tid': 'Parent', 'ftype_to_SO': {'3UTR': 'three_prime_UTR', '5UTR': 'five_prime_UTR', 'CDS': 'CDS', 'UTR3': 'three_prime_UTR', 'UTR5': 'five_prime_UTR', 'exon': 'exon', 'five_prime_UTR': 'five_prime_UTR', 'gene': 'gene', 'intron': 'intron', 'lnc_RNA': 'transcript', 'mRNA': 'transcript', 'miRNA': 'transcript', 'ncRNA': 'transcript', 'ncRNA_gene': 'gene', 'pre_miRNA': 'transcript', 'pseudogenic_transcript': 'transcript', 'rRNA': 'transcript', 'snRNA': 'transcript', 'snoRNA': 'transcript', 'tRNA': 'transcript', 'three_prime_UTR': 'three_prime_UTR', 'transcript': 'transcript'}, 'gene_name': 'gene_name', 'gid': 'ID', 'tid': 'ID', 'tx_gid': 'Parent'}, ('generic', 'gtf'): {'copied_fields': [], 'feat_tid': 'transcript_id', 'ftype_to_SO': {'3UTR': 'three_prime_UTR', '5UTR': 'five_prime_UTR', 'CDS': 'CDS', 'UTR3': 'three_prime_UTR', 'UTR5': 'five_prime_UTR', 'exon': 'exon', 'five_prime_UTR': 'five_prime_UTR', 'gene': 'gene', 'intron': 'intron', 'lnc_RNA': 'transcript', 'mRNA': 'transcript', 'miRNA': 'transcript', 'ncRNA': 'transcript', 'ncRNA_gene': 'gene', 'pre_miRNA': 'transcript', 'pseudogenic_transcript': 'transcript', 'rRNA': 'transcript', 'snRNA': 'transcript', 'snoRNA': 'transcript', 'tRNA': 'transcript', 'three_prime_UTR': 'three_prime_UTR', 'transcript': 'transcript'}, 'gene_name': 'gene_name', 'gid': 'gene_id', 'tid': 'transcript_id', 'tx_gid': 'gene_id'}, ('mirbase', 'gff'): {'copied_fields': ['source', 'Alias'], 'feat_tid': None, 'ftype_to_SO': {'miRNA': 'transcript', 'miRNA_primary_transcript': 'transcript'}, 'gene_name': 'Alias', 'gid': None, 'tid': 'ID', 'tx_gid': None}, ('mirgenedb', 'gff'): {'copied_fields': ['source', 'Alias'], 'feat_tid': None, 'ftype_to_SO': {'miRNA': 'transcript', 'pre_miRNA': 'transcript'}, 'gene_name': 'Alias', 'gid': None, 'tid': 'ID', 'tx_gid': None}, ('ucsc', 'gtf'): {'copied_fields': ['source', 'gene_type'], 'feat_tid': 'transcript_id', 'ftype_to_SO': {'3UTR': 'three_prime_UTR', '5UTR': 'five_prime_UTR', 'CDS': 'CDS', 'UTR3': 'three_prime_UTR', 'UTR5': 'five_prime_UTR', 'exon': 'exon', 'five_prime_UTR': 'five_prime_UTR', 'gene': 'gene', 'intron': 'intron', 'lnc_RNA': 'transcript', 'mRNA': 'transcript', 'miRNA': 'transcript', 'ncRNA': 'transcript', 'ncRNA_gene': 'gene', 'pre_miRNA': 'transcript', 'pseudogenic_transcript': 'transcript', 'rRNA': 'transcript', 'snRNA': 'transcript', 'snoRNA': 'transcript', 'tRNA': 'transcript', 'three_prime_UTR': 'three_prime_UTR', 'transcript': 'transcript'}, 'gene_name': 'gene_name', 'gid': None, 'tid': 'transcript_id', 'tx_gid': 'gene_id'}, ('wormbase', 'gff'): {'copied_fields': ['source', 'biotype', 'so_term_name'], 'feat_tid': 'Parent', 'ftype_to_SO': {'3UTR': 'three_prime_UTR', '5UTR': 'five_prime_UTR', 'CDS': 'CDS', 'UTR3': 'three_prime_UTR', 'UTR5': 'five_prime_UTR', 'exon': 'exon', 'five_prime_UTR': 'five_prime_UTR', 'gene': 'gene', 'intron': 'intron', 'lnc_RNA': 'transcript', 'mRNA': 'transcript', 'miRNA': 'transcript', 'ncRNA': 'transcript', 'ncRNA_gene': 'gene', 'pre_miRNA': 'transcript', 'pseudogenic_transcript': None, 'rRNA': 'transcript', 'snRNA': None, 'snoRNA': 'transcript', 'tRNA': 'transcript', 'three_prime_UTR': 'three_prime_UTR', 'transcript': 'transcript'}, 'gene_name': 'Name', 'gid': 'ID', 'tid': 'ID', 'tx_gid': 'Parent'}}: Maps info field names for various GFF flavours

class rnalib.constants.BamFlag(value, names=<not given>, *values, module=None, qualname=None, type=None, start=1, boundary=None)[source]

Bases: IntEnum

BAM flags, @see https://broadinstitute.github.io/picard/explain-flags.html

BAM_FPAIRED = 1

BAM_FPROPER_PAIR = 2

BAM_FUNMAP = 4

BAM_FMUNMAP = 8

BAM_FREVERSE = 16

BAM_FMREVERSE = 32

BAM_FREAD1 = 64

BAM_FREAD2 = 128

BAM_FSECONDARY = 256

BAM_FQCFAIL = 512

BAM_FDUP = 1024

BAM_SUPPLEMENTARY = 2048

rnalib.constants.DEFAULT_FLAG_FILTER = 3844: default BAM flag filter (int 3844); comparable to samtools view -F 3844; also used as default filter in IGV.

rnalib.constants.SEP = <IPython.core.display.Markdown object>: Markdown separator for jupyter notebooks; display(SEP)

rnalib.constants.mygeneinfo_fields = {'AnimalQTLdb': 'text', 'FLYBASE': 'keyword', 'HGNC': 'keyword', 'HPRD': 'keyword', 'MGI': 'keyword', 'MIM': 'keyword', 'RATMAP': 'keyword', 'RGD': 'keyword', 'SGD': 'keyword', 'TAIR': 'keyword', 'Vega': 'text', 'WormBase': 'keyword', 'Xenbase': 'keyword', 'ZFIN': 'keyword', 'accession': 'object', 'accession.genomic': 'text', 'accession.protein': 'text', 'accession.rna': 'text', 'accession.translation': 'object', 'alias': 'keyword', 'biocarta': 'text', 'clingen': 'object', 'clingen.clinical_validity': 'object', 'clingen.clinical_validity.classification': 'keyword', 'clingen.clinical_validity.classification_date': 'date', 'clingen.clinical_validity.disease_label': 'text', 'clingen.clinical_validity.gcep': 'text', 'clingen.clinical_validity.moi': 'keyword', 'clingen.clinical_validity.mondo': 'keyword', 'clingen.clinical_validity.online_report': 'text', 'clingen.clinical_validity.sop': 'keyword', 'ec': 'keyword', 'ensembl': 'object', 'ensembl.gene': 'keyword', 'ensembl.protein': 'keyword', 'ensembl.transcript': 'keyword', 'ensembl.translation': 'object', 'ensembl.type_of_gene': 'keyword', 'entrezgene': 'keyword', 'exac': 'object', 'exac.all': 'object', 'exac.bp': 'integer', 'exac.cds_end': 'integer', 'exac.cds_start': 'integer', 'exac.n_exons': 'integer', 'exac.nonpsych': 'object', 'exac.nontcga': 'object', 'exac.transcript': 'text', 'exons': 'object', 'exons_hg19': 'object', 'exons_mm10': 'object', 'exons_mm9': 'object', 'generif': 'object', 'generif.pubmed': 'long', 'generif.text': 'text', 'genomic_pos': 'object', 'genomic_pos.chr': 'keyword', 'genomic_pos.end': 'long', 'genomic_pos.start': 'long', 'genomic_pos.strand': 'byte', 'genomic_pos_hg19': 'object', 'genomic_pos_hg19.chr': 'keyword', 'genomic_pos_hg19.end': 'long', 'genomic_pos_hg19.start': 'long', 'genomic_pos_hg19.strand': 'byte', 'genomic_pos_mm9': 'object', 'genomic_pos_mm9.chr': 'keyword', 'genomic_pos_mm9.end': 'long', 'genomic_pos_mm9.start': 'long', 'genomic_pos_mm9.strand': 'byte', 'go': 'object', 'go.BP': 'object', 'go.BP.category': 'text', 'go.BP.evidence': 'text', 'go.BP.id': 'keyword', 'go.BP.pubmed': 'long', 'go.BP.term': 'text', 'go.CC': 'object', 'go.CC.category': 'text', 'go.CC.evidence': 'text', 'go.CC.id': 'keyword', 'go.CC.pubmed': 'long', 'go.CC.term': 'text', 'go.MF': 'object', 'go.MF.category': 'text', 'go.MF.evidence': 'text', 'go.MF.id': 'keyword', 'go.MF.pubmed': 'long', 'go.MF.term': 'text', 'homologene': 'object', 'homologene.genes': 'long', 'homologene.id': 'long', 'humancyc': 'text', 'interpro': 'object', 'interpro.desc': 'text', 'interpro.id': 'keyword', 'interpro.short_desc': 'text', 'ipi': 'keyword', 'kegg': 'text', 'locus_tag': 'keyword', 'map_location': 'text', 'miRBase': 'keyword', 'mousecyc': 'text', 'name': 'text', 'netpath': 'text', 'other_names': 'text', 'pantherdb': 'object', 'pantherdb.Araport': 'keyword', 'pantherdb.EcoGene': 'keyword', 'pantherdb.Ensembl': 'keyword', 'pantherdb.EnsemblGenome': 'keyword', 'pantherdb.FlyBase': 'keyword', 'pantherdb.Gene': 'keyword', 'pantherdb.GeneID': 'keyword', 'pantherdb.Gene_Name': 'keyword', 'pantherdb.Gene_ORFName': 'keyword', 'pantherdb.Gene_OrderedLocusName': 'keyword', 'pantherdb.HGNC': 'keyword', 'pantherdb.MGI': 'keyword', 'pantherdb.PomBase': 'keyword', 'pantherdb.RGD': 'keyword', 'pantherdb.SGD': 'keyword', 'pantherdb.TAIR': 'keyword', 'pantherdb.WormBase': 'keyword', 'pantherdb.ZFIN': 'keyword', 'pantherdb.dictyBase': 'keyword', 'pantherdb.ortholog': 'object', 'pantherdb.ortholog.Araport': 'keyword', 'pantherdb.ortholog.EcoGene': 'keyword', 'pantherdb.ortholog.Ensembl': 'keyword', 'pantherdb.ortholog.EnsemblGenome': 'keyword', 'pantherdb.ortholog.FlyBase': 'keyword', 'pantherdb.ortholog.Gene': 'keyword', 'pantherdb.ortholog.GeneCards': 'keyword', 'pantherdb.ortholog.GeneID': 'keyword', 'pantherdb.ortholog.Gene_Name': 'keyword', 'pantherdb.ortholog.Gene_ORFName': 'keyword', 'pantherdb.ortholog.Gene_OrderedLocusName': 'keyword', 'pantherdb.ortholog.HGNC': 'keyword', 'pantherdb.ortholog.MGI': 'keyword', 'pantherdb.ortholog.PomBase': 'keyword', 'pantherdb.ortholog.RGD': 'keyword', 'pantherdb.ortholog.SGD': 'keyword', 'pantherdb.ortholog.TAIR': 'keyword', 'pantherdb.ortholog.WormBase': 'keyword', 'pantherdb.ortholog.ZFIN': 'keyword', 'pantherdb.ortholog.dictyBase': 'keyword', 'pantherdb.ortholog.ortholog_type': 'keyword', 'pantherdb.ortholog.panther_family': 'keyword', 'pantherdb.ortholog.taxid': 'integer', 'pantherdb.ortholog.uniprot_kb': 'keyword', 'pantherdb.uniprot_kb': 'keyword', 'pathway': 'object', 'pathway.biocarta': 'object', 'pathway.biocarta.id': 'text', 'pathway.biocarta.name': 'text', 'pathway.humancyc': 'object', 'pathway.humancyc.id': 'text', 'pathway.humancyc.name': 'text', 'pathway.kegg': 'object', 'pathway.kegg.id': 'text', 'pathway.kegg.name': 'text', 'pathway.mousecyc': 'object', 'pathway.mousecyc.id': 'text', 'pathway.mousecyc.name': 'text', 'pathway.netpath': 'object', 'pathway.netpath.id': 'text', 'pathway.netpath.name': 'text', 'pathway.pharmgkb': 'object', 'pathway.pharmgkb.id': 'text', 'pathway.pharmgkb.name': 'text', 'pathway.pid': 'object', 'pathway.pid.id': 'text', 'pathway.pid.name': 'text', 'pathway.reactome': 'object', 'pathway.reactome.id': 'text', 'pathway.reactome.name': 'text', 'pathway.smpdb': 'object', 'pathway.smpdb.id': 'text', 'pathway.smpdb.name': 'text', 'pathway.wikipathways': 'object', 'pathway.wikipathways.id': 'text', 'pathway.wikipathways.name': 'text', 'pathway.yeastcyc': 'object', 'pathway.yeastcyc.id': 'text', 'pathway.yeastcyc.name': 'text', 'pdb': 'keyword', 'pfam': 'keyword', 'pharmgkb': 'keyword', 'pharos': 'object', 'pharos.target_id': 'integer', 'pid': 'text', 'pir': 'keyword', 'prosite': 'keyword', 'reactome': 'text', 'reagent': 'object', 'reagent.CM-LibrX-no-seq': 'object', 'reagent.CM-LibrX-no-seq.id': 'keyword', 'reagent.CM-LibrX-no-seq.relationship': 'text', 'reagent.CondMedia_CM_LibrAB': 'object', 'reagent.CondMedia_CM_LibrAB.id': 'keyword', 'reagent.CondMedia_CM_LibrAB.relationship': 'text', 'reagent.GNF_Qia_hs-genome_v1_siRNA': 'object', 'reagent.GNF_Qia_hs-genome_v1_siRNA.id': 'keyword', 'reagent.GNF_Qia_hs-genome_v1_siRNA.relationship': 'text', 'reagent.GNF_hs-GPCR_IDT-siRNA': 'object', 'reagent.GNF_hs-GPCR_IDT-siRNA.id': 'keyword', 'reagent.GNF_hs-GPCR_IDT-siRNA.relationship': 'text', 'reagent.GNF_hs-ORFeome1_1_reads': 'object', 'reagent.GNF_hs-ORFeome1_1_reads.id': 'keyword', 'reagent.GNF_hs-ORFeome1_1_reads.relationship': 'text', 'reagent.GNF_hs-Origene': 'object', 'reagent.GNF_hs-Origene.id': 'keyword', 'reagent.GNF_hs-Origene.relationship': 'text', 'reagent.GNF_hs-druggable_lenti-shRNA': 'object', 'reagent.GNF_hs-druggable_lenti-shRNA.id': 'keyword', 'reagent.GNF_hs-druggable_lenti-shRNA.relationship': 'text', 'reagent.GNF_hs-druggable_plasmid-shRNA': 'object', 'reagent.GNF_hs-druggable_plasmid-shRNA.id': 'keyword', 'reagent.GNF_hs-druggable_plasmid-shRNA.relationship': 'text', 'reagent.GNF_hs-druggable_siRNA': 'object', 'reagent.GNF_hs-druggable_siRNA.id': 'keyword', 'reagent.GNF_hs-druggable_siRNA.relationship': 'text', 'reagent.GNF_hs-oncomine_IDT-siRNA': 'object', 'reagent.GNF_hs-oncomine_IDT-siRNA.id': 'keyword', 'reagent.GNF_hs-oncomine_IDT-siRNA.relationship': 'text', 'reagent.GNF_hs-pkinase_IDT-siRNA': 'object', 'reagent.GNF_hs-pkinase_IDT-siRNA.id': 'keyword', 'reagent.GNF_hs-pkinase_IDT-siRNA.relationship': 'text', 'reagent.GNF_hs_LentiORF-HA-MYC': 'object', 'reagent.GNF_hs_LentiORF-HA-MYC.id': 'keyword', 'reagent.GNF_hs_LentiORF-HA-MYC.relationship': 'text', 'reagent.GNF_hs_LentiORF-Jred': 'object', 'reagent.GNF_hs_LentiORF-Jred.id': 'keyword', 'reagent.GNF_hs_LentiORF-Jred.relationship': 'text', 'reagent.GNF_mm+hs-MGC': 'object', 'reagent.GNF_mm+hs-MGC.id': 'keyword', 'reagent.GNF_mm+hs-MGC.relationship': 'text', 'reagent.GNF_mm+hs_RetroCDNA': 'object', 'reagent.GNF_mm+hs_RetroCDNA.id': 'keyword', 'reagent.GNF_mm+hs_RetroCDNA.relationship': 'text', 'reagent.GNF_mm-GIPZ_shRNA': 'object', 'reagent.GNF_mm-GIPZ_shRNA.id': 'keyword', 'reagent.GNF_mm-GIPZ_shRNA.relationship': 'text', 'reagent.GNF_mm-TLR_lenti_shRNA': 'object', 'reagent.GNF_mm-TLR_lenti_shRNA.id': 'keyword', 'reagent.GNF_mm-TLR_lenti_shRNA.relationship': 'text', 'reagent.GNF_mm-kinase_lenti-shRNA': 'object', 'reagent.GNF_mm-kinase_lenti-shRNA.id': 'keyword', 'reagent.GNF_mm-kinase_lenti-shRNA.relationship': 'text', 'reagent.GNF_mm-kinase_plasmid-shRNA': 'object', 'reagent.GNF_mm-kinase_plasmid-shRNA.id': 'keyword', 'reagent.GNF_mm-kinase_plasmid-shRNA.relationship': 'text', 'reagent.IDT_27mer_hs_ATPase_siRNAs': 'object', 'reagent.IDT_27mer_hs_ATPase_siRNAs.id': 'keyword', 'reagent.IDT_27mer_hs_ATPase_siRNAs.relationship': 'text', 'reagent.Invitrogen_IVTHSSIPKv2': 'object', 'reagent.Invitrogen_IVTHSSIPKv2.id': 'keyword', 'reagent.Invitrogen_IVTHSSIPKv2.relationship': 'text', 'reagent.MasterSecretomicsList': 'object', 'reagent.MasterSecretomicsList.id': 'keyword', 'reagent.MasterSecretomicsList.relationship': 'text', 'reagent.NIBRI_hs-Secretome_pDEST': 'object', 'reagent.NIBRI_hs-Secretome_pDEST.id': 'keyword', 'reagent.NIBRI_hs-Secretome_pDEST.relationship': 'text', 'reagent.NOVART_hs-genome_siRNA': 'object', 'reagent.NOVART_hs-genome_siRNA.id': 'keyword', 'reagent.NOVART_hs-genome_siRNA.relationship': 'text', 'reagent.Qiagen_mouse_QMIHSINHIBv1': 'object', 'reagent.Qiagen_mouse_QMIHSINHIBv1.id': 'keyword', 'reagent.Qiagen_mouse_QMIHSINHIBv1.relationship': 'text', 'reagent.Qiagen_mouse_QMIHSMIMv1': 'object', 'reagent.Qiagen_mouse_QMIHSMIMv1.id': 'keyword', 'reagent.Qiagen_mouse_QMIHSMIMv1.relationship': 'text', 'refseq': 'object', 'refseq.genomic': 'text', 'refseq.protein': 'text', 'refseq.rna': 'text', 'refseq.translation': 'object', 'reporter': 'object', 'reporter.AraGene-1_0': 'keyword', 'reporter.BovGene-1_0': 'keyword', 'reporter.CanGene-1_0': 'keyword', 'reporter.ChiGene-1_0': 'keyword', 'reporter.CyRGene-1_0': 'keyword', 'reporter.CynGene-1_0': 'keyword', 'reporter.DroGene-1_0': 'keyword', 'reporter.EleGene-1_0': 'keyword', 'reporter.EquGene-1_0': 'keyword', 'reporter.FelGene-1_0': 'keyword', 'reporter.GNF1H': 'keyword', 'reporter.GNF1M': 'keyword', 'reporter.GuiGene-1_0': 'keyword', 'reporter.HG-U133_Plus_2': 'keyword', 'reporter.HG-U95Av2': 'keyword', 'reporter.HG-U95B': 'keyword', 'reporter.HTA-2_0': 'keyword', 'reporter.HuEx-1_0': 'keyword', 'reporter.HuGene-1_1': 'keyword', 'reporter.HuGene-2_1': 'keyword', 'reporter.MG-U74Av2': 'keyword', 'reporter.MG-U74Bv2': 'keyword', 'reporter.MTA-1_0': 'keyword', 'reporter.MarGene-1_0': 'keyword', 'reporter.MoEx-1_0': 'keyword', 'reporter.MoGene-1_1': 'keyword', 'reporter.MoGene-2_1': 'keyword', 'reporter.Mouse430_2': 'keyword', 'reporter.PorGene-1_0': 'keyword', 'reporter.RCnGene-1_0': 'keyword', 'reporter.RG-U34A': 'keyword', 'reporter.RG-U34B': 'keyword', 'reporter.RJpGene-1_0': 'keyword', 'reporter.RUSGene-1_0': 'keyword', 'reporter.RaEx-1_0': 'keyword', 'reporter.RaGene-1_1': 'keyword', 'reporter.RaGene-2_1': 'keyword', 'reporter.RabGene-1_0': 'keyword', 'reporter.Rat230_2': 'keyword', 'reporter.RheGene-1_0': 'keyword', 'reporter.SoyGene-1_0': 'keyword', 'reporter.ZebGene-1_0': 'keyword', 'reporter.snowball': 'keyword', 'retired': 'long', 'smpdb': 'text', 'summary': 'text', 'symbol': 'keyword', 'taxid': 'integer', 'type_of_gene': 'keyword', 'umls': 'object', 'umls.cui': 'keyword', 'umls.protein_cui': 'keyword', 'unigene': 'keyword', 'uniprot': 'object', 'uniprot.Swiss-Prot': 'keyword', 'uniprot.TrEMBL': 'keyword', 'wikipathways': 'text', 'wikipedia': 'object', 'wikipedia.url_stub': 'text', 'yeastcyc': 'text'}: mygeneinfo fields