Parse everything available in an imported xml document resulted from
hpaXmlGet(), based on the Human Protein Atlas xml schema
(https://www.proteinatlas.org/download/proteinatlas.xsd). Unlike the
other hpaXml functions, which each extract one specific piece of
information, hpaXmlParse() generically walks the entire xml tree and
normalizes it into a flat, single-level named list of tibbles, similar to a
small relational database extracted from the xml file.
Arguments
- importedXml
Input an xml document object resulted from a
hpaXmlGet()call.
Value
This function returns a flat, named list of tibbles. See Details for how the tibbles are named and joined to each other.
Details
Every row, except the single top-level result$entry row, carries a
foreign key column named "<parent>_id" pointing back at the row (in
another tibble) it belongs to. For example, rows in
result$tissueCell carry a data_id that matches the
data_id of their parent row in result$data, and
result$tissueCell_level rows carry a tissueCell_id pointing
back at result$tissueCell.
Two kinds of tibble are produced. Tibbles for nested entities
(entry, data, patient, image,
antibody, ...) keep their plain tag name, since they represent the
same kind of record wherever they occur, and additionally have a surrogate
key column named "<name>_id" that their own children point at.
Tibbles for leaf/property-style elements are instead named
"<parent>_<tag>" (e.g. tissueCell_level,
patient_location), because some xml tags are reused with different
meaning under different parents (for example level means staining
intensity under tissueCell but RNA abundance under data);
nothing refers back to their rows, so they carry the parent's foreign key
only and have no surrogate key of their own.
In a leaf/property tibble, the element's own text content is held in a
column literally named "value" and its xml attributes keep their
own names as columns, so e.g. result$tissueCell_cellType$value
holds the cell type name. A leaf element that the schema guarantees can
never repeat gets no tibble at all and is merged into its parent's row
instead: its text content becomes a column named after the tag (e.g.
result$entry$name, result$data$tissue) and any attributes
become columns named "<tag>_<attribute>".
Because the function is driven entirely by the xml structure itself
(whether an xml tag is, per the schema, allowed to occur more than once)
rather than by hand-written per-element extraction code, its output shape
does not depend on which gene was parsed, gracefully tolerates xml files
that are missing elements the schema allows, and requires no code changes
to support new elements introduced by future HPA schema revisions.
hpaXmlParse() only includes tibbles for elements that are actually
present in the imported document; an element absent for a given gene (for
example an antibody with no western blot data) simply has no
corresponding entry in the returned list.
See also
Other xml functions:
hpaXml(),
hpaXmlAntibody(),
hpaXmlGet(),
hpaXmlProtClass(),
hpaXmlTissueExpr(),
hpaXmlTissueExprSum()
Examples
GCH1xml <- hpaXmlGet('ENSG00000131979')
hpaXmlParse(GCH1xml)
#> $antibody
#> # A tibble: 5 × 12
#> name start_position end_position identity_percent chain_id antibody_id id
#> <chr> <chr> <chr> <chr> <int> <int> <chr>
#> 1 HPA02… 65 183 100 1 1 NA
#> 2 HPA02… 65 183 100 2 2 NA
#> 3 HPA02… 65 183 100 3 3 NA
#> 4 HPA02… 65 183 100 4 4 NA
#> 5 NA NA NA NA NA 5 HPA0…
#> # ℹ 5 more variables: releaseVersion <chr>, releaseDate <chr>, entry_id <int>,
#> # antigenSequence_source <chr>, antigenSequence <chr>
#>
#> $antibodyTargetWeights
#> # A tibble: 1 × 3
#> source antibody_id antibodyTargetWeights_id
#> <chr> <int> <int>
#> 1 HPA 5 1
#>
#> $antibodyTargetWeights_weight
#> # A tibble: 3 × 3
#> value unit antibodyTargetWeights_id
#> <chr> <chr> <int>
#> 1 27.9 kDa 1
#> 2 25.8 kDa 1
#> 3 23.5 kDa 1
#>
#> $assayImage
#> # A tibble: 525 × 3
#> sample_id assayImage_id data_id
#> <int> <int> <int>
#> 1 1 1 NA
#> 2 2 2 NA
#> 3 3 3 NA
#> 4 4 4 NA
#> 5 5 5 NA
#> 6 6 6 NA
#> 7 7 7 NA
#> 8 8 8 NA
#> 9 9 9 NA
#> 10 10 10 NA
#> # ℹ 515 more rows
#>
#> $blotLanes
#> # A tibble: 1 × 2
#> westernBlot_id blotLanes_id
#> <int> <int>
#> 1 1 1
#>
#> $cancerExpression
#> # A tibble: 1 × 7
#> source technology assayType entry_id cancerExpression_id rnaCancerSpecificity
#> <chr> <chr> <chr> <int> <int> <chr>
#> 1 HPA RNA cancer 1 1 Low cancer specifici…
#> # ℹ 1 more variable: rnaCancerDistribution <chr>
#>
#> $cellExpression
#> # A tibble: 2 × 8
#> source technology entry_id cellExpression_id summary verification_type
#> <chr> <chr> <int> <int> <chr> <chr>
#> 1 HPA ICC/IF 1 1 Mainly localiz… reliability
#> 2 HPA ICC/IF NA 2 NA NA
#> # ℹ 2 more variables: verification <chr>, antibody_id <int>
#>
#> $cellTypeExpression
#> # A tibble: 1 × 7
#> technology assayType entry_id cellTypeExpression_id cellTypeDistribution
#> <chr> <chr> <int> <int> <chr>
#> 1 scRNAseq cell 1 1 Detected in many
#> # ℹ 2 more variables: cellTypeExpressionCluster_clusterID <chr>,
#> # cellTypeExpressionCluster <chr>
#>
#> $cellTypeExpression_singleCellTypeExpression
#> # A tibble: 154 × 5
#> name type unitRNA expRNA cellTypeExpression_id
#> <chr> <chr> <chr> <chr> <int>
#> 1 Brain excitatory neurons normalizedRNAE… nCPM 6.7 1
#> 2 Brain inhibitory neurons normalizedRNAE… nCPM 11.9 1
#> 3 Retinal amacrine cells normalizedRNAE… nCPM 3.5 1
#> 4 Retinal horizontal cells normalizedRNAE… nCPM 2.0 1
#> 5 Retinal ganglion cells normalizedRNAE… nCPM 3.9 1
#> 6 Retinal bipolar cells normalizedRNAE… nCPM 2.1 1
#> 7 Rod photoreceptor cells normalizedRNAE… nCPM 9.5 1
#> 8 Cone photoreceptor cells normalizedRNAE… nCPM 35.2 1
#> 9 Other brain neurons normalizedRNAE… nCPM 13.7 1
#> 10 Astrocytes normalizedRNAE… nCPM 1.3 1
#> # ℹ 144 more rows
#>
#> $cellTypeSpecificity
#> # A tibble: 1 × 3
#> category cellTypeExpression_id cellTypeSpecificity_id
#> <chr> <int> <int>
#> 1 Cell type enhanced 1 1
#>
#> $cellTypeSpecificity_cellType
#> # A tibble: 4 × 2
#> value cellTypeSpecificity_id
#> <chr> <int>
#> 1 monocytes 1
#> 2 Neuroendocrine cells 1
#> 3 Neutrophils 1
#> 4 Pancreatic islet cells 1
#>
#> $chain
#> # A tibble: 4 × 7
#> chain length gene ensembl_peptide_id ensembl_transcript_id structure_id
#> <chr> <chr> <chr> <chr> <chr> <int>
#> 1 A 250 GCH1 ENSP00000378890 ENST00000395514 1
#> 2 A 250 GCH1 ENSP00000419045 ENST00000491895 2
#> 3 A 233 GCH1 ENSP00000444011 ENST00000543643 3
#> 4 A 213 GCH1 ENSP00000445246 ENST00000536224 4
#> # ℹ 1 more variable: chain_id <int>
#>
#> $data
#> # A tibble: 540 × 26
#> tissueExpression_id data_id tissue_organ tissue_ontologyTerms tissue
#> <int> <int> <chr> <chr> <chr>
#> 1 1 1 Connective & soft ti… UBERON:0001013 Adipo…
#> 2 1 2 Endocrine tissues UBERON:0002369 Adren…
#> 3 1 3 Bone marrow & lympho… UBERON:0013689 Appen…
#> 4 1 4 Bone marrow & lympho… UBERON:0002371 Bone …
#> 5 1 5 Female tissues UBERON:0000310,UBER… Breast
#> 6 1 6 Respiratory system UBERON:0002185 Bronc…
#> 7 1 7 Brain UBERON:0001873 Cauda…
#> 8 1 8 Brain UBERON:0002037 Cereb…
#> 9 1 9 Brain UBERON:0000956 Cereb…
#> 10 1 10 Female tissues UBERON:0000002 Cervix
#> # ℹ 530 more rows
#> # ℹ 21 more variables: cancerExpression_id <int>,
#> # survivalAnalysis_prognosticType <chr>, survivalAnalysis_isPrognostic <chr>,
#> # survivalAnalysis_prognostic <chr>, survivalAnalysis_pValue <chr>,
#> # survivalAnalysis_source <chr>, survivalAnalysis_dataSource <chr>,
#> # cellExpression_id <int>, rnaExpression_id <int>, RNASample_sampleId <chr>,
#> # RNASample_unitRNA <chr>, RNASample_expRNA <chr>, RNASample_sex <chr>, …
#>
#> $data_RNASample
#> # A tibble: 1,436 × 6
#> sampleId unitRNA expRNA sex age data_id
#> <chr> <chr> <chr> <chr> <chr> <int>
#> 1 86 nTPM 0 Female 80 133
#> 2 115 nTPM 0 Female 45 133
#> 3 137 nTPM 0.4 Female 57 133
#> 4 329 nTPM 1 Female 74 133
#> 5 331 nTPM 1.5 Female 59 133
#> 6 87 nTPM 1.2 Female 62 134
#> 7 88 nTPM 5.7 Female 36 134
#> 8 89 nTPM 9.9 Female 63 134
#> 9 92 nTPM 9.7 Male 26 135
#> 10 93 nTPM 1.5 Female 37 135
#> # ℹ 1,426 more rows
#>
#> $data_level
#> # A tibble: 1,210 × 5
#> type value data_id unitRNA expRNA
#> <chr> <chr> <int> <chr> <chr>
#> 1 expression not detected 1 NA NA
#> 2 expression medium 2 NA NA
#> 3 expression low 3 NA NA
#> 4 expression low 4 NA NA
#> 5 expression low 5 NA NA
#> 6 expression low 6 NA NA
#> 7 expression not detected 7 NA NA
#> 8 expression not detected 8 NA NA
#> 9 expression not detected 9 NA NA
#> 10 expression medium 10 NA NA
#> # ℹ 1,200 more rows
#>
#> $data_location
#> # A tibble: 9 × 5
#> status GOId value data_id singleCellVariationIntensity
#> <chr> <chr> <chr> <int> <chr>
#> 1 additional GO:0005829 cytosol 81 NA
#> 2 additional GO:0031965 nuclear membrane 81 NA
#> 3 main GO:0005654 nucleoplasm 81 NA
#> 4 NA GO:0005654 nucleoplasm 538 NA
#> 5 NA GO:0005654 nucleoplasm 539 NA
#> 6 NA GO:0005829 cytosol 539 NA
#> 7 NA GO:0005654 nucleoplasm 540 true
#> 8 NA GO:0031965 nuclear membrane 540 NA
#> 9 NA GO:0005829 cytosol 540 NA
#>
#> $entry
#> # A tibble: 1 × 5
#> version url entry_id name predictedLocation
#> <chr> <chr> <int> <chr> <chr>
#> 1 25 https://v25.proteinatlas.org/ENSG000… 1 GCH1 Intracellular
#>
#> $entry_synonym
#> # A tibble: 5 × 2
#> value entry_id
#> <chr> <int>
#> 1 DYT14 1
#> 2 DYT5 1
#> 3 DYT5a 1
#> 4 GCH 1
#> 5 GTPCH1 1
#>
#> $identifier
#> # A tibble: 1 × 7
#> id db version assembly gencodeVersion entry_id identifier_id
#> <chr> <chr> <chr> <chr> <chr> <int> <int>
#> 1 ENSG00000131979 Ensembl 109 GRCh38.… 43 1 1
#>
#> $identifier_xref
#> # A tibble: 2 × 3
#> id db identifier_id
#> <chr> <chr> <int>
#> 1 P30793 Uniprot/SWISSPROT 1
#> 2 2643 NCBI GeneID 1
#>
#> $image
#> # A tibble: 540 × 13
#> imageType tissueExpression_id image_id tissue_organ tissue_ontologyTerms
#> <chr> <int> <int> <chr> <chr>
#> 1 selected 1 1 Liver & Gallbl… UBERON:0002107
#> 2 selected 1 2 Gastrointestin… UBERON:0001155
#> 3 selected 1 3 Kidney & Urina… UBERON:0002113
#> 4 selected 1 4 Male tissues UBERON:0000473
#> 5 selected 1 5 Bone marrow & … UBERON:0000029
#> 6 selected 1 6 Brain UBERON:0000956
#> 7 selected 1 7 Female tissues UBERON:0000996
#> 8 selected NA 8 NA NA
#> 9 selected 2 9 NA NA
#> 10 sampleImage NA 10 NA NA
#> # ℹ 530 more rows
#> # ℹ 8 more variables: tissue <chr>, cellExpression_id <int>, description <chr>,
#> # assayImage_id <int>, subAssay_id <int>, scale <chr>, westernBlot_id <int>,
#> # proteinArray_id <int>
#>
#> $image_channel
#> # A tibble: 24 × 3
#> color value image_id
#> <chr> <chr> <int>
#> 1 blue Nucleus 533
#> 2 red Microtubules 533
#> 3 green Target protein 533
#> 4 yellow ER 533
#> 5 blue Nucleus 534
#> 6 red Microtubules 534
#> 7 green Target protein 534
#> 8 yellow ER 534
#> 9 blue Nucleus 535
#> 10 red Microtubules 535
#> # ℹ 14 more rows
#>
#> $image_imageUrl
#> # A tibble: 540 × 2
#> value image_id
#> <chr> <int>
#> 1 https://images.proteinatlas.org/28612/64078_A_8_4_rna_selected.jpg 1
#> 2 https://images.proteinatlas.org/28612/64078_A_7_3_rna_selected.jpg 2
#> 3 https://images.proteinatlas.org/28612/64078_A_7_5_rna_selected.jpg 3
#> 4 https://images.proteinatlas.org/28612/64078_A_4_6_rna_selected.jpg 4
#> 5 https://images.proteinatlas.org/28612/64078_A_8_8_rna_selected.jpg 5
#> 6 https://images.proteinatlas.org/28612/64078_B_8_5_rna_selected.jpg 6
#> 7 https://images.proteinatlas.org/28612/64078_B_2_2_rna_selected.jpg 7
#> 8 https://images.proteinatlas.org/28612/256_C7_2_selected.jpg 8
#> 9 https://images.proteinatlas.org/28612/ihc_selected.jpg 9
#> 10 https://images.proteinatlas.org/28612/64078_B_3_8.jpg 10
#> # ℹ 530 more rows
#>
#> $image_imageUrlTif
#> # A tibble: 516 × 2
#> value image_id
#> <chr> <int>
#> 1 https://images.proteinatlas.org/28612/64078_B_4_5.tif 16
#> 2 https://images.proteinatlas.org/28612/64078_B_5_5.tif 17
#> 3 https://images.proteinatlas.org/28612/64078_B_6_5.tif 18
#> 4 https://images.proteinatlas.org/28612/64078_A_3_2.tif 19
#> 5 https://images.proteinatlas.org/28612/64078_A_1_2.tif 20
#> 6 https://images.proteinatlas.org/28612/64078_A_2_2.tif 21
#> 7 https://images.proteinatlas.org/28612/64078_B_4_4.tif 22
#> 8 https://images.proteinatlas.org/28612/64078_B_6_4.tif 23
#> 9 https://images.proteinatlas.org/28612/64078_B_5_4.tif 24
#> 10 https://images.proteinatlas.org/28612/64078_B_1_4.tif 25
#> # ℹ 506 more rows
#>
#> $lane
#> # A tibble: 6 × 4
#> laneId laneContent blotLanes_id lane_id
#> <chr> <chr> <int> <int>
#> 1 1 Marker 1 1
#> 2 2 RT-4 1 2
#> 3 3 U-251MG 1 3
#> 4 4 Human Plasma 1 4
#> 5 5 Liver 1 5
#> 6 6 Tonsil 1 6
#>
#> $lane_weight
#> # A tibble: 9 × 3
#> value unit lane_id
#> <chr> <chr> <int>
#> 1 230 kDa 1
#> 2 130 kDa 1
#> 3 95 kDa 1
#> 4 72 kDa 1
#> 5 56 kDa 1
#> 6 36 kDa 1
#> 7 28 kDa 1
#> 8 17 kDa 1
#> 9 11 kDa 1
#>
#> $patient
#> # A tibble: 344 × 6
#> data_id patient_id sex age patientId quantity
#> <int> <int> <chr> <chr> <chr> <chr>
#> 1 469 1 Female 23 2259 NA
#> 2 469 2 Female 77 2263 NA
#> 3 469 3 Female 89 3162 NA
#> 4 469 4 Female 39 3500 NA
#> 5 469 5 Male 59 3761 NA
#> 6 469 6 Male 63 3910 NA
#> 7 470 7 Male 57 1725 NA
#> 8 470 8 Male 61 1859 NA
#> 9 470 9 Female 59 3238 NA
#> 10 471 10 Male 14 1990 NA
#> # ℹ 334 more rows
#>
#> $patient_level
#> # A tibble: 410 × 3
#> type value patient_id
#> <chr> <chr> <int>
#> 1 staining Medium 140
#> 2 intensity Moderate 140
#> 3 staining High 141
#> 4 intensity Strong 141
#> 5 staining High 142
#> 6 intensity Strong 142
#> 7 staining Medium 143
#> 8 intensity Moderate 143
#> 9 staining Medium 144
#> 10 intensity Moderate 144
#> # ℹ 400 more rows
#>
#> $patient_location
#> # A tibble: 205 × 2
#> value patient_id
#> <chr> <int>
#> 1 cytoplasmic/membranous 140
#> 2 cytoplasmic/membranous 141
#> 3 cytoplasmic/membranous 142
#> 4 cytoplasmic/membranous 143
#> 5 cytoplasmic/membranous,nuclear 144
#> 6 cytoplasmic/membranous,nuclear 145
#> 7 none 146
#> 8 cytoplasmic/membranous 147
#> 9 cytoplasmic/membranous,nuclear 148
#> 10 cytoplasmic/membranous,nuclear 149
#> # ℹ 195 more rows
#>
#> $proteinArray
#> # A tibble: 1 × 8
#> source technology antibody_id proteinArray_id verification_type
#> <chr> <chr> <int> <int> <chr>
#> 1 HPA PA 5 1 validation
#> # ℹ 3 more variables: verification_description <chr>, verification <chr>,
#> # antibodyDilution_dilution <chr>
#>
#> $proteinClasses
#> # A tibble: 1 × 2
#> entry_id proteinClasses_id
#> <int> <int>
#> 1 1 1
#>
#> $proteinClasses_proteinClass
#> # A tibble: 17 × 5
#> source id parent_id name proteinClasses_id
#> <chr> <chr> <chr> <chr> <int>
#> 1 "" Ez "" Enzymes 1
#> 2 "ENZYME" Ec "Ez" ENZYME proteins 1
#> 3 "ENZYME" Eh "Ec" Hydrolases 1
#> 4 "Metabolic Atlas" Mp "" Metabolic proteins 1
#> 5 "HPA" Za "" Predicted intracellular … 1
#> 6 "HPA" Zm "Za" Intracellular proteins p… 1
#> 7 "UniProt" Dr "" Disease related genes 1
#> 8 "HPA" Pd "" Potential drug targets 1
#> 9 "KEGG" Ha "" Human disease related ge… 1
#> 10 "KEGG" Hd "Ha" Congenital disorders of … 1
#> 11 "KEGG" Hd4 "Hd" Congenital disorders of … 1
#> 12 "KEGG" Hk "Ha" Nervous system diseases 1
#> 13 "KEGG" Hk5 "Hk" Other nervous and sensor… 1
#> 14 "UniProt" Ua "" UniProt - Evidence at pr… 1
#> 15 "neXtProt" Nx "" Mapped to neXtProt 1
#> 16 "neXtProt" Na "Nx" neXtProt - Evidence at p… 1
#> 17 "Kim et al 2014" Ea "" Protein evidence (Kim et… 1
#>
#> $proteinEvidence
#> # A tibble: 1 × 3
#> evidence entry_id proteinEvidence_id
#> <chr> <int> <int>
#> 1 Evidence at protein level 1 1
#>
#> $proteinEvidence_evidence
#> # A tibble: 3 × 3
#> source evidence proteinEvidence_id
#> <chr> <chr> <int>
#> 1 HPA Evidence at protein level 1
#> 2 MS Not available 1
#> 3 UniProt Evidence at protein level 1
#>
#> $proteinstructure
#> # A tibble: 1 × 2
#> entry_id proteinstructure_id
#> <int> <int>
#> 1 1 1
#>
#> $rnaExpression
#> # A tibble: 11 × 9
#> source technology assayType entry_id rnaExpression_id rnaDistribution_desc…¹
#> <chr> <chr> <chr> <int> <int> <chr>
#> 1 HPA RNAseq consensus… 1 1 n>33% and n<all
#> 2 HPA RNAseq tissue 1 2 NA
#> 3 HPA RNAseq humanBrain 1 3 NA
#> 4 HPA RNAseq humanBrai… 1 4 n=all
#> 5 HPA RNAseq mouseBrai… 1 5 n>33% and n<all
#> 6 HPA RNAseq mouseBrain 1 6 NA
#> 7 HPA RNAseq pigBrainR… 1 7 n=all
#> 8 HPA RNAseq pigBrain 1 8 NA
#> 9 HPA RNAseq cellLine 1 9 n>33% and n<all
#> 10 HPA RNAseq immuneCell 1 10 n>33% and n<all
#> 11 HPA RNAseq immuneCel… 1 11 n>33% and n<all
#> # ℹ abbreviated name: ¹rnaDistribution_description
#> # ℹ 3 more variables: rnaDistribution <chr>,
#> # rnaExpressionCluster_clusterID <chr>, rnaExpressionCluster <chr>
#>
#> $rnaSpecificity
#> # A tibble: 7 × 6
#> description specificity rnaExpression_id rnaSpecificity_id immuneCell_lineage
#> <chr> <chr> <int> <int> <chr>
#> 1 At least fo… Tissue enh… 1 1 NA
#> 2 nTPM >= 1 i… Low region… 4 2 NA
#> 3 nTPM >= 1 i… Low region… 5 3 NA
#> 4 nTPM >= 1 i… Low region… 7 4 NA
#> 5 nTPM >= 1 i… Low cancer… 9 5 NA
#> 6 At least fo… Immune cel… 10 6 Monocytes
#> 7 nTPM >= 1 i… Low lineag… 11 7 NA
#> # ℹ 1 more variable: immuneCell <chr>
#>
#> $rnaSpecificity_tissue
#> # A tibble: 2 × 4
#> organ ontologyTerms value rnaSpecificity_id
#> <chr> <chr> <chr> <int>
#> 1 Bone marrow & Lymphoid tissues UBERON:0002371 bone marrow 1
#> 2 Liver & Gallbladder UBERON:0002107 liver 1
#>
#> $sample
#> # A tibble: 522 × 2
#> patient_id sample_id
#> <int> <int>
#> 1 1 1
#> 2 2 2
#> 3 3 3
#> 4 4 4
#> 5 5 5
#> 6 6 6
#> 7 7 7
#> 8 8 8
#> 9 9 9
#> 10 10 10
#> # ℹ 512 more rows
#>
#> $snomedParameters
#> # A tibble: 522 × 2
#> sample_id snomedParameters_id
#> <int> <int>
#> 1 1 1
#> 2 2 2
#> 3 3 3
#> 4 4 4
#> 5 5 5
#> 6 6 6
#> 7 7 7
#> 8 8 8
#> 9 9 9
#> 10 10 10
#> # ℹ 512 more rows
#>
#> $snomedParameters_snomed
#> # A tibble: 1,147 × 3
#> tissueDescription snomedCode snomedParameters_id
#> <chr> <chr> <int>
#> 1 Normal tissue, NOS M-00100 1
#> 2 Breast T-04000 1
#> 3 Normal tissue, NOS M-00100 2
#> 4 Basal cell carcinoma M-80903 2
#> 5 Cartilage tissue T-1X700 2
#> 6 Nasopharynx T-23000 2
#> 7 Oral tissue T-51000 2
#> 8 Normal tissue, NOS M-00100 3
#> 9 Basal cell carcinoma M-80903 3
#> 10 Skin T-01000 3
#> # ℹ 1,137 more rows
#>
#> $structure
#> # A tibble: 4 × 6
#> url name type method proteinstructure_id structure_id
#> <chr> <chr> <chr> <chr> <int> <int>
#> 1 https://v25.proteinatlas.… ENSP… pred… Alpha… 1 1
#> 2 https://v25.proteinatlas.… ENSP… pred… Alpha… 1 2
#> 3 https://v25.proteinatlas.… ENSP… pred… Alpha… 1 3
#> 4 https://v25.proteinatlas.… ENSP… pred… Alpha… 1 4
#>
#> $subAssay
#> # A tibble: 1 × 6
#> type subtype cellExpression_id subAssay_id verification_type verification
#> <chr> <chr> <int> <int> <chr> <chr>
#> 1 human human cell… 2 1 validation supported
#>
#> $tissueCell
#> # A tibble: 182 × 3
#> data_id tissueCell_id quantity
#> <int> <int> <chr>
#> 1 1 1 NA
#> 2 2 2 NA
#> 3 3 3 NA
#> 4 3 4 NA
#> 5 4 5 NA
#> 6 5 6 NA
#> 7 5 7 NA
#> 8 5 8 NA
#> 9 6 9 NA
#> 10 7 10 NA
#> # ℹ 172 more rows
#>
#> $tissueCell_cellType
#> # A tibble: 182 × 2
#> value tissueCell_id
#> <chr> <int>
#> 1 Adipocytes 1
#> 2 Glandular cells 2
#> 3 Glandular cells 3
#> 4 Lymphoid tissue 4
#> 5 Hematopoietic cells 5
#> 6 Adipocytes 6
#> 7 Glandular cells 7
#> 8 Myoepithelial cells 8
#> 9 Respiratory epithelial cells 9
#> 10 Glial cells 10
#> # ℹ 172 more rows
#>
#> $tissueCell_level
#> # A tibble: 300 × 4
#> type value tissueCell_id count
#> <chr> <chr> <int> <chr>
#> 1 expression not detected 1 NA
#> 2 expression medium 2 NA
#> 3 expression low 3 NA
#> 4 expression low 4 NA
#> 5 expression low 5 NA
#> 6 expression not detected 6 NA
#> 7 expression low 7 NA
#> 8 expression low 8 NA
#> 9 expression low 9 NA
#> 10 expression not detected 10 NA
#> # ℹ 290 more rows
#>
#> $tissueCell_location
#> # A tibble: 81 × 2
#> value tissueCell_id
#> <chr> <int>
#> 1 none 82
#> 2 cytoplasmic/membranous,nuclear 83
#> 3 cytoplasmic/membranous,nuclear 84
#> 4 cytoplasmic/membranous 85
#> 5 cytoplasmic/membranous,nuclear 86
#> 6 none 87
#> 7 cytoplasmic/membranous,nuclear 88
#> 8 cytoplasmic/membranous,nuclear 89
#> 9 cytoplasmic/membranous,nuclear 90
#> 10 cytoplasmic/membranous 91
#> # ℹ 71 more rows
#>
#> $tissueExpression
#> # A tibble: 3 × 11
#> source technology assayType entry_id tissueExpression_id summary_type summary
#> <chr> <chr> <chr> <int> <int> <chr> <chr>
#> 1 HPA IHC tissue 1 1 tissue Cytopla…
#> 2 HPA IHC tissue NA 2 tissue Basal c…
#> 3 HPA IHC cancer NA 3 cancer A major…
#> # ℹ 4 more variables: verification_type <chr>, verification_description <chr>,
#> # verification <chr>, antibody_id <int>
#>
#> $tissueExpression_validation
#> # A tibble: 2 × 3
#> type value tissueExpression_id
#> <chr> <chr> <int>
#> 1 RNAConsistency Low consistency between antibody sta… 2
#> 2 literatureConformity Partly consistent with extensive gen… 2
#>
#> $westernBlot
#> # A tibble: 1 × 8
#> source technology antibody_id westernBlot_id verification_type
#> <chr> <chr> <int> <int> <chr>
#> 1 HPA WB 5 1 validation
#> # ℹ 3 more variables: verification_description <chr>, verification <chr>,
#> # antibodyDilution_dilution <chr>
#>