gomesh2014

package module
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 Go to latest Published: May 5, 2016 License: Apache-2.0 Imports: 7 Imported by: 0

README

gomesh

Go library to read MEDLINE/PubMed Medical Subject Headings (MeSH) XML (2014)

MeSH Record Types

Data

MeSH XML download is here. "Download of any of the full data files requires the completion of an online Memorandum of Understanding." A tiny sample of this data is available in https://github.com/gnewton/gomesh/tree/master/testData

Example

Example usage: see gomesh or a running example of gomesh running at Dumontier Lab

TODO

  • Document core methods in README.md
  • Allow for loading then writing to SQLite then using SQLite so full data is not in memory (once done allow using SQLite as data source)

Acknowledgement

This work is a by-product of my graduate work at Carleton Univerity at Dumontier Lab

Documentation

Index

Constants

View Source 
const DESCRIPTOR_RECORD = "DescriptorRecord"
View Source 
const PHARMACOLOGICAL_RECORD = "PharmacologicalAction"
View Source 
const QUALIFIER_RECORD = "QualifierRecord"
View Source 
const SUPPLEMENTAL_RECORD = "SupplementalRecord"
View Source 
const TREE_SEPARATOR = "."

Variables

View Source 
var TOP_LEVEL = map[string]string{
	"A": "Anatomy",
	"B": "Organisms",
	"C": "Diseases",
	"D": "Chemicals and Drugs",
	"E": "Analytical, Diagnostic and Therapeutic Techniques and Equipment",
	"F": "Psychiatry and Psychology",
	"G": "Phenomena and Processes",
	"H": "Disciplines and Occupations",
	"I": "Anthropology, Education, Sociology and Social Phenomena",
	"J": "Technology, Industry, Agriculture",
	"K": "Humanities",
	"L": "Information Science",
	"M": "Named Groups",
	"N": "Health Care",
	"V": "Publication Characteristics",
	"Z": "Geographicals",
}

Functions

func DescriptorChannelFromFile 

func DescriptorChannelFromFile(filename string) (desChan chan *DescriptorRecord, file *os.File, err error)

func DescriptorChannelFromReader 

func DescriptorChannelFromReader(reader io.Reader) (chan *DescriptorRecord, error)

func DescriptorMapFromFile 

func DescriptorMapFromFile(filename string) (map[string]*DescriptorRecord, error)

func DescriptorMapFromReader 

func DescriptorMapFromReader(reader io.Reader) (map[string]*DescriptorRecord, error)

func MeshDescriptorNameMap 

func MeshDescriptorNameMap(uiMap map[string]*DescriptorRecord) map[string]*DescriptorRecord

func PharmacologicalChannelFromFile 

func PharmacologicalChannelFromFile(filename string) (pharmChan chan *PharmacologicalAction, file *os.File, err error)

func PharmacologicalChannelFromReader 

func PharmacologicalChannelFromReader(reader io.Reader) (chan *PharmacologicalAction, error)

func PharmacologicalMapFromFile 

func PharmacologicalMapFromFile(filename string) (map[string]*PharmacologicalAction, error)

func PharmacologicalMapFromReader 

func PharmacologicalMapFromReader(reader io.Reader) (map[string]*PharmacologicalAction, error)

func QualifierChannelFromFile 

func QualifierChannelFromFile(filename string) (qualChan chan *QualifierRecord, file *os.File, err error)

func QualifierChannelFromReader 

func QualifierChannelFromReader(reader io.Reader) (chan *QualifierRecord, error)

func QualifierMapFromFile 

func QualifierMapFromFile(filename string) (map[string]*QualifierRecord, error)

func QualifierMapFromReader 

func QualifierMapFromReader(reader io.Reader) (map[string]*QualifierRecord, error)

func SelfLinkDescriptor 

func SelfLinkDescriptor(m map[string]*DescriptorRecord)

func SupplementalChannelFromFile 

func SupplementalChannelFromFile(filename string) (suppChan chan *SupplementalRecord, file *os.File, err error)

func SupplementalChannelFromReader 

func SupplementalChannelFromReader(reader io.Reader) (chan *SupplementalRecord, error)

func SupplementalMapFromFile 

func SupplementalMapFromFile(filename string) (map[string]*SupplementalRecord, error)

func SupplementalMapFromReader 

func SupplementalMapFromReader(reader io.Reader) (map[string]*SupplementalRecord, error)

Types

type Abbreviation 

type Abbreviation struct {
	Abbreviation string `xml:",chardata"`
}

type AllowableQualifier 

type AllowableQualifier struct {
	QualifierReferredTo *QualifierReferredTo
	Abbreviation        Abbreviation
}

type AllowableQualifiersList 

type AllowableQualifiersList struct {
	AllowableQualifier []AllowableQualifier
}

type Concept 

type Concept struct {
	CASN1Name                   string                    `json:",omitempty"`
	ConceptName                 string                    `xml:">String"`
	ConceptRelationList         ConceptRelationList       `json:",omitempty"`
	ConceptUI                   string                    `json:",omitempty"`
	PreferredConceptYN          string                    `xml:",attr" json:",omitempty"`
	RegistryNumber              string                    `json:",omitempty"`
	RelatedRegistryNumberList   RelatedRegistryNumberList `json:",omitempty"`
	ScopeNote                   string                    `json:",omitempty"`
	SemanticTypeList            SemanticTypeList          `json:",omitempty"`
	TermList                    TermList                  `json:",omitempty"`
	TranslatorsEnglishScopeNote string                    `json:",omitempty"`
	TranslatorsScopeNote        string                    `json:",omitempty"`
}

type ConceptList 

type ConceptList struct {
	Concept []Concept `json:",omitempty"`
}

type ConceptRelation 

type ConceptRelation struct {
	Concept1UI   string
	Concept2UI   string
	RelationName string `xml:",attr" json:",omitempty"`
}

type ConceptRelationList 

type ConceptRelationList struct {
	ConceptRelation []ConceptRelation `json:",omitempty"`
}

type Date 

type Date struct {
	Year  string `json:",omitempty"`
	Month string `json:",omitempty"`
	Day   string `json:",omitempty"`
}

type DescriptorRecord 

type DescriptorRecord struct {
	ActiveMeSHYearList        []string `xml:">Year"`
	AllowableQualifiersList   AllowableQualifiersList
	Annotation                string                    `json:",omitempty"`
	ConceptList               ConceptList               `json:",omitempty"`
	ConsiderAlso              string                    `json:",omitempty"`
	DateCreated               Date                      `json:",omitempty"`
	DateEstablished           Date                      `json:",omitempty"`
	DateRevised               Date                      `json:",omitempty"`
	DescriptorName            string                    `xml:"DescriptorName>String"`
	DescriptorUI              string                    `json:",omitempty"`
	EntryCombinationList      EntryCombinationList      `json:",omitempty"`
	HistoryNote               string                    `json:",omitempty"`
	OnlineNote                string                    `json:",omitempty"`
	PharmacologicalActionList PharmacologicalActionList `json:",omitempty"`
	PreviousIndexingList      PreviousIndexingList      `json:",omitempty"`
	PublicMeSHNote            string                    `json:",omitempty"`
	RecordOriginatorsList     RecordOriginatorsList     `json:",omitempty"`
	RunningHead               string                    `json:",omitempty"`
	SeeRelatedList            SeeRelatedList            `json:",omitempty"`
	TreeNumberList            TreeNumberList            `json:",omitempty"`
}

type DescriptorRecordSet 

type DescriptorRecordSet struct {
	DescriptorRecord []DescriptorRecord
	LanguageCode     string `xml:",attr"`
}

type DescriptorReferredTo 

type DescriptorReferredTo struct {
	DescriptorUI     string            `json:",omitempty"`
	DescriptorName   string            `xml:"DescriptorName>String"`
	DescriptorRecord *DescriptorRecord `xml:"-" json:",omitempty"`
	Url              string            `json:",omitempty"`
}

type ECIN 

type ECIN struct {
	DescriptorReferredTo *DescriptorReferredTo `json:",omitempty"`
}

type ECOUT 

type ECOUT struct {
	DescriptorReferredTo *DescriptorReferredTo `json:",omitempty"`
}

type EntryCombination 

type EntryCombination struct {
	ECIN  ECIN  `json:",omitempty"`
	ECOUT ECOUT `json:",omitempty"`
}

type EntryCombinationList 

type EntryCombinationList struct {
	EntryCombination []EntryCombination `json:",omitempty"`
}

type HeadingMappedTo 

type HeadingMappedTo struct {
	DescriptorReferredTo *DescriptorReferredTo `json:",omitempty"`
}

type HeadingMappedToList 

type HeadingMappedToList struct {
	HeadingMappedTo []HeadingMappedTo `json:",omitempty"`
}

type IdEntry 

type IdEntry struct {
	Id    string
	Url   string
	Label string `json:",omitempty"`
}

type IndexingInformation 

type IndexingInformation struct {
	DescriptorReferredTo *DescriptorReferredTo `json:",omitempty"`
}

type IndexingInformationList 

type IndexingInformationList struct {
	IndexingInformation []IndexingInformation `json:",omitempty"`
}

type Node 

type Node struct {
	TreeNumber     string            `json:"treeNumber`
	NodeNumber     string            `json:"-"`
	Name           string            `json:",omitempty"`
	Children       []IdEntry         `json:",omitempty"`
	ChildrenMap    map[string]*Node  `json:"-"`
	AllDescriptors map[string]bool   `json:"-"`
	DescriptorUrl  string            `json:",omitempty"`
	Descriptor     *DescriptorRecord `json:"-"`
}

func MakeTree 

func MakeTree(m map[string]*DescriptorRecord) (root *Node)

func (*Node) Init 

func (node *Node) Init() *Node

func (*Node) Traverse 

func (node *Node) Traverse(depth int, nodeUser useNode)

type PharmacologicalAction 

type PharmacologicalAction struct {
	DescriptorReferredTo               *DescriptorReferredTo              `json:",omitempty"`
	PharmacologicalActionSubstanceList PharmacologicalActionSubstanceList `json:",omitempty"`
}

type PharmacologicalActionList 

type PharmacologicalActionList struct {
	PharmacologicalAction []PharmacologicalAction `json:",omitempty"`
}

type PharmacologicalActionSet 

type PharmacologicalActionSet struct {
	PharmacologicalAction []PharmacologicalAction
}

type PharmacologicalActionSubstanceList 

type PharmacologicalActionSubstanceList struct {
	Substance []Substance `json:",omitempty"`
}

type PreviousIndexingList 

type PreviousIndexingList struct {
	PreviousIndexing []string `json:",omitempty"`
}

type QualifierRecord 

type QualifierRecord struct {
	QualifierUI           string                `json:",omitempty"`
	QualifierName         string                `xml:"QualifierName>String" json:",omitempty"`
	DateCreated           Date                  `json:",omitempty"`
	DateRevised           Date                  `json:",omitempty"`
	DateEstablished       Date                  `json:",omitempty"`
	ActiveMeSHYearList    []string              `xml:">Year" json:",omitempty"`
	Annotation            string                `json:",omitempty"`
	HistoryNote           string                `json:",omitempty"`
	OnlineNote            string                `json:",omitempty"`
	TreeNumberList        TreeNumberList        `json:",omitempty"`
	TreeNodeAllowedList   TreeNodeAllowedList   `json:",omitempty"`
	RecordOriginatorsList RecordOriginatorsList `json:",omitempty"`
	ConceptList           ConceptList           `json:",omitempty"`
}

type QualifierRecordSet 

type QualifierRecordSet struct {
	QualifierRecord []*QualifierRecord
}

type QualifierReferredTo 

type QualifierReferredTo struct {
	QualifierUI     string
	QualifierName   string           `xml:"QualifierName>String"`
	QualifierRecord *QualifierRecord `xml:"-" json:",omitempty"`
	Url             string           `json:",omitempty"`
}

type Record 

type Record interface {
	// contains filtered or unexported methods
}

type RecordOriginator 

type RecordOriginator struct {
	RecordOriginator string `json:",omitempty"`
	RecordMaintainer string `json:",omitempty"`
	RecordAuthorizer string `json:",omitempty"`
}

type RecordOriginatorsList 

type RecordOriginatorsList struct {
	RecordOriginator []RecordOriginator `json:",omitempty"`
}

type RelatedRegistryNumber 

type RelatedRegistryNumber struct {
	RelatedRegistryNumber string `xml:",chardata"`
}

type RelatedRegistryNumberList 

type RelatedRegistryNumberList struct {
	RelatedRegistryNumber []RelatedRegistryNumber `json:",omitempty"`
}

type SeeRelatedDescriptor 

type SeeRelatedDescriptor struct {
	DescriptorReferredTo *DescriptorReferredTo `json:",omitempty"`
}

type SeeRelatedList 

type SeeRelatedList struct {
	SeeRelatedDescriptor []SeeRelatedDescriptor `json:",omitempty"`
}

type SemanticType 

type SemanticType struct {
	SemanticTypeUI   string `json:",omitempty"`
	SemanticTypeName string `json:",omitempty"`
}

type SemanticTypeList 

type SemanticTypeList struct {
	SemanticType []SemanticType `json:",omitempty"`
}

type Source 

type Source struct {
	Source string `json:",omitempty"`
}

type SourceList 

type SourceList struct {
	Source []Source `json:",omitempty"`
}

type Substance 

type Substance struct {
	RecordUI        string
	DescriptorUrl   string `json:",omitempty"`
	SupplementalUrl string `json:",omitempty"`
	RecordName      string `xml:"RecordName>String" json:",omitempty"`
}

type SupplementalRecord 

type SupplementalRecord struct {
	SupplementalRecordUI    string                  `json:",omitempty"`
	SupplementalRecordName  string                  `xml:"SupplementalRecordName>String" json:",omitempty"`
	DateCreated             Date                    `json:",omitempty"`
	DateEstablished         Date                    `json:",omitempty"`
	DateRevised             Date                    `json:",omitempty"`
	ActiveMeSHYearList      []string                `xml:">Year" json:",omitempty"`
	Note                    string                  `json:",omitempty"`
	Frequency               string                  `json:",omitempty"`
	HeadingMappedToList     HeadingMappedToList     `json:",omitempty"`
	IndexingInformationList IndexingInformationList `json:",omitempty"`
	SourceList              SourceList              `json:",omitempty"`
	RecordOriginatorsList   RecordOriginatorsList   `json:",omitempty"`
	ConceptList             ConceptList             `json:",omitempty"`
}

type SupplementalRecordSet 

type SupplementalRecordSet struct {
	SupplementalRecord []SupplementalRecord
}

type Term 

type Term struct {
	Abbreviation           string          `json:",omitempty"`
	ConceptPreferredTermYN string          `xml:",attr"`
	DateCreated            Date            `json:",omitempty"`
	EntryVersion           string          `json:",omitempty"`
	IsPermutedTermYN       string          `xml:",attr" json:",omitempty"`
	LexicalTag             string          `xml:",attr" json:",omitempty"`
	PrintFlagYN            string          `xml:",attr" json:",omitempty"`
	RecordPreferredTermYN  string          `xml:",attr" json:",omitempty"`
	SortVersion            string          `json:",omitempty"`
	String                 string          `json:",omitempty"`
	TermNote               string          `json:",omitempty"`
	TermUI                 string          `json:",omitempty"`
	ThesaurusIDlist        ThesaurusIDlist `json:",omitempty"`
}

type TermList 

type TermList struct {
	Term []Term `json:",omitempty"`
}

type ThesaurusIDlist 

type ThesaurusIDlist struct {
	ThesaurusID []string `json:",omitempty"`
}

type TreeNodeAllowed 

type TreeNodeAllowed struct {
	TreeNodeAllowed string `xml:",chardata" json:",omitempty"`
}

type TreeNodeAllowedList 

type TreeNodeAllowedList struct {
	TreeNodeAllowed []TreeNodeAllowed `json:",omitempty"`
}

type TreeNumber 

type TreeNumber struct {
	TreeNumber string `xml:",chardata"`
	Url        string `json:",omitempty"`
}

type TreeNumberList 

type TreeNumberList struct {
	TreeNumber []TreeNumber `json:",omitempty"`
}

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