tests/testthat/_snaps/drugbank-parser.md
In Dainanahan/dbparser: Drugs Databases Parser
parse DrugBank DB - default params
Code
dvobj$result
Output
$drugs
$drugs$general_information
# A tibble: 1 × 15
drugbank_id other_keys type created updated name description cas_number
<chr> <chr> <chr> <chr> <chr> <chr> <chr> <chr>
1 DB00001 BTD00024;BIOD0… biot… 2005-0… 2024-0… Lepi… "Lepirudin… 138068-37…
# ℹ 7 more variables: unii <chr>, average_mass <chr>, monoisotopic_mass <chr>,
# state <chr>, synthesis_reference <chr>, fda_label <chr>, msds <chr>
attr(,"class")
[1] "dvobject"
attr(,"original_db_info")
attr(,"original_db_info")$db_type
[1] "DrugBank"
attr(,"original_db_info")$db_version
[1] "5.1"
attr(,"original_db_info")$db_exported_date
[1] "2018-07-03"
parse DrugBank DB - small molecule
Code
dvobj$result
Output
$drugs
$drugs$general_information
# A tibble: 1 × 15
drugbank_id other_keys type created updated name description cas_number
<chr> <chr> <chr> <chr> <chr> <chr> <chr> <chr>
1 DB00006 BTD00076;EXPT0… smal… 2005-0… 2024-0… Biva… Bivalirudi… 128270-60…
# ℹ 7 more variables: unii <chr>, average_mass <chr>, monoisotopic_mass <chr>,
# state <chr>, synthesis_reference <chr>, fda_label <chr>, msds <chr>
$drugs$drug_classification
# A tibble: 1 × 9
description direct_parent kingdom superclass class subclass
<chr> <chr> <chr> <chr> <chr> <chr>
1 This compound belongs to the … Polypeptides Organi… Organic P… Poly… ""
# ℹ 3 more variables: alternative_parents <chr>, substituents <chr>,
# drugbank_id <chr>
$drugs$synonyms
# A tibble: 3 × 4
synonym language coder drugbank_id
<chr> <chr> <chr> <chr>
1 Bivalirudin english "inn/usan" DB00006
2 Bivalirudina spanish "" DB00006
3 Bivalirudinum latin "" DB00006
$drugs$pharmacology
# A tibble: 1 × 12
drugbank_id indication pharmacodynamics mechanism_of_action toxicity
<chr> <chr> <chr> <chr> <chr>
1 DB00006 For treatment of he… "Bivalirudin me… Inhibits the actio… Based o…
# ℹ 7 more variables: metabolism <chr>, absorption <chr>, half_life <chr>,
# protein_binding <chr>, route_of_elimination <chr>,
# volume_of_distribution <chr>, clearance <chr>
$drugs$international_brands
# A tibble: 2 × 3
brand company drugbank_id
<chr> <chr> <chr>
1 Angiox "" DB00006
2 Hirulog "" DB00006
$drugs$mixtures
# A tibble: 0 × 0
$drugs$packagers
# A tibble: 4 × 3
name url drugbank_id
<chr> <chr> <chr>
1 Ben Venue Laboratories Inc. "http://www.benvenue.com" DB00006
2 Oryx Pharmaceuticals Inc. "" DB00006
3 Sepracor Pharmaceuticals Inc. "http://www.sepracor.com" DB00006
4 The Medicines Co. "http://www.themedicinescompany.com" DB00006
$drugs$manufacturers
# A tibble: 1 × 4
manufacturer generic url drugbank_id
<chr> <chr> <chr> <chr>
1 The medicines co false "" DB00006
$drugs$prices
# A tibble: 1 × 5
description currency cost unit drugbank_id
<chr> <chr> <chr> <chr> <chr>
1 Angiomax 250 mg vial USD 780.0 vial DB00006
$drugs$categories
# A tibble: 10 × 3
category mesh_id drugbank_id
<chr> <chr> <chr>
1 Amino Acids, Peptides, and Proteins "D000602" DB00006
2 Anticoagulants "D000925" DB00006
3 Antithrombins "D000991" DB00006
4 Blood and Blood Forming Organs "" DB00006
5 Enzyme Inhibitors "D004791" DB00006
6 Hematologic Agents "D006401" DB00006
7 Peptides "D010455" DB00006
8 Protease Inhibitors "D011480" DB00006
9 Serine Protease Inhibitors "D015842" DB00006
10 Thrombin Inhibitors "" DB00006
$drugs$dosages
# A tibble: 17 × 4
form route strength drugbank_id
<chr> <chr> <chr> <chr>
1 "Injection, powder, lyophilized, for solution" Intrav… "250 mg… DB00006
2 "Injection, solution" Intrav… "250 mg… DB00006
3 "Injection, powder, lyophilized, for solution" Intrav… "250 mg" DB00006
4 "" Intrav… "250 mg" DB00006
5 "Injection, powder, for solution" Intrav… "250 MG" DB00006
6 "Injection" Intrac… "250 mg… DB00006
7 "Injection" Intrav… "250 mg… DB00006
8 "Injection, powder, lyophilized, for solution" Intrav… "250 mg… DB00006
9 "Injection, powder, lyophilized, for suspension" Intrav… "250 mg… DB00006
10 "Injection, powder, lyophilized, for solution" Intrav… "" DB00006
11 "Powder, for solution" Intrav… "250 mg… DB00006
12 "Injection" Intrav… "250 mg… DB00006
13 "Injection" Intrav… "500 mg… DB00006
14 "Solution" Intrav… "5 mg /… DB00006
15 "Injection, solution" Intrav… "5 mg/1… DB00006
16 "Powder" Intrav… "250 MG" DB00006
17 "Powder" Intrav… "" DB00006
$drugs$atc_codes
# A tibble: 1 × 10
atc_code level_1 code_1 level_2 code_2 level_3 code_3 level_4 code_4
<chr> <chr> <chr> <chr> <chr> <chr> <chr> <chr> <chr>
1 B01AE06 Direct thrombin … B01AE ANTITH… B01A ANTITH… B01 BLOOD … B
# ℹ 1 more variable: drugbank_id <chr>
$drugs$patents
# A tibble: 4 × 6
number country approved expires pediatric_extension drugbank_id
<chr> <chr> <chr> <chr> <chr> <chr>
1 5196404 United States 1993-03-23 2010-05-23 false DB00006
2 2065150 Canada 1999-12-14 2010-08-17 false DB00006
3 7598343 United States 2009-10-06 2029-01-27 true DB00006
4 7582727 United States 2009-09-01 2029-01-27 true DB00006
$drugs$drug_interactions
# A tibble: 639 × 4
target_drugbank_id name description drugbank_id
<chr> <chr> <chr> <chr>
1 DB06605 Apixaban Apixaban may incre… DB00006
2 DB06695 Dabigatran etexilate Dabigatran etexila… DB00006
3 DB01254 Dasatinib The risk or severi… DB00006
4 DB01609 Deferasirox The risk or severi… DB00006
5 DB01586 Ursodeoxycholic acid The risk or severi… DB00006
6 DB02123 Glycochenodeoxycholic Acid The risk or severi… DB00006
7 DB02659 Cholic Acid The risk or severi… DB00006
8 DB02691 Glycocholic acid The risk or severi… DB00006
9 DB03619 Deoxycholic acid The risk or severi… DB00006
10 DB04348 Taurocholic acid The risk or severi… DB00006
# ℹ 629 more rows
$drugs$sequences
# A tibble: 0 × 0
$drugs$calculated_properties
# A tibble: 26 × 4
kind value source drugbank_id
<chr> <chr> <chr> <chr>
1 logP -0.76 ALOGPS DB00006
2 logS -4.7 ALOGPS DB00006
3 Water Solubility 4.64e-02 g/l ALOGPS DB00006
4 logP -14 ChemA… DB00006
5 IUPAC Name (4S)-4-[(2S)-2-[(2S)-2-[(2S)-2-{2-… ChemA… DB00006
6 Traditional IUPAC Name bivalirudin ChemA… DB00006
7 Molecular Weight 2180.2853 ChemA… DB00006
8 Monoisotopic Weight 2178.985813062 ChemA… DB00006
9 SMILES CC[C@H](C)[C@H](NC(=O)[C@H](CCC(O)… ChemA… DB00006
10 Molecular Formula C98H138N24O33 ChemA… DB00006
# ℹ 16 more rows
$drugs$experimental_properties
# A tibble: 0 × 0
$drugs$external_identifiers
# A tibble: 12 × 3
resource identifier drugbank_id
<chr> <chr> <chr>
1 Drugs Product Database (DPD) 12945 DB00006
2 ChEBI 59173 DB00006
3 PubChem Compound 16129704 DB00006
4 PubChem Substance 46507415 DB00006
5 KEGG Drug D03136 DB00006
6 ChemSpider 10482069 DB00006
7 BindingDB 50248103 DB00006
8 PharmGKB PA10032 DB00006
9 Therapeutic Targets Database DAP000542 DB00006
10 Wikipedia Bivalirudin DB00006
11 ChEMBL CHEMBL2103749 DB00006
12 RxCUI 60819 DB00006
$drugs$pathway
$drugs$pathway$general_information
# A tibble: 1 × 4
smpdb_id name category drugbank_id
<chr> <chr> <chr> <chr>
1 SMP0000277 Bivalirudin Action Pathway drug_action DB00006
$drugs$pathway$pathway_drugs
# A tibble: 3 × 3
drugbank_id name smpdb_id
<chr> <chr> <chr>
1 DB00006 Bivalirudin SMP0000277
2 DB01022 Phylloquinone SMP0000277
3 DB01373 Calcium SMP0000277
$drugs$pathway$pathway_enzyme
# A tibble: 20 × 2
enzyme smpdb_id
<chr> <chr>
1 P00734 SMP0000277
2 P00748 SMP0000277
3 P02452 SMP0000277
4 P03952 SMP0000277
5 P03951 SMP0000277
6 P00740 SMP0000277
7 P00451 SMP0000277
8 P12259 SMP0000277
9 P00742 SMP0000277
10 P02671 SMP0000277
11 P02675 SMP0000277
12 P02679 SMP0000277
13 P00488 SMP0000277
14 P05160 SMP0000277
15 P00747 SMP0000277
16 P00750 SMP0000277
17 P08709 SMP0000277
18 P13726 SMP0000277
19 Q9BQB6 SMP0000277
20 P38435 SMP0000277
$drugs$reactions
$drugs$reactions$general_information
# A tibble: 0 × 0
$drugs$reactions$reactions_enzymes
# A tibble: 0 × 0
$drugs$snp_effects
# A tibble: 0 × 0
$drugs$snp_adverse_reactions
# A tibble: 0 × 0
$drugs$food_interactions
# A tibble: 2 × 2
food_interaction drugbank_id
<chr> <chr>
1 Avoid echinacea. DB00006
2 Avoid herbs and supplements with anticoagulant/antiplatelet activ… DB00006
$drugs$pdb_entries
# A tibble: 0 × 0
$drugs$ahfs_codes
# A tibble: 0 × 0
$drugs$affected_organisms
# A tibble: 1 × 2
affected_organism drugbank_id
<chr> <chr>
1 Humans and other mammals DB00006
$drugs$groups
# A tibble: 2 × 2
group drugbank_id
<chr> <chr>
1 approved DB00006
2 investigational DB00006
$drugs$external_links
# A tibble: 2 × 3
resource url drugbank_id
<chr> <chr> <chr>
1 RxList http://www.rxlist.com/cgi/generic/angiomax.htm DB00006
2 Drugs.com http://www.drugs.com/cdi/bivalirudin.html DB00006
$salts
# A tibble: 0 × 0
$products
# A tibble: 34 × 19
name labeller ndc_id ndc_product_code dpd_id ema_product_code ema_ma_number
<chr> <chr> <chr> <chr> <chr> <chr> <chr>
1 Angio… Cardina… "" "55154-2275" "" "" ""
2 Angio… The Med… "" "65293-001" "" "" ""
3 Angio… Sandoz … "" "0781-3447" "" "" ""
4 Angio… Sandoz … "" "" "0224… "" ""
5 Angio… MAIA Ph… "" "70511-141" "" "" ""
6 Angiox The Med… "" "" "" "EMEA/H/C/00056… "EU/1/04/289…
7 Bival… Accord … "" "16729-275" "" "" ""
8 Bival… Cipla U… "" "69097-601" "" "" ""
9 Bival… Mylan I… "" "67457-256" "" "" ""
10 Bival… Eugia U… "" "55150-210" "" "" ""
# ℹ 24 more rows
# ℹ 12 more variables: started_marketing_on <chr>, ended_marketing_on <chr>,
# dosage_form <chr>, strength <chr>, route <chr>,
# fda_application_number <chr>, generic <chr>, over_the_counter <chr>,
# approved <chr>, country <chr>, source <chr>, drugbank_id <chr>
$references
$references$drugs
$references$drugs$books
# A tibble: 0 × 0
$references$drugs$articles
# A tibble: 7 × 4
ref_id pubmed_id citation drugbank_id
<chr> <chr> <chr> <chr>
1 A17 16466327 Seybert AL, Coons JC, Zerumsky K: Treatment of h… DB00006
2 A18 17381384 Dager WE, Dougherty JA, Nguyen PH, Militello MA,… DB00006
3 A19 16553503 Dang CH, Durkalski VL, Nappi JM: Evaluation of t… DB00006
4 A20 11156732 Robson R: The use of bivalirudin in patients wit… DB00006
5 A21 21108549 Van De Car DA, Rao SV, Ohman EM: Bivalirudin: a … DB00006
6 A22 16614733 Shammas NW: Bivalirudin: pharmacology and clinic… DB00006
7 A23 12851152 Gleason TG, Chengelis CP, Jackson CB, Lindstrom … DB00006
$references$drugs$links
# A tibble: 0 × 0
$references$drugs$attachments
# A tibble: 0 × 0
$references$carriers
$references$carriers$books
# A tibble: 0 × 0
$references$carriers$articles
# A tibble: 0 × 0
$references$carriers$links
# A tibble: 0 × 0
$references$carriers$attachments
# A tibble: 0 × 0
$references$enzymes
$references$enzymes$books
# A tibble: 0 × 0
$references$enzymes$articles
# A tibble: 1 × 4
ref_id pubmed_id citation enzyme_id
<chr> <chr> <chr> <chr>
1 A17596 18701766 Rudolph V, Rudolph TK, Schopfer FJ, Bonacci G, Lau… BE0001075
$references$enzymes$links
# A tibble: 0 × 0
$references$enzymes$attachments
# A tibble: 0 × 0
$references$targets
$references$targets$books
# A tibble: 0 × 0
$references$targets$articles
# A tibble: 6 × 4
ref_id pubmed_id citation target_id
<chr> <chr> <chr> <chr>
1 A1733 11060732 Scatena R: Bivalirudin: a new generation antithrom… BE0000048
2 A1736 11504570 Bates ER: Bivalirudin for percutaneous coronary in… BE0000048
3 A1738 11833835 Gladwell TD: Bivalirudin: a direct thrombin inhibi… BE0000048
4 A1739 11923794 Kleiman NS, Klem J, Fernandes LS, Rubin H, Challa … BE0000048
5 A1741 11929334 Carswell CI, Plosker GL: Bivalirudin: a review of … BE0000048
6 A9 11752352 Chen X, Ji ZL, Chen YZ: TTD: Therapeutic Target Da… BE0000048
$references$targets$links
# A tibble: 0 × 0
$references$targets$attachments
# A tibble: 0 × 0
$references$transporters
$references$transporters$books
# A tibble: 0 × 0
$references$transporters$articles
# A tibble: 0 × 0
$references$transporters$links
# A tibble: 0 × 0
$references$transporters$attachments
# A tibble: 0 × 0
$cett
$cett$carriers
$cett$carriers$general_information
# A tibble: 0 × 0
$cett$carriers$actions
# A tibble: 0 × 0
$cett$carriers$polypeptides
$cett$carriers$polypeptides$general_information
# A tibble: 0 × 0
$cett$carriers$polypeptides$external_identy
# A tibble: 0 × 0
$cett$carriers$polypeptides$synonyms
# A tibble: 0 × 0
$cett$carriers$polypeptides$pfams
# A tibble: 0 × 0
$cett$carriers$polypeptides$go
# A tibble: 0 × 0
$cett$enzymes
$cett$enzymes$general_information
# A tibble: 1 × 8
enzyme_id name organism known_action position drugbank_id inhibition_strength
<chr> <chr> <chr> <chr> <chr> <chr> <chr>
1 BE0001075 Myel… Humans unknown 1 DB00006 unknown
# ℹ 1 more variable: induction_strength <chr>
$cett$enzymes$actions
# A tibble: 1 × 2
action enzyme_id
<chr> <chr>
1 inhibitor BE0001075
$cett$enzymes$polypeptides
$cett$enzymes$polypeptides$general_information
# A tibble: 1 × 20
polypeptide_id source name general_function specific_function gene_name locus
<chr> <chr> <chr> <chr> <chr> <chr> <chr>
1 P05164 Swiss… Myel… Peroxidase acti… Part of the host… MPO 17q2…
# ℹ 13 more variables: cellular_location <chr>, transmembrane_regions <chr>,
# signal_regions <chr>, theoretical_pi <chr>, molecular_weight <chr>,
# chromosome_location <chr>, organism <chr>, organism_ncbi_taxonomy_id <chr>,
# amino_acid_sequence <chr>, amino_acid_format <chr>, gene_sequence <chr>,
# gene_format <chr>, enzyme_id <chr>
$cett$enzymes$polypeptides$external_identy
# A tibble: 7 × 3
resource identifier enzyme_id
<chr> <chr> <chr>
1 HUGO Gene Nomenclature Committee (HGNC) HGNC:7218 BE0001075
2 GenAtlas MPO BE0001075
3 GenBank Gene Database J02694 BE0001075
4 GenBank Protein Database 189040 BE0001075
5 Guide to Pharmacology 2789 BE0001075
6 UniProtKB P05164 BE0001075
7 UniProt Accession PERM_HUMAN BE0001075
$cett$enzymes$polypeptides$synonyms
# A tibble: 2 × 2
synonym enzyme_id
<chr> <chr>
1 1.11.2.2 BE0001075
2 MPO BE0001075
$cett$enzymes$polypeptides$pfams
# A tibble: 1 × 3
identifier name enzyme_id
<chr> <chr> <chr>
1 PF03098 An_peroxidase BE0001075
$cett$enzymes$polypeptides$go
# A tibble: 24 × 3
category description enzyme_id
<chr> <chr> <chr>
1 component azurophil granule BE0001075
2 component extracellular exosome BE0001075
3 component extracellular space BE0001075
4 component lysosome BE0001075
5 component mitochondrion BE0001075
6 component nucleus BE0001075
7 component secretory granule BE0001075
8 function chromatin binding BE0001075
9 function heme binding BE0001075
10 function heparin binding BE0001075
# ℹ 14 more rows
$cett$targets
$cett$targets$general_information
# A tibble: 1 × 6
target_id name organism known_action position drugbank_id
<chr> <chr> <chr> <chr> <chr> <chr>
1 BE0000048 Prothrombin Humans yes 1 DB00006
$cett$targets$actions
# A tibble: 1 × 2
action target_id
<chr> <chr>
1 inhibitor BE0000048
$cett$targets$polypeptides
$cett$targets$polypeptides$general_information
# A tibble: 1 × 20
polypeptide_id source name general_function specific_function gene_name locus
<chr> <chr> <chr> <chr> <chr> <chr> <chr>
1 P00734 Swiss… Prot… Thrombospondin … Thrombin, which … F2 11p1…
# ℹ 13 more variables: cellular_location <chr>, transmembrane_regions <chr>,
# signal_regions <chr>, theoretical_pi <chr>, molecular_weight <chr>,
# chromosome_location <chr>, organism <chr>, organism_ncbi_taxonomy_id <chr>,
# amino_acid_sequence <chr>, amino_acid_format <chr>, gene_sequence <chr>,
# gene_format <chr>, target_id <chr>
$cett$targets$polypeptides$external_identy
# A tibble: 7 × 3
resource identifier target_id
<chr> <chr> <chr>
1 HUGO Gene Nomenclature Committee (HGNC) HGNC:3535 BE0000048
2 GenAtlas F2 BE0000048
3 GenBank Gene Database M17262 BE0000048
4 GenBank Protein Database 339641 BE0000048
5 Guide to Pharmacology 2362 BE0000048
6 UniProtKB P00734 BE0000048
7 UniProt Accession THRB_HUMAN BE0000048
$cett$targets$polypeptides$synonyms
# A tibble: 2 × 2
synonym target_id
<chr> <chr>
1 3.4.21.5 BE0000048
2 Coagulation factor II BE0000048
$cett$targets$polypeptides$pfams
# A tibble: 4 × 3
identifier name target_id
<chr> <chr> <chr>
1 PF00594 Gla BE0000048
2 PF00051 Kringle BE0000048
3 PF00089 Trypsin BE0000048
4 PF09396 Thrombin_light BE0000048
$cett$targets$polypeptides$go
# A tibble: 46 × 3
category description target_id
<chr> <chr> <chr>
1 component blood microparticle BE0000048
2 component cytosol BE0000048
3 component endoplasmic reticulum lumen BE0000048
4 component extracellular exosome BE0000048
5 component extracellular matrix BE0000048
6 component extracellular region BE0000048
7 component extracellular space BE0000048
8 component Golgi lumen BE0000048
9 component plasma membrane BE0000048
10 function calcium ion binding BE0000048
# ℹ 36 more rows
$cett$transporters
$cett$transporters$general_information
# A tibble: 0 × 0
$cett$transporters$actions
# A tibble: 0 × 0
$cett$transporters$polypeptides
$cett$transporters$polypeptides$general_information
# A tibble: 0 × 0
$cett$transporters$polypeptides$external_identy
# A tibble: 0 × 0
$cett$transporters$polypeptides$synonyms
# A tibble: 0 × 0
$cett$transporters$polypeptides$pfams
# A tibble: 0 × 0
$cett$transporters$polypeptides$go
# A tibble: 0 × 0
attr(,"class")
[1] "dvobject"
attr(,"original_db_info")
attr(,"original_db_info")$db_type
[1] "DrugBank"
attr(,"original_db_info")$db_version
[1] "5.1"
attr(,"original_db_info")$db_exported_date
[1] "2018-07-03"
parse DrugBank DB - zip file
Code
dvobj$result
Output
$drugs
$drugs$general_information
# A tibble: 1 × 15
drugbank_id other_keys type created updated name description cas_number
<chr> <chr> <chr> <chr> <chr> <chr> <chr> <chr>
1 DB00001 BTD00024;BIOD0… biot… 2005-0… 2018-0… Lepi… Lepirudin … 138068-37…
# ℹ 7 more variables: unii <chr>, average_mass <chr>, monoisotopic_mass <chr>,
# state <chr>, synthesis_reference <chr>, fda_label <chr>, msds <chr>
attr(,"class")
[1] "dvobject"
attr(,"original_db_info")
attr(,"original_db_info")$db_type
[1] "DrugBank"
attr(,"original_db_info")$db_version
[1] "5.1"
attr(,"original_db_info")$db_exported_date
[1] "2018-07-03"
Dainanahan/dbparser documentation built on April 20, 2024, 5:21 p.m.
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parse DrugBank DB - default params
Code
dvobj$result
Output
$drugs
$drugs$general_information
# A tibble: 1 × 15
drugbank_id other_keys type created updated name description cas_number
<chr> <chr> <chr> <chr> <chr> <chr> <chr> <chr>
1 DB00001 BTD00024;BIOD0… biot… 2005-0… 2024-0… Lepi… "Lepirudin… 138068-37…
# ℹ 7 more variables: unii <chr>, average_mass <chr>, monoisotopic_mass <chr>,
# state <chr>, synthesis_reference <chr>, fda_label <chr>, msds <chr>
attr(,"class")
[1] "dvobject"
attr(,"original_db_info")
attr(,"original_db_info")$db_type
[1] "DrugBank"
attr(,"original_db_info")$db_version
[1] "5.1"
attr(,"original_db_info")$db_exported_date
[1] "2018-07-03"
parse DrugBank DB - small molecule
Code
dvobj$result
Output
$drugs
$drugs$general_information
# A tibble: 1 × 15
drugbank_id other_keys type created updated name description cas_number
<chr> <chr> <chr> <chr> <chr> <chr> <chr> <chr>
1 DB00006 BTD00076;EXPT0… smal… 2005-0… 2024-0… Biva… Bivalirudi… 128270-60…
# ℹ 7 more variables: unii <chr>, average_mass <chr>, monoisotopic_mass <chr>,
# state <chr>, synthesis_reference <chr>, fda_label <chr>, msds <chr>
$drugs$drug_classification
# A tibble: 1 × 9
description direct_parent kingdom superclass class subclass
<chr> <chr> <chr> <chr> <chr> <chr>
1 This compound belongs to the … Polypeptides Organi… Organic P… Poly… ""
# ℹ 3 more variables: alternative_parents <chr>, substituents <chr>,
# drugbank_id <chr>
$drugs$synonyms
# A tibble: 3 × 4
synonym language coder drugbank_id
<chr> <chr> <chr> <chr>
1 Bivalirudin english "inn/usan" DB00006
2 Bivalirudina spanish "" DB00006
3 Bivalirudinum latin "" DB00006
$drugs$pharmacology
# A tibble: 1 × 12
drugbank_id indication pharmacodynamics mechanism_of_action toxicity
<chr> <chr> <chr> <chr> <chr>
1 DB00006 For treatment of he… "Bivalirudin me… Inhibits the actio… Based o…
# ℹ 7 more variables: metabolism <chr>, absorption <chr>, half_life <chr>,
# protein_binding <chr>, route_of_elimination <chr>,
# volume_of_distribution <chr>, clearance <chr>
$drugs$international_brands
# A tibble: 2 × 3
brand company drugbank_id
<chr> <chr> <chr>
1 Angiox "" DB00006
2 Hirulog "" DB00006
$drugs$mixtures
# A tibble: 0 × 0
$drugs$packagers
# A tibble: 4 × 3
name url drugbank_id
<chr> <chr> <chr>
1 Ben Venue Laboratories Inc. "http://www.benvenue.com" DB00006
2 Oryx Pharmaceuticals Inc. "" DB00006
3 Sepracor Pharmaceuticals Inc. "http://www.sepracor.com" DB00006
4 The Medicines Co. "http://www.themedicinescompany.com" DB00006
$drugs$manufacturers
# A tibble: 1 × 4
manufacturer generic url drugbank_id
<chr> <chr> <chr> <chr>
1 The medicines co false "" DB00006
$drugs$prices
# A tibble: 1 × 5
description currency cost unit drugbank_id
<chr> <chr> <chr> <chr> <chr>
1 Angiomax 250 mg vial USD 780.0 vial DB00006
$drugs$categories
# A tibble: 10 × 3
category mesh_id drugbank_id
<chr> <chr> <chr>
1 Amino Acids, Peptides, and Proteins "D000602" DB00006
2 Anticoagulants "D000925" DB00006
3 Antithrombins "D000991" DB00006
4 Blood and Blood Forming Organs "" DB00006
5 Enzyme Inhibitors "D004791" DB00006
6 Hematologic Agents "D006401" DB00006
7 Peptides "D010455" DB00006
8 Protease Inhibitors "D011480" DB00006
9 Serine Protease Inhibitors "D015842" DB00006
10 Thrombin Inhibitors "" DB00006
$drugs$dosages
# A tibble: 17 × 4
form route strength drugbank_id
<chr> <chr> <chr> <chr>
1 "Injection, powder, lyophilized, for solution" Intrav… "250 mg… DB00006
2 "Injection, solution" Intrav… "250 mg… DB00006
3 "Injection, powder, lyophilized, for solution" Intrav… "250 mg" DB00006
4 "" Intrav… "250 mg" DB00006
5 "Injection, powder, for solution" Intrav… "250 MG" DB00006
6 "Injection" Intrac… "250 mg… DB00006
7 "Injection" Intrav… "250 mg… DB00006
8 "Injection, powder, lyophilized, for solution" Intrav… "250 mg… DB00006
9 "Injection, powder, lyophilized, for suspension" Intrav… "250 mg… DB00006
10 "Injection, powder, lyophilized, for solution" Intrav… "" DB00006
11 "Powder, for solution" Intrav… "250 mg… DB00006
12 "Injection" Intrav… "250 mg… DB00006
13 "Injection" Intrav… "500 mg… DB00006
14 "Solution" Intrav… "5 mg /… DB00006
15 "Injection, solution" Intrav… "5 mg/1… DB00006
16 "Powder" Intrav… "250 MG" DB00006
17 "Powder" Intrav… "" DB00006
$drugs$atc_codes
# A tibble: 1 × 10
atc_code level_1 code_1 level_2 code_2 level_3 code_3 level_4 code_4
<chr> <chr> <chr> <chr> <chr> <chr> <chr> <chr> <chr>
1 B01AE06 Direct thrombin … B01AE ANTITH… B01A ANTITH… B01 BLOOD … B
# ℹ 1 more variable: drugbank_id <chr>
$drugs$patents
# A tibble: 4 × 6
number country approved expires pediatric_extension drugbank_id
<chr> <chr> <chr> <chr> <chr> <chr>
1 5196404 United States 1993-03-23 2010-05-23 false DB00006
2 2065150 Canada 1999-12-14 2010-08-17 false DB00006
3 7598343 United States 2009-10-06 2029-01-27 true DB00006
4 7582727 United States 2009-09-01 2029-01-27 true DB00006
$drugs$drug_interactions
# A tibble: 639 × 4
target_drugbank_id name description drugbank_id
<chr> <chr> <chr> <chr>
1 DB06605 Apixaban Apixaban may incre… DB00006
2 DB06695 Dabigatran etexilate Dabigatran etexila… DB00006
3 DB01254 Dasatinib The risk or severi… DB00006
4 DB01609 Deferasirox The risk or severi… DB00006
5 DB01586 Ursodeoxycholic acid The risk or severi… DB00006
6 DB02123 Glycochenodeoxycholic Acid The risk or severi… DB00006
7 DB02659 Cholic Acid The risk or severi… DB00006
8 DB02691 Glycocholic acid The risk or severi… DB00006
9 DB03619 Deoxycholic acid The risk or severi… DB00006
10 DB04348 Taurocholic acid The risk or severi… DB00006
# ℹ 629 more rows
$drugs$sequences
# A tibble: 0 × 0
$drugs$calculated_properties
# A tibble: 26 × 4
kind value source drugbank_id
<chr> <chr> <chr> <chr>
1 logP -0.76 ALOGPS DB00006
2 logS -4.7 ALOGPS DB00006
3 Water Solubility 4.64e-02 g/l ALOGPS DB00006
4 logP -14 ChemA… DB00006
5 IUPAC Name (4S)-4-[(2S)-2-[(2S)-2-[(2S)-2-{2-… ChemA… DB00006
6 Traditional IUPAC Name bivalirudin ChemA… DB00006
7 Molecular Weight 2180.2853 ChemA… DB00006
8 Monoisotopic Weight 2178.985813062 ChemA… DB00006
9 SMILES CC[C@H](C)[C@H](NC(=O)[C@H](CCC(O)… ChemA… DB00006
10 Molecular Formula C98H138N24O33 ChemA… DB00006
# ℹ 16 more rows
$drugs$experimental_properties
# A tibble: 0 × 0
$drugs$external_identifiers
# A tibble: 12 × 3
resource identifier drugbank_id
<chr> <chr> <chr>
1 Drugs Product Database (DPD) 12945 DB00006
2 ChEBI 59173 DB00006
3 PubChem Compound 16129704 DB00006
4 PubChem Substance 46507415 DB00006
5 KEGG Drug D03136 DB00006
6 ChemSpider 10482069 DB00006
7 BindingDB 50248103 DB00006
8 PharmGKB PA10032 DB00006
9 Therapeutic Targets Database DAP000542 DB00006
10 Wikipedia Bivalirudin DB00006
11 ChEMBL CHEMBL2103749 DB00006
12 RxCUI 60819 DB00006
$drugs$pathway
$drugs$pathway$general_information
# A tibble: 1 × 4
smpdb_id name category drugbank_id
<chr> <chr> <chr> <chr>
1 SMP0000277 Bivalirudin Action Pathway drug_action DB00006
$drugs$pathway$pathway_drugs
# A tibble: 3 × 3
drugbank_id name smpdb_id
<chr> <chr> <chr>
1 DB00006 Bivalirudin SMP0000277
2 DB01022 Phylloquinone SMP0000277
3 DB01373 Calcium SMP0000277
$drugs$pathway$pathway_enzyme
# A tibble: 20 × 2
enzyme smpdb_id
<chr> <chr>
1 P00734 SMP0000277
2 P00748 SMP0000277
3 P02452 SMP0000277
4 P03952 SMP0000277
5 P03951 SMP0000277
6 P00740 SMP0000277
7 P00451 SMP0000277
8 P12259 SMP0000277
9 P00742 SMP0000277
10 P02671 SMP0000277
11 P02675 SMP0000277
12 P02679 SMP0000277
13 P00488 SMP0000277
14 P05160 SMP0000277
15 P00747 SMP0000277
16 P00750 SMP0000277
17 P08709 SMP0000277
18 P13726 SMP0000277
19 Q9BQB6 SMP0000277
20 P38435 SMP0000277
$drugs$reactions
$drugs$reactions$general_information
# A tibble: 0 × 0
$drugs$reactions$reactions_enzymes
# A tibble: 0 × 0
$drugs$snp_effects
# A tibble: 0 × 0
$drugs$snp_adverse_reactions
# A tibble: 0 × 0
$drugs$food_interactions
# A tibble: 2 × 2
food_interaction drugbank_id
<chr> <chr>
1 Avoid echinacea. DB00006
2 Avoid herbs and supplements with anticoagulant/antiplatelet activ… DB00006
$drugs$pdb_entries
# A tibble: 0 × 0
$drugs$ahfs_codes
# A tibble: 0 × 0
$drugs$affected_organisms
# A tibble: 1 × 2
affected_organism drugbank_id
<chr> <chr>
1 Humans and other mammals DB00006
$drugs$groups
# A tibble: 2 × 2
group drugbank_id
<chr> <chr>
1 approved DB00006
2 investigational DB00006
$drugs$external_links
# A tibble: 2 × 3
resource url drugbank_id
<chr> <chr> <chr>
1 RxList http://www.rxlist.com/cgi/generic/angiomax.htm DB00006
2 Drugs.com http://www.drugs.com/cdi/bivalirudin.html DB00006
$salts
# A tibble: 0 × 0
$products
# A tibble: 34 × 19
name labeller ndc_id ndc_product_code dpd_id ema_product_code ema_ma_number
<chr> <chr> <chr> <chr> <chr> <chr> <chr>
1 Angio… Cardina… "" "55154-2275" "" "" ""
2 Angio… The Med… "" "65293-001" "" "" ""
3 Angio… Sandoz … "" "0781-3447" "" "" ""
4 Angio… Sandoz … "" "" "0224… "" ""
5 Angio… MAIA Ph… "" "70511-141" "" "" ""
6 Angiox The Med… "" "" "" "EMEA/H/C/00056… "EU/1/04/289…
7 Bival… Accord … "" "16729-275" "" "" ""
8 Bival… Cipla U… "" "69097-601" "" "" ""
9 Bival… Mylan I… "" "67457-256" "" "" ""
10 Bival… Eugia U… "" "55150-210" "" "" ""
# ℹ 24 more rows
# ℹ 12 more variables: started_marketing_on <chr>, ended_marketing_on <chr>,
# dosage_form <chr>, strength <chr>, route <chr>,
# fda_application_number <chr>, generic <chr>, over_the_counter <chr>,
# approved <chr>, country <chr>, source <chr>, drugbank_id <chr>
$references
$references$drugs
$references$drugs$books
# A tibble: 0 × 0
$references$drugs$articles
# A tibble: 7 × 4
ref_id pubmed_id citation drugbank_id
<chr> <chr> <chr> <chr>
1 A17 16466327 Seybert AL, Coons JC, Zerumsky K: Treatment of h… DB00006
2 A18 17381384 Dager WE, Dougherty JA, Nguyen PH, Militello MA,… DB00006
3 A19 16553503 Dang CH, Durkalski VL, Nappi JM: Evaluation of t… DB00006
4 A20 11156732 Robson R: The use of bivalirudin in patients wit… DB00006
5 A21 21108549 Van De Car DA, Rao SV, Ohman EM: Bivalirudin: a … DB00006
6 A22 16614733 Shammas NW: Bivalirudin: pharmacology and clinic… DB00006
7 A23 12851152 Gleason TG, Chengelis CP, Jackson CB, Lindstrom … DB00006
$references$drugs$links
# A tibble: 0 × 0
$references$drugs$attachments
# A tibble: 0 × 0
$references$carriers
$references$carriers$books
# A tibble: 0 × 0
$references$carriers$articles
# A tibble: 0 × 0
$references$carriers$links
# A tibble: 0 × 0
$references$carriers$attachments
# A tibble: 0 × 0
$references$enzymes
$references$enzymes$books
# A tibble: 0 × 0
$references$enzymes$articles
# A tibble: 1 × 4
ref_id pubmed_id citation enzyme_id
<chr> <chr> <chr> <chr>
1 A17596 18701766 Rudolph V, Rudolph TK, Schopfer FJ, Bonacci G, Lau… BE0001075
$references$enzymes$links
# A tibble: 0 × 0
$references$enzymes$attachments
# A tibble: 0 × 0
$references$targets
$references$targets$books
# A tibble: 0 × 0
$references$targets$articles
# A tibble: 6 × 4
ref_id pubmed_id citation target_id
<chr> <chr> <chr> <chr>
1 A1733 11060732 Scatena R: Bivalirudin: a new generation antithrom… BE0000048
2 A1736 11504570 Bates ER: Bivalirudin for percutaneous coronary in… BE0000048
3 A1738 11833835 Gladwell TD: Bivalirudin: a direct thrombin inhibi… BE0000048
4 A1739 11923794 Kleiman NS, Klem J, Fernandes LS, Rubin H, Challa … BE0000048
5 A1741 11929334 Carswell CI, Plosker GL: Bivalirudin: a review of … BE0000048
6 A9 11752352 Chen X, Ji ZL, Chen YZ: TTD: Therapeutic Target Da… BE0000048
$references$targets$links
# A tibble: 0 × 0
$references$targets$attachments
# A tibble: 0 × 0
$references$transporters
$references$transporters$books
# A tibble: 0 × 0
$references$transporters$articles
# A tibble: 0 × 0
$references$transporters$links
# A tibble: 0 × 0
$references$transporters$attachments
# A tibble: 0 × 0
$cett
$cett$carriers
$cett$carriers$general_information
# A tibble: 0 × 0
$cett$carriers$actions
# A tibble: 0 × 0
$cett$carriers$polypeptides
$cett$carriers$polypeptides$general_information
# A tibble: 0 × 0
$cett$carriers$polypeptides$external_identy
# A tibble: 0 × 0
$cett$carriers$polypeptides$synonyms
# A tibble: 0 × 0
$cett$carriers$polypeptides$pfams
# A tibble: 0 × 0
$cett$carriers$polypeptides$go
# A tibble: 0 × 0
$cett$enzymes
$cett$enzymes$general_information
# A tibble: 1 × 8
enzyme_id name organism known_action position drugbank_id inhibition_strength
<chr> <chr> <chr> <chr> <chr> <chr> <chr>
1 BE0001075 Myel… Humans unknown 1 DB00006 unknown
# ℹ 1 more variable: induction_strength <chr>
$cett$enzymes$actions
# A tibble: 1 × 2
action enzyme_id
<chr> <chr>
1 inhibitor BE0001075
$cett$enzymes$polypeptides
$cett$enzymes$polypeptides$general_information
# A tibble: 1 × 20
polypeptide_id source name general_function specific_function gene_name locus
<chr> <chr> <chr> <chr> <chr> <chr> <chr>
1 P05164 Swiss… Myel… Peroxidase acti… Part of the host… MPO 17q2…
# ℹ 13 more variables: cellular_location <chr>, transmembrane_regions <chr>,
# signal_regions <chr>, theoretical_pi <chr>, molecular_weight <chr>,
# chromosome_location <chr>, organism <chr>, organism_ncbi_taxonomy_id <chr>,
# amino_acid_sequence <chr>, amino_acid_format <chr>, gene_sequence <chr>,
# gene_format <chr>, enzyme_id <chr>
$cett$enzymes$polypeptides$external_identy
# A tibble: 7 × 3
resource identifier enzyme_id
<chr> <chr> <chr>
1 HUGO Gene Nomenclature Committee (HGNC) HGNC:7218 BE0001075
2 GenAtlas MPO BE0001075
3 GenBank Gene Database J02694 BE0001075
4 GenBank Protein Database 189040 BE0001075
5 Guide to Pharmacology 2789 BE0001075
6 UniProtKB P05164 BE0001075
7 UniProt Accession PERM_HUMAN BE0001075
$cett$enzymes$polypeptides$synonyms
# A tibble: 2 × 2
synonym enzyme_id
<chr> <chr>
1 1.11.2.2 BE0001075
2 MPO BE0001075
$cett$enzymes$polypeptides$pfams
# A tibble: 1 × 3
identifier name enzyme_id
<chr> <chr> <chr>
1 PF03098 An_peroxidase BE0001075
$cett$enzymes$polypeptides$go
# A tibble: 24 × 3
category description enzyme_id
<chr> <chr> <chr>
1 component azurophil granule BE0001075
2 component extracellular exosome BE0001075
3 component extracellular space BE0001075
4 component lysosome BE0001075
5 component mitochondrion BE0001075
6 component nucleus BE0001075
7 component secretory granule BE0001075
8 function chromatin binding BE0001075
9 function heme binding BE0001075
10 function heparin binding BE0001075
# ℹ 14 more rows
$cett$targets
$cett$targets$general_information
# A tibble: 1 × 6
target_id name organism known_action position drugbank_id
<chr> <chr> <chr> <chr> <chr> <chr>
1 BE0000048 Prothrombin Humans yes 1 DB00006
$cett$targets$actions
# A tibble: 1 × 2
action target_id
<chr> <chr>
1 inhibitor BE0000048
$cett$targets$polypeptides
$cett$targets$polypeptides$general_information
# A tibble: 1 × 20
polypeptide_id source name general_function specific_function gene_name locus
<chr> <chr> <chr> <chr> <chr> <chr> <chr>
1 P00734 Swiss… Prot… Thrombospondin … Thrombin, which … F2 11p1…
# ℹ 13 more variables: cellular_location <chr>, transmembrane_regions <chr>,
# signal_regions <chr>, theoretical_pi <chr>, molecular_weight <chr>,
# chromosome_location <chr>, organism <chr>, organism_ncbi_taxonomy_id <chr>,
# amino_acid_sequence <chr>, amino_acid_format <chr>, gene_sequence <chr>,
# gene_format <chr>, target_id <chr>
$cett$targets$polypeptides$external_identy
# A tibble: 7 × 3
resource identifier target_id
<chr> <chr> <chr>
1 HUGO Gene Nomenclature Committee (HGNC) HGNC:3535 BE0000048
2 GenAtlas F2 BE0000048
3 GenBank Gene Database M17262 BE0000048
4 GenBank Protein Database 339641 BE0000048
5 Guide to Pharmacology 2362 BE0000048
6 UniProtKB P00734 BE0000048
7 UniProt Accession THRB_HUMAN BE0000048
$cett$targets$polypeptides$synonyms
# A tibble: 2 × 2
synonym target_id
<chr> <chr>
1 3.4.21.5 BE0000048
2 Coagulation factor II BE0000048
$cett$targets$polypeptides$pfams
# A tibble: 4 × 3
identifier name target_id
<chr> <chr> <chr>
1 PF00594 Gla BE0000048
2 PF00051 Kringle BE0000048
3 PF00089 Trypsin BE0000048
4 PF09396 Thrombin_light BE0000048
$cett$targets$polypeptides$go
# A tibble: 46 × 3
category description target_id
<chr> <chr> <chr>
1 component blood microparticle BE0000048
2 component cytosol BE0000048
3 component endoplasmic reticulum lumen BE0000048
4 component extracellular exosome BE0000048
5 component extracellular matrix BE0000048
6 component extracellular region BE0000048
7 component extracellular space BE0000048
8 component Golgi lumen BE0000048
9 component plasma membrane BE0000048
10 function calcium ion binding BE0000048
# ℹ 36 more rows
$cett$transporters
$cett$transporters$general_information
# A tibble: 0 × 0
$cett$transporters$actions
# A tibble: 0 × 0
$cett$transporters$polypeptides
$cett$transporters$polypeptides$general_information
# A tibble: 0 × 0
$cett$transporters$polypeptides$external_identy
# A tibble: 0 × 0
$cett$transporters$polypeptides$synonyms
# A tibble: 0 × 0
$cett$transporters$polypeptides$pfams
# A tibble: 0 × 0
$cett$transporters$polypeptides$go
# A tibble: 0 × 0
attr(,"class")
[1] "dvobject"
attr(,"original_db_info")
attr(,"original_db_info")$db_type
[1] "DrugBank"
attr(,"original_db_info")$db_version
[1] "5.1"
attr(,"original_db_info")$db_exported_date
[1] "2018-07-03"
parse DrugBank DB - zip file
Code
dvobj$result
Output
$drugs
$drugs$general_information
# A tibble: 1 × 15
drugbank_id other_keys type created updated name description cas_number
<chr> <chr> <chr> <chr> <chr> <chr> <chr> <chr>
1 DB00001 BTD00024;BIOD0… biot… 2005-0… 2018-0… Lepi… Lepirudin … 138068-37…
# ℹ 7 more variables: unii <chr>, average_mass <chr>, monoisotopic_mass <chr>,
# state <chr>, synthesis_reference <chr>, fda_label <chr>, msds <chr>
attr(,"class")
[1] "dvobject"
attr(,"original_db_info")
attr(,"original_db_info")$db_type
[1] "DrugBank"
attr(,"original_db_info")$db_version
[1] "5.1"
attr(,"original_db_info")$db_exported_date
[1] "2018-07-03"
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