Hand investigation of records that don't match to fatcat metadata. ## Overview 811 such records from 2020-03-20 CORD-19 dataset. 221 have some DOI 242 have a PMCID 12 have a PMID jq 'select(.doi == "" and .pubmed_id =="" and .pmcid == "")' -c | wc -l => 364 jq 'select(.doi == "" and .pubmed_id =="" and .pmcid == "")' -c | jq .source_x -r | sort | uniq -c | sort -nr 288 WHO 76 Elsevier jq 'select(.doi == "" and .pubmed_id =="" and .pmcid == "")' -c | jq .title | sort | uniq -c | head => 62 have empty titles, all from Elsevier jq .title | sort | uniq -c | head => from full batch, 224 have empty titles; no duplicates 214 Elsevier 9 PMC 1 PMC_new ## Lacking Identifiers, Has Title jq 'select(.doi == "" and .pubmed_id =="" and .pmcid == "")' -c | jq 'select(.title != "")' -c => 302 such papers Random sample 10: "Surgical management strategies for orthopedic trauma patients under epidemic of novel coronavirus pneumonia" Chinese Journal of Trauma, 2020 => Volume: 36, Issue: 2, pp 124-128 => https://academic.microsoft.com/paper/3009524916/related "Molecular biology of microbial pathogenicity: Adhesion, invasion and receptors" FEMS Microbiology Letters, 1984 => elsevier => missing DOI => free PDF, hard to crawl (OUP) => https://fatcat.wiki/release/wbzyyyuhcfhnjfmuouygqyi7vy "Recommendations for general surgery clinical practice in novel coronavirus pneumonia situation" Chinese Journal of Surgery, 2020 => missing DOI and PMID => DOI not in crossref => free PDF download => https://fatcat.wiki/release/3przclac6jfarpru2ol4xafmie "Author index volume 20 (1983)" FEMS Microbiology Letters, 1983 => stub "Paying close attention to diabetic patients with novel coronavirus infection" Chinese Journal of Endocrinology and Metabolism, 2020 => https://academic.microsoft.com/paper/3010104673/related => no fatcat "The recommendation for management of the bereavements among the family members died with novel coronavirus pneumonia" Chinese Journal of Behavioral Medicine and Brain Science, 2020 => https://academic.microsoft.com/paper/3009517691/related => 1674-6554 => 10.3760/cma.j.issn.1674-6554.2020.... (?) => there are english and chinese websites for journal, but chinese more up-to-date => http://med.wanfangdata.com.cn/Periodical/zgxwyxkx => publisher resources: http://subject.med.wanfangdata.com.cn/Channel/7 https://translate.googleusercontent.com/translate_c?depth=1&rurl=translate.google.com&sl=auto&source=osdd&sp=nmt4&tl=en&u=http://subject.med.wanfangdata.com.cn/Channel/7&usg=ALkJrhj0J6IQM6RKNFYPKpMshQS9UcS2oQ "Singapore claims first use of antibody test to track coronavirus infections | Science | AAAS" Science Magazine, 2020 => https://fatcat.wiki/release/ovghasgr6bclbj2ksbnaz635ci => simply missing DOI "High resolution CT findings and clinical features of novel coronavirus pneumonia in Guangzhou" Chinese Journal of Radiology, 2020 => https://academic.microsoft.com/paper/3010637392/related => http://www.cjrjournal.org/ => https://fatcat.wiki/container/grktk23p5rayfncvh3bm6ylbwy (old only) => not seeing this paper in any recent (2020) issues "COVID-19 Update From China" JAMA, 2020 => seems to be an audio recording and/or video on "JN Learning" => https://edhub.ama-assn.org/jn-learning/audio-player/18234306 => https://edhub.ama-assn.org/jn-learning/video-player/18234510 => abstract matches "Coronavirus latest: death toll passes 2,000" Nature, 2020 => this is a commentary article which is getting continuously updated, with the title changing => DOI: 10.1038/d41586-020-00154-w => do have a wayback snapshot with exact title: => http://web.archive.org/web/20200220185055/https://www.nature.com/articles/d41586-020-00154-w Summary: - some informal material mixed in (commentary/opinion/video) - bunch of chinese papers, often with DOI, not indexed in western databases, but are in MAG. MAG identifiers mostly not included. could get metadata from wanfang data (company)? - some stub articles: eg, indexes - some exact title matches, missing identifier (pubmed_id, DOI) matches Top journals: 46 (none) 15 Chinese Journal of Laboratory Medicine => fatcat container, no papers 14 FEMS Microbiology Letters => fatcat container, OUP, many papers 11 Chinese Journal of Medical Science Research Management => no fatcat => 1006-1924 => https://portal.issn.org/resource/ISSN/1006-1924 => "Zhonghua yixue keyan guanli zazhi" 11 Chinese Journal of Hospital Administration 10 Chinese Journal of Radiology 10 Chinese Journal of Emergency Medicine 9 Chinese Journal of Preventive Medicine 9 Chinese Journal of Experimental Ophthalmology 9 Chinese Critical Care Medicine 8 Chongqing Medicine 8 Chinese Journal of Infectious Diseases => in fatcat (twice?) => "Zhonghua chuan ran bing za zhi" 7 Chinese Journal of Trauma => no fatcat => in MAG [...] ## DOIs jq 'select(.doi != "" and .pubmed_id =="" and .pmcid == "")' -c | jq 'select(.title != "")' -c => 194 such papers jq 'select(.doi != "" and .pubmed_id =="" and .pmcid == "")' -c | jq 'select(.title != "")' -c | jq .source_x -r | sort | uniq -c 176 Elsevier 5 medrxiv 13 WHO jq 'select(.doi != "" and .pubmed_id =="" and .pmcid == "")' -c | jq 'select(.title != "")' -c | jq .title -r | sort | uniq -c | sort -nr | head 22 Index 7 Subject Index 2 S 2 C 1 V Trying a sample of DOIs that didn't match: jq 'select(.doi != "" and .pubmed_id =="" and .pmcid == "")' -c | jq 'select(.title != "")' -c | shuf -n10 | jq .doi -r 10.1101/2020.01.31.20019935 => medrxiv, not sure why not in fatcat 10.1016/j.diagmicrobio.2004.10.002 => elsevier, not in fatcat 10.1016/B978-0-323-53045-3.00035-0 => no such doi 10.1016/B978-0-323-37591-7.00038-0 => no such doi 10.1016/B978-0-323-52993-8.00048-5 => no such doi 10.1016/B978-0-323-44887-1.00022-5 => no such doi 10.1016/B978-343721804-0.50036-3 => elsevier, index 10.1016/B978-0-323-44887-1.00044-4 => no such doi => https://www.us.elsevierhealth.com/kendigs-disorders-of-the-respiratory-tract-in-children-9780323448871.html 10.1016/B978-0-323-04579-7.00035-6 => no such doi 10.1016/B978-0-323-55512-8.00140-X => no such doi => 10.1016/B978-0-323-55512-8.00140-X => DOI is listed on elsevier homepage => https://www.sciencedirect.com/science/article/pii/B978032355512800140X Many of these "no such DOI" may be partially registered? Top journals (actually books?) with missing DOIs: bnewbold@orithena$ cat missing.json | jq .who_paper -c | jq 'select(.doi != "" and .pubmed_id =="" and .pmcid == "")' -c | jq 'select(.title != "")' -c | jq .journal | sort | uniq -c | sort -nr | head 28 "Mandell, Douglas, and Bennett's Principles and Practice of Infectious Diseases" 13 "Principles and Practice of Pediatric Infectious Diseases" 11 "Infectious Diseases" 9 "Hunter's Tropical Medicine and Emerging Infectious Diseases" 7 "Kendig's Disorders of the Respiratory Tract in Children" 5 "" 4 "Vaccine" 4 "The Dictionary of Cell & Molecular Biology" 4 "Clinical Immunology" 3 "Zakim and Boyer's Hepatology" [...] ## PMID/PMCID jq 'select(.doi == "" and .pubmed_id !="")' -c => 8 jq 'select(.doi == "" and .pmcid !="")' -c => 223 All of these PMIDs and PMCIDs seem to be valid. From a quick scan, they seem to not be in fatcat because there are already works there with DOIs. ## Recommendations In your data munging, filter out: - works with blank titles and no external identifier (eg, no DOI, PMCID, PMID, MAG ID) - works with blocklist titles (see below). I assume these got included due to fulltext search matches, but I think are just noise - works with titles which are a single capital letter (eg, "S", "C") Title blocklist (preceeded by count); usually I do these by lower-casing and striping non-alphanumeric characters before comparing: 348 Index 83 Subject Index 76 Subject index 69 Author index 68 Contents 67 Articles of Significant Interest Selected from This Issue by the Editors 66 Information for Authors 36 Graphical contents list 29 Table of Contents 21 In brief 20 Preface 20 Editorial Board 19 Author Index 18 Volume Contents 18 Research brief 18 Abstracts 15 Opportunities from the Center for Perioperative Education 13 Keyword index 12 PNAS Plus Significance Statements 11 In This Issue 10 Current Awareness on Comparative and Functional Genomics 9 Introduction 9 Highlights of this issue 9 Contents list 9 Abbreviations 8 QUIZ CORNER 8 Positions available 8 Journal Watch 8 Index of Authors 8 Editorial 8 Cumulative Index 7 Table of contents 7 Quiz Corner 7 Index of Subjects 7 INDEX 7 Foreword 7 Bibliography of the current world literature 6 Viral gastroenteritis 6 Public Health Watch 6 Contributors 6 Contents of Volume 6 Contents of other veterinary journals from Elsevier Highlights of this issue QUIZ CORNER Answers to Quiz Corner ## Notes There is some chinese journal registry number, eg "ISSN 1005-1201 CN 11-2149/R" Interesting sites to crawl or translate: http://medjournals.cn/index.do => 1 million papers http://rs.yiigle.com/yufabiao/1181337.htm => paper repository/host? http://subject.med.wanfangdata.com.cn/Channel/7?mark=34 => list of papers? wanfang data seems like a large publisher http://www.wanfangdata.com/about/about.asp => mainland china (beijing) => commerical/national holder of 40+ million papers => indexed by EBSCO ## Fetching Metata cat metadata/cord19.2020-03-27.missing.json | jq 'select(.doi != "") | .doi' -r | sort -u > missing_doi.tsv cat metadata/cord19.2020-03-27.missing.json | jq 'select(.pubmed_id != "") | .pubmed_id' -r | sort -u > missing_pmid.tsv cat metadata/cord19.2020-03-27.missing.json | jq 'select(.pmcid != "") | .pmcid' -r | sort -u > missing_pmcid.tsv cat missing_doi.tsv | parallel -j4 'http --headers head "https://doi.org/{}" | head -n1 | awk "{print \"{}\t\" \$2}"' > missing_doi_status.tsv cat missing_doi_status.tsv | rg '404$' | cut -f1 > unregistered_doi.tsv cat missing_doi_status.tsv | rg '302$' | cut -f1 | parallel http --json get "https://api.crossref.org/v1/works/http://dx.doi.org/{}" | jq .message -c | pv -l > missing_doi_crossref.json mkdir -p pubmed cat missing_pmcid.tsv | parallel -j1 'http get "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=pubmed&id={}&rettype=pubmed" > pubmed/{}.xml' cat missing_pmid.tsv | parallel -j1 'http get "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=pubmed&id={}&rettype=pubmed" > pubmed/{}.xml' cat pubmed/*.xml | rg -v '^<\?xml version' | rg -v '^' | rg -v '^' > pubmed_combined.xml # Edit file manually to add `` and `` wrapper. # in prod: ./fatcat_import.py pubmed --do-updates /tmp/pubmed_combined.xml /srv/fatcat/datasets/ISSN-to-ISSN-L.txt