The PubChemR package features the essential function get_pug_view, specifically developed to provide access to comprehensive summary reports and additional information not typically found in the primary PubChem Substance, Compound, or BioAssay records. Utilizing the PUG View service, a REST-style web service of PubChem, get_pug_view is primarily utilized for generating detailed summaries for the PubChem database record web pages. It can also function as a standalone programmatic web service.
PUG View is expertly designed to provide complete summary reports on individual PubChem records, offering a different approach compared to the PUG REST service, which delivers smaller bits of information about one or more PubChem records. The get_pug_view function sends requests to the PubChem PUG View API, allowing users to retrieve various types of data for a given identifier, including annotations and QR codes. It supports multiple output formats such as JSON and SVG, making it a versatile tool for users who need comprehensive information from PubChem’s database. This vignette aims to elucidate the structure and usage of the PUG View service, offering illustrative use cases to aid new users in understanding its operation and constructing effective requests.
get_pug_viewPUG View offers a versatile approach to access structured information from PubChem’s extensive database. Here’s how to leverage the get_pug_view function in R for accessing various data formats and specific record summaries:
Multiple Formats: PUG View supports various formats. For example, to retrieve JSON data:
result <- get_pug_view(annotation = "data", identifier = "1234", domain = "compound", output = "JSON")This code initializes a request to retrieve data from the PubChem database for the compound with the identifier “1234” (Gallopamil). The annotation parameter is set to “data” indicating that we want the compound data.
result
#>
#> PUG View Data from PubChem Database
#>
#> Request Details:
#> - Domain: Compound
#> - Annotation: data
#> - Identifier: 1234
#>
#> Pug View Details:
#> - RecordType (1): [<unnamed character>]
#> - RecordNumber (1): [<unnamed numeric>]
#> - RecordTitle (1): [<unnamed character>]
#> - Section (15): [<unnamed list>] Structures, Names and Identifiers, ... and 13 more.
#> - Reference (52): [<unnamed list>]
#>
#> NOTE: Run getter function 'retrieve()' with element name above to extract data from corresponding list.
#> See ?retrieve for details.The response provides an overview of the PUG View data for the requested compound, including the domain, annotation, identifier, and available sections. The retrieve() function can be used to extract data from specific sections.
To retrieve the record type:
retrieve(object = result, .slot = "RecordType", .to.data.frame = FALSE)
#> [1] "CID"This code extracts the record type, which is “CID” (Compound Identifier).
To retrieve the record number:
retrieve(object = result, .slot = "RecordNumber", .to.data.frame = FALSE)
#> [1] 1234This code extracts the record number, which is “1234”.
To retrieve the record title:
retrieve(object = result, .slot = "RecordTitle", .to.data.frame = FALSE)
#> [1] "Gallopamil"This code extracts the record title, which is “Gallopamil”.
To retrieve sections of the data:
section <- retrieve(object = result, .slot = "Section", .to.data.frame = FALSE)
section
#>
#> PUG View Data Sections
#>
#> Request Details:
#> - Record Type: CID
#> - Record Number: 1234
#> - Record Title: Gallopamil
#>
#> Section Details:
#> - Number of available sections: 15
#> - Section headings: Structures, Names and Identifiers, ... and 13 more.
#>
#> NOTE: Run getter function 'section()' to extract section data. To list available sections, run 'sectionList()'.
#> See ?section and ?sectionList for details.This code retrieves the sections of the data available for the compound. It provides an overview of the number of sections and their headings.
To list the available sections:
sectionList(section)
#> # A tibble: 15 × 2
#> SectionID Headings
#> <chr> <chr>
#> 1 S1 Structures
#> 2 S2 Names and Identifiers
#> 3 S3 Chemical and Physical Properties
#> 4 S4 Spectral Information
#> 5 S5 Related Records
#> 6 S6 Chemical Vendors
#> 7 S7 Drug and Medication Information
#> 8 S8 Pharmacology and Biochemistry
#> 9 S9 Use and Manufacturing
#> 10 S10 Associated Disorders and Diseases
#> 11 S11 Literature
#> 12 S12 Patents
#> 13 S13 Interactions and Pathways
#> 14 S14 Biological Test Results
#> 15 S15 ClassificationThis code lists all the sections available for the compound data, along with their section IDs and headings.
S1: Structures
After retrieving the main sections of the compound data, you can extract detailed information about specific sections. Here, we’ll focus on the “Structures” section (S1).
To retrieve the “Structures” section:
structures <- section(object = result, .id = "S1")This code retrieves the “Structures” section of the compound data. The output provides an overview of the section, including its Table of Contents (TOC) heading, description, and subsections.
structures
#>
#> PUG View Data Sections (Structures)
#>
#> Request Details:
#> - Record Type: CID
#> - Record Number: 1234
#> - Record Title: Gallopamil
#>
#> Section Details:
#> - TOCHeading (1): [<unnamed character>]
#> - Description (1): [<unnamed character>]
#> - Section (2): [<unnamed list>] 2D Structure, 3D Conformer, ... and 0 more.
#>
#> NOTE: Run getter function 'retrieve()' with element name above to extract data from corresponding list.
#> See ?retrieve for details.
#>
#> NOTE: Run getter function 'section()' to extract section data. To list available sections, run 'sectionList()'.
#> See ?section and ?sectionList for details.To extract the Table of Contents (TOC) heading of the “Structures” section:
retrieve(object = structures, .slot = "TOCHeading")
#> [1] "Structures"This code retrieves the TOC heading, which is “Structures”.
To extract the description of the “Structures” section:
retrieve(object = structures, .slot = "Description")
#> [1] "Structure depictions of this compound, including computationally generated two-dimensional (2D) and three-dimensional (3D) structures, as well as experimentally determined 3D single-crystal structures."This code retrieves the description of the section, providing an overview of the types of structures included.
To extract the subsections within the “Structures” section:
retrieve(object = structures, .slot = "Section")
#> [[1]]
#> [[1]]$TOCHeading
#> [1] "2D Structure"
#>
#> [[1]]$Description
#> [1] "A two-dimensional (2D) structure representation of the compound. Because this structure is processed through chemical structure standardization (Hähnke et al., J. Cheminform. 2018, 10, 36), it is not necessarily the same as the structures provided by individual data contributors. "
#>
#> [[1]]$URL
#> [1] "https://doi.org/10.1186/s13321-018-0293-8"
#>
#> [[1]]$DisplayControls
#> MoveToTop
#> TRUE
#>
#> [[1]]$Information
#> [[1]]$Information[[1]]
#> [[1]]$Information[[1]]$ReferenceNumber
#> [1] 37
#>
#> [[1]]$Information[[1]]$Value
#> [[1]]$Information[[1]]$Value$Boolean
#> [1] TRUE
#>
#>
#>
#>
#>
#> [[2]]
#> [[2]]$TOCHeading
#> [1] "3D Conformer"
#>
#> [[2]]$Description
#> [1] "A three-dimensional (3D) structure representation of the compound. This 3D structure is not experimentally determined, but computed by PubChem. This structure may or may not be the same as the inherent structure of the compound you would expect to see in vacuum or in the gas phase, because the underlying computational algorithm aims to generate a protein-bound structure, which would be observed in a protein-ligand complex. More detailed information on this conformer model can be found in Kim et al., J. Cheminform. 2013, 5, 1."
#>
#> [[2]]$URL
#> [1] "https://doi.org/10.1186/1758-2946-5-1"
#>
#> [[2]]$DisplayControls
#> MoveToTop
#> TRUE
#>
#> [[2]]$Information
#> [[2]]$Information[[1]]
#> [[2]]$Information[[1]]$ReferenceNumber
#> [1] 37
#>
#> [[2]]$Information[[1]]$Description
#> [1] "Gallopamil"
#>
#> [[2]]$Information[[1]]$Value
#> [[2]]$Information[[1]]$Value$Number
#> [1] 1234This code retrieves the details of the subsections within the “Structures” section. There are two subsections: “2D Structure” and “3D Conformer”.
Subsection: 2D Structure The “2D Structure” subsection provides a two-dimensional representation of the compound:
TOCHeading: “2D Structure” Description: A two-dimensional (2D) structure representation of the compound. This structure is processed through chemical structure standardization, meaning it may not be identical to structures provided by individual data contributors. URL: https://jcheminf.biomedcentral.com/articles/10.1186/s13321-018-0293-8
Subsection: 3D Conformer The “3D Conformer” subsection provides a three-dimensional representation of the compound:
TOCHeading: “3D Conformer” Description: A three-dimensional (3D) structure representation of the compound. This structure is computed by PubChem and aims to generate a protein-bound structure, which may differ from the inherent structure in vacuum or gas phase. URL: https://jcheminf.biomedcentral.com/articles/10.1186/1758-2946-5-1
This detailed extraction and interpretation provide a comprehensive understanding of the structure-related information available for the compound in the PubChem database.
Specific Headings: Retrieve data under specific headings for more targeted information. For instance, to get experimental properties:
result <- get_pug_view(annotation = "data", identifier = "2244", domain = "compound", output = "JSON", heading = "Experimental Properties")This code requests detailed data for the compound identified by “2244” under the heading “Experimental Properties”. The output format specified is JSON. The resulting object, result, contains the following details:
result
#>
#> PUG View Data from PubChem Database
#>
#> Request Details:
#> - Domain: Compound
#> - Annotation: data
#> - Identifier: 2244
#>
#> Pug View Details:
#> - RecordType (1): [<unnamed character>]
#> - RecordNumber (1): [<unnamed numeric>]
#> - RecordTitle (1): [<unnamed character>]
#> - Section (1): [<unnamed list>] Chemical and Physical Properties
#> - Reference (14): [<unnamed list>]
#>
#> NOTE: Run getter function 'retrieve()' with element name above to extract data from corresponding list.
#> See ?retrieve for details.The output shows the “Chemical and Physical Properties” section, with references and details specific to the compound identified as “2244”.
To extract the “Chemical and Physical Properties” section:
s1 <- section(object = result, .id = "S1")This code retrieves the “Chemical and Physical Properties” section from the result object. The output contains detailed information about this section:
s1
#>
#> PUG View Data Sections (Chemical and Physical Properties)
#>
#> Request Details:
#> - Record Type: CID
#> - Record Number: 2244
#> - Record Title: Aspirin
#>
#> Section Details:
#> - TOCHeading (1): [<unnamed character>]
#> - Description (1): [<unnamed character>]
#> - Section (1): [<unnamed list>] Experimental Properties
#>
#> NOTE: Run getter function 'retrieve()' with element name above to extract data from corresponding list.
#> See ?retrieve for details.
#>
#> NOTE: Run getter function 'section()' to extract section data. To list available sections, run 'sectionList()'.
#> See ?section and ?sectionList for details.This section contains the heading, description, and details about “Experimental Properties”.
To extract the “Experimental Properties” subsection:
s1_s1 <- section(object = s1, .id = "S1")This code retrieves the “Experimental Properties” subsection from the s1 object. The output contains detailed information about this subsection:
s1_s1
#>
#> PUG View Data Sections (Experimental Properties)
#>
#> Request Details:
#> - Record Type: CID
#> - Record Number: 2244
#> - Record Title: Aspirin
#>
#> Section Details:
#> - TOCHeading (1): [<unnamed character>]
#> - Description (1): [<unnamed character>]
#> - Section (16): [<unnamed list>] Physical Description, Color/Form, ... and 14 more.
#>
#> NOTE: Run getter function 'retrieve()' with element name above to extract data from corresponding list.
#> See ?retrieve for details.
#>
#> NOTE: Run getter function 'section()' to extract section data. To list available sections, run 'sectionList()'.
#> See ?section and ?sectionList for details.To extract a specific experimental property, such as LogP:
s1_s1_s10 <- section(object = s1_s1, .id = "S10")This code retrieves the “LogP” section from the s1_s1 object. The output contains detailed information about this section:
s1_s1_s10
#>
#> PUG View Data Sections (LogP)
#>
#> Request Details:
#> - Record Type: CID
#> - Record Number: 2244
#> - Record Title: Aspirin
#>
#> Section Details:
#> - TOCHeading (1): [<unnamed character>]
#> - Description (1): [<unnamed character>]
#> - Information (4): [<unnamed list>]
#>
#> NOTE: Run getter function 'retrieve()' with element name above to extract data from corresponding list.
#> See ?retrieve for details.This section contains the heading, description, and information related to the LogP property.
To extract the information within the “LogP” section:
retrieve(object = s1_s1_s10, .slot = "Information", .to.data.frame = FALSE)
#> [[1]]
#> [[1]]$ReferenceNumber
#> [1] 35
#>
#> [[1]]$Reference
#> [1] "https://www.fip.org/files/fip/BPS/BCS/Monographs/AcetylsalicylicAcid.pdf"
#>
#> [[1]]$Value
#> [[1]]$Value$Number
#> [1] 1.18
#>
#>
#>
#> [[2]]
#> [[2]]$ReferenceNumber
#> [1] 59
#>
#> [[2]]$Description
#> [1] "PEER REVIEWED"
#>
#> [[2]]$Reference
#> [1] "Hansch, C., Leo, A., D. Hoekman. Exploring QSAR - Hydrophobic, Electronic, and Steric Constants. Washington, DC: American Chemical Society., 1995., p. 54"
#>
#> [[2]]$Value
#> [[2]]$Value$StringWithMarkup
#> [[2]]$Value$StringWithMarkup[[1]]
#> String
#> "log Kow = 1.19"
#>
#>
#>
#>
#> [[3]]
#> [[3]]$ReferenceNumber
#> [1] 60
#>
#> [[3]]$Reference
#> [1] "HANSCH,C ET AL. (1995)"
#>
#> [[3]]$Value
#> [[3]]$Value$StringWithMarkup
#> [[3]]$Value$StringWithMarkup[[1]]
#> String
#> "1.19"
#>
#>
#>
#>
#> [[4]]
#> [[4]]$ReferenceNumber
#> [1] 77
#>
#> [[4]]$Name
#> [1] ""
#>
#> [[4]]$Value
#> [[4]]$Value$StringWithMarkup
#> [[4]]$Value$StringWithMarkup[[1]]
#> String
#> "1.19"Above code retrieves detailed information about the “LogP” property of the compound, including references and values:
This output shows four entries for the LogP property of the compound, each with a reference number, reference link or description, and the value of LogP (either as a number or a string with markup).
Compounds, Substances, and BioAssays: Access these records using their respective identifiers (CID, SID, AID). For example, to access a BioAssay record:
result <- get_pug_view(annotation = "data", identifier = "1", domain = "assay", output = "JSON")This code requests the full data for the BioAssay identified by “1”. The output format specified is JSON. The resulting object, result, contains the following details:
result
#>
#> PUG View Data from PubChem Database
#>
#> Request Details:
#> - Domain: Assay
#> - Annotation: data
#> - Identifier: 1
#>
#> Pug View Details:
#> - RecordType (1): [<unnamed character>]
#> - RecordNumber (1): [<unnamed numeric>]
#> - RecordTitle (1): [<unnamed character>]
#> - Section (10): [<unnamed list>] Record Description, Description, ... and 8 more.
#> - Reference (3): [<unnamed list>]
#>
#> NOTE: Run getter function 'retrieve()' with element name above to extract data from corresponding list.
#> See ?retrieve for details.The output shows the structure of the data available for the BioAssay, including 10 sections such as “Record Description” and “Description”.
To view these sub-sections:
sectionList(object = result)
#> # A tibble: 10 × 2
#> SectionID Headings
#> <chr> <chr>
#> 1 S1 Record Description
#> 2 S2 Description
#> 3 S3 Comment
#> 4 S4 Result Definitions
#> 5 S5 Data Table
#> 6 S6 Target
#> 7 S7 Entrez Crosslinks
#> 8 S8 Identity
#> 9 S9 Same-Project BioAssays
#> 10 S10 BioAssay AnnotationsThe code returns the list of sub-sections for AID 1:
To access a specific sub-section, such as BioAssay Annotations (S10):
record_description <- section(object = result, .id = "S10")
record_description
#>
#> PUG View Data Sections (BioAssay Annotations)
#>
#> Request Details:
#> - Record Type: AID
#> - Record Number: 1
#> - Record Title: NCI human tumor cell line growth inhibition assay. Data for the NCI-H23 Non-Small Cell Lung cell line
#>
#> Section Details:
#> - TOCHeading (1): [<unnamed character>]
#> - Description (1): [<unnamed character>]
#> - DisplayControls (1): [<named list>] CreateTable
#> - Information (3): [<unnamed list>]
#>
#> NOTE: Run getter function 'retrieve()' with element name above to extract data from corresponding list.
#> See ?retrieve for details.The output contains detailed information about the BioAssay Annotations section:
record_description
#>
#> PUG View Data Sections (BioAssay Annotations)
#>
#> Request Details:
#> - Record Type: AID
#> - Record Number: 1
#> - Record Title: NCI human tumor cell line growth inhibition assay. Data for the NCI-H23 Non-Small Cell Lung cell line
#>
#> Section Details:
#> - TOCHeading (1): [<unnamed character>]
#> - Description (1): [<unnamed character>]
#> - DisplayControls (1): [<named list>] CreateTable
#> - Information (3): [<unnamed list>]
#>
#> NOTE: Run getter function 'retrieve()' with element name above to extract data from corresponding list.
#> See ?retrieve for details.Now, we can use retrieve function to extract section details for “BioAssay Annotations”. For example, we can fetch the information details as follow:
To extract detailed information from the BioAssay Annotations section:
retrieve(object = record_description, .slot = "Information")
#> [[1]]
#> [[1]]$ReferenceNumber
#> [1] 3
#>
#> [[1]]$Name
#> [1] "Assay Format"
#>
#> [[1]]$Value
#> [[1]]$Value$StringWithMarkup
#> [[1]]$Value$StringWithMarkup[[1]]
#> String
#> "Cell-based"
#>
#>
#>
#>
#> [[2]]
#> [[2]]$ReferenceNumber
#> [1] 3
#>
#> [[2]]$Name
#> [1] "Assay Type"
#>
#> [[2]]$Value
#> [[2]]$Value$StringWithMarkup
#> [[2]]$Value$StringWithMarkup[[1]]
#> String
#> "Functional"
#>
#>
#>
#>
#> [[3]]
#> [[3]]$ReferenceNumber
#> [1] 3
#>
#> [[3]]$Name
#> [1] "Assay Cell Type"
#>
#> [[3]]$URL
#> [1] "https://pubchem.ncbi.nlm.nih.gov/cell/CHEMBL3307750"
#>
#> [[3]]$Value
#> [[3]]$Value$StringWithMarkup
#> [[3]]$Value$StringWithMarkup[[1]]
#> String
#> "NCI-H23"This output shows three entries for the BioAssay Annotations, each with a reference number, name, URL (if available), and value.
Patents, Genes, Proteins, Pathways, Taxonomies, Cell Lines, Elements: Each of these can be accessed using their specific identifiers or names. For instance, to retrieve information on a specific gene:
result <- get_pug_view(annotation = "data", identifier = "1", domain = "gene", output = "JSON")This code requests full data for the gene identified by “1”. The output format specified is JSON. The resulting object, result, contains the following details:
result
#>
#> PUG View Data from PubChem Database
#>
#> Request Details:
#> - Domain: Gene
#> - Annotation: data
#> - Identifier: 1
#>
#> Pug View Details:
#> - RecordType (1): [<unnamed character>]
#> - RecordNumber (1): [<unnamed numeric>]
#> - RecordTitle (1): [<unnamed character>]
#> - RecordExternalURL (1): [<unnamed character>]
#> - Section (13): [<unnamed list>] Record Description, Gene Information, ... and 11 more.
#> - Reference (22): [<unnamed list>]
#>
#> NOTE: Run getter function 'retrieve()' with element name above to extract data from corresponding list.
#> See ?retrieve for details.The output shows the structure of the data available for the gene, including 13 sections such as “Record Description” and “Gene Information”.
The code returns the title of the gene record:
retrieve(object = result, .slot = "RecordTitle")
#> # A tibble: 1 × 1
#> value
#> <chr>
#> 1 A1BG - alpha-1-B glycoprotein (human)This output shows the title of the gene identified by “1” is “A1BG - alpha-1-B glycoprotein (human)”.
The code returns the list of sub-sections for gene ID 1:
sectionList(object = result)
#> # A tibble: 13 × 2
#> SectionID Headings
#> <chr> <chr>
#> 1 S1 Record Description
#> 2 S2 Gene Information
#> 3 S3 Names and Identifiers
#> 4 S4 Related Records
#> 5 S5 Proteins
#> 6 S6 BioAssays
#> 7 S7 Diseases and Phenotypes
#> 8 S8 Interactions and Pathways
#> 9 S9 Expression
#> 10 S10 Target Development Level
#> 11 S11 Literature
#> 12 S12 Patents
#> 13 S13 ClassificationThese detailed interpretations illustrate how to access different types of records, view sub-sections, and extract specific information from PubChem using PUG REST. This approach is applicable for compounds, substances, BioAssays, genes, and other record types supported by PubChem.
Access by Heading: Retrieve specific types of information across PubChem’s databases. For example, to get all experimental viscosity measurements:
result <- get_pug_view(annotation = "annotations", identifier = "Viscosity", domain = "heading", output = "JSON")This code requests all annotations related to viscosity from the PubChem database. The output format specified is JSON. The resulting object, result, contains the following details:
result
#>
#> PUG View Data from PubChem Database
#>
#> Request Details:
#> - Domain: DomainSpecific (heading)
#> - Annotation: annotations
#> - Identifier: Viscosity
#>
#> Pug View Details:
#> - Annotation (820): [<unnamed list>]
#> - Page (1): [<unnamed numeric>]
#> - TotalPages (1): [<unnamed numeric>]
#>
#> NOTE: Run getter function 'retrieve()' with element name above to extract data from corresponding list.
#> See ?retrieve for details.To extract the annotations:
annotations <- retrieve(object = result, .slot = "Annotation", .to.data.frame = FALSE)The code returns the first few viscosity annotations. The following is an example of what the extracted annotations might look like:
head(annotations)
#> [[1]]
#> [[1]]$SourceName
#> [1] "Hazardous Substances Data Bank (HSDB)"
#>
#> [[1]]$SourceID
#> [1] "30"
#>
#> [[1]]$Name
#> [1] "NITROGLYCERIN"
#>
#> [[1]]$Description
#> [1] "The Hazardous Substances Data Bank (HSDB) is a toxicology database that focuses on the toxicology of potentially hazardous chemicals. It provides information on human exposure, industrial hygiene, emergency handling procedures, environmental fate, regulatory requirements, nanomaterials, and related areas. The information in HSDB has been assessed by a Scientific Review Panel."
#>
#> [[1]]$URL
#> [1] "https://pubchem.ncbi.nlm.nih.gov/source/hsdb/30"
#>
#> [[1]]$LicenseURL
#> [1] "https://www.nlm.nih.gov/web_policies.html"
#>
#> [[1]]$Data
#> [[1]]$Data[[1]]
#> [[1]]$Data[[1]]$TOCHeading
#> type #TOCHeading
#> "Compound" "Viscosity"
#>
#> [[1]]$Data[[1]]$Description
#> [1] "PEER REVIEWED"
#>
#> [[1]]$Data[[1]]$Reference
#> [1] "Kirk-Othmer Encyclopedia of Chemical Technology. 4th ed. Volumes 1: New York, NY. John Wiley and Sons, 1991-Present., p. V10 (1993) 22"
#>
#> [[1]]$Data[[1]]$Value
#> [[1]]$Data[[1]]$Value$StringWithMarkup
#> [[1]]$Data[[1]]$Value$StringWithMarkup[[1]]
#> String
#> "36.0 centipoise @ 20 °C"
#>
#>
#>
#>
#>
#> [[1]]$ANID
#> [1] 2
#>
#> [[1]]$LinkedRecords
#> [[1]]$LinkedRecords$CID
#> [1] 4510
#>
#>
#>
#> [[2]]
#> [[2]]$SourceName
#> [1] "Hazardous Substances Data Bank (HSDB)"
#>
#> [[2]]$SourceID
#> [1] "34"
#>
#> [[2]]$Name
#> [1] "IODINE, ELEMENTAL"
#>
#> [[2]]$Description
#> [1] "The Hazardous Substances Data Bank (HSDB) is a toxicology database that focuses on the toxicology of potentially hazardous chemicals. It provides information on human exposure, industrial hygiene, emergency handling procedures, environmental fate, regulatory requirements, nanomaterials, and related areas. The information in HSDB has been assessed by a Scientific Review Panel."
#>
#> [[2]]$URL
#> [1] "https://pubchem.ncbi.nlm.nih.gov/source/hsdb/34"
#>
#> [[2]]$LicenseURL
#> [1] "https://www.nlm.nih.gov/web_policies.html"
#>
#> [[2]]$Data
#> [[2]]$Data[[1]]
#> [[2]]$Data[[1]]$TOCHeading
#> type #TOCHeading
#> "Compound" "Viscosity"
#>
#> [[2]]$Data[[1]]$Description
#> [1] "PEER REVIEWED"
#>
#> [[2]]$Data[[1]]$Reference
#> [1] "Weast, R.C. (ed.) Handbook of Chemistry and Physics. 69th ed. Boca Raton, FL: CRC Press Inc., 1988-1989., p. F-43"
#>
#> [[2]]$Data[[1]]$Value
#> [[2]]$Data[[1]]$Value$StringWithMarkup
#> [[2]]$Data[[1]]$Value$StringWithMarkup[[1]]
#> String
#> "2.27 cP at 116 °C"
#>
#>
#>
#>
#>
#> [[2]]$ANID
#> [1] 5
#>
#> [[2]]$LinkedRecords
#> [[2]]$LinkedRecords$CID
#> [1] 807
#>
#>
#>
#> [[3]]
#> [[3]]$SourceName
#> [1] "Hazardous Substances Data Bank (HSDB)"
#>
#> [[3]]$SourceID
#> [1] "35"
#>
#> [[3]]$Name
#> [1] "BENZENE"
#>
#> [[3]]$Description
#> [1] "The Hazardous Substances Data Bank (HSDB) is a toxicology database that focuses on the toxicology of potentially hazardous chemicals. It provides information on human exposure, industrial hygiene, emergency handling procedures, environmental fate, regulatory requirements, nanomaterials, and related areas. The information in HSDB has been assessed by a Scientific Review Panel."
#>
#> [[3]]$URL
#> [1] "https://pubchem.ncbi.nlm.nih.gov/source/hsdb/35"
#>
#> [[3]]$LicenseURL
#> [1] "https://www.nlm.nih.gov/web_policies.html"
#>
#> [[3]]$Data
#> [[3]]$Data[[1]]
#> [[3]]$Data[[1]]$TOCHeading
#> type #TOCHeading
#> "Compound" "Viscosity"
#>
#> [[3]]$Data[[1]]$Description
#> [1] "PEER REVIEWED"
#>
#> [[3]]$Data[[1]]$Reference
#> [1] "Haynes, W.M. (ed.). CRC Handbook of Chemistry and Physics. 94th Edition. CRC Press LLC, Boca Raton: FL 2013-2014, p. 6-238"
#>
#> [[3]]$Data[[1]]$Value
#> [[3]]$Data[[1]]$Value$StringWithMarkup
#> [[3]]$Data[[1]]$Value$StringWithMarkup[[1]]
#> String
#> "0.604 mPa.s at 25 °C"
#>
#>
#>
#>
#>
#> [[3]]$ANID
#> [1] 6
#>
#> [[3]]$LinkedRecords
#> [[3]]$LinkedRecords$CID
#> [1] 241
#>
#>
#>
#> [[4]]
#> [[4]]$SourceName
#> [1] "Hazardous Substances Data Bank (HSDB)"
#>
#> [[4]]$SourceID
#> [1] "39"
#>
#> [[4]]$Name
#> [1] "EPICHLOROHYDRIN"
#>
#> [[4]]$Description
#> [1] "The Hazardous Substances Data Bank (HSDB) is a toxicology database that focuses on the toxicology of potentially hazardous chemicals. It provides information on human exposure, industrial hygiene, emergency handling procedures, environmental fate, regulatory requirements, nanomaterials, and related areas. The information in HSDB has been assessed by a Scientific Review Panel."
#>
#> [[4]]$URL
#> [1] "https://pubchem.ncbi.nlm.nih.gov/source/hsdb/39"
#>
#> [[4]]$LicenseURL
#> [1] "https://www.nlm.nih.gov/web_policies.html"
#>
#> [[4]]$Data
#> [[4]]$Data[[1]]
#> [[4]]$Data[[1]]$TOCHeading
#> type #TOCHeading
#> "Compound" "Viscosity"
#>
#> [[4]]$Data[[1]]$Description
#> [1] "PEER REVIEWED"
#>
#> [[4]]$Data[[1]]$Reference
#> [1] "Lewis, R.J., Sr (Ed.). Hawley's Condensed Chemical Dictionary. 13th ed. New York, NY: John Wiley & Sons, Inc. 1997., p. 449"
#>
#> [[4]]$Data[[1]]$Value
#> [[4]]$Data[[1]]$Value$StringWithMarkup
#> [[4]]$Data[[1]]$Value$StringWithMarkup[[1]]
#> String
#> "0.0103 poise at 25 °C"
#>
#>
#>
#>
#>
#> [[4]]$ANID
#> [1] 10
#>
#> [[4]]$LinkedRecords
#> [[4]]$LinkedRecords$CID
#> [1] 7835
#>
#>
#>
#> [[5]]
#> [[5]]$SourceName
#> [1] "Hazardous Substances Data Bank (HSDB)"
#>
#> [[5]]$SourceID
#> [1] "40"
#>
#> [[5]]$Name
#> [1] "ACETIC ACID"
#>
#> [[5]]$Description
#> [1] "The Hazardous Substances Data Bank (HSDB) is a toxicology database that focuses on the toxicology of potentially hazardous chemicals. It provides information on human exposure, industrial hygiene, emergency handling procedures, environmental fate, regulatory requirements, nanomaterials, and related areas. The information in HSDB has been assessed by a Scientific Review Panel."
#>
#> [[5]]$URL
#> [1] "https://pubchem.ncbi.nlm.nih.gov/source/hsdb/40"
#>
#> [[5]]$LicenseURL
#> [1] "https://www.nlm.nih.gov/web_policies.html"
#>
#> [[5]]$Data
#> [[5]]$Data[[1]]
#> [[5]]$Data[[1]]$TOCHeading
#> type #TOCHeading
#> "Compound" "Viscosity"
#>
#> [[5]]$Data[[1]]$Description
#> [1] "PEER REVIEWED"
#>
#> [[5]]$Data[[1]]$Reference
#> [1] "Haynes, W.M. (ed.). CRC Handbook of Chemistry and Physics. 94th Edition. CRC Press LLC, Boca Raton: FL 2013-2014, p. 6-232"
#>
#> [[5]]$Data[[1]]$Value
#> [[5]]$Data[[1]]$Value$StringWithMarkup
#> [[5]]$Data[[1]]$Value$StringWithMarkup[[1]]
#> String
#> "1.056 mPa-s at 25 °C"
#>
#>
#>
#>
#>
#> [[5]]$ANID
#> [1] 11
#>
#> [[5]]$LinkedRecords
#> [[5]]$LinkedRecords$CID
#> [1] 176
#>
#>
#>
#> [[6]]
#> [[6]]$SourceName
#> [1] "Hazardous Substances Data Bank (HSDB)"
#>
#> [[6]]$SourceID
#> [1] "41"
#>
#> [[6]]$Name
#> [1] "ACETONE"
#>
#> [[6]]$Description
#> [1] "The Hazardous Substances Data Bank (HSDB) is a toxicology database that focuses on the toxicology of potentially hazardous chemicals. It provides information on human exposure, industrial hygiene, emergency handling procedures, environmental fate, regulatory requirements, nanomaterials, and related areas. The information in HSDB has been assessed by a Scientific Review Panel."
#>
#> [[6]]$URL
#> [1] "https://pubchem.ncbi.nlm.nih.gov/source/hsdb/41"
#>
#> [[6]]$LicenseURL
#> [1] "https://www.nlm.nih.gov/web_policies.html"
#>
#> [[6]]$Data
#> [[6]]$Data[[1]]
#> [[6]]$Data[[1]]$TOCHeading
#> type #TOCHeading
#> "Compound" "Viscosity"
#>
#> [[6]]$Data[[1]]$Description
#> [1] "PEER REVIEWED"
#>
#> [[6]]$Data[[1]]$Reference
#> [1] "Howard HL; Acetone. Kirk-Othmer Encyclopedia of Chemical Technology. (1999-2015). New York, NY: John Wiley & Sons. Online Posting Date: Jan 14, 2011."
#>
#> [[6]]$Data[[1]]$Value
#> [[6]]$Data[[1]]$Value$StringWithMarkup
#> [[6]]$Data[[1]]$Value$StringWithMarkup[[1]]
#> String
#> "0.32 cP at 20 °C; 0.27 cP at 40 °C"
#>
#>
#>
#>
#>
#> [[6]]$ANID
#> [1] 12
#>
#> [[6]]$LinkedRecords
#> [[6]]$LinkedRecords$CID
#> [1] 180The output shows detailed information for each annotation entry, including the source, name, description, reference, and values.
Or equivalently, we can employ the following if the heading contains special characters not compatible with URL syntax:
result <- get_pug_view(annotation = "annotations", identifier = NULL, domain = "heading", output = "JSON", heading = "Viscosity")
result
#>
#> PUG View Data from PubChem Database
#>
#> Stopped with an ERROR. Details are below:
#>
#> - Message: 'identifier' cannot be NULL.Specify Heading Type: For headings referring to different record types, specify the heading type. For example, boiling point for compounds:
result <- get_pug_view(annotation = "annotations", identifier = "Boiling Point", domain = "heading", output = "JSON", headingType = "Compound")This code retrieves all annotations related to the boiling point of compounds. The resulting object, result, contains detailed data:
result
#>
#> PUG View Data from PubChem Database
#>
#> Request Details:
#> - Domain: DomainSpecific (heading)
#> - Annotation: annotations
#> - Identifier: Boiling%20Point
#>
#> Pug View Details:
#> - Annotation (1000): [<unnamed list>]
#> - Page (1): [<unnamed numeric>]
#> - TotalPages (1): [<unnamed numeric>]
#>
#> NOTE: Run getter function 'retrieve()' with element name above to extract data from corresponding list.
#> See ?retrieve for details.To extract the annotations:
annotations <- retrieve(object = result, .slot = "Annotation", .to.data.frame = FALSE)The output might include annotations like these:
head(annotations)
#> [[1]]
#> [[1]]$SourceName
#> [1] "Hazardous Substances Data Bank (HSDB)"
#>
#> [[1]]$SourceID
#> [1] "30"
#>
#> [[1]]$Name
#> [1] "NITROGLYCERIN"
#>
#> [[1]]$Description
#> [1] "The Hazardous Substances Data Bank (HSDB) is a toxicology database that focuses on the toxicology of potentially hazardous chemicals. It provides information on human exposure, industrial hygiene, emergency handling procedures, environmental fate, regulatory requirements, nanomaterials, and related areas. The information in HSDB has been assessed by a Scientific Review Panel."
#>
#> [[1]]$URL
#> [1] "https://pubchem.ncbi.nlm.nih.gov/source/hsdb/30"
#>
#> [[1]]$LicenseURL
#> [1] "https://www.nlm.nih.gov/web_policies.html"
#>
#> [[1]]$Data
#> [[1]]$Data[[1]]
#> [[1]]$Data[[1]]$TOCHeading
#> type #TOCHeading
#> "Compound" "Boiling Point"
#>
#> [[1]]$Data[[1]]$Description
#> [1] "PEER REVIEWED"
#>
#> [[1]]$Data[[1]]$Reference
#> [1] "O'Neil, M.J. (ed.). The Merck Index - An Encyclopedia of Chemicals, Drugs, and Biologicals. 13th Edition, Whitehouse Station, NJ: Merck and Co., Inc., 2001., p. 1185"
#>
#> [[1]]$Data[[1]]$Value
#> [[1]]$Data[[1]]$Value$StringWithMarkup
#> [[1]]$Data[[1]]$Value$StringWithMarkup[[1]]
#> String
#> "Explodes at 218 °C"
#>
#>
#>
#>
#> [[1]]$Data[[2]]
#> [[1]]$Data[[2]]$TOCHeading
#> type #TOCHeading
#> "Compound" "Boiling Point"
#>
#> [[1]]$Data[[2]]$Description
#> [1] "PEER REVIEWED"
#>
#> [[1]]$Data[[2]]$Reference
#> [1] "Weast, R.C. (ed.) Handbook of Chemistry and Physics. 69th ed. Boca Raton, FL: CRC Press Inc., 1988-1989., p. C-291"
#>
#> [[1]]$Data[[2]]$Value
#> [[1]]$Data[[2]]$Value$StringWithMarkup
#> [[1]]$Data[[2]]$Value$StringWithMarkup[[1]]
#> String
#> "BOILING POINT: 125 °C @ 2 MM HG"
#>
#>
#>
#>
#>
#> [[1]]$ANID
#> [1] 2
#>
#> [[1]]$LinkedRecords
#> [[1]]$LinkedRecords$CID
#> [1] 4510
#>
#>
#>
#> [[2]]
#> [[2]]$SourceName
#> [1] "Hazardous Substances Data Bank (HSDB)"
#>
#> [[2]]$SourceID
#> [1] "31"
#>
#> [[2]]$Name
#> [1] "ISOLAN"
#>
#> [[2]]$Description
#> [1] "The Hazardous Substances Data Bank (HSDB) is a toxicology database that focuses on the toxicology of potentially hazardous chemicals. It provides information on human exposure, industrial hygiene, emergency handling procedures, environmental fate, regulatory requirements, nanomaterials, and related areas. The information in HSDB has been assessed by a Scientific Review Panel."
#>
#> [[2]]$URL
#> [1] "https://pubchem.ncbi.nlm.nih.gov/source/hsdb/31"
#>
#> [[2]]$LicenseURL
#> [1] "https://www.nlm.nih.gov/web_policies.html"
#>
#> [[2]]$Data
#> [[2]]$Data[[1]]
#> [[2]]$Data[[1]]$TOCHeading
#> type #TOCHeading
#> "Compound" "Boiling Point"
#>
#> [[2]]$Data[[1]]$Description
#> [1] "PEER REVIEWED"
#>
#> [[2]]$Data[[1]]$Reference
#> [1] "Lewis, R.J. Sr.; Hawley's Condensed Chemical Dictionary 14th Edition. John Wiley & Sons, Inc. New York, NY 2001., p. 631"
#>
#> [[2]]$Data[[1]]$Value
#> [[2]]$Data[[1]]$Value$StringWithMarkup
#> [[2]]$Data[[1]]$Value$StringWithMarkup[[1]]
#> String
#> "103 °C at 0.7 mm Hg"
#>
#>
#>
#>
#>
#> [[2]]$ANID
#> [1] 3
#>
#> [[2]]$LinkedRecords
#> [[2]]$LinkedRecords$CID
#> [1] 8393
#>
#>
#>
#> [[3]]
#> [[3]]$SourceName
#> [1] "Hazardous Substances Data Bank (HSDB)"
#>
#> [[3]]$SourceID
#> [1] "33"
#>
#> [[3]]$Name
#> [1] "MERCURIC CHLORIDE"
#>
#> [[3]]$Description
#> [1] "The Hazardous Substances Data Bank (HSDB) is a toxicology database that focuses on the toxicology of potentially hazardous chemicals. It provides information on human exposure, industrial hygiene, emergency handling procedures, environmental fate, regulatory requirements, nanomaterials, and related areas. The information in HSDB has been assessed by a Scientific Review Panel."
#>
#> [[3]]$URL
#> [1] "https://pubchem.ncbi.nlm.nih.gov/source/hsdb/33"
#>
#> [[3]]$LicenseURL
#> [1] "https://www.nlm.nih.gov/web_policies.html"
#>
#> [[3]]$Data
#> [[3]]$Data[[1]]
#> [[3]]$Data[[1]]$TOCHeading
#> type #TOCHeading
#> "Compound" "Boiling Point"
#>
#> [[3]]$Data[[1]]$Description
#> [1] "PEER REVIEWED"
#>
#> [[3]]$Data[[1]]$Reference
#> [1] "Weiss, G.; Hazardous Chemicals Handbook. 1986, Noyes Data Corporation, Park Ridge, NJ 1986., p. 652"
#>
#> [[3]]$Data[[1]]$Value
#> [[3]]$Data[[1]]$Value$StringWithMarkup
#> [[3]]$Data[[1]]$Value$StringWithMarkup[[1]]
#> String
#> "302 °C"
#>
#>
#>
#>
#>
#> [[3]]$ANID
#> [1] 4
#>
#> [[3]]$LinkedRecords
#> [[3]]$LinkedRecords$CID
#> [1] 24085
#>
#>
#>
#> [[4]]
#> [[4]]$SourceName
#> [1] "Hazardous Substances Data Bank (HSDB)"
#>
#> [[4]]$SourceID
#> [1] "34"
#>
#> [[4]]$Name
#> [1] "IODINE, ELEMENTAL"
#>
#> [[4]]$Description
#> [1] "The Hazardous Substances Data Bank (HSDB) is a toxicology database that focuses on the toxicology of potentially hazardous chemicals. It provides information on human exposure, industrial hygiene, emergency handling procedures, environmental fate, regulatory requirements, nanomaterials, and related areas. The information in HSDB has been assessed by a Scientific Review Panel."
#>
#> [[4]]$URL
#> [1] "https://pubchem.ncbi.nlm.nih.gov/source/hsdb/34"
#>
#> [[4]]$LicenseURL
#> [1] "https://www.nlm.nih.gov/web_policies.html"
#>
#> [[4]]$Data
#> [[4]]$Data[[1]]
#> [[4]]$Data[[1]]$TOCHeading
#> type #TOCHeading
#> "Compound" "Boiling Point"
#>
#> [[4]]$Data[[1]]$Description
#> [1] "PEER REVIEWED"
#>
#> [[4]]$Data[[1]]$Reference
#> [1] "Lide, D.R. CRC Handbook of Chemistry and Physics 86TH Edition 2005-2006. CRC Press, Taylor & Francis, Boca Raton, FL 2005, p. 4-19"
#>
#> [[4]]$Data[[1]]$Value
#> [[4]]$Data[[1]]$Value$StringWithMarkup
#> [[4]]$Data[[1]]$Value$StringWithMarkup[[1]]
#> String
#> "184.4 °C"
#>
#>
#>
#>
#>
#> [[4]]$ANID
#> [1] 5
#>
#> [[4]]$LinkedRecords
#> [[4]]$LinkedRecords$CID
#> [1] 807
#>
#>
#>
#> [[5]]
#> [[5]]$SourceName
#> [1] "Hazardous Substances Data Bank (HSDB)"
#>
#> [[5]]$SourceID
#> [1] "35"
#>
#> [[5]]$Name
#> [1] "BENZENE"
#>
#> [[5]]$Description
#> [1] "The Hazardous Substances Data Bank (HSDB) is a toxicology database that focuses on the toxicology of potentially hazardous chemicals. It provides information on human exposure, industrial hygiene, emergency handling procedures, environmental fate, regulatory requirements, nanomaterials, and related areas. The information in HSDB has been assessed by a Scientific Review Panel."
#>
#> [[5]]$URL
#> [1] "https://pubchem.ncbi.nlm.nih.gov/source/hsdb/35"
#>
#> [[5]]$LicenseURL
#> [1] "https://www.nlm.nih.gov/web_policies.html"
#>
#> [[5]]$Data
#> [[5]]$Data[[1]]
#> [[5]]$Data[[1]]$TOCHeading
#> type #TOCHeading
#> "Compound" "Boiling Point"
#>
#> [[5]]$Data[[1]]$Description
#> [1] "PEER REVIEWED"
#>
#> [[5]]$Data[[1]]$Reference
#> [1] "Haynes, W.M. (ed.). CRC Handbook of Chemistry and Physics. 94th Edition. CRC Press LLC, Boca Raton: FL 2013-2014, p. 3-34"
#>
#> [[5]]$Data[[1]]$Value
#> [[5]]$Data[[1]]$Value$StringWithMarkup
#> [[5]]$Data[[1]]$Value$StringWithMarkup[[1]]
#> String
#> "80.08 °C"
#>
#>
#>
#>
#>
#> [[5]]$ANID
#> [1] 6
#>
#> [[5]]$LinkedRecords
#> [[5]]$LinkedRecords$CID
#> [1] 241
#>
#>
#>
#> [[6]]
#> [[6]]$SourceName
#> [1] "Hazardous Substances Data Bank (HSDB)"
#>
#> [[6]]$SourceID
#> [1] "36"
#>
#> [[6]]$Name
#> [1] "CAFFEINE"
#>
#> [[6]]$Description
#> [1] "The Hazardous Substances Data Bank (HSDB) is a toxicology database that focuses on the toxicology of potentially hazardous chemicals. It provides information on human exposure, industrial hygiene, emergency handling procedures, environmental fate, regulatory requirements, nanomaterials, and related areas. The information in HSDB has been assessed by a Scientific Review Panel."
#>
#> [[6]]$URL
#> [1] "https://pubchem.ncbi.nlm.nih.gov/source/hsdb/36"
#>
#> [[6]]$LicenseURL
#> [1] "https://www.nlm.nih.gov/web_policies.html"
#>
#> [[6]]$Data
#> [[6]]$Data[[1]]
#> [[6]]$Data[[1]]$TOCHeading
#> type #TOCHeading
#> "Compound" "Boiling Point"
#>
#> [[6]]$Data[[1]]$Description
#> [1] "PEER REVIEWED"
#>
#> [[6]]$Data[[1]]$Reference
#> [1] "O'Neil, M.J. (ed.). The Merck Index - An Encyclopedia of Chemicals, Drugs, and Biologicals. Cambridge, UK: Royal Society of Chemistry, 2013., p. 289"
#>
#> [[6]]$Data[[1]]$Value
#> [[6]]$Data[[1]]$Value$StringWithMarkup
#> [[6]]$Data[[1]]$Value$StringWithMarkup[[1]]
#> String
#> "178 °C (sublimes)"
#>
#>
#>
#>
#>
#> [[6]]$ANID
#> [1] 7
#>
#> [[6]]$LinkedRecords
#> [[6]]$LinkedRecords$CID
#> [1] 2519The extracted data will contain detailed boiling point information for the compound, along with references and source details.
These examples illustrate the versatility of the PubChem PUG REST API in retrieving specific annotations, allowing users to access detailed information efficiently and effectively.
Pagination: When accessing data from PubChem, you may encounter situations where the data spans multiple pages. In such cases, you can use the page parameter to navigate through the pages. Here’s how you can access different pages of data using the page parameter.
To access annotations related to CAS on the 10th page, you can use the following code:
result <- get_pug_view(annotation = "annotations", identifier = "CAS", domain = "heading", output = "JSON", page = "10")This code retrieves the 10th page of annotations related to CAS. The resulting object, result, contains detailed data about the annotations on that page.
result
#>
#> PUG View Data from PubChem Database
#>
#> Request Details:
#> - Domain: DomainSpecific (heading)
#> - Annotation: annotations
#> - Identifier: CAS
#>
#> Pug View Details:
#> - Annotation (1000): [<unnamed list>]
#> - Page (1): [<unnamed numeric>]
#> - TotalPages (1): [<unnamed numeric>]
#>
#> NOTE: Run getter function 'retrieve()' with element name above to extract data from corresponding list.
#> See ?retrieve for details.To extract the annotations, use the retrieve function:
annotations <- retrieve(object = result, .slot = "Annotation", .to.data.frame = FALSE)The head(annotations) code will provide a preview of the annotations. The detailed structure of the annotations is shown below:
head(annotations)
#> [[1]]
#> [[1]]$SourceName
#> [1] "CAMEO Chemicals"
#>
#> [[1]]$SourceID
#> [1] "19706"
#>
#> [[1]]$Name
#> [1] "O-ACETOTOLUIDIDE"
#>
#> [[1]]$Description
#> [1] "CAMEO Chemicals is a chemical database designed for people who are involved in hazardous material incident response and planning. CAMEO Chemicals contains a library with thousands of datasheets containing response-related information and recommendations for hazardous materials that are commonly transported, used, or stored in the United States. CAMEO Chemicals was developed by the National Oceanic and Atmospheric Administration's Office of Response and Restoration in partnership with the Environmental Protection Agency's Office of Emergency Management."
#>
#> [[1]]$URL
#> [1] "https://cameochemicals.noaa.gov/chemical/19706"
#>
#> [[1]]$LicenseNote
#> [1] "CAMEO Chemicals and all other CAMEO products are available at no charge to those organizations and individuals (recipients) responsible for the safe handling of chemicals. However, some of the chemical data itself is subject to the copyright restrictions of the companies or organizations that provided the data."
#>
#> [[1]]$LicenseURL
#> [1] "https://cameochemicals.noaa.gov/help/reference/terms_and_conditions.htm?d_f=false"
#>
#> [[1]]$Data
#> [[1]]$Data[[1]]
#> [[1]]$Data[[1]]$TOCHeading
#> type #TOCHeading
#> "Compound" "CAS"
#>
#> [[1]]$Data[[1]]$Value
#> [[1]]$Data[[1]]$Value$StringWithMarkup
#> [[1]]$Data[[1]]$Value$StringWithMarkup[[1]]
#> String
#> "120-66-1"
#>
#>
#>
#>
#>
#> [[1]]$ANID
#> [1] 759941
#>
#> [[1]]$LinkedRecords
#> [[1]]$LinkedRecords$CID
#> [1] 8443
#>
#>
#>
#> [[2]]
#> [[2]]$SourceName
#> [1] "CAMEO Chemicals"
#>
#> [[2]]$SourceID
#> [1] "19750"
#>
#> [[2]]$Name
#> [1] "O-AMINOAZOTOLUENE"
#>
#> [[2]]$Description
#> [1] "CAMEO Chemicals is a chemical database designed for people who are involved in hazardous material incident response and planning. CAMEO Chemicals contains a library with thousands of datasheets containing response-related information and recommendations for hazardous materials that are commonly transported, used, or stored in the United States. CAMEO Chemicals was developed by the National Oceanic and Atmospheric Administration's Office of Response and Restoration in partnership with the Environmental Protection Agency's Office of Emergency Management."
#>
#> [[2]]$URL
#> [1] "https://cameochemicals.noaa.gov/chemical/19750"
#>
#> [[2]]$LicenseNote
#> [1] "CAMEO Chemicals and all other CAMEO products are available at no charge to those organizations and individuals (recipients) responsible for the safe handling of chemicals. However, some of the chemical data itself is subject to the copyright restrictions of the companies or organizations that provided the data."
#>
#> [[2]]$LicenseURL
#> [1] "https://cameochemicals.noaa.gov/help/reference/terms_and_conditions.htm?d_f=false"
#>
#> [[2]]$Data
#> [[2]]$Data[[1]]
#> [[2]]$Data[[1]]$TOCHeading
#> type #TOCHeading
#> "Compound" "CAS"
#>
#> [[2]]$Data[[1]]$Value
#> [[2]]$Data[[1]]$Value$StringWithMarkup
#> [[2]]$Data[[1]]$Value$StringWithMarkup[[1]]
#> String
#> "97-56-3"
#>
#>
#>
#>
#>
#> [[2]]$ANID
#> [1] 759942
#>
#> [[2]]$LinkedRecords
#> [[2]]$LinkedRecords$CID
#> [1] 7340
#>
#>
#>
#> [[3]]
#> [[3]]$SourceName
#> [1] "CAMEO Chemicals"
#>
#> [[3]]$SourceID
#> [1] "19795"
#>
#> [[3]]$Name
#> [1] "O-AMINOPHENOL"
#>
#> [[3]]$Description
#> [1] "CAMEO Chemicals is a chemical database designed for people who are involved in hazardous material incident response and planning. CAMEO Chemicals contains a library with thousands of datasheets containing response-related information and recommendations for hazardous materials that are commonly transported, used, or stored in the United States. CAMEO Chemicals was developed by the National Oceanic and Atmospheric Administration's Office of Response and Restoration in partnership with the Environmental Protection Agency's Office of Emergency Management."
#>
#> [[3]]$URL
#> [1] "https://cameochemicals.noaa.gov/chemical/19795"
#>
#> [[3]]$LicenseNote
#> [1] "CAMEO Chemicals and all other CAMEO products are available at no charge to those organizations and individuals (recipients) responsible for the safe handling of chemicals. However, some of the chemical data itself is subject to the copyright restrictions of the companies or organizations that provided the data."
#>
#> [[3]]$LicenseURL
#> [1] "https://cameochemicals.noaa.gov/help/reference/terms_and_conditions.htm?d_f=false"
#>
#> [[3]]$Data
#> [[3]]$Data[[1]]
#> [[3]]$Data[[1]]$TOCHeading
#> type #TOCHeading
#> "Compound" "CAS"
#>
#> [[3]]$Data[[1]]$Value
#> [[3]]$Data[[1]]$Value$StringWithMarkup
#> [[3]]$Data[[1]]$Value$StringWithMarkup[[1]]
#> String
#> "95-55-6"
#>
#>
#>
#>
#>
#> [[3]]$ANID
#> [1] 759943
#>
#> [[3]]$LinkedRecords
#> [[3]]$LinkedRecords$CID
#> [1] 5801
#>
#>
#>
#> [[4]]
#> [[4]]$SourceName
#> [1] "CAMEO Chemicals"
#>
#> [[4]]$SourceID
#> [1] "19800"
#>
#> [[4]]$Name
#> [1] "O-AMINOPHTHALYL HYDRAZIDE"
#>
#> [[4]]$Description
#> [1] "CAMEO Chemicals is a chemical database designed for people who are involved in hazardous material incident response and planning. CAMEO Chemicals contains a library with thousands of datasheets containing response-related information and recommendations for hazardous materials that are commonly transported, used, or stored in the United States. CAMEO Chemicals was developed by the National Oceanic and Atmospheric Administration's Office of Response and Restoration in partnership with the Environmental Protection Agency's Office of Emergency Management."
#>
#> [[4]]$URL
#> [1] "https://cameochemicals.noaa.gov/chemical/19800"
#>
#> [[4]]$LicenseNote
#> [1] "CAMEO Chemicals and all other CAMEO products are available at no charge to those organizations and individuals (recipients) responsible for the safe handling of chemicals. However, some of the chemical data itself is subject to the copyright restrictions of the companies or organizations that provided the data."
#>
#> [[4]]$LicenseURL
#> [1] "https://cameochemicals.noaa.gov/help/reference/terms_and_conditions.htm?d_f=false"
#>
#> [[4]]$Data
#> [[4]]$Data[[1]]
#> [[4]]$Data[[1]]$TOCHeading
#> type #TOCHeading
#> "Compound" "CAS"
#>
#> [[4]]$Data[[1]]$Value
#> [[4]]$Data[[1]]$Value$StringWithMarkup
#> [[4]]$Data[[1]]$Value$StringWithMarkup[[1]]
#> String
#> "521-31-3"
#>
#>
#>
#>
#>
#> [[4]]$ANID
#> [1] 759944
#>
#> [[4]]$LinkedRecords
#> [[4]]$LinkedRecords$CID
#> [1] 10638
#>
#>
#>
#> [[5]]
#> [[5]]$SourceName
#> [1] "CAMEO Chemicals"
#>
#> [[5]]$SourceID
#> [1] "2488"
#>
#> [[5]]$Name
#> [1] "O-ANISIDINE"
#>
#> [[5]]$Description
#> [1] "CAMEO Chemicals is a chemical database designed for people who are involved in hazardous material incident response and planning. CAMEO Chemicals contains a library with thousands of datasheets containing response-related information and recommendations for hazardous materials that are commonly transported, used, or stored in the United States. CAMEO Chemicals was developed by the National Oceanic and Atmospheric Administration's Office of Response and Restoration in partnership with the Environmental Protection Agency's Office of Emergency Management."
#>
#> [[5]]$URL
#> [1] "https://cameochemicals.noaa.gov/chemical/2488"
#>
#> [[5]]$LicenseNote
#> [1] "CAMEO Chemicals and all other CAMEO products are available at no charge to those organizations and individuals (recipients) responsible for the safe handling of chemicals. However, some of the chemical data itself is subject to the copyright restrictions of the companies or organizations that provided the data."
#>
#> [[5]]$LicenseURL
#> [1] "https://cameochemicals.noaa.gov/help/reference/terms_and_conditions.htm?d_f=false"
#>
#> [[5]]$Data
#> [[5]]$Data[[1]]
#> [[5]]$Data[[1]]$TOCHeading
#> type #TOCHeading
#> "Compound" "CAS"
#>
#> [[5]]$Data[[1]]$Value
#> [[5]]$Data[[1]]$Value$StringWithMarkup
#> [[5]]$Data[[1]]$Value$StringWithMarkup[[1]]
#> String
#> "90-04-0"
#>
#>
#>
#>
#>
#> [[5]]$ANID
#> [1] 759945
#>
#> [[5]]$LinkedRecords
#> [[5]]$LinkedRecords$CID
#> [1] 7000
#>
#>
#>
#> [[6]]
#> [[6]]$SourceName
#> [1] "CAMEO Chemicals"
#>
#> [[6]]$SourceID
#> [1] "16104"
#>
#> [[6]]$Name
#> [1] "O-ANISIDINE HYDROCHLORIDE"
#>
#> [[6]]$Description
#> [1] "CAMEO Chemicals is a chemical database designed for people who are involved in hazardous material incident response and planning. CAMEO Chemicals contains a library with thousands of datasheets containing response-related information and recommendations for hazardous materials that are commonly transported, used, or stored in the United States. CAMEO Chemicals was developed by the National Oceanic and Atmospheric Administration's Office of Response and Restoration in partnership with the Environmental Protection Agency's Office of Emergency Management."
#>
#> [[6]]$URL
#> [1] "https://cameochemicals.noaa.gov/chemical/16104"
#>
#> [[6]]$LicenseNote
#> [1] "CAMEO Chemicals and all other CAMEO products are available at no charge to those organizations and individuals (recipients) responsible for the safe handling of chemicals. However, some of the chemical data itself is subject to the copyright restrictions of the companies or organizations that provided the data."
#>
#> [[6]]$LicenseURL
#> [1] "https://cameochemicals.noaa.gov/help/reference/terms_and_conditions.htm?d_f=false"
#>
#> [[6]]$Data
#> [[6]]$Data[[1]]
#> [[6]]$Data[[1]]$TOCHeading
#> type #TOCHeading
#> "Compound" "CAS"
#>
#> [[6]]$Data[[1]]$Value
#> [[6]]$Data[[1]]$Value$StringWithMarkup
#> [[6]]$Data[[1]]$Value$StringWithMarkup[[1]]
#> String
#> "134-29-2"
#>
#>
#>
#>
#>
#> [[6]]$ANID
#> [1] 759946
#>
#> [[6]]$LinkedRecords
#> [[6]]$LinkedRecords$CID
#> [1] 8638The extracted data provides detailed information on each annotation, including the source, name, description, and CAS number, along with relevant references and linked records. This approach allows you to efficiently access specific annotations even when dealing with large datasets that span multiple pages.
Depositors and SIDs: List all depositors for a given compound, categorized by source type.
The following code snippet retrieves detailed annotated data from the PubChem database for the compound with CID “1234”:
result <- get_pug_view(annotation = "categories", identifier = "1234", domain = "compound", output = "JSON")
result
#>
#> PUG View Data from PubChem Database
#>
#> Request Details:
#> - Domain: Compound
#> - Annotation: categories
#> - Identifier: 1234
#>
#> Pug View Details:
#> - RecordType (1): [<unnamed character>]
#> - RecordNumber (1): [<unnamed numeric>]
#> - Categories (8): [<unnamed list>]
#>
#> NOTE: Run getter function 'retrieve()' with element name above to extract data from corresponding list.
#> See ?retrieve for details.This code extracts the “Categories” data from the result using the retrieve() function. The extracted data is stored in the categories variable.
categories <- retrieve(object = result, .slot = "Categories", .to.data.frame = FALSE)The displayed output of head(categories) will show a list of categories, where each category contains:
The name of the category (e.g., “Chemical Vendors”) A link to a PubChem search for substances in this category A list of sources that have deposited data in this category, including: The Substance Identifier (SID) The source’s name and website URL The URL of the source’s page on PubChem The registry ID of the compound The URL to the detailed record of the source The categories the source belongs to
head(categories)
#> [[1]]
#> [[1]]$Category
#> [1] "Chemical Vendors"
#>
#> [[1]]$URL
#> [1] "https://www.ncbi.nlm.nih.gov/sites/entrez?cmd=search&db=pcsubstance&term=1234[StandardizedCID]+AND+%22Chemical+Vendors%22[SourceCategory]"
#>
#> [[1]]$Sources
#> [[1]]$Sources[[1]]
#> [[1]]$Sources[[1]]$SID
#> [1] 254789975
#>
#> [[1]]$Sources[[1]]$SourceName
#> [1] "BOC Sciences"
#>
#> [[1]]$Sources[[1]]$SourceURL
#> [1] "https://www.bocsci.com/"
#>
#> [[1]]$Sources[[1]]$SourceDetail
#> [1] "https://pubchem.ncbi.nlm.nih.gov/source/BOC%20Sciences"
#>
#> [[1]]$Sources[[1]]$RegistryID
#> [1] "16662-46-7"
#>
#> [[1]]$Sources[[1]]$SourceRecordURL
#> [1] "https://www.bocsci.com/3-cyano-3-3-4-5-trimethoxyphenyl-hex-6-yl-5-6-dimethoxyphenethyl-cas-16662-46-7-item-60526.html"
#>
#> [[1]]$Sources[[1]]$SourceCategories
#> [1] "Chemical Vendors"
#>
#>
#> [[1]]$Sources[[2]]
#> [[1]]$Sources[[2]]$SID
#> [1] 341112340
#>
#> [[1]]$Sources[[2]]$SourceName
#> [1] "BOC Sciences"
#>
#> [[1]]$Sources[[2]]$SourceURL
#> [1] "https://www.bocsci.com/"
#>
#> [[1]]$Sources[[2]]$SourceDetail
#> [1] "https://pubchem.ncbi.nlm.nih.gov/source/BOC%20Sciences"
#>
#> [[1]]$Sources[[2]]$RegistryID
#> [1] "16662-47-8"
#>
#> [[1]]$Sources[[2]]$SourceRecordURL
#> [1] "https://www.bocsci.com/product/gallopamil-cas-16662-47-8-60527.html"
#>
#> [[1]]$Sources[[2]]$SourceCategories
#> [1] "Chemical Vendors"
#>
#>
#> [[1]]$Sources[[3]]
#> [[1]]$Sources[[3]]$SID
#> [1] 443845441
#>
#> [[1]]$Sources[[3]]$SourceName
#> [1] "TargetMol"
#>
#> [[1]]$Sources[[3]]$SourceURL
#> [1] "https://www.targetmol.com/contact-us"
#>
#> [[1]]$Sources[[3]]$SourceDetail
#> [1] "https://pubchem.ncbi.nlm.nih.gov/source/TargetMol"
#>
#> [[1]]$Sources[[3]]$RegistryID
#> [1] "T11353"
#>
#> [[1]]$Sources[[3]]$SourceRecordURL
#> [1] "https://www.targetmol.com/compound/Gallopamil"
#>
#> [[1]]$Sources[[3]]$SourceCategories
#> [1] "Chemical Vendors"
#>
#>
#> [[1]]$Sources[[4]]
#> [[1]]$Sources[[4]]$SID
#> [1] 491505959
#>
#> [[1]]$Sources[[4]]$SourceName
#> [1] "10X CHEM"
#>
#> [[1]]$Sources[[4]]$SourceURL
#> [1] "https://www.10xchem.com/"
#>
#> [[1]]$Sources[[4]]$SourceDetail
#> [1] "https://pubchem.ncbi.nlm.nih.gov/source/10X%20CHEM"
#>
#> [[1]]$Sources[[4]]$RegistryID
#> [1] "TX001Y13"
#>
#> [[1]]$Sources[[4]]$SourceRecordURL
#> [1] "https://www.10xchem.com/prod/16662-47-8"
#>
#> [[1]]$Sources[[4]]$SourceCategories
#> [1] "Chemical Vendors"
#>
#>
#> [[1]]$Sources[[5]]
#> [[1]]$Sources[[5]]$SID
#> [1] 373325381
#>
#> [[1]]$Sources[[5]]$SourceName
#> [1] "Ambinter"
#>
#> [[1]]$Sources[[5]]$SourceURL
#> [1] "http://www.ambinter.com"
#>
#> [[1]]$Sources[[5]]$SourceDetail
#> [1] "https://pubchem.ncbi.nlm.nih.gov/source/Ambinter"
#>
#> [[1]]$Sources[[5]]$RegistryID
#> [1] "Amb21926585"
#>
#> [[1]]$Sources[[5]]$SourceRecordURL
#> [1] "http://www.ambinter.com/reference/21926585"
#>
#> [[1]]$Sources[[5]]$SourceCategories
#> [1] "Chemical Vendors"
#>
#>
#> [[1]]$Sources[[6]]
#> [[1]]$Sources[[6]]$SID
#> [1] 443331886
#>
#> [[1]]$Sources[[6]]$SourceName
#> [1] "AA BLOCKS"
#>
#> [[1]]$Sources[[6]]$SourceURL
#> [1] "https://www.aablocks.com"
#>
#> [[1]]$Sources[[6]]$SourceDetail
#> [1] "https://pubchem.ncbi.nlm.nih.gov/source/AA%20BLOCKS"
#>
#> [[1]]$Sources[[6]]$RegistryID
#> [1] "AA001WSN"
#>
#> [[1]]$Sources[[6]]$SourceRecordURL
#> [1] "https://www.aablocks.com/prod/16662-47-8"
#>
#> [[1]]$Sources[[6]]$SourceCategories
#> [1] "Chemical Vendors"
#>
#>
#> [[1]]$Sources[[7]]
#> [[1]]$Sources[[7]]$SID
#> [1] 438803399
#>
#> [[1]]$Sources[[7]]$SourceName
#> [1] "Smolecule"
#>
#> [[1]]$Sources[[7]]$SourceURL
#> [1] "https://www.smolecule.com/"
#>
#> [[1]]$Sources[[7]]$SourceDetail
#> [1] "https://pubchem.ncbi.nlm.nih.gov/source/Smolecule"
#>
#> [[1]]$Sources[[7]]$RegistryID
#> [1] "S572969"
#>
#> [[1]]$Sources[[7]]$SourceRecordURL
#> [1] "https://www.smolecule.com/products/s572969"
#>
#> [[1]]$Sources[[7]]$SourceCategories
#> [1] "Chemical Vendors"
#>
#>
#> [[1]]$Sources[[8]]
#> [[1]]$Sources[[8]]$SID
#> [1] 468739220
#>
#> [[1]]$Sources[[8]]$SourceName
#> [1] "J&H Chemical Co.,ltd"
#>
#> [[1]]$Sources[[8]]$SourceURL
#> [1] "http://www.jhechem.com"
#>
#> [[1]]$Sources[[8]]$SourceDetail
#> [1] "https://pubchem.ncbi.nlm.nih.gov/source/J&H%20Chemical%20Co.,ltd"
#>
#> [[1]]$Sources[[8]]$RegistryID
#> [1] "JH169373"
#>
#> [[1]]$Sources[[8]]$SourceRecordURL
#> [1] "http://www.jhechem.com/ProductDetail/169373"
#>
#> [[1]]$Sources[[8]]$SourceCategories
#> [1] "Chemical Vendors"
#>
#>
#> [[1]]$Sources[[9]]
#> [[1]]$Sources[[9]]$SID
#> [1] 434290301
#>
#> [[1]]$Sources[[9]]$SourceName
#> [1] "BLD Pharm"
#>
#> [[1]]$Sources[[9]]$SourceURL
#> [1] "https://www.bldpharm.com/"
#>
#> [[1]]$Sources[[9]]$SourceDetail
#> [1] "https://pubchem.ncbi.nlm.nih.gov/source/BLD%20Pharm"
#>
#> [[1]]$Sources[[9]]$RegistryID
#> [1] "BD238932"
#>
#> [[1]]$Sources[[9]]$SourceRecordURL
#> [1] "http://www.bldpharm.com/products/16662-47-8.html"
#>
#> [[1]]$Sources[[9]]$SourceCategories
#> [1] "Chemical Vendors"
#>
#>
#> [[1]]$Sources[[10]]
#> [[1]]$Sources[[10]]$SID
#> [1] 446164551
#>
#> [[1]]$Sources[[10]]$SourceName
#> [1] "MolCore"
#>
#> [[1]]$Sources[[10]]$SourceURL
#> [1] "https://www.001chemical.com/"
#>
#> [[1]]$Sources[[10]]$SourceDetail
#> [1] "https://pubchem.ncbi.nlm.nih.gov/source/MolCore"
#>
#> [[1]]$Sources[[10]]$RegistryID
#> [1] "DY114903"
#>
#> [[1]]$Sources[[10]]$SourceRecordURL
#> [1] "https://www.001chemical.com/chem/16662-47-8"
#>
#> [[1]]$Sources[[10]]$SourceCategories
#> [1] "Chemical Vendors"
#>
#>
#> [[1]]$Sources[[11]]
#> [[1]]$Sources[[11]]$SID
#> [1] 335977281
#>
#> [[1]]$Sources[[11]]$SourceName
#> [1] "MolCore"
#>
#> [[1]]$Sources[[11]]$SourceURL
#> [1] "https://www.molcore.com/"
#>
#> [[1]]$Sources[[11]]$SourceDetail
#> [1] "https://pubchem.ncbi.nlm.nih.gov/source/MolCore"
#>
#> [[1]]$Sources[[11]]$RegistryID
#> [1] "MC114903"
#>
#> [[1]]$Sources[[11]]$SourceRecordURL
#> [1] "https://www.molcore.com/product/16662-47-8"
#>
#> [[1]]$Sources[[11]]$SourceCategories
#> [1] "Chemical Vendors"
#>
#>
#> [[1]]$Sources[[12]]
#> [[1]]$Sources[[12]]$SID
#> [1] 91721411
#>
#> [[1]]$Sources[[12]]$SourceName
#> [1] "MolPort"
#>
#> [[1]]$Sources[[12]]$SourceURL
#> [1] "https://www.molport.com"
#>
#> [[1]]$Sources[[12]]$SourceDetail
#> [1] "https://pubchem.ncbi.nlm.nih.gov/source/MolPort"
#>
#> [[1]]$Sources[[12]]$RegistryID
#> [1] "MolPort-003-958-631"
#>
#> [[1]]$Sources[[12]]$SourceRecordURL
#> [1] "https://www.molport.com/shop/molecule-link/MolPort-003-958-631"
#>
#> [[1]]$Sources[[12]]$SourceCategories
#> [1] "Chemical Vendors"
#>
#>
#> [[1]]$Sources[[13]]
#> [[1]]$Sources[[13]]$SID
#> [1] 485297280
#>
#> [[1]]$Sources[[13]]$SourceName
#> [1] "LGC Standards"
#>
#> [[1]]$Sources[[13]]$SourceURL
#> [1] "https://www.lgcstandards.com/US/en/"
#>
#> [[1]]$Sources[[13]]$SourceDetail
#> [1] "https://pubchem.ncbi.nlm.nih.gov/source/LGC%20Standards"
#>
#> [[1]]$Sources[[13]]$RegistryID
#> [1] "TRC-M271768"
#>
#> [[1]]$Sources[[13]]$SourceRecordURL
#> [1] "https://www.lgcstandards.com/CA/en/p/TRC-M271768-100MG"
#>
#> [[1]]$Sources[[13]]$SourceCategories
#> [1] "Chemical Vendors"
#>
#>
#> [[1]]$Sources[[14]]
#> [[1]]$Sources[[14]]$SID
#> [1] 496060445
#>
#> [[1]]$Sources[[14]]$SourceName
#> [1] "LGC Standards"
#>
#> [[1]]$Sources[[14]]$SourceURL
#> [1] "https://www.lgcstandards.com/US/en/"
#>
#> [[1]]$Sources[[14]]$SourceDetail
#> [1] "https://pubchem.ncbi.nlm.nih.gov/source/LGC%20Standards"
#>
#> [[1]]$Sources[[14]]$RegistryID
#> [1] "TRC-M271768-100MG"
#>
#> [[1]]$Sources[[14]]$SourceRecordURL
#> [1] "https://www.lgcstandards.com/GB/en/p/TRC-M271768-100MG"
#>
#> [[1]]$Sources[[14]]$SourceCategories
#> [1] "Chemical Vendors"
#>
#>
#> [[1]]$Sources[[15]]
#> [[1]]$Sources[[15]]$SID
#> [1] 478133809
#>
#> [[1]]$Sources[[15]]$SourceName
#> [1] "Thoreauchem"
#>
#> [[1]]$Sources[[15]]$SourceURL
#> [1] "http://www.thoreauchem.com/"
#>
#> [[1]]$Sources[[15]]$SourceDetail
#> [1] "https://pubchem.ncbi.nlm.nih.gov/source/Thoreauchem"
#>
#> [[1]]$Sources[[15]]$RegistryID
#> [1] "TH-B02072"
#>
#> [[1]]$Sources[[15]]$SourceRecordURL
#> [1] "http://www.thoreauchem.com/prod/16161/"
#>
#> [[1]]$Sources[[15]]$SourceCategories
#> [1] "Chemical Vendors"
#>
#>
#> [[1]]$Sources[[16]]
#> [[1]]$Sources[[16]]$SID
#> [1] 468530044
#>
#> [[1]]$Sources[[16]]$SourceName
#> [1] "Starshine Chemical"
#>
#> [[1]]$Sources[[16]]$SourceURL
#> [1] "https://www.starshinechemical.com"
#>
#> [[1]]$Sources[[16]]$SourceDetail
#> [1] "https://pubchem.ncbi.nlm.nih.gov/source/Starshine%20Chemical"
#>
#> [[1]]$Sources[[16]]$RegistryID
#> [1] "starbld0087386"
#>
#> [[1]]$Sources[[16]]$SourceCategories
#> [1] "Chemical Vendors"
#>
#>
#> [[1]]$Sources[[17]]
#> [[1]]$Sources[[17]]$SID
#> [1] 375768453
#>
#> [[1]]$Sources[[17]]$SourceName
#> [1] "001Chemical"
#>
#> [[1]]$Sources[[17]]$SourceURL
#> [1] "https://www.001chemical.com/"
#>
#> [[1]]$Sources[[17]]$SourceDetail
#> [1] "https://pubchem.ncbi.nlm.nih.gov/source/001Chemical"
#>
#> [[1]]$Sources[[17]]$RegistryID
#> [1] "DY114903"
#>
#> [[1]]$Sources[[17]]$SourceRecordURL
#> [1] "https://www.001chemical.com/chem/16662-47-8"
#>
#> [[1]]$Sources[[17]]$SourceCategories
#> [1] "Chemical Vendors"
#>
#>
#> [[1]]$Sources[[18]]
#> [[1]]$Sources[[18]]$SID
#> [1] 381391039
#>
#> [[1]]$Sources[[18]]$SourceName
#> [1] "Achemtek"
#>
#> [[1]]$Sources[[18]]$SourceURL
#> [1] "http://achemtek.com/"
#>
#> [[1]]$Sources[[18]]$SourceDetail
#> [1] "https://pubchem.ncbi.nlm.nih.gov/source/Achemtek"
#>
#> [[1]]$Sources[[18]]$RegistryID
#> [1] "0102-012956"
#>
#> [[1]]$Sources[[18]]$SourceRecordURL
#> [1] "http://www.achemtek.com/16662-47-8"
#>
#> [[1]]$Sources[[18]]$SourceCategories
#> [1] "Chemical Vendors"
#>
#>
#> [[1]]$Sources[[19]]
#> [[1]]$Sources[[19]]$SID
#> [1] 445871730
#>
#> [[1]]$Sources[[19]]$SourceName
#> [1] "BenchChem"
#>
#> [[1]]$Sources[[19]]$SourceURL
#> [1] "https://www.benchchem.com/"
#>
#> [[1]]$Sources[[19]]$SourceDetail
#> [1] "https://pubchem.ncbi.nlm.nih.gov/source/BenchChem"
#>
#> [[1]]$Sources[[19]]$RegistryID
#> [1] "B102620"
#>
#> [[1]]$Sources[[19]]$SourceRecordURL
#> [1] "https://www.benchchem.com/product/b102620"
#>
#> [[1]]$Sources[[19]]$SourceCategories
#> [1] "Chemical Vendors"
#>
#>
#> [[1]]$Sources[[20]]
#> [[1]]$Sources[[20]]$SID
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#> [1] "Governmental Organizations" "NIH Initiatives"Similar Compounds: Get a list of compounds with similar structures and associated information:
result <- get_pug_view(annotation = "neighbors", identifier = "1234", domain = "compound", output = "JSON")This code fetches data related to compounds similar to the compound with CID “1234”. The result is stored in the result variable and contains information about similar compounds. The function parameters specify that we are looking for “neighbors” (compounds with similar structures) in the “compound” domain.
result
#>
#> PUG View Data from PubChem Database
#>
#> Stopped with an ERROR. Details are below:
#>
#> - Message: Error in API request
#> - Code: HTTP Error 400The Pug View Details section includes several lists of similar compounds categorized by different types of related information. Each type is followed by a list of IDs corresponding to similar compounds.
retrieve(object = result, .slot = "NeighborsOfType", .to.data.frame = FALSE)
#> Warning in retrieve.PugViewInstance(object = result, .slot = "NeighborsOfType", : 'object' encountered an error. Nothing to return.
#> See error details in 'object'.
#> NULLThe output displays lists of similar compounds categorized by various types such as:
PubMed URLs: Retrieve literature associated with a compound, organized by subheading:
result <- get_pug_view(annotation = "literature", identifier = "1234", domain = "compound", output = "JSON")This code fetches data related to the literature associated with the compound identified by CID “1234”. The result is stored in the result variable and contains information about the related literature. The function parameters specify that we are looking for “literature” in the “compound” domain.
result
#>
#> PUG View Data from PubChem Database
#>
#> Request Details:
#> - Domain: Compound
#> - Annotation: literature
#> - Identifier: 1234
#>
#> Pug View Details:
#> - RecordType (1): [<unnamed character>]
#> - RecordNumber (1): [<unnamed numeric>]
#> - AllURL (1): [<unnamed character>]
#> - Subheadings (15): [<unnamed list>]
#>
#> NOTE: Run getter function 'retrieve()' with element name above to extract data from corresponding list.
#> See ?retrieve for details.The Pug View Details section includes the AllURL slot, which contains URLs to the relevant literature. The following code retrieves the detailed information about the literature from the result object:
retrieve(object = result, .slot = "AllURL", .to.data.frame = FALSE)
#> [1] "https://www.ncbi.nlm.nih.gov/sites/entrez?cmd=search&db=pubmed&term=%22Gallopamil%22[Mesh%20Terms%3anoexp]"This URL directs to PubMed and shows the literature related to the compound “Gallopamil” identified by the CID “1234”.
NCBI LinkOut Records: List all LinkOut records for a substance, compound, or assay:
result <- get_pug_view(annotation = "linkout", identifier = "1234", domain = "compound", output = "JSON")
result
#>
#> PUG View Data from PubChem Database
#>
#> Request Details:
#> - Domain: Compound
#> - Annotation: linkout
#> - Identifier: 1234
#>
#> Pug View Details:
#> - RecordType (1): [<unnamed character>]
#> - RecordNumber (1): [<unnamed numeric>]
#> - ObjUrl (1): [<unnamed list>]
#>
#> NOTE: Run getter function 'retrieve()' with element name above to extract data from corresponding list.
#> See ?retrieve for details.The following code extracts the LinkOut data from the result:
retrieve(result, .slot = "ObjUrl", .to.data.frame = FALSE)
#> $Url
#> [1] "http://partnersolution.ingenuity.com/?cid=97ae3f91eab87a&p1=EntrezPubChem&p2=GV&s=&ipaUri=%2Fpa%2Fapi%2Fv2%2Fgeneview%3Fapplicationname%3DEntrezPubChem%26geneId%3DING:qkb%26geneidtype%3Dingenuity"
#>
#> $SubjectType
#> [1] "molecular interactions"
#>
#> $Category
#> [1] "Chemical Information"
#>
#> $Attribute
#> [1] "subscription/membership/fee required"
#>
#> $Provider
#> Name NameAbbr
#> "Ingenuity Pathways Analysis" "Ingenuity"
#> Id Url
#> "5628" "http://www.ingenuity.com"The example output shows details such as the URL, subject type, category, attribute, and provider information for the LinkOut record.
3D Protein Structures: List 3D protein structures associated with a compound:
result <- get_pug_view(annotation = "structure", identifier = "2244", domain = "compound", output = "JSON")
result
#>
#> PUG View Data from PubChem Database
#>
#> Request Details:
#> - Domain: Compound
#> - Annotation: structure
#> - Identifier: 2244
#>
#> Pug View Details:
#> - RecordType (1): [<unnamed character>]
#> - RecordNumber (1): [<unnamed numeric>]
#> - URL (1): [<unnamed character>]
#> - NumberOfStructures (1): [<unnamed numeric>]
#> - Structures (8): [<unnamed list>]
#>
#> NOTE: Run getter function 'retrieve()' with element name above to extract data from corresponding list.
#> See ?retrieve for details.The following code extracts the 3D structures data from the result:
retrieve(object = result, .slot = "Structures", .to.data.frame = FALSE)
#> [[1]]
#> [[1]]$MMDB_ID
#> [1] 230639
#>
#> [[1]]$PDB_ID
#> [1] "8J3W"
#>
#> [[1]]$URL
#> [1] "https://www.ncbi.nlm.nih.gov/Structure/mmdb/mmdbsrv.cgi?uid=230639"
#>
#> [[1]]$ImageURL
#> [1] "https://www.ncbi.nlm.nih.gov/Structure/mmdb/mmdbimage.fcgi?small=t&id=230639"
#>
#> [[1]]$Description
#> [1] "Cryo-EM structure of aspirin-bound ABCC4"
#>
#> [[1]]$Taxonomy
#> [[1]]$Taxonomy$ID
#> [1] 9606
#>
#> [[1]]$Taxonomy$Name
#> [1] "Homo sapiens"
#>
#>
#>
#> [[2]]
#> [[2]]$MMDB_ID
#> [1] 173465
#>
#> [[2]]$PDB_ID
#> [1] "6MQF"
#>
#> [[2]]$URL
#> [1] "https://www.ncbi.nlm.nih.gov/Structure/mmdb/mmdbsrv.cgi?uid=173465"
#>
#> [[2]]$ImageURL
#> [1] "https://www.ncbi.nlm.nih.gov/Structure/mmdb/mmdbimage.fcgi?small=t&id=173465"
#>
#> [[2]]$Description
#> [1] "Myotoxin II from Bothrops moojeni complexed with Acetylsalicylic acid"
#>
#> [[2]]$Taxonomy
#> [[2]]$Taxonomy$ID
#> [1] 98334
#>
#> [[2]]$Taxonomy$Name
#> [1] "Bothrops moojeni"
#>
#>
#>
#> [[3]]
#> [[3]]$MMDB_ID
#> [1] 115960
#>
#> [[3]]$PDB_ID
#> [1] "4NSB"
#>
#> [[3]]$URL
#> [1] "https://www.ncbi.nlm.nih.gov/Structure/mmdb/mmdbsrv.cgi?uid=115960"
#>
#> [[3]]$ImageURL
#> [1] "https://www.ncbi.nlm.nih.gov/Structure/mmdb/mmdbimage.fcgi?small=t&id=115960"
#>
#> [[3]]$Description
#> [1] "Crystal structure of the complex of signaling glycoprotein, SPB-40 and N-acetyl salicylic acid at 3.05 A resolution"
#>
#> [[3]]$Taxonomy
#> [[3]]$Taxonomy$ID
#> [1] 89462
#>
#> [[3]]$Taxonomy$Name
#> [1] "Bubalus bubalis"
#>
#>
#>
#> [[4]]
#> [[4]]$MMDB_ID
#> [1] 75951
#>
#> [[4]]$PDB_ID
#> [1] "3IAZ"
#>
#> [[4]]$URL
#> [1] "https://www.ncbi.nlm.nih.gov/Structure/mmdb/mmdbsrv.cgi?uid=75951"
#>
#> [[4]]$ImageURL
#> [1] "https://www.ncbi.nlm.nih.gov/Structure/mmdb/mmdbimage.fcgi?small=t&id=75951"
#>
#> [[4]]$Description
#> [1] "Structural basis of the prevention of NSAID-induced damage of the gastrointestinal tract by C-terminal half (C-lobe) of bovine colostrum protein lactoferrin: Binding and structural studies of the C-lobe complex with aspirin"
#>
#> [[4]]$Taxonomy
#> [[4]]$Taxonomy$ID
#> [1] 9913
#>
#> [[4]]$Taxonomy$Name
#> [1] "Bos taurus"
#>
#>
#>
#> [[5]]
#> [[5]]$MMDB_ID
#> [1] 70578
#>
#> [[5]]$PDB_ID
#> [1] "3GCL"
#>
#> [[5]]$URL
#> [1] "https://www.ncbi.nlm.nih.gov/Structure/mmdb/mmdbsrv.cgi?uid=70578"
#>
#> [[5]]$ImageURL
#> [1] "https://www.ncbi.nlm.nih.gov/Structure/mmdb/mmdbimage.fcgi?small=t&id=70578"
#>
#> [[5]]$Description
#> [1] "Mode of ligand binding and assignment of subsites in mammalian peroxidases: crystal structure of lactoperoxidase complexes with acetyl salycylic acid, salicylhydroxamic acid and benzylhydroxamic acid"
#>
#> [[5]]$Taxonomy
#> [[5]]$Taxonomy$ID
#> [1] 9913
#>
#> [[5]]$Taxonomy$Name
#> [1] "Bos taurus"
#>
#>
#>
#> [[6]]
#> [[6]]$MMDB_ID
#> [1] 54234
#>
#> [[6]]$PDB_ID
#> [1] "2QQT"
#>
#> [[6]]$URL
#> [1] "https://www.ncbi.nlm.nih.gov/Structure/mmdb/mmdbsrv.cgi?uid=54234"
#>
#> [[6]]$ImageURL
#> [1] "https://www.ncbi.nlm.nih.gov/Structure/mmdb/mmdbimage.fcgi?small=t&id=54234"
#>
#> [[6]]$Description
#> [1] "Crystal structure of the complex of bovine lactoperoxidase with acetyl salicylic acid at 2.5 A resolution"
#>
#> [[6]]$Taxonomy
#> [[6]]$Taxonomy$ID
#> [1] 9913
#>
#> [[6]]$Taxonomy$Name
#> [1] "Bos taurus"
#>
#>
#>
#> [[7]]
#> [[7]]$MMDB_ID
#> [1] 27954
#>
#> [[7]]$PDB_ID
#> [1] "1TGM"
#>
#> [[7]]$URL
#> [1] "https://www.ncbi.nlm.nih.gov/Structure/mmdb/mmdbsrv.cgi?uid=27954"
#>
#> [[7]]$ImageURL
#> [1] "https://www.ncbi.nlm.nih.gov/Structure/mmdb/mmdbimage.fcgi?small=t&id=27954"
#>
#> [[7]]$Description
#> [1] "Crystal structure of a complex formed between group II phospholipase A2 and aspirin at 1.86 A resolution"
#>
#> [[7]]$Taxonomy
#> [[7]]$Taxonomy$ID
#> [1] 31159
#>
#> [[7]]$Taxonomy$Name
#> [1] "Daboia russelii russelii"
#>
#>
#>
#> [[8]]
#> [[8]]$MMDB_ID
#> [1] 27242
#>
#> [[8]]$PDB_ID
#> [1] "1OXR"
#>
#> [[8]]$URL
#> [1] "https://www.ncbi.nlm.nih.gov/Structure/mmdb/mmdbsrv.cgi?uid=27242"
#>
#> [[8]]$ImageURL
#> [1] "https://www.ncbi.nlm.nih.gov/Structure/mmdb/mmdbimage.fcgi?small=t&id=27242"
#>
#> [[8]]$Description
#> [1] "Aspirin induces its Anti-inflammatory effects through its specific binding to Phospholipase A2: Crystal structure of the complex formed between Phospholipase A2 and Aspirin at 1.9A resolution"
#>
#> [[8]]$Taxonomy
#> [[8]]$Taxonomy$ID
#> [1] 195058
#>
#> [[8]]$Taxonomy$Name
#> [1] "Naja sagittifera"The extracted structures data includes details such as MMDB ID, PDB ID, URLs, descriptions, and taxonomy information for each structure associated with the compound.