pubmed

package
v0.0.0-...-3551151 Latest Latest
Warning

This package is not in the latest version of its module.

 Go to latest Published: Aug 28, 2023 License: MIT Imports: 6 Imported by: 0

Documentation

Index

Constants

This section is empty.

Variables

This section is empty.

Functions

func Convert 

func Convert(w io.Writer, r io.Reader) error

Convert converts a stream containing pubmed XML records into a stream of jsonlines.

Types

type Contrib 

type Contrib struct {
	Name        string `json:"name,omitempty"`
	Affiliation string `json:"aff,omitempty"`
	Identifier  string `json:"id,omitempty"`
}

Contrib is a contributor.

type PubmedArticle 

type PubmedArticle struct {
	XMLName         xml.Name `xml:"PubmedArticle"`
	Text            string   `xml:",chardata"`
	MedlineCitation struct {
		Text           string `xml:",chardata"`
		Status         string `xml:"Status,attr"`
		Owner          string `xml:"Owner,attr"`
		IndexingMethod string `xml:"IndexingMethod,attr"`
		PMID           struct {
			Text    string `xml:",chardata"` // 1, 2, 4, 3, 5, 6, 7, 8, 9...
			Version string `xml:"Version,attr"`
		} `xml:"PMID"`
		DateCompleted struct {
			Text  string `xml:",chardata"`
			Year  string `xml:"Year"`  // 1976, 1976, 1976, 1976, 1...
			Month string `xml:"Month"` // 01, 01, 01, 01, 01, 01, 0...
			Day   string `xml:"Day"`   // 16, 10, 10, 10, 10, 10, 2...
		} `xml:"DateCompleted"`
		DateRevised struct {
			Text  string `xml:",chardata"`
			Year  string `xml:"Year"`  // 2022, 2019, 2022, 2022, 2...
			Month string `xml:"Month"` // 02, 06, 01, 11, 06, 06, 0...
			Day   string `xml:"Day"`   // 18, 12, 29, 16, 12, 12, 2...
		} `xml:"DateRevised"`
		Article struct {
			Text     string `xml:",chardata"`
			PubModel string `xml:"PubModel,attr"`
			Journal  struct {
				Text string `xml:",chardata"`
				ISSN struct {
					Text     string `xml:",chardata"` // 0006-2944, 1090-2104, 109...
					IssnType string `xml:"IssnType,attr"`
				} `xml:"ISSN"`
				JournalIssue struct {
					Text        string `xml:",chardata"`
					CitedMedium string `xml:"CitedMedium,attr"`
					Volume      string `xml:"Volume"` // 13, 66, 66, 66, 66, 66, 2...
					Issue       string `xml:"Issue"`  // 2, 4, 4, 4, 4, 4, 16, 16,...
					PubDate     struct {
						Text        string `xml:",chardata"`
						Year        string `xml:"Year"`        // 1975, 1975, 1975, 1975, 1...
						Month       string `xml:"Month"`       // Jun, Oct, Oct, Oct, Oct, ...
						Day         string `xml:"Day"`         // 27, 27, 27, 27, 27, 15, 1...
						MedlineDate string `xml:"MedlineDate"` // 1975 Jul-Aug, 1975 Jul-Au...
						Season      string `xml:"Season"`      // Summer, Summer, Spring, S...
					} `xml:"PubDate"`
				} `xml:"JournalIssue"`
				Title           string `xml:"Title"`           // Biochemical medicine, Bio...
				ISOAbbreviation string `xml:"ISOAbbreviation"` // Biochem Med, Biochem Biop...
			} `xml:"Journal"`
			ArticleTitle struct {
				Text string `xml:",chardata"` // Formate assay in body flu...
			} `xml:"ArticleTitle"`
			Pagination struct {
				Text       string `xml:",chardata"`
				MedlinePgn string `xml:"MedlinePgn"` // 117-26, 1173-9, 1338-43, ...
			} `xml:"Pagination"`
			AuthorList struct {
				Text       string `xml:",chardata"`
				CompleteYN string `xml:"CompleteYN,attr"`
				Author     []struct {
					Text            string `xml:",chardata"`
					ValidYN         string `xml:"ValidYN,attr"`
					EqualContrib    string `xml:"EqualContrib,attr"`
					LastName        string `xml:"LastName"` // Makar, McMartin, Palese, ...
					ForeName        string `xml:"ForeName"` // A B, K E, M, T R, K S, R ...
					Initials        string `xml:"Initials"` // AB, KE, M, TR, KS, RH, UN...
					Suffix          string `xml:"Suffix"`   // Jr, 3rd, Jr, Jr, Jr, Jr, ...
					AffiliationInfo struct {
						Text        string `xml:",chardata"`
						Affiliation string `xml:"Affiliation"` // Pharmaceutical Research D...
					} `xml:"AffiliationInfo"`
					CollectiveName string `xml:"CollectiveName"` // The UCLA Bone Marrow Tran...
					Identifier     struct {
						Text   string `xml:",chardata"` // 0000-0002-6463-7460, 0000...
						Source string `xml:"Source,attr"`
					} `xml:"Identifier"`
				} `xml:"Author"`
			} `xml:"AuthorList"`
			Language  []string `xml:"Language"` // eng, eng, eng, eng, eng, ...
			GrantList struct {
				Text       string `xml:",chardata"`
				CompleteYN string `xml:"CompleteYN,attr"`
				Grant      []struct {
					Text    string `xml:",chardata"`
					GrantID string `xml:"GrantID"` // F32 AG064886, MC_UU_12013...
					Acronym string `xml:"Acronym"` // AG, BB_, MRC_, BB_, AG, M...
					Agency  string `xml:"Agency"`  // NIA NIH HHS, MRC, Biotech...
					Country string `xml:"Country"` // United States, United Kin...
				} `xml:"Grant"`
			} `xml:"GrantList"`
			PublicationTypeList struct {
				Text            string `xml:",chardata"`
				PublicationType []struct {
					Text string `xml:",chardata"` // Journal Article, Research...
					UI   string `xml:"UI,attr"`
				} `xml:"PublicationType"`
			} `xml:"PublicationTypeList"`
			Abstract struct {
				Text         string `xml:",chardata"`
				AbstractText []struct {
					Text  string `xml:",chardata"` // (--)-alpha-Bisabolol has ...
					Label string `xml:"Label,attr"`
				} `xml:"AbstractText"`
				CopyrightInformation string `xml:"CopyrightInformation"` // © OIE, 1992, © OIE, 199...
			} `xml:"Abstract"`
			VernacularTitle string `xml:"VernacularTitle"` // Biochemische Untersuchung...
			ELocationID     []struct {
				Text    string `xml:",chardata"` // 10.1139/m76-085, 10.1016/...
				EIdType string `xml:"EIdType,attr"`
				ValidYN string `xml:"ValidYN,attr"`
			} `xml:"ELocationID"`
			DataBankList struct {
				Text       string `xml:",chardata"`
				CompleteYN string `xml:"CompleteYN,attr"`
				DataBank   []struct {
					Text                string `xml:",chardata"`
					DataBankName        string `xml:"DataBankName"` // GENBANK, GENBANK, GENBANK...
					AccessionNumberList struct {
						Text            string   `xml:",chardata"`
						AccessionNumber []string `xml:"AccessionNumber"` // M10683, J02459, M17233, M...
					} `xml:"AccessionNumberList"`
				} `xml:"DataBank"`
			} `xml:"DataBankList"`
		} `xml:"Article"`
		MedlineJournalInfo struct {
			Text        string `xml:",chardata"`
			Country     string `xml:"Country"`     // United States, United Sta...
			MedlineTA   string `xml:"MedlineTA"`   // Biochem Med, Biochem Biop...
			NlmUniqueID string `xml:"NlmUniqueID"` // 0151424, 0372516, 0372516...
			ISSNLinking string `xml:"ISSNLinking"` // 0006-2944, 0006-291X, 000...
		} `xml:"MedlineJournalInfo"`
		ChemicalList struct {
			Text     string `xml:",chardata"`
			Chemical []struct {
				Text            string `xml:",chardata"`
				RegistryNumber  string `xml:"RegistryNumber"` // 0, 142M471B3J, EC 1.2.-, ...
				NameOfSubstance struct {
					Text string `xml:",chardata"` // Formates, Carbon Dioxide,...
					UI   string `xml:"UI,attr"`
				} `xml:"NameOfSubstance"`
			} `xml:"Chemical"`
		} `xml:"ChemicalList"`
		CitationSubset  string `xml:"CitationSubset"` // IM, IM, IM, IM, IM, IM, I...
		MeshHeadingList struct {
			Text        string `xml:",chardata"`
			MeshHeading []struct {
				Text           string `xml:",chardata"`
				DescriptorName struct {
					Text         string `xml:",chardata"` // Aldehyde Oxidoreductases,...
					UI           string `xml:"UI,attr"`
					MajorTopicYN string `xml:"MajorTopicYN,attr"`
					Type         string `xml:"Type,attr"`
				} `xml:"DescriptorName"`
				QualifierName []struct {
					Text         string `xml:",chardata"` // metabolism, analysis, blo...
					UI           string `xml:"UI,attr"`
					MajorTopicYN string `xml:"MajorTopicYN,attr"`
				} `xml:"QualifierName"`
			} `xml:"MeshHeading"`
		} `xml:"MeshHeadingList"`
		CommentsCorrectionsList struct {
			Text                string `xml:",chardata"`
			CommentsCorrections []struct {
				Text      string `xml:",chardata"`
				RefType   string `xml:"RefType,attr"`
				RefSource string `xml:"RefSource"` // Biochem Pharmacol. 1975 A...
				PMID      struct {
					Text    string `xml:",chardata"` // 8, 2, 21351112, 33403544,...
					Version string `xml:"Version,attr"`
				} `xml:"PMID"`
				Note string `xml:"Note"` // Gratwhol, A A [corrected ...
			} `xml:"CommentsCorrections"`
		} `xml:"CommentsCorrectionsList"`
		NumberOfReferences string `xml:"NumberOfReferences"` // 18, 115, 110, 27, 12, 53,...
		OtherID            []struct {
			Text   string `xml:",chardata"` // 76062498, 76062844, 76062...
			Source string `xml:"Source,attr"`
		} `xml:"OtherID"`
		PersonalNameSubjectList struct {
			Text                string `xml:",chardata"`
			PersonalNameSubject []struct {
				Text     string `xml:",chardata"`
				LastName string `xml:"LastName"` // Drake, Landsteiner, Avery...
				ForeName string `xml:"ForeName"` // N, K, O T, G, J, G F, B F...
				Initials string `xml:"Initials"` // N, K, OT, G, J, GF, BF, L...
				Suffix   string `xml:"Suffix"`   // <Suffix>2nd</Suffix>, Jr,...
			} `xml:"PersonalNameSubject"`
		} `xml:"PersonalNameSubjectList"`
		OtherAbstract []struct {
			Text         string `xml:",chardata"`
			Type         string `xml:"Type,attr"`
			Language     string `xml:"Language,attr"`
			AbstractText struct {
				Text string `xml:",chardata"` // A discussion of causes, d...
				Math []struct {
					Text string   `xml:",chardata"`
					Mml  string   `xml:"mml,attr"`
					Mn   []string `xml:"mn"` // 2, 5
					Mo   []string `xml:"mo"` // -, ×
					Msup struct {
						Text  string   `xml:",chardata"`
						Mn    []string `xml:"mn"`    // 10, 6, 10, -6, 10, -6, 10...
						Mtext string   `xml:"mtext"` // H, Na, Na
						Mo    string   `xml:"mo"`    // +, +, +
					} `xml:"msup"`
					Mtext []string `xml:"mtext"` // C, Na, H, C, H, C, Na, H,...
					Msub  struct {
						Text  string `xml:",chardata"`
						Mtext string `xml:"mtext"` // O, O, O, O
						Mn    string `xml:"mn"`    // 2, 3, 3, 2
					} `xml:"msub"`
					Msubsup struct {
						Text  string `xml:",chardata"`
						Mtext string `xml:"mtext"` // O
						Mn    string `xml:"mn"`    // 3
						Mo    string `xml:"mo"`    // -
					} `xml:"msubsup"`
				} `xml:"math"`
				DispFormula []struct {
					Text string `xml:",chardata"`
					Math struct {
						Text string `xml:",chardata"`
						Mml  string `xml:"mml,attr"`
						Msup struct {
							Text  string `xml:",chardata"`
							Mtext string `xml:"mtext"` // H
							Mo    string `xml:"mo"`    // +
						} `xml:"msup"`
						Mrow struct {
							Text string `xml:",chardata"`
							Msup []struct {
								Text string `xml:",chardata"`
								Mi   string `xml:"mi"` // a, b, c
								Mn   string `xml:"mn"` // 2, 2, 2
							} `xml:"msup"`
							Mo []string `xml:"mo"` // +, =
						} `xml:"mrow"`
					} `xml:"math"`
				} `xml:"DispFormula"`
			} `xml:"AbstractText"`
		} `xml:"OtherAbstract"`
		KeywordList []struct {
			Text    string `xml:",chardata"`
			Owner   string `xml:"Owner,attr"`
			Keyword []struct {
				Text         string `xml:",chardata"` // Diarrhea, Diarrhea, Infan...
				MajorTopicYN string `xml:"MajorTopicYN,attr"`
			} `xml:"Keyword"`
		} `xml:"KeywordList"`
		GeneralNote []struct {
			Text  string `xml:",chardata"` // TJ: INFECTION., 2 fn., KI...
			Owner string `xml:"Owner,attr"`
		} `xml:"GeneralNote"`
		SpaceFlightMission []string `xml:"SpaceFlightMission"` // Flight Experiment, Skylab...
		GeneSymbolList     struct {
			Text       string   `xml:",chardata"`
			GeneSymbol []string `xml:"GeneSymbol"` // Ir, Ir, abl, c-src, fyn, ...
		} `xml:"GeneSymbolList"`
		SupplMeshList struct {
			Text          string `xml:",chardata"`
			SupplMeshName []struct {
				Text string `xml:",chardata"` // VAC protocol, CAF protoco...
				Type string `xml:"Type,attr"`
				UI   string `xml:"UI,attr"`
			} `xml:"SupplMeshName"`
		} `xml:"SupplMeshList"`
		InvestigatorList struct {
			Text         string `xml:",chardata"`
			Investigator []struct {
				Text            string `xml:",chardata"`
				ValidYN         string `xml:"ValidYN,attr"`
				LastName        string `xml:"LastName"` // Llinas, Joyce, Haber, Wol...
				ForeName        string `xml:"ForeName"` // R R, G F, E, D J, G E, J,...
				Initials        string `xml:"Initials"` // RR, GF, E, DJ, GE, J, J, ...
				AffiliationInfo struct {
					Text        string `xml:",chardata"`
					Affiliation string `xml:"Affiliation"` // NY U Med Ctr, NY, Scripps...
				} `xml:"AffiliationInfo"`
				Suffix string `xml:"Suffix"` // 3rd, Jr, Jr
			} `xml:"Investigator"`
		} `xml:"InvestigatorList"`
		CoiStatement string `xml:"CoiStatement"` // disclosures M. Loreto Yan...
	} `xml:"MedlineCitation"`
	PubmedData struct {
		Text    string `xml:",chardata"`
		History struct {
			Text          string `xml:",chardata"`
			PubMedPubDate []struct {
				Text      string `xml:",chardata"`
				PubStatus string `xml:"PubStatus,attr"`
				Year      string `xml:"Year"`   // 1975, 1975, 1975, 1975, 1...
				Month     string `xml:"Month"`  // 6, 6, 6, 10, 10, 10, 10, ...
				Day       string `xml:"Day"`    // 1, 1, 1, 27, 27, 27, 27, ...
				Hour      string `xml:"Hour"`   // 0, 0, 0, 0, 0, 0, 0, 0, 0...
				Minute    string `xml:"Minute"` // 1, 0, 1, 0, 1, 0, 1, 0, 1...
			} `xml:"PubMedPubDate"`
		} `xml:"History"`
		PublicationStatus string `xml:"PublicationStatus"` // ppublish, ppublish, ppubl...
		ArticleIdList     struct {
			Text      string `xml:",chardata"`
			ArticleId []struct {
				Text   string `xml:",chardata"` // 1, 10.1016/0006-2944(75)9...
				IdType string `xml:"IdType,attr"`
			} `xml:"ArticleId"`
		} `xml:"ArticleIdList"`
		ReferenceList struct {
			Text      string `xml:",chardata"`
			Reference []struct {
				Text          string `xml:",chardata"`
				Citation      string `xml:"Citation"` // Hautarzt. 2020 Feb;71(2):...
				ArticleIdList struct {
					Text      string `xml:",chardata"`
					ArticleId struct {
						Text   string `xml:",chardata"` // 31659390, 25526014, 24803...
						IdType string `xml:"IdType,attr"`
					} `xml:"ArticleId"`
				} `xml:"ArticleIdList"`
			} `xml:"Reference"`
		} `xml:"ReferenceList"`
	} `xml:"PubmedData"`
}

PubmedArticle was generated 2023-08-02 10:56:01 by tir on reka.

type PubmedFlat 

type PubmedFlat struct {
	PMID        string `json:"pmid,omitempty"`
	DOI         string `json:"doi,omitempty"`
	PMCID       string `json:"pmc,omitempty"`
	PII         string `json:"pii,omitempty"`
	MID         string `json:"mid,omitempty"`
	Title       string `json:"title,omitempty"`
	Date        string `json:"date,omitempty"`
	DateRevised string `json:"revised,omitempty"`
	Container   struct {
		Name string `json:"name,omitempty"`
		ISSN string `json:"issn,omitempty"`
	} `json:"container,omitempty"`
	Contribs []Contrib `json:"contribs"`
}

PubmedFlat is a flat JSON structure for easier access.

Source Files

View all Source files

Jump to

Keyboard shortcuts

? : This menu
/ : Search site
f or F : Jump to
y or Y : Canonical URL
go.dev uses cookies from Google to deliver and enhance the quality of its services and to analyze traffic. Learn more.