diff --git a/package-lock.json b/package-lock.json index 4b9e42985..2aec12263 100644 --- a/package-lock.json +++ b/package-lock.json @@ -1,12 +1,12 @@ { "name": "factoid", - "version": "0.26.0", + "version": "0.27.0", "lockfileVersion": 2, "requires": true, "packages": { "": { "name": "factoid", - "version": "0.26.0", + "version": "0.27.0", "license": "MIT", "dependencies": { "@appsignal/express": "^0.5.1", diff --git a/package.json b/package.json index af38ac6a0..a590a40fa 100644 --- a/package.json +++ b/package.json @@ -137,5 +137,5 @@ "engines": { "node": ">=16.19.0" }, - "version": "0.26.0" + "version": "0.27.0" } diff --git a/src/client/components/accordion.js b/src/client/components/accordion.js new file mode 100644 index 000000000..9c71c0dba --- /dev/null +++ b/src/client/components/accordion.js @@ -0,0 +1,63 @@ +import h from 'react-hyperscript'; +import { Component } from 'react'; +import { makeClassList } from '../dom'; +import _ from 'lodash'; + + +export const ACCORDION_ITEM_FIELDS = { + TITLE: 'title', + DESCRIPTION: 'description' +}; + + +export class AccordionItem extends Component { + constructor(props){ + super(props); + + this.state = { + isOpen: false + }; + } + + toggleItem(){ + this.setState({ isOpen: !this.state.isOpen }); + } + + render(){ + const { title, description } = this.props.item; + const { isOpen } = this.state; + const content = _.isString( description ) ? [ h('p', description) ] : description; + return h('div.accordion-item', [ + h('div.accordion-item-header', { + className: makeClassList({ + 'open': isOpen + }), + onClick: () => this.toggleItem() + }, [ + h( 'p.accordion-item-header-title', title ), + isOpen ? h('i.material-icons.accordion-item-header-icon', 'expand_less') : + h('i.material-icons.accordion-item-header-icon', 'expand_more') + ]), + h('div.accordion-item-content', content ) + ]); + } +} + +export class Accordion extends Component { + constructor(props){ + super(props); + + this.state = { + }; + } + + render(){ + const { title, items } = this.props; + return h('div.accordion', [ + title ? h('h3.accordion-title', title ) : null, + h('div.accordion-items', items.map( (item, key) => h( AccordionItem, { key, item } ) ) ) + ]); + } +} + +export default Accordion; \ No newline at end of file diff --git a/src/client/components/editor/info-panel.js b/src/client/components/editor/info-panel.js index a718cd1e5..13d56549d 100644 --- a/src/client/components/editor/info-panel.js +++ b/src/client/components/editor/info-panel.js @@ -67,7 +67,7 @@ export class InfoPanel extends Component { const citation = document.citation(); // authorProfiles may not be existing for the older documents const authorProfiles = document.authorProfiles() || citation.authors.authorList; - const { pmid, title = 'Untitled article', reference, doi, abstract } = citation; + const { pmid, title = 'Untitled article', reference, doi, abstract, relations } = citation; const retractedPubType = _.find( citation.pubTypes, ['UI', 'D016441'] ); const retractFlag = retractedPubType ? h('span.editor-info-flag.super-salient-button.danger', retractedPubType.value) : null; @@ -75,6 +75,8 @@ export class InfoPanel extends Component { const hasArticleId = pmid != null || doi != null; const hasRelatedPapers = !_.isEmpty( document.relatedPapers() ); + const hasRelations = !_.isEmpty( relations ); + return h('div.editor-info-panel', [ h('div.editor-info-flags', [ retractFlag ]), @@ -103,6 +105,13 @@ export class InfoPanel extends Component { pmid ? h('a.editor-info-link.plain-link', { target: '_blank', href: `${PUBMED_LINK_BASE_URL}${pmid}` }, 'PubMed') : null, h('a.editor-info-link.plain-link', { target: '_blank', href: `${GOOGLE_SCHOLAR_BASE_URL}${( "\u0022" + title + "\u0022") }`}, 'Google Scholar') ]), + hasRelations ? + h('div.editor-info-relations', relations.map( ({ type, links }, i) => [ + h('div.editor-info-relation', { key: i.toString() }, [ + h('span.editor-info-relation-type', `${type} `), + h('span.editor-info-links', links.map( ({ url, reference }, j ) => h('a.editor-info-link.plain-link', { key: j.toString(), target: '_blank', href: url }, reference ) ) ) + ]) + ])): null, h('div.editor-info-main-sections', [ abstract ? h('div.editor-info-abstract-section.editor-info-main-section', [ h('div.editor-info-section-title', abstract ? 'Abstract': 'Summary'), diff --git a/src/client/components/element-info/entity-info.js b/src/client/components/element-info/entity-info.js index 3f182c53e..5979c657c 100644 --- a/src/client/components/element-info/entity-info.js +++ b/src/client/components/element-info/entity-info.js @@ -365,11 +365,6 @@ class EntityInfo extends DataComponent { let doc = p.document; let children = []; - const citation = doc.citation(); - const { pmid } = citation; - - const hasPubmedMetadata = pmid != null; - let Loader = ({ loading = true }) => h('div.entity-info-matches-loading' + (loading ? '.entity-info-matches-loading-active' : ''), [ loading ? h('i.icon.icon-spinner') : h('i.material-icons', 'remove') ]); @@ -612,6 +607,7 @@ class EntityInfo extends DataComponent { if( isComplex(s.element.type()) ){ const entityNames = s.element.participants().map(ppt => ppt.name()); children.push( h('div.entity-info-assoc', targetFromAssoc({ type, name, entityNames }, true )) ); + if (hasRelatedPapers) { children.push( h('div.entity-info-reld-papers-title', `Recommended articles`) ); diff --git a/src/client/components/home.js b/src/client/components/home.js index 82c2153be..12e198f17 100644 --- a/src/client/components/home.js +++ b/src/client/components/home.js @@ -7,6 +7,7 @@ import { Carousel, CAROUSEL_CONTENT } from './carousel'; import { tryPromise } from '../../util'; import { formatDistanceToNow } from 'date-fns'; import DocumentSearch from '../document-search'; +import Accordion from './accordion.js'; import { TWITTER_ACCOUNT_NAME, SAMPLE_DOC_ID, EMAIL_ADDRESS_INFO } from '../../config'; import _ from 'lodash'; @@ -377,7 +378,8 @@ class Home extends Component { h('a.home-nav-link', [ h(ContactPopover) ]), - h('a.home-nav-link', { href: `https://twitter.com/${TWITTER_ACCOUNT_NAME}`, target: '_blank' }, 'Twitter') + h('a.home-nav-link', { href: `https://twitter.com/${TWITTER_ACCOUNT_NAME}`, target: '_blank' }, 'Twitter'), + h('a.home-nav-link', { href: '#faq' }, 'FAQ') ]) ]), h('div.home-intro', [ @@ -557,6 +559,136 @@ class Home extends Component { ]) ]) ]), + h('div.home-section.home-fluid-section.home-fluid-section-no-figure', [ + h('div.home-fluid-section-copy', [ + h( Accordion, { + title: [ h('span', { id: 'faq' }, 'Frequently Asked Questions')], + items: [ + { title: 'What is Biofactoid?', description: [ + h('p', [ + 'A tool to map ', + h('a.plain-link', { href: 'https://en.wikipedia.org/wiki/Biological_pathway', target: '_blank' }, 'biological pathways'), + ' assembled from author-curated results in papers.' + ]) + ]}, + { title: 'What problem does Biofactoid help solve?', description: [ + h('p', 'Think about the last time you snapped a photo of your friends or family (or your pet). Your phone automatically identified and focused on all the faces, but, whether you were aware of it or not, it also labelled those faces (and cars, food, cute babies) so that it could organise your album by the places, people, pets and things within the images.'), + h('p', 'Wouldn’t it be great if all of the scientific details in a paper were readily identifiable by computers so that information across the literature could be precisely related and combined?'), + h('p', [ + 'Despite the fact that scientific papers are distributed digitally, the content itself -- plain text and images -- remains rooted in the print era. Unfortunately, knowledge in the text and figures in papers is extremely challenging for computers to accurately extract and use. We traditionally rely on expert curators at biological resources (e.g., ', + h('a.plain-link', { href: 'https://www.uniprot.org/', target: '_blank' }, 'UniProt'), + ') to read papers and enter the information in a format that a computer can work with. However, this is expensive and there are too many papers for expert curators to handle at the same time.' + ]), + h('p', 'Biofactoid rethinks the way information in papers is captured by enabling curation by authors of scientific articles, which is accurate, since authors are authoritative experts on their studies, and scales to support comprehensive, up-to-the-minute coverage of the literature.') + ]}, + { title: 'What kind of information does Biofactoid contain?', description: 'Functional relationships (e.g., binding, transcription) between molecules and chemicals. For instance, "NAD+ binds to mouse PARP1".'}, + { title: 'Which species does Biofactoid support?', description: [ + h('p', [ + 'Humans and major model organisms including: ', + h('em', 'M. musculus'), ', ', + h('em', 'R. norvegicus'), ', ', + h('em', 'S. cerevisiae'), ', ', + h('em', 'D. melanogaster'), ', ', + h('em', 'E. coli'), ', ', + h('em', 'C. elegans'), ', ', + h('em', 'D. rerio'), ', ', + h('em', 'A. thaliana'), ', as well as ', + h('em', 'SARS-CoV-2.') + ]) + ]}, + { title: 'Can anyone submit an article?', description: [ + h('p', [ + h('span', 'Any author of a primary research article is welcome to submit content to Biofactoid. Authors access the curation tool via a private web link. Author names and emails are associated with Biofactoid records and matched against corresponding author and '), + h('a.plain-link', { href: 'https://orcid.org/', target: '_blank' }, 'Open Researcher and Contributor ID (ORCID)'), + h('span', ' information (when available) for each article. The Biofactoid website displays the name of the author who created the record, linked to their ORCID.') + ]) + ]}, + { title: 'How long does it take?', description: 'A typical author spends a total of 6 minutes to add information from a paper; this usually involves 3 interactions. More than a quarter of users finish in less than 3 minutes.' }, + { title: 'Do I need to create an account?', description: 'No. All Biofactoid data is freely and openly available for all to use, download and redistribute without restriction. Authors curate their paper by following a private web link. Email addresses remain private and are never shared.' }, + { title: 'How does Biofactoid compare to other pathway databases like Reactome or STRING?', description: [ + h('p', 'Biofactoid collects pathway and network data and makes it available as a resource to support many different uses. Biofactoid data can be searched as is, as a knowledge resource. It can also provide input data for pathway and network analyses, such as the following:'), + h('ul', [ + h('li', [ + 'STRING collects data from other sources, such as Biocarta, BioCyc, Gene Ontology, KEGG, and Reactome; ', + h('u', 'Biofactoid is a primary source of curated data') + ]), + h('li', 'Reactome curates a defined set of human pathways from select papers, focusing on a consensus (i.e. "textbook") interpretation of biological processes; Biofactoid supports author-curation of all papers with pathway results') + ]) + ]}, + { title: 'How is Biofactoid data is used?', description: [ + h('p', 'Biofactoid collects pathway and network data and makes it available as a resource to support many different uses. Biofactoid data can be searched as is, as a knowledge resource. It can also provide input data for pathway and network analyses, such as the following:'), + h('ul', [ + h('li', [ + h('b', 'Interpreting long lists of genes from large-scale experiments'), + h('ul', [ + h('p', 'Comprehensive quantification of DNA, RNA and proteins in biological samples yields long lists of measured entities (e.g. differentially expressed genes) which are difficult to interpret. Pathway enrichment analysis summarises gene lists as a smaller, more easily interpretable list of affected pathways. Pathway data is obtained from manually curated resources.'), + h('li', [ + h('a.plain-link', { href: 'https://www.science.org/doi/full/10.1126/scisignal.aan3580', target: '_blank' }, 'Integrated in vivo multiomics analysis identifies p21-activated kinase signaling as a driver of colitis.'), + ' Sci. Signal 11 (2018)' + ]), + h('li', [ + h('a.plain-link', { href: 'https://www.nature.com/articles/nature13108', target: '_blank' }, 'Epigenomic alterations define lethal CIMP-positive ependymomas of infancy.'), + ' Nature 506 (2014)' + ]), + h('li', [ + h('a.plain-link', { href: 'https://www.nature.com/articles/nature13483', target: '_blank' }, 'DNA-damage-induced differentiation of leukaemic cells as an anti-cancer barrier.'), + ' Nature 514 (2014)' + ]) + ]) + ]), + h('li', [ + h('b', 'Exploring the mechanistic neighbourhood of a gene or drug'), + h('ul', [ + h('p', 'Functional screens (e.g., RNAi) and genetic screens can implicate one or a few genes in a phenotype. However, complex cellular networks of gene products and chemicals underlie most genotype-to-phenotype relationships. An integrated resource of curated biological relationships enables researchers to explore a neighbourhood of direct and indirect mechanistic interactions for a protein (or drug) of interest.'), + h('li', [ + 'Search engines: ', + h('a.plain-link', { href: 'https://string-db.org/', target: '_blank' }, 'STRING'), + h('span', ', '), + h('a.plain-link', { href: 'https://genemania.org/', target: '_blank' }, 'GeneMANIA'), + h('span', ', '), + h('a.plain-link', { href: 'https://apps.pathwaycommons.org/', target: '_blank' }, 'Pathway Commons Search') + ]) + ]), + ]), + h('li', [ + h('b', 'Network analysis'), + h('ul', [ + h('p', 'The research community has used pathway and interaction data in a wide variety of computational analyses:'), + h('li', [ + h('em', 'Constructing quantitative dynamical models from curated pathways'), + h('ul', [ + h('li', [ + h('a.plain-link', { href: 'https://pubmed.ncbi.nlm.nih.gov/24273241/', target: '_blank' }, 'Pathway Commons at virtual cell: use of pathway data for mathematical.'), + ' Bioinformatics 15:30 (2014)' + ]) + ]), + ]), + h('li', [ + h('em', 'Using curated pathways to assemble a kinase signalling network that explains kinase data'), + h('ul', [ + h('li', [ + h('a.plain-link', { href: 'https://www.nature.com/articles/nmeth.3773', target: '_blank' }, 'DREAM Challenge: Hill, S. M. et al. Inferring causal molecular networks: empirical assessment through a community-based effort.'), + ' Nat. Methods 13 (2016)' + ]) + ]), + ]), + h('li', [ + h('em', 'Using curated pathways to explain mutually exclusive mutations in cancer'), + h('ul', [ + h('li', [ + h('a.plain-link', { href: 'https://genomebiology.biomedcentral.com/articles/10.1186/s13059-015-0612-6', target: '_blank' }, 'Systematic identification of cancer driving signaling pathways based on mutual exclusivity of genomic alterations.'), + ' Genome Biology 16:45 (2015)' + ]) + ]), + ]) + ]) + ]) + ]) + ]} + ] + }) + ]) + ]), h('div.home-section.home-search-results', [ this.state.searchMode ? ( this.state.searching ? ( diff --git a/src/server/routes/api/document/crossref/map.js b/src/server/routes/api/document/crossref/map.js index 6227fc87c..fa6e82b68 100644 --- a/src/server/routes/api/document/crossref/map.js +++ b/src/server/routes/api/document/crossref/map.js @@ -1,6 +1,6 @@ import _ from 'lodash'; import { format } from 'date-fns'; -import { createPubmedArticle } from '../../../../../util/pubmed'; +import { COMMENTSCORRECTIONS_REFTYPE, createPubmedArticle } from '../../../../../util/pubmed'; /** * getAbstract @@ -169,6 +169,50 @@ const getPublicationTypeList = record => { return PublicationTypeList; }; +const getCommentsCorrectionsList = record => { + const CommentsCorrectionsList = []; + const CRRELATION_REFTYPE_MAP = new Map([ + ['is-preprint-of', COMMENTSCORRECTIONS_REFTYPE.UpdateIn], + ['has-preprint', COMMENTSCORRECTIONS_REFTYPE.UpdateOf], + ['is-comment-on', COMMENTSCORRECTIONS_REFTYPE.CommentOn], + ['has-comment', COMMENTSCORRECTIONS_REFTYPE.CommentIn], + ['isSupplementedBy', COMMENTSCORRECTIONS_REFTYPE.AssociatedDataset] + ]); + const CRRELATION_IDTYPES = new Set([ + 'doi', + 'pmid' + ]); + const { relation } = record; + if( relation ){ + for (let crRelationType of Object.keys(relation)) { + if( CRRELATION_REFTYPE_MAP.has( crRelationType ) ){ + const RefType = CRRELATION_REFTYPE_MAP.get( crRelationType ); + const relations = relation[crRelationType]; + for (let rel of relations) { + const { id, 'id-type': idType } = rel; + if( CRRELATION_IDTYPES.has( idType ) ){ + const CommentsCorrections = { + RefType, + PMID: null, + DOI: null, + RefSource: '' + }; + if( idType === 'doi' ){ + _.set(CommentsCorrections, 'DOI', id); + _.set(CommentsCorrections, 'RefSource', `doi: ${id}`); + } else if( idType === 'pmid' ){ + _.set(CommentsCorrections, 'PMID', id); + _.set(CommentsCorrections, 'RefSource', `pmid: ${id}`); + } + CommentsCorrectionsList.push(CommentsCorrections); + } + } + } + } + } + return CommentsCorrectionsList; +}; + const getMedlineCitation = record => { const { abstract, title, author } = record; const Abstract = getAbstract( abstract ); @@ -176,7 +220,8 @@ const getMedlineCitation = record => { const AuthorList = asAuthorList( author ); const Journal = getJournal( record ); const PublicationTypeList = getPublicationTypeList( record ); - const MedlineCitation = { Article: { Abstract, ArticleTitle, AuthorList, Journal, PublicationTypeList } }; + const CommentsCorrectionsList = getCommentsCorrectionsList( record ); + const MedlineCitation = { Article: { Abstract, ArticleTitle, AuthorList, Journal, PublicationTypeList }, CommentsCorrectionsList }; return MedlineCitation; }; diff --git a/src/server/routes/api/document/crossref/works.js b/src/server/routes/api/document/crossref/works.js index b1c57e184..567a08dd6 100644 --- a/src/server/routes/api/document/crossref/works.js +++ b/src/server/routes/api/document/crossref/works.js @@ -3,7 +3,7 @@ import logger from '../../../../logger'; import { search, get } from './api.js'; import { toPubMedArticle } from './map'; -import { isDoi } from '../../../../../util'; +import { HTTPStatusError, isDoi } from '../../../../../util'; import { ArticleIDError } from '../../../../../util/pubmed'; const ID_TYPE = Object.freeze({ @@ -111,7 +111,19 @@ const findPreprint = async paperId => { } } catch( err ) { - logger.error( `${err.name}: ${err.message}` ); + if( err instanceof HTTPStatusError ){ + const { response } = err; + const { url, headers } = response; + logger.error( `crossref.findPreprint threw ${err.name}: ${err.message}` ); + logger.error( `fetch URL: ${url}` ); + logger.error( headers.raw() ); + + } else if( err instanceof ArticleIDError ){ + logger.debug( `crossref.findPreprint threw ${err.name}: ${err.message}` ); + + } else { + logger.error( `crossref.findPreprint threw ${err.name}: ${err.message}` ); + } throw err; } }; diff --git a/src/server/routes/api/document/pubmed/fetchPubmed.js b/src/server/routes/api/document/pubmed/fetchPubmed.js index c9b381cf7..babdc848f 100644 --- a/src/server/routes/api/document/pubmed/fetchPubmed.js +++ b/src/server/routes/api/document/pubmed/fetchPubmed.js @@ -244,6 +244,42 @@ const getChemicalList = MedlineCitation => { return getElementsByName( ChemicalList, 'Chemical' ).map( getChemical ); }; + +const getCommentsCorrections = CommentsCorrections => { + const extractDOI = str => { + const doiRegex = /^doi: (?10\.\d{4,9}\/[-._;()/:A-Z0-9]+)$/i; + const matches = str.match( doiRegex ); + const DOI = _.get( matches, ['groups', 'DOI'], null ); + return DOI; + }; +// +// + const RefType = getElementAttribute( CommentsCorrections, 'RefType' ); + const PMID = getElementByName( CommentsCorrections, 'PMID' ) ? getElementText( getElementByName( CommentsCorrections, 'PMID' ) ): null; + const RefSource = getElementText( getElementByName( CommentsCorrections, 'RefSource' ) ); + const DOI = extractDOI( RefSource ); + return { RefType, PMID, RefSource, DOI }; +}; + +// +const getCommentsCorrectionsList = MedlineCitation => { + const CommentsCorrectionsList = getElementByName( MedlineCitation, 'CommentsCorrectionsList' ); + return getElementsByName( CommentsCorrectionsList, 'CommentsCorrections' ).map( getCommentsCorrections ); +}; + // // @@ -313,6 +349,7 @@ const getMedlineCitation = PubmedArticle => { const Article = getArticle( MedlineCitation ); const ChemicalList = getElementByName( MedlineCitation, 'ChemicalList' ) ? getChemicalList( MedlineCitation ): []; + const CommentsCorrectionsList = getElementByName( MedlineCitation, 'CommentsCorrectionsList' ) ? getCommentsCorrectionsList( MedlineCitation ): []; const KeywordList = getElementByName( MedlineCitation, 'KeywordList' ) ? getKeywordList( MedlineCitation ): []; const MeshheadingList = getElementByName( MedlineCitation, 'MeshHeadingList' ) ? getMeshheadingList( MedlineCitation ): []; const InvestigatorList = getElementByName( MedlineCitation, 'InvestigatorList' ) ? getInvestigatorList( MedlineCitation ): []; @@ -320,6 +357,7 @@ const getMedlineCitation = PubmedArticle => { return { Article, ChemicalList, + CommentsCorrectionsList, KeywordList, MeshheadingList, InvestigatorList diff --git a/src/server/routes/api/document/pubmed/index.js b/src/server/routes/api/document/pubmed/index.js index 2762f427c..5ee2df294 100644 --- a/src/server/routes/api/document/pubmed/index.js +++ b/src/server/routes/api/document/pubmed/index.js @@ -7,7 +7,7 @@ import { ArticleIDError, getPubmedCitation } from '../../../../../util/pubmed'; import { DEMO_ID } from '../../../../../config'; -import { isDigits, isDoi } from '../../../../../util'; +import { HTTPStatusError, isDigits, isDoi } from '../../../../../util'; const ID_TYPE = Object.freeze({ DOI: 'doi', @@ -93,6 +93,7 @@ const getPubmedArticle = async paperId => { try { const IdType = paperId2Type( paperId ); const fieldOpts = IdType === ID_TYPE.TITLE ? { field: ID_TYPE.TITLE } : {}; + // TODO - this should fetch when PMID-like, search otherwise const { searchHits } = await searchPubmed( paperId, fieldOpts ); const PubmedArticle = await findMatchingPubmedArticle( paperId, IdType, searchHits ); @@ -103,7 +104,19 @@ const getPubmedArticle = async paperId => { } } catch( err ) { - logger.error( `${err.name}: ${err.message}` ); + if( err instanceof HTTPStatusError ){ + const { response } = err; + const { url, headers } = response; + logger.error( `pubmed.getPubmedArticle threw ${err.name}: ${err.message}` ); + logger.error( `fetch URL: ${url}` ); + logger.error( headers.raw() ); + + } else if( err instanceof ArticleIDError ){ + logger.debug( `pubmed.getPubmedArticle threw ${err.name}: ${err.message}` ); + + } else { + logger.error( `pubmed.getPubmedArticle threw ${err.name}: ${err.message}` ); + } throw err; } } diff --git a/src/styles/accordion.css b/src/styles/accordion.css new file mode 100644 index 000000000..0d130fb53 --- /dev/null +++ b/src/styles/accordion.css @@ -0,0 +1,64 @@ +.accordion { + margin: auto; + width: 70%; + padding: 10px; +} + +.accordion-item { + padding: 1em 0.5em; + border-bottom: 1px solid rgb(234, 234, 234); +} + +.accordion-item-header { + position: relative; +} + +.accordion-item-header .accordion-item-header-title { + margin: 0; + max-width: 90%; +} + +.accordion-item-header:hover { + cursor: pointer; +} + +.accordion-item-header-icon { + position: absolute; + top: 50%; + right: 0; + transform: translateY(-50%); +} + +.accordion .accordion-item-content { + padding: 0 1em; + opacity: 0; + max-height: 0; + overflow: hidden; + + & p { + color: #000; + } + + & ul { + margin-top: 0; + } + + & li { + margin: 0; + } +} + +.accordion .accordion-item .accordion-item-header.open { + margin-bottom: 15px; +} + +.accordion .accordion-item .accordion-item-header.open + .accordion-item-content { + max-height: 2000px; + opacity: 1; +} + +@media (max-width: 750px) { + .accordion { + width: 100%; + } +} diff --git a/src/styles/editor/editor.css b/src/styles/editor/editor.css index 2e3b8be8e..0fdee2502 100644 --- a/src/styles/editor/editor.css +++ b/src/styles/editor/editor.css @@ -317,6 +317,18 @@ line-height: 1.4; } +.editor-info-relations { + margin-bottom: 0.8em; +} + +.editor-info-relation { + margin: 0.25em 0; +} + +.editor-info-relation-type { + font-style: italic; +} + .editor-info-author-spacer { margin-right: 0.333em; } diff --git a/src/styles/home.css b/src/styles/home.css index 731dd800b..2732dd617 100644 --- a/src/styles/home.css +++ b/src/styles/home.css @@ -660,9 +660,9 @@ } } -.home-search-doc-top { - /* flex: 1 1 auto; */ -} +/* .home-search-doc-top { + flex: 1 1 auto; +} */ .home-search-doc-title { position: relative; @@ -886,7 +886,7 @@ display: none; } - ..home-intro-figure-sm-alt-section { + .home-intro-figure-sm-alt-section { display: block; } diff --git a/src/styles/index.css b/src/styles/index.css index d4693a150..d4248022f 100644 --- a/src/styles/index.css +++ b/src/styles/index.css @@ -6,6 +6,7 @@ @import "./custom-icons.css"; @import "./popover"; @import "./carousel.css"; +@import "./accordion.css"; @import "./related-papers.css"; @import "./react-tabs.css"; @import "./init-app.css"; diff --git a/src/styles/related-papers.css b/src/styles/related-papers.css index 3f2cf4a67..2138f4b45 100644 --- a/src/styles/related-papers.css +++ b/src/styles/related-papers.css @@ -28,6 +28,7 @@ display: flex; flex-direction: column; justify-content: space-between; + min-width: 15em; } .related-paper-title { diff --git a/src/util/fetch.js b/src/util/fetch.js index eb3a628a8..b571ff06e 100644 --- a/src/util/fetch.js +++ b/src/util/fetch.js @@ -4,11 +4,12 @@ * Class representing a Fetch Response error */ class HTTPStatusError extends Error { - constructor( message, status, statusText ) { + constructor( message, status, statusText, response ) { super( message ); this.status = status; this.statusText = statusText; this.name = 'HTTPStatusError'; + this.response = response; } } @@ -24,7 +25,7 @@ class HTTPStatusError extends Error { const checkHTTPStatus = response => { const { statusText, status, ok } = response; if ( !ok ) { - throw new HTTPStatusError( `${statusText} (${status})`, status, statusText ); + throw new HTTPStatusError( `${statusText} (${status})`, status, statusText, response ); } return response; }; diff --git a/src/util/pubmed.js b/src/util/pubmed.js index 13ced4a5f..84f1b8be6 100644 --- a/src/util/pubmed.js +++ b/src/util/pubmed.js @@ -1,8 +1,32 @@ import _ from 'lodash'; import { parse as dateParse } from 'date-fns'; +import { DOI_LINK_BASE_URL, PUBMED_LINK_BASE_URL } from '../config'; +import { fromCamelCase, onlyCapitalizeFirst } from './strings'; const NUM_AUTHORS_SHOWING = 4; +const COMMENTSCORRECTIONS_REFTYPE = Object.freeze({ + AssociatedDataset: 'AssociatedDataset', + AssociatedPublication: 'AssociatedPublication', + CommentOn: 'CommentOn', + CommentIn: 'CommentIn', + ErratumIn: 'ErratumIn', + ErratumFor: 'ErratumFor', + ExpressionOfConcernIn: 'ExpressionOfConcernIn', + ExpressionOfConcernFor: 'ExpressionOfConcernFor', + RepublishedFrom: 'RepublishedFrom', + RepublishedIn: 'RepublishedIn', + RetractionOf: 'RetractionOf', + RetractionIn: 'RetractionIn', + UpdateIn: 'UpdateIn', + UpdateOf: 'UpdateOf', + SummaryForPatientsIn: 'SummaryForPatientsIn', + OriginalReportIn: 'OriginalReportIn', + ReprintOf: 'ReprintOf', + ReprintIn: 'ReprintIn', + Cites: 'Cites' +}); + /** * getAuthorName * @@ -209,6 +233,27 @@ const getReferenceString = Journal => { const getArticleId = ( PubmedArticle, IdType ) => _.get( _.find( _.get( PubmedArticle, ['PubmedData', 'ArticleIdList'], [] ), [ 'IdType', IdType ] ), 'id', null ); +const getRelations = PubmedArticle => { + const formatRefSource = refSource => _.trimEnd( refSource, ':;' );// ? _.first( refSource.split(';') ) : 'link'; + const commentsCorrections2Link = ({ RefSource, PMID, DOI }) => { + const hasPMID = !_.isNil( PMID ); + const hasDOI = !_.isNil( DOI ); + if( !hasPMID && !hasDOI ) return null; + const reference = formatRefSource( RefSource ); + const url = hasPMID ? `${PUBMED_LINK_BASE_URL}${PMID}` : `${DOI_LINK_BASE_URL}${DOI}`; + return ({ reference, url }); + }; + const raw = _.get( PubmedArticle, [ 'MedlineCitation', 'CommentsCorrectionsList' ], [] ); + const groups = _.groupBy( raw, 'RefType' ); + const relations = _.toPairs( groups ).map( ( [ RefType, CommentsCorrectionsList ] ) => { + const type = onlyCapitalizeFirst( fromCamelCase( RefType ) ); + const links = CommentsCorrectionsList.map( commentsCorrections2Link ); + return ({ type, links }); + }); + + return _.compact( relations ); +}; + /** * getPubmedCitation * @@ -238,8 +283,9 @@ const getPubmedCitation = PubmedArticle => { const doi = getArticleId( PubmedArticle, 'doi' ); const pubTypes = _.get( Article, 'PublicationTypeList' ); //required const { ISODate } = getPubDate( _.get( Article, ['Journal', 'JournalIssue'] ) ); + const relations = getRelations( PubmedArticle ); - return { title, authors, reference, abstract, pmid, doi, pubTypes, ISODate }; + return { title, authors, reference, abstract, pmid, doi, pubTypes, ISODate, relations }; }; /** @@ -278,6 +324,7 @@ const createPubmedArticle = ({ articleTitle = null, journalName = null, publicat PublicationTypeList: [] }, ChemicalList: [], + CommentsCorrectionsList: [], InvestigatorList: [], KeywordList: [], MeshheadingList: [] @@ -303,4 +350,4 @@ class ArticleIDError extends Error { } } -export { getPubmedCitation, createPubmedArticle, ArticleIDError, findOrcidIdentifier }; \ No newline at end of file +export { getPubmedCitation, createPubmedArticle, ArticleIDError, findOrcidIdentifier, COMMENTSCORRECTIONS_REFTYPE }; \ No newline at end of file diff --git a/src/util/strings.js b/src/util/strings.js index 4d879fed8..40fa7daec 100644 --- a/src/util/strings.js +++ b/src/util/strings.js @@ -30,4 +30,12 @@ const stripFinalPeriod = text => { return text; }; -export { stringDistanceMetric, longestCommonPrefixLength, truncateString, stripFinalPeriod }; +const fromCamelCase = str => { + return str.replace(/([a-z])([A-Z])/g, '$1 $2'); +}; + +const onlyCapitalizeFirst = str => { + return str.charAt(0).toUpperCase() + str.slice(1).toLowerCase(); +}; + +export { stringDistanceMetric, longestCommonPrefixLength, truncateString, stripFinalPeriod, fromCamelCase, onlyCapitalizeFirst }; diff --git a/test/crossRef/10.7554_elife.86689.3.json b/test/crossRef/10.7554_elife.86689.3.json new file mode 100644 index 000000000..2fcae4fa3 --- /dev/null +++ b/test/crossRef/10.7554_elife.86689.3.json @@ -0,0 +1,331 @@ +{ + "indexed": { + "date-parts": [ + [ + 2024, + 3, + 4 + ] + ], + "date-time": "2024-03-04T21:37:09Z", + "timestamp": 1709588229648 + }, + "posted": { + "date-parts": [ + [ + 2023, + 8, + 25 + ] + ] + }, + "group-title": "elife", + "reference-count": 0, + "publisher": "eLife Sciences Publications, Ltd", + "license": [ + { + "start": { + "date-parts": [ + [ + 2023, + 8, + 25 + ] + ], + "date-time": "2023-08-25T00:00:00Z", + "timestamp": 1692921600000 + }, + "content-version": "unspecified", + "delay-in-days": 0, + "URL": "http:\/\/creativecommons.org\/licenses\/by\/4.0\/" + } + ], + "content-domain": { + "domain": [], + "crossmark-restriction": false + }, + "short-container-title": [], + "abstract": "The primary cilium plays important roles in regulating cell differentiation, signal transduction, and tissue organization. Dysfunction of the primary cilium can lead to ciliopathies and cancer. The formation and organization of the primary cilium are highly associated with cell polarity proteins, such as the apical polarity protein CRB3. However, the molecular mechanisms by which CRB3 regulates ciliogenesis and the location of CRB3 remain unknown. Here, we show that CRB3, as a navigator, regulates vesicle trafficking in γ-TuRC assembly during ciliogenesis and cilium-related Hh and Wnt signaling pathways in tumorigenesis. Crb3 knockout mice display severe defects of the primary cilium in the mammary ductal lumen and renal tubule, while mammary epithelial-specific Crb3 knockout mice exhibit the promotion of ductal epithelial hyperplasia and tumorigenesis. CRB3 is essential for lumen formation and ciliary assembly in the mammary epithelium. We demonstrate that CRB3 localizes to the basal body and that CRB3 trafficking is mediated by Rab11-positive endosomes. Significantly, CRB3 interacts with Rab11 to navigate GCP6\/Rab11 trafficking vesicles to CEP290, resulting in intact γ-TuRC assembly. In addition, CRB3-depleted cells are unresponsive to the activation of the Hh signaling pathway, while CRB3 regulates the Wnt signaling pathway. Therefore, our studies reveal the molecular mechanisms by which CRB3 recognizes Rab11-positive endosomes to facilitate ciliogenesis, and regulates cilium-related signaling pathways in tumorigenesis.<\/jats:p>", + "DOI": "10.7554\/elife.86689.3", + "type": "posted-content", + "created": { + "date-parts": [ + [ + 2023, + 8, + 25 + ] + ], + "date-time": "2023-08-25T11:05:14Z", + "timestamp": 1692961514000 + }, + "source": "Crossref", + "is-referenced-by-count": 0, + "title": [ + "CRB3 navigates Rab11 trafficking vesicles to promote γTuRC assembly during ciliogenesis" + ], + "prefix": "10.7554", + "author": [ + { + "given": "Bo", + "family": "Wang", + "sequence": "first", + "affiliation": [ + { + "name": "Center for Translational Medicine, the First Affiliated Hospital of Xi’an Jiaotong University, Xi’an 710061, Shaanxi, P.R. China" + }, + { + "name": "Key Laboratory for Tumor Precision Medicine of Shaanxi Province, the First Affiliated Hospital of Xi’an Jiaotong University, Xi’an 710061, Shaanxi, P.R. China" + } + ] + }, + { + "given": "Zheyong", + "family": "Liang", + "sequence": "additional", + "affiliation": [ + { + "name": "Center for Translational Medicine, the First Affiliated Hospital of Xi’an Jiaotong University, Xi’an 710061, Shaanxi, P.R. China" + }, + { + "name": "Department of Cardiovascular Surgery, the First Affiliated Hospital of Xi’an Jiaotong University, Xi’an 710061, Shaanxi, P.R. China" + } + ] + }, + { + "given": "Tan", + "family": "tan", + "sequence": "additional", + "affiliation": [ + { + "name": "Center for Precision Medicine, Affiliated to The First People’s Hospital of Chenzhou, University of South China, Chenzhou 423000, Hunan, P.R. China" + } + ] + }, + { + "given": "Miao", + "family": "Zhang", + "sequence": "additional", + "affiliation": [ + { + "name": "Center for Translational Medicine, the First Affiliated Hospital of Xi’an Jiaotong University, Xi’an 710061, Shaanxi, P.R. China" + }, + { + "name": "Key Laboratory for Tumor Precision Medicine of Shaanxi Province, the First Affiliated Hospital of Xi’an Jiaotong University, Xi’an 710061, Shaanxi, P.R. China" + } + ] + }, + { + "given": "Yina", + "family": "Jiang", + "sequence": "additional", + "affiliation": [ + { + "name": "Department of Pathology, the First Affiliated Hospital of Xi’an Jiaotong University, Xi’an 710061, Shaanxi, P.R. China" + } + ] + }, + { + "given": "Yangyang", + "family": "Shang", + "sequence": "additional", + "affiliation": [ + { + "name": "Center for Translational Medicine, the First Affiliated Hospital of Xi’an Jiaotong University, Xi’an 710061, Shaanxi, P.R. China" + }, + { + "name": "Key Laboratory for Tumor Precision Medicine of Shaanxi Province, the First Affiliated Hospital of Xi’an Jiaotong University, Xi’an 710061, Shaanxi, P.R. China" + } + ] + }, + { + "given": "Xiaoqian", + "family": "Gao", + "sequence": "additional", + "affiliation": [ + { + "name": "Center for Translational Medicine, the First Affiliated Hospital of Xi’an Jiaotong University, Xi’an 710061, Shaanxi, P.R. China" + }, + { + "name": "Key Laboratory for Tumor Precision Medicine of Shaanxi Province, the First Affiliated Hospital of Xi’an Jiaotong University, Xi’an 710061, Shaanxi, P.R. China" + } + ] + }, + { + "given": "Shaoran", + "family": "Song", + "sequence": "additional", + "affiliation": [ + { + "name": "Center for Translational Medicine, the First Affiliated Hospital of Xi’an Jiaotong University, Xi’an 710061, Shaanxi, P.R. China" + }, + { + "name": "Key Laboratory for Tumor Precision Medicine of Shaanxi Province, the First Affiliated Hospital of Xi’an Jiaotong University, Xi’an 710061, Shaanxi, P.R. China" + } + ] + }, + { + "given": "Ruiqi", + "family": "Wang", + "sequence": "additional", + "affiliation": [ + { + "name": "Center for Translational Medicine, the First Affiliated Hospital of Xi’an Jiaotong University, Xi’an 710061, Shaanxi, P.R. China" + }, + { + "name": "Key Laboratory for Tumor Precision Medicine of Shaanxi Province, the First Affiliated Hospital of Xi’an Jiaotong University, Xi’an 710061, Shaanxi, P.R. China" + } + ] + }, + { + "given": "He", + "family": "Chen", + "sequence": "additional", + "affiliation": [ + { + "name": "Center for Translational Medicine, the First Affiliated Hospital of Xi’an Jiaotong University, Xi’an 710061, Shaanxi, P.R. China" + }, + { + "name": "Key Laboratory for Tumor Precision Medicine of Shaanxi Province, the First Affiliated Hospital of Xi’an Jiaotong University, Xi’an 710061, Shaanxi, P.R. China" + } + ] + }, + { + "given": "Jie", + "family": "Liu", + "sequence": "additional", + "affiliation": [ + { + "name": "Center for Translational Medicine, the First Affiliated Hospital of Xi’an Jiaotong University, Xi’an 710061, Shaanxi, P.R. China" + }, + { + "name": "Key Laboratory for Tumor Precision Medicine of Shaanxi Province, the First Affiliated Hospital of Xi’an Jiaotong University, Xi’an 710061, Shaanxi, P.R. China" + } + ] + }, + { + "given": "Juan", + "family": "Li", + "sequence": "additional", + "affiliation": [ + { + "name": "Center for Translational Medicine, the First Affiliated Hospital of Xi’an Jiaotong University, Xi’an 710061, Shaanxi, P.R. China" + }, + { + "name": "Key Laboratory for Tumor Precision Medicine of Shaanxi Province, the First Affiliated Hospital of Xi’an Jiaotong University, Xi’an 710061, Shaanxi, P.R. China" + } + ] + }, + { + "given": "Yu", + "family": "Ren", + "sequence": "additional", + "affiliation": [ + { + "name": "Department of Breast Surgery, the First Affiliated Hospital of Xi’an Jiaotong University, Xi’an 710061, Shaanxi, P.R. China" + } + ] + }, + { + "given": "Peijun", + "family": "Liu", + "sequence": "additional", + "affiliation": [ + { + "name": "Center for Translational Medicine, the First Affiliated Hospital of Xi’an Jiaotong University, Xi’an 710061, Shaanxi, P.R. China" + }, + { + "name": "Key Laboratory for Tumor Precision Medicine of Shaanxi Province, the First Affiliated Hospital of Xi’an Jiaotong University, Xi’an 710061, Shaanxi, P.R. China" + } + ] + } + ], + "member": "4374", + "container-title": [], + "original-title": [], + "deposited": { + "date-parts": [ + [ + 2023, + 8, + 25 + ] + ], + "date-time": "2023-08-25T11:05:14Z", + "timestamp": 1692961514000 + }, + "score": 1, + "resource": { + "primary": { + "URL": "https:\/\/elifesciences.org\/reviewed-preprints\/86689v3" + } + }, + "subtitle": [], + "short-title": [], + "issued": { + "date-parts": [ + [ + 2023, + 8, + 25 + ] + ] + }, + "references-count": 0, + "URL": "http:\/\/dx.doi.org\/10.7554\/elife.86689.3", + "relation": { + "has-version": [ + { + "id-type": "doi", + "id": "10.7554\/eLife.86689.2", + "asserted-by": "subject" + }, + { + "id-type": "doi", + "id": "10.7554\/eLife.86689.4", + "asserted-by": "object" + } + ], + "is-version-of": [ + { + "id-type": "doi", + "id": "10.1101\/2023.02.15.528649", + "asserted-by": "subject" + } + ], + "has-review": [ + { + "id-type": "doi", + "id": "10.7554\/eLife.86689.3.sa2", + "asserted-by": "object" + }, + { + "id-type": "doi", + "id": "10.7554\/eLife.86689.3.sa1", + "asserted-by": "object" + }, + { + "id-type": "doi", + "id": "10.7554\/eLife.86689.3.sa0", + "asserted-by": "object" + } + ], + "is-preprint-of": [ + { + "id-type": "doi", + "id": "10.7554\/eLife.86689.4", + "asserted-by": "object" + } + ] + }, + "published": { + "date-parts": [ + [ + 2023, + 8, + 25 + ] + ] + }, + "subtype": "preprint" +} \ No newline at end of file diff --git a/test/crossref/map.js b/test/crossref/map.js index 522ca73ef..39de9d509 100644 --- a/test/crossref/map.js +++ b/test/crossref/map.js @@ -9,6 +9,7 @@ import work_doi_4 from './10.1101_2022.09.28.22280453.json'; import work_doi_5 from './10.1016_j.molcel.2019.06.008.json'; import work_doi_6 from './10.7554_eLife.68292.json'; import work_doi_7 from './10.3030_101067344.json'; +import work_doi_8 from './10.7554_elife.86689.3.json'; describe('map', function(){ @@ -97,6 +98,32 @@ describe('map', function(){ }); // PublicationTypeList + describe('CommentsCorrectionsList', () => { + + describe('RefType: UpdateIn', () => { + const RefType = 'UpdateIn'; + const { MedlineCitation: { CommentsCorrectionsList } } = toPubMedArticle( work_doi_8 ); + + it('Should contain a CommentsCorrectionsList with an element', () => { + expect( CommentsCorrectionsList.length ).to.not.equal( 0 ); + }); + + it('Should have a CommentsCorrections with attributes: RefType, RefSource, DOI', () => { + const commentsCorrections = _.find(CommentsCorrectionsList, ['RefType', RefType ]); + expect( commentsCorrections ).to.have.property( 'DOI' ); + expect( commentsCorrections ).to.have.property( 'RefType' ); + expect( commentsCorrections ).to.have.property( 'RefSource' ); + }); + + it('Should have a CommentsCorrections with DOI-based values: RefSource, DOI', () => { + const commentsCorrections = _.find(CommentsCorrectionsList, ['RefType', RefType ]); + expect( commentsCorrections.DOI ).to.match(/^10\.\d{4,9}\/[-._;()/:A-Z0-9]+$/i); + expect( commentsCorrections.RefSource ).to.match(/^doi: 10\.\d{4,9}\/[-._;()/:A-Z0-9]+$/i); + }); + }); + + }); // CommentsCorrectionsList + }); // Article }); // type: posted-content, subtype: preprint @@ -170,7 +197,7 @@ describe('map', function(){ describe('article 2', () => { describe('MedlineCitation > Article', () => { - const { MedlineCitation: { Article } } = toPubMedArticle( work_doi_6 ); + const { MedlineCitation: { Article, CommentsCorrectionsList } } = toPubMedArticle( work_doi_6 ); describe('Text fields (ArticleTitle, Abstract)', () => { it('Should correctly map Abstract and ArticleTitle', () => { @@ -232,6 +259,31 @@ describe('map', function(){ }); // PublicationTypeList + describe('CommentsCorrectionsList', () => { + + describe('RefType: UpdateOf', () => { + const RefType = 'UpdateOf'; + + it('Should contain a CommentsCorrectionsList with an element', () => { + expect( CommentsCorrectionsList.length ).to.not.equal( 0 ); + }); + + it('Should have a CommentsCorrections with attributes: RefType, RefSource, DOI', () => { + const commentsCorrections = _.find(CommentsCorrectionsList, ['RefType', RefType ]); + expect( commentsCorrections ).to.have.property( 'DOI' ); + expect( commentsCorrections ).to.have.property( 'RefType' ); + expect( commentsCorrections ).to.have.property( 'RefSource' ); + }); + + it('Should have a CommentsCorrections with DOI-based values: RefSource, DOI', () => { + const commentsCorrections = _.find(CommentsCorrectionsList, ['RefType', RefType ]); + expect( commentsCorrections.DOI ).to.match(/^10\.\d{4,9}\/[-._;()/:A-Z0-9]+$/i); + expect( commentsCorrections.RefSource ).to.match(/^doi: 10\.\d{4,9}\/[-._;()/:A-Z0-9]+$/i); + }); + }); + + }); // CommentsCorrectionsList + }); // article 2 diff --git a/test/pubmed/fetchPubmed.js b/test/pubmed/fetchPubmed.js index 23959460a..f21fd422f 100644 --- a/test/pubmed/fetchPubmed.js +++ b/test/pubmed/fetchPubmed.js @@ -5,6 +5,7 @@ import { expect } from 'chai'; import convert from 'xml-js'; import { pubmedDataConverter } from '../../src/server/routes/api/document/pubmed/fetchPubmed'; +import { isDigits, isDoi } from '../../src/util'; const TEST_PUBMED_DATA = new Map([ ['151222', 'pmid_151222.xml'], // MedlineDate @@ -12,7 +13,9 @@ const TEST_PUBMED_DATA = new Map([ ['29440426', 'pmid_29440426.xml'], // PubMedData ['30078747', 'pmid_30078747.xml'], // InvestigatorList ['30115697', 'pmid_30115697.xml'], // Markup; Identifier - ['31511694', 'pmid_31511694.xml'] + ['31511694', 'pmid_31511694.xml'], + ['9500320', 'pmid_9500320.xml'], //CommentsCorrections - RetractionIn etc + ['38289659', 'pmid_38289659.xml'] //CommentsCorrections RefSource: doi string ]); const xml2jsOpts = {}; @@ -215,8 +218,9 @@ describe('fetchPubmed', function(){ it('Should have item with top-level attributes', () => { if( !_.isEmpty( Identifier ) ){ - expect( Identifier ).to.have.property( 'Identifier[0].Source' ); - expect( Identifier ).to.have.property( 'Identifier[0].id' ); + let first = _.first( Identifier ); + expect( first ).to.have.property( 'Source' ); + expect( first ).to.have.property( 'id' ); } }); @@ -277,6 +281,46 @@ describe('fetchPubmed', function(){ });//ChemicalList + describe( 'CommentsCorrectionsList', () => { + + let CommentsCorrectionsList; + before( () => { + CommentsCorrectionsList = _.get( MedlineCitation, 'CommentsCorrectionsList' ); + }); + + it('Should be a list, when exists', () => { + if( CommentsCorrectionsList ){ // Optional + expect( CommentsCorrectionsList ).to.be.an.instanceof(Array); + } + }); + + it('Should have required attributes, when exists', () => { + if( CommentsCorrectionsList ){ // Optional + for (const CommentsCorrections of CommentsCorrectionsList) { + expect( CommentsCorrections ).to.have.property( 'RefSource' ); + expect( CommentsCorrections ).to.have.property( 'PMID' ); + expect( CommentsCorrections ).to.have.property( 'DOI' ); + expect( CommentsCorrections ).to.have.property( 'RefType' ); + } + } + }); + + it('Should have correctly formatted PMID and DOI, when not null', () => { + if( CommentsCorrectionsList ){ // Optional + for (const CommentsCorrections of CommentsCorrectionsList) { + if( CommentsCorrections.PMID !== null ){ + expect( isDigits( CommentsCorrections.PMID ) ).to.be.true; + } + if( CommentsCorrections.DOI !== null ){ + expect( isDoi( CommentsCorrections.DOI ) ).to.be.true; + } + } + } + }); + + });//CommentsCorrectionsList + + describe( 'KeywordList', () => { let KeywordList; diff --git a/test/pubmed/pmid_38289659.xml b/test/pubmed/pmid_38289659.xml new file mode 100644 index 000000000..571c61026 --- /dev/null +++ b/test/pubmed/pmid_38289659.xml @@ -0,0 +1,1175 @@ + + + + + + 38289659 + + 2024 + 01 + 31 + + + 2024 + 03 + 20 + +
+ + 2050-084X + + 12 + + 2024 + Jan + 30 + + + eLife + Elife + + Orai-mediated calcium entry determines activity of central dopaminergic neurons by regulation of gene expression. + RP88808 + 10.7554/eLife.88808 + + Maturation and fine-tuning of neural circuits frequently require neuromodulatory signals that set the excitability threshold, neuronal connectivity, and synaptic strength. Here, we present a mechanistic study of how neuromodulator-stimulated intracellular Ca + 2+ signals, through the store-operated Ca + 2+ channel Orai, regulate intrinsic neuronal properties by control of developmental gene expression in flight-promoting central dopaminergic neurons (fpDANs). The fpDANs receive cholinergic inputs for release of dopamine at a central brain tripartite synapse that sustains flight (Sharma and Hasan, 2020). Cholinergic inputs act on the muscarinic acetylcholine receptor to stimulate intracellular Ca + 2+ release through the endoplasmic reticulum (ER) localised inositol 1,4,5-trisphosphate receptor followed by ER-store depletion and Orai-mediated store-operated Ca + 2+ entry (SOCE). Analysis of gene expression in fpDANs followed by genetic, cellular, and molecular studies identified Orai-mediated Ca + 2+ entry as a key regulator of excitability in fpDANs during circuit maturation. SOCE activates the transcription factor trithorax-like (Trl), which in turn drives expression of a set of genes, including + Set2, that encodes a histone 3 lysine 36 methyltransferase (H3K36me3). Set2 function establishes a positive feedback loop, essential for receiving neuromodulatory cholinergic inputs and sustaining SOCE. Chromatin-modifying activity of Set2 changes the epigenetic status of fpDANs and drives expression of key ion channel and signalling genes that determine fpDAN activity. Loss of activity reduces the axonal arborisation of fpDANs within the MB lobe and prevents dopamine release required for the maintenance of long flight. + + © 2023, Mitra et al. + + + + Mitra + Rishav + R + 0000-0001-6840-6160 + + National Centre for Biological Sciences, Tata Institute of Fundamental Research, Bangalore, India. + + + + Richhariya + Shlesha + S + + National Centre for Biological Sciences, Tata Institute of Fundamental Research, Bangalore, India. + + + Department of Biology, Brandeis University, Waltham, United States. + + + + Hasan + Gaiti + G + 0000-0001-7194-383X + + National Centre for Biological Sciences, Tata Institute of Fundamental Research, Bangalore, India. + + + + eng + + + GEO + + GSE230134 + GSE47280 + GSE47319 + + + + + + BT/PR28450/MED/122/2018 + Department of Biotechnology, Ministry of Science and Technology, India + + + + + Journal Article + + + 2024 + 01 + 30 + +
+ + England + Elife + 101579614 + 2050-084X + + + + SY7Q814VUP + Calcium + + + VTD58H1Z2X + Dopamine + + + 0 + Calcium, Dietary + + + EC 2.1.1.43 + Histone-Lysine N-Methyltransferase + + + 0 + Cholinergic Agents + + + IM + + + doi: 10.1101/2023.05.24.542083 + + + doi: 10.7554/eLife.88808.1 + + + doi: 10.7554/eLife.88808.2 + + + doi: 10.7554/eLife.88808.3 + + + + + Calcium + + + Dopaminergic Neurons + + + Dopamine + + + Calcium, Dietary + + + Histone-Lysine N-Methyltransferase + + + Cholinergic Agents + + + + D. melanogaster + Drosophila flight + PPL1 DANs + SOCE + genetics + genomics + histone modifications + neuromodulation + neuroscience + trithorax-like/GAF + + RM, SR, GH No competing interests declared + + + + + 2024 + 1 + 31 + 6 + 43 + + + 2024 + 1 + 30 + 12 + 44 + + + 2024 + 1 + 30 + 11 + 54 + + + 2024 + 1 + 30 + + + epublish + + 38289659 + PMC10945566 + 10.7554/eLife.88808 + 88808 + + + + Agrawal N, Venkiteswaran G, Sadaf S, Padmanabhan N, Banerjee S, Hasan G. 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+ + 0140-6736 + + 351 + 9103 + + 1998 + Feb + 28 + + + Lancet (London, England) + Lancet + + Ileal-lymphoid-nodular hyperplasia, non-specific colitis, and pervasive developmental disorder in children. + + 637 + 641 + 637-41 + + + We investigated a consecutive series of children with chronic enterocolitis and regressive developmental disorder. + 12 children (mean age 6 years [range 3-10], 11 boys) were referred to a paediatric gastroenterology unit with a history of normal development followed by loss of acquired skills, including language, together with diarrhoea and abdominal pain. Children underwent gastroenterological, neurological, and developmental assessment and review of developmental records. Ileocolonoscopy and biopsy sampling, magnetic-resonance imaging (MRI), electroencephalography (EEG), and lumbar puncture were done under sedation. Barium follow-through radiography was done where possible. Biochemical, haematological, and immunological profiles were examined. + Onset of behavioural symptoms was associated, by the parents, with measles, mumps, and rubella vaccination in eight of the 12 children, with measles infection in one child, and otitis media in another. All 12 children had intestinal abnormalities, ranging from lymphoid nodular hyperplasia to aphthoid ulceration. Histology showed patchy chronic inflammation in the colon in 11 children and reactive ileal lymphoid hyperplasia in seven, but no granulomas. Behavioural disorders included autism (nine), disintegrative psychosis (one), and possible postviral or vaccinal encephalitis (two). There were no focal neurological abnormalities and MRI and EEG tests were normal. Abnormal laboratory results were significantly raised urinary methylmalonic acid compared with age-matched controls (p=0.003), low haemoglobin in four children, and a low serum IgA in four children. + We identified associated gastrointestinal disease and developmental regression in a group of previously normal children, which was generally associated in time with possible environmental triggers. + + + + Wakefield + A J + AJ + + Inflammatory Bowel Disease Study Group, University Department of Medicine, Royal Free Hospital and School of Medicine, London, UK. + + + + Murch + S H + SH + + + Anthony + A + A + + + Linnell + J + J + + + Casson + D M + DM + + + Malik + M + M + + + Berelowitz + M + M + + + Dhillon + A P + AP + + + Thomson + M A + MA + + + Harvey + P + P + + + Valentine + A + A + + + Davies + S E + SE + + + Walker-Smith + J A + JA + + + eng + + Journal Article + Research Support, Non-U.S. Gov't + Retracted Publication + +
+ + England + Lancet + 2985213R + 0140-6736 + + + + 0 + Measles Vaccine + + + 0 + Measles-Mumps-Rubella Vaccine + + + 0 + Mumps Vaccine + + + 0 + Rubella Vaccine + + + 0 + Vaccines, Combined + + + IM + + + Lancet. 1998 Feb 28;351(9103):611-2 + 9500313 + + + Lancet. 1998 Mar 21;351(9106):905; author reply 908-9 + 9525390 + + + Lancet. 1998 Mar 21;351(9106):905-6; author reply 908-9 + 9525391 + + + Lancet. 1998 Mar 21;351(9106):906; author reply 908-9 + 9525392 + + + Lancet. 1998 Mar 21;351(9106):906-7; author reply 908-9 + 9525393 + + + Lancet. 1998 Mar 21;351(9106):907; author reply 908-9 + 9525394 + + + Lancet. 1998 Mar 21;351(9106):907; author reply 908-9 + 9525395 + + + Lancet. 1998 Mar 21;351(9106):907-8; author reply 908-9 + 9525396 + + + Lancet. 1998 May 2;351(9112):1355; author reply 1356 + 9643815 + + + Lancet. 1998 May 2;351(9112):1355; author reply 1356 + 9643816 + + + Lancet. 1998 May 2;351(9112):1355-6; author reply 1356 + 9643817 + + + Lancet. 1998 May 2;351(9112):1356 + 9643818 + + + Lancet. 1998 May 2;351(9112):1357 + 9643820 + + + Lancet. 1998 May 2;351(9112):1357 + 9643821 + + + Lancet. 1998 May 2;351(9112):1357-8 + 9643822 + + + Lancet. 1998 May 2;351(9112):1358 + 9643823 + + + Lancet. 1998 Jul 18;352(9123):234-5 + 9683237 + + + Lancet. 2000 Jul 8;356(9224):160-1 + 10963264 + + + Lancet. 2000 Jul 8;356(9224):161 + 10963266 + + + Lancet. 2000 Jul 8;356(9224):161-2 + 10963267 + + + Lancet. 2002 Jun 15;359(9323):2051-2 + 12086756 + + + Lancet. 2004 Mar 6;363(9411):747-9 + 15016482 + + + Lancet. 2004 Mar 6;363(9411):750 + 15016483 + + + Lancet. 2004 Mar 6;363(9411):820-1 + 15022645 + + + Lancet. 2004 Mar 6;363(9411):821-2 + 15022648 + + + Lancet. 2004 Mar 6;363(9411):822-3 + 15022649 + + + Lancet. 2004 Mar 6;363(9411):823-4 + 15022650 + + + Lancet. 2010 Feb 6;375(9713):445 + 20137807 + + + Eur J Gastroenterol Hepatol. 2011 Nov;23 (11):1082 + 21971344 + + + + + Child + + + Child, Preschool + + + Developmental Disabilities + etiology + + + Enterocolitis + etiology + + + Female + + + Humans + + + Hyperplasia + pathology + + + Ileum + pathology + + + Lymphoid Tissue + pathology + + + Male + + + Measles + complications + + + Measles Vaccine + adverse effects + + + Measles-Mumps-Rubella Vaccine + + + Mumps Vaccine + adverse effects + + + Otitis Media + complications + + + Rubella Vaccine + adverse effects + + + Vaccines, Combined + adverse effects + + + + + + + 1998 + 3 + 21 + + + 1998 + 3 + 21 + 0 + 1 + + + 1998 + 3 + 21 + 0 + 0 + + + ppublish + + 9500320 + 10.1016/s0140-6736(97)11096-0 + S0140673697110960 + + + + \ No newline at end of file diff --git a/test/pubmed/searchPubmed.js b/test/pubmed/searchPubmed.js index 35528c83d..fbd52ac63 100644 --- a/test/pubmed/searchPubmed.js +++ b/test/pubmed/searchPubmed.js @@ -1,7 +1,7 @@ import _ from 'lodash'; import { expect } from 'chai'; -import { searchPubmed, pubmedDataConverter } from '../../src/server/routes/api/document/pubmed/searchPubmed'; +import { pubmedDataConverter } from '../../src/server/routes/api/document/pubmed/searchPubmed'; import searchPubmedData from './searchPubmedData'; const TEST_PUBMED_DATA = new Map( _.entries( searchPubmedData ) ); @@ -15,15 +15,15 @@ const DEFAULT_ESEARCH_PARAMS = { }; describe('searchPubmed', function(){ - + describe('pubmedDataConverter', function(){ - + describe( 'undefined term', () => { - let pubmedInfo; + let pubmedInfo; const queryType = 'undefined_term'; const json = TEST_PUBMED_DATA.get( queryType ); - + before( async () => { pubmedInfo = await pubmedDataConverter( json ); }); @@ -31,7 +31,7 @@ describe('searchPubmed', function(){ it('Should return a result', () => { expect( pubmedInfo ).to.exist; }); - + it('Should contain top-level attributes', () => { expect( pubmedInfo ).to.have.property( 'count' ); expect( pubmedInfo ).to.have.property( 'searchHits' ); @@ -45,15 +45,15 @@ describe('searchPubmed', function(){ expect( pubmedInfo.query_key ).to.be.a('null'); expect( pubmedInfo.webenv ).to.be.a('null'); }); - + }); // empty term describe( 'empty term', () => { - let pubmedInfo; + let pubmedInfo; const queryType = 'empty_term'; const json = TEST_PUBMED_DATA.get( queryType ); - + before( async () => { pubmedInfo = await pubmedDataConverter( json ); }); @@ -61,7 +61,7 @@ describe('searchPubmed', function(){ it('Should return a result', () => { expect( pubmedInfo ).to.exist; }); - + it('Should contain top-level attributes', () => { expect( pubmedInfo ).to.have.property( 'count' ); expect( pubmedInfo ).to.have.property( 'searchHits' ); @@ -75,15 +75,15 @@ describe('searchPubmed', function(){ expect( pubmedInfo.query_key ).to.not.be.a('null'); expect( pubmedInfo.webenv ).to.not.be.a('null'); }); - + }); // empty term describe( 'unique term', () => { - let pubmedInfo; + let pubmedInfo; const queryType = 'unique_term'; const json = TEST_PUBMED_DATA.get( queryType ); - + before( async () => { pubmedInfo = await pubmedDataConverter( json ); }); @@ -91,7 +91,7 @@ describe('searchPubmed', function(){ it('Should return a result', () => { expect( pubmedInfo ).to.exist; }); - + it('Should contain top-level attributes', () => { expect( pubmedInfo ).to.have.property( 'count' ); expect( pubmedInfo ).to.have.property( 'searchHits' ); @@ -105,16 +105,16 @@ describe('searchPubmed', function(){ expect( pubmedInfo.query_key ).to.not.be.a('null'); expect( pubmedInfo.webenv ).to.not.be.a('null'); }); - + }); // unique term describe( 'nonunique term', () => { - let pubmedInfo; + let pubmedInfo; const queryType = 'nonunique_term'; const json = TEST_PUBMED_DATA.get( queryType ); - + before( async () => { pubmedInfo = await pubmedDataConverter( json ); }); @@ -122,7 +122,7 @@ describe('searchPubmed', function(){ it('Should return a result', () => { expect( pubmedInfo ).to.exist; }); - + it('Should contain top-level attributes', () => { expect( pubmedInfo ).to.have.property( 'count' ); expect( pubmedInfo ).to.have.property( 'searchHits' ); @@ -136,7 +136,7 @@ describe('searchPubmed', function(){ expect( pubmedInfo.query_key ).to.not.be.a('null'); expect( pubmedInfo.webenv ).to.not.be.a('null'); }); - + }); // nonunique term }); // pubmedDataConverter