diff --git a/src/codecs/crossref/__file_snapshots__/article-elife-50356.xml b/src/codecs/crossref/__file_snapshots__/article-elife-50356.xml index 0be45b50d..e9cae7e0b 100644 --- a/src/codecs/crossref/__file_snapshots__/article-elife-50356.xml +++ b/src/codecs/crossref/__file_snapshots__/article-elife-50356.xml @@ -50,6 +50,421 @@ 10.5555/12345 https://example.org + + + European Journal of Internal Medicine + Abuhasira + 49 + 2018 + Medical use of Cannabis and cannabinoids containing products - Regulations in Europe and north america + + + American Journal of Physiology-Endocrinology and Metabolism + Adashi + 244 + 1983 + Direct antigonadal activity of cannabinoids: suppression of rat granulosa cell functions + + + BMC Complementary and Alternative Medicine + Armour + 19 + 2019 + Self-management strategies amongst Australian women with endometriosis: a national online survey + + + PNAS + Arosh + 112 + 2015 + Molecular and preclinical basis to inhibit PGE2 receptors EP2 and EP4 as a novel nonsteroidal therapy for endometriosis + + + PNAS + Berkley + 101 + 2004 + Innervation of ectopic endometrium in a rat model of endometriosis + + + Nature Medicine + Bilkei-Gorzo + 23 + 2017 + A chronic low dose of Δ9-tetrahydrocannabinol (THC) restores cognitive function in old mice + + + Pain + Bushnell + 156 + 2015 + Effect of environment on the long-term consequences of chronic pain + + + Biological Psychiatry + Busquets-Garcia + 70 + 2011 + Differential role of anandamide and 2-arachidonoylglycerol in memory and anxiety-like responses + + + Neuropsychopharmacology + Busquets-Garcia + 43 + 2018 + Hippocampal protein kinase C signaling mediates the Short-Term memory impairment induced by Delta9-Tetrahydrocannabinol + + + PLOS ONE + Byers + 7 + 2012 + Mouse estrous cycle identification tool and images + + + BMJ + Campbell + 323 + 2001 + Are cannabinoids an effective and safe treatment option in the management of pain? A qualitative systematic review + + + Neuropharmacology + Célérier + 50 + 2006 + Influence of the anabolic-androgenic steroid nandrolone on cannabinoid dependence + + + Nature Medicine + Corder + 23 + 2017 + Loss of μ opioid receptor signaling in nociceptors, but not microglia, abrogates morphine tolerance without disrupting analgesia + + + Science + Corder + 363 + 2019 + An amygdalar neural ensemble that encodes the unpleasantness of pain + + + Nature Reviews Neuroscience + Curran + 17 + 2016 + Keep off the grass? Cannabis, cognition and addiction + + + Journal of Clinical Investigation + Cutando + 123 + 2013 + Microglial activation underlies cerebellar deficits produced by repeated Cannabis exposure + + + European Journal of Pharmacology + De + 491 + 2004 + Pharmacological characterization of the chronic constriction injury model of neuropathic pain + + + PLOS ONE + El-Talatini + 4 + 2009 + Localisation and function of the endocannabinoid system in the human ovary + + + Metabolic Brain Disease + Filho + 34 + 2019 + Peritoneal endometriosis induces time-related depressive- and anxiety-like alterations in female rats: involvement of hippocampal pro-oxidative and BDNF alterations + + + Biological Psychiatry + Flores + 75 + 2014 + The hypocretin/orexin receptor-1 as a novel target to modulate cannabinoid reward + + + Journal of Experimental Zoology + Forsberg + 175 + 1970 + An estradiol mitotic rate inhibiting effect in the müllerian epithelium in neonatal mice + + + Fertility and Sterility + Fourquet + 96 + 2011 + Quantification of the impact of endometriosis symptoms on health-related quality of life and work productivity + + + Current Opinion in Obstetrics and Gynecology + Garry + 16 + 2004 + The effectiveness of laparoscopic excision of endometriosis + + + Scientific Reports + Greaves + 7 + 2017 + EP2 receptor antagonism reduces peripheral and central hyperalgesia in a preclinical mouse model of endometriosis + + + Psychopharmacology + Greene + 235 + 2018 + Cannabidiol modulation of antinociceptive tolerance to Δ9-tetrahydrocannabinol + + + British Journal of Pharmacology + Gunasekaran + 158 + 2009 + Reintoxication: the release of fat-stored Delta(9)-tetrahydrocannabinol (THC) into blood is enhanced by food deprivation or ACTH exposure + + + European Journal of Obstetrics & Gynecology and Reproductive Biology + Hansen + 169 + 2013 + The influence of endometriosis-related symptoms on work life and work ability: a study of danish endometriosis patients in employment + + + Planta Medica + Harris + 82 + 2016 + Effects of Delta-9-Tetrahydrocannabinol and cannabidiol on Cisplatin-Induced neuropathy in mice + + + Pharmacology Biochemistry and Behavior + Kasten + 163 + 2017 + Acute and long-term effects of Δ9-tetrahydrocannabinol on object recognition and anxiety-like activity are age- and strain-dependent in mice + + + British Journal of Pharmacology + King + 174 + 2017 + Single and combined effects of Δ9 -tetrahydrocannabinol and cannabidiol in a mouse model of chemotherapy-induced neuropathic pain + + + Learning & Memory + Kubilius + 25 + 2018 + Highway to hell or magic smoke? The dose-dependence of Δ9-THC in place conditioning paradigms + + + Pain + La + 156 + 2015 + Role of the endocannabinoid system in the emotional manifestations of osteoarthritis pain + + + NeuroReport + LaFleur + 29 + 2018 + Sex differences in antinociceptive response to Δ-9-tetrahydrocannabinol and CP 55,940 in the mouse Formalin test + + + The American Journal of Pathology + Leconte + 177 + 2010 + Antiproliferative effects of cannabinoid agonists on deep infiltrating endometriosis + + + Biology of Reproduction + Li + 99 + 2018 + Endometriosis alters brain electrophysiology, gene expression and increases pain sensitization, anxiety, and depression in female mice + + + British Journal of Pharmacology + Lopez-Rodriguez + 171 + 2014 + Sex-dependent long-term effects of adolescent exposure to THC and/or MDMA on neuroinflammation and serotoninergic and cannabinoid systems in rats + + + European Journal of Internal Medicine + MacCallum + 49 + 2018 + Practical considerations in medical Cannabis administration and dosing + + + Human Reproduction + Márki + 32 + 2017 + Physical pain and emotion regulation as the main predictive factors of health-related quality of life in women living with endometriosis + + + Women's Health + Miller + 11 + 2015 + The importance of pelvic nerve fibers in endometriosis + + + Neuropsychopharmacology + Morrison + 36 + 2011 + Disruption of frontal θ coherence by Δ9-tetrahydrocannabinol is associated with positive psychotic symptoms + + + Reproduction + Myers + 127 + 2004 + Methods for quantifying follicular numbers within the mouse ovary + + + Reproduction + Numazawa + 64 + 1982 + Morphometric studies on ovarian follicles and corpora lutea during the oestrous cycle in the mouse + + + Nature Neuroscience + Puighermanal + 12 + 2009 + Cannabinoid modulation of hippocampal long-term memory is mediated by mTOR signaling + + + Neuropsychopharmacology + Puighermanal + 38 + 2013 + Dissociation of the pharmacological effects of THC by mTOR blockade + + + Nature Reviews Endocrinology + Ross + 13 + 2017 + The emotional cost of contraception + + + Neurobiology of Aging + Sarne + 61 + 2018 + Reversal of age-related cognitive impairments in mice by an extremely low dose of tetrahydrocannabinol + + + JAMA Psychiatry + Skovlund + 73 + 2016 + Association of hormonal contraception with depression + + + Human Reproduction + Somigliana + 14 + 1999 + Endometrial ability to implant in ectopic sites can be prevented by interleukin-12 in a murine model of endometriosis + + + BMJ Open + Sperschneider + 9 + 2019 + Does endometriosis affect professional life? A matched case-control study in Switzerland, Germany and Austria + + + Pain + Stockings + 159 + 2018 + Cannabis and cannabinoids for the treatment of people with chronic noncancer pain conditions: a systematic review and meta-analysis of controlled and observational studies + + + Human Reproduction + Tokushige + 21 + 2006 + High density of small nerve fibres in the functional layer of the endometrium in women with endometriosis + + + Journal of Pain Research + Ueberall + 12 + 2019 + Effectiveness and tolerability of THC:cbd oromucosal spray as add-on measure in patients with severe chronic pain: analysis of 12-week open-label real-world data provided by the german pain e-Registry]]> + + + PLOS Biology + Viñals + 40 + 2015 + Cognitive impairment induced by Delta9- tetrahydrocannabinol occurs through heteromers between cannabinoid CB 1 and serotonin 5-HT 2A receptors 1 + + + Drug and Alcohol Dependence + Wakley + 143 + 2014 + Sex differences in antinociceptive tolerance to delta-9-tetrahydrocannabinol in the rat + + + Journal of Ovarian Research + Walker + 12 + 2019 + The role of the endocannabinoid system in female reproductive tissues + + + Human Reproduction + Wang + 24 + 2009 + Rich innervation of deep infiltrating endometriosis + + + European Journal of Pharmacology + Williams + 584 + 2008 + Decreased basal endogenous opioid levels in diabetic rodents: effects on morphine and delta-9-tetrahydrocannabinoid-induced antinociception + + + Pain + You + 159 + 2018 + Cognitive impairment in a rat model of neuropathic pain: role of hippocampal microtubule stability + + + Medical Radiology + Zondervan + 4 + 2019 + Endometriosis + + \ No newline at end of file diff --git a/src/codecs/crossref/__file_snapshots__/article-plosone-0229075.xml b/src/codecs/crossref/__file_snapshots__/article-plosone-0229075.xml new file mode 100644 index 000000000..5440a47f1 --- /dev/null +++ b/src/codecs/crossref/__file_snapshots__/article-plosone-0229075.xml @@ -0,0 +1,355 @@ + + + + 0000000000000000000000000000000000000000000000000000000000000000 + 1605068020541 + + Stencila + doi@stenci.la + + Stencila + + + + Article + + + Lucía + Trilla-Fuertes + + + Natalia + Miranda + + + Daniel + Castellano + + + Rocío + López-Vacas + + + Carlos A. + Farfán Tello + + + Guillermo + de Velasco + + + Felipe + Villacampa + + + Elena + López-Camacho + + + Guillermo + Prado-Vázquez + + + Andrea + Zapater-Moros + + + Enrique + Espinosa + + + Juan Ángel + Fresno Vara + + + Álvaro + Pinto + + + Angelo + Gámez-Pozo + + + + miRNA profiling in renal carcinoma suggest the existence of a group of pro-angionenic tumors in localized clear cell renal carcinoma + + + 02 + 28 + 2020 + + + 01 + 28 + 2020 + + +

Renal cell carcinoma comprises a variety of entities, the most common being the clear-cell, papillary and chromophobe subtypes. These subtypes are related to different clinical evolution; however, most therapies have been developed for clear-cell carcinoma and there is not a specific treatment based on different subtypes. In this study, one hundred and sixty-four paraffin samples from primary nephrectomies for localized tumors were analyzed. MiRNAs were isolated and measured by microRNA arrays. Significance Analysis of Microarrays and Consensus Cluster algorithm were used to characterize different renal subtypes. The analyses showed that chromophobe renal tumors are a homogeneous group characterized by an overexpression of miR 1229, miR 10a, miR 182, miR 1208, miR 222, miR 221, miR 891b, miR 629-5p and miR 221-5p. On the other hand, clear cell renal carcinomas presented two different groups inside this histological subtype, with differences in miRNAs that regulate focal adhesion, transcription, apoptosis and angiogenesis processes. Specifically, one of the defined groups had an overexpression of proangiogenic microRNAs miR185, miR126 and miR130a. In conclusion, differences in miRNA expression profiles between histological renal subtypes were established. In addition, clear cell renal carcinomas had different expression of proangiogenic miRNAs. With the emergence of antiangiogenic drugs, these differences could be used as therapeutic targets in the future or as a selection method for tailoring personalized treatments.

+ + + 10.5555/12345 + https://example.org + + + + CA Cancer J Clin + Siegel + 69 + 1 + 2019 + Cancer statistics, 2019 + + + Urol Clin North Am + Janzen + 30 + 4 + 2003 + Surveillance after radical or partial nephrectomy for localized renal cell carcinoma and management of recurrent disease + + + Semin Oncol + Janowitz + 40 + 4 + 2013 + Adjuvant therapy in renal cell carcinoma-past, present, and future + + + Ann Oncol + Staehler + 29 + 10 + 2018 + Adjuvant sunitinib in patients with high-risk renal cell carcinoma: safety, therapy management, and patient-reported outcomes in the S-TRAC trial + + + Kidney Cancer + Lawrence + 2 + 2 + 2018 + What Survival Benefits are Needed to Make Adjuvant Sorafenib Worthwhile After Resection of Intermediate- or High-Risk Renal Cell Carcinoma? Clinical Investigators' Preferences in the SORCE Trial + + + J Clin Oncol + Motzer + 35 + 35 + 2017 + Randomized Phase III Trial of Adjuvant Pazopanib Versus Placebo After Nephrectomy in Patients With Localized or Locally Advanced Renal Cell Carcinoma + + + Ann Oncol + Gross-Goupil + 29 + 12 + 2018 + Axitinib versus placebo as an adjuvant treatment of renal cell carcinoma: results from the phase III, randomized ATLAS trial + + + Eur Urol + Moch + 70 + 1 + 2016 + The 2016 WHO Classification of Tumours of the Urinary System and Male Genital Organs-Part A: Renal, Penile, and Testicular Tumours + + + Cell Rep + Ricketts + 23 + 1 + 2018 + The Cancer Genome Atlas Comprehensive Molecular Characterization of Renal Cell Carcinoma + + + N Engl J Med + Linehan + 374 + 2 + 2016 + Comprehensive Molecular Characterization of Papillary Renal-Cell Carcinoma + + + J Hematol Oncol + Wang + 7 + 2014 + Circulating miRNAs in cancer: from detection to therapy + + + PLoS One + Kakimoto + 11 + 9 + 2016 + MicroRNA Stability in FFPE Tissue Samples: Dependence on GC Content + + + Clin Epigenetics + Si + 11 + 1 + 2019 + The role and mechanisms of action of microRNAs in cancer drug resistance + + + Annu Rev Pathol + Lee + 4 + 2009 + MicroRNAs in cancer + + + Cancer Res + Gámez-Pozo + 2015 + Combined label-free quantitative proteomics and microRNA expression analysis of breast cancer unravel molecular differences with clinical implications + + + Neoplasia + Gámez-Pozo + 14 + 12 + 2012 + MicroRNA expression profiling of peripheral blood samples predicts resistance to first-line sunitinib in advanced renal cell carcinoma patients + + + BMC Res Notes + López-Romero + 3 + 2010 + Processing of Agilent microRNA array data + + + Biostatistics + Johnson + 8 + 1 + 2007 + Adjusting batch effects in microarray expression data using empirical Bayes methods + + + Machine learning + Monti + 52 + 1 + 2003 + Consensus Clustering: A Resampling-Based Method for Class Discovery and Visualization of Gene Expression Microarray Data + + + Biotechniques + Saeed + 34 + 2 + 2003 + TM4: a free, open-source system for microarray data management and analysis + + + Proc Natl Acad Sci U S A + Tusher + 98 + 9 + 2001 + Significance analysis of microarrays applied to the ionizing radiation response + + + J Biomed Inform + Dweep + 44 + 5 + 2011 + miRWalk—database: prediction of possible miRNA binding sites by "walking" the genes of three genomes + + + BMC Bioinformatics + Chen + 14 + 2013 + Enrichr: interactive and collaborative HTML5 gene list enrichment analysis tool + + + Br J Cancer + Silva-Santos + 109 + 10 + 2013 + MicroRNA profile: a promising ancillary tool for accurate renal cell tumour diagnosis + + + Eur Urol + Youssef + 59 + 5 + 2011 + Accurate molecular classification of kidney cancer subtypes using microRNA signature + + + Diagn Mol Pathol + Powers + 20 + 2 + 2011 + Molecular classification of adult renal epithelial neoplasms using microRNA expression and virtual karyotyping + + + Urol Oncol + Ma + 33 + 4 + 2015 + MicroRNA-185 inhibits cell proliferation and induces cell apoptosis by targeting VEGFA directly in von Hippel-Lindau-inactivated clear cell renal cell carcinoma + + + Tumour Biol + Yuan + 35 + 12 + 2014 + Elevated microRNA-185 is associated with high vascular endothelial growth factor receptor 2 expression levels and high microvessel density in clear cell renal cell carcinoma + + + Proc Natl Acad Sci U S A + Harris + 105 + 5 + 2008 + MicroRNA-126 regulates endothelial expression of vascular cell adhesion molecule 1 + + + Dev Cell + Fish + 15 + 2 + 2008 + miR-126 regulates angiogenic signaling and vascular integrity + + + Am J Pathol + Khella + 185 + 3 + 2015 + Low expression of miR-126 is a prognostic marker for metastatic clear cell renal cell carcinoma + + + Blood + Chen + 111 + 3 + 2008 + Regulation of angiogenesis through a microRNA (miR-130a) that down-regulates antiangiogenic homeobox genes GAX and HOXA5 + + + Ann Oncol + Bex + 28 + 4 + 2017 + Adjuvant sunitinib in renal cell carcinoma: from evidence to recommendation + + + + + \ No newline at end of file diff --git a/src/codecs/crossref/crossref.test.ts b/src/codecs/crossref/crossref.test.ts index 00ff7febb..3d99cd059 100644 --- a/src/codecs/crossref/crossref.test.ts +++ b/src/codecs/crossref/crossref.test.ts @@ -4,6 +4,7 @@ import * as vfile from '../../util/vfile' import { nockRecord, snapshot } from '../../__tests__/helpers' import { YamlCodec } from '../yaml' import * as elife50356 from '../../__fixtures__/article/journal/elife/50356.json' +import * as plosone0229075 from '../../__fixtures__/article/journal/plosone/0229075.json' // Mocks to avoid changes in ids and timestamps between test runs jest.mock('crypto') @@ -37,6 +38,15 @@ describe('encode', () => { ).toMatchFile(snapshot('article-elife-50356.xml')) }) + test('PLOS article', async () => { + expect( + await crossref.dump(plosone0229075, { + doi: '10.5555/12345', + url: 'https://example.org', + }) + ).toMatchFile(snapshot('article-plosone-0229075.xml')) + }) + test('review of eLife article', async () => { const review = schema.review({ authors: [ diff --git a/src/codecs/crossref/index.ts b/src/codecs/crossref/index.ts index ab6bcba64..18dd6caff 100644 --- a/src/codecs/crossref/index.ts +++ b/src/codecs/crossref/index.ts @@ -91,7 +91,6 @@ export class CrossrefCodec extends Codec implements Codec { version = '4.4.2', } = {} - // The root XMl document to create const doc = { declaration: { attributes: { @@ -140,9 +139,7 @@ function encodeNode( doi: string, url: string ): xml.Element | undefined { - // @ts-ignore TODO: Replace with schema.isA('Review', node) - if (schema.nodeType(node) === 'Review') { - // @ts-ignore + if (schema.isA('Review', node)) { return encodePeerReview(node, doi, url) } else if (schema.isCreativeWork(node)) { return encodePostedContent(node, doi, url) @@ -192,8 +189,8 @@ function encodePeerReview( for (const identifier of itemReviewed.identifiers ?? []) { if (schema.isA('PropertyValue', identifier)) { const { name, value } = identifier - if (name?.toLowerCase() === 'doi') { - itemReviewedDoi = `${value}` + if (name?.toLowerCase() === 'doi' && typeof value === 'string') { + itemReviewedDoi = value } } } @@ -240,6 +237,7 @@ function encodePostedContent( datePublished, description, genre = [], + references, title, } = work @@ -268,7 +266,8 @@ function encodePostedContent( ? encodeDate('acceptance_date', dateAccepted) : null, abstract, - encodeDoiData(doi, url) + encodeDoiData(doi, url), + encodeCitationList(references) ) } @@ -357,3 +356,113 @@ function encodeProgramRelatedItem( function encodeDoiData(doi: string, url: string): xml.Element { return xml.elem('doi_data', xml.elem('doi', doi), xml.elem('resource', url)) } + +function encodeCitationList( + references: schema.CreativeWork['references'] +): xml.Element | null { + if (references === undefined) return null + return xml.elem( + 'citation_list', + ...references.map((work, index) => { + if (typeof work === 'string') { + return xml.elem( + 'citation', + { key: `ref${index + 1}` }, + xml.elem('unstructured_citation', work) + ) + } + + return xml.elem( + 'citation', + { key: `ref${index + 1}` }, + encodeJournalTitle(work), + encodeAuthor(work), + encodeVolume(work), + encodeIssue(work), + encodeCYear(work), + encodeDoi(work), + encodeArticleTitle(work) + ) + }) + ) +} + +function encodeJournalTitle(work: schema.CreativeWork): xml.Element | null { + let isPartOf = work.isPartOf + while (isPartOf) { + if (schema.isA('Periodical', isPartOf)) + return xml.elem( + 'journal_title', + TxtCodec.stringify(isPartOf.title ?? isPartOf.name ?? 'Unknown') + ) + isPartOf = isPartOf.isPartOf + } + return null +} + +function encodeAuthor(work: schema.CreativeWork): xml.Element | null { + const firstAuthor = work.authors?.[0] + const firstAuthorName = schema.isA('Person', firstAuthor) + ? firstAuthor.familyNames?.[0] ?? firstAuthor.name + : firstAuthor?.name + return firstAuthorName !== undefined + ? xml.elem('author', firstAuthorName) + : null +} + +function encodeVolume(work: schema.CreativeWork): xml.Element | null { + let isPartOf = work.isPartOf + while (isPartOf) { + if ( + schema.isA('PublicationVolume', isPartOf) && + isPartOf.volumeNumber !== undefined + ) + return xml.elem('volume', isPartOf.volumeNumber.toString()) + isPartOf = isPartOf.isPartOf + } + return null +} + +function encodeIssue(work: schema.CreativeWork): xml.Element | null { + let isPartOf = work.isPartOf + while (isPartOf) { + if ( + schema.isA('PublicationIssue', isPartOf) && + isPartOf.issueNumber !== undefined + ) + return xml.elem('issue', isPartOf.issueNumber.toString()) + isPartOf = isPartOf.isPartOf + } + return null +} + +function encodeCYear(work: schema.CreativeWork): xml.Element | null { + const date = + work.datePublished ?? + work.dateAccepted ?? + work.dateReceived ?? + work.dateCreated + if (date !== undefined) { + const value = typeof date === 'string' ? date : date.value + return xml.elem('cYear', value.substr(0, 4)) + } + return null +} + +function encodeDoi(work: schema.CreativeWork): xml.Element | null { + for (const identifier of work.identifiers ?? []) { + if ( + schema.isA('PropertyValue', identifier) && + identifier.name?.toLowerCase() === 'doi' && + typeof identifier.value === 'string' + ) + return xml.elem('doi', identifier.value) + } + return null +} + +function encodeArticleTitle(work: schema.CreativeWork): xml.Element | null { + return work.title !== undefined + ? xml.elem('article_title', TxtCodec.stringify(work.title)) + : null +}