@larsgw/formica 0.9.2 → 0.10.0

package/src/bin/generate-linked-data.ts

@@ -1,762 +0,0 @@
-#!/usr/bin/env node
-
-import { existsSync as doesFileExist, promises as fs } from 'fs'
-import * as path from 'path'
-import * as util from 'util'
-
-import type { JsonLdDocument, NodeObject } from 'jsonld'
-import * as jsonld from 'jsonld'
-import * as N3 from 'n3'
-
-import { catalog } from '../index'
-import { WorkResource } from '../resources/resource'
-import { parseCsv } from '../csv'
-
-const SHEETS = ['catalog', 'authors', 'places', 'publishers', 'taxa'] as const
-
-interface Resource {
-    metadata: ResourceMetadata,
-    taxa: AmendedTaxon[],
-}
-
-interface Catalog {
-    catalog: catalog.Entities,
-    authors: catalog.Entities,
-    places: catalog.Entities,
-    publishers: catalog.Entities,
-    taxa: catalog.Entities,
-
-    resources: Record<ResourceId, Resource>,
-}
-
-const PREFIX = 'https://purl.org/identification-resources/'
-const HANDLE_PREFIX = 'https://hdl.handle.net/'
-const SCOPES: Record<string, [string, string]> = {
-    // animal life stage
-    'adults': ['dwciri:lifeStage', 'http://rs.gbif.org/vocabulary/gbif/life_stage/adult'],
-    'pupae': ['dwciri:lifeStage', 'http://rs.gbif.org/vocabulary/gbif/life_stage/pupa'],
-    'juveniles': ['dwciri:lifeStage', 'http://rs.gbif.org/vocabulary/gbif/life_stage/juvenile'],
-    'subimagos': ['dwciri:lifeStage', 'http://rs.gbif.org/vocabulary/gbif/life_stage/juvenile'],
-    'larvae': ['dwciri:lifeStage', 'http://rs.gbif.org/vocabulary/gbif/life_stage/larva'],
-    'larvae (instar V)': ['dwciri:lifeStage', 'http://rs.gbif.org/vocabulary/gbif/life_stage/larva'],
-    'larvae (instar IV)': ['dwciri:lifeStage', 'http://rs.gbif.org/vocabulary/gbif/life_stage/larva'],
-    'larvae (instar III)': ['dwciri:lifeStage', 'http://rs.gbif.org/vocabulary/gbif/life_stage/larva'],
-    'larvae (instar I)': ['dwciri:lifeStage', 'http://rs.gbif.org/vocabulary/gbif/life_stage/larva'],
-    'nymphs': ['dwciri:lifeStage', 'http://rs.gbif.org/vocabulary/gbif/life_stage/larva'],
-    'nypmhs': ['dwciri:lifeStage', 'http://rs.gbif.org/vocabulary/gbif/life_stage/larva'],
-    'nymphs (instar V)': ['dwciri:lifeStage', 'http://rs.gbif.org/vocabulary/gbif/life_stage/larva'],
-    'nymphs (instar IV)': ['dwciri:lifeStage', 'http://rs.gbif.org/vocabulary/gbif/life_stage/larva'],
-    'eggs': ['dwciri:lifeStage', 'http://rs.gbif.org/vocabulary/gbif/life_stage/embryo'],
-
-    // plant life stage
-    'flowering plants': ['dwciri:lifeStage', 'http://rs.gbif.org/vocabulary/gbif/life_stage/adult'],
-    'fruiting plants': ['dwciri:lifeStage', 'http://rs.gbif.org/vocabulary/gbif/life_stage/adult'],
-    'without sporangia': ['dwciri:lifeStage', 'http://rs.gbif.org/vocabulary/gbif/life_stage/juvenile'],
-    'with sporangia': ['dwciri:lifeStage', 'http://rs.gbif.org/vocabulary/gbif/life_stage/adult'],
-    'teleomorphs': ['dwciri:lifeStage', 'http://rs.gbif.org/vocabulary/gbif/life_stage/adult'],
-
-    // sex
-    'females': ['dwciri:sex', 'http://rs.gbif.org/vocabulary/gbif/sex/female'],
-    'males': ['dwciri:sex', 'http://rs.gbif.org/vocabulary/gbif/sex/male'],
-    'male': ['dwciri:sex', 'http://rs.gbif.org/vocabulary/gbif/sex/male'],
-
-    // caste
-    'queens': ['dwc:caste', 'queen'],
-    'workers': ['dwc:caste', 'worker'],
-    'soldiers': ['dwc:caste', 'soldier'],
-    'alatae': ['dwc:caste', 'alate'],
-    'apterae': ['dwc:caste', 'aptera'],
-    'viviparae': ['dwc:caste', 'vivipara'],
-
-    // evidence
-    'nests': ['ac:subjectPartLiteral', 'nest'],
-    'galls': ['ac:subjectPartLiteral', 'gall'],
-    'puparia': ['ac:subjectPartLiteral', 'puparium'],
-    'eggcases': ['ac:subjectPart', 'http://rs.tdwg.org/acpart/values/p0031'],
-    'bones': ['ac:subjectPartLiteral', 'skeleton'],
-    'bones (skulls)': ['ac:subjectPart', 'http://rs.tdwg.org/acpart/values/p0027'],
-    'bones (upper jaws)': ['ac:subjectPart', 'http://rs.tdwg.org/acpart/values/p0028'],
-    'bones (lower jaws)': ['ac:subjectPart', 'http://rs.tdwg.org/acpart/values/p0029'],
-}
-const PREFIXES = {
-    'ac': 'http://rs.tdwg.org/ac/terms/',
-    'bibo': 'http://purl.org/ontology/bibo/',
-    'dcterms': 'http://purl.org/dc/terms/',
-    'dwc': 'http://rs.tdwg.org/dwc/terms/',
-    'dwciri': 'http://rs.tdwg.org/dwc/iri/',
-    'foaf': 'http://xmlns.com/foaf/0.1/',
-    'owl': 'http://www.w3.org/2002/07/owl#',
-    'rdfs': 'http://www.w3.org/2000/01/rdf-schema#',
-    'schema': 'https://schema.org/',
-    'xsd': 'http://www.w3.org/2001/XMLSchema#',
-}
-const DWC_FIELDS: Record<string, string> = {
-    scientificName: 'dwc:scientificName',
-    scientificNameAuthorship: 'dwc:scientificNameAuthorship',
-    genericName: 'dwc:genericName',
-    infragenericEpithet: 'dwc:infragenericEpithet',
-    specificEpithet: 'dwc:specificEpithet',
-    infraspecificEpithet: 'dwc:infraspecificEpithet',
-    taxonRank: 'dwc:taxonRank',
-    taxonRemarks: 'dwc:taxonRemarks',
-    taxonomicStatus: 'dwc:taxonomicStatus',
-    verbatimIdentification: 'dwc:verbatimIdentification',
-}
-const GBIF_RANKS = ['kingdom', 'phylum', 'class', 'order', 'family', 'genus', 'species', 'subspecies']
-const GBIF_VOCAB_RANKS = ['domain', 'kingdom', 'subkingdom', 'superphylum', 'phylum', 'subphylum', 'superclass', 'class', 'subclass', 'supercohort', 'cohort', 'subcohort', 'superorder', 'order', 'suborder', 'infraorder', 'superfamily', 'family', 'subfamily', 'tribe', 'subtribe', 'genus', 'subgenus', 'section', 'subsection', 'series', 'subseries', 'speciesAggregate', 'species', 'subspecificAggregate', 'subspecies', 'variety', 'subvariety', 'form', 'subform', 'cultivarGroup', 'cultivar', 'strain']
-const STATUSES: Record<string, string> = {
-    'accepted': 'http://rs.gbif.org/vocabulary/gbif/taxonomicStatus/accepted',
-    'misapplied': 'http://rs.gbif.org/vocabulary/gbif/taxonomicStatus/misapplied',
-    'proparte synonym': 'http://rs.gbif.org/vocabulary/gbif/taxonomicStatus/proParteSynonym',
-    'synonym': 'http://rs.gbif.org/vocabulary/gbif/taxonomicStatus/synonym',
-}
-
-function getCoveringTaxon (taxa: catalog.Entity[]): string|null {
-    if (taxa.length === 1 && !taxa[0].has('gbif')) {
-        return `${PREFIX}taxon/${taxa[0].get('id')}`
-    }
-
-    function getAncestors (taxon: catalog.Entity): string[] {
-        const [...parents] = (taxon.get('parent_taxa') ?? []) as string[]
-        if (taxon.has('gbif')) {
-            parents.push(taxon.get('gbif') as string)
-        }
-        return parents
-    }
-
-    const ancestors = getAncestors(taxa[0])
-    for (const taxon of taxa.slice(1)) {
-        const otherAncestors = getAncestors(taxon)
-
-        for (let i = 0; i < ancestors.length; i++) {
-            if (ancestors[i] !== otherAncestors[i]) {
-                ancestors.splice(i)
-            }
-        }
-    }
-
-    return ancestors.length ? makeGbifUri(ancestors[ancestors.length - 1])['@id'] as string : null
-}
-
-function mapEntities (names: string[], entities: catalog.Entity[]): catalog.Entity[] {
-    const result = []
-
-    for (const name of names) {
-        const entity = entities.find(entity => {
-            const values = entity.get('name')
-            return Array.isArray(values) ? values.includes(name) : values === name
-        })
-
-        if (!entity) {
-            console.error('Unmapped entity:', name)
-            continue
-        }
-
-        result.push(entity as catalog.Entity)
-    }
-
-    return result
-}
-
-function makeWikidataUri (qid: string): NodeObject {
-    return { '@id': `http://www.wikidata.org/entity/${qid}` }
-}
-
-function makeGbifUri (id: string): NodeObject {
-    return { '@id': `https://gbif.org/species/${id}` }
-}
-
-function makeWorkUri (id: string): NodeObject {
-    return { '@id': `${PREFIX}catalog/${id}` }
-}
-
-function makeScientificNameUri (id: string): NodeObject {
-    const resource = id.split(':').slice(0, -1).join(':')
-    return { '@id': `${PREFIX}resource/${resource}#${id}` }
-}
-
-function makeTaxonRankUri (rank: string): NodeObject|string {
-    if (GBIF_VOCAB_RANKS.includes(rank)) {
-        return { '@id': `http://rs.gbif.org/vocabulary/gbif/rank/${rank}` }
-    } else {
-        return rank
-    }
-}
-
-function makeTaxonomicStatusUri (status: keyof typeof STATUSES): NodeObject {
-    return { '@id': STATUSES[status] }
-}
-
-function makeLinkedDataForAuthor (author: catalog.Entity): NodeObject {
-    const node: NodeObject = {
-        '@id': `${PREFIX}author/${author.get('id')}`,
-        '@type': 'foaf:Person',
-        'foaf:name': author.get('display_name')
-    }
-
-    if (author.has('qid')) {
-        node['owl:sameAs'] = makeWikidataUri(author.get('qid') as string)
-    }
-
-    return node
-}
-
-function makeLinkedDataForPlace (place: catalog.Entity): NodeObject {
-    const node: NodeObject = {
-        '@id': `${PREFIX}place/${place.get('id')}`,
-        '@type': 'dcterms:Location',
-        'dcterms:title': place.get('display_name'),
-    }
-
-    if (place.has('qid')) {
-        node['owl:sameAs'] = makeWikidataUri(place.get('qid') as string)
-    }
-
-    return node
-}
-
-function makeLinkedDataForPublisher (publisher: catalog.Entity): NodeObject {
-    const node: NodeObject = {
-        '@id': `${PREFIX}publisher/${publisher.get('id')}`,
-        '@type': 'foaf:Organization',
-        'foaf:name': publisher.get('display_name')
-    }
-
-    if (publisher.has('qid')) {
-        node['owl:sameAs'] = makeWikidataUri(publisher.get('qid') as string)
-    }
-
-    return node
-}
-
-function makeLinkedDataForTaxon (taxon: catalog.Entity): NodeObject {
-    const node: NodeObject = {
-        '@id': `${PREFIX}taxon/${taxon.get('id')}`,
-        '@type': 'dwc:Taxon',
-        'dwc:scientificName': taxon.get('name'),
-    }
-
-    if (taxon.has('rank')) {
-        node['dwc:taxonRank'] = makeTaxonRankUri(taxon.get('rank') as string)
-    }
-
-    const ids = []
-    if (taxon.has('qid')) {
-        ids.push(makeWikidataUri(taxon.get('qid') as string))
-    }
-    if (taxon.has('gbif')) {
-        ids.push(makeGbifUri(taxon.get('gbif') as string))
-    }
-    if (ids.length) {
-        node['owl:sameAs'] = ids
-    }
-
-    return node
-}
-
-function makeLinkedDataForTaxa (files: Catalog): NodeObject[] {
-    const nodes = []
-    const gbifTaxa: Record<string, NodeObject> = {}
-
-    for (const taxon of files.taxa.entities) {
-        const node = makeLinkedDataForTaxon(taxon)
-
-        const ancestors = taxon.get('ancestors_gbif') ?? []
-        if (ancestors.length) {
-            node['dwc:parentNameUsageID'] = makeGbifUri(ancestors[ancestors.length - 1])
-        } else if (taxon.get('id') !== 'T141') {
-            node['dwc:parentNameUsageID'] = { '@id': `${PREFIX}taxon/T141` }
-        }
-
-        for (let i = 0; i < ancestors.length; i++) {
-            gbifTaxa[ancestors[i]] = {
-                ...makeGbifUri(ancestors[i]),
-                'dwc:taxonRank': makeTaxonRankUri(GBIF_RANKS[i]),
-                'dwc:parentNameUsageID': i ? makeGbifUri(ancestors[i - 1]) : { '@id': `${PREFIX}taxon/T141` }
-            }
-        }
-
-        if (taxon.has('children_gbif')) {
-            const children = taxon.get('children_gbif') as string[]
-            node['@reverse'] = { 'dwc:parentNameUsageID': children.map(makeGbifUri) as unknown as string }
-
-            const childRank = GBIF_RANKS[ancestors.length]
-            for (const child of children) {
-                gbifTaxa[child] = {
-                    ...makeGbifUri(child),
-                    'dwc:taxonRank': makeTaxonRankUri(childRank),
-                }
-            }
-        }
-
-        nodes.push(node)
-    }
-
-    nodes.push(...Object.values(gbifTaxa))
-
-    return nodes
-}
-
-function makeLinkedDataForScientificName (name: AmendedTaxon): NodeObject {
-    const node: NodeObject = {
-        ...makeScientificNameUri(name.scientificNameID),
-        '@type': 'dwc:Taxon',
-    }
-
-    for (const field in DWC_FIELDS) {
-        const value = name[field as keyof AmendedTaxon]
-        if (value) {
-            node[DWC_FIELDS[field]] = value as string
-        }
-    }
-
-    if (GBIF_VOCAB_RANKS.includes(name.taxonRank)) {
-        node[DWC_FIELDS.taxonRank] = makeTaxonRankUri(name.taxonRank)
-    }
-
-    if (name.taxonomicStatus in STATUSES) {
-        node[DWC_FIELDS.taxonomicStatus] = makeTaxonomicStatusUri(name.taxonomicStatus)
-    } else {
-        console.error('Unmapped taxonomic status:', name.taxonomicStatus)
-    }
-
-    if (name.acceptedNameUsageID) {
-        node['dwc:acceptedNameUsageID'] = makeScientificNameUri(name.acceptedNameUsageID)
-    }
-
-    if (name.parentNameUsageID) {
-        node['dwc:parentNameUsageID'] = makeScientificNameUri(name.parentNameUsageID)
-    }
-
-    const identifiers = []
-    if (name.gbifTaxonID) {
-        identifiers.push(makeGbifUri(name.gbifTaxonID))
-    }
-    if (name.colTaxonID) {
-        identifiers.push({ '@id': `https://www.checklistbank.org/dataset/309120/taxon/${name.colTaxonID}` })
-    }
-
-    if (identifiers.length) {
-        node['dwc:taxonID'] = identifiers
-    }
-
-    return node
-}
-
-function makeLinkedDataForResource (work: catalog.Entity, files: Catalog, resourceId?: ResourceId): NodeObject {
-    const resource = new WorkResource({})
-
-    if (!resourceId) {
-        resourceId = `${work.get('id')}:0`
-    }
-
-    if (files.resources[resourceId] && files.resources[resourceId].metadata.catalog) {
-        resource.fields = files.resources[resourceId].metadata.catalog as Record<string, Value>
-    }
-
-    if (!resource.has('language')) {
-        resource.fields.language = work.get('language') as Value
-    }
-
-    const node: NodeObject = {
-        ...makeLinkedDataForWork(resource, files),
-        '@id': `${PREFIX}resource/${resourceId}`,
-        '@type': 'bibo:DocumentPart',
-    }
-
-    const types = resource.get('key_type') ?? work.get('key_type') ?? []
-
-    if (types.includes('matrix') || types.includes('algorithm')) {
-        node['dcterms:type'] = { '@id': 'http://purl.org/dc/dcmitype/Software' }
-    } else if (types.includes('key') || types.includes('reference') || types.includes('supplement')) {
-        node['dcterms:type'] = { '@id': 'http://purl.org/dc/dcmitype/Text' }
-    } else if (types.includes('gallery') || types.includes('collection')) {
-        node['dcterms:type'] = { '@id': 'http://purl.org/dc/dcmitype/Collection' }
-    } else if (types.includes('checklist')) {
-        node['dcterms:type'] = { '@id': 'http://purl.org/dc/dcmitype/Dataset' }
-    }
-
-    if (types.includes('key') || types.includes('matrix')) {
-        node['ac:subtype'] = { '@id': 'http://rs.tdwg.org/acsubtype/values/IdentificationKey' }
-    }
-
-    const taxonNames = resource.get('taxon') ?? work.get('taxon')
-    if (taxonNames) {
-        const taxa = mapEntities(taxonNames as string[], files.taxa.entities)
-        const coveringTaxon = taxa.length ? getCoveringTaxon(taxa) : null
-        if (coveringTaxon !== null) {
-            node['ac:taxonCoverage'] = { '@id': coveringTaxon }
-        }
-
-        node['dwc:taxonID'] = taxa.map(taxon => ({ '@id': `${PREFIX}taxon/${taxon.get('id')}` }))
-    }
-
-    const scopes = resource.get('scope') ?? work.get('scope')
-    if (scopes) {
-        for (const scope of scopes as string[]) {
-            if (!SCOPES[scope]) {
-                console.error('Unmapped scope:', scope)
-                continue
-            }
-
-            const [property, ...values] = SCOPES[scope]
-
-            if (!Array.isArray(node[property])) {
-                node[property] = []
-            }
-
-            for (const value of values) {
-                if (value.startsWith('http')) {
-                    (node[property] as unknown[]).push({ '@id': value })
-                } else {
-                    (node[property] as unknown[]).push(value)
-                }
-            }
-        }
-    }
-
-    const region = resource.get('region') ?? work.get('region')
-    if (region) {
-        const places = mapEntities(region as string[], files.places.entities).map(place => ({ '@id': `${PREFIX}place/${place.get('id')}` }))
-        node['dcterms:spatial'] = places
-    }
-
-    const tags: string[] = []
-
-    const taxonScopes = resource.get('taxon_scope') ?? work.get('taxon_scope')
-    if (taxonScopes) {
-        tags.push(...taxonScopes as string[])
-    } else if ((resource.get('complete') ?? work.get('complete')) === 'FALSE') {
-        tags.push('not intended to be complete')
-    }
-
-    const targetTaxa = resource.get('target_taxa') ?? work.get('target_taxa')
-    if (targetTaxa) {
-        const first = (targetTaxa as string[]).slice(0, -1).map(rank => rank + ',')
-        const last = targetTaxa[targetTaxa.length - 1]
-        const list = first.length ? first.join('') + ' or ' + last : last
-        tags.push(`for identification to ${list}`)
-    }
-
-    if (tags.length) {
-        node['ac:tag'] = tags
-    }
-
-    if (files.resources[resourceId].taxa) {
-        const leafs = new Set(files.resources[resourceId].taxa.map(taxon => taxon.scientificNameID))
-        const taxa = []
-        for (const taxon of files.resources[resourceId].taxa) {
-            taxa.push(makeLinkedDataForScientificName(taxon))
-
-            if (taxon.parentNameUsageID) {
-                leafs.delete(taxon.parentNameUsageID)
-            }
-        }
-
-        node['dcterms:subject'] = taxa
-        node['ac:taxonCount'] = leafs.size
-    }
-
-    return node
-}
-
-function makeLinkedDataForWork (work: catalog.Entity, files: Catalog): NodeObject {
-    const id = work.get('id') as string
-    const node: NodeObject = makeWorkUri(id)
-
-    const languages = work.get('language') as string[]
-    node['dcterms:language'] = languages.map(language => ({ '@id': `http://id.loc.gov/vocabulary/iso639-1/${language}` }))
-
-    if (work.has('title')) {
-        const title = work.get('title') as string[]
-        if (title.length > languages.length) {
-            title.splice(0, title.length, title.join('; '))
-        }
-        node['dcterms:title'] = title.map((value, i) => ({ '@value': value, '@language': languages[i] }))
-    }
-
-    if (work.has('pages') && (work.get('pages') as string).includes('-')) {
-        const containers = work.has('part_of') ? (work.get('part_of') as string[]).map(id => files.catalog.get(id)) : []
-        if (containers.find(container => container.get('entry_type') === 'online')) {
-            node['@type'] = 'bibo:BookSection'
-        } else {
-            node['@type'] = 'bibo:AcademicArticle'
-        }
-    } else if (work.get('entry_type') === 'online') {
-        node['@type'] = 'bibo:Website'
-    } else {
-        node['@type'] = 'bibo:Book'
-    }
-
-    if (work.has('author')) {
-        const authors = mapEntities(work.get('author') as string[], files.authors.entities).map(author => ({ '@id': `${PREFIX}author/${author.get('id')}` }))
-        node['bibo:authorList'] = { '@list': authors }
-        node['dcterms:creator'] = authors
-    }
-
-    if (work.has('url')) {
-        const urls = work.get('url') as string[]
-
-        const handle = urls.find(url => url.startsWith(HANDLE_PREFIX))
-        if (handle) {
-            node['bibo:handle'] = { '@id': handle.slice(HANDLE_PREFIX.length) }
-        }
-
-        node['schema:url'] = urls.map(url => ({ '@id': url }))
-    }
-
-    if (work.has('fulltext_url')) {
-        const urls = work.get('fulltext_url') as string[]
-
-        node['schema:encoding'] = urls.map(url => ({ '@type': 'schema:MediaObject', 'schema:contentUrl': { '@id': url } }))
-    }
-
-    if (work.has('archive_url')) {
-        node['schema:archivedAt'] = (work.get('archive_url') as string[]).map(url => ({ '@id': url }))
-    }
-
-    if (work.has('date')) {
-        const date = work.get('date') as string
-        let dateType = 'rdfs:Literal'
-        if (date.match(/^\d{4}-\d{2}-\d{2}$/)) {
-            dateType = 'xsd:date'
-        } else if (date.match(/^\d{4}-\d{2}$/)) {
-            dateType = 'xsd:gYearMonth'
-        } else if (date.match(/^\d{4}$/)) {
-            dateType = 'xsd:gYear'
-        }
-
-        node['dcterms:issued'] = { '@value': work.get('date'), '@type': dateType }
-    }
-
-    if (work.has('publisher')) {
-        const publishers = mapEntities(work.get('publisher') as string[], files.publishers.entities).map(publisher => ({ '@id': `${PREFIX}publisher/${publisher.get('id')}` }))
-        node['dcterms:publisher'] = publishers
-    }
-
-    if (work.has('ISSN')) {
-        node['bibo:issn'] = work.get('ISSN')
-    }
-
-    if (work.has('ISBN')) {
-        const isbns = work.get('ISBN') as string[]
-
-        for (const isbn of isbns) {
-            if (isbn.length === 13) {
-                node['bibo:isbn13'] = isbn
-            } else if (isbn.length === 10) {
-                node['bibo:isbn10'] = isbn
-            } else {
-                node['bibo:isbn'] = isbn
-            }
-        }
-    }
-
-    if (work.has('QID')) {
-        node['bibo:uri'] = makeWikidataUri(work.get('QID') as string)
-    }
-
-    if (work.has('DOI')) {
-        node['bibo:doi'] = work.get('DOI')
-    }
-
-    if (work.has('volume')) {
-        node['bibo:volume'] = work.get('volume')
-    }
-
-    if (work.has('issue')) {
-        node['bibo:issue'] = work.get('issue')
-    }
-
-    if (work.has('pages')) {
-        const pages = work.get('pages') as string
-        const range = pages.split('-')
-
-        if (pages.match(/^\d+$/)) {
-            node['bibo:numPages'] = parseInt(pages)
-        } else if (range.length === 2) {
-            node['bibo:pages'] = pages
-
-            const [start, end] = range.map(part => parseInt(part))
-            if (!isNaN(start)) {
-                node['bibo:pageStart'] = start
-            }
-            if (!isNaN(end)) {
-                node['bibo:pageEnd'] = end
-            }
-            if (!isNaN(start) && !isNaN(end)) {
-                node['bibo:numPages'] = end - start + 1
-            }
-        } else {
-            node['bibo:pages'] = pages
-        }
-    }
-
-    if (work.has('edition')) {
-        node['bibo:edition'] = work.get('edition')
-    }
-
-    if (work.has('license')) {
-        const licenses = work.get('license') as string[]
-        node['dcterms:rights'] = licenses.map(license => {
-            if (license === '<public domain>' || license.match(/^<.+\?>$/)) {
-                return license.slice(1, -1)
-            } else {
-                return { '@id': `https://spdx.org/licenses/${license}.html` }
-            }
-        })
-    }
-
-    return node
-}
-
-function makeLinkedDataForWorks (files: Catalog): NodeObject[] {
-    const nodes: Record<string, NodeObject> = {}
-    const works = files.catalog
-
-    for (const work of works.entities) {
-        nodes[work.get('id') as string] = makeLinkedDataForWork(work, files)
-    }
-
-    for (const work of works.entities) {
-        const id = work.get('id') as string
-        const node = nodes[id]
-        const language = work.get('language') as string[]
-
-        if (work.has('part_of')) {
-            const containers = work.get('part_of') as string[]
-
-            if ((work.get('key_type') as string[]).includes('supplement')) {
-                node['bibo:annotates'] = containers.map(makeWorkUri)
-            } else {
-                node['dcterms:isPartOf'] = containers.map(makeWorkUri)
-
-                for (const container of containers) {
-                    if (!Array.isArray(nodes[container]['dcterms:hasPart'])) {
-                        nodes[container]['dcterms:hasPart'] = []
-                    }
-                    (nodes[container]['dcterms:hasPart'] as NodeObject[]).push(makeWorkUri(id))
-                }
-            }
-        }
-
-        if (work.has('listed_in')) {
-            const referers = work.get('listed_in') as string[]
-            node['bibo:citedBy'] = node['dcterms:isReferencedBy'] = referers.map(makeWorkUri)
-
-            for (const referer of referers) {
-                nodes[referer]['bibo:cites'] = nodes[referer]['dcterms:references'] = makeWorkUri(id)
-            }
-        }
-
-        if (work.has('version_of')) {
-            const originals = work.get('version_of') as string[]
-            const originalLanguages = originals.map(id => ((works.get(id) as catalog.Entity).get('language') as string[]).join())
-            node['bibo:translationOf'] = originals.filter((_, i) => originalLanguages[i] !== language.join()).map(makeWorkUri)
-            node['dcterms:isVersionOf'] = originals.filter(id => work.get('id') !== id).map(makeWorkUri)
-        }
-
-        let resourceIndex = 1
-        let resourceId
-        while ((resourceId = `${id}:${resourceIndex++}`) in files.resources) {
-            const resource = makeLinkedDataForResource(work, files, resourceId)
-
-            if (!Array.isArray(node['dcterms:hasPart'])) {
-                node['dcterms:hasPart'] = []
-            }
-            (node['dcterms:hasPart'] as NodeObject[]).push(resource)
-
-            if (!Array.isArray(resource['dcterms:isPartOf'])) {
-                resource['dcterms:isPartOf'] = []
-            }
-            (resource['dcterms:isPartOf'] as NodeObject[]).push({ '@id': node['@id'] })
-        }
-    }
-
-    return Object.values(nodes)
-}
-
-async function writeOutput (document: JsonLdDocument, format = 'jsonld'): Promise<void> {
-    if (format === 'jsonld') {
-        process.stdout.write(JSON.stringify(document, null, 2))
-        return
-    }
-
-    const nquads = await jsonld.toRDF(document, { format: 'application/n-quads' }) as string
-    if (format === 'nquads') {
-        process.stdout.write(nquads)
-        return
-    }
-
-    const parser = new N3.StreamParser()
-    const writer = new N3.StreamWriter({ prefixes: PREFIXES })
-    parser.write(nquads)
-    parser.pipe(writer)
-    writer.pipe(process.stdout)
-}
-
-async function main (): Promise<void> {
-    const args = util.parseArgs({
-        allowPositionals: true,
-        options: {
-            format: {
-                type: 'string',
-                short: 'f',
-                default: 'jsonld',
-            }
-        },
-    })
-    const directory = path.resolve(args.positionals[0])
-
-    const files = {} as Catalog
-    for (const sheet of SHEETS) {
-        const filePath = path.join(directory, `${sheet}.csv`)
-        if (!doesFileExist(filePath)) {
-            throw new Error(`File "${sheet}.csv" must be provided`)
-        }
-
-        const file = await fs.readFile(filePath, 'utf8')
-        files[sheet] = catalog.loadData(file, sheet)
-    }
-
-    files.resources = {}
-    const resources = JSON.parse(await fs.readFile(path.join(directory, 'resources', 'index.json'), 'utf8'))
-    for (const id in resources) {
-        const filePath = path.join(directory, 'resources', 'dwc', id.split(':').join('-') + '.csv')
-        const file = await fs.readFile(filePath, 'utf8')
-        const [header, ...rows] = parseCsv(file)
-        const taxa = rows.map(row => row.reduce((object, value, index) => {
-            object[header[index]] = value
-            return object
-        }, {} as Record<string, string>) as unknown as AmendedTaxon)
-
-        files.resources[id] = { metadata: resources[id], taxa }
-    }
-
-    const graph: NodeObject[] = [
-        ...makeLinkedDataForWorks(files),
-        ...makeLinkedDataForTaxa(files),
-    ]
-
-    for (const entity of files.authors.entities) {
-        graph.push(makeLinkedDataForAuthor(entity))
-    }
-    for (const entity of files.places.entities) {
-        graph.push(makeLinkedDataForPlace(entity))
-    }
-    for (const entity of files.publishers.entities) {
-        graph.push(makeLinkedDataForPublisher(entity))
-    }
-
-    const document: JsonLdDocument = {
-        '@context': PREFIXES,
-        '@graph': graph
-    }
-
-    writeOutput(document, args.values.format)
-}
-
-main().catch((error: Error) => {
-    console.error(error)
-    process.exit(1)
-})