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Use of JATS data to compile a bibliographic database / JATS-Con-Asia-20151019-04-Toshinori-Kurosawa

Use of JATS data to compile a bibliographic database / JATS-Con-Asia-20151019-04-Toshinori-Kurosawa

JATS-Con Asia
Monday, October 19, 2015

General Session:
Speaker 2 "Use of JATS data to compile a bibliographic database"
-Toshinori Kurosawa, NPO Japan Medical Abstracts Society (JAMAS)
Abstract: http://jats-con-asia.strikingly.com/#speakers
Materials: https://speakerdeck.com/jatsconasiasc/jats-con-asia-20151019-04-toshinori-kurosawa
Video: https://vimeo.com/150207491

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  1. Use of JATS Data in Creating Ichushi Web Database JATS-Con

    Asia 2015/10/19 NPO Japan Medical Abstracts Society Database Management Division Toshinori Kurosawa 1
  2. 2 About Us ▪Organization Japan Medical Abstracts Society (JAMAS, Ichushi)

    Non-profit organization. ▪Activities Produce medical bibliographic & abstract database and provide “Ichushi Web”(which is just like PubMed).
  3. 3 ▪History Established in 1903. Since then we have continued

    publication of Ichushi for over 110 years. Shiro Amako (1865~1930) : Fouder of JAMAS
  4. 4 ▪Database detail Coverage: Totally about 6,000 journals published in

    Japan. (currently about 3,000) Target fields are Medicine, Dentistry, Pharmacology, Nursing science and other related fields. Number of Records: 10 million articles. Keywords: Indexing keywords and subheadings to all articles manually with thesaurus which is based on MeSH.
  5. ▪Users Corporate users: about 2,500 Personal users: about 7,000 ▪Usage

    Login: about 18,000 per day Search: about 80,000 per day 5
  6. Data Creation Flow 7 Journals ICHUSHI In-house system Ichushi-Web Users

    ・Bibliographic data ・Abstract ・Keywords ・Link inforamation to fulltext The problem is ・・・ Almost all of journals are submitted by Printed Version.
  7. Collecting Journals by XML data 8 In 2007, for the

    purpose of efficient data processing, we started collecting journals by XML data that Ichushi original DTD. Unfortunately, because of local DTD, it did not become widespread. (Only a few publishers have submitted by Ichushi DTD.)
  8. 9 In 2014, we launched the accepting JATS data. Number

    of Journals submitted by JATS data has been increasing gradually, but in Japan, it is still difficult to get electronic data from pubulishers. Format Number of Journals JATS 62 JAMAS DTD 14 Total 76 (2.5%) Acceptable Tag Set ・Journal Archiving and Interchange (green) ・Journal Publishing (blue)
  9. Publisher JATS Data Flow 10 JATS ICHUSHI Ichushi Web Parser

    Bibliographic data Abstract Citation data DOI URL Ichushi Link Service JALC e-journal Link to fulltext by DOI Get Citation data with fulltext link DOI server
  10. 11 JATS for Ichushi Web Extract bibliographic and abstract data

    from <journal-meta>, <article-meta>. ・Ichushi Journal ID To identify Journals exactly, it is recommended to put Ichushi Journal ID in <journal-id>. sample: <journal-id journal-id-type="ichushi">J01858</journal-id> ・Abstract Use <abstract> data only if we have license. Otherwise, we make our own abstract.
  11. 12 ・Article subtitle Decide whether or not to get article

    subtitle value with attribute of <subj-group>. sample: <article-categories> <subj-group subj-group-type="features-heading-cat"> <subject>Special</subject> <subj-group subj-group-type="features-heading-title"> <subject>Mass-Screening</subject> <subj-group subj-group-type="normal-heading-title"> <subject>Cardiac Infarction</subject> </subj-group> </subj-group> </subj-group> </article-categories> <title-group> <article-title>Dietary instruction</article-title> </title-group> Article subtitle: “Mass-Screening Cardiac Infarction” Article title: “Dietary instruction” In this case, subj-group-type “features-heading-cat” is not target. ・Element in value Cut elements appeared in value. (emphasis elements etc.) sample: <article-title>An experimental <italic>in vitro</italic> study</article-title> Article title: “An experimental in vitro study”
  12. 13 JATS for Ichushi Link Service Ichushi Link Service is

    optional service for citation link. If publishers send us citation data in JATS, we get link information to fulltext for each citaion. And publishers can get back citation data with fulltext link in their site. Target of fulltext links are Crossref, J-STAGE and other japanese e-journals. Both <mixed-citation> and <element-citation> data can be accepted.
  13. 14 <mixed-citation publication-type="journal"> <string-name> <surname>Woodford-Williams</surname>, <given-names>E</given-names> </string-name>, <string-name> <surname>Watson</surname>, <given-names>D</given-names>

    </string-name>, and <string-name> <surname>Bushby</surname>, <given-names>C</given-names> </string-name>. <article-title>The day hospital in the community care of the elderly</article-title>. <source>Gerontology Clinic</source>. <year iso-8601-date="1962">1962</year>; <volume>4</volume>( <issue>4</issue>): <fpage>241</fpage>-<lpage>256</lpage>. </mixed-citation> mixed-citation sample:
  14. ICHUSHI 15 Publisher JATS Parser Citation data Extract below and

    get Link ID from outside services ・Title ・Author ・Journal ・Volume ・Issue ・Page ・Published year Crossref J-STAGE PubMed Other japanese e-journals e-journal Ichushi Link Service get citation data with fulltext link
  15. 17 JATS for DOI deposit Deposit DOI through JALC on

    behalf of publishers. Publisher JATS ICHUSHI Parser JALC XML JALC convert deposit DOI assign DOI prefix support team contact personnel assign DOI prefix assignDOI request to get DOI request DOI prefix
  16. 18 Future ・Popularize JATS in scholarly publishing field through the

    activities of XML Scholary Publishing Association(XSPA). ・Prepare for BITS Although our collection is only Journal Articles now, we have a plan to add book data near future.