### Example Usage of getUnichemSources Source: https://bhklab.github.io/AnnotationGx/reference/getUnichemSources.html An example demonstrating how to call the getUnichemSources function, which requires an internet connection. The example is wrapped in an interactive check to ensure it only runs when expected. ```R # Requires internet connection to UniChem if (interactive()) { getUnichemSources() } ``` -------------------------------- ### Examples Source: https://bhklab.github.io/AnnotationGx/reference/getPubchemAnnotationHeadings.html Examples of using the getPubchemAnnotationHeadings function with different parameters. ```R getPubchemAnnotationHeadings() #> Heading Type #> #> 1: 11B NMR Spectra Compound #> 2: 13C NMR Spectra Compound #> 3: 15N NMR Spectra Compound #> 4: 17O NMR Spectra Compound #> 5: 19F NMR Spectra Compound #> --- #> 697: Withdrawn Compound #> 698: WormBase ID Gene #> 699: WormBase ID Protein #> 700: Xenbase Gene ID Gene #> 701: ZFIN ID Gene ``` ```R getPubchemAnnotationHeadings(type = "Compound") #> Heading Type #> #> 1: 11B NMR Spectra Compound #> 2: 13C NMR Spectra Compound #> 3: 15N NMR Spectra Compound #> 4: 17O NMR Spectra Compound #> 5: 19F NMR Spectra Compound #> --- #> 529: WHO Essential Medicines Compound #> 530: Wikidata Compound #> 531: Wikipedia Compound #> 532: Wiley References Compound #> 533: Withdrawn Compound ``` ```R getPubchemAnnotationHeadings(heading = "ChEMBL*") #> Heading Type #> #> 1: ChEMBL Cell Line ID Cell #> 2: ChEMBL ID Compound #> 3: ChEMBL Target ID Protein ``` ```R getPubchemAnnotationHeadings(type = "Compound", heading = "ChEMBL*") #> Heading Type #> #> 1: ChEMBL ID Compound ``` -------------------------------- ### Install AnnotationGx from GitHub Source: https://bhklab.github.io/AnnotationGx/index.html Instructions for installing the AnnotationGx package from GitHub, including building manual and vignettes. ```r remotes::install_github( "bhklab/AnnotationGx", build_manual=TRUE, build_vignettes=TRUE ) ``` -------------------------------- ### Example Usage Source: https://bhklab.github.io/AnnotationGx/reference/mapCID2Properties.html Example of how to use the mapCID2Properties function. ```R mapCID2Properties(ids = c(123, 456), properties = c("MolecularWeight", "CanonicalSMILES")) #> CID MolecularWeight ConnectivitySMILES #> #> 1: 123 144.18 C(CC(=O)N)CN=C(N)N #> 2: 456 132.08 C(=O)(C(=O)O)NC(=O)N ``` -------------------------------- ### Example usage of getOncotreeVersions Source: https://bhklab.github.io/AnnotationGx/reference/getOncotreeVersions.html Example of how to use the getOncotreeVersions function. Requires internet connection to Oncotree API. ```R # Requires internet connection to Oncotree API if (interactive()) { getOncotreeVersions() } ``` -------------------------------- ### Examples Source: https://bhklab.github.io/AnnotationGx/reference/getPubchemProperties.html Example of how to use the getPubchemProperties function, requiring an internet connection. ```r # Requires internet connection to PubChem if (interactive()) { getPubchemProperties() } ``` -------------------------------- ### Examples Source: https://bhklab.github.io/AnnotationGx/reference/annotatePubchemCompound.html Examples of how to use the annotatePubchemCompound function. ```R annotatePubchemCompound(cid = 2244) #> [1] "CHEMBL25" annotatePubchemCompound(cid = c(2244, 67890), heading = "CAS") #> [1] "50-78-2" "407-59-0" ``` -------------------------------- ### Getting available resources from ChEMBL Source: https://bhklab.github.io/AnnotationGx/articles/ChEMBL.html Example of using the `getChemblResources()` function to list all queryable resources in the ChEMBL API. ```r getChemblResources() #> [1] "activity" "assay" #> [3] "atc_class" "binding_site" #> [5] "biotherapeutic" "cell_line" #> [7] "chembl_id_lookup" "compound_record" #> [9] "compound_structural_alert" "document" #> [11] "document_similarity" "document_term" #> [13] "drug" "drug_indication" #> [15] "drug_warning" "go_slim" #> [17] "image" "mechanism" #> [19] "metabolism" "molecule" #> [21] "molecule_form" "organism" #> [23] "protein_classification" "similarity" #> [25] "source" "status" #> [27] "substructure" "target" #> [29] "target_component" "target_relation" #> [31] "tissue" "xref_source" ``` -------------------------------- ### Example Source: https://bhklab.github.io/AnnotationGx/reference/queryChemblAPI.html An example of how to query the ChEMBL API for mechanisms related to a molecule. ```R queryChemblAPI("mechanism", "molecule_chembl_id", "in", "CHEMBL1413") #> $mechanisms #> action_type binding_site_comment direct_interaction disease_efficacy #> 1 CHELATING AGENT NA 1 1 #> 2 CHELATING AGENT NA 1 1 #> max_phase mec_id #> 1 4 2200 #> 2 4 2224 #> mechanism_comment #> 1 Trivalent metal cations chelating agent; inhibition of the metal-dependent enzymes that are responsible for the degradation of peroxides within the fungal cell #> 2 Trivalent metal cations chelating agent; inhibition of the metal-dependent enzymes that are responsible for the degradation of peroxides within the fungal cell #> mechanism_of_action #> 1 Iron chelating agent #> 2 Aluminium chelating agent #> mechanism_refs #> 1 20964457, 23416050, Ciclopirox#cite_note-pmid12760852-4, PubMed, PubMed, Wikipedia, http://europepmc.org/abstract/MED/20964457, http://europepmc.org/abstract/MED/23416050, http://en.wikipedia.org/wiki/Ciclopirox#cite_note-pmid12760852-4 #> 2 20964457, 23416050, Ciclopirox#cite_note-pmid12760852-4, PubMed, PubMed, Wikipedia, http://europepmc.org/abstract/MED/20964457, http://europepmc.org/abstract/MED/23416050, http://en.wikipedia.org/wiki/Ciclopirox#cite_note-pmid12760852-4 #> molecular_mechanism molecule_chembl_id parent_molecule_chembl_id record_id #> 1 1 CHEMBL1413 CHEMBL1413 1343970 #> 2 1 CHEMBL1413 CHEMBL1413 1343970 #> selectivity_comment site_id target_chembl_id variant_sequence #> 1 NA NA CHEMBL2363058 NA #> 2 NA NA CHEMBL2366381 NA #> #> $page_meta #> $page_meta$limit #> [1] 20 #> #> $page_meta$`next` #> NULL #> #> $page_meta$offset #> [1] 0 #> #> $page_meta$previous #> NULL #> #> $page_meta$total_count #> [1] 2 #> #> ``` -------------------------------- ### Load AnnotationGx Package Source: https://bhklab.github.io/AnnotationGx/index.html Example of loading the AnnotationGx package and accessing its help documentation. ```r library(AnnotationGx) help(package="AnnotationGx") ``` -------------------------------- ### Example usage of getPubchemCompound Source: https://bhklab.github.io/AnnotationGx/reference/getPubchemCompound.html Example demonstrating how to retrieve compound information including Title, MolecularFormula, InChIKey, and CanonicalSMILES for given compound IDs. ```R properties <- c("Title", "MolecularFormula", "InChIKey", "CanonicalSMILES") getPubchemCompound(c(3672, 176870), from = "cid", to = "property", properties = properties) ``` -------------------------------- ### Example Usage of getOncotreeMainTypes Source: https://bhklab.github.io/AnnotationGx/reference/getOncotreeMainTypes.html Example of how to use the getOncotreeMainTypes function. Requires an internet connection to the Oncotree API. ```R # Requires internet connection to Oncotree API if (interactive()) { getOncotreeMainTypes() } ``` -------------------------------- ### Examples of getPubchemStatus Source: https://bhklab.github.io/AnnotationGx/reference/getPubchemStatus.html Shows example outputs of getPubchemStatus with different arguments, including returning messages and suppressing print messages. ```r getPubchemStatus() #> Throttling status: #> Request Count status: Green (0%) #> Request Time status: Green (0%) #> Service status: Green (7%) getPubchemStatus(returnMessage = TRUE) #> Throttling status: #> Request Count status: Green (1%) #> Request Time status: Green (0%) #> Service status: Yellow (57%) #> [17:23:12][WARNING]The request limit has been reached or is close to being reached. #> $request_count #> $request_count$status #> [1] "Green" #> #> $request_count$percent #> [1] 1 #> #> #> $request_time #> $request_time$status #> [1] "Green" #> #> $request_time$percent #> [1] 0 #> #> #> $service #> $service$status #> [1] "Yellow" #> #> $service$percent #> [1] 57 #> #> getPubchemStatus(printMessage = FALSE) #> [17:23:12][WARNING]The request limit has been reached or is close to being reached. ``` -------------------------------- ### Examples Source: https://bhklab.github.io/AnnotationGx/reference/GDSC_sampleMetadata.html Display the first few rows of the GDSC_sampleMetadata dataset. ```R data(GDSC_sampleMetadata) head(GDSC_sampleMetadata) ``` -------------------------------- ### Example Usage of queryUnichemCompound Source: https://bhklab.github.io/AnnotationGx/reference/queryUnichemCompound.html An example demonstrating how to use the queryUnichemCompound function to query for a compound by sourceID and compound ID, showing the returned external and UniChem mappings. ```R queryUnichemCompound(type = "sourceID", compound = "444795", sourceID = 22) #> $External_Mappings #> compoundID Name NameLong sourceID #> #> 1: CHEMBL38 chembl ChEMBL 1 #> 2: DB00755 drugbank DrugBank 2 #> 3: 3KV rcsb_pdb RCSB PDB 3 #> 4: REA rcsb_pdb RCSB PDB 3 #> 5: REA pdbe Protein Data Bank in Europe 5 #> --- #> 206: NCT06358677 clinicaltrials Clinical Trials 46 #> 207: NCT06439888 clinicaltrials Clinical Trials 46 #> 208: NCT06484920 clinicaltrials Clinical Trials 46 #> 209: PD001430 probes_and_drugs Probes&Drugs 49 #> 210: VITAAC CCDC CSD (Cambridge Structural Database) 50 #> sourceURL #> #> 1: https://www.ebi.ac.uk/chembldb/compound/inspect/CHEMBL38 #> 2: https://go.drugbank.com/drugs/DB00755 #> 3: https://www.rcsb.org/ligand/3KV #> 4: https://www.rcsb.org/ligand/REA #> 5: https://www.ebi.ac.uk/pdbe-srv/pdbechem/chemicalCompound/show/REA #> --- #> 206: https://clinicaltrials.gov/study/NCT06358677 #> 207: https://clinicaltrials.gov/study/NCT06439888 #> 208: https://clinicaltrials.gov/study/NCT06484920 #> 209: https://www.probes-drugs.org/compounds/PD001430 #> 210: https://www.ccdc.cam.ac.uk/structures/search?sid=UNICHEM&pid=csd:VITAAC #> #> $UniChem_Mappings #> $UniChem_Mappings$UniChem.UCI #> [1] 538323 #> #> $UniChem_Mappings$UniChem.InchiKey #> [1] "SHGAZHPCJJPHSC-YCNIQYBTSA-N" #> #> $UniChem_Mappings$UniChem.Inchi #> [1] "InChI=1S/C20H28O2/c1-15(8-6-9-16(2)14-19(21)22)11-12-18-17(3)10-7-13-20(18,4)5/h6,8-9,11-12,14H,7,10,13H2,1-5H3,(H,21,22)/b9-6+,12-11+,15-8+,16-14+" #> #> $UniChem_Mappings$UniChem.formula #> [1] "C20H28O2" #> #> $UniChem_Mappings$UniChem.connections #> [1] "1-15(8-6-9-16(2)14-19(21)22)11-12-18-17(3)10-7-13-20(18,4)5" #> #> $UniChem_Mappings$UniChem.hAtoms #> [1] "6,8-9,11-12,14H,7,10,13H2,1-5H3,(H,21,22)" #> #> ``` -------------------------------- ### Example Source: https://bhklab.github.io/AnnotationGx/reference/mapCell2Accession.html An example of how to use the mapCell2Accession function to map cell line IDs to accession numbers. ```R mapCell2Accession(ids = c("A549", "MCF7")) #> Querying Cellosaurus... ■■■■■■■■■■■■■■■■ 50% | ETA: 1s #> Querying Cellosaurus... ■■■■■■■■■■■■■■■■■■■■■■■■■■■■■■■ 100% | ETA: 0s #> cellLineName accession query #> #> 1: A-549 CVCL_0023 A549 #> 2: MCF-7 CVCL_0031 MCF7 ``` -------------------------------- ### Example Usage of cleanCharacterStrings Source: https://bhklab.github.io/AnnotationGx/reference/cleanCharacterStrings.html Demonstrates how to use the cleanCharacterStrings function to clean a sample input string. ```R cleanCharacterStrings("Cisplatin: 1 mg/mL (1.5 mM); 5 mM in DMSO") #> [1] "CISPLATIN" ``` -------------------------------- ### Example ChEMBL API Query Source: https://bhklab.github.io/AnnotationGx/articles/ChEMBL.html An example query to retrieve mechanisms for a specific molecule ChEMBL ID. ```text https://www.ebi.ac.uk/chembl/api/data/mechanism?molecule_chembl_id__in=CHEMBL1413&format=json ``` -------------------------------- ### Standard GNU GPL Notice Source: https://bhklab.github.io/AnnotationGx/LICENSE.html This is the standard notice to be attached to the start of each source file for a new program to ensure it is free software under the GNU General Public License. ```text Copyright (C) This program is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version. This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details. You should have received a copy of the GNU General Public License along with this program. If not, see . ``` -------------------------------- ### Example 1 Source: https://bhklab.github.io/AnnotationGx/reference/annotateCellAccession.html Annotating a cell line with default parameters. ```R annotateCellAccession("CVCL_0031") #> cellLineName accession category #> #> 1: MCF-7 CVCL_0031 Cancer cell line #> date ageAtSampling #> #> 1: Created: 04-04-12; Last updated: 27-11-25; Version: 54 69Y #> sexOfCell #> #> 1: Female #> synonyms #> #> 1: MCF 7,MCF.7,MCF7,Michigan Cancer Foundation-7,ssMCF-7,ssMCF7,...[9] #> diseases crossReferences hierarchy comments #> #> 1: ``` -------------------------------- ### Interactive Mode Notice Source: https://bhklab.github.io/AnnotationGx/LICENSE.html This is a short notice to be displayed when a program starts in interactive mode, informing users about its copyright and licensing terms. ```text Copyright (C) This program comes with ABSOLUTELY NO WARRANTY; for details type 'show w'. This is free software, and you are welcome to redistribute it under certain conditions; type 'show c' for details. ``` -------------------------------- ### Example CCLE sample metadata Source: https://bhklab.github.io/AnnotationGx/articles/AnnotationStandards.html This code snippet shows the first few rows of the CCLE sample metadata, illustrating column names like CCLE_ID, depMapID, Name, and CCLE_ID_parsed. ```r # "sample" refers to the cell line names data(CCLE_sampleMetadata) head(CCLE_sampleMetadata) #> CCLE_ID depMapID Name CCLE_ID_parsed #> #> 1: DMS53_LUNG ACH-000698 DMS 53 DMS53 #> 2: SW1116_LARGE_INTESTINE ACH-000489 SW1116 SW1116 #> 3: NCIH1694_LUNG ACH-000431 NCI-H1694 NCIH1694 #> 4: P3HR1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE ACH-000707 P3HR-1 P3HR1 #> 5: HUT78_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE ACH-000509 HuT 78 HUT78 #> 6: UMUC3_URINARY_TRACT ACH-000522 UM-UC-3 UMUC3 ``` -------------------------------- ### Standardize Names Function Example Source: https://bhklab.github.io/AnnotationGx/reference/standardize_names.html Demonstrates the usage of the standardize_names function with a sample character vector and shows the expected output. ```r standardize_names(c("John Doe", "Jane Smith (Manager)", "Alice, PhD")) #> [1] "JOHNDOE" "JANESMITH" "ALICE" # Output: [1] "JOHNDOE" "JANESMITH" "ALICE" ``` -------------------------------- ### Handle multimapping by selecting the first CID Source: https://bhklab.github.io/AnnotationGx/articles/PubChemAPI.html Illustrates how to use the `first = TRUE` argument in mapCompound2CID to get only the first CID when a name maps to multiple CIDs. ```R mapCompound2CID(drugs, first = TRUE) #> name cids #> #> 1: Aspirin 2244 #> 2: Erlotinib 176870 #> 3: Acadesine 17513 #> 4: Camptothecin 24360 #> 5: Vincaleukoblastine 13342 #> 6: Cisplatin 5460033 ``` -------------------------------- ### Get annotation headings for a specific type Source: https://bhklab.github.io/AnnotationGx/articles/PubChemAPI.html Fetches all annotation headings available for a given PubChem compound type. ```R getPubchemAnnotationHeadings(type = "Compound") #> Heading Type #> #> 1: 11B NMR Spectra Compound #> 2: 13C NMR Spectra Compound #> 3: 15N NMR Spectra Compound #> 4: 17O NMR Spectra Compound #> 5: 19F NMR Spectra Compound #> --- #> 529: WHO Essential Medicines Compound #> 530: Wikidata Compound #> 531: Wikipedia Compound #> 532: Wiley References Compound #> 533: Withdrawn Compound ``` -------------------------------- ### Get All Available Annotation Headings Source: https://bhklab.github.io/AnnotationGx/articles/PubChemAPI.html This function retrieves all available annotation headings and their corresponding types from PubChem. ```r getPubchemAnnotationHeadings() #> Heading Type #> #> 1: 11B NMR Spectra Compound #> 2: 13C NMR Spectra Compound #> 3: 15N NMR Spectra Compound #> 4: 17O NMR Spectra Compound #> 5: 19F NMR Spectra Compound #> --- #> 697: Withdrawn Compound #> 698: WormBase ID Gene #> 699: WormBase ID Protein #> 700: Xenbase Gene ID Gene #> 701: ZFIN ID Gene ``` -------------------------------- ### Example CCLE treatment metadata Source: https://bhklab.github.io/AnnotationGx/articles/AnnotationStandards.html This code snippet shows the first few rows of the CCLE treatment metadata, illustrating the column name CCLE.treatmentid. ```r # "treatment" refers to the drug names data(CCLE_treatmentMetadata) head(CCLE_treatmentMetadata) #> CCLE.treatmentid #> #> 1: Erlotinib #> 2: Lapatinib #> 3: PHA-665752 #> 4: PF-2341066 #> 5: TAE684 #> 6: Vandetanib ``` -------------------------------- ### Example Usage of getOncotreeTumorTypes Source: https://bhklab.github.io/AnnotationGx/reference/getOncotreeTumorTypes.html Example of how to use the getOncotreeTumorTypes function, which requires an internet connection to the Oncotree API. ```R # Requires internet connection to Oncotree API if (interactive()) { getOncotreeTumorTypes() } ``` -------------------------------- ### Getting fields for a specific resource Source: https://bhklab.github.io/AnnotationGx/articles/ChEMBL.html Example of using the `getChemblResourceFields()` function to list queryable fields for a given ChEMBL resource. ```r getChemblResourceFields("mechanism") ``` -------------------------------- ### Load AnnotationGx package Source: https://bhklab.github.io/AnnotationGx/articles/Introduction.html R code to load the AnnotationGx package into the current R session. ```R library("AnnotationGx") ``` -------------------------------- ### Load AnnotationGx library Source: https://bhklab.github.io/AnnotationGx/articles/AnnotationStandards.html This code snippet demonstrates how to load the AnnotationGx library in R. ```r library(AnnotationGx) ``` -------------------------------- ### Get available Oncotree versions Source: https://bhklab.github.io/AnnotationGx/reference/getOncotreeVersions.html This function retrieves the available versions of Oncotree. ```R getOncotreeVersions() ``` -------------------------------- ### Get the Chembl filter types Source: https://bhklab.github.io/AnnotationGx/reference/getChemblFilterTypes.html This function retrieves the Chembl filter types. ```R getChemblFilterTypes() ``` -------------------------------- ### Get Oncotree Main Types Function Source: https://bhklab.github.io/AnnotationGx/reference/getOncotreeMainTypes.html This function retrieves the main types from the Oncotree database. ```R getOncotreeMainTypes() ``` -------------------------------- ### Get Oncotree Tumor Types Function Source: https://bhklab.github.io/AnnotationGx/reference/getOncotreeTumorTypes.html This function retrieves the tumor types from the Oncotree database. ```R getOncotreeTumorTypes() ``` -------------------------------- ### Usage Source: https://bhklab.github.io/AnnotationGx/reference/gCSI_sampleMetadata.html This snippet shows how to access the gCSI_sampleMetadata object. ```r gCSI_sampleMetadata ``` -------------------------------- ### Get Chembl Resource Fields Function Usage Source: https://bhklab.github.io/AnnotationGx/reference/getChemblResourceFields.html This R code snippet demonstrates how to use the getChemblResourceFields function to retrieve fields for the 'molecule' resource from the ChEMBL database. ```R getChemblResourceFields("molecule") #> [1] "atc_classifications" "availability_type" "biotherapeutic" #> [4] "black_box_warning" "chemical_probe" "chirality" #> [7] "cross_references" "dosed_ingredient" "first_approval" #> [10] "first_in_class" "helm_notation" "inorganic_flag" #> [13] "max_phase" "molecule_chembl_id" "molecule_hierarchy" #> [16] "molecule_properties" "molecule_structures" "molecule_synonyms" #> [19] "molecule_type" "natural_product" "oral" #> [22] "orphan" "parenteral" "polymer_flag" #> [25] "pref_name" "prodrug" "score" #> [28] "structure_type" "therapeutic_flag" "topical" #> [31] "usan_stem" "usan_stem_definition" "usan_substem" #> [34] "usan_year" "veterinary" "withdrawn_flag" ``` -------------------------------- ### Usage of CTRP_sampleMetadata Source: https://bhklab.github.io/AnnotationGx/reference/CTRP_sampleMetadata.html Shows how to access the CTRP_sampleMetadata object. ```R CTRP_sampleMetadata ``` -------------------------------- ### Example 2 Source: https://bhklab.github.io/AnnotationGx/reference/annotateCellAccession.html Annotating a cell line with specific annotation types. ```R annotateCellAccession("CVCL_0031", to = c("id", "ac", "hi", "sy")) #> cellLineName accession ageAtSampling sexOfCell #> #> 1: MCF-7 CVCL_0031 #> synonyms diseases #> #> 1: MCF 7,MCF.7,MCF7,Michigan Cancer Foundation-7,ssMCF-7,ssMCF7,...[9] #> crossReferences hierarchy comments #> #> 1: ``` -------------------------------- ### Get available UniChem sources Source: https://bhklab.github.io/AnnotationGx/articles/Unichem.html This code snippet demonstrates how to retrieve a list of available database identifiers from UniChem. By default, it returns the database shortname and UniChem's ID for it. Passing `all_columns = TRUE` returns all available columns. ```r getUnichemSources() #> Name SourceID #> #> 1: probes_and_drugs 49 #> 2: pubchem 22 #> 3: bindingdb 31 #> 4: lipidmaps 33 #> 5: fdasrs 14 #> 6: nmrshiftdb2 24 #> 7: drugcentral 34 #> 8: chembl 1 #> 9: rcsb_pdb 3 #> 10: rhea 38 #> 11: surechembl 15 #> 12: brenda 37 #> 13: swisslipids 41 #> 14: CCDC 50 #> 15: molport 28 #> 16: gtopdb 4 #> 17: chebi 7 #> 18: drugbank 2 #> 19: hmdb 18 #> 20: pdbe 5 #> 21: comptox 32 #> 22: clinicaltrials 46 #> Name SourceID #> ``` -------------------------------- ### Example GDSC sample metadata Source: https://bhklab.github.io/AnnotationGx/articles/AnnotationStandards.html This code snippet shows the first few rows of the GDSC sample metadata, demonstrating standardized column names like GDSC.Sample_Name and GDSC.COSMIC_ID, following both Standard 1 and Standard 2. ```r data(GDSC_sampleMetadata) head(GDSC_sampleMetadata) #> GDSC.Sample_Name GDSC.COSMIC_ID #> #> 1: A253 906794 #> 2: BB30-HNC 753531 #> 3: BB49-HNC 753532 #> 4: BHY 753535 #> 5: BICR10 1290724 #> 6: BICR22 1240121 ``` -------------------------------- ### Get the Cellosaurus API version Source: https://bhklab.github.io/AnnotationGx/reference/cellosaurusAPIVersion.html This function retrieves the version of the Cellosaurus API. ```R cellosaurusAPIVersion() ``` ```R cellosaurusAPIVersion() #> [1] "1.0.4" ``` -------------------------------- ### Load AnnotationGx and set options Source: https://bhklab.github.io/AnnotationGx/articles/Cellosaurus.html Loads the AnnotationGx library and sets logging options to suppress informational messages. ```R library(AnnotationGx) library(data.table) # set options to warn to quiet info logs options("log_level" = "WARN") ``` -------------------------------- ### Usage of getPubchemStatus Source: https://bhklab.github.io/AnnotationGx/reference/getPubchemStatus.html Demonstrates how to call the getPubchemStatus function with default and custom arguments. ```r getPubchemStatus( returnMessage = FALSE, printMessage = TRUE, url = "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/name/Aspirin/cids/JSON" ) ``` -------------------------------- ### Get OncoTree Versions Source: https://bhklab.github.io/AnnotationGx/articles/OncoTree.html The `getOncotreeVersions` function retrieves the available OncoTree release. ```r getOncotreeVersions() #> api_identifier #> #> 1: oncotree_latest_stable #> 2: oncotree_2025_10_03 #> 3: oncotree_2025_04_08 #> 4: oncotree_development #> 5: oncotree_candidate_release #> 6: oncotree_2021_11_02 #> 7: oncotree_2020_10_01 #> 8: oncotree_2020_04_01 #> 9: oncotree_2020_02_06 #> 10: oncotree_2020_02_01 #> 11: oncotree_2019_12_01 #> 12: oncotree_2019_08_01 #> 13: oncotree_2019_05_01 #> 14: oncotree_2019_03_01 #> 15: oncotree_2019_02_01 #> 16: oncotree_2018_11_01 #> 17: oncotree_2018_09_01 #> 18: oncotree_2018_08_01 #> 19: oncotree_2018_07_01 #> 20: oncotree_2018_06_15 #> 21: oncotree_2018_06_01 #> 22: oncotree_2018_05_01 #> 23: oncotree_2018_04_01 #> 24: oncotree_2018_03_01 #> 25: oncotree_2018_02_01 #> 26: oncotree_2018_01_01 #> 27: oncotree_2017_11_01 #> 28: oncotree_2017_10_05 #> 29: oncotree_2017_06_21 #> 30: oncotree_legacy_1.1 #> api_identifier #> #> description #> #> 1: This is the latest approved version for public use. #> 2: Stable OncoTree released on date 2025-10-03 #> 3: Stable OncoTree released on date 2025-04-08 #> 4: Latest OncoTree under development (subject to change without notice) #> 5: This version of the OncoTree reflects upcoming changes which have been approved for the next public release of oncotree. It also includes a small number of nodes which will not be included in the next public release (see the news page for more details). The next public release may possibly include additional oncotree nodes, if approved. #> 6: Stable OncoTree released on date 2021-11-02 #> 7: Stable OncoTree released on date 2020-10-01 #> 8: Stable OncoTree released on date 2020-04-01 ``` -------------------------------- ### Usage Source: https://bhklab.github.io/AnnotationGx/reference/CCLE_sampleMetadata.html This snippet shows how to access the CCLE_sampleMetadata object. ```R CCLE_sampleMetadata ``` -------------------------------- ### Basic Usage Source: https://bhklab.github.io/AnnotationGx/reference/getChemblMechanism.html Retrieves all mechanism data for a given ChEMBL ID. ```r getChemblMechanism("CHEMBL1413") #> action_type binding_site_comment direct_interaction disease_efficacy #> #> 1: CHELATING AGENT NA 1 1 #> 2: CHELATING AGENT NA 1 1 #> max_phase mec_id #> #> 1: 4 2200 #> 2: 4 2224 #> mechanism_comment #> #> 1: Trivalent metal cations chelating agent; inhibition of the metal-dependent enzymes that are responsible for the degradation of peroxides within the fungal cell #> 2: Trivalent metal cations chelating agent; inhibition of the metal-dependent enzymes that are responsible for the degradation of peroxides within the fungal cell #> mechanism_of_action mechanism_refs molecular_mechanism #> #> 1: Iron chelating agent 1 #> 2: Aluminium chelating agent 1 #> molecule_chembl_id parent_molecule_chembl_id record_id selectivity_comment #> #> 1: CHEMBL1413 CHEMBL1413 1343970 NA #> 2: CHEMBL1413 CHEMBL1413 1343970 NA #> site_id target_chembl_id variant_sequence #> #> 1: NA CHEMBL2363058 NA #> 2: NA CHEMBL2366381 NA ``` -------------------------------- ### R Function Signature Source: https://bhklab.github.io/AnnotationGx/reference/getChemblMechanism.html The usage signature for the getChemblMechanism function in R. ```R getChemblMechanism( chembl.ID, resources = "mechanism", field = "molecule_chembl_id", filter_type = "in", returnURL = FALSE, raw = FALSE ) ``` -------------------------------- ### Load AnnotationGx library and CTRP treatment metadata Source: https://bhklab.github.io/AnnotationGx/articles/CTRP-Treatment-Annotation.html Loads the AnnotationGx library and the CTRP_treatmentMetadata dataset. ```R library(AnnotationGx) data(CTRP_treatmentMetadata) ```