The PubChemR package introduces a pivotal function,
get_pug_rest, designed to facilitate seamless access to the
vast chemical data repository of PubChem. This function leverages the
capabilities of PubChem’s Power User Gateway (PUG) REST service,
providing a straightforward and efficient means for users to
programmatically interact with PubChem’s extensive database. This
vignette aims to elucidate the structure and usage of the PUG REST
service, offering a range of illustrative use cases to aid new users in
understanding its operation and constructing effective requests.
PUG REST, standing for Power User Gateway RESTful interface, is a simplified access route to PubChem’s data and services. It is designed for scripts, web page embedded JavaScript, and third-party applications, eliminating the need for the more complex XML and SOAP envelopes required by other PUG variants. PUG REST’s design revolves around the PubChem identifier (SID for substances, CID for compounds, and AID for assays) and is structured into three main request components: input (identifiers), operation (actions on identifiers), and output (desired information format).
Usage Policy:
get_pug_restOverview
The get_pug_rest function in the PubChemR
package provides a versatile interface to access a wide range of
chemical data from the PubChem database. This section of the vignette
focuses on various methods to retrieve chemical structure information
and other related data using the PUG REST service. The function is
designed to be flexible, accommodating different input methods,
operations, and output formats.
This function sends a request to the PubChem PUG REST API to retrieve various types of data for a given identifier. It supports fetching data in different formats and allows saving the output.
get_pug_rest(
identifier = NULL,
namespace = "cid",
domain = "compound",
operation = NULL,
output = "JSON",
searchtype = NULL,
property = NULL,
options = NULL,
save = FALSE,
dpi = 300,
path = NULL,
file_name = NULL,
...
)Arguments
identifier: A vector of identifiers for the query, either numeric or character. This is the main input for querying the PubChem database.
namespace: A character string specifying the namespace for the request. Default is ‘cid’. This defines the type of identifier being used, such as ‘cid’ (Compound ID), ‘sid’ (Substance ID), etc.
domain: A character string specifying the domain for the request. Default is ‘compound’. This indicates the type of entity being queried, such as ‘compound’, ‘substance’, etc.
operation: An optional character string specifying the operation for the request. This can be used to specify particular actions or methods within the API.
output: A character string specifying the output format. Possible values are ‘SDF’, ‘JSON’, ‘JSONP’, ‘CSV’, ‘TXT’, and ‘PNG’. Default is ‘JSON’. This defines the format in which the data will be returned.
searchtype: An optional character string specifying the search type. This allows for specifying the nature of the search being performed.
property: An optional character string specifying the property for the request. This can be used to filter or specify particular properties of the data being retrieved.
options: A list of additional options for the request. This allows for further customization and fine-tuning of the request parameters.
save: A logical value indicating whether to save the output as a file or image. Default is FALSE. When set to TRUE, the function will save the retrieved data to a specified file.
dpi: An integer specifying the DPI for image output. Default is 300. This is relevant when the output format is an image, determining the resolution of the saved image.
path: A character string specifying the directory path where the file will be saved. If not provided, the current working directory is used.
file_name: A character string of length 1. Defines the name of the file (without file extension) to save. If NULL, the default file name is set as “files_downloaded”.
…: Additional arguments to be passed to the request.
Value
The function returns different types of content based on the specified output format:
JSON: Returns a list. CSV and TXT: Returns a data frame. SDF: Returns an SDF file of the requested identifier. PNG: Returns an image object or saves an image file.
In the context of the PubChem PUG REST API, the input methods define how records of interest are specified for a request. There are several ways to define this input, with the most common methods being outlined below:
1. By Identifier: The most straightforward method to specify input is by using identifiers directly. These identifiers can be Substance IDs (SIDs) or Compound IDs (CIDs). For example, to retrieve the names of a substance with CID 2244, you can use the get_pug_rest function as follows:
result <- get_pug_rest(identifier = "2244", namespace = "cid", domain = "compound", output = "JSON")
result
#>
#> An object of class 'PugRestInstance'
#>
#> Request Details:
#> - Domain: Compound
#> - Namespace: CID
#> - Operation: <NULL>
#> - Identifier: 2244
#>
#> NOTE: Run getter function 'pubChemData(...)' to extract raw data retrieved from PubChem Database.
#> See ?pubChemData for details.The pubChemData function then processes the result to extract and display the retrieved data. Here’s an interpretation of the output for CID 2244:
pubChemDataResult <- pubChemData(result)The JSON response contains detailed information about the compound identified by CID 2244. The PC_Compounds array holds the compound data, and within it, each element corresponds to a specific compound.
For CID 2244, the following information is retrieved:
ID: Confirms the compound identifier is CID 2244.
pubChemDataResult$PC_Compounds[[1]]$id
#> $id
#> cid
#> 2244Atoms: Details the atomic composition, with an aid array listing the atom IDs and an element array listing the atomic numbers (e.g., 6 for carbon, 8 for oxygen, 1 for hydrogen).
pubChemDataResult$PC_Compounds[[1]]$atoms
#> $aid
#> [1] 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21
#>
#> $element
#> [1] 8 8 8 8 6 6 6 6 6 6 6 6 6 1 1 1 1 1 1 1 1Bonds: Describes the bonds between atoms, including arrays for the IDs of the atoms involved (aid1 and aid2) and the bond order.
pubChemDataResult$PC_Compounds[[1]]$bonds
#> $aid1
#> [1] 1 1 2 2 3 4 5 5 6 6 7 7 8 8 9 9 10 12 13 13 13
#>
#> $aid2
#> [1] 5 12 11 21 11 12 6 7 8 11 9 14 10 15 10 16 17 13 18 19 20
#>
#> $order
#> [1] 1 1 1 1 2 2 1 2 2 1 1 1 1 1 2 1 1 1 1 1 1Coordinates: Provides the spatial coordinates (x and y) for each atom, which can be used to visualize the molecular structure.
pubChemDataResult$PC_Compounds[[1]]$coords
#> [[1]]
#> [[1]]$type
#> [1] 1 5 255
#>
#> [[1]]$aid
#> [1] 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21
#>
#> [[1]]$conformers
#> [[1]]$conformers[[1]]
#> [[1]]$conformers[[1]]$x
#> [1] 3.7321 6.3301 4.5981 2.8660 4.5981 5.4641 4.5981 6.3301 5.4641 6.3301 5.4641 2.8660 2.0000 4.0611 6.8671 5.4641
#> [17] 6.8671 2.3100 1.4631 1.6900 6.3301
#>
#> [[1]]$conformers[[1]]$y
#> [1] -0.0600 1.4400 1.4400 -1.5600 -0.5600 -0.0600 -1.5600 -0.5600 -2.0600 -1.5600 0.9400 -0.5600 -0.0600 -1.8700
#> [15] -0.2500 -2.6800 -1.8700 0.4769 0.2500 -0.5969 2.0600
#>
#> [[1]]$conformers[[1]]$style
#> [[1]]$conformers[[1]]$style$annotation
#> [1] 8 8 8 8 8 8
#>
#> [[1]]$conformers[[1]]$style$aid1
#> [1] 5 5 6 7 8 9
#>
#> [[1]]$conformers[[1]]$style$aid2
#> [1] 6 7 8 9 10 10Charge: Indicates the compound’s charge, which is 0 in this case.
pubChemDataResult$PC_Compounds[[1]]$charge
#> [1] 0Properties: Lists various properties of the compound, including:
Compound Complexity: A measure of the molecular complexity.
pubChemDataResult$PC_Compounds[[1]]$props[[2]]
#> $urn
#> $urn$label
#> [1] "Compound Complexity"
#>
#> $urn$datatype
#> [1] 7
#>
#> $urn$implementation
#> [1] "E_COMPLEXITY"
#>
#> $urn$version
#> [1] "3.4.8.18"
#>
#> $urn$software
#> [1] "Cactvs"
#>
#> $urn$source
#> [1] "Xemistry GmbH"
#>
#> $urn$release
#> [1] "2025.04.14"
#>
#>
#> $value
#> fval
#> 212Hydrogen Bond Acceptor/Donor Count: Indicates the number of hydrogen bond acceptors and donors.
pubChemDataResult$PC_Compounds[[1]]$props[[3]]
#> $urn
#> $urn$label
#> [1] "Count"
#>
#> $urn$name
#> [1] "Hydrogen Bond Acceptor"
#>
#> $urn$datatype
#> [1] 5
#>
#> $urn$implementation
#> [1] "E_NHACCEPTORS"
#>
#> $urn$version
#> [1] "3.4.8.18"
#>
#> $urn$software
#> [1] "Cactvs"
#>
#> $urn$source
#> [1] "Xemistry GmbH"
#>
#> $urn$release
#> [1] "2025.04.14"
#>
#>
#> $value
#> ival
#> 4pubChemDataResult$PC_Compounds[[1]]$props[[4]]
#> $urn
#> $urn$label
#> [1] "Count"
#>
#> $urn$name
#> [1] "Hydrogen Bond Donor"
#>
#> $urn$datatype
#> [1] 5
#>
#> $urn$implementation
#> [1] "E_NHDONORS"
#>
#> $urn$version
#> [1] "3.4.8.18"
#>
#> $urn$software
#> [1] "Cactvs"
#>
#> $urn$source
#> [1] "Xemistry GmbH"
#>
#> $urn$release
#> [1] "2025.04.14"
#>
#>
#> $value
#> ival
#> 1Rotatable Bond Count: The number of rotatable bonds, which impacts the molecule’s flexibility.
pubChemDataResult$PC_Compounds[[1]]$props[[5]]
#> $urn
#> $urn$label
#> [1] "Count"
#>
#> $urn$name
#> [1] "Rotatable Bond"
#>
#> $urn$datatype
#> [1] 5
#>
#> $urn$implementation
#> [1] "E_NROTBONDS"
#>
#> $urn$version
#> [1] "3.4.8.18"
#>
#> $urn$software
#> [1] "Cactvs"
#>
#> $urn$source
#> [1] "Xemistry GmbH"
#>
#> $urn$release
#> [1] "2025.04.14"
#>
#>
#> $value
#> ival
#> 3IUPAC Names: Various standardized names for the compound, such as “2-acetoxybenzoic acid” and “2-acetyloxybenzoic acid”.
pubChemDataResult$PC_Compounds[[1]]$props[[7]]
#> $urn
#> $urn$label
#> [1] "IUPAC Name"
#>
#> $urn$name
#> [1] "Allowed"
#>
#> $urn$datatype
#> [1] 1
#>
#> $urn$version
#> [1] "2.7.0"
#>
#> $urn$software
#> [1] "Lexichem TK"
#>
#> $urn$source
#> [1] "OpenEye Scientific Software"
#>
#> $urn$release
#> [1] "2025.04.14"
#>
#>
#> $value
#> sval
#> "2-acetoxybenzoic acid"InChI and InChIKey: Standardized identifiers for the chemical structure.
pubChemDataResult$PC_Compounds[[1]]$props[[13]]
#> $urn
#> $urn$label
#> [1] "InChI"
#>
#> $urn$name
#> [1] "Standard"
#>
#> $urn$datatype
#> [1] 1
#>
#> $urn$version
#> [1] "1.07.2"
#>
#> $urn$software
#> [1] "InChI"
#>
#> $urn$source
#> [1] "iupac.org"
#>
#> $urn$release
#> [1] "2025.04.14"
#>
#>
#> $value
#> sval
#> "InChI=1S/C9H8O4/c1-6(10)13-8-5-3-2-4-7(8)9(11)12/h2-5H,1H3,(H,11,12)"pubChemDataResult$PC_Compounds[[1]]$props[[14]]
#> $urn
#> $urn$label
#> [1] "InChIKey"
#>
#> $urn$name
#> [1] "Standard"
#>
#> $urn$datatype
#> [1] 1
#>
#> $urn$version
#> [1] "1.07.2"
#>
#> $urn$software
#> [1] "InChI"
#>
#> $urn$source
#> [1] "iupac.org"
#>
#> $urn$release
#> [1] "2025.04.14"
#>
#>
#> $value
#> sval
#> "BSYNRYMUTXBXSQ-UHFFFAOYSA-N"Log P: The partition coefficient, indicating the compound’s hydrophobicity.
pubChemDataResult$PC_Compounds[[1]]$props[[15]]
#> $urn
#> $urn$label
#> [1] "Log P"
#>
#> $urn$name
#> [1] "XLogP3"
#>
#> $urn$datatype
#> [1] 7
#>
#> $urn$version
#> [1] "3.0"
#>
#> $urn$source
#> [1] "sioc-ccbg.ac.cn"
#>
#> $urn$release
#> [1] "2025.04.14"
#>
#>
#> $value
#> fval
#> 1.2Molecular Formula: The chemical formula of the compound, which is C9H8O4.
pubChemDataResult$PC_Compounds[[1]]$props[[17]]
#> $urn
#> $urn$label
#> [1] "Molecular Formula"
#>
#> $urn$datatype
#> [1] 1
#>
#> $urn$version
#> [1] "2.2"
#>
#> $urn$software
#> [1] "PubChem"
#>
#> $urn$source
#> [1] "ncbi.nlm.nih.gov"
#>
#> $urn$release
#> [1] "2025.04.14"
#>
#>
#> $value
#> sval
#> "C9H8O4"Molecular Weight: The compound’s molecular weight, 180.16 g/mol.
pubChemDataResult$PC_Compounds[[1]]$props[[18]]
#> $urn
#> $urn$label
#> [1] "Molecular Weight"
#>
#> $urn$datatype
#> [1] 1
#>
#> $urn$version
#> [1] "2.2"
#>
#> $urn$software
#> [1] "PubChem"
#>
#> $urn$source
#> [1] "ncbi.nlm.nih.gov"
#>
#> $urn$release
#> [1] "2025.04.14"
#>
#>
#> $value
#> sval
#> "180.16"SMILES: Canonical and isomeric Simplified Molecular Input Line Entry System (SMILES) strings, which are text representations of the chemical structure. Topological Polar Surface Area: A measure of the molecule’s surface area that can form hydrogen bonds.
pubChemDataResult$PC_Compounds[[1]]$props[[19]]
#> $urn
#> $urn$label
#> [1] "SMILES"
#>
#> $urn$name
#> [1] "Absolute"
#>
#> $urn$datatype
#> [1] 1
#>
#> $urn$version
#> [1] "2.3.0"
#>
#> $urn$software
#> [1] "OEChem"
#>
#> $urn$source
#> [1] "OpenEye Scientific Software"
#>
#> $urn$release
#> [1] "2025.04.14"
#>
#>
#> $value
#> sval
#> "CC(=O)OC1=CC=CC=C1C(=O)O"For multiple IDs, a vector of IDs can be used. For instance, to retrieve a CSV table of compound properties:
result <- get_pug_rest(identifier = c("1","2","3","4","5"), namespace = "cid", domain = "compound", property = c("MolecularFormula","MolecularWeight","CanonicalSMILES"), output = "CSV")
result
#>
#> An object of class 'PugRestInstance'
#>
#> Request Details:
#> - Domain: Compound
#> - Namespace: CID
#> - Operation: <NULL>
#> - Identifier: 1, 2, ... and 3 more.
#>
#> NOTE: Run getter function 'pubChemData(...)' to extract raw data retrieved from PubChem Database.
#> See ?pubChemData for details.The output of this request, when processed with pubChemData, provides a data frame containing the specified properties for each CID:
pubChemData(result)
#> CID MolecularFormula MolecularWeight ConnectivitySMILES
#> 1 1 C9H17NO4 203.24 CC(=O)OC(CC(=O)[O-])C[N+](C)(C)C
#> 2 2 C9H18NO4+ 204.24 CC(=O)OC(CC(=O)O)C[N+](C)(C)C
#> 3 3 C7H8O4 156.14 C1=CC(C(C(=C1)C(=O)O)O)O
#> 4 4 C3H9NO 75.11 CC(CN)O
#> 5 5 C3H8NO5P 169.07 C(C(=O)COP(=O)(O)O)NEach row in the table corresponds to a different CID and lists the requested properties, facilitating easy comparison and further analysis.
2. By Name: In addition to using direct identifiers, you can refer to a chemical by its common name. This method allows users to search for compounds using familiar names instead of numerical identifiers. It’s important to note that a single name might correspond to multiple records in the PubChem database. For example, the name “glucose” can refer to several different compounds or isomers. Here’s how you can retrieve Compound IDs (CIDs) for “glucose”:
result <- get_pug_rest(identifier = "glucose", namespace = "name", domain = "compound", operation = "cids", output = "TXT")
result
#>
#> An object of class 'PugRestInstance'
#>
#> Request Details:
#> - Domain: Compound
#> - Namespace: Name
#> - Operation: cids
#> - Identifier: glucose
#>
#> NOTE: Run getter function 'pubChemData(...)' to extract raw data retrieved from PubChem Database.
#> See ?pubChemData for details.The pubChemData function is then used to process the result and extract the retrieved data. The function retrieves the output in data frame. The output indicates that the search for “glucose” returned a single CID:
pubChemData(result)
#> Text
#> 1 5793This output reveals that the common name “glucose” corresponds to the CID 5793. This CID can then be used in further queries to retrieve detailed information about the compound, such as its molecular structure, properties, and associated bioactivities.
Using a common name for searching can simplify the process, especially when the numerical identifiers are not known. However, because a name can map to multiple records, the results might need further filtering or validation to ensure they correspond to the specific compound of interest.
3. By Structure Identity: Another method to specify a compound in PubChem PUG REST API requests is by using structural identifiers such as SMILES or InChI keys. This approach allows for precise identification of chemical structures by providing a textual representation of the molecule. For example, to retrieve the CID for the SMILES string “CCCC” (which represents butane), you can use the following code:
result <- get_pug_rest(identifier = "CCCC", namespace = "smiles", domain = "compound", operation = "cids", output = "TXT")
result
#>
#> An object of class 'PugRestInstance'
#>
#> Request Details:
#> - Domain: Compound
#> - Namespace: SMILES
#> - Operation: cids
#> - Identifier: CCCC
#>
#> NOTE: Run getter function 'pubChemData(...)' to extract raw data retrieved from PubChem Database.
#> See ?pubChemData for details.When the pubChemData(result) function is executed, it retrieves the output in data frame. The output indicates that the search for the SMILES string “CCCC” returned a single CID:
pubChemData(result)
#> Text
#> 1 7843This output reveals that the SMILES string “CCCC” corresponds to the CID 7843. This CID can then be used in further queries to gather detailed information about the compound, such as its molecular structure, physical and chemical properties, biological activities, and more.
Using structure-based identifiers like SMILES or InChI keys is particularly useful for precise and unambiguous chemical searches, as these identifiers provide a detailed representation of the molecule’s structure. This method ensures that the exact compound of interest is identified, reducing the risk of ambiguity that might arise with common names or other identifiers.
4. By Fast (Synchronous) Structure Search: In PubChem PUG REST API, fast (synchronous) structure search allows for quicker searches by identity, similarity, substructure, and superstructure, often returning results in a single call. This method is efficient for obtaining results quickly and is useful for various types of structural queries.
To illustrate, let’s perform a fast identity search for the compound with CID 5793, using the same connectivity option:
result <- get_pug_rest(identifier = "5793", namespace = "cid", domain = "compound", operation = "cids", output = "TXT", searchtype = "fastidentity", options = list(identity_type = "same_connectivity"))
result
#>
#> An object of class 'PugRestInstance'
#>
#> Request Details:
#> - Domain: Compound
#> - Namespace: CID
#> - Operation: cids
#> - Identifier: 5793
#>
#> NOTE: Run getter function 'pubChemData(...)' to extract raw data retrieved from PubChem Database.
#> See ?pubChemData for details.When the following code executed, it retrieves the output in data frame, listing all CIDs that match the fast identity search criteria.
pubChemData(result)
#> Text
#> 1 5793
#> 2 206
#> 3 6036
#> 4 18950
#> 5 64689
#> 6 66371
#> 7 79025
#> 8 81696
#> 9 104724
#> 10 185698
#> 11 439353
#> 12 439357
#> 13 439507
#> 14 439583
#> 15 439680
#> 16 441032
#> 17 441033
#> 18 441034
#> 19 441035
#> 20 444314
#> 21 448388
#> 22 448702
#> 23 451187
#> 24 451188
#> 25 451189
#> 26 452245
#> 27 455147
#> 28 657055
#> 29 1549080
#> 30 2724488
#> 31 3000450
#> 32 3034742
#> 33 5319264
#> 34 6102790
#> 35 6321330
#> 36 6323336
#> 37 6400264
#> 38 6560213
#> 39 6971003
#> 40 6971007
#> 41 6971016
#> 42 6971096
#> 43 6971097
#> 44 6971098
#> 45 6992021
#> 46 6992084
#> 47 7018164
#> 48 7043897
#> 49 7044038
#> 50 7098663
#> 51 7098664
#> 52 7157007
#> 53 9794056
#> 54 9815418
#> 55 9834129
#> 56 9899007
#> 57 10035228
#> 58 10081060
#> 59 10103794
#> 60 10130220
#> 61 10197954
#> 62 10219674
#> 63 10219763
#> 64 10313382
#> 65 10329946
#> 66 10899282
#> 67 10954241
#> 68 11019447
#> 69 11030410
#> 70 11344362
#> 71 11367383
#> 72 11412863
#> 73 11480819
#> 74 11492034
#> 75 11571906
#> 76 11571917
#> 77 11600783
#> 78 11651921
#> 79 11672764
#> 80 11959770
#> 81 11970126
#> 82 12003287
#> 83 12193653
#> 84 12285853
#> 85 12285856
#> 86 12285861
#> 87 12285862
#> 88 12285863
#> 89 12285866
#> 90 12285868
#> 91 12285869
#> 92 12285870
#> 93 12285871
#> 94 12285873
#> 95 12285877
#> 96 12285878
#> 97 12285879
#> 98 12285885
#> 99 12285886
#> 100 12285889
#> 101 12285890
#> 102 12285891
#> 103 12285892
#> 104 12285893
#> 105 12285894
#> 106 16054987
#> 107 16211884
#> 108 16211941
#> 109 16211984
#> 110 16211986
#> 111 16212959
#> 112 16212960
#> 113 16212966
#> 114 16213546
#> 115 16213640
#> 116 16213872
#> 117 16217112
#> 118 16219580
#> 119 21355827
#> 120 22825318
#> 121 22836365
#> 122 22836366
#> 123 23424086
#> 124 24728695
#> 125 24802149
#> 126 24802163
#> 127 24802281
#> 128 24892722
#> 129 42626680
#> 130 44328781
#> 131 44328785
#> 132 46188479
#> 133 46780441
#> 134 46897877
#> 135 50939543
#> 136 51340651
#> 137 54445180
#> 138 54445181
#> 139 54445182
#> 140 56845432
#> 141 56845995
#> 142 57197748
#> 143 57288387
#> 144 57483528
#> 145 57691826
#> 146 57973135
#> 147 58070804
#> 148 58265153
#> 149 58265160
#> 150 58265166
#> 151 58265178
#> 152 58265190
#> 153 58265196
#> 154 58300638
#> 155 58594768
#> 156 58595959
#> 157 58618581
#> 158 58969552
#> 159 59034276
#> 160 59036328
#> 161 59040622
#> 162 59083882
#> 163 59105109
#> 164 59125088
#> 165 59146659
#> 166 59383280
#> 167 59445439
#> 168 59503407
#> 169 59503411
#> 170 59886072
#> 171 59965103
#> 172 60052896
#> 173 60078648
#> 174 66629908
#> 175 67518639
#> 176 67615000
#> 177 67615455
#> 178 67641738
#> 179 67938791
#> 180 67944215
#> 181 67944290
#> 182 67950444
#> 183 68167579
#> 184 68324677
#> 185 68334110
#> 186 69528681
#> 187 70443535
#> 188 70543261
#> 189 71309028
#> 190 71309128
#> 191 71309129
#> 192 71309140
#> 193 71309397
#> 194 71309503
#> 195 71309513
#> 196 71309514
#> 197 71309671
#> 198 71309852
#> 199 71309905
#> 200 71309908
#> 201 71309927
#> 202 71317094
#> 203 71317095
#> 204 71317096
#> 205 71317097
#> 206 71317182
#> 207 71777654
#> 208 75357255
#> 209 76973265
#> 210 86278404
#> 211 87297824
#> 212 87929779
#> 213 87931119
#> 214 88255060
#> 215 88547603
#> 216 88974141
#> 217 89000581
#> 218 89200515
#> 219 89332529
#> 220 89374440
#> 221 89424182
#> 222 89742272
#> 223 89855666
#> 224 90057933
#> 225 90159939
#> 226 90346255
#> 227 90470917
#> 228 90472751
#> 229 90472752
#> 230 90472753
#> 231 90472761
#> 232 90472762
#> 233 90472770
#> 234 90473076
#> 235 90781811
#> 236 90895196
#> 237 91057721
#> 238 92043367
#> 239 92043446
#> 240 101015849
#> 241 101033892
#> 242 101254308
#> 243 101254309
#> 244 101254310
#> 245 101254311
#> 246 101254312
#> 247 101254313
#> 248 101254314
#> 249 101254315
#> 250 101469918
#> 251 101513786
#> 252 101718250
#> 253 101718251
#> 254 101796201
#> 255 102089288
#> 256 102447462
#> 257 102447463
#> 258 102601142
#> 259 102601177
#> 260 102601371
#> 261 102601743
#> 262 102601816
#> 263 117064633
#> 264 117064644
#> 265 117065485
#> 266 117633116
#> 267 117768413
#> 268 117938207
#> 269 118797420
#> 270 118797610
#> 271 118797621
#> 272 118797622
#> 273 118855887
#> 274 118855889
#> 275 118855904
#> 276 118855910
#> 277 118855920
#> 278 118855925
#> 279 118924468
#> 280 121494046
#> 281 121494058
#> 282 122360911
#> 283 122522140
#> 284 125309563
#> 285 125353406
#> 286 125363512
#> 287 126704391
#> 288 129629038
#> 289 131698424
#> 290 131698425
#> 291 131698450
#> 292 131699179
#> 293 131842051
#> 294 131966764
#> 295 132939819
#> 296 132939820
#> 297 133119158
#> 298 133119249
#> 299 133121364
#> 300 133662560
#> 301 133662561
#> 302 133662562
#> 303 134695353
#> 304 134860471
#> 305 136898365
#> 306 137554722
#> 307 139025182
#> 308 140565377
#> 309 141697522
#> 310 142119910
#> 311 145874935
#> 312 153238571
#> 313 153238579
#> 314 154008122
#> 315 154724068
#> 316 155920671
#> 317 156615593
#> 318 161581717
#> 319 162642814
#> 320 166450901
#> 321 166606713
#> 322 168357285
#> 323 168358828
#> 324 168361185
#> 325 168361364
#> 326 168361934
#> 327 168362043
#> 328 168363258
#> 329 168364204
#> 330 168365395
#> 331 168365574
#> 332 168366670
#> 333 168371870
#> 334 168372103
#> 335 168375045
#> 336 168375837
#> 337 168375921
#> 338 169440996
#> 339 169440997
#> 340 169493886
#> 341 169493887
#> 342 169494552
#> 343 172182394
#> 344 172402795
#> 345 172406756
#> 346 172526287
#> 347 173755368
#> 348 173756423
#> 349 173965749
#> 350 175675661
#> 351 175692688
#> 352 175749077
#> 353 175753235
#> 354 175754449
#> 355 175792189
#> 356 175879469
#> 357 175926561
#> 358 175926562
#> 359 175931896
#> 360 176160654
#> 361 176214393
#> 362 176229955
#> 363 176244429The output indicates that there are numerous compounds with similar connectivity to the compound identified by CID 5793. Each row in the output represents a different CID that shares the same connectivity pattern as the original compound. This extensive list includes hundreds of CIDs, showcasing the effectiveness of the fast identity search in identifying structurally related compounds quickly.
This method is advantageous for researchers needing to identify compounds with similar structures for further study, such as drug development, chemical analysis, or bioactivity screening. The fast response time and comprehensive results make it a valuable tool for various chemical and pharmaceutical applications.
5. By Cross-Reference (XRef): The cross-reference (XRef) method allows for reverse lookup of records using a cross-reference value. This method is particularly useful for linking external identifiers, such as patent numbers, to records in the PubChem database. For example, to find all SIDs linked to a specific patent identifier, you can use the following code:
result <- get_pug_rest(identifier = "US20050159403A1", namespace = "xref/PatentID", domain = "substance", operation = "sids", output = "JSON")
result
#>
#> An object of class 'PugRestInstance'
#>
#> Request Details:
#> - Domain: Substance
#> - Namespace: DomainSpecific
#> - Operation: sids
#> - Identifier: US20050159403A1
#>
#> NOTE: Run getter function 'pubChemData(...)' to extract raw data retrieved from PubChem Database.
#> See ?pubChemData for details.pubChemData function retrieves all SIDs that are linked to the specified patent identifier. The output indicates that the specified patent identifier “US20050159403A1” is linked to a large number of SIDs. Each SID represents a different substance that has been referenced in the patent.
pubChemData(result)
#> $IdentifierList
#> $IdentifierList$SID
#> [1] 127377127 127382334 127386382 127387376 127394906 127397376 127401897 127417654 127421022 127427561 127429426
#> [12] 127432264 127440404 127440428 127445646 127449926 127457867 127460434 127463574 127464134 127494894 127496937
#> [23] 127498548 127529998 127543991 127546018 127550965 127560184 127566278 127568614 127579066 127599056 127600815
#> [34] 127611817 127623534 127625503 127632433 127671807 127679107 127688846 127691718 127697988 127711332 127715174
#> [45] 127721611 127722233 127724090 127724974 127727269 127740859 127774458 127786062 127790664 127793921 127794507
#> [56] 127795243 127815192 127824113 127825299 127832880 127835824 127841389 127851147 127855878 127884538 127887083
#> [67] 127907515 127915891 127918344 127926702 127931871 127943403 127949193 127959361 127959362 127961945 127968700
#> [78] 127974435 127988890 128003687 128016428 128024305 128030061 128033308 128033392 128037075 128041901 128043208
#> [89] 128054804 128071903 128075872 128078936 128080424 128086739 128096360 128107971 128108063 128108066 128112623
#> [100] 128116501 128122481 128133149 128139949 128147430 128149266 128164707 128171553 128181006 128199891 128202584
#> [111] 128204869 128208747 128209556 128214152 128216313 128231608 128233622 128235075 128239224 128247683 128253922
#> [122] 128254582 128257870 128265053 128273912 128287030 128289228 128292761 128310374 128310447 128311517 128313782
#> [133] 128319875 128321254 128324845 128327185 128328645 128338633 128344584 128358565 128360063 128361597 128370060
#> [144] 128375029 128381421 128383506 128383593 128385126 128390596 128391357 128391640 128397827 128407104 128414752
#> [155] 128417831 128417970 128421724 128427165 128429151 128431035 128453144 128454426 128459192 128479099 128485819
#> [166] 128490532 128490533 128496172 128504855 128514984 128515903 128531133 128539521 128548161 128550853 128555702
#> [177] 128571383 128573137 128579725 128582246 128587585 128600655 128620771 128624545 128627105 128628584 128632557
#> [188] 128632828 128633726 128633902 128634258 128639692 128642692 128646882 128649366 128675326 128675957 128689052
#> [199] 128690685 128693396 128694828 128699310 128702849 128706476 128716066 128720357 128723298 128723509 128731938
#> [210] 128749024 128749163 128751829 128757815 128766098 128776154 128783768 128789021 128789967 128791547 128796670
#> [221] 128801133 128801849 128804888 128804889 128808454 128815642 128821150 128833107 128837247 128846910 128856633
#> [232] 128862719 128865088 128873754 128874253 128880985 128881190 128894056 128894682 128905743 128908713 128915047
#> [243] 128915536 128921696 128931918 128934857 128935768 128953776 128955396 128970283 128981506 128988380 128997690
#> [254] 129001067 129007663 129014483 129015035 129015817 129016179 129017989 129017990 129026427 129044226 129053129
#> [265] 129054986 129068688 129068801 129079556 129084855 129102578 129104885 129111825 129113828 129115030 129122432
#> [276] 129128697 129130686 129133094 129136176 129140081 129141617 129142896 129148181 129162993 129168398 129173408
#> [287] 129173457 129176810 129177288 129184645 129192608 129202881 129203714 129205760 129209673 129218442 129224837
#> [298] 129228814 129233871 129233873 129233874 129255832 129266266 129272170 129288442 129292073 129294634 129302252
#> [309] 129309716 129310311 129313799 129317146 129328896 129333065 129337106 129337589 129345232 129349967 129351897
#> [320] 129359174 129365621 129366270 129370686 129371805 129374061 129376455 129378267 129379472 129383430 129384458
#> [331] 129389744 129403822 129421538 129440903 129455218 129456175 129457573 129462203 129479103 129489229 129493774
#> [342] 129504746 129508593 129517263 129521307 129526420 129534168 129538802 129547789 129551052 129551258 129555666
#> [353] 129562150 129573817 129586364 129598381 129614967 129617515 129624957 129625178 129625510 129627772 129627879
#> [364] 129629301 129632951 129670298 129672175 129685831 129688258 129702886 129706999 129709395 129711942 129715311
#> [375] 129726350 129728891 129729719 129736495 129738647 129764614 129770055 129776398 129781417 129797152 129808214
#> [386] 129809046 129809280 129811709 129815623 129815624 129818107 129838999 129842321 129844561 129845709 129855419
#> [397] 129865464 129871639 129873187 129873949 129879637 129880907 129894085 129894756 129894757 129906668 129908561
#> [408] 129912020 129921074 129935955 129936330 129941294 129945069 129950653 129962601 129975648 134359275 134393961
#> [419] 134412235 135747269 135752889 135754219 135763149 135798297 135802614 135806152 135826617 135837077 135842328
#> [430] 135847369 135857922 135878265 135887484 135892282 135900333 135900801 135946050 135971530 136022349 136022812
#> [441] 136044641 136052383 136057158 136072993 136080169 136099624 136116271 136118214 136126969 136156103 136157629
#> [452] 136161084 136172216 136222651 136227638 136234395 136261580 136265581 136269831 136272977 136273523 136275074
#> [463] 136291195 136291391 136302881 136314053 136324561 136326756 137349406 137349415 139042442 139667196 140037191
#> [474] 140037194 140254002 140254003 140254004 140254005 140254006 140254007 140254008 140254009 140254010 140254011
#> [485] 140254012 140254013 140254014 140254015 140254016 140254017 140254018 140254019 140254020 140254021 140254022
#> [496] 140254023 140254024 140254025 140254026 140254027 140254028 140254029 140254030 140254031 140254032 140254033
#> [507] 140254034 140254035 140254036 140254037 140254038 140254039 140254040 140254041 140254042 140254043 140254044
#> [518] 140254045 140254046 140254047 140254048 140254049 140254050 140254051 140254052 140254053 140254054 140254055
#> [529] 140254056 140254057 140254058 140254059 140254060 140254061 140254062 140254063 140254064 140254065 140254066
#> [540] 140254067 140254068 140254069 140254070 140254071 140254072 140254073 140254074 140254075 140254076 140254077
#> [551] 140254078 140254079 140254080 140254081 140254082 140254083 140254084 140254085 140254086 140254087 140254088
#> [562] 140254089 140254090 140254091 140254092 140254093 140254094 140254095 140254096 140254097 140254098 140254099
#> [573] 140254100 140262425 140262449 140262456 140262460 140262471 140262478 140262480 140262481 140262486 140262491
#> [584] 140262504 140297441 140297443 140343485 140343488 140343490 140343491 140343493 140343497 140343499 140343505
#> [595] 140492225 141972099 141972100 141989468 142047558 142047559 142059950 142086609 142090637 142093192 142106350
#> [606] 142106351 142106355 142106365 142106373 142130212 142216111 142266779 142289307 142290035 142292362 142292867
#> [617] 142300477 142301161 142355996 142359434 142359441 142365242 142395042 142395064 142396928 142396930 142396931
#> [628] 142398573 142405238 142418631 142438154 142448656 142456985 142456989 142456990 142456991 142456995 142457001
#> [639] 142457025 142457027 142457031 142457036 142457040 142457045 142457053 142457055 142457058 142457059 142457063
#> [650] 142457067 142457072 142457075 142457076 142457077 142457082 142457086 142457092 142457095 142457098 142457099
#> [661] 142457106 142457115 142457119 142457130 142457134 142457138 142457141 142457144 142457146 142457150 142457151
#> [672] 142457164 142457170 142457176 142457178 142457181 142457183 142457188 142457195 142457199 142457201 142457202
#> [683] 142457210 142457212 142457213 142457217 142472709 142504653 142517754 142718650 142794296 142794297 142794298
#> [694] 142976674 142976694 143004316 143078051 143078053 143078054 143078056 143078060 143078078 143078326 143091452
#> [705] 143251864 143251865 143251867 143251868 143251869 143251871 143251875 143251881 143251883 143251885 143251886
#> [716] 143251887 143251888 143251890 143251892 143251894 143251895 143274528 143298830 143319100 226393239 226393684
#> [727] 226394178 226394363 226394481 226394839 226395327 226395557 226395726 226395832 226396049 226396082 226396083
#> [738] 226396198 226396401 226396445 226396464 226396553 226396598 226396617 226396621 226396627 226396776 226396908
#> [749] 226397214 226397418 226397954 226397955 226398150 226398151 226398302 226399315 226399316 226399355 226399517
#> [760] 226399589 226399655 226400044 226400304 226400424 226400518 226401770 226405489 226405836 226406284 226406322
#> [771] 226406323 226406337 226406888 226407848 226408379 226408395 226408853 226408859 226409030 226409597 226409697
#> [782] 226410719 226411068 226411348 226411370 226411403 226412544 226412844 226412845 226412937 226413104 226413385
#> [793] 226413386 226413604 226413605 226413606 226413636 226414206 226414262 226414263 226414297 226414324 226419993
#> [804] 226419994 226420042 226420160 226420161 226420292 226420293 226420456 226420457 226420566 226420567 226420640
#> [815] 226420681 226420720 226420751 226420773 226420774 226420775 226420787 226420804 226420877 226421001 226421002
#> [826] 226421003 226421699 226421728 226423326 226423740 226423826 226424221 226424268 226424269 226424411 226424412
#> [837] 226424915 226425111 226425112 226425266 226425785 226425786 226425915 226425916 226426085 226426288 226426344
#> [848] 226426345 226426582 226426623 226426904 226427860 226427861 226428721 226428722 226428885 226429123 226429124
#> [859] 226432865 226432866 226433067 226433069 226433070 226433090 226433091 226433125 226433126 226433141 226433192
#> [870] 226433193 226433202 226433203 226433344 226433345 226433523 226433524 226433876 226434160 226434771 226440330
#> [881] 226441562 226443823 226445144 226447692 226457181 226457266 226457330 226457331 226457556 226458114 226458225
#> [892] 226458539 226459695 226461214 226462543 226471608 226471621 226472159 226472161 226487293 226487863 226487864
#> [903] 226489321 226490310 226490791 226492265 226492375 226492435 226492437 226492438 226493640 226494285 226494502
#> [914] 226495017 226495025 226497342 226503391 226503607 226506442 226506563 226516040 226520272 226521124 226522490
#> [925] 226542800 226553920 226554136 226564914 226567033 226567034 226567043 226567109 226567110 226567180 226567194
#> [936] 226567379 226567380 226567400 226567435 226567443 226567450 226567458 226567459 226567556 226567567 226567574
#> [947] 226567579 226567629 226567646 226567656 226567670 226567681 226567699 226567701 226567702 226567706 226567717
#> [958] 226567727 226567759 226567799 226567800 226567820 226567824 226567833 226567848 226567862 226567886 226567894
#> [969] 226567923 226567935 226567950 226567961 226567989 226568036 226568060 226568061 226568066 226568082 226568123
#> [980] 226568127 226568139 226568146 226568177 226568234 226568241 226568245 226568264 226568294 226568315 226568346
#> [991] 226568349 226568359 226568362 226568364 226568408 226568416 226568417 226568432 226568449 226568457
#> [ reached getOption("max.print") -- omitted 708 entries ]This result provides a comprehensive list of substances associated with the specified patent, allowing for further exploration and analysis within the PubChem database.
Once you’ve specified the records of interest in PUG REST, the next step is to define what information you want to retrieve about these records. PUG REST excels in providing access to specific data points about each record, such as individual properties or cross-references, without the need to download and sift through large datasets.
1. Full Records: PUG REST allows the retrieval of entire records in various formats like JSON, CSV, TXT, and SDF. For example, to retrieve the record for aspirin (CID 2244) in SDF format:
result <- get_pug_rest(identifier = "2244", namespace = "cid", domain = "compound", output = "SDF")Multiple records can also be requested in a single call, though large lists may be subject to timeouts.
2. Images: Images of chemical structures can be retrieved by specifying PNG format. This works with various input methods, including chemical names, SMILES strings, and InChI keys. For example, to get an image for the chemical name “lipitor”:
get_pug_rest(identifier = "lipitor", namespace = "name", domain = "compound", output = "PNG")
#>
#> An object of class 'PugRestInstance'
#>
#> Request Details:
#> - Domain: Compound
#> - Namespace: Name
#> - Operation: <NULL>
#> - Identifier: lipitor
#>
#> NOTE: Run getter function 'pubChemData(...)' to extract raw data retrieved from PubChem Database.
#> See ?pubChemData for details.3. Compound Properties: Pre-computed properties for PubChem compounds are accessible individually or in tables. For instance, to get the molecular weight of a compound:
result <- get_pug_rest(identifier = "2244", namespace = "cid", domain = "compound", property = "MolecularWeight", output = "TXT")
result
#>
#> An object of class 'PugRestInstance'
#>
#> Request Details:
#> - Domain: Compound
#> - Namespace: CID
#> - Operation: <NULL>
#> - Identifier: 2244
#>
#> NOTE: Run getter function 'pubChemData(...)' to extract raw data retrieved from PubChem Database.
#> See ?pubChemData for details.pubChemData(result)
#> Text
#> 1 180.16Or to retrieve a CSV table of multiple compounds and properties:
result <- get_pug_rest(identifier = c("1","2","3","4","5"), namespace = "cid", domain = "compound", property = c("MolecularWeight", "MolecularFormula", "HBondDonorCount", "HBondAcceptorCount", "InChIKey", "InChI"), output = "CSV")pubChemData(result)
#> CID MolecularWeight MolecularFormula HBondDonorCount HBondAcceptorCount InChIKey
#> 1 1 203.24 C9H17NO4 0 4 RDHQFKQIGNGIED-UHFFFAOYSA-N
#> 2 2 204.24 C9H18NO4+ 1 4 RDHQFKQIGNGIED-UHFFFAOYSA-O
#> 3 3 156.14 C7H8O4 3 4 INCSWYKICIYAHB-UHFFFAOYSA-N
#> 4 4 75.11 C3H9NO 2 2 HXKKHQJGJAFBHI-UHFFFAOYSA-N
#> 5 5 169.07 C3H8NO5P 3 6 HIQNVODXENYOFK-UHFFFAOYSA-N
#> InChI
#> 1 InChI=1S/C9H17NO4/c1-7(11)14-8(5-9(12)13)6-10(2,3)4/h8H,5-6H2,1-4H3
#> 2 InChI=1S/C9H17NO4/c1-7(11)14-8(5-9(12)13)6-10(2,3)4/h8H,5-6H2,1-4H3/p+1
#> 3 InChI=1S/C7H8O4/c8-5-3-1-2-4(6(5)9)7(10)11/h1-3,5-6,8-9H,(H,10,11)
#> 4 InChI=1S/C3H9NO/c1-3(5)2-4/h3,5H,2,4H2,1H3
#> 5 InChI=1S/C3H8NO5P/c4-1-3(5)2-9-10(6,7)8/h1-2,4H2,(H2,6,7,8)4. Synonyms: To view all synonyms of a compound, such as Vioxx:
result <- get_pug_rest(identifier = "vioxx", namespace = "name", domain = "compound", operation = "synonyms", output = "JSON")
result
#>
#> An object of class 'PugRestInstance'
#>
#> Request Details:
#> - Domain: Compound
#> - Namespace: Name
#> - Operation: synonyms
#> - Identifier: vioxx
#>
#> NOTE: Run getter function 'pubChemData(...)' to extract raw data retrieved from PubChem Database.
#> See ?pubChemData for details.pubChemData(result)
#> $InformationList
#> $InformationList$Information
#> $InformationList$Information[[1]]
#> $InformationList$Information[[1]]$CID
#> [1] 5090
#>
#> $InformationList$Information[[1]]$Synonym
#> [1] "rofecoxib"
#> [2] "162011-90-7"
#> [3] "Vioxx"
#> [4] "Ceoxx"
#> [5] "MK 966"
#> [6] "4-(4-(Methylsulfonyl)phenyl)-3-phenylfuran-2(5H)-one"
#> [7] "Vioxx Dolor"
#> [8] "MK-966"
#> [9] "4-[4-(methylsulfonyl)phenyl]-3-phenyl-2(5H)-furanone"
#> [10] "4-[4-(methylsulfonyl)phenyl]-3-phenylfuran-2(5H)-one"
#> [11] "MK0966"
#> [12] "MK-0966"
#> [13] "rofecoxibum"
#> [14] "TRM-201"
#> [15] "0QTW8Z7MCR"
#> [16] "NSC-720256"
#> [17] "NSC-758705"
#> [18] "CHEBI:8887"
#> [19] "TRM201"
#> [20] "DTXSID2023567"
#> [21] "M01AH02"
#> [22] "3-phenyl-4-[4-(methylsulfonyl)phenyl]-2(5H)-furanone"
#> [23] "4-(4-(Methylsulfonyl)phenyl)-3-phenyl-2(5H)-furanone"
#> [24] "4-(4-methylsulfonylphenyl)-3-phenyl-5H-furan-2-one"
#> [25] "DTXCID903567"
#> [26] "NSC720256"
#> [27] "3-phenyl-4-(4-(methylsulfonyl)phenyl)-2(5H)-furanone"
#> [28] "RefChem:55985"
#> [29] "4-(4'-(Methylsulfonyl)phenyl)-3-phenyl-2(5H)-furanone"
#> [30] "803-260-0"
#> [31] "MK 0966"
#> [32] "3-(4-methylsulfonylphenyl)-4-phenyl-2H-furan-5-one"
#> [33] "2(5H)-Furanone, 4-[4-(methylsulfonyl)phenyl]-3-phenyl-"
#> [34] "C17H14O4S"
#> [35] "MK966"
#> [36] "4-(4-methanesulfonylphenyl)-3-phenyl-2,5-dihydrofuran-2-one"
#> [37] "MFCD00935806"
#> [38] "CHEMBL122"
#> [39] "4-(p-(Methylsulfonyl)phenyl)-3-phenyl-2(5H)-furanone"
#> [40] "refecoxib"
#> [41] "NCGC00095118-01"
#> [42] "2(5H)-Furanone, 4-(4-(methylsulfonyl)phenyl)-3-phenyl-"
#> [43] "Vioxx (trademark)"
#> [44] "SMR000466331"
#> [45] "CCRIS 8967"
#> [46] "Vioxx (TN)"
#> [47] "HSDB 7262"
#> [48] "SR-01000762904"
#> [49] "UNII-0QTW8Z7MCR"
#> [50] "Rofecoxib (JAN/USAN/INN)"
#> [51] "Rofecoxib [USAN:INN:BAN]"
#> [52] "3-Phenyl-4-(4-(methylsulfonyl)phenyl))-2(5H)-furanone"
#> [53] "Rofecoxib (Vioxx)"
#> [54] "Rofecoxib [USAN]"
#> [55] "Rofecoxib (Standard)"
#> [56] "KS-1107"
#> [57] "MK 0996"
#> [58] "Spectrum_000119"
#> [59] "ROFECOXIB [INN]"
#> [60] "ROFECOXIB [JAN]"
#> [61] "SpecPlus_000669"
#> [62] "ROFECOXIB [MI]"
#> [63] "ROFECOXIB [HSDB]"
#> [64] "Spectrum2_000446"
#> [65] "Spectrum3_001153"
#> [66] "Spectrum4_000631"
#> [67] "Spectrum5_001598"
#> [68] "ROFECOXIB [VANDF]"
#> [69] "ROFECOXIB [MART.]"
#> [70] "ROFECOXIB [WHO-DD]"
#> [71] "SCHEMBL3050"
#> [72] "BSPBio_002705"
#> [73] "KBioGR_001242"
#> [74] "KBioGR_002345"
#> [75] "KBioSS_000559"
#> [76] "KBioSS_002348"
#> [77] "MLS000759440"
#> [78] "MLS001165770"
#> [79] "MLS001195623"
#> [80] "MLS001424113"
#> [81] "MLS006010091"
#> [82] "BIDD:GT0399"
#> [83] "DivK1c_006765"
#> [84] "SPECTRUM1504235"
#> [85] "Rofecoxib - Bio-X trade mark"
#> [86] "SPBio_000492"
#> [87] "3-(4-methanesulfonylphenyl)-2-phenyl-2-buten-4-olide"
#> [88] "GTPL2893"
#> [89] "orb1309482"
#> [90] "ROFECOXIB [ORANGE BOOK]"
#> [91] "BDBM22369"
#> [92] "KBio1_001709"
#> [93] "KBio2_000559"
#> [94] "KBio2_002345"
#> [95] "KBio2_003127"
#> [96] "KBio2_004913"
#> [97] "KBio2_005695"
#> [98] "KBio2_007481"
#> [99] "KBio3_002205"
#> [100] "KBio3_002825"
#> [101] "EX-A708"
#> [102] "cMAP_000024"
#> [103] "GLXC-05865"
#> [104] "HMS1922H11"
#> [105] "HMS2051G16"
#> [106] "HMS2089H20"
#> [107] "HMS2093E04"
#> [108] "HMS2232G21"
#> [109] "HMS3371P11"
#> [110] "HMS3393G16"
#> [111] "HMS3651F16"
#> [112] "HMS3713B07"
#> [113] "HMS3750I17"
#> [114] "HMS3885E05"
#> [115] "HMS5081K08"
#> [116] "Pharmakon1600-01504235"
#> [117] "BCP03619"
#> [118] "MSK10084"
#> [119] "UWA68493"
#> [120] "Tox21_111430"
#> [121] "CCG-40253"
#> [122] "HY-17372R"
#> [123] "NSC758705"
#> [124] "s3043"
#> [125] "STK635144"
#> [126] "AKOS000280931"
#> [127] "AB07701"
#> [128] "CS-0997"
#> [129] "DB00533"
#> [130] "FV28711"
#> [131] "NC00132"
#> [132] "NSC 720256"
#> [133] "NSC 758705"
#> [134] "SB19518"
#> [135] "NCGC00095118-02"
#> [136] "NCGC00095118-03"
#> [137] "NCGC00095118-04"
#> [138] "NCGC00095118-05"
#> [139] "NCGC00095118-08"
#> [140] "NCGC00095118-17"
#> [141] "NCGC00095118-18"
#> [142] "AC-28318"
#> [143] "BR164362"
#> [144] "HY-17372"
#> [145] "NCI60_041175"
#> [146] "SBI-0206774.P001"
#> [147] "CAS-162011-90-7"
#> [148] "NS00003940"
#> [149] "R0206"
#> [150] "SW219668-1"
#> [151] "C07590"
#> [152] "D00568"
#> [153] "AB00052090-06"
#> [154] "AB00052090-08"
#> [155] "AB00052090_09"
#> [156] "AB00052090_10"
#> [157] "EN300-7364304"
#> [158] "011R907"
#> [159] "L000912"
#> [160] "Q411412"
#> [161] "SR-01000762904-3"
#> [162] "SR-01000762904-5"
#> [163] "BRD-K21733600-001-02-6"
#> [164] "BRD-K21733600-001-06-7"
#> [165] "BRD-K21733600-001-14-1"
#> [166] "BRD-K21733600-001-15-8"
#> [167] "BRD-K21733600-001-19-0"
#> [168] "BRD-K21733600-001-23-2"
#> [169] "BRD-K21733600-001-24-0"
#> [170] "3-(4-methanesulfonyl-phenyl)-2-phenyl-2-buten-4-olide"
#> [171] "Z2037279770"
#> [172] "2(5H)-Furanone, 4-[4-(methyl-sulfonyl)phenyl]-3-phenyl-"
#> [173] "3-(Phenyl)-4-(4-(methylsulfonyl)phenyl)-2-(5H)-furanone"
#> [174] "3-Phenyl-4-(4-(Methylsulfonyl)Phenyl)-2-(5H)-Furanone"
#> [175] "4-(4-METHANESULFONYL-PHENYL)-3-PHENYL-5H-FURAN-2-ONE"
#> [176] "4-(4-methylsulfonylphenyl)-3-phenyl-2,5-dihydro-2-furanone"
#> [177] "4-4-(Methylsulfonyl)phenyl-3-phenyl-2(5H)-furanone;Rofecoxib"5. Cross-References (XRefs): PUG REST provides access to various cross-references. For example, to retrieve MMDB identifiers for protein structures containing aspirin:
result <- get_pug_rest(identifier = "2244", namespace = "cid", domain = "compound", operation = c("xrefs","MMDBID"), output = "JSON")
result
#>
#> An object of class 'PugRestInstance'
#>
#> Request Details:
#> - Domain: Compound
#> - Namespace: CID
#> - Operation: xrefs
#> - Identifier: 2244
#>
#> NOTE: Run getter function 'pubChemData(...)' to extract raw data retrieved from PubChem Database.
#> See ?pubChemData for details.pubChemData(result)
#> $InformationList
#> $InformationList$Information
#> $InformationList$Information[[1]]
#> $InformationList$Information[[1]]$CID
#> [1] 2244
#>
#> $InformationList$Information[[1]]$MMDBID
#> [1] 115960 173465 230639 27242 27954 54234 70578 75951Or to find all patent identifiers associated with a given SID:
result <- get_pug_rest(identifier = "137349406", namespace = "sid", domain = "substance", operation = c("xrefs","PatentID"), output = "TXT")
result
#>
#> An object of class 'PugRestInstance'
#>
#> Request Details:
#> - Domain: Substance
#> - Namespace: SID
#> - Operation: xrefs
#> - Identifier: 137349406
#>
#> NOTE: Run getter function 'pubChemData(...)' to extract raw data retrieved from PubChem Database.
#> See ?pubChemData for details.pubChemData(result)
#> Text
#> 1 US20030181500A1
#> 2 US20050059720A1
#> 3 US20050124633A1
#> 4 US20050124634A1
#> 5 US20050159403A1
#> 6 US20060008862A1
#> 7 US20060135506A1
#> 8 US20070142442A1
#> 9 US20070179152A1
#> 10 US20070196421A1
#> 11 US20070197957A1
#> 12 US20070198063A1
#> 13 US20070208134A1
#> 14 US20070299043A1
#> 15 US20080125595A1
#> 16 US20090075960A1
#> 17 US20100144696A1
#> 18 US20100144697A1
#> 19 US20100267704A1
#> 20 US20110098273A1
#> 21 US20110177999A1
#> 22 US20110201811A1
#> 23 US7485653
#> 24 US7488721
#> 25 US7585978These examples illustrate the versatility of PUG REST in fetching specific data efficiently. It’s an ideal tool for users who need quick access to particular pieces of information from the vast PubChem database without the overhead of processing bulk data.
PubChem BioAssays are complex entities containing a wealth of data. PUG REST provides access to both complete assay records and specific components of BioAssay data, allowing users to efficiently retrieve the information they need.
1. Assay Description: To obtain the description section of a BioAssay, which includes authorship, general description, protocol, and data readout definitions, use a request like:
result <- get_pug_rest(identifier = "504526", namespace = "aid", domain = "assay", operation = "description", output = "JSON")
result
#>
#> An object of class 'PugRestInstance'
#>
#> Request Details:
#> - Domain: Assay
#> - Namespace: AID
#> - Operation: description
#> - Identifier: 504526
#>
#> NOTE: Run getter function 'pubChemData(...)' to extract raw data retrieved from PubChem Database.
#> See ?pubChemData for details.pubChemData(result)
#> $PC_AssayContainer
#> $PC_AssayContainer[[1]]
#> $PC_AssayContainer[[1]]$assay
#> $PC_AssayContainer[[1]]$assay$descr
#> $PC_AssayContainer[[1]]$assay$descr$aid
#> id version
#> 504526 1
#>
#> $PC_AssayContainer[[1]]$assay$descr$aid_source
#> $PC_AssayContainer[[1]]$assay$descr$aid_source$db
#> $PC_AssayContainer[[1]]$assay$descr$aid_source$db$name
#> [1] "Southern Research Specialized Biocontainment Screening Center"
#>
#> $PC_AssayContainer[[1]]$assay$descr$aid_source$db$source_id
#> str
#> "RSV_DR6"
#>
#> $PC_AssayContainer[[1]]$assay$descr$aid_source$db$date
#> $PC_AssayContainer[[1]]$assay$descr$aid_source$db$date$std
#> year month day
#> 2012 3 18
#>
#>
#>
#>
#> $PC_AssayContainer[[1]]$assay$descr$name
#> [1] "A Cell Based HTS Approach for the Discovery of New Inhibitors of Respiratory syncytial virus (RSV) using synthesized compounds (6)"
#>
#> $PC_AssayContainer[[1]]$assay$descr$description
#> [1] "Southern Research's Specialized Biocontainment Screening Center (SRSBSC)"
#> [2] "Southern Research Institute (Birmingham, Alabama)"
#> [3] "NIH Molecular Libraries Probe Centers Network (MLPCN)"
#> [4] "Assay Provider: Dr. William Severson, Southern Research Institute "
#> [5] "Grant number: 1 R03 MH082403-01A1"
#> [6] ""
#> [7] "Assay Rationale and Summary: Currently, there are no commercially available vaccines to protect humans against Respiratory syncytial virus (RSV). RSV is associated with substantial morbidity and mortality and is the most common cause of bronchiolitis and pneumonia among infants and children under one year of age. Nevertheless, severe lower respiratory tract disease may occur at any age, especially among the elderly or among those with compromised cardiac, pulmonary, or immune systems. The existing therapies for the acute infection are ribavirin and the prophylactic humanized monoclonal antibody (Synagis from MedImmune) that is limited to use in high risk pediatric patients. The economic impact of RSV infections due to hospitalizations and indirect medical costs is greater than $ 650 million annually. The assay provider has developed and validated an HTS assay that measures cytopathic effect (CPE) induced in HEp-2 cells by RSV infection, using a luminescent-based detection system for signal endpoint. We anticipate that the proposed studies utilizing the Molecular Libraries Probes Production Network (MLPCN) HTS resources will generate multiple scaffolds targeting various junctures in the RSV viral lifecycle. These may be furthered developed into probes to construct novel single or combination therapeutics. "
#>
#> $PC_AssayContainer[[1]]$assay$descr$protocol
#> [1] "Cell Culture: HEp-2 cells (ATCC CCL-23, American Tissue Culture Type) were maintained as adherent cell lines in Optimem 1 with 2 mM L-glutamine and 10% fetal bovine serum (FBS) at 37oC in a humidified 5% CO2 atmosphere. Cells were passaged as needed and harvested from flasks using 0.05% trypsin-EDTA. "
#> [2] ""
#> [3] "Assay Media - Preparation of Complete DMEM/F12: 50 mL Pen/Strep/Glutamine (Gibco, Cat. No. 10378) was added to four liters of room temperature DMEM/F12 (Sigma, Cat. No. D6434) and the pH adjusted to 7.5 using 1N NaOH. The medium was sterile filtered through a 0.2 um filter and 10 mL of HI-FBS was added per 500 mL of media."
#> [4] ""
#> [5] "RSV culture: Human respiratory syncytial virus (HRSV) strain Long (ATCC VR-26) was used for screening. The RSV stock was prepared in HEp-2 cells using an initial stock obtained from ATCC. Briefly, HEp-2 cells were grown in two T-175 flasks to 50% confluence in Dulbecco's Modified Eagle Medium: Nutrient Mixture F-12 (CDMEM/F12), pH 7.5 with 2.5 mM L-glutamine, 2% FBS and 125 U of penicillin, 125 ug of streptomycin per ml. 0.2 ml of RSV was added to 25 ml of CDMEM/F12. After three days incubation at 37 degrees C, 5% C02 and high humidity, the supernatant was harvested and the cell debris pelleted by centrifuging at 1,000 rpm for 5 minutes at 18 degrees C. Trehalose and FBS were added to a final concentration of 10% each and the supernatant was aliquoted (1 ml per tube) fast freeze using 100% Ethanol dry ice for five minutes and stored at -80 degrees C. These virus stocks were titrated in HEp-2 cells using an agarose overlay plaque method and the titer was 6.0E+07 pfu/ml. "
#> [6] ""
#> [7] "Dose Response Compound Preparation: For dose response screening, compounds or carrier control (DMSO) were diluted to 6x in Complete DMEM/F12. Test compounds were serially diluted 1:2 resulting in an 8 point dose response dilution series. (final plate well concentration ranging from 50 uM to 0.39 uM and a final DMSO concentration of 0.5%). Twenty ul of each dilution was dispensed to assay plates (3% DMSO) in triplicate."
#> [8] "Control Drug: The positive control drug for this assay, ribavirin [1] (No. 196066, MP Biomedicals, Solon, OH) was solubilized in DMSO. It was diluted and added to the assay plates as described for test compounds. Final concentration for ribavirin was 100uM. All wells contained 0.5% DMSO."
#> [9] ""
#> [10] "Preparation of HEp-2 cells: Cells were harvested and resuspended to 178,000 cells per ml in Complete DMEM/F12."
#> [11] ""
#> [12] "Assay Set up: Sixty ul of HEp-2 cells (10,595 cells/well) forty ul of media and 20 ul of 3% DMSO were plated in the cell control wells. Sixty ul of HEp-2 cells (10,595 cells/well), forty ul of a 1:500 dilution of virus (viral MOI = 0.45) and 20 ul of compound or ribavirin control drug were added to the virus control and compound wells. All cell plating was conducted using a Matrix WellMate and cells were maintained at room temperature with stirring during the plating process. The assay plates were incubated for six days at 37 degrees C, 5% CO2 and 90% relative humidity. "
#> [13] ""
#> [14] "Data Analysis: Eight control wells containing cells only and four wells containing cells and virus were included on each assay plate and used to calculate Z' value for each plate and to normalize the data on a per plate basis. Results are reported as percent (%) CPE inhibition and were calculated using the following formula: % CPE inhibition = 100*(Test Cmpd - Med Virus)/(Med Cells - Med Virus). Four ribavirin positive control wells were included on each plate for quality control purposes. To quantify the viral cytopathic effect, IC50s were calculated for each substance using the 4 parameter Levenburg-Marquardt algorithm with the minimum and maximum parameters locked at 0 and 100, respectively. "
#>
#> $PC_AssayContainer[[1]]$assay$descr$comment
#> [1] "Possible artifacts in this assay include, but are not limited to, compounds that interfere with the luciferase reaction, absorb luminescence, or precipitate."
#> [2] ""
#> [3] "Compounds that demonstrated at least 50% inhibition and were considered active. "
#> [4] ""
#> [5] "The following tiered system has been implemented at Southern Research Institute for use with the PubChem Score. Compounds in the primary screen are scored on a scale of 0-40 based on inhibitory activity where a score of 40 corresponds to 100% inhibition. In the initial confirmatory dose response screen, active compounds were scored on a scale of 41-80 based on the IC50 result while compounds that did not confirm as actives were given the score of 0. In assays using purified and synthesized compounds a scale of 81-100 based on the IC50 result is used to denote a high level of confidence in both the substance and the data. Compounds that did not confirm activity were given the score of 0."
#>
#> $PC_AssayContainer[[1]]$assay$descr$xref
#> $PC_AssayContainer[[1]]$assay$descr$xref[[1]]
#> $PC_AssayContainer[[1]]$assay$descr$xref[[1]]$xref
#> aid
#> 2391
#>
#> $PC_AssayContainer[[1]]$assay$descr$xref[[1]]$comment
#> [1] "Primary and confirmatory screen."
#>
#>
#> $PC_AssayContainer[[1]]$assay$descr$xref[[2]]
#> $PC_AssayContainer[[1]]$assay$descr$xref[[2]]$xref
#> aid
#> 2410
#>
#> $PC_AssayContainer[[1]]$assay$descr$xref[[2]]$comment
#> [1] "Cytotoxicity of primary screen hits."
#>
#>
#> $PC_AssayContainer[[1]]$assay$descr$xref[[3]]
#> $PC_AssayContainer[[1]]$assay$descr$xref[[3]]$xref
#> aid
#> 449732
#>
#> $PC_AssayContainer[[1]]$assay$descr$xref[[3]]$comment
#> [1] "TCID50 on selected compounds."
#>
#>
#> $PC_AssayContainer[[1]]$assay$descr$xref[[4]]
#> $PC_AssayContainer[[1]]$assay$descr$xref[[4]]$xref
#> aid
#> 488972
#>
#> $PC_AssayContainer[[1]]$assay$descr$xref[[4]]$comment
#> [1] "Confirmatory screen (2) on purified and synthesized compounds."
#>
#>
#> $PC_AssayContainer[[1]]$assay$descr$xref[[5]]
#> $PC_AssayContainer[[1]]$assay$descr$xref[[5]]$xref
#> aid
#> 488976
#>
#> $PC_AssayContainer[[1]]$assay$descr$xref[[5]]$comment
#> [1] "Cytotoxicity screen (2) on purified and synthesized compounds."
#>
#>
#> $PC_AssayContainer[[1]]$assay$descr$xref[[6]]
#> $PC_AssayContainer[[1]]$assay$descr$xref[[6]]$xref
#> aid
#> 2440
#>
#> $PC_AssayContainer[[1]]$assay$descr$xref[[6]]$comment
#> [1] "Summary AID."
#>
#>
#> $PC_AssayContainer[[1]]$assay$descr$xref[[7]]
#> $PC_AssayContainer[[1]]$assay$descr$xref[[7]]$xref
#> aid
#> 492966
#>
#> $PC_AssayContainer[[1]]$assay$descr$xref[[7]]$comment
#> [1] "Confirmatory screen (3) on purified and synthesized compounds."
#>
#>
#> $PC_AssayContainer[[1]]$assay$descr$xref[[8]]
#> $PC_AssayContainer[[1]]$assay$descr$xref[[8]]$xref
#> aid
#> 492968
#>
#> $PC_AssayContainer[[1]]$assay$descr$xref[[8]]$comment
#> [1] "Cytotoxicity screen (3) on purified and synthesized compounds."
#>
#>
#> $PC_AssayContainer[[1]]$assay$descr$xref[[9]]
#> $PC_AssayContainer[[1]]$assay$descr$xref[[9]]$xref
#> aid
#> 493016
#>
#> $PC_AssayContainer[[1]]$assay$descr$xref[[9]]$comment
#> [1] "Confirmatory screen (4) on purified and synthesized compounds."
#>
#>
#> $PC_AssayContainer[[1]]$assay$descr$xref[[10]]
#> $PC_AssayContainer[[1]]$assay$descr$xref[[10]]$xref
#> aid
#> 493015
#>
#> $PC_AssayContainer[[1]]$assay$descr$xref[[10]]$comment
#> [1] "Cytotoxicity screen (4) on purified and synthesized compounds."
#>
#>
#> $PC_AssayContainer[[1]]$assay$descr$xref[[11]]
#> $PC_AssayContainer[[1]]$assay$descr$xref[[11]]$xref
#> aid
#> 493088
#>
#> $PC_AssayContainer[[1]]$assay$descr$xref[[11]]$comment
#> [1] "Confirmatory screen (5) on purified and synthesized compounds."
#>
#>
#> $PC_AssayContainer[[1]]$assay$descr$xref[[12]]
#> $PC_AssayContainer[[1]]$assay$descr$xref[[12]]$xref
#> aid
#> 493090
#>
#> $PC_AssayContainer[[1]]$assay$descr$xref[[12]]$comment
#> [1] "Cytotoxicity screen (5) on purified and synthesized compounds."
#>
#>
#> $PC_AssayContainer[[1]]$assay$descr$xref[[13]]
#> $PC_AssayContainer[[1]]$assay$descr$xref[[13]]$xref
#> taxonomy
#> 12814
#>
#>
#>
#> $PC_AssayContainer[[1]]$assay$descr$results
#> $PC_AssayContainer[[1]]$assay$descr$results[[1]]
#> $PC_AssayContainer[[1]]$assay$descr$results[[1]]$tid
#> [1] 1
#>
#> $PC_AssayContainer[[1]]$assay$descr$results[[1]]$name
#> [1] "IC50 Modifier"
#>
#> $PC_AssayContainer[[1]]$assay$descr$results[[1]]$type
#> [1] 4
#>
#> $PC_AssayContainer[[1]]$assay$descr$results[[1]]$unit
#> [1] 254
#>
#>
#> $PC_AssayContainer[[1]]$assay$descr$results[[2]]
#> $PC_AssayContainer[[1]]$assay$descr$results[[2]]$tid
#> [1] 2
#>
#> $PC_AssayContainer[[1]]$assay$descr$results[[2]]$name
#> [1] "IC50"
#>
#> $PC_AssayContainer[[1]]$assay$descr$results[[2]]$type
#> [1] 1
#>
#> $PC_AssayContainer[[1]]$assay$descr$results[[2]]$unit
#> [1] 5
#>
#> $PC_AssayContainer[[1]]$assay$descr$results[[2]]$ac
#> [1] TRUE
#>
#>
#> $PC_AssayContainer[[1]]$assay$descr$results[[3]]
#> $PC_AssayContainer[[1]]$assay$descr$results[[3]]$tid
#> [1] 3
#>
#> $PC_AssayContainer[[1]]$assay$descr$results[[3]]$name
#> [1] "% CPE Inhibition @ 50 uM"
#>
#> $PC_AssayContainer[[1]]$assay$descr$results[[3]]$description
#> [1] "Inhibition of cytopathic effect of virus at 50 uM"
#>
#> $PC_AssayContainer[[1]]$assay$descr$results[[3]]$type
#> [1] 1
#>
#> $PC_AssayContainer[[1]]$assay$descr$results[[3]]$unit
#> [1] 15
#>
#> $PC_AssayContainer[[1]]$assay$descr$results[[3]]$tc
#> concentration unit dr_id
#> 50 5 1
#>
#>
#> $PC_AssayContainer[[1]]$assay$descr$results[[4]]
#> $PC_AssayContainer[[1]]$assay$descr$results[[4]]$tid
#> [1] 4
#>
#> $PC_AssayContainer[[1]]$assay$descr$results[[4]]$name
#> [1] "% CPE Inhibition @ 25 uM"
#>
#> $PC_AssayContainer[[1]]$assay$descr$results[[4]]$description
#> [1] "Inhibition of cytopathic effect of virus at 25 uM"
#>
#> $PC_AssayContainer[[1]]$assay$descr$results[[4]]$type
#> [1] 1
#>
#> $PC_AssayContainer[[1]]$assay$descr$results[[4]]$unit
#> [1] 15
#>
#> $PC_AssayContainer[[1]]$assay$descr$results[[4]]$tc
#> concentration unit dr_id
#> 25 5 1
#>
#>
#> $PC_AssayContainer[[1]]$assay$descr$results[[5]]
#> $PC_AssayContainer[[1]]$assay$descr$results[[5]]$tid
#> [1] 5
#>
#> $PC_AssayContainer[[1]]$assay$descr$results[[5]]$name
#> [1] "% CPE Inhibition @ 12.5 uM"
#>
#> $PC_AssayContainer[[1]]$assay$descr$results[[5]]$description
#> [1] "Inhibition of cytopathic effect of virus at 12.50 uM"
#>
#> $PC_AssayContainer[[1]]$assay$descr$results[[5]]$type
#> [1] 1
#>
#> $PC_AssayContainer[[1]]$assay$descr$results[[5]]$unit
#> [1] 15
#>
#> $PC_AssayContainer[[1]]$assay$descr$results[[5]]$tc
#> concentration unit dr_id
#> 12.5 5.0 1.0
#>
#>
#> $PC_AssayContainer[[1]]$assay$descr$results[[6]]
#> $PC_AssayContainer[[1]]$assay$descr$results[[6]]$tid
#> [1] 6
#>
#> $PC_AssayContainer[[1]]$assay$descr$results[[6]]$name
#> [1] "% CPE Inhibition @ 6.25 uM"
#>
#> $PC_AssayContainer[[1]]$assay$descr$results[[6]]$description
#> [1] "Inhibition of cytopathic effect of virus at 6.25 uM"
#>
#> $PC_AssayContainer[[1]]$assay$descr$results[[6]]$type
#> [1] 1
#>
#> $PC_AssayContainer[[1]]$assay$descr$results[[6]]$unit
#> [1] 15
#>
#> $PC_AssayContainer[[1]]$assay$descr$results[[6]]$tc
#> concentration unit dr_id
#> 6.25 5.00 1.00
#>
#>
#> $PC_AssayContainer[[1]]$assay$descr$results[[7]]
#> $PC_AssayContainer[[1]]$assay$descr$results[[7]]$tid
#> [1] 7
#>
#> $PC_AssayContainer[[1]]$assay$descr$results[[7]]$name
#> [1] "% CPE Inhibition @ 3.125 uM"
#>
#> $PC_AssayContainer[[1]]$assay$descr$results[[7]]$description
#> [1] "Inhibition of cytopathic effect of virus at 3.125 uM"
#>
#> $PC_AssayContainer[[1]]$assay$descr$results[[7]]$type
#> [1] 1
#>
#> $PC_AssayContainer[[1]]$assay$descr$results[[7]]$unit
#> [1] 15
#>
#> $PC_AssayContainer[[1]]$assay$descr$results[[7]]$tc
#> concentration unit dr_id
#> 3.125 5.000 1.000
#>
#>
#> $PC_AssayContainer[[1]]$assay$descr$results[[8]]
#> $PC_AssayContainer[[1]]$assay$descr$results[[8]]$tid
#> [1] 8
#>
#> $PC_AssayContainer[[1]]$assay$descr$results[[8]]$name
#> [1] "% CPE Inhibition @ 1.563 uM"
#>
#> $PC_AssayContainer[[1]]$assay$descr$results[[8]]$description
#> [1] "Inhibition of cytopathic effect of virus at 1.563 uM"
#>
#> $PC_AssayContainer[[1]]$assay$descr$results[[8]]$type
#> [1] 1
#>
#> $PC_AssayContainer[[1]]$assay$descr$results[[8]]$unit
#> [1] 15
#>
#> $PC_AssayContainer[[1]]$assay$descr$results[[8]]$tc
#> concentration unit dr_id
#> 1.563 5.000 1.000
#>
#>
#> $PC_AssayContainer[[1]]$assay$descr$results[[9]]
#> $PC_AssayContainer[[1]]$assay$descr$results[[9]]$tid
#> [1] 9
#>
#> $PC_AssayContainer[[1]]$assay$descr$results[[9]]$name
#> [1] "% CPE Inhibition @ 0.781 uM"
#>
#> $PC_AssayContainer[[1]]$assay$descr$results[[9]]$description
#> [1] "Inhibition of cytopathic effect of virus at 0.781 uM"
#>
#> $PC_AssayContainer[[1]]$assay$descr$results[[9]]$type
#> [1] 1
#>
#> $PC_AssayContainer[[1]]$assay$descr$results[[9]]$unit
#> [1] 15
#>
#> $PC_AssayContainer[[1]]$assay$descr$results[[9]]$tc
#> concentration unit dr_id
#> 0.781 5.000 1.000
#>
#>
#> $PC_AssayContainer[[1]]$assay$descr$results[[10]]
#> $PC_AssayContainer[[1]]$assay$descr$results[[10]]$tid
#> [1] 10
#>
#> $PC_AssayContainer[[1]]$assay$descr$results[[10]]$name
#> [1] "% CPE Inhibition @ 0.391 uM"
#>
#> $PC_AssayContainer[[1]]$assay$descr$results[[10]]$description
#> [1] "Inhibition of cytopathic effect of virus at 0.391 uM"
#>
#> $PC_AssayContainer[[1]]$assay$descr$results[[10]]$type
#> [1] 1
#>
#> $PC_AssayContainer[[1]]$assay$descr$results[[10]]$unit
#> [1] 15
#>
#> $PC_AssayContainer[[1]]$assay$descr$results[[10]]$tc
#> concentration unit dr_id
#> 0.391 5.000 1.000
#>
#>
#>
#> $PC_AssayContainer[[1]]$assay$descr$revision
#> [1] 1
#>
#> $PC_AssayContainer[[1]]$assay$descr$activity_outcome_method
#> [1] 2
#>
#> $PC_AssayContainer[[1]]$assay$descr$dr
#> $PC_AssayContainer[[1]]$assay$descr$dr[[1]]
#> $PC_AssayContainer[[1]]$assay$descr$dr[[1]]$id
#> [1] 1
#>
#> $PC_AssayContainer[[1]]$assay$descr$dr[[1]]$descr
#> [1] "CR Plot Labels 1"
#>
#> $PC_AssayContainer[[1]]$assay$descr$dr[[1]]$dn
#> [1] "Concentration"
#>
#> $PC_AssayContainer[[1]]$assay$descr$dr[[1]]$rn
#> [1] "Response"
#>
#>
#>
#> $PC_AssayContainer[[1]]$assay$descr$grant_number
#> [1] "1R03 MH084847-01"
#>
#> $PC_AssayContainer[[1]]$assay$descr$project_category
#> [1] 2For a simplified summary format that includes target information, active and inactive SID and CID counts:
result <- get_pug_rest(identifier = "1000", namespace = "aid", domain = "assay", operation = "summary", output = "JSON")
result
#>
#> An object of class 'PugRestInstance'
#>
#> Request Details:
#> - Domain: Assay
#> - Namespace: AID
#> - Operation: summary
#> - Identifier: 1000
#>
#> NOTE: Run getter function 'pubChemData(...)' to extract raw data retrieved from PubChem Database.
#> See ?pubChemData for details.pubChemData(result)
#> $AssaySummaries
#> $AssaySummaries$AssaySummary
#> $AssaySummaries$AssaySummary[[1]]
#> $AssaySummaries$AssaySummary[[1]]$AID
#> [1] 1000
#>
#> $AssaySummaries$AssaySummary[[1]]$SourceName
#> [1] "SRMLSC"
#>
#> $AssaySummaries$AssaySummary[[1]]$SourceID
#> [1] "SPE-MK-Sec"
#>
#> $AssaySummaries$AssaySummary[[1]]$Name
#> [1] "Screening for Inhibitors of the Mevalonate Pathway in Streptococcus Pneumoniae - MK Secondary Assay"
#>
#> $AssaySummaries$AssaySummary[[1]]$Description
#> [1] "Southern Research Molecular Libraries Screening Center (SRMLSC) "
#> [2] "Southern Research Institute (Birmingham, Alabama) "
#> [3] "NIH Molecular Libraries Screening Centers Network (MLSCN) "
#> [4] "Assay Provider: Dr. Thomas S. Leyh, Albert Einstein College of medicine of Yeshiva University "
#> [5] "Award: R03 MH078936-01"
#> [6] ""
#> [7] "Streptococcus pneumonia (SP) takes the lives of nearly 4,000 people daily and antibiotic resistant strains are becoming an increasing problem. Because of this, the discovery of drugs targeting novel pathways such as the mevalonate pathway has become increasingly important. The pathway produces isopentyl diphosphate (the molecular building block of isoprenoids) and is essential for the survival of the pathogen in mouse lung and serum. The mevalonate pathway is comprised of three consecutive reactions that are catalyzed by the enzymes mevalonate kinase (MK; E.C. 2.7.1.36), phosphomevalonate kinase (PMK; E.C. 2.7.4.2), and diphosphomevalonate decarboxylase (PDM-DC; E.C. 4.1.1.33). MK catalyzes the ATP dependent conversion of (R)-mevalonate to ADP plus (R)-5-phosphomevalonate. "
#> [8] ""
#> [9] "The activity of MK was measured spectrophotometrically by coupling the formation of ADP to the reactions of pyruvate kinase and lactate dehydrogenase. The rate of ADP formation was quantitated by the reduction of absorbance (OD340) due to the oxidation of NADH to NAD by lactate dehydrogenase. A kinetic assay was chosen to minimize interference by compounds that absorbed at 340 nm."
#> [10] ""
#> [11] "A total of 57 compounds were initially screened at a final concentration of 100 uM. Compounds with more than 20% inhibition at 100 uM were then tested in dose response assays at seven concentrations, ranging from 100 uM to 0.0156 uM depending on the % inhibition for each compound in the initial 100 uM screen. To confirm that the compounds were specifically inhibiting MK and not one of the other enzymes in the assay, the compounds were tested in parallel in an assay that contained hexokinase as the enzyme instead of MK and glucose as the substrate instead of mevalonate. None of the compounds tested inhibited in this 'coupling enzymes' assay."
#>
#> $AssaySummaries$AssaySummary[[1]]$Protocol
#> [1] "Mevalonate Kinase Protocol for 1 mL cuvet assay"
#> [2] ""
#> [3] "Purified recombinant MK enzyme was provided by Dr. Thomas Leyh, Albert Einstein College of Medicine of Yeshiva University. "
#> [4] ""
#> [5] "590 uL of MK reagent mix which included NADH, mevalonate, ATP, phosphoenolpyruvate, MgCl2, KCl, pyruvate kinase, and lactate dehydrogenase in buffer was added to each UV-VIS semimicro cuvet. Compounds were then added to the cuvets in 10 uL volumes in DMSO. The reaction was initiated with the addition of 400 uL of MK, diluted in assay buffer. The final concentrations in the reaction were 0.4 mM NADH, 0.2 mM melalonate, 6 mM MgCl2, 50 mM KCl, 5 mM ATP, 2 mM potassium phosphoenolpyruvate, 3 units/mL each of rabbit muscle pyruvate kinase and rabbit muscle lactate dehydrogenase, 1% DMSO, and 60 nM Mevalonate Kinase (MK) diluted in 50 mM HEPES buffer (pH 7.8) in a final volume of 1000 uL. The cuvets were immediately transferred to a CARY 3E UV-Visible Spectrophotometer and absorbance was measured at 340 nm for 3 minutes. Each compound was tested in triplicate for the initial 100 uM screen and for the dose response assays each concentration was in triplicate. Full reaction controls were assays with 10 uL of DMSO added instead of compound. Background controls were assays in which 400 uL of assay buffer was added instead of MK. "
#> [6] ""
#> [7] "The 'coupling enzyme' assays were performed as above by replacing MK with hexokinase and mevalonate with glucose."
#>
#> $AssaySummaries$AssaySummary[[1]]$Comment
#> [1] "Percent inhibition in the single dose assay was determined by comparing the reaction rates of the compounds to that of the rate for the full reaction after subtracting the background rate using the following equation: "
#> [2] ""
#> [3] "% Inhib = 100*(1-((cmpd rate-bkgrd rate)/ (full rx rate-bkgrd rate))) "
#> [4] ""
#> [5] "Dose response curves were analyzed using the four parameter logistic formula in SigmaPlot Enzyme Kinetics software."
#> [6] " "
#> [7] "In this confirmatory dose response screen active compounds were scored on a scale of 41-80 using an inverted linear correlation to EC50s between 0 and 40 uM. Compounds that did not confirm as actives in the dose response screen were given the score 0. "
#>
#> $AssaySummaries$AssaySummary[[1]]$NumberOfTIDs
#> [1] 27
#>
#> $AssaySummaries$AssaySummary[[1]]$HasScore
#> [1] TRUE
#>
#> $AssaySummaries$AssaySummary[[1]]$Method
#> [1] "confirmatory"
#>
#> $AssaySummaries$AssaySummary[[1]]$Target
#> $AssaySummaries$AssaySummary[[1]]$Target[[1]]
#> Accession Name
#> "YP_815859" "mevalonate kinase"
#>
#>
#> $AssaySummaries$AssaySummary[[1]]$Version
#> [1] 1
#>
#> $AssaySummaries$AssaySummary[[1]]$Revision
#> [1] 2
#>
#> $AssaySummaries$AssaySummary[[1]]$LastDataChange
#> Year Month Day
#> 2008 3 5
#>
#> $AssaySummaries$AssaySummary[[1]]$SIDCountAll
#> [1] 57
#>
#> $AssaySummaries$AssaySummary[[1]]$SIDCountActive
#> [1] 36
#>
#> $AssaySummaries$AssaySummary[[1]]$SIDCountInactive
#> [1] 21
#>
#> $AssaySummaries$AssaySummary[[1]]$SIDCountInconclusive
#> [1] 0
#>
#> $AssaySummaries$AssaySummary[[1]]$SIDCountUnspecified
#> [1] 0
#>
#> $AssaySummaries$AssaySummary[[1]]$SIDCountProbe
#> [1] 0
#>
#> $AssaySummaries$AssaySummary[[1]]$CIDCountAll
#> [1] 57
#>
#> $AssaySummaries$AssaySummary[[1]]$CIDCountActive
#> [1] 36
#>
#> $AssaySummaries$AssaySummary[[1]]$CIDCountInactive
#> [1] 21
#>
#> $AssaySummaries$AssaySummary[[1]]$CIDCountInconclusive
#> [1] 0
#>
#> $AssaySummaries$AssaySummary[[1]]$CIDCountUnspecified
#> [1] 0
#>
#> $AssaySummaries$AssaySummary[[1]]$CIDCountProbe
#> [1] 02. Assay Data: To retrieve the entire data set of an assay in CSV format:
result <- get_pug_rest(identifier = "504526", namespace = "aid", domain = "assay", output = "CSV")
result
#>
#> An object of class 'PugRestInstance'
#>
#> Request Details:
#> - Domain: Assay
#> - Namespace: AID
#> - Operation: <NULL>
#> - Identifier: 504526
#>
#> NOTE: Run getter function 'pubChemData(...)' to extract raw data retrieved from PubChem Database.
#> See ?pubChemData for details.pubChemData(result)
#> PUBCHEM_RESULT_TAG PUBCHEM_SID PUBCHEM_CID
#> 1 RESULT_TYPE NA NA
#> 2 RESULT_DESCR NA NA
#> 3 RESULT_UNIT NA NA
#> 4 RESULT_IS_ACTIVE_CONCENTRATION NA NA
#> 5 RESULT_ATTR_CONC_MICROMOL NA NA
#> 6 1 103061373 6619281
#> 7 2 103904139 2971528
#> 8 3 109967230 50897767
#> 9 4 109967232 50897761
#> 10 5 109967235 50897759
#> 11 6 104222572 22429344
#> 12 7 104169543 49842897
#> 13 8 104169547 6619281
#> 14 9 104169544 49842896
#> 15 10 104169548 49842898
#> 16 11 103904144 4969604
#> 17 12 109967231 50897764
#> 18 13 109967233 50897765
#> 19 14 109967234 50897766
#> 20 15 109967236 50897760
#> 21 16 109967237 50897763
#> 22 17 109967238 50897762
#> 23 18 109967239 50897768
#> 24 19 104222567 49852456
#> 25 20 104222568 49852454
#> 26 21 104222569 22429370
#> 27 22 104222570 15996204
#> 28 23 104222571 49852455
#> 29 24 104169545 1077725
#> 30 25 104169546 5308867
#> PUBCHEM_EXT_DATASOURCE_SMILES PUBCHEM_ACTIVITY_OUTCOME
#> 1
#> 2
#> 3
#> 4
#> 5
#> 6 COC1=CC=CC=C1CNC(=O)C2CCN(CC2)S(=O)(=O)C3=CC=CC4=NON=C43 Active
#> 7 C1CC2=CC=CC=C2N(C1)S(=O)(=O)C3=CC=C(C=C3)NC(=O)C4CC=CCC4C(=O)O Active
#> 8 CC1=CC=C(C=C1)CN2C3=CC=CC=C3C(=O)N(C2=O)CC4=CC=C(C=C4)C(=O)NCCOC Active
#> 9 CC1=C(C=C(C=C1)Cl)NC(=O)[C@@H]2CCCN2S(=O)(=O)C3=CC=CC4=C3N=CC=C4 Active
#> 10 CC1=C(C=C(C=C1)OC)NC(=O)[C@@H]2CCCN2S(=O)(=O)C3=CC=CC4=C3N=CC=C4 Active
#> 11 C1CN(CCC1C(=O)NCC2=CC=CC=C2Cl)S(=O)(=O)C3=CC=CC4=NON=C43 Active
#> 12 CC1=CC(=C(C=C1)C)NC(=O)[C@@H]2CCCN2S(=O)(=O)C3=CC=CC4=C3N=CC=C4 Active
#> 13 COC1=CC=CC=C1CNC(=O)C2CCN(CC2)S(=O)(=O)C3=CC=CC4=NON=C43 Active
#> 14 CC1=C(C(=CC=C1)C)NC(=O)[C@@H]2CCCN2S(=O)(=O)C3=CC=CC4=C3N=CC=C4 Active
#> 15 COC1=CC=CC=C1CNC(=O)[C@@H]2CCCN2S(=O)(=O)C3=CC=CC4=C3N=CC=C4 Active
#> 16 COC1=CC=CC=C1NCC(=O)NC2=C(C=CC(=C2)S(=O)(=O)N3CCOCC3)N4CCOCC4 Inactive
#> 17 CC1=CC=C(C=C1)CN2C3=C(C=CC(=C3)Cl)C(=O)N(C2=O)CC4=CC=C(C=C4)C(=O)NCCCOC Inactive
#> 18 CC1=C(C=C(C=C1)C(C)C)NC(=O)[C@@H]2CCCN2S(=O)(=O)C3=CC=CC4=C3N=CC=C4 Inactive
#> 19 CC1=CC(=C(C=C1)OC)NC(=O)[C@@H]2CCCN2S(=O)(=O)C3=CC=CC4=C3N=CC=C4 Inactive
#> 20 CC1=CC(=C(C=C1)Cl)NC(=O)[C@@H]2CCCN2S(=O)(=O)C3=CC=CC4=C3N=CC=C4 Inactive
#> 21 CC1=C(C=C(C=C1)C(F)(F)F)NC(=O)[C@@H]2CCCN2S(=O)(=O)C3=CC=CC4=C3N=CC=C4 Inactive
#> 22 CC1=C(C=C(C=C1)C(C)(C)C)NC(=O)[C@@H]2CCCN2S(=O)(=O)C3=CC=CC4=C3N=CC=C4 Inactive
#> 23 COCCCNC(=O)C1=CC=C(C=C1)CN2C(=O)C3=CC=CC=C3N(C2=O)CC4=CC=CC=C4 Inactive
#> 24 COC1=CC=CC=C1CNC(=O)C2CCN(CC2)S(=O)(=O)C3=CC=CC4=C3N=CS4 Inactive
#> 25 COC1=CC=CC=C1CNC(=O)C2CCN(CC2)CC3=CC=CC4=NON=C43 Inactive
#> 26 COC1=CC=CC(=C1)CNC(=O)C2CCN(CC2)S(=O)(=O)C3=CC=CC4=NON=C43 Inactive
#> 27 COC1=CC=C(C=C1)CNC(=O)C2CCN(CC2)S(=O)(=O)C3=CC=CC4=NON=C43 Inactive
#> 28 CC1=CC=CC=C1CNC(=O)C2CCN(CC2)S(=O)(=O)C3=CC=CC4=NON=C43 Inactive
#> 29 COC1=CC=CC=C1CNC(=O)C2CCN(CC2)S(=O)(=O)C3=CC=CC=C3 Inactive
#> 30 COC1=CC=CC=C1CNC(=O)C2CCN(CC2)S(=O)(=O)C3=CC=CC4=C3N=CC=C4 Inactive
#> PUBCHEM_ACTIVITY_SCORE PUBCHEM_ACTIVITY_URL PUBCHEM_ASSAYDATA_COMMENT IC50.Modifier IC50
#> 1 NA NA NA STRING FLOAT
#> 2 NA NA NA
#> 3 NA NA NA NONE MICROMOLAR
#> 4 NA NA NA TRUE
#> 5 NA NA NA
#> 6 99 NA NA 3.6
#> 7 88 NA NA 31.4
#> 8 99 NA NA 2.32
#> 9 100 NA NA 0.22
#> 10 99 NA NA 3.51
#> 11 98 NA NA 6.9
#> 12 98 NA NA 5.1
#> 13 99 NA NA 4.7
#> 14 87 NA NA 34.6
#> 15 93 NA NA 18.8
#> 16 81 NA NA > 50
#> 17 81 NA NA > 50
#> 18 81 NA NA > 50
#> 19 81 NA NA > 50
#> 20 81 NA NA > 50
#> 21 81 NA NA > 50
#> 22 81 NA NA > 50
#> 23 81 NA NA > 50
#> 24 81 NA NA > 50
#> 25 81 NA NA > 50
#> 26 81 NA NA > 50
#> 27 81 NA NA > 50
#> 28 81 NA NA > 50
#> 29 81 NA NA > 50
#> 30 81 NA NA > 50
#> X..CPE.Inhibition...50.uM X..CPE.Inhibition...25.uM
#> 1 FLOAT FLOAT
#> 2 Inhibition of cytopathic effect of virus at 50 uM Inhibition of cytopathic effect of virus at 25 uM
#> 3 PERCENT PERCENT
#> 4
#> 5 50 25
#> 6 78.38 97.5
#> 7 47.67 68.41
#> 8 107.05 90.78
#> 9 7.51 9.47
#> 10 88.79 90.14
#> 11 78.03 86.65
#> 12 43.94 91.27
#> 13 85.88 92.21
#> 14 59.74 42.48
#> 15 72.51 61.24
#> 16 0.42 0.56
#> 17 2.59 2.63
#> 18 30.79 21.08
#> 19 9.1 11.2
#> 20 3.2 6.08
#> 21 12.15 3.83
#> 22 2.49 4.66
#> 23 2.1 2.52
#> 24 0.59 0.77
#> 25 0.58 0.54
#> 26 0.96 0.98
#> 27 1.83 1.5
#> 28 2 2.18
#> 29 0.55 0.69
#> 30 0.51 0.51
#> X..CPE.Inhibition...12.5.uM X..CPE.Inhibition...6.25.uM
#> 1 FLOAT FLOAT
#> 2 Inhibition of cytopathic effect of virus at 12.50 uM Inhibition of cytopathic effect of virus at 6.25 uM
#> 3 PERCENT PERCENT
#> 4
#> 5 12.5 6.25
#> 6 94.84 95.43
#> 7 16.83 2.14
#> 8 87.53 101.19
#> 9 60.4 79.75
#> 10 77.74 66.47
#> 11 83.45 47.02
#> 12 82.68 66.81
#> 13 91.99 78.58
#> 14 21.56 8.54
#> 15 40.57 19
#> 16 0.62 0.43
#> 17 2.32 2.49
#> 18 27.55 17.89
#> 19 10.88 7.76
#> 20 34.16 17.15
#> 21 8.53 39.9
#> 22 4.19 3.38
#> 23 1.87 1.93
#> 24 0.76 0.94
#> 25 0.53 0.49
#> 26 0.94 0.89
#> 27 1.11 0.77
#> 28 1.73 1.56
#> 29 0.74 0.88
#> 30 0.52 0.43
#> X..CPE.Inhibition...3.125.uM X..CPE.Inhibition...1.563.uM
#> 1 FLOAT FLOAT
#> 2 Inhibition of cytopathic effect of virus at 3.125 uM Inhibition of cytopathic effect of virus at 1.563 uM
#> 3 PERCENT PERCENT
#> 4
#> 5 3.125 1.563
#> 6 35.06 3.21
#> 7 1.07 0.93
#> 8 80.54 15.81
#> 9 72.51 59.35
#> 10 48.34 32.2
#> 11 12.2 2.23
#> 12 39.43 18.27
#> 13 14.87 2.15
#> 14 4.49 2.69
#> 15 8.08 3.66
#> 16 0.51 0.38
#> 17 1.96 1.8
#> 18 6.44 3.41
#> 19 4.61 3.29
#> 20 8.56 4.66
#> 21 30.03 14.27
#> 22 2.38 1.7
#> 23 1.62 1.42
#> 24 0.79 0.8
#> 25 0.5 0.39
#> 26 1.09 0.98
#> 27 0.64 0.51
#> 28 1.19 0.93
#> 29 0.95 0.78
#> 30 0.58 0.46
#> X..CPE.Inhibition...0.781.uM X..CPE.Inhibition...0.391.uM
#> 1 FLOAT FLOAT
#> 2 Inhibition of cytopathic effect of virus at 0.781 uM Inhibition of cytopathic effect of virus at 0.391 uM
#> 3 PERCENT PERCENT
#> 4
#> 5 0.781 0.391
#> 6 1.08 0.7
#> 7 0.84 0.74
#> 8 4.66 2.32
#> 9 35.87 13.62
#> 10 15.81 5.72
#> 11 0.77 0.65
#> 12 6.99 4.01
#> 13 0.79 0.54
#> 14 1.51 0.94
#> 15 1.59 1.04
#> 16 0.44 0.45
#> 17 1.19 1.06
#> 18 2.54 1.48
#> 19 2.06 1.52
#> 20 3.13 1.93
#> 21 5.48 3.58
#> 22 1.37 1.06
#> 23 1.31 1.27
#> 24 0.77 0.73
#> 25 0.36 0.53
#> 26 0.89 0.71
#> 27 0.48 0.57
#> 28 0.8 0.74
#> 29 0.75 0.7
#> 30 0.62 0.51For a subset of data rows, specify the SIDs:
result <- get_pug_rest(identifier = "504526", namespace = "aid", domain = "assay", operation = "JSON?sid=104169547,109967232", output = "JSON")
result
#>
#> An object of class 'PugRestInstance'
#>
#> Request Details:
#> - Domain: Assay
#> - Namespace: AID
#> - Operation: JSON?sid=104169547,109967232
#> - Identifier: 504526
#>
#> NOTE: Run getter function 'pubChemData(...)' to extract raw data retrieved from PubChem Database.
#> See ?pubChemData for details.result <- pubChemData(result)
result$PC_AssaySubmit$assay
#> $descr
#> $descr$aid
#> id version
#> 504526 1
#>
#> $descr$aid_source
#> $descr$aid_source$db
#> $descr$aid_source$db$name
#> [1] "Southern Research Specialized Biocontainment Screening Center"
#>
#> $descr$aid_source$db$source_id
#> str
#> "RSV_DR6"
#>
#> $descr$aid_source$db$date
#> $descr$aid_source$db$date$std
#> year month day
#> 2012 3 18
#>
#>
#>
#>
#> $descr$name
#> [1] "A Cell Based HTS Approach for the Discovery of New Inhibitors of Respiratory syncytial virus (RSV) using synthesized compounds (6)"
#>
#> $descr$description
#> [1] "Southern Research's Specialized Biocontainment Screening Center (SRSBSC)"
#> [2] "Southern Research Institute (Birmingham, Alabama)"
#> [3] "NIH Molecular Libraries Probe Centers Network (MLPCN)"
#> [4] "Assay Provider: Dr. William Severson, Southern Research Institute "
#> [5] "Grant number: 1 R03 MH082403-01A1"
#> [6] ""
#> [7] "Assay Rationale and Summary: Currently, there are no commercially available vaccines to protect humans against Respiratory syncytial virus (RSV). RSV is associated with substantial morbidity and mortality and is the most common cause of bronchiolitis and pneumonia among infants and children under one year of age. Nevertheless, severe lower respiratory tract disease may occur at any age, especially among the elderly or among those with compromised cardiac, pulmonary, or immune systems. The existing therapies for the acute infection are ribavirin and the prophylactic humanized monoclonal antibody (Synagis from MedImmune) that is limited to use in high risk pediatric patients. The economic impact of RSV infections due to hospitalizations and indirect medical costs is greater than $ 650 million annually. The assay provider has developed and validated an HTS assay that measures cytopathic effect (CPE) induced in HEp-2 cells by RSV infection, using a luminescent-based detection system for signal endpoint. We anticipate that the proposed studies utilizing the Molecular Libraries Probes Production Network (MLPCN) HTS resources will generate multiple scaffolds targeting various junctures in the RSV viral lifecycle. These may be furthered developed into probes to construct novel single or combination therapeutics. "
#>
#> $descr$protocol
#> [1] "Cell Culture: HEp-2 cells (ATCC CCL-23, American Tissue Culture Type) were maintained as adherent cell lines in Optimem 1 with 2 mM L-glutamine and 10% fetal bovine serum (FBS) at 37oC in a humidified 5% CO2 atmosphere. Cells were passaged as needed and harvested from flasks using 0.05% trypsin-EDTA. "
#> [2] ""
#> [3] "Assay Media - Preparation of Complete DMEM/F12: 50 mL Pen/Strep/Glutamine (Gibco, Cat. No. 10378) was added to four liters of room temperature DMEM/F12 (Sigma, Cat. No. D6434) and the pH adjusted to 7.5 using 1N NaOH. The medium was sterile filtered through a 0.2 um filter and 10 mL of HI-FBS was added per 500 mL of media."
#> [4] ""
#> [5] "RSV culture: Human respiratory syncytial virus (HRSV) strain Long (ATCC VR-26) was used for screening. The RSV stock was prepared in HEp-2 cells using an initial stock obtained from ATCC. Briefly, HEp-2 cells were grown in two T-175 flasks to 50% confluence in Dulbecco's Modified Eagle Medium: Nutrient Mixture F-12 (CDMEM/F12), pH 7.5 with 2.5 mM L-glutamine, 2% FBS and 125 U of penicillin, 125 ug of streptomycin per ml. 0.2 ml of RSV was added to 25 ml of CDMEM/F12. After three days incubation at 37 degrees C, 5% C02 and high humidity, the supernatant was harvested and the cell debris pelleted by centrifuging at 1,000 rpm for 5 minutes at 18 degrees C. Trehalose and FBS were added to a final concentration of 10% each and the supernatant was aliquoted (1 ml per tube) fast freeze using 100% Ethanol dry ice for five minutes and stored at -80 degrees C. These virus stocks were titrated in HEp-2 cells using an agarose overlay plaque method and the titer was 6.0E+07 pfu/ml. "
#> [6] ""
#> [7] "Dose Response Compound Preparation: For dose response screening, compounds or carrier control (DMSO) were diluted to 6x in Complete DMEM/F12. Test compounds were serially diluted 1:2 resulting in an 8 point dose response dilution series. (final plate well concentration ranging from 50 uM to 0.39 uM and a final DMSO concentration of 0.5%). Twenty ul of each dilution was dispensed to assay plates (3% DMSO) in triplicate."
#> [8] "Control Drug: The positive control drug for this assay, ribavirin [1] (No. 196066, MP Biomedicals, Solon, OH) was solubilized in DMSO. It was diluted and added to the assay plates as described for test compounds. Final concentration for ribavirin was 100uM. All wells contained 0.5% DMSO."
#> [9] ""
#> [10] "Preparation of HEp-2 cells: Cells were harvested and resuspended to 178,000 cells per ml in Complete DMEM/F12."
#> [11] ""
#> [12] "Assay Set up: Sixty ul of HEp-2 cells (10,595 cells/well) forty ul of media and 20 ul of 3% DMSO were plated in the cell control wells. Sixty ul of HEp-2 cells (10,595 cells/well), forty ul of a 1:500 dilution of virus (viral MOI = 0.45) and 20 ul of compound or ribavirin control drug were added to the virus control and compound wells. All cell plating was conducted using a Matrix WellMate and cells were maintained at room temperature with stirring during the plating process. The assay plates were incubated for six days at 37 degrees C, 5% CO2 and 90% relative humidity. "
#> [13] ""
#> [14] "Data Analysis: Eight control wells containing cells only and four wells containing cells and virus were included on each assay plate and used to calculate Z' value for each plate and to normalize the data on a per plate basis. Results are reported as percent (%) CPE inhibition and were calculated using the following formula: % CPE inhibition = 100*(Test Cmpd - Med Virus)/(Med Cells - Med Virus). Four ribavirin positive control wells were included on each plate for quality control purposes. To quantify the viral cytopathic effect, IC50s were calculated for each substance using the 4 parameter Levenburg-Marquardt algorithm with the minimum and maximum parameters locked at 0 and 100, respectively. "
#>
#> $descr$comment
#> [1] "Possible artifacts in this assay include, but are not limited to, compounds that interfere with the luciferase reaction, absorb luminescence, or precipitate."
#> [2] ""
#> [3] "Compounds that demonstrated at least 50% inhibition and were considered active. "
#> [4] ""
#> [5] "The following tiered system has been implemented at Southern Research Institute for use with the PubChem Score. Compounds in the primary screen are scored on a scale of 0-40 based on inhibitory activity where a score of 40 corresponds to 100% inhibition. In the initial confirmatory dose response screen, active compounds were scored on a scale of 41-80 based on the IC50 result while compounds that did not confirm as actives were given the score of 0. In assays using purified and synthesized compounds a scale of 81-100 based on the IC50 result is used to denote a high level of confidence in both the substance and the data. Compounds that did not confirm activity were given the score of 0."
#>
#> $descr$xref
#> $descr$xref[[1]]
#> $descr$xref[[1]]$xref
#> aid
#> 2391
#>
#> $descr$xref[[1]]$comment
#> [1] "Primary and confirmatory screen."
#>
#>
#> $descr$xref[[2]]
#> $descr$xref[[2]]$xref
#> aid
#> 2410
#>
#> $descr$xref[[2]]$comment
#> [1] "Cytotoxicity of primary screen hits."
#>
#>
#> $descr$xref[[3]]
#> $descr$xref[[3]]$xref
#> aid
#> 449732
#>
#> $descr$xref[[3]]$comment
#> [1] "TCID50 on selected compounds."
#>
#>
#> $descr$xref[[4]]
#> $descr$xref[[4]]$xref
#> aid
#> 488972
#>
#> $descr$xref[[4]]$comment
#> [1] "Confirmatory screen (2) on purified and synthesized compounds."
#>
#>
#> $descr$xref[[5]]
#> $descr$xref[[5]]$xref
#> aid
#> 488976
#>
#> $descr$xref[[5]]$comment
#> [1] "Cytotoxicity screen (2) on purified and synthesized compounds."
#>
#>
#> $descr$xref[[6]]
#> $descr$xref[[6]]$xref
#> aid
#> 2440
#>
#> $descr$xref[[6]]$comment
#> [1] "Summary AID."
#>
#>
#> $descr$xref[[7]]
#> $descr$xref[[7]]$xref
#> aid
#> 492966
#>
#> $descr$xref[[7]]$comment
#> [1] "Confirmatory screen (3) on purified and synthesized compounds."
#>
#>
#> $descr$xref[[8]]
#> $descr$xref[[8]]$xref
#> aid
#> 492968
#>
#> $descr$xref[[8]]$comment
#> [1] "Cytotoxicity screen (3) on purified and synthesized compounds."
#>
#>
#> $descr$xref[[9]]
#> $descr$xref[[9]]$xref
#> aid
#> 493016
#>
#> $descr$xref[[9]]$comment
#> [1] "Confirmatory screen (4) on purified and synthesized compounds."
#>
#>
#> $descr$xref[[10]]
#> $descr$xref[[10]]$xref
#> aid
#> 493015
#>
#> $descr$xref[[10]]$comment
#> [1] "Cytotoxicity screen (4) on purified and synthesized compounds."
#>
#>
#> $descr$xref[[11]]
#> $descr$xref[[11]]$xref
#> aid
#> 493088
#>
#> $descr$xref[[11]]$comment
#> [1] "Confirmatory screen (5) on purified and synthesized compounds."
#>
#>
#> $descr$xref[[12]]
#> $descr$xref[[12]]$xref
#> aid
#> 493090
#>
#> $descr$xref[[12]]$comment
#> [1] "Cytotoxicity screen (5) on purified and synthesized compounds."
#>
#>
#> $descr$xref[[13]]
#> $descr$xref[[13]]$xref
#> taxonomy
#> 12814
#>
#>
#>
#> $descr$results
#> $descr$results[[1]]
#> $descr$results[[1]]$tid
#> [1] 1
#>
#> $descr$results[[1]]$name
#> [1] "IC50 Modifier"
#>
#> $descr$results[[1]]$type
#> [1] 4
#>
#> $descr$results[[1]]$unit
#> [1] 254
#>
#>
#> $descr$results[[2]]
#> $descr$results[[2]]$tid
#> [1] 2
#>
#> $descr$results[[2]]$name
#> [1] "IC50"
#>
#> $descr$results[[2]]$type
#> [1] 1
#>
#> $descr$results[[2]]$unit
#> [1] 5
#>
#> $descr$results[[2]]$ac
#> [1] TRUE
#>
#>
#> $descr$results[[3]]
#> $descr$results[[3]]$tid
#> [1] 3
#>
#> $descr$results[[3]]$name
#> [1] "% CPE Inhibition @ 50 uM"
#>
#> $descr$results[[3]]$description
#> [1] "Inhibition of cytopathic effect of virus at 50 uM"
#>
#> $descr$results[[3]]$type
#> [1] 1
#>
#> $descr$results[[3]]$unit
#> [1] 15
#>
#> $descr$results[[3]]$tc
#> concentration unit dr_id
#> 50 5 1
#>
#>
#> $descr$results[[4]]
#> $descr$results[[4]]$tid
#> [1] 4
#>
#> $descr$results[[4]]$name
#> [1] "% CPE Inhibition @ 25 uM"
#>
#> $descr$results[[4]]$description
#> [1] "Inhibition of cytopathic effect of virus at 25 uM"
#>
#> $descr$results[[4]]$type
#> [1] 1
#>
#> $descr$results[[4]]$unit
#> [1] 15
#>
#> $descr$results[[4]]$tc
#> concentration unit dr_id
#> 25 5 1
#>
#>
#> $descr$results[[5]]
#> $descr$results[[5]]$tid
#> [1] 5
#>
#> $descr$results[[5]]$name
#> [1] "% CPE Inhibition @ 12.5 uM"
#>
#> $descr$results[[5]]$description
#> [1] "Inhibition of cytopathic effect of virus at 12.50 uM"
#>
#> $descr$results[[5]]$type
#> [1] 1
#>
#> $descr$results[[5]]$unit
#> [1] 15
#>
#> $descr$results[[5]]$tc
#> concentration unit dr_id
#> 12.5 5.0 1.0
#>
#>
#> $descr$results[[6]]
#> $descr$results[[6]]$tid
#> [1] 6
#>
#> $descr$results[[6]]$name
#> [1] "% CPE Inhibition @ 6.25 uM"
#>
#> $descr$results[[6]]$description
#> [1] "Inhibition of cytopathic effect of virus at 6.25 uM"
#>
#> $descr$results[[6]]$type
#> [1] 1
#>
#> $descr$results[[6]]$unit
#> [1] 15
#>
#> $descr$results[[6]]$tc
#> concentration unit dr_id
#> 6.25 5.00 1.00
#>
#>
#> $descr$results[[7]]
#> $descr$results[[7]]$tid
#> [1] 7
#>
#> $descr$results[[7]]$name
#> [1] "% CPE Inhibition @ 3.125 uM"
#>
#> $descr$results[[7]]$description
#> [1] "Inhibition of cytopathic effect of virus at 3.125 uM"
#>
#> $descr$results[[7]]$type
#> [1] 1
#>
#> $descr$results[[7]]$unit
#> [1] 15
#>
#> $descr$results[[7]]$tc
#> concentration unit dr_id
#> 3.125 5.000 1.000
#>
#>
#> $descr$results[[8]]
#> $descr$results[[8]]$tid
#> [1] 8
#>
#> $descr$results[[8]]$name
#> [1] "% CPE Inhibition @ 1.563 uM"
#>
#> $descr$results[[8]]$description
#> [1] "Inhibition of cytopathic effect of virus at 1.563 uM"
#>
#> $descr$results[[8]]$type
#> [1] 1
#>
#> $descr$results[[8]]$unit
#> [1] 15
#>
#> $descr$results[[8]]$tc
#> concentration unit dr_id
#> 1.563 5.000 1.000
#>
#>
#> $descr$results[[9]]
#> $descr$results[[9]]$tid
#> [1] 9
#>
#> $descr$results[[9]]$name
#> [1] "% CPE Inhibition @ 0.781 uM"
#>
#> $descr$results[[9]]$description
#> [1] "Inhibition of cytopathic effect of virus at 0.781 uM"
#>
#> $descr$results[[9]]$type
#> [1] 1
#>
#> $descr$results[[9]]$unit
#> [1] 15
#>
#> $descr$results[[9]]$tc
#> concentration unit dr_id
#> 0.781 5.000 1.000
#>
#>
#> $descr$results[[10]]
#> $descr$results[[10]]$tid
#> [1] 10
#>
#> $descr$results[[10]]$name
#> [1] "% CPE Inhibition @ 0.391 uM"
#>
#> $descr$results[[10]]$description
#> [1] "Inhibition of cytopathic effect of virus at 0.391 uM"
#>
#> $descr$results[[10]]$type
#> [1] 1
#>
#> $descr$results[[10]]$unit
#> [1] 15
#>
#> $descr$results[[10]]$tc
#> concentration unit dr_id
#> 0.391 5.000 1.000
#>
#>
#>
#> $descr$revision
#> [1] 1
#>
#> $descr$activity_outcome_method
#> [1] 2
#>
#> $descr$dr
#> $descr$dr[[1]]
#> $descr$dr[[1]]$id
#> [1] 1
#>
#> $descr$dr[[1]]$descr
#> [1] "CR Plot Labels 1"
#>
#> $descr$dr[[1]]$dn
#> [1] "Concentration"
#>
#> $descr$dr[[1]]$rn
#> [1] "Response"
#>
#>
#>
#> $descr$grant_number
#> [1] "1R03 MH084847-01"
#>
#> $descr$project_category
#> [1] 2For concise data (e.g., active concentration readout) with additional information:
result <- get_pug_rest(identifier = "504526", namespace = "aid", domain = "assay", operation = "concise", output = "JSON")
result
#>
#> An object of class 'PugRestInstance'
#>
#> Request Details:
#> - Domain: Assay
#> - Namespace: AID
#> - Operation: concise
#> - Identifier: 504526
#>
#> NOTE: Run getter function 'pubChemData(...)' to extract raw data retrieved from PubChem Database.
#> See ?pubChemData for details.pubChemData(result)
#> $Table
#> $Table$Columns
#> $Table$Columns$Column
#> [1] "AID" "SID" "CID" "Activity Outcome" "Target Accession"
#> [6] "Target GeneID" "Activity Value [uM]" "Activity Name" "Assay Name" "Assay Type"
#> [11] "PubMed ID" "RNAi"
#>
#>
#> $Table$Row
#> $Table$Row[[1]]
#> $Table$Row[[1]]$Cell
#> [1] "504526"
#> [2] "103061373"
#> [3] "6619281"
#> [4] "Active"
#> [5] ""
#> [6] ""
#> [7] "3.6"
#> [8] "IC50"
#> [9] "A Cell Based HTS Approach for the Discovery of New Inhibitors of Respiratory syncytial virus (RSV) using synthesized compounds (6)"
#> [10] "Confirmatory"
#> [11] ""
#> [12] ""
#>
#>
#> $Table$Row[[2]]
#> $Table$Row[[2]]$Cell
#> [1] "504526"
#> [2] "103904139"
#> [3] "2971528"
#> [4] "Active"
#> [5] ""
#> [6] ""
#> [7] "31.4"
#> [8] "IC50"
#> [9] "A Cell Based HTS Approach for the Discovery of New Inhibitors of Respiratory syncytial virus (RSV) using synthesized compounds (6)"
#> [10] "Confirmatory"
#> [11] ""
#> [12] ""
#>
#>
#> $Table$Row[[3]]
#> $Table$Row[[3]]$Cell
#> [1] "504526"
#> [2] "103904144"
#> [3] "4969604"
#> [4] "Inactive"
#> [5] ""
#> [6] ""
#> [7] "50"
#> [8] "IC50"
#> [9] "A Cell Based HTS Approach for the Discovery of New Inhibitors of Respiratory syncytial virus (RSV) using synthesized compounds (6)"
#> [10] "Confirmatory"
#> [11] ""
#> [12] ""
#>
#>
#> $Table$Row[[4]]
#> $Table$Row[[4]]$Cell
#> [1] "504526"
#> [2] "104169543"
#> [3] "49842897"
#> [4] "Active"
#> [5] ""
#> [6] ""
#> [7] "5.1"
#> [8] "IC50"
#> [9] "A Cell Based HTS Approach for the Discovery of New Inhibitors of Respiratory syncytial virus (RSV) using synthesized compounds (6)"
#> [10] "Confirmatory"
#> [11] ""
#> [12] ""
#>
#>
#> $Table$Row[[5]]
#> $Table$Row[[5]]$Cell
#> [1] "504526"
#> [2] "104169544"
#> [3] "49842896"
#> [4] "Active"
#> [5] ""
#> [6] ""
#> [7] "34.6"
#> [8] "IC50"
#> [9] "A Cell Based HTS Approach for the Discovery of New Inhibitors of Respiratory syncytial virus (RSV) using synthesized compounds (6)"
#> [10] "Confirmatory"
#> [11] ""
#> [12] ""
#>
#>
#> $Table$Row[[6]]
#> $Table$Row[[6]]$Cell
#> [1] "504526"
#> [2] "104169545"
#> [3] "1077725"
#> [4] "Inactive"
#> [5] ""
#> [6] ""
#> [7] "50"
#> [8] "IC50"
#> [9] "A Cell Based HTS Approach for the Discovery of New Inhibitors of Respiratory syncytial virus (RSV) using synthesized compounds (6)"
#> [10] "Confirmatory"
#> [11] ""
#> [12] ""
#>
#>
#> $Table$Row[[7]]
#> $Table$Row[[7]]$Cell
#> [1] "504526"
#> [2] "104169546"
#> [3] "5308867"
#> [4] "Inactive"
#> [5] ""
#> [6] ""
#> [7] "50"
#> [8] "IC50"
#> [9] "A Cell Based HTS Approach for the Discovery of New Inhibitors of Respiratory syncytial virus (RSV) using synthesized compounds (6)"
#> [10] "Confirmatory"
#> [11] ""
#> [12] ""
#>
#>
#> $Table$Row[[8]]
#> $Table$Row[[8]]$Cell
#> [1] "504526"
#> [2] "104169547"
#> [3] "6619281"
#> [4] "Active"
#> [5] ""
#> [6] ""
#> [7] "4.7"
#> [8] "IC50"
#> [9] "A Cell Based HTS Approach for the Discovery of New Inhibitors of Respiratory syncytial virus (RSV) using synthesized compounds (6)"
#> [10] "Confirmatory"
#> [11] ""
#> [12] ""
#>
#>
#> $Table$Row[[9]]
#> $Table$Row[[9]]$Cell
#> [1] "504526"
#> [2] "104169548"
#> [3] "49842898"
#> [4] "Active"
#> [5] ""
#> [6] ""
#> [7] "18.8"
#> [8] "IC50"
#> [9] "A Cell Based HTS Approach for the Discovery of New Inhibitors of Respiratory syncytial virus (RSV) using synthesized compounds (6)"
#> [10] "Confirmatory"
#> [11] ""
#> [12] ""
#>
#>
#> $Table$Row[[10]]
#> $Table$Row[[10]]$Cell
#> [1] "504526"
#> [2] "104222567"
#> [3] "49852456"
#> [4] "Inactive"
#> [5] ""
#> [6] ""
#> [7] "50"
#> [8] "IC50"
#> [9] "A Cell Based HTS Approach for the Discovery of New Inhibitors of Respiratory syncytial virus (RSV) using synthesized compounds (6)"
#> [10] "Confirmatory"
#> [11] ""
#> [12] ""
#>
#>
#> $Table$Row[[11]]
#> $Table$Row[[11]]$Cell
#> [1] "504526"
#> [2] "104222568"
#> [3] "49852454"
#> [4] "Inactive"
#> [5] ""
#> [6] ""
#> [7] "50"
#> [8] "IC50"
#> [9] "A Cell Based HTS Approach for the Discovery of New Inhibitors of Respiratory syncytial virus (RSV) using synthesized compounds (6)"
#> [10] "Confirmatory"
#> [11] ""
#> [12] ""
#>
#>
#> $Table$Row[[12]]
#> $Table$Row[[12]]$Cell
#> [1] "504526"
#> [2] "104222569"
#> [3] "22429370"
#> [4] "Inactive"
#> [5] ""
#> [6] ""
#> [7] "50"
#> [8] "IC50"
#> [9] "A Cell Based HTS Approach for the Discovery of New Inhibitors of Respiratory syncytial virus (RSV) using synthesized compounds (6)"
#> [10] "Confirmatory"
#> [11] ""
#> [12] ""
#>
#>
#> $Table$Row[[13]]
#> $Table$Row[[13]]$Cell
#> [1] "504526"
#> [2] "104222570"
#> [3] "15996204"
#> [4] "Inactive"
#> [5] ""
#> [6] ""
#> [7] "50"
#> [8] "IC50"
#> [9] "A Cell Based HTS Approach for the Discovery of New Inhibitors of Respiratory syncytial virus (RSV) using synthesized compounds (6)"
#> [10] "Confirmatory"
#> [11] ""
#> [12] ""
#>
#>
#> $Table$Row[[14]]
#> $Table$Row[[14]]$Cell
#> [1] "504526"
#> [2] "104222571"
#> [3] "49852455"
#> [4] "Inactive"
#> [5] ""
#> [6] ""
#> [7] "50"
#> [8] "IC50"
#> [9] "A Cell Based HTS Approach for the Discovery of New Inhibitors of Respiratory syncytial virus (RSV) using synthesized compounds (6)"
#> [10] "Confirmatory"
#> [11] ""
#> [12] ""
#>
#>
#> $Table$Row[[15]]
#> $Table$Row[[15]]$Cell
#> [1] "504526"
#> [2] "104222572"
#> [3] "22429344"
#> [4] "Active"
#> [5] ""
#> [6] ""
#> [7] "6.9"
#> [8] "IC50"
#> [9] "A Cell Based HTS Approach for the Discovery of New Inhibitors of Respiratory syncytial virus (RSV) using synthesized compounds (6)"
#> [10] "Confirmatory"
#> [11] ""
#> [12] ""
#>
#>
#> $Table$Row[[16]]
#> $Table$Row[[16]]$Cell
#> [1] "504526"
#> [2] "109967230"
#> [3] "50897767"
#> [4] "Active"
#> [5] ""
#> [6] ""
#> [7] "2.32"
#> [8] "IC50"
#> [9] "A Cell Based HTS Approach for the Discovery of New Inhibitors of Respiratory syncytial virus (RSV) using synthesized compounds (6)"
#> [10] "Confirmatory"
#> [11] ""
#> [12] ""
#>
#>
#> $Table$Row[[17]]
#> $Table$Row[[17]]$Cell
#> [1] "504526"
#> [2] "109967231"
#> [3] "50897764"
#> [4] "Inactive"
#> [5] ""
#> [6] ""
#> [7] "50"
#> [8] "IC50"
#> [9] "A Cell Based HTS Approach for the Discovery of New Inhibitors of Respiratory syncytial virus (RSV) using synthesized compounds (6)"
#> [10] "Confirmatory"
#> [11] ""
#> [12] ""
#>
#>
#> $Table$Row[[18]]
#> $Table$Row[[18]]$Cell
#> [1] "504526"
#> [2] "109967232"
#> [3] "50897761"
#> [4] "Active"
#> [5] ""
#> [6] ""
#> [7] "0.22"
#> [8] "IC50"
#> [9] "A Cell Based HTS Approach for the Discovery of New Inhibitors of Respiratory syncytial virus (RSV) using synthesized compounds (6)"
#> [10] "Confirmatory"
#> [11] ""
#> [12] ""
#>
#>
#> $Table$Row[[19]]
#> $Table$Row[[19]]$Cell
#> [1] "504526"
#> [2] "109967233"
#> [3] "50897765"
#> [4] "Inactive"
#> [5] ""
#> [6] ""
#> [7] "50"
#> [8] "IC50"
#> [9] "A Cell Based HTS Approach for the Discovery of New Inhibitors of Respiratory syncytial virus (RSV) using synthesized compounds (6)"
#> [10] "Confirmatory"
#> [11] ""
#> [12] ""
#>
#>
#> $Table$Row[[20]]
#> $Table$Row[[20]]$Cell
#> [1] "504526"
#> [2] "109967234"
#> [3] "50897766"
#> [4] "Inactive"
#> [5] ""
#> [6] ""
#> [7] "50"
#> [8] "IC50"
#> [9] "A Cell Based HTS Approach for the Discovery of New Inhibitors of Respiratory syncytial virus (RSV) using synthesized compounds (6)"
#> [10] "Confirmatory"
#> [11] ""
#> [12] ""
#>
#>
#> $Table$Row[[21]]
#> $Table$Row[[21]]$Cell
#> [1] "504526"
#> [2] "109967235"
#> [3] "50897759"
#> [4] "Active"
#> [5] ""
#> [6] ""
#> [7] "3.51"
#> [8] "IC50"
#> [9] "A Cell Based HTS Approach for the Discovery of New Inhibitors of Respiratory syncytial virus (RSV) using synthesized compounds (6)"
#> [10] "Confirmatory"
#> [11] ""
#> [12] ""
#>
#>
#> $Table$Row[[22]]
#> $Table$Row[[22]]$Cell
#> [1] "504526"
#> [2] "109967236"
#> [3] "50897760"
#> [4] "Inactive"
#> [5] ""
#> [6] ""
#> [7] "50"
#> [8] "IC50"
#> [9] "A Cell Based HTS Approach for the Discovery of New Inhibitors of Respiratory syncytial virus (RSV) using synthesized compounds (6)"
#> [10] "Confirmatory"
#> [11] ""
#> [12] ""
#>
#>
#> $Table$Row[[23]]
#> $Table$Row[[23]]$Cell
#> [1] "504526"
#> [2] "109967237"
#> [3] "50897763"
#> [4] "Inactive"
#> [5] ""
#> [6] ""
#> [7] "50"
#> [8] "IC50"
#> [9] "A Cell Based HTS Approach for the Discovery of New Inhibitors of Respiratory syncytial virus (RSV) using synthesized compounds (6)"
#> [10] "Confirmatory"
#> [11] ""
#> [12] ""
#>
#>
#> $Table$Row[[24]]
#> $Table$Row[[24]]$Cell
#> [1] "504526"
#> [2] "109967238"
#> [3] "50897762"
#> [4] "Inactive"
#> [5] ""
#> [6] ""
#> [7] "50"
#> [8] "IC50"
#> [9] "A Cell Based HTS Approach for the Discovery of New Inhibitors of Respiratory syncytial virus (RSV) using synthesized compounds (6)"
#> [10] "Confirmatory"
#> [11] ""
#> [12] ""
#>
#>
#> $Table$Row[[25]]
#> $Table$Row[[25]]$Cell
#> [1] "504526"
#> [2] "109967239"
#> [3] "50897768"
#> [4] "Inactive"
#> [5] ""
#> [6] ""
#> [7] "50"
#> [8] "IC50"
#> [9] "A Cell Based HTS Approach for the Discovery of New Inhibitors of Respiratory syncytial virus (RSV) using synthesized compounds (6)"
#> [10] "Confirmatory"
#> [11] ""
#> [12] ""For dose-response curve data:
result <- get_pug_rest(identifier = "504526", namespace = "aid", domain = "assay", operation = "doseresponse/CSV?sid=104169547,109967232", output = "CSV")
result
#>
#> An object of class 'PugRestInstance'
#>
#> Request Details:
#> - Domain: Assay
#> - Namespace: AID
#> - Operation: doseresponse/CSV?sid=104169547,109967232
#> - Identifier: 504526
#>
#> NOTE: Run getter function 'pubChemData(...)' to extract raw data retrieved from PubChem Database.
#> See ?pubChemData for details.pubChemData(result)
#> AID SID Concentration Concentration.Unit Response Response.Unit
#> 1 504526 103061373 50.000 uM 78.38 %
#> 2 504526 103061373 25.000 uM 97.50 %
#> 3 504526 103061373 12.500 uM 94.84 %
#> 4 504526 103061373 6.250 uM 95.43 %
#> 5 504526 103061373 3.125 uM 35.06 %
#> 6 504526 103061373 1.563 uM 3.21 %
#> 7 504526 103061373 0.781 uM 1.08 %
#> 8 504526 103061373 0.391 uM 0.70 %
#> 9 504526 103904139 50.000 uM 47.67 %
#> 10 504526 103904139 25.000 uM 68.41 %
#> 11 504526 103904139 12.500 uM 16.83 %
#> 12 504526 103904139 6.250 uM 2.14 %
#> 13 504526 103904139 3.125 uM 1.07 %
#> 14 504526 103904139 1.563 uM 0.93 %
#> 15 504526 103904139 0.781 uM 0.84 %
#> 16 504526 103904139 0.391 uM 0.74 %
#> 17 504526 103904144 50.000 uM 0.42 %
#> 18 504526 103904144 25.000 uM 0.56 %
#> 19 504526 103904144 12.500 uM 0.62 %
#> 20 504526 103904144 6.250 uM 0.43 %
#> 21 504526 103904144 3.125 uM 0.51 %
#> 22 504526 103904144 1.563 uM 0.38 %
#> 23 504526 103904144 0.781 uM 0.44 %
#> 24 504526 103904144 0.391 uM 0.45 %
#> 25 504526 104169543 50.000 uM 43.94 %
#> 26 504526 104169543 25.000 uM 91.27 %
#> 27 504526 104169543 12.500 uM 82.68 %
#> 28 504526 104169543 6.250 uM 66.81 %
#> 29 504526 104169543 3.125 uM 39.43 %
#> 30 504526 104169543 1.563 uM 18.27 %
#> 31 504526 104169543 0.781 uM 6.99 %
#> 32 504526 104169543 0.391 uM 4.01 %
#> 33 504526 104169544 50.000 uM 59.74 %
#> 34 504526 104169544 25.000 uM 42.48 %
#> 35 504526 104169544 12.500 uM 21.56 %
#> 36 504526 104169544 6.250 uM 8.54 %
#> 37 504526 104169544 3.125 uM 4.49 %
#> 38 504526 104169544 1.563 uM 2.69 %
#> 39 504526 104169544 0.781 uM 1.51 %
#> 40 504526 104169544 0.391 uM 0.94 %
#> 41 504526 104169545 50.000 uM 0.55 %
#> 42 504526 104169545 25.000 uM 0.69 %
#> 43 504526 104169545 12.500 uM 0.74 %
#> 44 504526 104169545 6.250 uM 0.88 %
#> 45 504526 104169545 3.125 uM 0.95 %
#> 46 504526 104169545 1.563 uM 0.78 %
#> 47 504526 104169545 0.781 uM 0.75 %
#> 48 504526 104169545 0.391 uM 0.70 %
#> 49 504526 104169546 50.000 uM 0.51 %
#> 50 504526 104169546 25.000 uM 0.51 %
#> 51 504526 104169546 12.500 uM 0.52 %
#> 52 504526 104169546 6.250 uM 0.43 %
#> 53 504526 104169546 3.125 uM 0.58 %
#> 54 504526 104169546 1.563 uM 0.46 %
#> 55 504526 104169546 0.781 uM 0.62 %
#> 56 504526 104169546 0.391 uM 0.51 %
#> 57 504526 104169547 50.000 uM 85.88 %
#> 58 504526 104169547 25.000 uM 92.21 %
#> 59 504526 104169547 12.500 uM 91.99 %
#> 60 504526 104169547 6.250 uM 78.58 %
#> 61 504526 104169547 3.125 uM 14.87 %
#> 62 504526 104169547 1.563 uM 2.15 %
#> 63 504526 104169547 0.781 uM 0.79 %
#> 64 504526 104169547 0.391 uM 0.54 %
#> 65 504526 104169548 50.000 uM 72.51 %
#> 66 504526 104169548 25.000 uM 61.24 %
#> 67 504526 104169548 12.500 uM 40.57 %
#> 68 504526 104169548 6.250 uM 19.00 %
#> 69 504526 104169548 3.125 uM 8.08 %
#> 70 504526 104169548 1.563 uM 3.66 %
#> 71 504526 104169548 0.781 uM 1.59 %
#> 72 504526 104169548 0.391 uM 1.04 %
#> 73 504526 104222567 50.000 uM 0.59 %
#> 74 504526 104222567 25.000 uM 0.77 %
#> 75 504526 104222567 12.500 uM 0.76 %
#> 76 504526 104222567 6.250 uM 0.94 %
#> 77 504526 104222567 3.125 uM 0.79 %
#> 78 504526 104222567 1.563 uM 0.80 %
#> 79 504526 104222567 0.781 uM 0.77 %
#> 80 504526 104222567 0.391 uM 0.73 %
#> 81 504526 104222568 50.000 uM 0.58 %
#> 82 504526 104222568 25.000 uM 0.54 %
#> 83 504526 104222568 12.500 uM 0.53 %
#> 84 504526 104222568 6.250 uM 0.49 %
#> 85 504526 104222568 3.125 uM 0.50 %
#> 86 504526 104222568 1.563 uM 0.39 %
#> 87 504526 104222568 0.781 uM 0.36 %
#> 88 504526 104222568 0.391 uM 0.53 %
#> 89 504526 104222569 50.000 uM 0.96 %
#> 90 504526 104222569 25.000 uM 0.98 %
#> 91 504526 104222569 12.500 uM 0.94 %
#> 92 504526 104222569 6.250 uM 0.89 %
#> 93 504526 104222569 3.125 uM 1.09 %
#> 94 504526 104222569 1.563 uM 0.98 %
#> 95 504526 104222569 0.781 uM 0.89 %
#> 96 504526 104222569 0.391 uM 0.71 %
#> 97 504526 104222570 50.000 uM 1.83 %
#> 98 504526 104222570 25.000 uM 1.50 %
#> 99 504526 104222570 12.500 uM 1.11 %
#> 100 504526 104222570 6.250 uM 0.77 %
#> 101 504526 104222570 3.125 uM 0.64 %
#> 102 504526 104222570 1.563 uM 0.51 %
#> 103 504526 104222570 0.781 uM 0.48 %
#> 104 504526 104222570 0.391 uM 0.57 %
#> 105 504526 104222571 50.000 uM 2.00 %
#> 106 504526 104222571 25.000 uM 2.18 %
#> 107 504526 104222571 12.500 uM 1.73 %
#> 108 504526 104222571 6.250 uM 1.56 %
#> 109 504526 104222571 3.125 uM 1.19 %
#> 110 504526 104222571 1.563 uM 0.93 %
#> 111 504526 104222571 0.781 uM 0.80 %
#> 112 504526 104222571 0.391 uM 0.74 %
#> 113 504526 104222572 50.000 uM 78.03 %
#> 114 504526 104222572 25.000 uM 86.65 %
#> 115 504526 104222572 12.500 uM 83.45 %
#> 116 504526 104222572 6.250 uM 47.02 %
#> 117 504526 104222572 3.125 uM 12.20 %
#> 118 504526 104222572 1.563 uM 2.23 %
#> 119 504526 104222572 0.781 uM 0.77 %
#> 120 504526 104222572 0.391 uM 0.65 %
#> 121 504526 109967230 50.000 uM 107.05 %
#> 122 504526 109967230 25.000 uM 90.78 %
#> 123 504526 109967230 12.500 uM 87.53 %
#> 124 504526 109967230 6.250 uM 101.19 %
#> 125 504526 109967230 3.125 uM 80.54 %
#> 126 504526 109967230 1.563 uM 15.81 %
#> 127 504526 109967230 0.781 uM 4.66 %
#> 128 504526 109967230 0.391 uM 2.32 %
#> 129 504526 109967231 50.000 uM 2.59 %
#> 130 504526 109967231 25.000 uM 2.63 %
#> 131 504526 109967231 12.500 uM 2.32 %
#> 132 504526 109967231 6.250 uM 2.49 %
#> 133 504526 109967231 3.125 uM 1.96 %
#> 134 504526 109967231 1.563 uM 1.80 %
#> 135 504526 109967231 0.781 uM 1.19 %
#> 136 504526 109967231 0.391 uM 1.06 %
#> 137 504526 109967232 50.000 uM 7.51 %
#> 138 504526 109967232 25.000 uM 9.47 %
#> 139 504526 109967232 12.500 uM 60.40 %
#> 140 504526 109967232 6.250 uM 79.75 %
#> 141 504526 109967232 3.125 uM 72.51 %
#> 142 504526 109967232 1.563 uM 59.35 %
#> 143 504526 109967232 0.781 uM 35.87 %
#> 144 504526 109967232 0.391 uM 13.62 %
#> 145 504526 109967233 50.000 uM 30.79 %
#> 146 504526 109967233 25.000 uM 21.08 %
#> 147 504526 109967233 12.500 uM 27.55 %
#> 148 504526 109967233 6.250 uM 17.89 %
#> 149 504526 109967233 3.125 uM 6.44 %
#> 150 504526 109967233 1.563 uM 3.41 %
#> 151 504526 109967233 0.781 uM 2.54 %
#> 152 504526 109967233 0.391 uM 1.48 %
#> 153 504526 109967234 50.000 uM 9.10 %
#> 154 504526 109967234 25.000 uM 11.20 %
#> 155 504526 109967234 12.500 uM 10.88 %
#> 156 504526 109967234 6.250 uM 7.76 %
#> 157 504526 109967234 3.125 uM 4.61 %
#> 158 504526 109967234 1.563 uM 3.29 %
#> 159 504526 109967234 0.781 uM 2.06 %
#> 160 504526 109967234 0.391 uM 1.52 %
#> 161 504526 109967235 50.000 uM 88.79 %
#> 162 504526 109967235 25.000 uM 90.14 %
#> 163 504526 109967235 12.500 uM 77.74 %
#> 164 504526 109967235 6.250 uM 66.47 %
#> 165 504526 109967235 3.125 uM 48.34 %
#> 166 504526 109967235 1.563 uM 32.20 %
#> [ reached 'max' / getOption("max.print") -- omitted 34 rows ]3. Targets: To retrieve assay targets, including protein or gene identifiers:
result <- get_pug_rest(identifier = c("490","1000"), namespace = "aid", domain = "assay", operation = "targets/ProteinGI,ProteinName,GeneID,GeneSymbol", output = "JSON")
result
#>
#> An object of class 'PugRestInstance'
#>
#> Request Details:
#> - Domain: Assay
#> - Namespace: AID
#> - Operation: targets/ProteinGI,ProteinName,GeneID,GeneSymbol
#> - Identifier: 490, 1000
#>
#> NOTE: Run getter function 'pubChemData(...)' to extract raw data retrieved from PubChem Database.
#> See ?pubChemData for details.pubChemData(result)
#> $InformationList
#> $InformationList$Information
#> $InformationList$Information[[1]]
#> $InformationList$Information[[1]]$AID
#> [1] 1000
#>
#> $InformationList$Information[[1]]$GI
#> [1] 116516899
#>
#> $InformationList$Information[[1]]$ProteinName
#> [1] "mevalonate kinase"To select assays via target identifier:
result <- get_pug_rest(identifier = "USP2", namespace = "target/genesymbol", domain = "assay", operation = "aids", output = "TXT")
result
#>
#> An object of class 'PugRestInstance'
#>
#> Request Details:
#> - Domain: Assay
#> - Namespace: DomainSpecific
#> - Operation: aids
#> - Identifier: USP2
#>
#> NOTE: Run getter function 'pubChemData(...)' to extract raw data retrieved from PubChem Database.
#> See ?pubChemData for details.pubChemData(result)
#> Text
#> 1 927
#> 2 1455
#> 3 1904
#> 4 2281
#> 5 463106
#> 6 463254
#> 7 493168
#> 8 493170
#> 9 504793
#> 10 504794
#> 11 504804
#> 12 504805
#> 13 504808
#> 14 624099
#> 15 624345
#> 16 651626
#> 17 651810
#> 18 651811
#> 19 652172
#> 20 652173
#> 21 652174
#> 22 652243
#> 23 652259
#> 24 652272
#> 25 686937
#> 26 686938
#> 27 686943
#> 28 686990
#> 29 694822
#> 30 720505
#> 31 743454
#> 32 755342
#> 33 761504
#> 34 1053208
#> 35 1117281
#> 36 1117357
#> 37 1128595
#> 38 1128604
#> 39 1159506
#> 40 1159578
#> 41 1159584
#> 42 1159615
#> 43 1197975
#> 44 1224826
#> 45 1224828
#> 46 1224830
#> 47 1383944
#> 48 1383945
#> 49 1383947
#> 50 1383948
#> 51 1383950
#> 52 1383951
#> 53 1489184
#> 54 1489185
#> 55 1491550
#> 56 1508587
#> 57 1508588
#> 58 1558721
#> 59 1561164
#> 60 1649123
#> 61 1680000
#> 62 1692429
#> 63 1794863
#> 64 1802686
#> 65 1802687
#> 66 1857650
#> 67 1881105
#> 68 1897518
#> 69 1925871
#> 70 1930792
#> 71 1930821
#> 72 1930826
#> 73 1930827
#> 74 1947415
#> 75 1947418
#> 76 1947449
#> 77 1947457
#> 78 1947524
#> 79 19742014. Activity Name: To select BioAssays by the name of the primary activity column:
result <- get_pug_rest(identifier = "EC50", namespace = "activity", domain = "assay", operation = "aids", output = "JSON")
result
#>
#> An object of class 'PugRestInstance'
#>
#> Request Details:
#> - Domain: Assay
#> - Namespace: DomainSpecific
#> - Operation: aids
#> - Identifier: EC50
#>
#> NOTE: Run getter function 'pubChemData(...)' to extract raw data retrieved from PubChem Database.
#> See ?pubChemData for details.pubChemData(result)
#> $IdentifierList
#> $IdentifierList$AID
#> [1] 430 431 618 620 696 718 737 773 854 872 874 876 936 1001 1045 1047 1050 1062
#> [19] 1078 1192 1196 1197 1198 1200 1221 1222 1223 1224 1228 1232 1234 1241 1243 1244 1245 1247
#> [37] 1248 1252 1266 1268 1269 1270 1271 1280 1281 1282 1283 1287 1289 1290 1291 1292 1293 1294
#> [55] 1295 1299 1302 1319 1320 1322 1323 1324 1327 1328 1329 1330 1331 1333 1334 1335 1336 1337
#> [73] 1339 1340 1341 1364 1365 1366 1367 1368 1369 1370 1371 1372 1373 1374 1375 1394 1397 1404
#> [91] 1406 1412 1414 1442 1444 1450 1465 1470 1508 1522 1528 1538 1562 1566 1578 1625 1659 1660
#> [109] 1679 1681 1682 1684 1686 1689 1690 1701 1723 1735 1736 1737 1738 1743 1744 1753 1757 1764
#> [127] 1767 1769 1777 1871 1872 1884 1888 1889 1891 1895 1896 1897 1900 1902 1914 1915 1923 1928
#> [145] 1929 1930 1932 1933 1934 1935 1936 1938 1939 1959 1960 1961 1964 1966 1988 1990 1994 1999
#> [163] 2002 2003 2008 2009 2010 2019 2020 2021 2022 2027 2031 2033 2036 2037 2038 2039 2040 2041
#> [181] 2042 2043 2044 2045 2046 2047 2048 2050 2051 2053 2055 2075 2077 2080 2081 2084 2086 2089
#> [199] 2096 2102 2121 2124 2133 2137 2138 2145 2150 2151 2181 2182 2183 2185 2186 2188 2190 2191
#> [217] 2192 2193 2194 2197 2199 2207 2208 2209 2210 2211 2212 2219 2220 2224 2252 2253 2284 2286
#> [235] 2294 2295 2296 2298 2307 2310 2311 2327 2343 2344 2347 2352 2359 2370 2376 2382 2387 2388
#> [253] 2396 2398 2400 2423 2425 2428 2434 2438 2442 2443 2446 2450 2452 2453 2454 2456 2457 2458
#> [271] 2460 2463 2467 2468 2470 2471 2473 2477 2484 2486 2492 2493 2497 2500 2510 2511 2518 2519
#> [289] 2525 2548 2583 2586 2603 2607 2608 2609 2610 2611 2630 2631 2633 2635 2638 2651 2654 2670
#> [307] 2683 2696 2704 2723 2724 2725 2735 2738 2739 2740 2742 2743 2744 2745 2753 2765 2807 2809
#> [325] 2814 2821 2823 2826 2827 2828 2829 2835 2843 2844 2901 2996 2997 2999 3004 3005 3006 3008
#> [343] 3009 3015 3058 3059 3189 3385 3423 3490 3492 3502 3503 3506 3507 3508 3509 3510 3513 3516
#> [361] 3517 3519 3706 3709 3901 3902 3903 3904 3905 3906 3907 3909 4494 4495 4496 4497 4498 4499
#> [379] 4500 4501 4502 4520 4521 4550 4567 4571 4572 4573 4574 4575 4576 4577 4578 4579 4580 4581
#> [397] 4582 4666 4667 4779 4871 4872 4936 4937 4938 4939 4972 4973 4974 5161 5162 5163 5165 5383
#> [415] 5459 5460 5461 5462 5464 5465 5466 5467 5468 5702 5841 5842 5843 6140 6142 6147 6148 6209
#> [433] 6220 6224 6225 6226 6228 6229 6250 6267 6274 6275 6276 6377 6380 6398 6399 8455 8619 8848
#> [451] 8849 9404 9405 9448 9454 9465 9467 9468 9635 9809 9810 9811 9812 9813 10054 19923 30287 30288
#> [469] 30289 30291 30292 30293 30294 30295 30296 30481 30504 30505 30506 30507 30508 30509 30510 30630 30631 30632
#> [487] 30633 30634 30792 30816 30817 30818 31103 31131 31260 31261 31262 31264 31265 31266 31267 31268 31269 31447
#> [505] 31454 31829 32070 32145 32146 32147 32148 32149 32150 32151 32464 32465 32785 32836 32967 32970 32972 33156
#> [523] 33162 33163 33164 33505 33767 33768 33769 33770 33950 34073 34074 34264 34265 34266 34267 34268 34269 34270
#> [541] 34309 34436 34438 34439 34440 34584 34592 34594 34596 34598 34600 34747 34748 35160 35381 35384 35390 35445
#> [559] 35446 35447 35448 35449 35451 35452 35453 35586 35618 35832 35922 35956 35957 35958 35959 35985 35987 35988
#> [577] 35989 35990 35991 35992 35993 35994 36027 36045 36046 36065 36133 36134 36135 36232 36233 36246 36261 36262
#> [595] 36352 36385 36416 36417 36419 36420 36421 36434 36435 36436 36437 36470 36512 36513 36524 36525 36526 36527
#> [613] 36578 36579 36580 36581 36626 36627 36628 36629 36656 36657 36665 36674 36675 36682 36683 36763 37036 37345
#> [631] 37346 37347 37348 37349 37350 37497 38017 38035 38326 38516 38518 38519 38533 38534 38535 38600 38694 38695
#> [649] 38696 38742 38799 38801 38802 38803 38804 38805 39027 39064 39165 39218 39867 39967 39968 40109 40110 40111
#> [667] 40112 40114 40115 40116 40117 40118 40119 40121 40122 40126 40844 40846 41017 41018 41032 41036 41037 41039
#> [685] 41040 41041 41045 41130 41137 41159 41160 41161 41162 41163 41165 41198 41199 41204 41207 41441 41442 41445
#> [703] 41512 41513 41528 41529 41530 41531 41543 41569 41570 41592 41600 41601 41634 41636 41650 41651 41652 41653
#> [721] 41654 41655 41656 41657 41658 41660 41663 41664 41665 41666 41667 41668 41669 41777 41778 41779 41780 41781
#> [739] 41783 41785 41786 41788 41789 41790 41791 41792 41910 41937 41938 41939 41940 41941 41964 42046 42047 42048
#> [757] 42049 42050 42052 42053 42092 42107 42117 42122 42220 42231 42233 42359 42382 42383 42398 42399 42593 42620
#> [775] 42621 42622 42776 42777 42778 42831 42847 42899 43083 43236 43237 43238 43239 43240 43241 43385 43386 43387
#> [793] 43388 43389 43390 43391 43392 43393 43394 43395 43396 43397 43398 43978 43979 43986 43987 43988 43990 44004
#> [811] 44005 44006 44208 44209 44211 44212 44213 44214 44215 44216 44217 44235 44340 44352 44384 44385 44393 44394
#> [829] 44398 44399 44405 44411 44412 44541 44542 44545 44546 44553 44560 44562 44563 44569 44570 44571 44591 44604
#> [847] 44608 44610 44627 44631 44641 44642 44645 44646 44647 44664 44665 44666 44667 44668 44669 44719 44735 44737
#> [865] 44739 44740 44741 44789 44790 44791 44792 44793 44794 44795 44796 44814 44816 44817 44818 44819 44820 44821
#> [883] 44822 44823 44824 44825 44826 44827 44828 44829 44830 44831 44832 44874 44998 44999 45000 45001 45002 45003
#> [901] 45004 45025 45026 45027 45028 45029 45035 45036 45037 45060 45061 45062 45063 45064 45065 45066 45067 45069
#> [919] 45070 45071 45072 45114 45115 45290 45292 45351 45354 45355 45356 45357 45358 45359 45360 45361 45362 45363
#> [937] 45364 45365 45366 45367 45368 45369 45370 45371 45372 45373 45374 45376 45378 45379 45380 45381 45382 45385
#> [955] 45386 45387 45388 45389 45390 45391 45392 45412 45518 45519 45520 45521 45522 45523 45524 45525 45526 45527
#> [973] 45528 45529 45530 45531 45532 45533 45534 45535 45536 45540 45541 45542 45543 45549 45550 45551 45552 45553
#> [991] 45554 45555 45682 45683 45684 45685 45686 45687 45688 45689
#> [ reached getOption("max.print") -- omitted 40108 entries ]These examples demonstrate the flexibility of PUG REST in accessing specific BioAssay data. Users can efficiently retrieve detailed descriptions, comprehensive data sets, concise readouts, and target information, making it a valuable tool for researchers and scientists working with BioAssay data.
PubChem provides various methods to access gene data, making it a valuable resource for genetic research. Here’s how you can utilize PUG REST to access gene-related information:
1. Gene Input Methods:
result <- get_pug_rest(identifier = "1956,13649", namespace = "geneid", domain = "gene", operation = "summary", output = "JSON")
result
#>
#> An object of class 'PugRestInstance'
#>
#> Request Details:
#> - Domain: Gene
#> - Namespace: DomainSpecific
#> - Operation: summary
#> - Identifier: 1956,13649
#>
#> NOTE: Run getter function 'pubChemData(...)' to extract raw data retrieved from PubChem Database.
#> See ?pubChemData for details.pubChemData(result)
#> $GeneSummaries
#> $GeneSummaries$GeneSummary
#> $GeneSummaries$GeneSummary[[1]]
#> $GeneSummaries$GeneSummary[[1]]$GeneID
#> [1] 1956
#>
#> $GeneSummaries$GeneSummary[[1]]$Symbol
#> [1] "EGFR"
#>
#> $GeneSummaries$GeneSummary[[1]]$Name
#> [1] "epidermal growth factor receptor"
#>
#> $GeneSummaries$GeneSummary[[1]]$TaxonomyID
#> [1] 9606
#>
#> $GeneSummaries$GeneSummary[[1]]$Taxonomy
#> [1] "Homo sapiens (human)"
#>
#> $GeneSummaries$GeneSummary[[1]]$Description
#> [1] "The protein encoded by this gene is a transmembrane glycoprotein that is a member of the protein kinase superfamily. This protein is a receptor for members of the epidermal growth factor family. EGFR is a cell surface protein that binds to epidermal growth factor, thus inducing receptor dimerization and tyrosine autophosphorylation leading to cell proliferation. Mutations in this gene are associated with lung cancer. EGFR is a component of the cytokine storm which contributes to a severe form of Coronavirus Disease 2019 (COVID-19) resulting from infection with severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2). [provided by RefSeq, Jul 2020]"
#>
#> $GeneSummaries$GeneSummary[[1]]$Synonym
#> [1] "ERBB"
#> [2] "ERBB1"
#> [3] "ERRP"
#> [4] "HER1"
#> [5] "NISBD2"
#> [6] "NNCIS"
#> [7] "PIG61"
#> [8] "mENA"
#> [9] "EGFR vIII"
#> [10] "avian erythroblastic leukemia viral (v-erb-b) oncogene homolog"
#> [11] "cell growth inhibiting protein 40"
#> [12] "cell proliferation-inducing protein 61"
#> [13] "epidermal growth factor receptor tyrosine kinase domain"
#> [14] "erb-b2 receptor tyrosine kinase 1"
#> [15] "proto-oncogene c-ErbB-1"
#> [16] "receptor tyrosine-protein kinase erbB-1"
#>
#>
#> $GeneSummaries$GeneSummary[[2]]
#> $GeneSummaries$GeneSummary[[2]]$GeneID
#> [1] 13649
#>
#> $GeneSummaries$GeneSummary[[2]]$Symbol
#> [1] "Egfr"
#>
#> $GeneSummaries$GeneSummary[[2]]$Name
#> [1] "epidermal growth factor receptor"
#>
#> $GeneSummaries$GeneSummary[[2]]$TaxonomyID
#> [1] 10090
#>
#> $GeneSummaries$GeneSummary[[2]]$Taxonomy
#> [1] "Mus musculus (house mouse)"
#>
#> $GeneSummaries$GeneSummary[[2]]$Description
#> [1] "Enables epidermal growth factor binding activity and epidermal growth factor receptor activity. Involved in ERBB2-EGFR signaling pathway; cellular response to amino acid stimulus; and positive regulation of fibroblast proliferation. Acts upstream of or within several processes, including eyelid development in camera-type eye; protein modification process; and regulation of epidermal growth factor receptor signaling pathway. Located in several cellular components, including basolateral plasma membrane; endocytic vesicle; and perinuclear region of cytoplasm. Is active in plasma membrane. Is expressed in several structures, including alimentary system; brain; integumental system; limb; and sensory organ. Used to study Coronavirus infectious disease and aortic valve disease. Human ortholog(s) of this gene implicated in several diseases, including colorectal cancer; lung cancer (multiple); pancreatic cancer; prostate cancer; and pulmonary tuberculosis. Orthologous to human EGFR (epidermal growth factor receptor). [provided by Alliance of Genome Resources, Apr 2025]"
#>
#> $GeneSummaries$GeneSummary[[2]]$Synonym
#> [1] "9030024J15Rik"
#> [2] "Erbb"
#> [3] "Errb1"
#> [4] "Errp"
#> [5] "Wa5"
#> [6] "wa-2"
#> [7] "wa2"
#> [8] "avian erythroblastic leukemia viral (v-erb-b) oncogene homolog"
#> [9] "waved 2"result <- get_pug_rest(identifier = "EGFR", namespace = "genesymbol", domain = "gene", operation = "summary", output = "JSON")
result
#>
#> An object of class 'PugRestInstance'
#>
#> Request Details:
#> - Domain: Gene
#> - Namespace: DomainSpecific
#> - Operation: summary
#> - Identifier: EGFR
#>
#> NOTE: Run getter function 'pubChemData(...)' to extract raw data retrieved from PubChem Database.
#> See ?pubChemData for details.pubChemData(result)
#> $GeneSummaries
#> $GeneSummaries$GeneSummary
#> $GeneSummaries$GeneSummary[[1]]
#> $GeneSummaries$GeneSummary[[1]]$GeneID
#> [1] 1956
#>
#> $GeneSummaries$GeneSummary[[1]]$Symbol
#> [1] "EGFR"
#>
#> $GeneSummaries$GeneSummary[[1]]$Name
#> [1] "epidermal growth factor receptor"
#>
#> $GeneSummaries$GeneSummary[[1]]$TaxonomyID
#> [1] 9606
#>
#> $GeneSummaries$GeneSummary[[1]]$Taxonomy
#> [1] "Homo sapiens (human)"
#>
#> $GeneSummaries$GeneSummary[[1]]$Description
#> [1] "The protein encoded by this gene is a transmembrane glycoprotein that is a member of the protein kinase superfamily. This protein is a receptor for members of the epidermal growth factor family. EGFR is a cell surface protein that binds to epidermal growth factor, thus inducing receptor dimerization and tyrosine autophosphorylation leading to cell proliferation. Mutations in this gene are associated with lung cancer. EGFR is a component of the cytokine storm which contributes to a severe form of Coronavirus Disease 2019 (COVID-19) resulting from infection with severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2). [provided by RefSeq, Jul 2020]"
#>
#> $GeneSummaries$GeneSummary[[1]]$Synonym
#> [1] "ERBB"
#> [2] "ERBB1"
#> [3] "ERRP"
#> [4] "HER1"
#> [5] "NISBD2"
#> [6] "NNCIS"
#> [7] "PIG61"
#> [8] "mENA"
#> [9] "EGFR vIII"
#> [10] "avian erythroblastic leukemia viral (v-erb-b) oncogene homolog"
#> [11] "cell growth inhibiting protein 40"
#> [12] "cell proliferation-inducing protein 61"
#> [13] "epidermal growth factor receptor tyrosine kinase domain"
#> [14] "erb-b2 receptor tyrosine kinase 1"
#> [15] "proto-oncogene c-ErbB-1"
#> [16] "receptor tyrosine-protein kinase erbB-1"result <- get_pug_rest(identifier = "ERBB1", namespace = "synonym", domain = "gene", operation = "summary", output = "JSON")
result
#>
#> An object of class 'PugRestInstance'
#>
#> Request Details:
#> - Domain: Gene
#> - Namespace: DomainSpecific
#> - Operation: summary
#> - Identifier: ERBB1
#>
#> NOTE: Run getter function 'pubChemData(...)' to extract raw data retrieved from PubChem Database.
#> See ?pubChemData for details.pubChemData(result)
#> $GeneSummaries
#> $GeneSummaries$GeneSummary
#> $GeneSummaries$GeneSummary[[1]]
#> $GeneSummaries$GeneSummary[[1]]$GeneID
#> [1] 1956
#>
#> $GeneSummaries$GeneSummary[[1]]$Symbol
#> [1] "EGFR"
#>
#> $GeneSummaries$GeneSummary[[1]]$Name
#> [1] "epidermal growth factor receptor"
#>
#> $GeneSummaries$GeneSummary[[1]]$TaxonomyID
#> [1] 9606
#>
#> $GeneSummaries$GeneSummary[[1]]$Taxonomy
#> [1] "Homo sapiens (human)"
#>
#> $GeneSummaries$GeneSummary[[1]]$Description
#> [1] "The protein encoded by this gene is a transmembrane glycoprotein that is a member of the protein kinase superfamily. This protein is a receptor for members of the epidermal growth factor family. EGFR is a cell surface protein that binds to epidermal growth factor, thus inducing receptor dimerization and tyrosine autophosphorylation leading to cell proliferation. Mutations in this gene are associated with lung cancer. EGFR is a component of the cytokine storm which contributes to a severe form of Coronavirus Disease 2019 (COVID-19) resulting from infection with severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2). [provided by RefSeq, Jul 2020]"
#>
#> $GeneSummaries$GeneSummary[[1]]$Synonym
#> [1] "ERBB"
#> [2] "ERBB1"
#> [3] "ERRP"
#> [4] "HER1"
#> [5] "NISBD2"
#> [6] "NNCIS"
#> [7] "PIG61"
#> [8] "mENA"
#> [9] "EGFR vIII"
#> [10] "avian erythroblastic leukemia viral (v-erb-b) oncogene homolog"
#> [11] "cell growth inhibiting protein 40"
#> [12] "cell proliferation-inducing protein 61"
#> [13] "epidermal growth factor receptor tyrosine kinase domain"
#> [14] "erb-b2 receptor tyrosine kinase 1"
#> [15] "proto-oncogene c-ErbB-1"
#> [16] "receptor tyrosine-protein kinase erbB-1"
#>
#>
#> $GeneSummaries$GeneSummary[[2]]
#> $GeneSummaries$GeneSummary[[2]]$GeneID
#> [1] 24329
#>
#> $GeneSummaries$GeneSummary[[2]]$Symbol
#> [1] "Egfr"
#>
#> $GeneSummaries$GeneSummary[[2]]$Name
#> [1] "epidermal growth factor receptor"
#>
#> $GeneSummaries$GeneSummary[[2]]$TaxonomyID
#> [1] 10116
#>
#> $GeneSummaries$GeneSummary[[2]]$Taxonomy
#> [1] "Rattus norvegicus (Norway rat)"
#>
#> $GeneSummaries$GeneSummary[[2]]$Description
#> [1] "Enables several functions, including calmodulin binding activity; enzyme binding activity; and epidermal growth factor binding activity. Involved in several processes, including blood vessel diameter maintenance; positive regulation of cell communication; and protein phosphorylation. Located in several cellular components, including apical plasma membrane; basolateral plasma membrane; and cytoplasmic vesicle. Is active in glutamatergic synapse and synaptic membrane. Used to study bronchiolo-alveolar adenocarcinoma; dilated cardiomyopathy; and high grade glioma. Biomarker of several diseases, including Parkinsonism; lung disease (multiple); median neuropathy; nicotine dependence; and peptic esophagitis. Human ortholog(s) of this gene implicated in several diseases, including colorectal cancer; lung cancer (multiple); pancreatic cancer; prostate cancer; and pulmonary tuberculosis. Orthologous to human EGFR (epidermal growth factor receptor). [provided by Alliance of Genome Resources, Jul 2025]"
#>
#> $GeneSummaries$GeneSummary[[2]]$Synonym
#> [1] "ERBB1"
#> [2] "ErbB-1"
#> [3] "Errp"
#> [4] "EGFR-related peptide"
#> [5] "Epidermal growth factor receptor formerly avian erythroblastic leukemia viral (v-erbB) oncogene homolog (Erbb1)"
#> [6] "avian erythroblastic leukemia viral (v-erbB) oncogene homolog"
#> [7] "epidermal growth factor receptor, formerly avian erythroblastic leukemia viral (v-erbB) oncogene homolog (Erbb1)"
#>
#>
#> $GeneSummaries$GeneSummary[[3]]
#> $GeneSummaries$GeneSummary[[3]]$GeneID
#> [1] 724072
#>
#> $GeneSummaries$GeneSummary[[3]]$Symbol
#> [1] "egfr.L"
#>
#> $GeneSummaries$GeneSummary[[3]]$Name
#> [1] "epidermal growth factor receptor L homeolog"
#>
#> $GeneSummaries$GeneSummary[[3]]$TaxonomyID
#> [1] 8355
#>
#> $GeneSummaries$GeneSummary[[3]]$Taxonomy
#> [1] "Xenopus laevis (African clawed frog)"
#>
#> $GeneSummaries$GeneSummary[[3]]$Description
#> [1] "Predicted to enable ATP binding activity and transmembrane receptor protein tyrosine kinase activity. Predicted to act upstream of or within ERBB signaling pathway; regulation of cell population proliferation; and regulation of signal transduction. Predicted to be located in membrane. Is expressed in musculoskeletal system; nervous system; pharyngeal arch; and primary germ layer. Human ortholog(s) of this gene implicated in several diseases, including colorectal cancer; lung cancer (multiple); pancreatic cancer; prostate cancer; and pulmonary tuberculosis. Orthologous to human EGFR (epidermal growth factor receptor). [provided by Alliance of Genome Resources, Apr 2025]"
#>
#> $GeneSummaries$GeneSummary[[3]]$Synonym
#> [1] "XEgfr" "egfr" "erbb"
#> [4] "erbb1" "her1" "epidermal growth factor receptor"
#>
#>
#> $GeneSummaries$GeneSummary[[4]]
#> $GeneSummaries$GeneSummary[[4]]$GeneID
#> [1] 100492965
#>
#> $GeneSummaries$GeneSummary[[4]]$Symbol
#> [1] "egfr"
#>
#> $GeneSummaries$GeneSummary[[4]]$Name
#> [1] "epidermal growth factor receptor"
#>
#> $GeneSummaries$GeneSummary[[4]]$TaxonomyID
#> [1] 8364
#>
#> $GeneSummaries$GeneSummary[[4]]$Taxonomy
#> [1] "Xenopus tropicalis (tropical clawed frog)"
#>
#> $GeneSummaries$GeneSummary[[4]]$Description
#> [1] "Predicted to enable epidermal growth factor binding activity and transmembrane receptor protein tyrosine kinase activity. Predicted to be involved in several processes, including epidermal growth factor receptor signaling pathway; positive regulation of MAPK cascade; and positive regulation of epithelial cell proliferation. Predicted to act upstream of or within ERBB signaling pathway; regulation of cell population proliferation; and regulation of signal transduction. Predicted to be located in membrane. Predicted to be part of receptor complex. Predicted to be active in basal plasma membrane. Human ortholog(s) of this gene implicated in several diseases, including colorectal cancer; lung cancer (multiple); pancreatic cancer; prostate cancer; and pulmonary tuberculosis. Orthologous to human EGFR (epidermal growth factor receptor). [provided by Alliance of Genome Resources, Apr 2025]"
#>
#> $GeneSummaries$GeneSummary[[4]]$Synonym
#> [1] "XEgfr" "erbb" "erbb1" "her1"
#>
#>
#> $GeneSummaries$GeneSummary[[5]]
#> $GeneSummaries$GeneSummary[[5]]$GeneID
#> [1] 100537376
#>
#> $GeneSummaries$GeneSummary[[5]]$Symbol
#> [1] "egfrb"
#>
#> $GeneSummaries$GeneSummary[[5]]$Name
#> [1] "epidermal growth factor receptor b (erythroblastic leukemia viral (v-erb-b) oncogene homolog, avian)"
#>
#> $GeneSummaries$GeneSummary[[5]]$TaxonomyID
#> [1] 7955
#>
#> $GeneSummaries$GeneSummary[[5]]$Taxonomy
#> [1] "Danio rerio (zebrafish)"
#>
#> $GeneSummaries$GeneSummary[[5]]$Description
#> [1] "Is expressed in liver and ovary. Human ortholog(s) of this gene implicated in several diseases, including colorectal cancer; lung cancer (multiple); pancreatic cancer; prostate cancer; and pulmonary tuberculosis. Orthologous to human EGFR (epidermal growth factor receptor). [provided by Alliance of Genome Resources, Jul 2025]"
#>
#> $GeneSummaries$GeneSummary[[5]]$Synonym
#> [1] "erbb1" "erbb1b"
#>
#>
#> $GeneSummaries$GeneSummary[[6]]
#> $GeneSummaries$GeneSummary[[6]]$GeneID
#> [1] 108719997
#>
#> $GeneSummaries$GeneSummary[[6]]$Symbol
#> [1] "egfr.S"
#>
#> $GeneSummaries$GeneSummary[[6]]$Name
#> [1] "epidermal growth factor receptor S homeolog"
#>
#> $GeneSummaries$GeneSummary[[6]]$TaxonomyID
#> [1] 8355
#>
#> $GeneSummaries$GeneSummary[[6]]$Taxonomy
#> [1] "Xenopus laevis (African clawed frog)"
#>
#> $GeneSummaries$GeneSummary[[6]]$Description
#> [1] "Predicted to enable ATP binding activity and transmembrane receptor protein tyrosine kinase activity. Predicted to act upstream of or within ERBB signaling pathway; regulation of cell population proliferation; and regulation of signal transduction. Predicted to be located in membrane. Human ortholog(s) of this gene implicated in several diseases, including colorectal cancer; lung cancer (multiple); pancreatic cancer; prostate cancer; and pulmonary tuberculosis. Orthologous to human EGFR (epidermal growth factor receptor). [provided by Alliance of Genome Resources, Apr 2025]"
#>
#> $GeneSummaries$GeneSummary[[6]]$Synonym
#> [1] "XEgfr" "erbb" "erbb1"
#> [4] "her1" "epidermal growth factor receptor"2. Available Gene Data:
result <- get_pug_rest(identifier = "1956,13649", namespace = "geneid", domain = "gene", operation = "summary", output = "JSON")
result
#>
#> An object of class 'PugRestInstance'
#>
#> Request Details:
#> - Domain: Gene
#> - Namespace: DomainSpecific
#> - Operation: summary
#> - Identifier: 1956,13649
#>
#> NOTE: Run getter function 'pubChemData(...)' to extract raw data retrieved from PubChem Database.
#> See ?pubChemData for details.pubChemData(result)
#> $GeneSummaries
#> $GeneSummaries$GeneSummary
#> $GeneSummaries$GeneSummary[[1]]
#> $GeneSummaries$GeneSummary[[1]]$GeneID
#> [1] 1956
#>
#> $GeneSummaries$GeneSummary[[1]]$Symbol
#> [1] "EGFR"
#>
#> $GeneSummaries$GeneSummary[[1]]$Name
#> [1] "epidermal growth factor receptor"
#>
#> $GeneSummaries$GeneSummary[[1]]$TaxonomyID
#> [1] 9606
#>
#> $GeneSummaries$GeneSummary[[1]]$Taxonomy
#> [1] "Homo sapiens (human)"
#>
#> $GeneSummaries$GeneSummary[[1]]$Description
#> [1] "The protein encoded by this gene is a transmembrane glycoprotein that is a member of the protein kinase superfamily. This protein is a receptor for members of the epidermal growth factor family. EGFR is a cell surface protein that binds to epidermal growth factor, thus inducing receptor dimerization and tyrosine autophosphorylation leading to cell proliferation. Mutations in this gene are associated with lung cancer. EGFR is a component of the cytokine storm which contributes to a severe form of Coronavirus Disease 2019 (COVID-19) resulting from infection with severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2). [provided by RefSeq, Jul 2020]"
#>
#> $GeneSummaries$GeneSummary[[1]]$Synonym
#> [1] "ERBB"
#> [2] "ERBB1"
#> [3] "ERRP"
#> [4] "HER1"
#> [5] "NISBD2"
#> [6] "NNCIS"
#> [7] "PIG61"
#> [8] "mENA"
#> [9] "EGFR vIII"
#> [10] "avian erythroblastic leukemia viral (v-erb-b) oncogene homolog"
#> [11] "cell growth inhibiting protein 40"
#> [12] "cell proliferation-inducing protein 61"
#> [13] "epidermal growth factor receptor tyrosine kinase domain"
#> [14] "erb-b2 receptor tyrosine kinase 1"
#> [15] "proto-oncogene c-ErbB-1"
#> [16] "receptor tyrosine-protein kinase erbB-1"
#>
#>
#> $GeneSummaries$GeneSummary[[2]]
#> $GeneSummaries$GeneSummary[[2]]$GeneID
#> [1] 13649
#>
#> $GeneSummaries$GeneSummary[[2]]$Symbol
#> [1] "Egfr"
#>
#> $GeneSummaries$GeneSummary[[2]]$Name
#> [1] "epidermal growth factor receptor"
#>
#> $GeneSummaries$GeneSummary[[2]]$TaxonomyID
#> [1] 10090
#>
#> $GeneSummaries$GeneSummary[[2]]$Taxonomy
#> [1] "Mus musculus (house mouse)"
#>
#> $GeneSummaries$GeneSummary[[2]]$Description
#> [1] "Enables epidermal growth factor binding activity and epidermal growth factor receptor activity. Involved in ERBB2-EGFR signaling pathway; cellular response to amino acid stimulus; and positive regulation of fibroblast proliferation. Acts upstream of or within several processes, including eyelid development in camera-type eye; protein modification process; and regulation of epidermal growth factor receptor signaling pathway. Located in several cellular components, including basolateral plasma membrane; endocytic vesicle; and perinuclear region of cytoplasm. Is active in plasma membrane. Is expressed in several structures, including alimentary system; brain; integumental system; limb; and sensory organ. Used to study Coronavirus infectious disease and aortic valve disease. Human ortholog(s) of this gene implicated in several diseases, including colorectal cancer; lung cancer (multiple); pancreatic cancer; prostate cancer; and pulmonary tuberculosis. Orthologous to human EGFR (epidermal growth factor receptor). [provided by Alliance of Genome Resources, Apr 2025]"
#>
#> $GeneSummaries$GeneSummary[[2]]$Synonym
#> [1] "9030024J15Rik"
#> [2] "Erbb"
#> [3] "Errb1"
#> [4] "Errp"
#> [5] "Wa5"
#> [6] "wa-2"
#> [7] "wa2"
#> [8] "avian erythroblastic leukemia viral (v-erb-b) oncogene homolog"
#> [9] "waved 2"result <- get_pug_rest(identifier = "13649", namespace = "geneid", domain = "gene", operation = "aids", output = "TXT")
result
#>
#> An object of class 'PugRestInstance'
#>
#> Request Details:
#> - Domain: Gene
#> - Namespace: DomainSpecific
#> - Operation: aids
#> - Identifier: 13649
#>
#> NOTE: Run getter function 'pubChemData(...)' to extract raw data retrieved from PubChem Database.
#> See ?pubChemData for details.pubChemData(result)
#> Text
#> 1 66438
#> 2 69721
#> 3 69722
#> 4 69724
#> 5 69727
#> 6 69728
#> 7 69729
#> 8 69730
#> 9 106697
#> 10 209326
#> 11 241562
#> 12 241823
#> 13 337238
#> 14 337243
#> 15 337244
#> 16 415757
#> 17 415758
#> 18 415759
#> 19 415760
#> 20 1053208
#> 21 1224826
#> 22 1224828
#> 23 1527521
#> 24 1740135
#> 25 1815786
#> 26 1815820
#> 27 1862914
#> 28 1896806
#> 29 1972653
#> 30 1975403
#> 31 1977970result <- get_pug_rest(identifier = "13649", namespace = "geneid", domain = "gene", operation = "concise", output = "JSON")
result
#>
#> An object of class 'PugRestInstance'
#>
#> Request Details:
#> - Domain: Gene
#> - Namespace: DomainSpecific
#> - Operation: concise
#> - Identifier: 13649
#>
#> NOTE: Run getter function 'pubChemData(...)' to extract raw data retrieved from PubChem Database.
#> See ?pubChemData for details.pubChemData(result)
#> $Table
#> $Table$Columns
#> $Table$Columns$Column
#> [1] "AID" "SID" "CID" "Activity Outcome" "Target Accession"
#> [6] "Activity Name" "Activity Qualifier" "Activity Value [uM]" "Assay Name" "Assay Type"
#> [11] "PubMed ID" "RNAi"
#>
#>
#> $Table$Row
#> $Table$Row[[1]]
#> $Table$Row[[1]]$Cell
#> [1] "66438"
#> [2] "103250953"
#> [3] "25017867"
#> [4] "Active"
#> [5] "Q01279"
#> [6] "Effective concentration"
#> [7] "="
#> [8] "0.01"
#> [9] "Inhibition of epidermal growth factor binding in C3H10T1/2 cells"
#> [10] "Confirmatory"
#> [11] "1597853"
#> [12] ""
#>
#>
#> $Table$Row[[2]]
#> $Table$Row[[2]]$Cell
#> [1] "66438"
#> [2] "103432098"
#> [3] "454217"
#> [4] "Active"
#> [5] "Q01279"
#> [6] "Effective concentration"
#> [7] "="
#> [8] "0.22"
#> [9] "Inhibition of epidermal growth factor binding in C3H10T1/2 cells"
#> [10] "Confirmatory"
#> [11] "1597853"
#> [12] ""
#>
#>
#> $Table$Row[[3]]
#> $Table$Row[[3]]$Cell
#> [1] "69721"
#> [2] "103358917"
#> [3] "135512509"
#> [4] "Unspecified"
#> [5] "Q01279"
#> [6] "IC50"
#> [7] "="
#> [8] "22.7"
#> [9] "Inhibition of Epidermal growth factor receptor mediated mitogenesis of NIH3T3 cells"
#> [10] "Confirmatory"
#> [11] "9748366"
#> [12] ""
#>
#>
#> $Table$Row[[4]]
#> $Table$Row[[4]]$Cell
#> [1] "69721"
#> [2] "103358918"
#> [3] "135434086"
#> [4] "Unspecified"
#> [5] "Q01279"
#> [6] "IC50"
#> [7] "="
#> [8] "36.9"
#> [9] "Inhibition of Epidermal growth factor receptor mediated mitogenesis of NIH3T3 cells"
#> [10] "Confirmatory"
#> [11] "9748366"
#> [12] ""
#>
#>
#> $Table$Row[[5]]
#> $Table$Row[[5]]$Cell
#> [1] "69721"
#> [2] "103358919"
#> [3] "135455949"
#> [4] "Unspecified"
#> [5] "Q01279"
#> [6] "IC50"
#> [7] "="
#> [8] "11.3"
#> [9] "Inhibition of Epidermal growth factor receptor mediated mitogenesis of NIH3T3 cells"
#> [10] "Confirmatory"
#> [11] "9748366"
#> [12] ""
#>
#>
#> $Table$Row[[6]]
#> $Table$Row[[6]]$Cell
#> [1] "69722"
#> [2] "103253186"
#> [3] "5328592"
#> [4] "Unspecified"
#> [5] "Q01279"
#> [6] "IC50"
#> [7] ">"
#> [8] "100"
#> [9] "Inhibition of epidermal growth factor receptor (EGFR-mediated tyrosine autophosphorylation in mouse fibroblasts."
#> [10] "Confirmatory"
#> [11] "8027985"
#> [12] ""
#>
#>
#> $Table$Row[[7]]
#> $Table$Row[[7]]$Cell
#> [1] "69722"
#> [2] "103253755"
#> [3] "5328614"
#> [4] "Unspecified"
#> [5] "Q01279"
#> [6] "IC50"
#> [7] ">"
#> [8] "100"
#> [9] "Inhibition of epidermal growth factor receptor (EGFR-mediated tyrosine autophosphorylation in mouse fibroblasts."
#> [10] "Confirmatory"
#> [11] "8027985"
#> [12] ""
#>
#>
#> $Table$Row[[8]]
#> $Table$Row[[8]]$Cell
#> [1] "69722"
#> [2] "103254313"
#> [3] "5328618"
#> [4] "Unspecified"
#> [5] "Q01279"
#> [6] "IC50"
#> [7] ">"
#> [8] "100"
#> [9] "Inhibition of epidermal growth factor receptor (EGFR-mediated tyrosine autophosphorylation in mouse fibroblasts."
#> [10] "Confirmatory"
#> [11] "8027985"
#> [12] ""
#>
#>
#> $Table$Row[[9]]
#> $Table$Row[[9]]$Cell
#> [1] "69722"
#> [2] "103254592"
#> [3] "5328617"
#> [4] "Unspecified"
#> [5] "Q01279"
#> [6] "IC50"
#> [7] ">"
#> [8] "25"
#> [9] "Inhibition of epidermal growth factor receptor (EGFR-mediated tyrosine autophosphorylation in mouse fibroblasts."
#> [10] "Confirmatory"
#> [11] "8027985"
#> [12] ""
#>
#>
#> $Table$Row[[10]]
#> $Table$Row[[10]]$Cell
#> [1] "69724"
#> [2] "103237764"
#> [3] "5328042"
#> [4] "Active"
#> [5] "Q01279"
#> [6] "IC50"
#> [7] "="
#> [8] "0.04"
#> [9] "Inhibition of epidermal growth factor receptor tyrosine kinase (EGFR TK)"
#> [10] "Confirmatory"
#> [11] "14640561"
#> [12] ""
#>
#>
#> $Table$Row[[11]]
#> $Table$Row[[11]]$Cell
#> [1] "69724"
#> [2] "103373305"
#> [3] "9882519"
#> [4] "Active"
#> [5] "Q01279"
#> [6] "IC50"
#> [7] "="
#> [8] "0.2"
#> [9] "Inhibition of epidermal growth factor receptor tyrosine kinase (EGFR TK)"
#> [10] "Confirmatory"
#> [11] "14640561"
#> [12] ""
#>
#>
#> $Table$Row[[12]]
#> $Table$Row[[12]]$Cell
#> [1] "69724"
#> [2] "103373788"
#> [3] "9885081"
#> [4] "Active"
#> [5] "Q01279"
#> [6] "IC50"
#> [7] "="
#> [8] "0.07"
#> [9] "Inhibition of epidermal growth factor receptor tyrosine kinase (EGFR TK)"
#> [10] "Confirmatory"
#> [11] "14640561"
#> [12] ""
#>
#>
#> $Table$Row[[13]]
#> $Table$Row[[13]]$Cell
#> [1] "69724"
#> [2] "103399645"
#> [3] "11198415"
#> [4] "Active"
#> [5] "Q01279"
#> [6] "IC50"
#> [7] "="
#> [8] "0.578"
#> [9] "Inhibition of epidermal growth factor receptor tyrosine kinase (EGFR TK)"
#> [10] "Confirmatory"
#> [11] "14640561"
#> [12] ""
#>
#>
#> $Table$Row[[14]]
#> $Table$Row[[14]]$Cell
#> [1] "69724"
#> [2] "103399736"
#> [3] "10094127"
#> [4] "Active"
#> [5] "Q01279"
#> [6] "IC50"
#> [7] "="
#> [8] "0.13"
#> [9] "Inhibition of epidermal growth factor receptor tyrosine kinase (EGFR TK)"
#> [10] "Confirmatory"
#> [11] "14640561"
#> [12] ""
#>
#>
#> $Table$Row[[15]]
#> $Table$Row[[15]]$Cell
#> [1] "69724"
#> [2] "103399893"
#> [3] "11349700"
#> [4] "Active"
#> [5] "Q01279"
#> [6] "IC50"
#> [7] "="
#> [8] "0.11"
#> [9] "Inhibition of epidermal growth factor receptor tyrosine kinase (EGFR TK)"
#> [10] "Confirmatory"
#> [11] "14640561"
#> [12] ""
#>
#>
#> $Table$Row[[16]]
#> $Table$Row[[16]]$Cell
#> [1] "69727"
#> [2] "103167027"
#> [3] "5280343"
#> [4] "Unspecified"
#> [5] "Q01279"
#> [6] ""
#> [7] ""
#> [8] ""
#> [9] "Inhibition of epidermal growth factor (EGF) receptor from A431 cell membranes at 150 uM"
#> [10] "Other"
#> [11] "8201603"
#> [12] ""
#>
#>
#> $Table$Row[[17]]
#> $Table$Row[[17]]$Cell
#> [1] "69728"
#> [2] "103399857"
#> [3] "44368090"
#> [4] "Inactive"
#> [5] "Q01279"
#> [6] ""
#> [7] ""
#> [8] ""
#> [9] "Inhibition of epidermal growth factor receptor tyrosine kinase (EGFR TK) (inactive)"
#> [10] "Other"
#> [11] "14640561"
#> [12] ""
#>
#>
#> $Table$Row[[18]]
#> $Table$Row[[18]]$Cell
#> [1] "69729"
#> [2] "103167027"
#> [3] "5280343"
#> [4] "Unspecified"
#> [5] "Q01279"
#> [6] ""
#> [7] ""
#> [8] ""
#> [9] "Inhibition of epidermal growth factor (EGF) receptor from A431 cell membranes at 150 uM"
#> [10] "Other"
#> [11] "8201603"
#> [12] ""
#>
#>
#> $Table$Row[[19]]
#> $Table$Row[[19]]$Cell
#> [1] "69730"
#> [2] "103226434"
#> [3] "10318571"
#> [4] "Active"
#> [5] "Q01279"
#> [6] "IC50"
#> [7] "="
#> [8] "4"
#> [9] "Inhibition of epidermal growth factor receptor phosphorylation in BaF3 mouse lymphoid cells."
#> [10] "Confirmatory"
#> [11] "11462983"
#> [12] ""
#>
#>
#> $Table$Row[[20]]
#> $Table$Row[[20]]$Cell
#> [1] "69730"
#> [2] "103350640"
#> [3] "10406106"
#> [4] "Unspecified"
#> [5] "Q01279"
#> [6] "IC50"
#> [7] "="
#> [8] "14"
#> [9] "Inhibition of epidermal growth factor receptor phosphorylation in BaF3 mouse lymphoid cells."
#> [10] "Confirmatory"
#> [11] "11462983"
#> [12] ""
#>
#>
#> $Table$Row[[21]]
#> $Table$Row[[21]]$Cell
#> [1] "69730"
#> [2] "103378973"
#> [3] "10738302"
#> [4] "Unspecified"
#> [5] "Q01279"
#> [6] "IC50"
#> [7] "="
#> [8] "33"
#> [9] "Inhibition of epidermal growth factor receptor phosphorylation in BaF3 mouse lymphoid cells."
#> [10] "Confirmatory"
#> [11] "11462983"
#> [12] ""
#>
#>
#> $Table$Row[[22]]
#> $Table$Row[[22]]$Cell
#> [1] "69730"
#> [2] "103378974"
#> [3] "10761144"
#> [4] "Unspecified"
#> [5] "Q01279"
#> [6] "IC50"
#> [7] ">"
#> [8] "200"
#> [9] "Inhibition of epidermal growth factor receptor phosphorylation in BaF3 mouse lymphoid cells."
#> [10] "Confirmatory"
#> [11] "11462983"
#> [12] ""
#>
#>
#> $Table$Row[[23]]
#> $Table$Row[[23]]$Cell
#> [1] "69730"
#> [2] "103379003"
#> [3] "10044189"
#> [4] "Unspecified"
#> [5] "Q01279"
#> [6] "IC50"
#> [7] "="
#> [8] "500"
#> [9] "Inhibition of epidermal growth factor receptor phosphorylation in BaF3 mouse lymphoid cells."
#> [10] "Confirmatory"
#> [11] "11462983"
#> [12] ""
#>
#>
#> $Table$Row[[24]]
#> $Table$Row[[24]]$Cell
#> [1] "69730"
#> [2] "103379199"
#> [3] "10428841"
#> [4] "Active"
#> [5] "Q01279"
#> [6] "IC50"
#> [7] "="
#> [8] "8"
#> [9] "Inhibition of epidermal growth factor receptor phosphorylation in BaF3 mouse lymphoid cells."
#> [10] "Confirmatory"
#> [11] "11462983"
#> [12] ""
#>
#>
#> $Table$Row[[25]]
#> $Table$Row[[25]]$Cell
#> [1] "69730"
#> [2] "103379200"
#> [3] "10716388"
#> [4] "Unspecified"
#> [5] "Q01279"
#> [6] "IC50"
#> [7] ">"
#> [8] "100"
#> [9] "Inhibition of epidermal growth factor receptor phosphorylation in BaF3 mouse lymphoid cells."
#> [10] "Confirmatory"
#> [11] "11462983"
#> [12] ""
#>
#>
#> $Table$Row[[26]]
#> $Table$Row[[26]]$Cell
#> [1] "69730"
#> [2] "103379360"
#> [3] "10452792"
#> [4] "Unspecified"
#> [5] "Q01279"
#> [6] "IC50"
#> [7] ">"
#> [8] "50"
#> [9] "Inhibition of epidermal growth factor receptor phosphorylation in BaF3 mouse lymphoid cells."
#> [10] "Confirmatory"
#> [11] "11462983"
#> [12] ""
#>
#>
#> $Table$Row[[27]]
#> $Table$Row[[27]]$Cell
#> [1] "69730"
#> [2] "103379591"
#> [3] "10620637"
#> [4] "Unspecified"
#> [5] "Q01279"
#> [6] "IC50"
#> [7] "="
#> [8] "300"
#> [9] "Inhibition of epidermal growth factor receptor phosphorylation in BaF3 mouse lymphoid cells."
#> [10] "Confirmatory"
#> [11] "11462983"
#> [12] ""
#>
#>
#> $Table$Row[[28]]
#> $Table$Row[[28]]$Cell
#> [1] "69730"
#> [2] "103379616"
#> [3] "10593843"
#> [4] "Unspecified"
#> [5] "Q01279"
#> [6] "IC50"
#> [7] ">"
#> [8] "100"
#> [9] "Inhibition of epidermal growth factor receptor phosphorylation in BaF3 mouse lymphoid cells."
#> [10] "Confirmatory"
#> [11] "11462983"
#> [12] ""
#>
#>
#> $Table$Row[[29]]
#> $Table$Row[[29]]$Cell
#> [1] "69730"
#> [2] "103379617"
#> [3] "10787405"
#> [4] "Active"
#> [5] "Q01279"
#> [6] "IC50"
#> [7] "="
#> [8] "4"
#> [9] "Inhibition of epidermal growth factor receptor phosphorylation in BaF3 mouse lymphoid cells."
#> [10] "Confirmatory"
#> [11] "11462983"
#> [12] ""
#>
#>
#> $Table$Row[[30]]
#> $Table$Row[[30]]$Cell
#> [1] "69730"
#> [2] "103379660"
#> [3] "10343317"
#> [4] "Unspecified"
#> [5] "Q01279"
#> [6] "IC50"
#> [7] "="
#> [8] "35"
#> [9] "Inhibition of epidermal growth factor receptor phosphorylation in BaF3 mouse lymphoid cells."
#> [10] "Confirmatory"
#> [11] "11462983"
#> [12] ""
#>
#>
#> $Table$Row[[31]]
#> $Table$Row[[31]]$Cell
#> [1] "69730"
#> [2] "103379661"
#> [3] "10499929"
#> [4] "Unspecified"
#> [5] "Q01279"
#> [6] "IC50"
#> [7] "="
#> [8] "15"
#> [9] "Inhibition of epidermal growth factor receptor phosphorylation in BaF3 mouse lymphoid cells."
#> [10] "Confirmatory"
#> [11] "11462983"
#> [12] ""
#>
#>
#> $Table$Row[[32]]
#> $Table$Row[[32]]$Cell
#> [1] "69730"
#> [2] "103379682"
#> [3] "10500718"
#> [4] "Active"
#> [5] "Q01279"
#> [6] "IC50"
#> [7] "="
#> [8] "1"
#> [9] "Inhibition of epidermal growth factor receptor phosphorylation in BaF3 mouse lymphoid cells."
#> [10] "Confirmatory"
#> [11] "11462983"
#> [12] ""
#>
#>
#> $Table$Row[[33]]
#> $Table$Row[[33]]$Cell
#> [1] "69730"
#> [2] "103379908"
#> [3] "10619651"
#> [4] "Active"
#> [5] "Q01279"
#> [6] "IC50"
#> [7] "="
#> [8] "10"
#> [9] "Inhibition of epidermal growth factor receptor phosphorylation in BaF3 mouse lymphoid cells."
#> [10] "Confirmatory"
#> [11] "11462983"
#> [12] ""
#>
#>
#> $Table$Row[[34]]
#> $Table$Row[[34]]$Cell
#> [1] "69730"
#> [2] "103379909"
#> [3] "10504027"
#> [4] "Unspecified"
#> [5] "Q01279"
#> [6] "IC50"
#> [7] "="
#> [8] "35"
#> [9] "Inhibition of epidermal growth factor receptor phosphorylation in BaF3 mouse lymphoid cells."
#> [10] "Confirmatory"
#> [11] "11462983"
#> [12] ""
#>
#>
#> $Table$Row[[35]]
#> $Table$Row[[35]]$Cell
#> [1] "69730"
#> [2] "103379910"
#> [3] "10740438"
#> [4] "Unspecified"
#> [5] "Q01279"
#> [6] "IC50"
#> [7] "="
#> [8] "46"
#> [9] "Inhibition of epidermal growth factor receptor phosphorylation in BaF3 mouse lymphoid cells."
#> [10] "Confirmatory"
#> [11] "11462983"
#> [12] ""
#>
#>
#> $Table$Row[[36]]
#> $Table$Row[[36]]$Cell
#> [1] "106697"
#> [2] "103166113"
#> [3] "10499619"
#> [4] "Active"
#> [5] "Q01279"
#> [6] "IC50"
#> [7] "="
#> [8] "9.55"
#> [9] "Inhibition of EGF-dependent mouse keratinocyte MK cell proliferation"
#> [10] "Confirmatory"
#> [11] "10090785"
#> [12] ""
#>
#>
#> $Table$Row[[37]]
#> $Table$Row[[37]]$Cell
#> [1] "106697"
#> [2] "103166157"
#> [3] "9978638"
#> [4] "Active"
#> [5] "Q01279"
#> [6] "IC50"
#> [7] "="
#> [8] "4.93"
#> [9] "Inhibition of EGF-dependent mouse keratinocyte MK cell proliferation"
#> [10] "Confirmatory"
#> [11] "10090785"
#> [12] ""
#>
#>
#> $Table$Row[[38]]
#> $Table$Row[[38]]$Cell
#> [1] "106697"
#> [2] "103166217"
#> [3] "10590515"
#> [4] "Unspecified"
#> [5] "Q01279"
#> [6] "IC50"
#> [7] "="
#> [8] "45.2"
#> [9] "Inhibition of EGF-dependent mouse keratinocyte MK cell proliferation"
#> [10] "Confirmatory"
#> [11] "10090785"
#> [12] ""
#>
#>
#> $Table$Row[[39]]
#> $Table$Row[[39]]$Cell
#> [1] "106697"
#> [2] "103166266"
#> [3] "10803234"
#> [4] "Unspecified"
#> [5] "Q01279"
#> [6] "IC50"
#> [7] "="
#> [8] "10.2"
#> [9] "Inhibition of EGF-dependent mouse keratinocyte MK cell proliferation"
#> [10] "Confirmatory"
#> [11] "10090785"
#> [12] ""
#>
#>
#> $Table$Row[[40]]
#> $Table$Row[[40]]$Cell
#> [1] "106697"
#> [2] "103166322"
#> [3] "2051"
#> [4] "Active"
#> [5] "Q01279"
#> [6] "IC50"
#> [7] "<"
#> [8] "0.1"
#> [9] "Inhibition of EGF-dependent mouse keratinocyte MK cell proliferation"
#> [10] "Confirmatory"
#> [11] "10090785"
#> [12] ""
#>
#>
#> $Table$Row[[41]]
#> $Table$Row[[41]]$Cell
#> [1] "106697"
#> [2] "103166323"
#> [3] "10850934"
#> [4] "Unspecified"
#> [5] "Q01279"
#> [6] "IC50"
#> [7] "="
#> [8] "16"
#> [9] "Inhibition of EGF-dependent mouse keratinocyte MK cell proliferation"
#> [10] "Confirmatory"
#> [11] "10090785"
#> [12] ""
#>
#>
#> $Table$Row[[42]]
#> $Table$Row[[42]]$Cell
#> [1] "106697"
#> [2] "103166405"
#> [3] "9883384"
#> [4] "Active"
#> [5] "Q01279"
#> [6] "IC50"
#> [7] "="
#> [8] "2.83"
#> [9] "Inhibition of EGF-dependent mouse keratinocyte MK cell proliferation"
#> [10] "Confirmatory"
#> [11] "10090785"
#> [12] ""
#>
#>
#> $Table$Row[[43]]
#> $Table$Row[[43]]$Cell
#> [1] "106697"
#> [2] "103166415"
#> [3] "10494548"
#> [4] "Unspecified"
#> [5] "Q01279"
#> [6] "IC50"
#> [7] "="
#> [8] "11.4"
#> [9] "Inhibition of EGF-dependent mouse keratinocyte MK cell proliferation"
#> [10] "Confirmatory"
#> [11] "10090785"
#> [12] ""
#>
#>
#> $Table$Row[[44]]
#> $Table$Row[[44]]$Cell
#> [1] "106697"
#> [2] "103166416"
#> [3] "689033"
#> [4] "Unspecified"
#> [5] "Q01279"
#> [6] "IC50"
#> [7] "="
#> [8] "46.2"
#> [9] "Inhibition of EGF-dependent mouse keratinocyte MK cell proliferation"
#> [10] "Confirmatory"
#> [11] "10090785"
#> [12] ""
#>
#>
#> $Table$Row[[45]]
#> $Table$Row[[45]]$Cell
#> [1] "209326"
#> [2] "103257455"
#> [3] "2428"
#> [4] "Active"
#> [5] "Q01279"
#> [6] "IC50"
#> [7] "="
#> [8] "0.046"
#> [9] "Inhibition of EGF-mediated mitogenesis in Swiss 3T3 cells"
#> [10] "Confirmatory"
#> [11] "8632415"
#> [12] ""
#>
#>
#> $Table$Row[[46]]
#> $Table$Row[[46]]$Cell
#> [1] "241562"
#> [2] "103439646"
#> [3] "10209082"
#> [4] "Unspecified"
#> [5] "Q01279"
#> [6] "IC50"
#> [7] ">"
#> [8] "10"
#> [9] "Inhibition of Epidermal growth factor receptor in P19 cells"
#> [10] "Confirmatory"
#> [11] "15771419"
#> [12] ""
#>
#>
#> $Table$Row[[47]]
#> $Table$Row[[47]]$Cell
#> [1] "241562"
#> [2] "103439659"
#> [3] "10185160"
#> [4] "Unspecified"
#> [5] "Q01279"
#> [6] "IC50"
#> [7] ">"
#> [8] "10"
#> [9] "Inhibition of Epidermal growth factor receptor in P19 cells"
#> [10] "Confirmatory"
#> [11] "15771419"
#> [12] ""
#>
#>
#> $Table$Row[[48]]
#> $Table$Row[[48]]$Cell
#> [1] "241562"
#> [2] "103439663"
#> [3] "10143584"
#> [4] "Unspecified"
#> [5] "Q01279"
#> [6] "IC50"
#> [7] ">"
#> [8] "10"
#> [9] "Inhibition of Epidermal growth factor receptor in P19 cells"
#> [10] "Confirmatory"
#> [11] "15771419"
#> [12] ""
#>
#>
#> $Table$Row[[49]]
#> $Table$Row[[49]]$Cell
#> [1] "241562"
#> [2] "103439672"
#> [3] "10163439"
#> [4] "Unspecified"
#> [5] "Q01279"
#> [6] "IC50"
#> [7] ">"
#> [8] "10"
#> [9] "Inhibition of Epidermal growth factor receptor in P19 cells"
#> [10] "Confirmatory"
#> [11] "15771419"
#> [12] ""
#>
#>
#> $Table$Row[[50]]
#> $Table$Row[[50]]$Cell
#> [1] "241562"
#> [2] "103439700"
#> [3] "10302405"
#> [4] "Unspecified"
#> [5] "Q01279"
#> [6] "IC50"
#> [7] ">"
#> [8] "10"
#> [9] "Inhibition of Epidermal growth factor receptor in P19 cells"
#> [10] "Confirmatory"
#> [11] "15771419"
#> [12] ""
#>
#>
#> $Table$Row[[51]]
#> $Table$Row[[51]]$Cell
#> [1] "241562"
#> [2] "103439717"
#> [3] "10187378"
#> [4] "Unspecified"
#> [5] "Q01279"
#> [6] "IC50"
#> [7] ">"
#> [8] "10"
#> [9] "Inhibition of Epidermal growth factor receptor in P19 cells"
#> [10] "Confirmatory"
#> [11] "15771419"
#> [12] ""
#>
#>
#> $Table$Row[[52]]
#> $Table$Row[[52]]$Cell
#> [1] "241562"
#> [2] "123092436"
#> [3] "44259"
#> [4] "Unspecified"
#> [5] "Q01279"
#> [6] "IC50"
#> [7] ">"
#> [8] "10"
#> [9] "Inhibition of Epidermal growth factor receptor in P19 cells"
#> [10] "Confirmatory"
#> [11] "15771419"
#> [12] ""
#>
#>
#> $Table$Row[[53]]
#> $Table$Row[[53]]$Cell
#> [1] "241823"
#> [2] "103452251"
#> [3] "22732319"
#> [4] "Inconclusive"
#> [5] "Q01279"
#> [6] ""
#> [7] ""
#> [8] ""
#> [9] "Inhibition of Epidermal growth factor receptor tyrosine kinase activity; not tested"
#> [10] "Other"
#> [11] "15454232"
#> [12] ""
#>
#>
#> $Table$Row[[54]]
#> $Table$Row[[54]]$Cell
#> [1] "337238"
#> [2] "103194285"
#> [3] "4075"
#> [4] "Unspecified"
#> [5] "Q01279"
#> [6] ""
#> [7] ""
#> [8] ""
#> [9] "Inhibition of mouse EGFR by liquid scintillation counting"
#> [10] "Other"
#> [11] "2614420"
#> [12] ""
#>
#>
#> $Table$Row[[55]]
#> $Table$Row[[55]]$Cell
#> [1] "337238"
#> [2] "103227545"
#> [3] "5328552"
#> [4] "Unspecified"
#> [5] "Q01279"
#> [6] ""
#> [7] ""
#> [8] ""
#> [9] "Inhibition of mouse EGFR by liquid scintillation counting"
#> [10] "Other"
#> [11] "2614420"
#> [12] ""
#>
#>
#> $Table$Row[[56]]
#> $Table$Row[[56]]$Cell
#> [1] "337238"
#> [2] "103319670"
#> [3] "3894"
#> [4] "Unspecified"
#> [5] "Q01279"
#> [6] ""
#> [7] ""
#> [8] ""
#> [9] "Inhibition of mouse EGFR by liquid scintillation counting"
#> [10] "Other"
#> [11] "2614420"
#> [12] ""
#>
#>
#> $Table$Row[[57]]
#> $Table$Row[[57]]$Cell
#> [1] "337238"
#> [2] "103319671"
#> [3] "3896"
#> [4] "Unspecified"
#> [5] "Q01279"
#> [6] ""
#> [7] ""
#> [8] ""
#> [9] "Inhibition of mouse EGFR by liquid scintillation counting"
#> [10] "Other"
#> [11] "2614420"
#> [12] ""
#>
#>
#> $Table$Row[[58]]
#> $Table$Row[[58]]$Cell
#> [1] "337238"
#> [2] "103529702"
#> [3] "65083"
#> [4] "Unspecified"
#> [5] "Q01279"
#> [6] ""
#> [7] ""
#> [8] ""
#> [9] "Inhibition of mouse EGFR by liquid scintillation counting"
#> [10] "Other"
#> [11] "2614420"
#> [12] ""
#>
#>
#> $Table$Row[[59]]
#> $Table$Row[[59]]$Cell
#> [1] "337238"
#> [2] "103529722"
#> [3] "70949"
#> [4] "Unspecified"
#> [5] "Q01279"
#> [6] ""
#> [7] ""
#> [8] ""
#> [9] "Inhibition of mouse EGFR by liquid scintillation counting"
#> [10] "Other"
#> [11] "2614420"
#> [12] ""
#>
#>
#> $Table$Row[[60]]
#> $Table$Row[[60]]$Cell
#> [1] "337238"
#> [2] "103618685"
#> [3] "3895"
#> [4] "Unspecified"
#> [5] "Q01279"
#> [6] ""
#> [7] ""
#> [8] ""
#> [9] "Inhibition of mouse EGFR by liquid scintillation counting"
#> [10] "Other"
#> [11] "2614420"
#> [12] ""
#>
#>
#> $Table$Row[[61]]
#> $Table$Row[[61]]$Cell
#> [1] "337238"
#> [2] "103618686"
#> [3] "44593598"
#> [4] "Unspecified"
#> [5] "Q01279"
#> [6] ""
#> [7] ""
#> [8] ""
#> [9] "Inhibition of mouse EGFR by liquid scintillation counting"
#> [10] "Other"
#> [11] "2614420"
#> [12] ""
#>
#>
#> $Table$Row[[62]]
#> $Table$Row[[62]]$Cell
#> [1] "337238"
#> [2] "103618687"
#> [3] "44593599"
#> [4] "Unspecified"
#> [5] "Q01279"
#> [6] ""
#> [7] ""
#> [8] ""
#> [9] "Inhibition of mouse EGFR by liquid scintillation counting"
#> [10] "Other"
#> [11] "2614420"
#> [12] ""
#>
#>
#> $Table$Row[[63]]
#> $Table$Row[[63]]$Cell
#> [1] "337238"
#> [2] "103618691"
#> [3] "375472"
#> [4] "Unspecified"
#> [5] "Q01279"
#> [6] ""
#> [7] ""
#> [8] ""
#> [9] "Inhibition of mouse EGFR by liquid scintillation counting"
#> [10] "Other"
#> [11] "2614420"
#> [12] ""
#>
#>
#> $Table$Row[[64]]
#> $Table$Row[[64]]$Cell
#> [1] "337238"
#> [2] "123092436"
#> [3] "44259"
#> [4] "Unspecified"
#> [5] "Q01279"
#> [6] ""
#> [7] ""
#> [8] ""
#> [9] "Inhibition of mouse EGFR by liquid scintillation counting"
#> [10] "Other"
#> [11] "2614420"
#> [12] ""
#>
#>
#> $Table$Row[[65]]
#> $Table$Row[[65]]$Cell
#> [1] "337243"
#> [2] "103319670"
#> [3] "3894"
#> [4] "Active"
#> [5] "Q01279"
#> [6] ""
#> [7] ""
#> [8] ""
#> [9] "Inhibition of mouse EGFR using [32P]gammaATP as substrate by competitive Lineweaver-Burke plot"
#> [10] "Other"
#> [11] "2614420"
#> [12] ""
#>
#>
#> $Table$Row[[66]]
#> $Table$Row[[66]]$Cell
#> [1] "337244"
#> [2] "103319670"
#> [3] "3894"
#> [4] "Active"
#> [5] "Q01279"
#> [6] ""
#> [7] ""
#> [8] ""
#> [9] "Inhibition of mouse EGFR using tridecapeptide as substrate by uncompetitive Lineweaver-Burke plot"
#> [10] "Other"
#> [11] "2614420"
#> [12] ""
#>
#>
#> $Table$Row[[67]]
#> $Table$Row[[67]]$Cell
#> [1] "415757"
#> [2] "103294831"
#> [3] "5289418"
#> [4] "Active"
#> [5] "Q01279"
#> [6] ""
#> [7] ""
#> [8] ""
#> [9] "Inhibition of EGF-stimulated EGFR phosphorylation in mouse HER14 cells by immunoblotting"
#> [10] "Other"
#> [11] "9139660"
#> [12] ""
#>
#>
#> $Table$Row[[68]]
#> $Table$Row[[68]]$Cell
#> [1] "415757"
#> [2] "103295395"
#> [3] "5941540"
#> [4] "Active"
#> [5] "Q01279"
#> [6] ""
#> [7] ""
#> [8] ""
#> [9] "Inhibition of EGF-stimulated EGFR phosphorylation in mouse HER14 cells by immunoblotting"
#> [10] "Other"
#> [11] "9139660"
#> [12] ""
#>
#>
#> $Table$Row[[69]]
#> $Table$Row[[69]]$Cell
#> [1] "415758"
#> [2] "103294831"
#> [3] "5289418"
#> [4] "Active"
#> [5] "Q01279"
#> [6] ""
#> [7] ""
#> [8] ""
#> [9] "Inhibition of EGFR in mouse HER14 cells assessed as inhibition of EGF-stimulated Shc phosphorylation by immunoblotting"
#> [10] "Other"
#> [11] "9139660"
#> [12] ""
#>
#>
#> $Table$Row[[70]]
#> $Table$Row[[70]]$Cell
#> [1] "415758"
#> [2] "103295395"
#> [3] "5941540"
#> [4] "Active"
#> [5] "Q01279"
#> [6] ""
#> [7] ""
#> [8] ""
#> [9] "Inhibition of EGFR in mouse HER14 cells assessed as inhibition of EGF-stimulated Shc phosphorylation by immunoblotting"
#> [10] "Other"
#> [11] "9139660"
#> [12] ""
#>
#>
#> $Table$Row[[71]]
#> $Table$Row[[71]]$Cell
#> [1] "415759"
#> [2] "103294831"
#> [3] "5289418"
#> [4] "Active"
#> [5] "Q01279"
#> [6] ""
#> [7] ""
#> [8] ""
#> [9] "Inhibition of EGFR in mouse HER14 cells assessed as inhibition of EGF-stimulated ERK2 activation by immunoblotting"
#> [10] "Other"
#> [11] "9139660"
#> [12] ""
#>
#>
#> $Table$Row[[72]]
#> $Table$Row[[72]]$Cell
#> [1] "415759"
#> [2] "103295395"
#> [3] "5941540"
#> [4] "Active"
#> [5] "Q01279"
#> [6] ""
#> [7] ""
#> [8] ""
#> [9] "Inhibition of EGFR in mouse HER14 cells assessed as inhibition of EGF-stimulated ERK2 activation by immunoblotting"
#> [10] "Other"
#> [11] "9139660"
#> [12] ""
#>
#>
#> $Table$Row[[73]]
#> $Table$Row[[73]]$Cell
#> [1] "415760"
#> [2] "103294831"
#> [3] "5289418"
#> [4] "Inactive"
#> [5] "Q01279"
#> [6] ""
#> [7] ""
#> [8] ""
#> [9] "Inhibition of EGFR phosphorylation in mouse NIH/3T3 cells at 200 uM"
#> [10] "Other"
#> [11] "9139660"
#> [12] ""
#>
#>
#> $Table$Row[[74]]
#> $Table$Row[[74]]$Cell
#> [1] "415760"
#> [2] "103295395"
#> [3] "5941540"
#> [4] "Inactive"
#> [5] "Q01279"
#> [6] ""
#> [7] ""
#> [8] ""
#> [9] "Inhibition of EGFR phosphorylation in mouse NIH/3T3 cells at 200 uM"
#> [10] "Other"
#> [11] "9139660"
#> [12] ""
#>
#>
#> $Table$Row[[75]]
#> $Table$Row[[75]]$Cell
#> [1] "1053208"
#> [2] "152302885"
#> [3] ""
#> [4] "Inactive"
#> [5] ""
#> [6] ""
#> [7] ""
#> [8] ""
#> [9] "A screen to identify the genes that modify the response of osteosarcoma to doxorubicin in mouse - Primary Screen"
#> [10] "Screening"
#> [11] "25862761"
#> [12] "1"
#>
#>
#> $Table$Row[[76]]
#> $Table$Row[[76]]$Cell
#> [1] "1224826"
#> [2] "315466459"
#> [3] ""
#> [4] "Inactive"
#> [5] ""
#> [6] ""
#> [7] ""
#> [8] ""
#> [9] "Genome-wide siRNA screen of genes regulating the Lipopolysaccharide-induced NF-kappaB and TNF-alpha responses in mouse macrophages_Primary screen TNF readout"
#> [10] "Summary"
#> [11] ""
#> [12] "1"
#>
#>
#> $Table$Row[[77]]
#> $Table$Row[[77]]$Cell
#> [1] "1224828"
#> [2] "315466459"
#> [3] ""
#> [4] "Inactive"
#> [5] ""
#> [6] ""
#> [7] ""
#> [8] ""
#> [9] "Genome-wide siRNA screen of genes regulating the Lipopolysaccharide-induced NF-kappaB and TNF-alpha responses in mouse macrophages_Primary screen NFkB readout"
#> [10] "Summary"
#> [11] ""
#> [12] "1"
#>
#>
#> $Table$Row[[78]]
#> $Table$Row[[78]]$Cell
#> [1] "1527521"
#> [2] "312367127"
#> [3] "71496458"
#> [4] "Active"
#> [5] "Q01279"
#> [6] "IC50"
#> [7] "="
#> [8] "0.081"
#> [9] "Inhibition of wild type EGFR in mouse BAF3 cells assessed as reduction in cell proliferation incubated for 72 hrs by Celltiter-Glo luminescent cell viability assay"
#> [10] "Confirmatory"
#> [11] "31689114"
#> [12] ""
#>
#>
#> $Table$Row[[79]]
#> $Table$Row[[79]]$Cell
#> [1] "1527521"
#> [2] "440110169"
#> [3] "139593669"
#> [4] "Unspecified"
#> [5] "Q01279"
#> [6] "IC50"
#> [7] ">"
#> [8] "10"
#> [9] "Inhibition of wild type EGFR in mouse BAF3 cells assessed as reduction in cell proliferation incubated for 72 hrs by Celltiter-Glo luminescent cell viability assay"
#> [10] "Confirmatory"
#> [11] "31689114"
#> [12] ""
#>
#>
#> $Table$Row[[80]]
#> $Table$Row[[80]]$Cell
#> [1] "1527521"
#> [2] "440119817"
#> [3] "155517202"
#> [4] "Inconclusive"
#> [5] "Q01279"
#> [6] "IC50"
#> [7] ""
#> [8] ""
#> [9] "Inhibition of wild type EGFR in mouse BAF3 cells assessed as reduction in cell proliferation incubated for 72 hrs by Celltiter-Glo luminescent cell viability assay"
#> [10] "Confirmatory"
#> [11] "31689114"
#> [12] ""
#>
#>
#> $Table$Row[[81]]
#> $Table$Row[[81]]$Cell
#> [1] "1527521"
#> [2] "440125045"
#> [3] "139447864"
#> [4] "Active"
#> [5] "Q01279"
#> [6] "IC50"
#> [7] "="
#> [8] "3.6"
#> [9] "Inhibition of wild type EGFR in mouse BAF3 cells assessed as reduction in cell proliferation incubated for 72 hrs by Celltiter-Glo luminescent cell viability assay"
#> [10] "Confirmatory"
#> [11] "31689114"
#> [12] ""
#>
#>
#> $Table$Row[[82]]
#> $Table$Row[[82]]$Cell
#> [1] "1527521"
#> [2] "440160302"
#> [3] "139593670"
#> [4] "Active"
#> [5] "Q01279"
#> [6] "IC50"
#> [7] "="
#> [8] "1.3"
#> [9] "Inhibition of wild type EGFR in mouse BAF3 cells assessed as reduction in cell proliferation incubated for 72 hrs by Celltiter-Glo luminescent cell viability assay"
#> [10] "Confirmatory"
#> [11] "31689114"
#> [12] ""
#>
#>
#> $Table$Row[[83]]
#> $Table$Row[[83]]$Cell
#> [1] "1527521"
#> [2] "440163841"
#> [3] "139447649"
#> [4] "Active"
#> [5] "Q01279"
#> [6] "IC50"
#> [7] "="
#> [8] "5.1"
#> [9] "Inhibition of wild type EGFR in mouse BAF3 cells assessed as reduction in cell proliferation incubated for 72 hrs by Celltiter-Glo luminescent cell viability assay"
#> [10] "Confirmatory"
#> [11] "31689114"
#> [12] ""
#>
#>
#> $Table$Row[[84]]
#> $Table$Row[[84]]$Cell
#> [1] "1527521"
#> [2] "440172005"
#> [3] "139447554"
#> [4] "Active"
#> [5] "Q01279"
#> [6] "IC50"
#> [7] "="
#> [8] "0.7"
#> [9] "Inhibition of wild type EGFR in mouse BAF3 cells assessed as reduction in cell proliferation incubated for 72 hrs by Celltiter-Glo luminescent cell viability assay"
#> [10] "Confirmatory"
#> [11] "31689114"
#> [12] ""
#>
#>
#> $Table$Row[[85]]
#> $Table$Row[[85]]$Cell
#> [1] "1527521"
#> [2] "440176009"
#> [3] "139600318"
#> [4] "Active"
#> [5] "Q01279"
#> [6] "IC50"
#> [7] "="
#> [8] "0.19"
#> [9] "Inhibition of wild type EGFR in mouse BAF3 cells assessed as reduction in cell proliferation incubated for 72 hrs by Celltiter-Glo luminescent cell viability assay"
#> [10] "Confirmatory"
#> [11] "31689114"
#> [12] ""
#>
#>
#> $Table$Row[[86]]
#> $Table$Row[[86]]$Cell
#> [1] "1527521"
#> [2] "440182946"
#> [3] "155444794"
#> [4] "Active"
#> [5] "Q01279"
#> [6] "IC50"
#> [7] "="
#> [8] "2.3"
#> [9] "Inhibition of wild type EGFR in mouse BAF3 cells assessed as reduction in cell proliferation incubated for 72 hrs by Celltiter-Glo luminescent cell viability assay"
#> [10] "Confirmatory"
#> [11] "31689114"
#> [12] ""
#>
#>
#> $Table$Row[[87]]
#> $Table$Row[[87]]$Cell
#> [1] "1527521"
#> [2] "440203081"
#> [3] "155444797"
#> [4] "Active"
#> [5] "Q01279"
#> [6] "IC50"
#> [7] "="
#> [8] "1.1"
#> [9] "Inhibition of wild type EGFR in mouse BAF3 cells assessed as reduction in cell proliferation incubated for 72 hrs by Celltiter-Glo luminescent cell viability assay"
#> [10] "Confirmatory"
#> [11] "31689114"
#> [12] ""
#>
#>
#> $Table$Row[[88]]
#> $Table$Row[[88]]$Cell
#> [1] "1527521"
#> [2] "440207922"
#> [3] "155444848"
#> [4] "Active"
#> [5] "Q01279"
#> [6] "IC50"
#> [7] "="
#> [8] "0.27"
#> [9] "Inhibition of wild type EGFR in mouse BAF3 cells assessed as reduction in cell proliferation incubated for 72 hrs by Celltiter-Glo luminescent cell viability assay"
#> [10] "Confirmatory"
#> [11] "31689114"
#> [12] ""
#>
#>
#> $Table$Row[[89]]
#> $Table$Row[[89]]$Cell
#> [1] "1527521"
#> [2] "440227038"
#> [3] "139593668"
#> [4] "Inconclusive"
#> [5] "Q01279"
#> [6] "IC50"
#> [7] ""
#> [8] ""
#> [9] "Inhibition of wild type EGFR in mouse BAF3 cells assessed as reduction in cell proliferation incubated for 72 hrs by Celltiter-Glo luminescent cell viability assay"
#> [10] "Confirmatory"
#> [11] "31689114"
#> [12] ""
#>
#>
#> $Table$Row[[90]]
#> $Table$Row[[90]]$Cell
#> [1] "1740135"
#> [2] "312367127"
#> [3] "71496458"
#> [4] "Active"
#> [5] "Q01279"
#> [6] "GI50"
#> [7] "="
#> [8] "2.6"
#> [9] "Inhibition of wild type EGFR in mouse BaF3 cells assessed as reduction in cell proliferation incubated for 72 hrs by Celltiter-Glo luminescent cell viability assay"
#> [10] "Confirmatory"
#> [11] "32619886"
#> [12] ""
#>
#>
#> $Table$Row[[91]]
#> $Table$Row[[91]]$Cell
#> [1] "1740135"
#> [2] "461515468"
#> [3] "162643657"
#> [4] "Inconclusive"
#> [5] "Q01279"
#> [6] "GI50"
#> [7] ""
#> [8] ""
#> [9] "Inhibition of wild type EGFR in mouse BaF3 cells assessed as reduction in cell proliferation incubated for 72 hrs by Celltiter-Glo luminescent cell viability assay"
#> [10] "Confirmatory"
#> [11] "32619886"
#> [12] ""
#>
#>
#> $Table$Row[[92]]
#> $Table$Row[[92]]$Cell
#> [1] "1740135"
#> [2] "461515649"
#> [3] "162643790"
#> [4] "Active"
#> [5] "Q01279"
#> [6] "GI50"
#> [7] "="
#> [8] "9.23"
#> [9] "Inhibition of wild type EGFR in mouse BaF3 cells assessed as reduction in cell proliferation incubated for 72 hrs by Celltiter-Glo luminescent cell viability assay"
#> [10] "Confirmatory"
#> [11] "32619886"
#> [12] ""
#>
#>
#> $Table$Row[[93]]
#> $Table$Row[[93]]$Cell
#> [1] "1740135"
#> [2] "461542097"
#> [3] "162662364"
#> [4] "Active"
#> [5] "Q01279"
#> [6] "GI50"
#> [7] "="
#> [8] "3.91"
#> [9] "Inhibition of wild type EGFR in mouse BaF3 cells assessed as reduction in cell proliferation incubated for 72 hrs by Celltiter-Glo luminescent cell viability assay"
#> [10] "Confirmatory"
#> [11] "32619886"
#> [12] ""
#>
#>
#> $Table$Row[[94]]
#> $Table$Row[[94]]$Cell
#> [1] "1740135"
#> [2] "461543217"
#> [3] "162663118"
#> [4] "Unspecified"
#> [5] "Q01279"
#> [6] "GI50"
#> [7] ">"
#> [8] "10"
#> [9] "Inhibition of wild type EGFR in mouse BaF3 cells assessed as reduction in cell proliferation incubated for 72 hrs by Celltiter-Glo luminescent cell viability assay"
#> [10] "Confirmatory"
#> [11] "32619886"
#> [12] ""
#>
#>
#> $Table$Row[[95]]
#> $Table$Row[[95]]$Cell
#> [1] "1740135"
#> [2] "461546315"
#> [3] "162665339"
#> [4] "Unspecified"
#> [5] "Q01279"
#> [6] "GI50"
#> [7] ">"
#> [8] "10"
#> [9] "Inhibition of wild type EGFR in mouse BaF3 cells assessed as reduction in cell proliferation incubated for 72 hrs by Celltiter-Glo luminescent cell viability assay"
#> [10] "Confirmatory"
#> [11] "32619886"
#> [12] ""
#>
#>
#> $Table$Row[[96]]
#> $Table$Row[[96]]$Cell
#> [1] "1740135"
#> [2] "461547480"
#> [3] "162666122"
#> [4] "Active"
#> [5] "Q01279"
#> [6] "GI50"
#> [7] "="
#> [8] "4.27"
#> [9] "Inhibition of wild type EGFR in mouse BaF3 cells assessed as reduction in cell proliferation incubated for 72 hrs by Celltiter-Glo luminescent cell viability assay"
#> [10] "Confirmatory"
#> [11] "32619886"
#> [12] ""
#>
#>
#> $Table$Row[[97]]
#> $Table$Row[[97]]$Cell
#> [1] "1740135"
#> [2] "461549927"
#> [3] "162667840"
#> [4] "Active"
#> [5] "Q01279"
#> [6] "GI50"
#> [7] "="
#> [8] "3.79"
#> [9] "Inhibition of wild type EGFR in mouse BaF3 cells assessed as reduction in cell proliferation incubated for 72 hrs by Celltiter-Glo luminescent cell viability assay"
#> [10] "Confirmatory"
#> [11] "32619886"
#> [12] ""
#>
#>
#> $Table$Row[[98]]
#> $Table$Row[[98]]$Cell
#> [1] "1740135"
#> [2] "461550238"
#> [3] "162668052"
#> [4] "Active"
#> [5] "Q01279"
#> [6] "GI50"
#> [7] "="
#> [8] "2.65"
#> [9] "Inhibition of wild type EGFR in mouse BaF3 cells assessed as reduction in cell proliferation incubated for 72 hrs by Celltiter-Glo luminescent cell viability assay"
#> [10] "Confirmatory"
#> [11] "32619886"
#> [12] ""
#>
#>
#> $Table$Row[[99]]
#> $Table$Row[[99]]$Cell
#> [1] "1740135"
#> [2] "461550466"
#> [3] "162668204"
#> [4] "Unspecified"
#> [5] "Q01279"
#> [6] "GI50"
#> [7] ">"
#> [8] "10"
#> [9] "Inhibition of wild type EGFR in mouse BaF3 cells assessed as reduction in cell proliferation incubated for 72 hrs by Celltiter-Glo luminescent cell viability assay"
#> [10] "Confirmatory"
#> [11] "32619886"
#> [12] ""
#>
#>
#> $Table$Row[[100]]
#> $Table$Row[[100]]$Cell
#> [1] "1740135"
#> [2] "461555362"
#> [3] "162671649"
#> [4] "Inconclusive"
#> [5] "Q01279"
#> [6] "GI50"
#> [7] ""
#> [8] ""
#> [9] "Inhibition of wild type EGFR in mouse BaF3 cells assessed as reduction in cell proliferation incubated for 72 hrs by Celltiter-Glo luminescent cell viability assay"
#> [10] "Confirmatory"
#> [11] "32619886"
#> [12] ""
#>
#>
#> $Table$Row[[101]]
#> $Table$Row[[101]]$Cell
#> [1] "1740135"
#> [2] "461557317"
#> [3] "162673094"
#> [4] "Active"
#> [5] "Q01279"
#> [6] "GI50"
#> [7] "="
#> [8] "9.23"
#> [9] "Inhibition of wild type EGFR in mouse BaF3 cells assessed as reduction in cell proliferation incubated for 72 hrs by Celltiter-Glo luminescent cell viability assay"
#> [10] "Confirmatory"
#> [11] "32619886"
#> [12] ""
#>
#>
#> $Table$Row[[102]]
#> $Table$Row[[102]]$Cell
#> [1] "1740135"
#> [2] "461557891"
#> [3] "162673491"
#> [4] "Active"
#> [5] "Q01279"
#> [6] "GI50"
#> [7] "="
#> [8] "3.79"
#> [9] "Inhibition of wild type EGFR in mouse BaF3 cells assessed as reduction in cell proliferation incubated for 72 hrs by Celltiter-Glo luminescent cell viability assay"
#> [10] "Confirmatory"
#> [11] "32619886"
#> [12] ""
#>
#>
#> $Table$Row[[103]]
#> $Table$Row[[103]]$Cell
#> [1] "1740135"
#> [2] "461558880"
#> [3] "162674154"
#> [4] "Inconclusive"
#> [5] "Q01279"
#> [6] "GI50"
#> [7] ""
#> [8] ""
#> [9] "Inhibition of wild type EGFR in mouse BaF3 cells assessed as reduction in cell proliferation incubated for 72 hrs by Celltiter-Glo luminescent cell viability assay"
#> [10] "Confirmatory"
#> [11] "32619886"
#> [12] ""
#>
#>
#> $Table$Row[[104]]
#> $Table$Row[[104]]$Cell
#> [1] "1740135"
#> [2] "461562991"
#> [3] "162677073"
#> [4] "Unspecified"
#> [5] "Q01279"
#> [6] "GI50"
#> [7] ">"
#> [8] "10"
#> [9] "Inhibition of wild type EGFR in mouse BaF3 cells assessed as reduction in cell proliferation incubated for 72 hrs by Celltiter-Glo luminescent cell viability assay"
#> [10] "Confirmatory"
#> [11] "32619886"
#> [12] ""
#>
#>
#> $Table$Row[[105]]
#> $Table$Row[[105]]$Cell
#> [1] "1815786"
#> [2] "475982343"
#> [3] "166627448"
#> [4] "Unspecified"
#> [5] "Q01279"
#> [6] ""
#> [7] ""
#> [8] ""
#> [9] "Inhibition of EGFR phosphorylation in mouse BaF3 cells expressing EGFR 19Del/T790M/C797S triple mutant measured after 2 hrs by Western blotting"
#> [10] "Other"
#> [11] "35178175"
#> [12] ""
#>
#>
#> $Table$Row[[106]]
#> $Table$Row[[106]]$Cell
#> [1] "1815820"
#> [2] "475982343"
#> [3] "166627448"
#> [4] "Unspecified"
#> [5] "Q01279"
#> [6] ""
#> [7] ""
#> [8] ""
#> [9] "Inhibition of EGFR phosphorylation in mouse BaF3 cells expressing EGFR L858R/T790M/C797S triple mutant measured after 2 hrs by Western blotting"
#> [10] "Other"
#> [11] "35178175"
#> [12] ""
#>
#>
#> $Table$Row[[107]]
#> $Table$Row[[107]]$Cell
#> [1] "1862914"
#> [2] "482063640"
#> [3] "155431347"
#> [4] "Active"
#> [5] "Q01279"
#> [6] ""
#> [7] ""
#> [8] ""
#> [9] "In vivo inhibition of EGFR phosphorylation in nude mouse implanted with mouse BaF3 cells harboring EGFR del18/T790M/C797S triple mutant at 20 mg/kg, po administered as single dose and measured upto 24 hrs by Western blot analysis"
#> [10] "Other"
#> [11] "35810715"
#> [12] ""
#>
#>
#> $Table$Row[[108]]
#> $Table$Row[[108]]$Cell
#> [1] "1896806"
#> [2] "482061797"
#> [3] "166176964"
#> [4] "Unspecified"
#> [5] "Q01279"
#> [6] ""
#> [7] ""
#> [8] ""
#> [9] "Inhibition of Wild type EGFR in mouse BaF3 cells assessed as protein phosphorylation at 10 to 1000 nM incubated for 8 hrs by Western blot analysis"
#> [10] "Other"
#> [11] "36384036"
#> [12] ""
#>
#>
#> $Table$Row[[109]]
#> $Table$Row[[109]]$Cell
#> [1] "1896806"
#> [2] "482062269"
#> [3] "168280117"
#> [4] "Unspecified"
#> [5] "Q01279"
#> [6] ""
#> [7] ""
#> [8] ""
#> [9] "Inhibition of Wild type EGFR in mouse BaF3 cells assessed as protein phosphorylation at 10 to 1000 nM incubated for 8 hrs by Western blot analysis"
#> [10] "Other"
#> [11] "36384036"
#> [12] ""
#>
#>
#> $Table$Row[[110]]
#> $Table$Row[[110]]$Cell
#> [1] "1972653"
#> [2] "174505192"
#> [3] "11511120"
#> [4] "Active"
#> [5] "Q01279"
#> [6] "IC50"
#> [7] "="
#> [8] "0.01995"
#> [9] "Inhibition of C-terminal his6-tagged mouse EGFR by TR-FRET assay"
#> [10] "Confirmatory"
#> [11] "37647129"
#> [12] ""
#>
#>
#> $Table$Row[[111]]
#> $Table$Row[[111]]$Cell
#> [1] "1972653"
#> [2] "504828024"
#> [3] "172462736"
#> [4] "Active"
#> [5] "Q01279"
#> [6] "IC50"
#> [7] "="
#> [8] "0.05012"
#> [9] "Inhibition of C-terminal his6-tagged mouse EGFR by TR-FRET assay"
#> [10] "Confirmatory"
#> [11] "37647129"
#> [12] ""
#>
#>
#> $Table$Row[[112]]
#> $Table$Row[[112]]$Cell
#> [1] "1972653"
#> [2] "504838405"
#> [3] "172470044"
#> [4] "Active"
#> [5] "Q01279"
#> [6] "IC50"
#> [7] "="
#> [8] "0.15849"
#> [9] "Inhibition of C-terminal his6-tagged mouse EGFR by TR-FRET assay"
#> [10] "Confirmatory"
#> [11] "37647129"
#> [12] ""
#>
#>
#> $Table$Row[[113]]
#> $Table$Row[[113]]$Cell
#> [1] "1972653"
#> [2] "504840308"
#> [3] "172471323"
#> [4] "Active"
#> [5] "Q01279"
#> [6] "IC50"
#> [7] "="
#> [8] "0.007943"
#> [9] "Inhibition of C-terminal his6-tagged mouse EGFR by TR-FRET assay"
#> [10] "Confirmatory"
#> [11] "37647129"
#> [12] ""
#>
#>
#> $Table$Row[[114]]
#> $Table$Row[[114]]$Cell
#> [1] "1975403"
#> [2] "440197370"
#> [3] "25740"
#> [4] "Unspecified"
#> [5] "Q01279"
#> [6] "IC50"
#> [7] "="
#> [8] "199.526"
#> [9] "Displacement of probe N-(4-(4-(3-((4-((3-chloro-4-fluorophenyl)amino)-7-methoxyquinazolin-6-yl)oxy)propyl)piperazin-1-yl)-4-oxobutyl)-3-(5,5-difluoro-7,9-dimethyl-5H-5l4,6l4-dipyrrolo[1,2-c:2',1'-f][1,3,2]diazaborinin-3-yl)propenamide from C-terminal His-tagged wild type mouse EGFR incubated for 30 mins by probe displacement based TR-FRET assay"
#> [10] "Confirmatory"
#> [11] "37418825"
#> [12] ""
#>
#>
#> $Table$Row[[115]]
#> $Table$Row[[115]]$Cell
#> [1] "1975403"
#> [2] "504793989"
#> [3] "28958571"
#> [4] "Unspecified"
#> [5] "Q01279"
#> [6] "IC50"
#> [7] ">"
#> [8] "1000"
#> [9] "Displacement of probe N-(4-(4-(3-((4-((3-chloro-4-fluorophenyl)amino)-7-methoxyquinazolin-6-yl)oxy)propyl)piperazin-1-yl)-4-oxobutyl)-3-(5,5-difluoro-7,9-dimethyl-5H-5l4,6l4-dipyrrolo[1,2-c:2',1'-f][1,3,2]diazaborinin-3-yl)propenamide from C-terminal His-tagged wild type mouse EGFR incubated for 30 mins by probe displacement based TR-FRET assay"
#> [10] "Confirmatory"
#> [11] "37418825"
#> [12] ""
#>
#>
#> $Table$Row[[116]]
#> $Table$Row[[116]]$Cell
#> [1] "1975403"
#> [2] "504810459"
#> [3] "172450561"
#> [4] "Unspecified"
#> [5] "Q01279"
#> [6] "IC50"
#> [7] "="
#> [8] "125.893"
#> [9] "Displacement of probe N-(4-(4-(3-((4-((3-chloro-4-fluorophenyl)amino)-7-methoxyquinazolin-6-yl)oxy)propyl)piperazin-1-yl)-4-oxobutyl)-3-(5,5-difluoro-7,9-dimethyl-5H-5l4,6l4-dipyrrolo[1,2-c:2',1'-f][1,3,2]diazaborinin-3-yl)propenamide from C-terminal His-tagged wild type mouse EGFR incubated for 30 mins by probe displacement based TR-FRET assay"
#> [10] "Confirmatory"
#> [11] "37418825"
#> [12] ""
#>
#>
#> $Table$Row[[117]]
#> $Table$Row[[117]]$Cell
#> [1] "1975403"
#> [2] "504811151"
#> [3] "16645749"
#> [4] "Unspecified"
#> [5] "Q01279"
#> [6] "IC50"
#> [7] "="
#> [8] "398.107"
#> [9] "Displacement of probe N-(4-(4-(3-((4-((3-chloro-4-fluorophenyl)amino)-7-methoxyquinazolin-6-yl)oxy)propyl)piperazin-1-yl)-4-oxobutyl)-3-(5,5-difluoro-7,9-dimethyl-5H-5l4,6l4-dipyrrolo[1,2-c:2',1'-f][1,3,2]diazaborinin-3-yl)propenamide from C-terminal His-tagged wild type mouse EGFR incubated for 30 mins by probe displacement based TR-FRET assay"
#> [10] "Confirmatory"
#> [11] "37418825"
#> [12] ""
#>
#>
#> $Table$Row[[118]]
#> $Table$Row[[118]]$Cell
#> [1] "1975403"
#> [2] "504817004"
#> [3] "172455097"
#> [4] "Unspecified"
#> [5] "Q01279"
#> [6] "IC50"
#> [7] ">"
#> [8] "1000"
#> [9] "Displacement of probe N-(4-(4-(3-((4-((3-chloro-4-fluorophenyl)amino)-7-methoxyquinazolin-6-yl)oxy)propyl)piperazin-1-yl)-4-oxobutyl)-3-(5,5-difluoro-7,9-dimethyl-5H-5l4,6l4-dipyrrolo[1,2-c:2',1'-f][1,3,2]diazaborinin-3-yl)propenamide from C-terminal His-tagged wild type mouse EGFR incubated for 30 mins by probe displacement based TR-FRET assay"
#> [10] "Confirmatory"
#> [11] "37418825"
#> [12] ""
#>
#>
#> $Table$Row[[119]]
#> $Table$Row[[119]]$Cell
#> [1] "1975403"
#> [2] "504824391"
#> [3] "116653986"
#> [4] "Unspecified"
#> [5] "Q01279"
#> [6] "IC50"
#> [7] ">"
#> [8] "1000"
#> [9] "Displacement of probe N-(4-(4-(3-((4-((3-chloro-4-fluorophenyl)amino)-7-methoxyquinazolin-6-yl)oxy)propyl)piperazin-1-yl)-4-oxobutyl)-3-(5,5-difluoro-7,9-dimethyl-5H-5l4,6l4-dipyrrolo[1,2-c:2',1'-f][1,3,2]diazaborinin-3-yl)propenamide from C-terminal His-tagged wild type mouse EGFR incubated for 30 mins by probe displacement based TR-FRET assay"
#> [10] "Confirmatory"
#> [11] "37418825"
#> [12] ""
#>
#>
#> $Table$Row[[120]]
#> $Table$Row[[120]]$Cell
#> [1] "1975403"
#> [2] "504828130"
#> [3] "47401324"
#> [4] "Unspecified"
#> [5] "Q01279"
#> [6] "IC50"
#> [7] "="
#> [8] "794.328"
#> [9] "Displacement of probe N-(4-(4-(3-((4-((3-chloro-4-fluorophenyl)amino)-7-methoxyquinazolin-6-yl)oxy)propyl)piperazin-1-yl)-4-oxobutyl)-3-(5,5-difluoro-7,9-dimethyl-5H-5l4,6l4-dipyrrolo[1,2-c:2',1'-f][1,3,2]diazaborinin-3-yl)propenamide from C-terminal His-tagged wild type mouse EGFR incubated for 30 mins by probe displacement based TR-FRET assay"
#> [10] "Confirmatory"
#> [11] "37418825"
#> [12] ""
#>
#>
#> $Table$Row[[121]]
#> $Table$Row[[121]]$Cell
#> [1] "1975403"
#> [2] "504839027"
#> [3] "110755096"
#> [4] "Unspecified"
#> [5] "Q01279"
#> [6] "IC50"
#> [7] "="
#> [8] "100"
#> [9] "Displacement of probe N-(4-(4-(3-((4-((3-chloro-4-fluorophenyl)amino)-7-methoxyquinazolin-6-yl)oxy)propyl)piperazin-1-yl)-4-oxobutyl)-3-(5,5-difluoro-7,9-dimethyl-5H-5l4,6l4-dipyrrolo[1,2-c:2',1'-f][1,3,2]diazaborinin-3-yl)propenamide from C-terminal His-tagged wild type mouse EGFR incubated for 30 mins by probe displacement based TR-FRET assay"
#> [10] "Confirmatory"
#> [11] "37418825"
#> [12] ""
#>
#>
#> $Table$Row[[122]]
#> $Table$Row[[122]]$Cell
#> [1] "1977970"
#> [2] "312367127"
#> [3] "71496458"
#> [4] "Active"
#> [5] "Q01279"
#> [6] "IC50"
#> [7] "="
#> [8] "0.009"
#> [9] "Inhibition of wild type EGFR in mouse BaF3 cells assessed as cell growth inhibition measured after 72 hrs by CellTiter-Glo assay"
#> [10] "Confirmatory"
#> [11] "37952262"
#> [12] ""
#>
#>
#> $Table$Row[[123]]
#> $Table$Row[[123]]$Cell
#> [1] "1977970"
#> [2] "404712229"
#> [3] "45370166"
#> [4] "Unspecified"
#> [5] "Q01279"
#> [6] "IC50"
#> [7] ">"
#> [8] "10"
#> [9] "Inhibition of wild type EGFR in mouse BaF3 cells assessed as cell growth inhibition measured after 72 hrs by CellTiter-Glo assay"
#> [10] "Confirmatory"
#> [11] "37952262"
#> [12] ""
#>
#>
#> $Table$Row[[124]]
#> $Table$Row[[124]]$Cell
#> [1] "1977970"
#> [2] "504823183"
#> [3] "169450484"
#> [4] "Active"
#> [5] "Q01279"
#> [6] "IC50"
#> [7] "="
#> [8] "1.45"
#> [9] "Inhibition of wild type EGFR in mouse BaF3 cells assessed as cell growth inhibition measured after 72 hrs by CellTiter-Glo assay"
#> [10] "Confirmatory"
#> [11] "37952262"
#> [12] ""result <- get_pug_rest(identifier = "13649", namespace = "geneid", domain = "gene", operation = "pwaccs", output = "TXT")
result
#>
#> An object of class 'PugRestInstance'
#>
#> Request Details:
#> - Domain: Gene
#> - Namespace: DomainSpecific
#> - Operation: pwaccs
#> - Identifier: 13649
#>
#> NOTE: Run getter function 'pubChemData(...)' to extract raw data retrieved from PubChem Database.
#> See ?pubChemData for details.pubChemData(result)
#> Text
#> 1 PANTHER:P06664
#> 2 PathBank:SMP0120900
#> 3 PathBank:SMP0120901
#> 4 Reactome:R-MMU-1227986
#> 5 Reactome:R-MMU-1236394
#> 6 Reactome:R-MMU-1266738
#> 7 Reactome:R-MMU-157118
#> 8 Reactome:R-MMU-162582
#> 9 Reactome:R-MMU-177929
#> 10 Reactome:R-MMU-179812
#> 11 Reactome:R-MMU-180292
#> 12 Reactome:R-MMU-180336
#> 13 Reactome:R-MMU-182971
#> 14 Reactome:R-MMU-199991
#> 15 Reactome:R-MMU-212718
#> 16 Reactome:R-MMU-2179392
#> 17 Reactome:R-MMU-372790
#> 18 Reactome:R-MMU-373760
#> 19 Reactome:R-MMU-388396
#> 20 Reactome:R-MMU-416476
#> 21 Reactome:R-MMU-422475
#> 22 Reactome:R-MMU-445144
#> 23 Reactome:R-MMU-5653656
#> 24 Reactome:R-MMU-881907
#> 25 Reactome:R-MMU-8848021
#> 26 Reactome:R-MMU-8856825
#> 27 Reactome:R-MMU-8856828
#> 28 Reactome:R-MMU-8857538
#> 29 Reactome:R-MMU-8939211
#> 30 Reactome:R-MMU-9006927
#> 31 Reactome:R-MMU-9006931
#> 32 Reactome:R-MMU-9006934
#> 33 Reactome:R-MMU-9009391
#> 34 Reactome:R-MMU-9012852
#> 35 Reactome:R-MMU-9013507
#> 36 Reactome:R-MMU-9675108
#> 37 WikiPathways:WP1261
#> 38 WikiPathways:WP265
#> 39 WikiPathways:WP2841
#> 40 WikiPathways:WP339
#> 41 WikiPathways:WP3663
#> 42 WikiPathways:WP488
#> 43 WikiPathways:WP493
#> 44 WikiPathways:WP523
#> 45 WikiPathways:WP5242
#> 46 WikiPathways:WP572
#> 47 WikiPathways:WP85These methods offer a comprehensive way to access and analyze gene-related data in PubChem, catering to various research needs in genetics and molecular biology.
PubChem provides a versatile platform for accessing detailed protein data, essential for researchers in biochemistry and molecular biology. Here’s how you can utilize PUG REST for protein-related queries:
1. Protein Input Methods:
result <- get_pug_rest(identifier = "P00533,P01422", namespace = "accession", domain = "protein", operation = "summary", output = "JSON")
result
#>
#> An object of class 'PugRestInstance'
#>
#> Request Details:
#> - Domain: Protein
#> - Namespace: DomainSpecific
#> - Operation: summary
#> - Identifier: P00533,P01422
#>
#> NOTE: Run getter function 'pubChemData(...)' to extract raw data retrieved from PubChem Database.
#> See ?pubChemData for details.pubChemData(result)
#> $ProteinSummaries
#> $ProteinSummaries$ProteinSummary
#> $ProteinSummaries$ProteinSummary[[1]]
#> $ProteinSummaries$ProteinSummary[[1]]$ProteinAccession
#> [1] "P00533"
#>
#> $ProteinSummaries$ProteinSummary[[1]]$Name
#> [1] "Epidermal growth factor receptor"
#>
#> $ProteinSummaries$ProteinSummary[[1]]$TaxonomyID
#> [1] 9606
#>
#> $ProteinSummaries$ProteinSummary[[1]]$Taxonomy
#> [1] "Homo sapiens (human)"
#>
#> $ProteinSummaries$ProteinSummary[[1]]$Synonym
#> [1] "EC 2.7.10.1" "Proto-oncogene c-ErbB-1"
#> [3] "Receptor tyrosine-protein kinase erbB-1"
#>
#>
#> $ProteinSummaries$ProteinSummary[[2]]
#> $ProteinSummaries$ProteinSummary[[2]]$ProteinAccession
#> [1] "P01422"
#>
#> $ProteinSummaries$ProteinSummary[[2]]$Name
#> [1] "Short neurotoxin 2"
#>
#> $ProteinSummaries$ProteinSummary[[2]]$TaxonomyID
#> [1] 96794
#>
#> $ProteinSummaries$ProteinSummary[[2]]$Taxonomy
#> [1] "Naja annulifera (banded Egyptian cobra)"
#>
#> $ProteinSummaries$ProteinSummary[[2]]$Synonym
#> [1] "Toxin CM-14" "Toxin V-N-I2"By Protein Synonym: Access protein data using synonyms or identifiers from external sources. For example, using a ChEMBL ID:
result <- get_pug_rest(identifier = "ChEMBL:CHEMBL203", namespace = "synonym", domain = "protein", operation = "summary", output = "JSON")
result
#>
#> An object of class 'PugRestInstance'
#>
#> Request Details:
#> - Domain: Protein
#> - Namespace: DomainSpecific
#> - Operation: summary
#> - Identifier: ChEMBL:CHEMBL203
#>
#> NOTE: Run getter function 'pubChemData(...)' to extract raw data retrieved from PubChem Database.
#> See ?pubChemData for details.pubChemData(result)
#> $ProteinSummaries
#> $ProteinSummaries$ProteinSummary
#> $ProteinSummaries$ProteinSummary[[1]]
#> $ProteinSummaries$ProteinSummary[[1]]$ProteinAccession
#> [1] "P00533"
#>
#> $ProteinSummaries$ProteinSummary[[1]]$Name
#> [1] "Epidermal growth factor receptor"
#>
#> $ProteinSummaries$ProteinSummary[[1]]$TaxonomyID
#> [1] 9606
#>
#> $ProteinSummaries$ProteinSummary[[1]]$Taxonomy
#> [1] "Homo sapiens (human)"
#>
#> $ProteinSummaries$ProteinSummary[[1]]$Synonym
#> [1] "EC 2.7.10.1" "Proto-oncogene c-ErbB-1"
#> [3] "Receptor tyrosine-protein kinase erbB-1"2. Available Protein Data:
result <- get_pug_rest(identifier = "P00533,P01422", namespace = "accession", domain = "protein", operation = "summary", output = "JSON")
result
#>
#> An object of class 'PugRestInstance'
#>
#> Request Details:
#> - Domain: Protein
#> - Namespace: DomainSpecific
#> - Operation: summary
#> - Identifier: P00533,P01422
#>
#> NOTE: Run getter function 'pubChemData(...)' to extract raw data retrieved from PubChem Database.
#> See ?pubChemData for details.pubChemData(result)
#> $ProteinSummaries
#> $ProteinSummaries$ProteinSummary
#> $ProteinSummaries$ProteinSummary[[1]]
#> $ProteinSummaries$ProteinSummary[[1]]$ProteinAccession
#> [1] "P00533"
#>
#> $ProteinSummaries$ProteinSummary[[1]]$Name
#> [1] "Epidermal growth factor receptor"
#>
#> $ProteinSummaries$ProteinSummary[[1]]$TaxonomyID
#> [1] 9606
#>
#> $ProteinSummaries$ProteinSummary[[1]]$Taxonomy
#> [1] "Homo sapiens (human)"
#>
#> $ProteinSummaries$ProteinSummary[[1]]$Synonym
#> [1] "EC 2.7.10.1" "Proto-oncogene c-ErbB-1"
#> [3] "Receptor tyrosine-protein kinase erbB-1"
#>
#>
#> $ProteinSummaries$ProteinSummary[[2]]
#> $ProteinSummaries$ProteinSummary[[2]]$ProteinAccession
#> [1] "P01422"
#>
#> $ProteinSummaries$ProteinSummary[[2]]$Name
#> [1] "Short neurotoxin 2"
#>
#> $ProteinSummaries$ProteinSummary[[2]]$TaxonomyID
#> [1] 96794
#>
#> $ProteinSummaries$ProteinSummary[[2]]$Taxonomy
#> [1] "Naja annulifera (banded Egyptian cobra)"
#>
#> $ProteinSummaries$ProteinSummary[[2]]$Synonym
#> [1] "Toxin CM-14" "Toxin V-N-I2"Assays from Protein: Retrieves a list of AIDs tested against a specific protein. For example, for protein accession P00533:
result <- get_pug_rest(identifier = "P00533", namespace = "accession", domain = "protein", operation = "aids", output = "TXT")
result
#>
#> An object of class 'PugRestInstance'
#>
#> Request Details:
#> - Domain: Protein
#> - Namespace: DomainSpecific
#> - Operation: aids
#> - Identifier: P00533
#>
#> NOTE: Run getter function 'pubChemData(...)' to extract raw data retrieved from PubChem Database.
#> See ?pubChemData for details.pubChemData(result)
#> Text
#> 1 1433
#> 2 1726
#> 3 1727
#> 4 1729
#> 5 1731
#> 6 1742
#> 7 1982
#> 8 3364
#> 9 3365
#> 10 7884
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#> 700 439896
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#> 707 441963
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#> 800 480262
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#> 999 625519
#> 1000 626081
#> [ reached 'max' / getOption("max.print") -- omitted 4485 rows ]Bioactivities from Protein: Returns concise bioactivity data for a specific protein. For example:
result <- get_pug_rest(identifier = "Q01279", namespace = "accession", domain = "protein", operation = "concise", output = "JSON")
result
#>
#> An object of class 'PugRestInstance'
#>
#> Request Details:
#> - Domain: Protein
#> - Namespace: DomainSpecific
#> - Operation: concise
#> - Identifier: Q01279
#>
#> NOTE: Run getter function 'pubChemData(...)' to extract raw data retrieved from PubChem Database.
#> See ?pubChemData for details.pubChemData(result)
#> $Table
#> $Table$Columns
#> $Table$Columns$Column
#> [1] "AID" "SID" "CID" "Activity Outcome" "Target GeneID"
#> [6] "Activity Name" "Activity Qualifier" "Activity Value [uM]" "Assay Name" "Assay Type"
#> [11] "PubMed ID"
#>
#>
#> $Table$Row
#> $Table$Row[[1]]
#> $Table$Row[[1]]$Cell
#> [1] "66438"
#> [2] "103250953"
#> [3] "25017867"
#> [4] "Active"
#> [5] "13649"
#> [6] "Effective concentration"
#> [7] "="
#> [8] "0.01"
#> [9] "Inhibition of epidermal growth factor binding in C3H10T1/2 cells"
#> [10] "Confirmatory"
#> [11] "1597853"
#>
#>
#> $Table$Row[[2]]
#> $Table$Row[[2]]$Cell
#> [1] "66438"
#> [2] "103432098"
#> [3] "454217"
#> [4] "Active"
#> [5] "13649"
#> [6] "Effective concentration"
#> [7] "="
#> [8] "0.22"
#> [9] "Inhibition of epidermal growth factor binding in C3H10T1/2 cells"
#> [10] "Confirmatory"
#> [11] "1597853"
#>
#>
#> $Table$Row[[3]]
#> $Table$Row[[3]]$Cell
#> [1] "69721"
#> [2] "103358917"
#> [3] "135512509"
#> [4] "Unspecified"
#> [5] "13649"
#> [6] "IC50"
#> [7] "="
#> [8] "22.7"
#> [9] "Inhibition of Epidermal growth factor receptor mediated mitogenesis of NIH3T3 cells"
#> [10] "Confirmatory"
#> [11] "9748366"
#>
#>
#> $Table$Row[[4]]
#> $Table$Row[[4]]$Cell
#> [1] "69721"
#> [2] "103358918"
#> [3] "135434086"
#> [4] "Unspecified"
#> [5] "13649"
#> [6] "IC50"
#> [7] "="
#> [8] "36.9"
#> [9] "Inhibition of Epidermal growth factor receptor mediated mitogenesis of NIH3T3 cells"
#> [10] "Confirmatory"
#> [11] "9748366"
#>
#>
#> $Table$Row[[5]]
#> $Table$Row[[5]]$Cell
#> [1] "69721"
#> [2] "103358919"
#> [3] "135455949"
#> [4] "Unspecified"
#> [5] "13649"
#> [6] "IC50"
#> [7] "="
#> [8] "11.3"
#> [9] "Inhibition of Epidermal growth factor receptor mediated mitogenesis of NIH3T3 cells"
#> [10] "Confirmatory"
#> [11] "9748366"
#>
#>
#> $Table$Row[[6]]
#> $Table$Row[[6]]$Cell
#> [1] "69722"
#> [2] "103253186"
#> [3] "5328592"
#> [4] "Unspecified"
#> [5] "13649"
#> [6] "IC50"
#> [7] ">"
#> [8] "100"
#> [9] "Inhibition of epidermal growth factor receptor (EGFR-mediated tyrosine autophosphorylation in mouse fibroblasts."
#> [10] "Confirmatory"
#> [11] "8027985"
#>
#>
#> $Table$Row[[7]]
#> $Table$Row[[7]]$Cell
#> [1] "69722"
#> [2] "103253755"
#> [3] "5328614"
#> [4] "Unspecified"
#> [5] "13649"
#> [6] "IC50"
#> [7] ">"
#> [8] "100"
#> [9] "Inhibition of epidermal growth factor receptor (EGFR-mediated tyrosine autophosphorylation in mouse fibroblasts."
#> [10] "Confirmatory"
#> [11] "8027985"
#>
#>
#> $Table$Row[[8]]
#> $Table$Row[[8]]$Cell
#> [1] "69722"
#> [2] "103254313"
#> [3] "5328618"
#> [4] "Unspecified"
#> [5] "13649"
#> [6] "IC50"
#> [7] ">"
#> [8] "100"
#> [9] "Inhibition of epidermal growth factor receptor (EGFR-mediated tyrosine autophosphorylation in mouse fibroblasts."
#> [10] "Confirmatory"
#> [11] "8027985"
#>
#>
#> $Table$Row[[9]]
#> $Table$Row[[9]]$Cell
#> [1] "69722"
#> [2] "103254592"
#> [3] "5328617"
#> [4] "Unspecified"
#> [5] "13649"
#> [6] "IC50"
#> [7] ">"
#> [8] "25"
#> [9] "Inhibition of epidermal growth factor receptor (EGFR-mediated tyrosine autophosphorylation in mouse fibroblasts."
#> [10] "Confirmatory"
#> [11] "8027985"
#>
#>
#> $Table$Row[[10]]
#> $Table$Row[[10]]$Cell
#> [1] "69724"
#> [2] "103237764"
#> [3] "5328042"
#> [4] "Active"
#> [5] "13649"
#> [6] "IC50"
#> [7] "="
#> [8] "0.04"
#> [9] "Inhibition of epidermal growth factor receptor tyrosine kinase (EGFR TK)"
#> [10] "Confirmatory"
#> [11] "14640561"
#>
#>
#> $Table$Row[[11]]
#> $Table$Row[[11]]$Cell
#> [1] "69724"
#> [2] "103373305"
#> [3] "9882519"
#> [4] "Active"
#> [5] "13649"
#> [6] "IC50"
#> [7] "="
#> [8] "0.2"
#> [9] "Inhibition of epidermal growth factor receptor tyrosine kinase (EGFR TK)"
#> [10] "Confirmatory"
#> [11] "14640561"
#>
#>
#> $Table$Row[[12]]
#> $Table$Row[[12]]$Cell
#> [1] "69724"
#> [2] "103373788"
#> [3] "9885081"
#> [4] "Active"
#> [5] "13649"
#> [6] "IC50"
#> [7] "="
#> [8] "0.07"
#> [9] "Inhibition of epidermal growth factor receptor tyrosine kinase (EGFR TK)"
#> [10] "Confirmatory"
#> [11] "14640561"
#>
#>
#> $Table$Row[[13]]
#> $Table$Row[[13]]$Cell
#> [1] "69724"
#> [2] "103399645"
#> [3] "11198415"
#> [4] "Active"
#> [5] "13649"
#> [6] "IC50"
#> [7] "="
#> [8] "0.578"
#> [9] "Inhibition of epidermal growth factor receptor tyrosine kinase (EGFR TK)"
#> [10] "Confirmatory"
#> [11] "14640561"
#>
#>
#> $Table$Row[[14]]
#> $Table$Row[[14]]$Cell
#> [1] "69724"
#> [2] "103399736"
#> [3] "10094127"
#> [4] "Active"
#> [5] "13649"
#> [6] "IC50"
#> [7] "="
#> [8] "0.13"
#> [9] "Inhibition of epidermal growth factor receptor tyrosine kinase (EGFR TK)"
#> [10] "Confirmatory"
#> [11] "14640561"
#>
#>
#> $Table$Row[[15]]
#> $Table$Row[[15]]$Cell
#> [1] "69724"
#> [2] "103399893"
#> [3] "11349700"
#> [4] "Active"
#> [5] "13649"
#> [6] "IC50"
#> [7] "="
#> [8] "0.11"
#> [9] "Inhibition of epidermal growth factor receptor tyrosine kinase (EGFR TK)"
#> [10] "Confirmatory"
#> [11] "14640561"
#>
#>
#> $Table$Row[[16]]
#> $Table$Row[[16]]$Cell
#> [1] "69727"
#> [2] "103167027"
#> [3] "5280343"
#> [4] "Unspecified"
#> [5] "13649"
#> [6] ""
#> [7] ""
#> [8] ""
#> [9] "Inhibition of epidermal growth factor (EGF) receptor from A431 cell membranes at 150 uM"
#> [10] "Other"
#> [11] "8201603"
#>
#>
#> $Table$Row[[17]]
#> $Table$Row[[17]]$Cell
#> [1] "69728"
#> [2] "103399857"
#> [3] "44368090"
#> [4] "Inactive"
#> [5] "13649"
#> [6] ""
#> [7] ""
#> [8] ""
#> [9] "Inhibition of epidermal growth factor receptor tyrosine kinase (EGFR TK) (inactive)"
#> [10] "Other"
#> [11] "14640561"
#>
#>
#> $Table$Row[[18]]
#> $Table$Row[[18]]$Cell
#> [1] "69729"
#> [2] "103167027"
#> [3] "5280343"
#> [4] "Unspecified"
#> [5] "13649"
#> [6] ""
#> [7] ""
#> [8] ""
#> [9] "Inhibition of epidermal growth factor (EGF) receptor from A431 cell membranes at 150 uM"
#> [10] "Other"
#> [11] "8201603"
#>
#>
#> $Table$Row[[19]]
#> $Table$Row[[19]]$Cell
#> [1] "69730"
#> [2] "103226434"
#> [3] "10318571"
#> [4] "Active"
#> [5] "13649"
#> [6] "IC50"
#> [7] "="
#> [8] "4"
#> [9] "Inhibition of epidermal growth factor receptor phosphorylation in BaF3 mouse lymphoid cells."
#> [10] "Confirmatory"
#> [11] "11462983"
#>
#>
#> $Table$Row[[20]]
#> $Table$Row[[20]]$Cell
#> [1] "69730"
#> [2] "103350640"
#> [3] "10406106"
#> [4] "Unspecified"
#> [5] "13649"
#> [6] "IC50"
#> [7] "="
#> [8] "14"
#> [9] "Inhibition of epidermal growth factor receptor phosphorylation in BaF3 mouse lymphoid cells."
#> [10] "Confirmatory"
#> [11] "11462983"
#>
#>
#> $Table$Row[[21]]
#> $Table$Row[[21]]$Cell
#> [1] "69730"
#> [2] "103378973"
#> [3] "10738302"
#> [4] "Unspecified"
#> [5] "13649"
#> [6] "IC50"
#> [7] "="
#> [8] "33"
#> [9] "Inhibition of epidermal growth factor receptor phosphorylation in BaF3 mouse lymphoid cells."
#> [10] "Confirmatory"
#> [11] "11462983"
#>
#>
#> $Table$Row[[22]]
#> $Table$Row[[22]]$Cell
#> [1] "69730"
#> [2] "103378974"
#> [3] "10761144"
#> [4] "Unspecified"
#> [5] "13649"
#> [6] "IC50"
#> [7] ">"
#> [8] "200"
#> [9] "Inhibition of epidermal growth factor receptor phosphorylation in BaF3 mouse lymphoid cells."
#> [10] "Confirmatory"
#> [11] "11462983"
#>
#>
#> $Table$Row[[23]]
#> $Table$Row[[23]]$Cell
#> [1] "69730"
#> [2] "103379003"
#> [3] "10044189"
#> [4] "Unspecified"
#> [5] "13649"
#> [6] "IC50"
#> [7] "="
#> [8] "500"
#> [9] "Inhibition of epidermal growth factor receptor phosphorylation in BaF3 mouse lymphoid cells."
#> [10] "Confirmatory"
#> [11] "11462983"
#>
#>
#> $Table$Row[[24]]
#> $Table$Row[[24]]$Cell
#> [1] "69730"
#> [2] "103379199"
#> [3] "10428841"
#> [4] "Active"
#> [5] "13649"
#> [6] "IC50"
#> [7] "="
#> [8] "8"
#> [9] "Inhibition of epidermal growth factor receptor phosphorylation in BaF3 mouse lymphoid cells."
#> [10] "Confirmatory"
#> [11] "11462983"
#>
#>
#> $Table$Row[[25]]
#> $Table$Row[[25]]$Cell
#> [1] "69730"
#> [2] "103379200"
#> [3] "10716388"
#> [4] "Unspecified"
#> [5] "13649"
#> [6] "IC50"
#> [7] ">"
#> [8] "100"
#> [9] "Inhibition of epidermal growth factor receptor phosphorylation in BaF3 mouse lymphoid cells."
#> [10] "Confirmatory"
#> [11] "11462983"
#>
#>
#> $Table$Row[[26]]
#> $Table$Row[[26]]$Cell
#> [1] "69730"
#> [2] "103379360"
#> [3] "10452792"
#> [4] "Unspecified"
#> [5] "13649"
#> [6] "IC50"
#> [7] ">"
#> [8] "50"
#> [9] "Inhibition of epidermal growth factor receptor phosphorylation in BaF3 mouse lymphoid cells."
#> [10] "Confirmatory"
#> [11] "11462983"
#>
#>
#> $Table$Row[[27]]
#> $Table$Row[[27]]$Cell
#> [1] "69730"
#> [2] "103379591"
#> [3] "10620637"
#> [4] "Unspecified"
#> [5] "13649"
#> [6] "IC50"
#> [7] "="
#> [8] "300"
#> [9] "Inhibition of epidermal growth factor receptor phosphorylation in BaF3 mouse lymphoid cells."
#> [10] "Confirmatory"
#> [11] "11462983"
#>
#>
#> $Table$Row[[28]]
#> $Table$Row[[28]]$Cell
#> [1] "69730"
#> [2] "103379616"
#> [3] "10593843"
#> [4] "Unspecified"
#> [5] "13649"
#> [6] "IC50"
#> [7] ">"
#> [8] "100"
#> [9] "Inhibition of epidermal growth factor receptor phosphorylation in BaF3 mouse lymphoid cells."
#> [10] "Confirmatory"
#> [11] "11462983"
#>
#>
#> $Table$Row[[29]]
#> $Table$Row[[29]]$Cell
#> [1] "69730"
#> [2] "103379617"
#> [3] "10787405"
#> [4] "Active"
#> [5] "13649"
#> [6] "IC50"
#> [7] "="
#> [8] "4"
#> [9] "Inhibition of epidermal growth factor receptor phosphorylation in BaF3 mouse lymphoid cells."
#> [10] "Confirmatory"
#> [11] "11462983"
#>
#>
#> $Table$Row[[30]]
#> $Table$Row[[30]]$Cell
#> [1] "69730"
#> [2] "103379660"
#> [3] "10343317"
#> [4] "Unspecified"
#> [5] "13649"
#> [6] "IC50"
#> [7] "="
#> [8] "35"
#> [9] "Inhibition of epidermal growth factor receptor phosphorylation in BaF3 mouse lymphoid cells."
#> [10] "Confirmatory"
#> [11] "11462983"
#>
#>
#> $Table$Row[[31]]
#> $Table$Row[[31]]$Cell
#> [1] "69730"
#> [2] "103379661"
#> [3] "10499929"
#> [4] "Unspecified"
#> [5] "13649"
#> [6] "IC50"
#> [7] "="
#> [8] "15"
#> [9] "Inhibition of epidermal growth factor receptor phosphorylation in BaF3 mouse lymphoid cells."
#> [10] "Confirmatory"
#> [11] "11462983"
#>
#>
#> $Table$Row[[32]]
#> $Table$Row[[32]]$Cell
#> [1] "69730"
#> [2] "103379682"
#> [3] "10500718"
#> [4] "Active"
#> [5] "13649"
#> [6] "IC50"
#> [7] "="
#> [8] "1"
#> [9] "Inhibition of epidermal growth factor receptor phosphorylation in BaF3 mouse lymphoid cells."
#> [10] "Confirmatory"
#> [11] "11462983"
#>
#>
#> $Table$Row[[33]]
#> $Table$Row[[33]]$Cell
#> [1] "69730"
#> [2] "103379908"
#> [3] "10619651"
#> [4] "Active"
#> [5] "13649"
#> [6] "IC50"
#> [7] "="
#> [8] "10"
#> [9] "Inhibition of epidermal growth factor receptor phosphorylation in BaF3 mouse lymphoid cells."
#> [10] "Confirmatory"
#> [11] "11462983"
#>
#>
#> $Table$Row[[34]]
#> $Table$Row[[34]]$Cell
#> [1] "69730"
#> [2] "103379909"
#> [3] "10504027"
#> [4] "Unspecified"
#> [5] "13649"
#> [6] "IC50"
#> [7] "="
#> [8] "35"
#> [9] "Inhibition of epidermal growth factor receptor phosphorylation in BaF3 mouse lymphoid cells."
#> [10] "Confirmatory"
#> [11] "11462983"
#>
#>
#> $Table$Row[[35]]
#> $Table$Row[[35]]$Cell
#> [1] "69730"
#> [2] "103379910"
#> [3] "10740438"
#> [4] "Unspecified"
#> [5] "13649"
#> [6] "IC50"
#> [7] "="
#> [8] "46"
#> [9] "Inhibition of epidermal growth factor receptor phosphorylation in BaF3 mouse lymphoid cells."
#> [10] "Confirmatory"
#> [11] "11462983"
#>
#>
#> $Table$Row[[36]]
#> $Table$Row[[36]]$Cell
#> [1] "106697"
#> [2] "103166113"
#> [3] "10499619"
#> [4] "Active"
#> [5] "13649"
#> [6] "IC50"
#> [7] "="
#> [8] "9.55"
#> [9] "Inhibition of EGF-dependent mouse keratinocyte MK cell proliferation"
#> [10] "Confirmatory"
#> [11] "10090785"
#>
#>
#> $Table$Row[[37]]
#> $Table$Row[[37]]$Cell
#> [1] "106697"
#> [2] "103166157"
#> [3] "9978638"
#> [4] "Active"
#> [5] "13649"
#> [6] "IC50"
#> [7] "="
#> [8] "4.93"
#> [9] "Inhibition of EGF-dependent mouse keratinocyte MK cell proliferation"
#> [10] "Confirmatory"
#> [11] "10090785"
#>
#>
#> $Table$Row[[38]]
#> $Table$Row[[38]]$Cell
#> [1] "106697"
#> [2] "103166217"
#> [3] "10590515"
#> [4] "Unspecified"
#> [5] "13649"
#> [6] "IC50"
#> [7] "="
#> [8] "45.2"
#> [9] "Inhibition of EGF-dependent mouse keratinocyte MK cell proliferation"
#> [10] "Confirmatory"
#> [11] "10090785"
#>
#>
#> $Table$Row[[39]]
#> $Table$Row[[39]]$Cell
#> [1] "106697"
#> [2] "103166266"
#> [3] "10803234"
#> [4] "Unspecified"
#> [5] "13649"
#> [6] "IC50"
#> [7] "="
#> [8] "10.2"
#> [9] "Inhibition of EGF-dependent mouse keratinocyte MK cell proliferation"
#> [10] "Confirmatory"
#> [11] "10090785"
#>
#>
#> $Table$Row[[40]]
#> $Table$Row[[40]]$Cell
#> [1] "106697"
#> [2] "103166322"
#> [3] "2051"
#> [4] "Active"
#> [5] "13649"
#> [6] "IC50"
#> [7] "<"
#> [8] "0.1"
#> [9] "Inhibition of EGF-dependent mouse keratinocyte MK cell proliferation"
#> [10] "Confirmatory"
#> [11] "10090785"
#>
#>
#> $Table$Row[[41]]
#> $Table$Row[[41]]$Cell
#> [1] "106697"
#> [2] "103166323"
#> [3] "10850934"
#> [4] "Unspecified"
#> [5] "13649"
#> [6] "IC50"
#> [7] "="
#> [8] "16"
#> [9] "Inhibition of EGF-dependent mouse keratinocyte MK cell proliferation"
#> [10] "Confirmatory"
#> [11] "10090785"
#>
#>
#> $Table$Row[[42]]
#> $Table$Row[[42]]$Cell
#> [1] "106697"
#> [2] "103166405"
#> [3] "9883384"
#> [4] "Active"
#> [5] "13649"
#> [6] "IC50"
#> [7] "="
#> [8] "2.83"
#> [9] "Inhibition of EGF-dependent mouse keratinocyte MK cell proliferation"
#> [10] "Confirmatory"
#> [11] "10090785"
#>
#>
#> $Table$Row[[43]]
#> $Table$Row[[43]]$Cell
#> [1] "106697"
#> [2] "103166415"
#> [3] "10494548"
#> [4] "Unspecified"
#> [5] "13649"
#> [6] "IC50"
#> [7] "="
#> [8] "11.4"
#> [9] "Inhibition of EGF-dependent mouse keratinocyte MK cell proliferation"
#> [10] "Confirmatory"
#> [11] "10090785"
#>
#>
#> $Table$Row[[44]]
#> $Table$Row[[44]]$Cell
#> [1] "106697"
#> [2] "103166416"
#> [3] "689033"
#> [4] "Unspecified"
#> [5] "13649"
#> [6] "IC50"
#> [7] "="
#> [8] "46.2"
#> [9] "Inhibition of EGF-dependent mouse keratinocyte MK cell proliferation"
#> [10] "Confirmatory"
#> [11] "10090785"
#>
#>
#> $Table$Row[[45]]
#> $Table$Row[[45]]$Cell
#> [1] "209326"
#> [2] "103257455"
#> [3] "2428"
#> [4] "Active"
#> [5] "13649"
#> [6] "IC50"
#> [7] "="
#> [8] "0.046"
#> [9] "Inhibition of EGF-mediated mitogenesis in Swiss 3T3 cells"
#> [10] "Confirmatory"
#> [11] "8632415"
#>
#>
#> $Table$Row[[46]]
#> $Table$Row[[46]]$Cell
#> [1] "241562"
#> [2] "103439646"
#> [3] "10209082"
#> [4] "Unspecified"
#> [5] "13649"
#> [6] "IC50"
#> [7] ">"
#> [8] "10"
#> [9] "Inhibition of Epidermal growth factor receptor in P19 cells"
#> [10] "Confirmatory"
#> [11] "15771419"
#>
#>
#> $Table$Row[[47]]
#> $Table$Row[[47]]$Cell
#> [1] "241562"
#> [2] "103439659"
#> [3] "10185160"
#> [4] "Unspecified"
#> [5] "13649"
#> [6] "IC50"
#> [7] ">"
#> [8] "10"
#> [9] "Inhibition of Epidermal growth factor receptor in P19 cells"
#> [10] "Confirmatory"
#> [11] "15771419"
#>
#>
#> $Table$Row[[48]]
#> $Table$Row[[48]]$Cell
#> [1] "241562"
#> [2] "103439663"
#> [3] "10143584"
#> [4] "Unspecified"
#> [5] "13649"
#> [6] "IC50"
#> [7] ">"
#> [8] "10"
#> [9] "Inhibition of Epidermal growth factor receptor in P19 cells"
#> [10] "Confirmatory"
#> [11] "15771419"
#>
#>
#> $Table$Row[[49]]
#> $Table$Row[[49]]$Cell
#> [1] "241562"
#> [2] "103439672"
#> [3] "10163439"
#> [4] "Unspecified"
#> [5] "13649"
#> [6] "IC50"
#> [7] ">"
#> [8] "10"
#> [9] "Inhibition of Epidermal growth factor receptor in P19 cells"
#> [10] "Confirmatory"
#> [11] "15771419"
#>
#>
#> $Table$Row[[50]]
#> $Table$Row[[50]]$Cell
#> [1] "241562"
#> [2] "103439700"
#> [3] "10302405"
#> [4] "Unspecified"
#> [5] "13649"
#> [6] "IC50"
#> [7] ">"
#> [8] "10"
#> [9] "Inhibition of Epidermal growth factor receptor in P19 cells"
#> [10] "Confirmatory"
#> [11] "15771419"
#>
#>
#> $Table$Row[[51]]
#> $Table$Row[[51]]$Cell
#> [1] "241562"
#> [2] "103439717"
#> [3] "10187378"
#> [4] "Unspecified"
#> [5] "13649"
#> [6] "IC50"
#> [7] ">"
#> [8] "10"
#> [9] "Inhibition of Epidermal growth factor receptor in P19 cells"
#> [10] "Confirmatory"
#> [11] "15771419"
#>
#>
#> $Table$Row[[52]]
#> $Table$Row[[52]]$Cell
#> [1] "241562"
#> [2] "123092436"
#> [3] "44259"
#> [4] "Unspecified"
#> [5] "13649"
#> [6] "IC50"
#> [7] ">"
#> [8] "10"
#> [9] "Inhibition of Epidermal growth factor receptor in P19 cells"
#> [10] "Confirmatory"
#> [11] "15771419"
#>
#>
#> $Table$Row[[53]]
#> $Table$Row[[53]]$Cell
#> [1] "241823"
#> [2] "103452251"
#> [3] "22732319"
#> [4] "Inconclusive"
#> [5] "13649"
#> [6] ""
#> [7] ""
#> [8] ""
#> [9] "Inhibition of Epidermal growth factor receptor tyrosine kinase activity; not tested"
#> [10] "Other"
#> [11] "15454232"
#>
#>
#> $Table$Row[[54]]
#> $Table$Row[[54]]$Cell
#> [1] "337238"
#> [2] "103194285"
#> [3] "4075"
#> [4] "Unspecified"
#> [5] "13649"
#> [6] ""
#> [7] ""
#> [8] ""
#> [9] "Inhibition of mouse EGFR by liquid scintillation counting"
#> [10] "Other"
#> [11] "2614420"
#>
#>
#> $Table$Row[[55]]
#> $Table$Row[[55]]$Cell
#> [1] "337238"
#> [2] "103227545"
#> [3] "5328552"
#> [4] "Unspecified"
#> [5] "13649"
#> [6] ""
#> [7] ""
#> [8] ""
#> [9] "Inhibition of mouse EGFR by liquid scintillation counting"
#> [10] "Other"
#> [11] "2614420"
#>
#>
#> $Table$Row[[56]]
#> $Table$Row[[56]]$Cell
#> [1] "337238"
#> [2] "103319670"
#> [3] "3894"
#> [4] "Unspecified"
#> [5] "13649"
#> [6] ""
#> [7] ""
#> [8] ""
#> [9] "Inhibition of mouse EGFR by liquid scintillation counting"
#> [10] "Other"
#> [11] "2614420"
#>
#>
#> $Table$Row[[57]]
#> $Table$Row[[57]]$Cell
#> [1] "337238"
#> [2] "103319671"
#> [3] "3896"
#> [4] "Unspecified"
#> [5] "13649"
#> [6] ""
#> [7] ""
#> [8] ""
#> [9] "Inhibition of mouse EGFR by liquid scintillation counting"
#> [10] "Other"
#> [11] "2614420"
#>
#>
#> $Table$Row[[58]]
#> $Table$Row[[58]]$Cell
#> [1] "337238"
#> [2] "103529702"
#> [3] "65083"
#> [4] "Unspecified"
#> [5] "13649"
#> [6] ""
#> [7] ""
#> [8] ""
#> [9] "Inhibition of mouse EGFR by liquid scintillation counting"
#> [10] "Other"
#> [11] "2614420"
#>
#>
#> $Table$Row[[59]]
#> $Table$Row[[59]]$Cell
#> [1] "337238"
#> [2] "103529722"
#> [3] "70949"
#> [4] "Unspecified"
#> [5] "13649"
#> [6] ""
#> [7] ""
#> [8] ""
#> [9] "Inhibition of mouse EGFR by liquid scintillation counting"
#> [10] "Other"
#> [11] "2614420"
#>
#>
#> $Table$Row[[60]]
#> $Table$Row[[60]]$Cell
#> [1] "337238"
#> [2] "103618685"
#> [3] "3895"
#> [4] "Unspecified"
#> [5] "13649"
#> [6] ""
#> [7] ""
#> [8] ""
#> [9] "Inhibition of mouse EGFR by liquid scintillation counting"
#> [10] "Other"
#> [11] "2614420"
#>
#>
#> $Table$Row[[61]]
#> $Table$Row[[61]]$Cell
#> [1] "337238"
#> [2] "103618686"
#> [3] "44593598"
#> [4] "Unspecified"
#> [5] "13649"
#> [6] ""
#> [7] ""
#> [8] ""
#> [9] "Inhibition of mouse EGFR by liquid scintillation counting"
#> [10] "Other"
#> [11] "2614420"
#>
#>
#> $Table$Row[[62]]
#> $Table$Row[[62]]$Cell
#> [1] "337238"
#> [2] "103618687"
#> [3] "44593599"
#> [4] "Unspecified"
#> [5] "13649"
#> [6] ""
#> [7] ""
#> [8] ""
#> [9] "Inhibition of mouse EGFR by liquid scintillation counting"
#> [10] "Other"
#> [11] "2614420"
#>
#>
#> $Table$Row[[63]]
#> $Table$Row[[63]]$Cell
#> [1] "337238"
#> [2] "103618691"
#> [3] "375472"
#> [4] "Unspecified"
#> [5] "13649"
#> [6] ""
#> [7] ""
#> [8] ""
#> [9] "Inhibition of mouse EGFR by liquid scintillation counting"
#> [10] "Other"
#> [11] "2614420"
#>
#>
#> $Table$Row[[64]]
#> $Table$Row[[64]]$Cell
#> [1] "337238"
#> [2] "123092436"
#> [3] "44259"
#> [4] "Unspecified"
#> [5] "13649"
#> [6] ""
#> [7] ""
#> [8] ""
#> [9] "Inhibition of mouse EGFR by liquid scintillation counting"
#> [10] "Other"
#> [11] "2614420"
#>
#>
#> $Table$Row[[65]]
#> $Table$Row[[65]]$Cell
#> [1] "337243"
#> [2] "103319670"
#> [3] "3894"
#> [4] "Active"
#> [5] "13649"
#> [6] ""
#> [7] ""
#> [8] ""
#> [9] "Inhibition of mouse EGFR using [32P]gammaATP as substrate by competitive Lineweaver-Burke plot"
#> [10] "Other"
#> [11] "2614420"
#>
#>
#> $Table$Row[[66]]
#> $Table$Row[[66]]$Cell
#> [1] "337244"
#> [2] "103319670"
#> [3] "3894"
#> [4] "Active"
#> [5] "13649"
#> [6] ""
#> [7] ""
#> [8] ""
#> [9] "Inhibition of mouse EGFR using tridecapeptide as substrate by uncompetitive Lineweaver-Burke plot"
#> [10] "Other"
#> [11] "2614420"
#>
#>
#> $Table$Row[[67]]
#> $Table$Row[[67]]$Cell
#> [1] "415757"
#> [2] "103294831"
#> [3] "5289418"
#> [4] "Active"
#> [5] "13649"
#> [6] ""
#> [7] ""
#> [8] ""
#> [9] "Inhibition of EGF-stimulated EGFR phosphorylation in mouse HER14 cells by immunoblotting"
#> [10] "Other"
#> [11] "9139660"
#>
#>
#> $Table$Row[[68]]
#> $Table$Row[[68]]$Cell
#> [1] "415757"
#> [2] "103295395"
#> [3] "5941540"
#> [4] "Active"
#> [5] "13649"
#> [6] ""
#> [7] ""
#> [8] ""
#> [9] "Inhibition of EGF-stimulated EGFR phosphorylation in mouse HER14 cells by immunoblotting"
#> [10] "Other"
#> [11] "9139660"
#>
#>
#> $Table$Row[[69]]
#> $Table$Row[[69]]$Cell
#> [1] "415758"
#> [2] "103294831"
#> [3] "5289418"
#> [4] "Active"
#> [5] "13649"
#> [6] ""
#> [7] ""
#> [8] ""
#> [9] "Inhibition of EGFR in mouse HER14 cells assessed as inhibition of EGF-stimulated Shc phosphorylation by immunoblotting"
#> [10] "Other"
#> [11] "9139660"
#>
#>
#> $Table$Row[[70]]
#> $Table$Row[[70]]$Cell
#> [1] "415758"
#> [2] "103295395"
#> [3] "5941540"
#> [4] "Active"
#> [5] "13649"
#> [6] ""
#> [7] ""
#> [8] ""
#> [9] "Inhibition of EGFR in mouse HER14 cells assessed as inhibition of EGF-stimulated Shc phosphorylation by immunoblotting"
#> [10] "Other"
#> [11] "9139660"
#>
#>
#> $Table$Row[[71]]
#> $Table$Row[[71]]$Cell
#> [1] "415759"
#> [2] "103294831"
#> [3] "5289418"
#> [4] "Active"
#> [5] "13649"
#> [6] ""
#> [7] ""
#> [8] ""
#> [9] "Inhibition of EGFR in mouse HER14 cells assessed as inhibition of EGF-stimulated ERK2 activation by immunoblotting"
#> [10] "Other"
#> [11] "9139660"
#>
#>
#> $Table$Row[[72]]
#> $Table$Row[[72]]$Cell
#> [1] "415759"
#> [2] "103295395"
#> [3] "5941540"
#> [4] "Active"
#> [5] "13649"
#> [6] ""
#> [7] ""
#> [8] ""
#> [9] "Inhibition of EGFR in mouse HER14 cells assessed as inhibition of EGF-stimulated ERK2 activation by immunoblotting"
#> [10] "Other"
#> [11] "9139660"
#>
#>
#> $Table$Row[[73]]
#> $Table$Row[[73]]$Cell
#> [1] "415760"
#> [2] "103294831"
#> [3] "5289418"
#> [4] "Inactive"
#> [5] "13649"
#> [6] ""
#> [7] ""
#> [8] ""
#> [9] "Inhibition of EGFR phosphorylation in mouse NIH/3T3 cells at 200 uM"
#> [10] "Other"
#> [11] "9139660"
#>
#>
#> $Table$Row[[74]]
#> $Table$Row[[74]]$Cell
#> [1] "415760"
#> [2] "103295395"
#> [3] "5941540"
#> [4] "Inactive"
#> [5] "13649"
#> [6] ""
#> [7] ""
#> [8] ""
#> [9] "Inhibition of EGFR phosphorylation in mouse NIH/3T3 cells at 200 uM"
#> [10] "Other"
#> [11] "9139660"
#>
#>
#> $Table$Row[[75]]
#> $Table$Row[[75]]$Cell
#> [1] "1527521"
#> [2] "312367127"
#> [3] "71496458"
#> [4] "Active"
#> [5] "13649"
#> [6] "IC50"
#> [7] "="
#> [8] "0.081"
#> [9] "Inhibition of wild type EGFR in mouse BAF3 cells assessed as reduction in cell proliferation incubated for 72 hrs by Celltiter-Glo luminescent cell viability assay"
#> [10] "Confirmatory"
#> [11] "31689114"
#>
#>
#> $Table$Row[[76]]
#> $Table$Row[[76]]$Cell
#> [1] "1527521"
#> [2] "440110169"
#> [3] "139593669"
#> [4] "Unspecified"
#> [5] "13649"
#> [6] "IC50"
#> [7] ">"
#> [8] "10"
#> [9] "Inhibition of wild type EGFR in mouse BAF3 cells assessed as reduction in cell proliferation incubated for 72 hrs by Celltiter-Glo luminescent cell viability assay"
#> [10] "Confirmatory"
#> [11] "31689114"
#>
#>
#> $Table$Row[[77]]
#> $Table$Row[[77]]$Cell
#> [1] "1527521"
#> [2] "440119817"
#> [3] "155517202"
#> [4] "Inconclusive"
#> [5] "13649"
#> [6] "IC50"
#> [7] ""
#> [8] ""
#> [9] "Inhibition of wild type EGFR in mouse BAF3 cells assessed as reduction in cell proliferation incubated for 72 hrs by Celltiter-Glo luminescent cell viability assay"
#> [10] "Confirmatory"
#> [11] "31689114"
#>
#>
#> $Table$Row[[78]]
#> $Table$Row[[78]]$Cell
#> [1] "1527521"
#> [2] "440125045"
#> [3] "139447864"
#> [4] "Active"
#> [5] "13649"
#> [6] "IC50"
#> [7] "="
#> [8] "3.6"
#> [9] "Inhibition of wild type EGFR in mouse BAF3 cells assessed as reduction in cell proliferation incubated for 72 hrs by Celltiter-Glo luminescent cell viability assay"
#> [10] "Confirmatory"
#> [11] "31689114"
#>
#>
#> $Table$Row[[79]]
#> $Table$Row[[79]]$Cell
#> [1] "1527521"
#> [2] "440160302"
#> [3] "139593670"
#> [4] "Active"
#> [5] "13649"
#> [6] "IC50"
#> [7] "="
#> [8] "1.3"
#> [9] "Inhibition of wild type EGFR in mouse BAF3 cells assessed as reduction in cell proliferation incubated for 72 hrs by Celltiter-Glo luminescent cell viability assay"
#> [10] "Confirmatory"
#> [11] "31689114"
#>
#>
#> $Table$Row[[80]]
#> $Table$Row[[80]]$Cell
#> [1] "1527521"
#> [2] "440163841"
#> [3] "139447649"
#> [4] "Active"
#> [5] "13649"
#> [6] "IC50"
#> [7] "="
#> [8] "5.1"
#> [9] "Inhibition of wild type EGFR in mouse BAF3 cells assessed as reduction in cell proliferation incubated for 72 hrs by Celltiter-Glo luminescent cell viability assay"
#> [10] "Confirmatory"
#> [11] "31689114"
#>
#>
#> $Table$Row[[81]]
#> $Table$Row[[81]]$Cell
#> [1] "1527521"
#> [2] "440172005"
#> [3] "139447554"
#> [4] "Active"
#> [5] "13649"
#> [6] "IC50"
#> [7] "="
#> [8] "0.7"
#> [9] "Inhibition of wild type EGFR in mouse BAF3 cells assessed as reduction in cell proliferation incubated for 72 hrs by Celltiter-Glo luminescent cell viability assay"
#> [10] "Confirmatory"
#> [11] "31689114"
#>
#>
#> $Table$Row[[82]]
#> $Table$Row[[82]]$Cell
#> [1] "1527521"
#> [2] "440176009"
#> [3] "139600318"
#> [4] "Active"
#> [5] "13649"
#> [6] "IC50"
#> [7] "="
#> [8] "0.19"
#> [9] "Inhibition of wild type EGFR in mouse BAF3 cells assessed as reduction in cell proliferation incubated for 72 hrs by Celltiter-Glo luminescent cell viability assay"
#> [10] "Confirmatory"
#> [11] "31689114"
#>
#>
#> $Table$Row[[83]]
#> $Table$Row[[83]]$Cell
#> [1] "1527521"
#> [2] "440182946"
#> [3] "155444794"
#> [4] "Active"
#> [5] "13649"
#> [6] "IC50"
#> [7] "="
#> [8] "2.3"
#> [9] "Inhibition of wild type EGFR in mouse BAF3 cells assessed as reduction in cell proliferation incubated for 72 hrs by Celltiter-Glo luminescent cell viability assay"
#> [10] "Confirmatory"
#> [11] "31689114"
#>
#>
#> $Table$Row[[84]]
#> $Table$Row[[84]]$Cell
#> [1] "1527521"
#> [2] "440203081"
#> [3] "155444797"
#> [4] "Active"
#> [5] "13649"
#> [6] "IC50"
#> [7] "="
#> [8] "1.1"
#> [9] "Inhibition of wild type EGFR in mouse BAF3 cells assessed as reduction in cell proliferation incubated for 72 hrs by Celltiter-Glo luminescent cell viability assay"
#> [10] "Confirmatory"
#> [11] "31689114"
#>
#>
#> $Table$Row[[85]]
#> $Table$Row[[85]]$Cell
#> [1] "1527521"
#> [2] "440207922"
#> [3] "155444848"
#> [4] "Active"
#> [5] "13649"
#> [6] "IC50"
#> [7] "="
#> [8] "0.27"
#> [9] "Inhibition of wild type EGFR in mouse BAF3 cells assessed as reduction in cell proliferation incubated for 72 hrs by Celltiter-Glo luminescent cell viability assay"
#> [10] "Confirmatory"
#> [11] "31689114"
#>
#>
#> $Table$Row[[86]]
#> $Table$Row[[86]]$Cell
#> [1] "1527521"
#> [2] "440227038"
#> [3] "139593668"
#> [4] "Inconclusive"
#> [5] "13649"
#> [6] "IC50"
#> [7] ""
#> [8] ""
#> [9] "Inhibition of wild type EGFR in mouse BAF3 cells assessed as reduction in cell proliferation incubated for 72 hrs by Celltiter-Glo luminescent cell viability assay"
#> [10] "Confirmatory"
#> [11] "31689114"
#>
#>
#> $Table$Row[[87]]
#> $Table$Row[[87]]$Cell
#> [1] "1740135"
#> [2] "312367127"
#> [3] "71496458"
#> [4] "Active"
#> [5] "13649"
#> [6] "GI50"
#> [7] "="
#> [8] "2.6"
#> [9] "Inhibition of wild type EGFR in mouse BaF3 cells assessed as reduction in cell proliferation incubated for 72 hrs by Celltiter-Glo luminescent cell viability assay"
#> [10] "Confirmatory"
#> [11] "32619886"
#>
#>
#> $Table$Row[[88]]
#> $Table$Row[[88]]$Cell
#> [1] "1740135"
#> [2] "461515468"
#> [3] "162643657"
#> [4] "Inconclusive"
#> [5] "13649"
#> [6] "GI50"
#> [7] ""
#> [8] ""
#> [9] "Inhibition of wild type EGFR in mouse BaF3 cells assessed as reduction in cell proliferation incubated for 72 hrs by Celltiter-Glo luminescent cell viability assay"
#> [10] "Confirmatory"
#> [11] "32619886"
#>
#>
#> $Table$Row[[89]]
#> $Table$Row[[89]]$Cell
#> [1] "1740135"
#> [2] "461515649"
#> [3] "162643790"
#> [4] "Active"
#> [5] "13649"
#> [6] "GI50"
#> [7] "="
#> [8] "9.23"
#> [9] "Inhibition of wild type EGFR in mouse BaF3 cells assessed as reduction in cell proliferation incubated for 72 hrs by Celltiter-Glo luminescent cell viability assay"
#> [10] "Confirmatory"
#> [11] "32619886"
#>
#>
#> $Table$Row[[90]]
#> $Table$Row[[90]]$Cell
#> [1] "1740135"
#> [2] "461542097"
#> [3] "162662364"
#> [4] "Active"
#> [5] "13649"
#> [6] "GI50"
#> [7] "="
#> [8] "3.91"
#> [9] "Inhibition of wild type EGFR in mouse BaF3 cells assessed as reduction in cell proliferation incubated for 72 hrs by Celltiter-Glo luminescent cell viability assay"
#> [10] "Confirmatory"
#> [11] "32619886"
#>
#>
#> $Table$Row[[91]]
#> $Table$Row[[91]]$Cell
#> [1] "1740135"
#> [2] "461543217"
#> [3] "162663118"
#> [4] "Unspecified"
#> [5] "13649"
#> [6] "GI50"
#> [7] ">"
#> [8] "10"
#> [9] "Inhibition of wild type EGFR in mouse BaF3 cells assessed as reduction in cell proliferation incubated for 72 hrs by Celltiter-Glo luminescent cell viability assay"
#> [10] "Confirmatory"
#> [11] "32619886"
#>
#>
#> $Table$Row[[92]]
#> $Table$Row[[92]]$Cell
#> [1] "1740135"
#> [2] "461546315"
#> [3] "162665339"
#> [4] "Unspecified"
#> [5] "13649"
#> [6] "GI50"
#> [7] ">"
#> [8] "10"
#> [9] "Inhibition of wild type EGFR in mouse BaF3 cells assessed as reduction in cell proliferation incubated for 72 hrs by Celltiter-Glo luminescent cell viability assay"
#> [10] "Confirmatory"
#> [11] "32619886"
#>
#>
#> $Table$Row[[93]]
#> $Table$Row[[93]]$Cell
#> [1] "1740135"
#> [2] "461547480"
#> [3] "162666122"
#> [4] "Active"
#> [5] "13649"
#> [6] "GI50"
#> [7] "="
#> [8] "4.27"
#> [9] "Inhibition of wild type EGFR in mouse BaF3 cells assessed as reduction in cell proliferation incubated for 72 hrs by Celltiter-Glo luminescent cell viability assay"
#> [10] "Confirmatory"
#> [11] "32619886"
#>
#>
#> $Table$Row[[94]]
#> $Table$Row[[94]]$Cell
#> [1] "1740135"
#> [2] "461549927"
#> [3] "162667840"
#> [4] "Active"
#> [5] "13649"
#> [6] "GI50"
#> [7] "="
#> [8] "3.79"
#> [9] "Inhibition of wild type EGFR in mouse BaF3 cells assessed as reduction in cell proliferation incubated for 72 hrs by Celltiter-Glo luminescent cell viability assay"
#> [10] "Confirmatory"
#> [11] "32619886"
#>
#>
#> $Table$Row[[95]]
#> $Table$Row[[95]]$Cell
#> [1] "1740135"
#> [2] "461550238"
#> [3] "162668052"
#> [4] "Active"
#> [5] "13649"
#> [6] "GI50"
#> [7] "="
#> [8] "2.65"
#> [9] "Inhibition of wild type EGFR in mouse BaF3 cells assessed as reduction in cell proliferation incubated for 72 hrs by Celltiter-Glo luminescent cell viability assay"
#> [10] "Confirmatory"
#> [11] "32619886"
#>
#>
#> $Table$Row[[96]]
#> $Table$Row[[96]]$Cell
#> [1] "1740135"
#> [2] "461550466"
#> [3] "162668204"
#> [4] "Unspecified"
#> [5] "13649"
#> [6] "GI50"
#> [7] ">"
#> [8] "10"
#> [9] "Inhibition of wild type EGFR in mouse BaF3 cells assessed as reduction in cell proliferation incubated for 72 hrs by Celltiter-Glo luminescent cell viability assay"
#> [10] "Confirmatory"
#> [11] "32619886"
#>
#>
#> $Table$Row[[97]]
#> $Table$Row[[97]]$Cell
#> [1] "1740135"
#> [2] "461555362"
#> [3] "162671649"
#> [4] "Inconclusive"
#> [5] "13649"
#> [6] "GI50"
#> [7] ""
#> [8] ""
#> [9] "Inhibition of wild type EGFR in mouse BaF3 cells assessed as reduction in cell proliferation incubated for 72 hrs by Celltiter-Glo luminescent cell viability assay"
#> [10] "Confirmatory"
#> [11] "32619886"
#>
#>
#> $Table$Row[[98]]
#> $Table$Row[[98]]$Cell
#> [1] "1740135"
#> [2] "461557317"
#> [3] "162673094"
#> [4] "Active"
#> [5] "13649"
#> [6] "GI50"
#> [7] "="
#> [8] "9.23"
#> [9] "Inhibition of wild type EGFR in mouse BaF3 cells assessed as reduction in cell proliferation incubated for 72 hrs by Celltiter-Glo luminescent cell viability assay"
#> [10] "Confirmatory"
#> [11] "32619886"
#>
#>
#> $Table$Row[[99]]
#> $Table$Row[[99]]$Cell
#> [1] "1740135"
#> [2] "461557891"
#> [3] "162673491"
#> [4] "Active"
#> [5] "13649"
#> [6] "GI50"
#> [7] "="
#> [8] "3.79"
#> [9] "Inhibition of wild type EGFR in mouse BaF3 cells assessed as reduction in cell proliferation incubated for 72 hrs by Celltiter-Glo luminescent cell viability assay"
#> [10] "Confirmatory"
#> [11] "32619886"
#>
#>
#> $Table$Row[[100]]
#> $Table$Row[[100]]$Cell
#> [1] "1740135"
#> [2] "461558880"
#> [3] "162674154"
#> [4] "Inconclusive"
#> [5] "13649"
#> [6] "GI50"
#> [7] ""
#> [8] ""
#> [9] "Inhibition of wild type EGFR in mouse BaF3 cells assessed as reduction in cell proliferation incubated for 72 hrs by Celltiter-Glo luminescent cell viability assay"
#> [10] "Confirmatory"
#> [11] "32619886"
#>
#>
#> $Table$Row[[101]]
#> $Table$Row[[101]]$Cell
#> [1] "1740135"
#> [2] "461562991"
#> [3] "162677073"
#> [4] "Unspecified"
#> [5] "13649"
#> [6] "GI50"
#> [7] ">"
#> [8] "10"
#> [9] "Inhibition of wild type EGFR in mouse BaF3 cells assessed as reduction in cell proliferation incubated for 72 hrs by Celltiter-Glo luminescent cell viability assay"
#> [10] "Confirmatory"
#> [11] "32619886"
#>
#>
#> $Table$Row[[102]]
#> $Table$Row[[102]]$Cell
#> [1] "1815786"
#> [2] "475982343"
#> [3] "166627448"
#> [4] "Unspecified"
#> [5] "13649"
#> [6] ""
#> [7] ""
#> [8] ""
#> [9] "Inhibition of EGFR phosphorylation in mouse BaF3 cells expressing EGFR 19Del/T790M/C797S triple mutant measured after 2 hrs by Western blotting"
#> [10] "Other"
#> [11] "35178175"
#>
#>
#> $Table$Row[[103]]
#> $Table$Row[[103]]$Cell
#> [1] "1815820"
#> [2] "475982343"
#> [3] "166627448"
#> [4] "Unspecified"
#> [5] "13649"
#> [6] ""
#> [7] ""
#> [8] ""
#> [9] "Inhibition of EGFR phosphorylation in mouse BaF3 cells expressing EGFR L858R/T790M/C797S triple mutant measured after 2 hrs by Western blotting"
#> [10] "Other"
#> [11] "35178175"
#>
#>
#> $Table$Row[[104]]
#> $Table$Row[[104]]$Cell
#> [1] "1862914"
#> [2] "482063640"
#> [3] "155431347"
#> [4] "Active"
#> [5] "13649"
#> [6] ""
#> [7] ""
#> [8] ""
#> [9] "In vivo inhibition of EGFR phosphorylation in nude mouse implanted with mouse BaF3 cells harboring EGFR del18/T790M/C797S triple mutant at 20 mg/kg, po administered as single dose and measured upto 24 hrs by Western blot analysis"
#> [10] "Other"
#> [11] "35810715"
#>
#>
#> $Table$Row[[105]]
#> $Table$Row[[105]]$Cell
#> [1] "1896806"
#> [2] "482061797"
#> [3] "166176964"
#> [4] "Unspecified"
#> [5] "13649"
#> [6] ""
#> [7] ""
#> [8] ""
#> [9] "Inhibition of Wild type EGFR in mouse BaF3 cells assessed as protein phosphorylation at 10 to 1000 nM incubated for 8 hrs by Western blot analysis"
#> [10] "Other"
#> [11] "36384036"
#>
#>
#> $Table$Row[[106]]
#> $Table$Row[[106]]$Cell
#> [1] "1896806"
#> [2] "482062269"
#> [3] "168280117"
#> [4] "Unspecified"
#> [5] "13649"
#> [6] ""
#> [7] ""
#> [8] ""
#> [9] "Inhibition of Wild type EGFR in mouse BaF3 cells assessed as protein phosphorylation at 10 to 1000 nM incubated for 8 hrs by Western blot analysis"
#> [10] "Other"
#> [11] "36384036"
#>
#>
#> $Table$Row[[107]]
#> $Table$Row[[107]]$Cell
#> [1] "1972653"
#> [2] "174505192"
#> [3] "11511120"
#> [4] "Active"
#> [5] "13649"
#> [6] "IC50"
#> [7] "="
#> [8] "0.01995"
#> [9] "Inhibition of C-terminal his6-tagged mouse EGFR by TR-FRET assay"
#> [10] "Confirmatory"
#> [11] "37647129"
#>
#>
#> $Table$Row[[108]]
#> $Table$Row[[108]]$Cell
#> [1] "1972653"
#> [2] "504828024"
#> [3] "172462736"
#> [4] "Active"
#> [5] "13649"
#> [6] "IC50"
#> [7] "="
#> [8] "0.05012"
#> [9] "Inhibition of C-terminal his6-tagged mouse EGFR by TR-FRET assay"
#> [10] "Confirmatory"
#> [11] "37647129"
#>
#>
#> $Table$Row[[109]]
#> $Table$Row[[109]]$Cell
#> [1] "1972653"
#> [2] "504838405"
#> [3] "172470044"
#> [4] "Active"
#> [5] "13649"
#> [6] "IC50"
#> [7] "="
#> [8] "0.15849"
#> [9] "Inhibition of C-terminal his6-tagged mouse EGFR by TR-FRET assay"
#> [10] "Confirmatory"
#> [11] "37647129"
#>
#>
#> $Table$Row[[110]]
#> $Table$Row[[110]]$Cell
#> [1] "1972653"
#> [2] "504840308"
#> [3] "172471323"
#> [4] "Active"
#> [5] "13649"
#> [6] "IC50"
#> [7] "="
#> [8] "0.007943"
#> [9] "Inhibition of C-terminal his6-tagged mouse EGFR by TR-FRET assay"
#> [10] "Confirmatory"
#> [11] "37647129"
#>
#>
#> $Table$Row[[111]]
#> $Table$Row[[111]]$Cell
#> [1] "1975403"
#> [2] "440197370"
#> [3] "25740"
#> [4] "Unspecified"
#> [5] "13649"
#> [6] "IC50"
#> [7] "="
#> [8] "199.526"
#> [9] "Displacement of probe N-(4-(4-(3-((4-((3-chloro-4-fluorophenyl)amino)-7-methoxyquinazolin-6-yl)oxy)propyl)piperazin-1-yl)-4-oxobutyl)-3-(5,5-difluoro-7,9-dimethyl-5H-5l4,6l4-dipyrrolo[1,2-c:2',1'-f][1,3,2]diazaborinin-3-yl)propenamide from C-terminal His-tagged wild type mouse EGFR incubated for 30 mins by probe displacement based TR-FRET assay"
#> [10] "Confirmatory"
#> [11] "37418825"
#>
#>
#> $Table$Row[[112]]
#> $Table$Row[[112]]$Cell
#> [1] "1975403"
#> [2] "504793989"
#> [3] "28958571"
#> [4] "Unspecified"
#> [5] "13649"
#> [6] "IC50"
#> [7] ">"
#> [8] "1000"
#> [9] "Displacement of probe N-(4-(4-(3-((4-((3-chloro-4-fluorophenyl)amino)-7-methoxyquinazolin-6-yl)oxy)propyl)piperazin-1-yl)-4-oxobutyl)-3-(5,5-difluoro-7,9-dimethyl-5H-5l4,6l4-dipyrrolo[1,2-c:2',1'-f][1,3,2]diazaborinin-3-yl)propenamide from C-terminal His-tagged wild type mouse EGFR incubated for 30 mins by probe displacement based TR-FRET assay"
#> [10] "Confirmatory"
#> [11] "37418825"
#>
#>
#> $Table$Row[[113]]
#> $Table$Row[[113]]$Cell
#> [1] "1975403"
#> [2] "504810459"
#> [3] "172450561"
#> [4] "Unspecified"
#> [5] "13649"
#> [6] "IC50"
#> [7] "="
#> [8] "125.893"
#> [9] "Displacement of probe N-(4-(4-(3-((4-((3-chloro-4-fluorophenyl)amino)-7-methoxyquinazolin-6-yl)oxy)propyl)piperazin-1-yl)-4-oxobutyl)-3-(5,5-difluoro-7,9-dimethyl-5H-5l4,6l4-dipyrrolo[1,2-c:2',1'-f][1,3,2]diazaborinin-3-yl)propenamide from C-terminal His-tagged wild type mouse EGFR incubated for 30 mins by probe displacement based TR-FRET assay"
#> [10] "Confirmatory"
#> [11] "37418825"
#>
#>
#> $Table$Row[[114]]
#> $Table$Row[[114]]$Cell
#> [1] "1975403"
#> [2] "504811151"
#> [3] "16645749"
#> [4] "Unspecified"
#> [5] "13649"
#> [6] "IC50"
#> [7] "="
#> [8] "398.107"
#> [9] "Displacement of probe N-(4-(4-(3-((4-((3-chloro-4-fluorophenyl)amino)-7-methoxyquinazolin-6-yl)oxy)propyl)piperazin-1-yl)-4-oxobutyl)-3-(5,5-difluoro-7,9-dimethyl-5H-5l4,6l4-dipyrrolo[1,2-c:2',1'-f][1,3,2]diazaborinin-3-yl)propenamide from C-terminal His-tagged wild type mouse EGFR incubated for 30 mins by probe displacement based TR-FRET assay"
#> [10] "Confirmatory"
#> [11] "37418825"
#>
#>
#> $Table$Row[[115]]
#> $Table$Row[[115]]$Cell
#> [1] "1975403"
#> [2] "504817004"
#> [3] "172455097"
#> [4] "Unspecified"
#> [5] "13649"
#> [6] "IC50"
#> [7] ">"
#> [8] "1000"
#> [9] "Displacement of probe N-(4-(4-(3-((4-((3-chloro-4-fluorophenyl)amino)-7-methoxyquinazolin-6-yl)oxy)propyl)piperazin-1-yl)-4-oxobutyl)-3-(5,5-difluoro-7,9-dimethyl-5H-5l4,6l4-dipyrrolo[1,2-c:2',1'-f][1,3,2]diazaborinin-3-yl)propenamide from C-terminal His-tagged wild type mouse EGFR incubated for 30 mins by probe displacement based TR-FRET assay"
#> [10] "Confirmatory"
#> [11] "37418825"
#>
#>
#> $Table$Row[[116]]
#> $Table$Row[[116]]$Cell
#> [1] "1975403"
#> [2] "504824391"
#> [3] "116653986"
#> [4] "Unspecified"
#> [5] "13649"
#> [6] "IC50"
#> [7] ">"
#> [8] "1000"
#> [9] "Displacement of probe N-(4-(4-(3-((4-((3-chloro-4-fluorophenyl)amino)-7-methoxyquinazolin-6-yl)oxy)propyl)piperazin-1-yl)-4-oxobutyl)-3-(5,5-difluoro-7,9-dimethyl-5H-5l4,6l4-dipyrrolo[1,2-c:2',1'-f][1,3,2]diazaborinin-3-yl)propenamide from C-terminal His-tagged wild type mouse EGFR incubated for 30 mins by probe displacement based TR-FRET assay"
#> [10] "Confirmatory"
#> [11] "37418825"
#>
#>
#> $Table$Row[[117]]
#> $Table$Row[[117]]$Cell
#> [1] "1975403"
#> [2] "504828130"
#> [3] "47401324"
#> [4] "Unspecified"
#> [5] "13649"
#> [6] "IC50"
#> [7] "="
#> [8] "794.328"
#> [9] "Displacement of probe N-(4-(4-(3-((4-((3-chloro-4-fluorophenyl)amino)-7-methoxyquinazolin-6-yl)oxy)propyl)piperazin-1-yl)-4-oxobutyl)-3-(5,5-difluoro-7,9-dimethyl-5H-5l4,6l4-dipyrrolo[1,2-c:2',1'-f][1,3,2]diazaborinin-3-yl)propenamide from C-terminal His-tagged wild type mouse EGFR incubated for 30 mins by probe displacement based TR-FRET assay"
#> [10] "Confirmatory"
#> [11] "37418825"
#>
#>
#> $Table$Row[[118]]
#> $Table$Row[[118]]$Cell
#> [1] "1975403"
#> [2] "504839027"
#> [3] "110755096"
#> [4] "Unspecified"
#> [5] "13649"
#> [6] "IC50"
#> [7] "="
#> [8] "100"
#> [9] "Displacement of probe N-(4-(4-(3-((4-((3-chloro-4-fluorophenyl)amino)-7-methoxyquinazolin-6-yl)oxy)propyl)piperazin-1-yl)-4-oxobutyl)-3-(5,5-difluoro-7,9-dimethyl-5H-5l4,6l4-dipyrrolo[1,2-c:2',1'-f][1,3,2]diazaborinin-3-yl)propenamide from C-terminal His-tagged wild type mouse EGFR incubated for 30 mins by probe displacement based TR-FRET assay"
#> [10] "Confirmatory"
#> [11] "37418825"
#>
#>
#> $Table$Row[[119]]
#> $Table$Row[[119]]$Cell
#> [1] "1977970"
#> [2] "312367127"
#> [3] "71496458"
#> [4] "Active"
#> [5] "13649"
#> [6] "IC50"
#> [7] "="
#> [8] "0.009"
#> [9] "Inhibition of wild type EGFR in mouse BaF3 cells assessed as cell growth inhibition measured after 72 hrs by CellTiter-Glo assay"
#> [10] "Confirmatory"
#> [11] "37952262"
#>
#>
#> $Table$Row[[120]]
#> $Table$Row[[120]]$Cell
#> [1] "1977970"
#> [2] "404712229"
#> [3] "45370166"
#> [4] "Unspecified"
#> [5] "13649"
#> [6] "IC50"
#> [7] ">"
#> [8] "10"
#> [9] "Inhibition of wild type EGFR in mouse BaF3 cells assessed as cell growth inhibition measured after 72 hrs by CellTiter-Glo assay"
#> [10] "Confirmatory"
#> [11] "37952262"
#>
#>
#> $Table$Row[[121]]
#> $Table$Row[[121]]$Cell
#> [1] "1977970"
#> [2] "504823183"
#> [3] "169450484"
#> [4] "Active"
#> [5] "13649"
#> [6] "IC50"
#> [7] "="
#> [8] "1.45"
#> [9] "Inhibition of wild type EGFR in mouse BaF3 cells assessed as cell growth inhibition measured after 72 hrs by CellTiter-Glo assay"
#> [10] "Confirmatory"
#> [11] "37952262"Pathways from Protein: Provides a list of pathways involving a specific protein. For example, for protein accession P00533:
result <- get_pug_rest(identifier = "P00533", namespace = "accession", domain = "protein", operation = "pwaccs", output = "TXT")
result
#>
#> An object of class 'PugRestInstance'
#>
#> Request Details:
#> - Domain: Protein
#> - Namespace: DomainSpecific
#> - Operation: pwaccs
#> - Identifier: P00533
#>
#> NOTE: Run getter function 'pubChemData(...)' to extract raw data retrieved from PubChem Database.
#> See ?pubChemData for details.pubChemData(result)
#> Text
#> 1 PathBank:SMP0000472
#> 2 PathBank:SMP0000473
#> 3 PathBank:SMP0000474
#> 4 PathBank:SMP0000475
#> 5 PathBank:SMP0000476
#> 6 PathBank:SMP0063810
#> 7 PathBank:SMP0063811
#> 8 Pathway Interaction Database:a6b1_a6b4_integrin_pathway
#> 9 Pathway Interaction Database:ajdiss_2pathway
#> 10 Pathway Interaction Database:arf6_pathway
#> 11 Pathway Interaction Database:ecadherin_keratinocyte_pathway
#> 12 Pathway Interaction Database:ecadherin_stabilization_pathway
#> 13 Pathway Interaction Database:erbb1_downstream_pathway
#> 14 Pathway Interaction Database:erbb1_internalization_pathway
#> 15 Pathway Interaction Database:erbb_network_pathway
#> 16 Pathway Interaction Database:et_egfrpathway
#> 17 Pathway Interaction Database:lysophospholipid_pathway
#> 18 Pathway Interaction Database:p53downstreampathway
#> 19 Pathway Interaction Database:ptp1bpathway
#> 20 Pathway Interaction Database:shp2_pathway
#> 21 Pathway Interaction Database:syndecan_3_pathway
#> 22 Pathway Interaction Database:tcptp_pathway
#> 23 Pathway Interaction Database:telomerasepathway
#> 24 Pathway Interaction Database:txa2pathway
#> 25 Pathway Interaction Database:upa_upar_pathway
#> 26 PharmGKB:PA152325160
#> 27 PharmGKB:PA154426903
#> 28 PharmGKB:PA162356267
#> 29 PharmGKB:PA165980050
#> 30 Reactome:R-HSA-1227986
#> 31 Reactome:R-HSA-1227990
#> 32 Reactome:R-HSA-1236394
#> 33 Reactome:R-HSA-1266738
#> 34 Reactome:R-HSA-157118
#> 35 Reactome:R-HSA-162582
#> 36 Reactome:R-HSA-1643685
#> 37 Reactome:R-HSA-1643713
#> 38 Reactome:R-HSA-177929
#> 39 Reactome:R-HSA-179812
#> 40 Reactome:R-HSA-180292
#> 41 Reactome:R-HSA-180336
#> 42 Reactome:R-HSA-182971
#> 43 Reactome:R-HSA-199991
#> 44 Reactome:R-HSA-212436
#> 45 Reactome:R-HSA-212718
#> 46 Reactome:R-HSA-2179392
#> 47 Reactome:R-HSA-372790
#> 48 Reactome:R-HSA-373760
#> 49 Reactome:R-HSA-388396
#> 50 Reactome:R-HSA-416476
#> 51 Reactome:R-HSA-422475
#> 52 Reactome:R-HSA-445144
#> 53 Reactome:R-HSA-5637810
#> 54 Reactome:R-HSA-5637812
#> 55 Reactome:R-HSA-5638302
#> 56 Reactome:R-HSA-5638303
#> 57 Reactome:R-HSA-5653656
#> 58 Reactome:R-HSA-5663202
#> 59 Reactome:R-HSA-73857
#> 60 Reactome:R-HSA-74160
#> 61 Reactome:R-HSA-881907
#> 62 Reactome:R-HSA-8848021
#> 63 Reactome:R-HSA-8856825
#> 64 Reactome:R-HSA-8856828
#> 65 Reactome:R-HSA-8857538
#> 66 Reactome:R-HSA-8864260
#> 67 Reactome:R-HSA-8866910
#> 68 Reactome:R-HSA-8939211
#> 69 Reactome:R-HSA-9006927
#> 70 Reactome:R-HSA-9006931
#> 71 Reactome:R-HSA-9006934
#> 72 Reactome:R-HSA-9009391
#> 73 Reactome:R-HSA-9012852
#> 74 Reactome:R-HSA-9013507
#> 75 Reactome:R-HSA-9634638
#> 76 Reactome:R-HSA-9664565
#> 77 Reactome:R-HSA-9665348
#> 78 Reactome:R-HSA-9665686
#> 79 Reactome:R-HSA-9675108
#> 80 WikiPathways:WP1984
#> 81 WikiPathways:WP2643
#> 82 WikiPathways:WP2840
#> 83 WikiPathways:WP5144
#> 84 WikiPathways:WP5158
#> 85 WikiPathways:WP5322These methods offer a comprehensive approach to accessing and analyzing protein-related data in PubChem, supporting a wide range of research applications in the fields of biochemistry, molecular biology, and pharmacology.
PubChem’s PUG REST service offers a detailed and comprehensive approach to accessing pathway information, crucial for researchers in fields like bioinformatics, pharmacology, and molecular biology. Here’s how to utilize PUG REST for pathway-related queries:
1. Pathway Input Methods:
By Pathway Accession: The primary method to access pathway data in PubChem. Pathway Accession is formatted as Source:ID. For example, to get a summary for the Reactome pathway R-HSA-70171 in JSON format:
result <- get_pug_rest(identifier = "Reactome:R-HSA-70171", namespace = "pwacc", domain = "pathway", operation = "summary", output = "JSON")
result
#>
#> An object of class 'PugRestInstance'
#>
#> Request Details:
#> - Domain: DomainSpecific (pathway)
#> - Namespace: DomainSpecific
#> - Operation: summary
#> - Identifier: Reactome:R-HSA-70171
#>
#> NOTE: Run getter function 'pubChemData(...)' to extract raw data retrieved from PubChem Database.
#> See ?pubChemData for details.pubChemData(result)
#> $PathwaySummaries
#> $PathwaySummaries$PathwaySummary
#> $PathwaySummaries$PathwaySummary[[1]]
#> $PathwaySummaries$PathwaySummary[[1]]$PathwayAccession
#> [1] "Reactome:R-HSA-70171"
#>
#> $PathwaySummaries$PathwaySummary[[1]]$SourceName
#> [1] "Reactome"
#>
#> $PathwaySummaries$PathwaySummary[[1]]$SourceID
#> [1] "R-HSA-70171"
#>
#> $PathwaySummaries$PathwaySummary[[1]]$SourceURL
#> [1] "https://reactome.org/content/detail/R-HSA-70171"
#>
#> $PathwaySummaries$PathwaySummary[[1]]$Name
#> [1] "Glycolysis"
#>
#> $PathwaySummaries$PathwaySummary[[1]]$Type
#> [1] "organism_specific"
#>
#> $PathwaySummaries$PathwaySummary[[1]]$Category
#> [1] "pathway"
#>
#> $PathwaySummaries$PathwaySummary[[1]]$Description
#> [1] "The reactions of glycolysis (e.g., van Wijk and van Solinge 2005) convert glucose 6-phosphate to pyruvate. The entire process is cytosolic. Glucose 6-phosphate is reversibly isomerized to form fructose 6-phosphate. Phosphofructokinase 1 catalyzes the physiologically irreversible phosphorylation of fructose 6-phosphate to form fructose 1,6-bisphosphate. In six reversible reactions, fructose 1,6-bisphosphate is converted to two molecules of phosphoenolpyruvate and two molecules of NAD+ are reduced to NADH + H+. Each molecule of phosphoenolpyruvate reacts with ADP to form ATP and pyruvate in a physiologically irreversible reaction. Under aerobic conditions the NADH +H+ can be reoxidized to NAD+ via electron transport to yield additional ATP, while under anaerobic conditions or in cells lacking mitochondria NAD+ can be regenerated via the reduction of pyruvate to lactate."
#>
#> $PathwaySummaries$PathwaySummary[[1]]$TaxonomyID
#> [1] 9606
#>
#> $PathwaySummaries$PathwaySummary[[1]]$Taxonomy
#> [1] "Homo sapiens (human)"2. Available Pathway Data:
Pathway Summary: Returns a summary including PathwayAccession, SourceName, Name, Type, Category, Description, TaxonomyID, and Taxonomy. For example:
result <- get_pug_rest(identifier = "Reactome:R-HSA-70171,BioCyc:HUMAN_PWY-4983", namespace = "pwacc", domain = "pathway", operation = "summary", output = "JSON")
result
#>
#> An object of class 'PugRestInstance'
#>
#> Request Details:
#> - Domain: DomainSpecific (pathway)
#> - Namespace: DomainSpecific
#> - Operation: summary
#> - Identifier: Reactome:R-HSA-70171,BioCyc:HUMAN_PWY-4983
#>
#> NOTE: Run getter function 'pubChemData(...)' to extract raw data retrieved from PubChem Database.
#> See ?pubChemData for details.pubChemData(result)
#> $PathwaySummaries
#> $PathwaySummaries$PathwaySummary
#> $PathwaySummaries$PathwaySummary[[1]]
#> $PathwaySummaries$PathwaySummary[[1]]$PathwayAccession
#> [1] "Reactome:R-HSA-70171"
#>
#> $PathwaySummaries$PathwaySummary[[1]]$SourceName
#> [1] "Reactome"
#>
#> $PathwaySummaries$PathwaySummary[[1]]$SourceID
#> [1] "R-HSA-70171"
#>
#> $PathwaySummaries$PathwaySummary[[1]]$SourceURL
#> [1] "https://reactome.org/content/detail/R-HSA-70171"
#>
#> $PathwaySummaries$PathwaySummary[[1]]$Name
#> [1] "Glycolysis"
#>
#> $PathwaySummaries$PathwaySummary[[1]]$Type
#> [1] "organism_specific"
#>
#> $PathwaySummaries$PathwaySummary[[1]]$Category
#> [1] "pathway"
#>
#> $PathwaySummaries$PathwaySummary[[1]]$Description
#> [1] "The reactions of glycolysis (e.g., van Wijk and van Solinge 2005) convert glucose 6-phosphate to pyruvate. The entire process is cytosolic. Glucose 6-phosphate is reversibly isomerized to form fructose 6-phosphate. Phosphofructokinase 1 catalyzes the physiologically irreversible phosphorylation of fructose 6-phosphate to form fructose 1,6-bisphosphate. In six reversible reactions, fructose 1,6-bisphosphate is converted to two molecules of phosphoenolpyruvate and two molecules of NAD+ are reduced to NADH + H+. Each molecule of phosphoenolpyruvate reacts with ADP to form ATP and pyruvate in a physiologically irreversible reaction. Under aerobic conditions the NADH +H+ can be reoxidized to NAD+ via electron transport to yield additional ATP, while under anaerobic conditions or in cells lacking mitochondria NAD+ can be regenerated via the reduction of pyruvate to lactate."
#>
#> $PathwaySummaries$PathwaySummary[[1]]$TaxonomyID
#> [1] 9606
#>
#> $PathwaySummaries$PathwaySummary[[1]]$Taxonomy
#> [1] "Homo sapiens (human)"
#>
#>
#> $PathwaySummaries$PathwaySummary[[2]]
#> $PathwaySummaries$PathwaySummary[[2]]$PathwayAccession
#> [1] "BioCyc:HUMAN_PWY-4983"
#>
#> $PathwaySummaries$PathwaySummary[[2]]$SourceName
#> [1] "BioCyc"
#>
#> $PathwaySummaries$PathwaySummary[[2]]$SourceID
#> [1] "PWY-4983"
#>
#> $PathwaySummaries$PathwaySummary[[2]]$SourceURL
#> [1] "https://biocyc.org/pathway?orgid=HUMAN&id=PWY-4983"
#>
#> $PathwaySummaries$PathwaySummary[[2]]$Name
#> [1] "citrulline-nitric oxide cycle"
#>
#> $PathwaySummaries$PathwaySummary[[2]]$Type
#> [1] "organism_specific"
#>
#> $PathwaySummaries$PathwaySummary[[2]]$Category
#> [1] "pathway"
#>
#> $PathwaySummaries$PathwaySummary[[2]]$Description
#> [1] "<b>General Background</b>\n\n|FRAME: NITRIC-OXIDE \"Nitric oxide\"| (NO) is the active moiety of the endothelium-derived relaxing factor. In the vasculature NO relaxes smooth muscle and inhibits platelet and leukocyte adhesion. Outside the vasculature, NO participates in the immunologic response to infection. It serves as a neurotransmitter and plays an important role in cell signaling in the nervous system, and in synaptic plasticity. \n\nNitric oxide synthases are a family of enzymes responsible for the NADPH dependent synthesis of nitric oxide from |FRAME: ARG| and oxygen in the |FRAME: PWY-4983|.\n\n<b>About this Pathway</b>\n\n|FRAME: NITRIC-OXIDE \"Nitric oxide\"| can be synthesized by three nitric oxide synthases from |FRAME: ARG| generating |FRAME:L-CITRULLINE| as a by-product. In this cycle, arginine forms NO and citrulline, and is subsequently regenerated from citrulline by the action of the enzymes |FRAME:CPLX-6641| and |FRAME:CPLX-6661|. These two enzymes are shared with the |FRAME: PWY-4984|. Citrulline is also required in |FRAME: PWY-4921|.\n\nThe citrulline-NO cycle functions in many different types of cells. It has been demonstrated in epithelial cells, chondrocytes, endothelial cells, macrophages and neurons |CITS: [2236071]||CITS:[1731766]|.\n\nThe enzymes |FRAME: CPLX-6641| and |FRAME: CPLX-6661| confer cells with the capacity to produce NO without the need for exogenous arginine. In vascular smooth muscle cells |FRAME: CPLX-6661| is constitutively expressed but |FRAME: CPLX-6641| is inducible by cytokines and bacterial endotoxin |CITS:[7511585]|."
#>
#> $PathwaySummaries$PathwaySummary[[2]]$TaxonomyID
#> [1] 9606
#>
#> $PathwaySummaries$PathwaySummary[[2]]$Taxonomy
#> [1] "Homo sapiens (human)"Compounds from Pathway: Retrieves a list of compounds involved in a specific pathway. For example, for the Reactome pathway R-HSA-70171:
result <- get_pug_rest(identifier = "Reactome:R-HSA-70171", namespace = "pwacc", domain = "pathway", operation = "cids", output = "TXT")
result
#>
#> An object of class 'PugRestInstance'
#>
#> Request Details:
#> - Domain: DomainSpecific (pathway)
#> - Namespace: DomainSpecific
#> - Operation: cids
#> - Identifier: Reactome:R-HSA-70171
#>
#> NOTE: Run getter function 'pubChemData(...)' to extract raw data retrieved from PubChem Database.
#> See ?pubChemData for details.pubChemData(result)
#> Text
#> 1 223
#> 2 813
#> 3 888
#> 4 962
#> 5 1038
#> 6 5793
#> 7 31348
#> 8 65246
#> 9 107735
#> 10 152306
#> 11 3674425
#> 12 3681305
#> 13 4643300
#> 14 5459820
#> 15 5460765
#> 16 5461108
#> 17 7058055
#> 18 7059571
#> 19 15938965
#> 20 15938971
#> 21 21117974
#> 22 21604863
#> 23 21604864
#> 24 21604869
#> 25 24794350
#> 26 25200383
#> 27 25201676
#> 28 25244770
#> 29 25245548
#> 30 40467846
#> 31 45266541
#> 32 46878409Genes from Pathway: Provides a list of genes involved in a specific pathway. For example, for the Reactome pathway R-HSA-70171:
result <- get_pug_rest(identifier = "Reactome:R-HSA-70171", namespace = "pwacc", domain = "pathway", operation = "geneids", output = "TXT")
result
#>
#> An object of class 'PugRestInstance'
#>
#> Request Details:
#> - Domain: DomainSpecific (pathway)
#> - Namespace: DomainSpecific
#> - Operation: geneids
#> - Identifier: Reactome:R-HSA-70171
#>
#> NOTE: Run getter function 'pubChemData(...)' to extract raw data retrieved from PubChem Database.
#> See ?pubChemData for details.pubChemData(result)
#> Text
#> 1 226
#> 2 229
#> 3 230
#> 4 669
#> 5 2023
#> 6 2026
#> 7 2027
#> 8 2597
#> 9 2645
#> 10 2646
#> 11 2821
#> 12 4927
#> 13 5207
#> 14 5208
#> 15 5209
#> 16 5210
#> 17 5211
#> 18 5213
#> 19 5214
#> 20 5223
#> 21 5224
#> 22 5230
#> 23 5232
#> 24 5528
#> 25 5903
#> 26 6396
#> 27 7167
#> 28 7175
#> 29 8021
#> 30 8086
#> 31 8480
#> 32 9631
#> 33 9688
#> 34 9972
#> 35 10007
#> 36 10762
#> 37 11097
#> 38 23165
#> 39 23225
#> 40 23279
#> 41 23511
#> 42 23636
#> 43 26330
#> 44 53371
#> 45 55706
#> 46 55746
#> 47 57122
#> 48 79023
#> 49 79902
#> 50 83440
#> 51 129401
#> 52 132789
#> 53 283209
#> 54 348995
#> 55 387712Proteins from Pathway: Returns a list of proteins involved in a given pathway. For example, for the Reactome pathway R-HSA-70171:
result <- get_pug_rest(identifier = "Reactome:R-HSA-70171", namespace = "pwacc", domain = "pathway", operation = "accessions", output = "TXT")
result
#>
#> An object of class 'PugRestInstance'
#>
#> Request Details:
#> - Domain: DomainSpecific (pathway)
#> - Namespace: DomainSpecific
#> - Operation: accessions
#> - Identifier: Reactome:R-HSA-70171
#>
#> NOTE: Run getter function 'pubChemData(...)' to extract raw data retrieved from PubChem Database.
#> See ?pubChemData for details.pubChemData(result)
#> Text
#> 1 A6NNW6
#> 2 O14556
#> 3 O15504
#> 4 O60825
#> 5 O75694
#> 6 P00558
#> 7 P04075
#> 8 P04406
#> 9 P05062
#> 10 P06733
#> 11 P06744
#> 12 P07205
#> 13 P07738
#> 14 P08237
#> 15 P09104
#> 16 P09972
#> 17 P12270
#> 18 P13929
#> 19 P14618-1
#> 20 P14618-2
#> 21 P15259
#> 22 P16118
#> 23 P17858
#> 24 P18669
#> 25 P35557
#> 26 P35658
#> 27 P37198
#> 28 P46926
#> 29 P49790
#> 30 P49792
#> 31 P52948-5
#> 32 P55735
#> 33 P57740
#> 34 P60174
#> 35 P78406
#> 36 Q01813
#> 37 Q12769
#> 38 Q14397
#> 39 Q14738
#> 40 Q16875
#> 41 Q16877
#> 42 Q5SRE5
#> 43 Q6PCE3
#> 44 Q7Z3B4
#> 45 Q8N1F7
#> 46 Q8NFH3
#> 47 Q8NFH4
#> 48 Q8NFH5
#> 49 Q8TDQ7
#> 50 Q8TEM1
#> 51 Q8WUM0
#> 52 Q92621
#> 53 Q96EE3-1
#> 54 Q96EE3-2
#> 55 Q99567
#> 56 Q9BRR6
#> 57 Q9BTX1
#> 58 Q9BW27
#> 59 Q9NRG9
#> 60 Q9UKX7These methods offer a streamlined and efficient way to access and analyze pathway-related data in PubChem, supporting a wide range of research applications in bioinformatics, molecular biology, and related fields.
PubChem’s PUG REST service provides a comprehensive approach to accessing taxonomy information, essential for researchers in fields like biology, pharmacology, and environmental science. Here’s how to utilize PUG REST for taxonomy-related queries:
1. Taxonomy Input Methods:
By Taxonomy ID: The primary method to access taxonomy data in PubChem using NCBI Taxonomy identifiers. For example, to get a summary for human (Taxonomy ID 9606) and SARS-CoV-2 (Taxonomy ID 2697049) in JSON format:
result <- get_pug_rest(identifier = "9606,2697049", namespace = "taxid", domain = "taxonomy", operation = "summary", output = "JSON")
result
#>
#> An object of class 'PugRestInstance'
#>
#> Request Details:
#> - Domain: Taxonomy
#> - Namespace: DomainSpecific
#> - Operation: summary
#> - Identifier: 9606,2697049
#>
#> NOTE: Run getter function 'pubChemData(...)' to extract raw data retrieved from PubChem Database.
#> See ?pubChemData for details.pubChemData(result)
#> $TaxonomySummaries
#> $TaxonomySummaries$TaxonomySummary
#> $TaxonomySummaries$TaxonomySummary[[1]]
#> $TaxonomySummaries$TaxonomySummary[[1]]$TaxonomyID
#> [1] 9606
#>
#> $TaxonomySummaries$TaxonomySummary[[1]]$ScientificName
#> [1] "Homo sapiens"
#>
#> $TaxonomySummaries$TaxonomySummary[[1]]$CommonName
#> [1] "human"
#>
#> $TaxonomySummaries$TaxonomySummary[[1]]$Rank
#> [1] "species"
#>
#> $TaxonomySummaries$TaxonomySummary[[1]]$RankedLineage
#> Species Genus Family Order Class Phylum Kingdom Superkingdom
#> "" "Homo" "Hominidae" "Primates" "Mammalia" "Chordata" "Metazoa" "Eukaryota"
#>
#> $TaxonomySummaries$TaxonomySummary[[1]]$Synonym
#> [1] "Homo sapiens Linnaeus, 1758" "Homo sapiens" "human"
#>
#>
#> $TaxonomySummaries$TaxonomySummary[[2]]
#> $TaxonomySummaries$TaxonomySummary[[2]]$TaxonomyID
#> [1] 2697049
#>
#> $TaxonomySummaries$TaxonomySummary[[2]]$ScientificName
#> [1] "Severe acute respiratory syndrome coronavirus 2"
#>
#> $TaxonomySummaries$TaxonomySummary[[2]]$CommonName
#> [1] ""
#>
#> $TaxonomySummaries$TaxonomySummary[[2]]$Rank
#> [1] "no rank"
#>
#> $TaxonomySummaries$TaxonomySummary[[2]]$RankedLineage
#> Species Genus
#> "Severe acute respiratory syndrome-related coronavirus" "Betacoronavirus"
#> Family Order
#> "Coronaviridae" "Nidovirales"
#> Class Phylum
#> "Pisoniviricetes" "Pisuviricota"
#> Kingdom Superkingdom
#> "Orthornavirae" "Viruses"
#>
#> $TaxonomySummaries$TaxonomySummary[[2]]$Synonym
#> [1] "2019-nCoV" "COVID-19 virus"
#> [3] "HCoV-19" "Human coronavirus 2019"
#> [5] "SARS-2" "SARS2"
#> [7] "SARS-CoV2" "Severe acute respiratory syndrome coronavirus 2"By Taxonomy Synonym: Access taxonomy data using synonyms like scientific or common names. For example, for Homo sapiens:
result <- get_pug_rest(identifier = "Homo sapiens", namespace = "synonym", domain = "taxonomy", operation = "summary", output = "JSON")
result
#>
#> An object of class 'PugRestInstance'
#>
#> Request Details:
#> - Domain: Taxonomy
#> - Namespace: DomainSpecific
#> - Operation: summary
#> - Identifier: Homo sapiens
#>
#> NOTE: Run getter function 'pubChemData(...)' to extract raw data retrieved from PubChem Database.
#> See ?pubChemData for details.pubChemData(result)
#> $TaxonomySummaries
#> $TaxonomySummaries$TaxonomySummary
#> $TaxonomySummaries$TaxonomySummary[[1]]
#> $TaxonomySummaries$TaxonomySummary[[1]]$TaxonomyID
#> [1] 9606
#>
#> $TaxonomySummaries$TaxonomySummary[[1]]$ScientificName
#> [1] "Homo sapiens"
#>
#> $TaxonomySummaries$TaxonomySummary[[1]]$CommonName
#> [1] "human"
#>
#> $TaxonomySummaries$TaxonomySummary[[1]]$Rank
#> [1] "species"
#>
#> $TaxonomySummaries$TaxonomySummary[[1]]$RankedLineage
#> Species Genus Family Order Class Phylum Kingdom Superkingdom
#> "" "Homo" "Hominidae" "Primates" "Mammalia" "Chordata" "Metazoa" "Eukaryota"
#>
#> $TaxonomySummaries$TaxonomySummary[[1]]$Synonym
#> [1] "Homo sapiens Linnaeus, 1758" "Homo sapiens" "human"
#>
#>
#> $TaxonomySummaries$TaxonomySummary[[2]]
#> $TaxonomySummaries$TaxonomySummary[[2]]$TaxonomyID
#> [1] 1003795096
#>
#> $TaxonomySummaries$TaxonomySummary[[2]]$ScientificName
#> [1] "Homo sapiens"
#>
#> $TaxonomySummaries$TaxonomySummary[[2]]$CommonName
#> [1] ""
#>
#> $TaxonomySummaries$TaxonomySummary[[2]]$Rank
#> [1] "species"
#>
#> $TaxonomySummaries$TaxonomySummary[[2]]$Synonym
#> [1] "Humans" "man" "Homo sapiens" "Human"2. Available Taxonomy Data:
Taxonomy Summary: Returns a summary including TaxonomyID, ScientificName, CommonName, Rank, RankedLineage, and Synonyms. For example:
result <- get_pug_rest(identifier = "9606,10090,10116", namespace = "taxid", domain = "taxonomy", operation = "summary", output = "JSON")
result
#>
#> An object of class 'PugRestInstance'
#>
#> Request Details:
#> - Domain: Taxonomy
#> - Namespace: DomainSpecific
#> - Operation: summary
#> - Identifier: 9606,10090,10116
#>
#> NOTE: Run getter function 'pubChemData(...)' to extract raw data retrieved from PubChem Database.
#> See ?pubChemData for details.pubChemData(result)
#> $TaxonomySummaries
#> $TaxonomySummaries$TaxonomySummary
#> $TaxonomySummaries$TaxonomySummary[[1]]
#> $TaxonomySummaries$TaxonomySummary[[1]]$TaxonomyID
#> [1] 9606
#>
#> $TaxonomySummaries$TaxonomySummary[[1]]$ScientificName
#> [1] "Homo sapiens"
#>
#> $TaxonomySummaries$TaxonomySummary[[1]]$CommonName
#> [1] "human"
#>
#> $TaxonomySummaries$TaxonomySummary[[1]]$Rank
#> [1] "species"
#>
#> $TaxonomySummaries$TaxonomySummary[[1]]$RankedLineage
#> Species Genus Family Order Class Phylum Kingdom Superkingdom
#> "" "Homo" "Hominidae" "Primates" "Mammalia" "Chordata" "Metazoa" "Eukaryota"
#>
#> $TaxonomySummaries$TaxonomySummary[[1]]$Synonym
#> [1] "Homo sapiens Linnaeus, 1758" "Homo sapiens" "human"
#>
#>
#> $TaxonomySummaries$TaxonomySummary[[2]]
#> $TaxonomySummaries$TaxonomySummary[[2]]$TaxonomyID
#> [1] 10090
#>
#> $TaxonomySummaries$TaxonomySummary[[2]]$ScientificName
#> [1] "Mus musculus"
#>
#> $TaxonomySummaries$TaxonomySummary[[2]]$CommonName
#> [1] "house mouse"
#>
#> $TaxonomySummaries$TaxonomySummary[[2]]$Rank
#> [1] "species"
#>
#> $TaxonomySummaries$TaxonomySummary[[2]]$RankedLineage
#> Species Genus Family Order Class Phylum Kingdom Superkingdom
#> "" "Mus" "Muridae" "Rodentia" "Mammalia" "Chordata" "Metazoa" "Eukaryota"
#>
#> $TaxonomySummaries$TaxonomySummary[[2]]$Synonym
#> [1] "house mouse" "mouse" "Mus musculus Linnaeus, 1758"
#> [4] "Mus musculus"
#>
#>
#> $TaxonomySummaries$TaxonomySummary[[3]]
#> $TaxonomySummaries$TaxonomySummary[[3]]$TaxonomyID
#> [1] 10116
#>
#> $TaxonomySummaries$TaxonomySummary[[3]]$ScientificName
#> [1] "Rattus norvegicus"
#>
#> $TaxonomySummaries$TaxonomySummary[[3]]$CommonName
#> [1] "Norway rat"
#>
#> $TaxonomySummaries$TaxonomySummary[[3]]$Rank
#> [1] "species"
#>
#> $TaxonomySummaries$TaxonomySummary[[3]]$RankedLineage
#> Species Genus Family Order Class Phylum Kingdom Superkingdom
#> "" "Rattus" "Muridae" "Rodentia" "Mammalia" "Chordata" "Metazoa" "Eukaryota"
#>
#> $TaxonomySummaries$TaxonomySummary[[3]]$Synonym
#> [1] "brown rat" "Mus norvegicus Berkenhout, 1769" "Mus norvegicus"
#> [4] "Norway rat" "rat" "rats"
#> [7] "Rattus norvegicus"Assays and Bioactivities: Retrieves a list of assays (AIDs) associated with a given taxonomy. For example, for SARS-CoV-2:
result <- get_pug_rest(identifier = "2697049", namespace = "taxid", domain = "taxonomy", operation = "aids", output = "TXT")
result
#>
#> An object of class 'PugRestInstance'
#>
#> Request Details:
#> - Domain: Taxonomy
#> - Namespace: DomainSpecific
#> - Operation: aids
#> - Identifier: 2697049
#>
#> NOTE: Run getter function 'pubChemData(...)' to extract raw data retrieved from PubChem Database.
#> See ?pubChemData for details.pubChemData(result)
#> Text
#> 1 1409578
#> 2 1409579
#> 3 1409582
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#> 848 2030734
#> 849 2030737
#> 850 2030740
#> 851 2030743
#> 852 2030745
#> 853 2030746
#> 854 2033302
#> 855 2035436
#> 856 2036558
#> 857 2039315
#> 858 2039316To aggregate concise bioactivity data from each AID:
result <- get_pug_rest(identifier = "1409578", namespace = "aid", domain = "assay", operation = "concise", output = "JSON")
result
#>
#> An object of class 'PugRestInstance'
#>
#> Request Details:
#> - Domain: Assay
#> - Namespace: AID
#> - Operation: concise
#> - Identifier: 1409578
#>
#> NOTE: Run getter function 'pubChemData(...)' to extract raw data retrieved from PubChem Database.
#> See ?pubChemData for details.pubChemData(result)
#> $Table
#> $Table$Columns
#> $Table$Columns$Column
#> [1] "AID" "SID" "CID" "Activity Outcome" "Target Accession"
#> [6] "Target GeneID" "Activity Value [uM]" "Activity Name" "Assay Name" "Assay Type"
#> [11] "PubMed ID" "RNAi"
#>
#>
#> $Table$Row
#> $Table$Row[[1]]
#> $Table$Row[[1]]$Cell
#> [1] "1409578"
#> [2] "103196897"
#> [3] "11199915"
#> [4] "Active"
#> [5] ""
#> [6] ""
#> [7] "0.22"
#> [8] "EC50"
#> [9] "Determination of antiviral efficacy in high-content imaging assay in Vero E6 cells infected with SARS-CoV-2 (USA-WA1/2020 isolate) at MOI 0.75 after 24 hrs"
#> [10] "Confirmatory"
#> [11] ""
#> [12] ""
#>
#>
#> $Table$Row[[2]]
#> $Table$Row[[2]]$Cell
#> [1] "1409578"
#> [2] "103224052"
#> [3] "2247"
#> [4] "Active"
#> [5] ""
#> [6] ""
#> [7] "1.1"
#> [8] "EC50"
#> [9] "Determination of antiviral efficacy in high-content imaging assay in Vero E6 cells infected with SARS-CoV-2 (USA-WA1/2020 isolate) at MOI 0.75 after 24 hrs"
#> [10] "Confirmatory"
#> [11] ""
#> [12] ""
#>
#>
#> $Table$Row[[3]]
#> $Table$Row[[3]]$Cell
#> [1] "1409578"
#> [2] "103246927"
#> [3] "208917"
#> [4] "Active"
#> [5] ""
#> [6] ""
#> [7] "1.1"
#> [8] "EC50"
#> [9] "Determination of antiviral efficacy in high-content imaging assay in Vero E6 cells infected with SARS-CoV-2 (USA-WA1/2020 isolate) at MOI 0.75 after 24 hrs"
#> [10] "Confirmatory"
#> [11] ""
#> [12] ""
#>
#>
#> $Table$Row[[4]]
#> $Table$Row[[4]]$Cell
#> [1] "1409578"
#> [2] "103281094"
#> [3] "9801987"
#> [4] "Active"
#> [5] ""
#> [6] ""
#> [7] "0.75"
#> [8] "EC50"
#> [9] "Determination of antiviral efficacy in high-content imaging assay in Vero E6 cells infected with SARS-CoV-2 (USA-WA1/2020 isolate) at MOI 0.75 after 24 hrs"
#> [10] "Confirmatory"
#> [11] ""
#> [12] ""
#>
#>
#> $Table$Row[[5]]
#> $Table$Row[[5]]$Cell
#> [1] "1409578"
#> [2] "103368147"
#> [3] "6476696"
#> [4] "Active"
#> [5] ""
#> [6] ""
#> [7] "0.25"
#> [8] "EC50"
#> [9] "Determination of antiviral efficacy in high-content imaging assay in Vero E6 cells infected with SARS-CoV-2 (USA-WA1/2020 isolate) at MOI 0.75 after 24 hrs"
#> [10] "Confirmatory"
#> [11] ""
#> [12] ""
#>
#>
#> $Table$Row[[6]]
#> $Table$Row[[6]]$Cell
#> [1] "1409578"
#> [2] "103389209"
#> [3] "10316203"
#> [4] "Active"
#> [5] ""
#> [6] ""
#> [7] "1.2"
#> [8] "EC50"
#> [9] "Determination of antiviral efficacy in high-content imaging assay in Vero E6 cells infected with SARS-CoV-2 (USA-WA1/2020 isolate) at MOI 0.75 after 24 hrs"
#> [10] "Confirmatory"
#> [11] ""
#> [12] ""
#>
#>
#> $Table$Row[[7]]
#> $Table$Row[[7]]$Cell
#> [1] "1409578"
#> [2] "103439840"
#> [3] "73078"
#> [4] "Active"
#> [5] ""
#> [6] ""
#> [7] "1.1"
#> [8] "EC50"
#> [9] "Determination of antiviral efficacy in high-content imaging assay in Vero E6 cells infected with SARS-CoV-2 (USA-WA1/2020 isolate) at MOI 0.75 after 24 hrs"
#> [10] "Confirmatory"
#> [11] ""
#> [12] ""
#>
#>
#> $Table$Row[[8]]
#> $Table$Row[[8]]$Cell
#> [1] "1409578"
#> [2] "103467980"
#> [3] "11591924"
#> [4] "Active"
#> [5] ""
#> [6] ""
#> [7] "1.2"
#> [8] "EC50"
#> [9] "Determination of antiviral efficacy in high-content imaging assay in Vero E6 cells infected with SARS-CoV-2 (USA-WA1/2020 isolate) at MOI 0.75 after 24 hrs"
#> [10] "Confirmatory"
#> [11] ""
#> [12] ""
#>
#>
#> $Table$Row[[9]]
#> $Table$Row[[9]]$Cell
#> [1] "1409578"
#> [2] "103490076"
#> [3] "15984102"
#> [4] "Active"
#> [5] ""
#> [6] ""
#> [7] "0.95"
#> [8] "EC50"
#> [9] "Determination of antiviral efficacy in high-content imaging assay in Vero E6 cells infected with SARS-CoV-2 (USA-WA1/2020 isolate) at MOI 0.75 after 24 hrs"
#> [10] "Confirmatory"
#> [11] ""
#> [12] ""
#>
#>
#> $Table$Row[[10]]
#> $Table$Row[[10]]$Cell
#> [1] "1409578"
#> [2] "103626512"
#> [3] "44579921"
#> [4] "Active"
#> [5] ""
#> [6] ""
#> [7] "1.6"
#> [8] "EC50"
#> [9] "Determination of antiviral efficacy in high-content imaging assay in Vero E6 cells infected with SARS-CoV-2 (USA-WA1/2020 isolate) at MOI 0.75 after 24 hrs"
#> [10] "Confirmatory"
#> [11] ""
#> [12] ""
#>
#>
#> $Table$Row[[11]]
#> $Table$Row[[11]]$Cell
#> [1] "1409578"
#> [2] "381838043"
#> [3] "121304016"
#> [4] "Active"
#> [5] ""
#> [6] ""
#> [7] "0.62"
#> [8] "EC50"
#> [9] "Determination of antiviral efficacy in high-content imaging assay in Vero E6 cells infected with SARS-CoV-2 (USA-WA1/2020 isolate) at MOI 0.75 after 24 hrs"
#> [10] "Confirmatory"
#> [11] ""
#> [12] ""
#>
#>
#> $Table$Row[[12]]
#> $Table$Row[[12]]$Cell
#> [1] "1409578"
#> [2] "404718364"
#> [3] "10173277"
#> [4] "Active"
#> [5] ""
#> [6] ""
#> [7] "0.023"
#> [8] "EC50"
#> [9] "Determination of antiviral efficacy in high-content imaging assay in Vero E6 cells infected with SARS-CoV-2 (USA-WA1/2020 isolate) at MOI 0.75 after 24 hrs"
#> [10] "Confirmatory"
#> [11] ""
#> [12] ""
#>
#>
#> $Table$Row[[13]]
#> $Table$Row[[13]]$Cell
#> [1] "1409578"
#> [2] "405270384"
#> [3] "73715817"
#> [4] "Active"
#> [5] ""
#> [6] ""
#> [7] "0.19"
#> [8] "EC50"
#> [9] "Determination of antiviral efficacy in high-content imaging assay in Vero E6 cells infected with SARS-CoV-2 (USA-WA1/2020 isolate) at MOI 0.75 after 24 hrs"
#> [10] "Confirmatory"
#> [11] ""
#> [12] ""
#>
#>
#> $Table$Row[[14]]
#> $Table$Row[[14]]$Cell
#> [1] "1409578"
#> [2] "405270481"
#> [3] "3025960"
#> [4] "Active"
#> [5] ""
#> [6] ""
#> [7] "1.2"
#> [8] "EC50"
#> [9] "Determination of antiviral efficacy in high-content imaging assay in Vero E6 cells infected with SARS-CoV-2 (USA-WA1/2020 isolate) at MOI 0.75 after 24 hrs"
#> [10] "Confirmatory"
#> [11] ""
#> [12] ""
#>
#>
#> $Table$Row[[15]]
#> $Table$Row[[15]]$Cell
#> [1] "1409578"
#> [2] "405270549"
#> [3] "11527774"
#> [4] "Active"
#> [5] ""
#> [6] ""
#> [7] "0.14"
#> [8] "EC50"
#> [9] "Determination of antiviral efficacy in high-content imaging assay in Vero E6 cells infected with SARS-CoV-2 (USA-WA1/2020 isolate) at MOI 0.75 after 24 hrs"
#> [10] "Confirmatory"
#> [11] ""
#> [12] ""
#>
#>
#> $Table$Row[[16]]
#> $Table$Row[[16]]$Cell
#> [1] "1409578"
#> [2] "405270558"
#> [3] "70945511"
#> [4] "Active"
#> [5] ""
#> [6] ""
#> [7] "0.3"
#> [8] "EC50"
#> [9] "Determination of antiviral efficacy in high-content imaging assay in Vero E6 cells infected with SARS-CoV-2 (USA-WA1/2020 isolate) at MOI 0.75 after 24 hrs"
#> [10] "Confirmatory"
#> [11] ""
#> [12] ""
#>
#>
#> $Table$Row[[17]]
#> $Table$Row[[17]]$Cell
#> [1] "1409578"
#> [2] "405270636"
#> [3] "21476448"
#> [4] "Active"
#> [5] ""
#> [6] ""
#> [7] "0.95"
#> [8] "EC50"
#> [9] "Determination of antiviral efficacy in high-content imaging assay in Vero E6 cells infected with SARS-CoV-2 (USA-WA1/2020 isolate) at MOI 0.75 after 24 hrs"
#> [10] "Confirmatory"
#> [11] ""
#> [12] ""
#>
#>
#> $Table$Row[[18]]
#> $Table$Row[[18]]$Cell
#> [1] "1409578"
#> [2] "405270669"
#> [3] "11582982"
#> [4] "Active"
#> [5] ""
#> [6] ""
#> [7] "0.5"
#> [8] "EC50"
#> [9] "Determination of antiviral efficacy in high-content imaging assay in Vero E6 cells infected with SARS-CoV-2 (USA-WA1/2020 isolate) at MOI 0.75 after 24 hrs"
#> [10] "Confirmatory"
#> [11] ""
#> [12] ""These methods offer a streamlined and efficient way to access and analyze taxonomy-related data in PubChem, supporting a wide range of research applications in biology, pharmacology, environmental science, and related fields.
PubChem’s PUG REST service offers a valuable resource for accessing detailed information about various cell lines, crucial for research in cellular biology, pharmacology, and related fields. Here’s how to effectively use PUG REST for cell line-related queries:
1. Cell Line Input Methods:
By Cell Line Accession: Utilize Cellosaurus and ChEMBL cell line accessions for precise data retrieval. For example:
result <- get_pug_rest(identifier = "CHEMBL3308376,CVCL_0045", namespace = "cellacc", domain = "cell", operation = "summary", output = "JSON")
result
#>
#> An object of class 'PugRestInstance'
#>
#> Request Details:
#> - Domain: Cell
#> - Namespace: DomainSpecific
#> - Operation: summary
#> - Identifier: CHEMBL3308376,CVCL_0045
#>
#> NOTE: Run getter function 'pubChemData(...)' to extract raw data retrieved from PubChem Database.
#> See ?pubChemData for details.pubChemData(result)
#> $CellSummaries
#> $CellSummaries$CellSummary
#> $CellSummaries$CellSummary[[1]]
#> $CellSummaries$CellSummary[[1]]$CellAccession
#> [1] "CVCL_0030"
#>
#> $CellSummaries$CellSummary[[1]]$Name
#> [1] "HeLa"
#>
#> $CellSummaries$CellSummary[[1]]$Sex
#> [1] "Female"
#>
#> $CellSummaries$CellSummary[[1]]$Category
#> [1] "Cancer cell line"
#>
#> $CellSummaries$CellSummary[[1]]$SourceTissue
#> [1] "uterine cervix"
#>
#> $CellSummaries$CellSummary[[1]]$SourceTaxonomyID
#> [1] 9606
#>
#> $CellSummaries$CellSummary[[1]]$SourceOrganism
#> [1] "Homo sapiens (human)"
#>
#> $CellSummaries$CellSummary[[1]]$Synonym
#> [1] "HELA" "Hela" "He La" "He-La"
#> [5] "HeLa-CCL2" "Henrietta Lacks cells" "Helacyton gartleri"
#>
#>
#> $CellSummaries$CellSummary[[2]]
#> $CellSummaries$CellSummary[[2]]$CellAccession
#> [1] "CVCL_0045"
#>
#> $CellSummaries$CellSummary[[2]]$Name
#> [1] "HEK293"
#>
#> $CellSummaries$CellSummary[[2]]$Sex
#> [1] "Female"
#>
#> $CellSummaries$CellSummary[[2]]$Category
#> [1] "Transformed cell line"
#>
#> $CellSummaries$CellSummary[[2]]$SourceTissue
#> [1] "kidney"
#>
#> $CellSummaries$CellSummary[[2]]$SourceTaxonomyID
#> [1] 9606
#>
#> $CellSummaries$CellSummary[[2]]$SourceOrganism
#> [1] "Homo sapiens (human)"
#>
#> $CellSummaries$CellSummary[[2]]$Synonym
#> [1] "Hek293" "HEK-293" "HEK/293"
#> [4] "(HEK)293" "HEK 293" "HEK;293"
#> [7] "293" "293 HEK" "293 Ad5"
#> [10] "Graham 293" "Graham-293" "Human Embryonic Kidney 293"By Cell Line Synonym: Access data using cell line names or other synonyms. For instance, for the HeLa cell line:
result <- get_pug_rest(identifier = "HeLa", namespace = "synonym", domain = "cell", operation = "summary", output = "JSON")
result
#>
#> An object of class 'PugRestInstance'
#>
#> Request Details:
#> - Domain: Cell
#> - Namespace: DomainSpecific
#> - Operation: summary
#> - Identifier: HeLa
#>
#> NOTE: Run getter function 'pubChemData(...)' to extract raw data retrieved from PubChem Database.
#> See ?pubChemData for details.pubChemData(result)
#> $CellSummaries
#> $CellSummaries$CellSummary
#> $CellSummaries$CellSummary[[1]]
#> $CellSummaries$CellSummary[[1]]$CellAccession
#> [1] "CVCL_0030"
#>
#> $CellSummaries$CellSummary[[1]]$Name
#> [1] "HeLa"
#>
#> $CellSummaries$CellSummary[[1]]$Sex
#> [1] "Female"
#>
#> $CellSummaries$CellSummary[[1]]$Category
#> [1] "Cancer cell line"
#>
#> $CellSummaries$CellSummary[[1]]$SourceTissue
#> [1] "uterine cervix"
#>
#> $CellSummaries$CellSummary[[1]]$SourceTaxonomyID
#> [1] 9606
#>
#> $CellSummaries$CellSummary[[1]]$SourceOrganism
#> [1] "Homo sapiens (human)"
#>
#> $CellSummaries$CellSummary[[1]]$Synonym
#> [1] "HELA" "Hela" "He La" "He-La"
#> [5] "HeLa-CCL2" "Henrietta Lacks cells" "Helacyton gartleri"2. Available Cell Line Data:
Cell Line Summary: Provides a comprehensive overview including CellAccession, Name, Sex, Category, SourceTissue, SourceTaxonomyID, SourceOrganism, and Synonyms. For example:
result <- get_pug_rest(identifier = "CVCL_0030,CVCL_0045", namespace = "cellacc", domain = "cell", operation = "summary", output = "JSON")
result
#>
#> An object of class 'PugRestInstance'
#>
#> Request Details:
#> - Domain: Cell
#> - Namespace: DomainSpecific
#> - Operation: summary
#> - Identifier: CVCL_0030,CVCL_0045
#>
#> NOTE: Run getter function 'pubChemData(...)' to extract raw data retrieved from PubChem Database.
#> See ?pubChemData for details.pubChemData(result)
#> $CellSummaries
#> $CellSummaries$CellSummary
#> $CellSummaries$CellSummary[[1]]
#> $CellSummaries$CellSummary[[1]]$CellAccession
#> [1] "CVCL_0030"
#>
#> $CellSummaries$CellSummary[[1]]$Name
#> [1] "HeLa"
#>
#> $CellSummaries$CellSummary[[1]]$Sex
#> [1] "Female"
#>
#> $CellSummaries$CellSummary[[1]]$Category
#> [1] "Cancer cell line"
#>
#> $CellSummaries$CellSummary[[1]]$SourceTissue
#> [1] "uterine cervix"
#>
#> $CellSummaries$CellSummary[[1]]$SourceTaxonomyID
#> [1] 9606
#>
#> $CellSummaries$CellSummary[[1]]$SourceOrganism
#> [1] "Homo sapiens (human)"
#>
#> $CellSummaries$CellSummary[[1]]$Synonym
#> [1] "HELA" "Hela" "He La" "He-La"
#> [5] "HeLa-CCL2" "Henrietta Lacks cells" "Helacyton gartleri"
#>
#>
#> $CellSummaries$CellSummary[[2]]
#> $CellSummaries$CellSummary[[2]]$CellAccession
#> [1] "CVCL_0045"
#>
#> $CellSummaries$CellSummary[[2]]$Name
#> [1] "HEK293"
#>
#> $CellSummaries$CellSummary[[2]]$Sex
#> [1] "Female"
#>
#> $CellSummaries$CellSummary[[2]]$Category
#> [1] "Transformed cell line"
#>
#> $CellSummaries$CellSummary[[2]]$SourceTissue
#> [1] "kidney"
#>
#> $CellSummaries$CellSummary[[2]]$SourceTaxonomyID
#> [1] 9606
#>
#> $CellSummaries$CellSummary[[2]]$SourceOrganism
#> [1] "Homo sapiens (human)"
#>
#> $CellSummaries$CellSummary[[2]]$Synonym
#> [1] "Hek293" "HEK-293" "HEK/293"
#> [4] "(HEK)293" "HEK 293" "HEK;293"
#> [7] "293" "293 HEK" "293 Ad5"
#> [10] "Graham 293" "Graham-293" "Human Embryonic Kidney 293"Assays and Bioactivities from Cell Line: Retrieves a list of assays (AIDs) tested on a specific cell line. For example, for HeLa:
result <- get_pug_rest(identifier = "HeLa", namespace = "synonym", domain = "cell", operation = "aids", output = "TXT")
result
#>
#> An object of class 'PugRestInstance'
#>
#> Request Details:
#> - Domain: Cell
#> - Namespace: DomainSpecific
#> - Operation: aids
#> - Identifier: HeLa
#>
#> NOTE: Run getter function 'pubChemData(...)' to extract raw data retrieved from PubChem Database.
#> See ?pubChemData for details.pubChemData(result)
#> Text
#> 1 1259
#> 2 1302
#> 3 1374
#> 4 1665
#> 5 1898
#> 6 3506
#> 7 3507
#> 8 3517
#> 9 3518
#> 10 3523
#> 11 3793
#> 12 3798
#> 13 3811
#> 14 3840
#> 15 3852
#> 16 3853
#> 17 3861
#> 18 3865
#> 19 3866
#> 20 3867
#> 21 3868
#> 22 3897
#> 23 3898
#> 24 3899
#> 25 3901
#> 26 3909
#> 27 3934
#> 28 3939
#> 29 4235
#> 30 4236
#> 31 4263
#> 32 4264
#> 33 4265
#> 34 5668
#> 35 6205
#> 36 6208
#> 37 6510
#> 38 6533
#> 39 6534
#> 40 6535
#> 41 6536
#> 42 6537
#> 43 6542
#> 44 6544
#> 45 6547
#> 46 6550
#> 47 6551
#> 48 6552
#> 49 6553
#> 50 6558
#> 51 29738
#> 52 32842
#> 53 42620
#> 54 42621
#> 55 42622
#> 56 51103
#> 57 53964
#> 58 54327
#> 59 54482
#> 60 54483
#> 61 54487
#> 62 54504
#> 63 54505
#> 64 56801
#> 65 56802
#> 66 56804
#> 67 56809
#> 68 56871
#> 69 57063
#> 70 57136
#> 71 57384
#> 72 57385
#> 73 57387
#> 74 70186
#> 75 70354
#> 76 70505
#> 77 70661
#> 78 73604
#> 79 79740
#> 80 79741
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#> 83 79746
#> 84 79747
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#> 88 79752
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#> 94 79759
#> 95 79760
#> 96 79761
#> 97 79885
#> 98 79886
#> 99 79887
#> 100 79888
#> 101 79889
#> 102 79890
#> 103 79891
#> 104 79892
#> 105 79893
#> 106 79894
#> 107 79895
#> 108 79896
#> 109 79897
#> 110 79898
#> 111 79899
#> 112 79900
#> 113 79901
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#> 115 79903
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#> 117 79905
#> 118 79906
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#> 120 79908
#> 121 79909
#> 122 79910
#> 123 79911
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#> 127 79915
#> 128 79916
#> 129 81365
#> 130 81366
#> 131 81367
#> 132 81368
#> 133 81369
#> 134 81370
#> 135 81375
#> 136 81376
#> 137 81377
#> 138 81887
#> 139 81888
#> 140 84636
#> 141 84637
#> 142 84638
#> 143 84639
#> 144 86317
#> 145 86318
#> 146 86319
#> 147 86320
#> 148 86321
#> 149 86322
#> 150 86323
#> 151 86324
#> 152 86325
#> 153 86326
#> 154 86327
#> 155 86328
#> 156 86329
#> 157 86330
#> 158 86331
#> 159 86332
#> 160 86333
#> 161 86334
#> 162 86335
#> 163 86336
#> 164 86337
#> 165 86338
#> 166 86339
#> 167 86340
#> 168 86341
#> 169 86342
#> 170 86343
#> 171 86344
#> 172 86345
#> 173 86346
#> 174 86347
#> 175 86348
#> 176 86349
#> 177 86350
#> 178 86351
#> 179 86352
#> 180 86353
#> 181 86354
#> 182 86355
#> 183 86356
#> 184 86357
#> 185 86481
#> 186 86482
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#> 204 86500
#> 205 86501
#> 206 86502
#> 207 86503
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#> 209 86505
#> 210 86506
#> 211 86507
#> 212 86508
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#> 1000 216534
#> [ reached 'max' / getOption("max.print") -- omitted 14442 rows ]To aggregate concise bioactivity data from each AID:
result <- get_pug_rest(identifier = "79900", namespace = "aid", domain = "assay", operation = "concise", output = "JSON")
result
#>
#> An object of class 'PugRestInstance'
#>
#> Request Details:
#> - Domain: Assay
#> - Namespace: AID
#> - Operation: concise
#> - Identifier: 79900
#>
#> NOTE: Run getter function 'pubChemData(...)' to extract raw data retrieved from PubChem Database.
#> See ?pubChemData for details.pubChemData(result)
#> $Table
#> $Table$Columns
#> $Table$Columns$Column
#> [1] "AID" "SID" "CID" "Activity Outcome" "Target Accession"
#> [6] "Target GeneID" "Activity Value [uM]" "Activity Name" "Assay Name" "Assay Type"
#> [11] "PubMed ID" "RNAi"
#>
#>
#> $Table$Row
#> $Table$Row[[1]]
#> $Table$Row[[1]]$Cell
#> [1] "79900"
#> [2] "103416777"
#> [3] "6476829"
#> [4] "Active"
#> [5] ""
#> [6] ""
#> [7] "0.162"
#> [8] "EC50"
#> [9] "Tested for antirhinoviral activity of compound against HRV 25 infected H1HeLa cells; Cytotoxicity at > 10 uM"
#> [10] "Confirmatory"
#> [11] "11858991"
#> [12] ""These methods provide an efficient and targeted approach to access and analyze cell line-related data in PubChem, supporting a wide range of research applications in cellular biology, pharmacology, and related fields.