Monday, October 19, 2015
Speaker 2 "Use of JATS data to compile a bibliographic database"
-Toshinori Kurosawa, NPO Japan Medical Abstracts Society (JAMAS)
Use of JATS Data in Creating
Ichushi Web Database
NPO Japan Medical Abstracts Society
Database Management Division
Japan Medical Abstracts Society (JAMAS, Ichushi)
Produce medical bibliographic & abstract database and
provide “Ichushi Web”(which is just like PubMed).
Established in 1903.
Since then we have continued publication of Ichushi
for over 110 years.
Shiro Amako (1865～1930) : Fouder of JAMAS
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.
Indexing keywords and subheadings to all articles
manually with thesaurus which is based on MeSH.
Corporate users: about 2,500
Personal users: about 7,000
Login: about 18,000 per day
Search: about 80,000 per day
Ichushi Web Interface
Data Creation Flow
･Link inforamation to fulltext
The problem is ･･･
Almost all of journals are submitted by Printed Version.
Collecting Journals by XML data
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
(Only a few publishers have submitted by Ichushi DTD.)
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
JAMAS DTD 14
Total 76 (2.5%)
Acceptable Tag Set
･Journal Archiving and Interchange (green)
･Journal Publishing (blue)
JATS Data Flow
Link to fulltext
Get Citation data
with fulltext link
JATS for Ichushi Web
Extract bibliographic and abstract data from
･Ichushi Journal ID
To identify Journals exactly, it is recommended to put
Ichushi Journal ID in .
Use data only if we have license.
Otherwise, we make our own abstract.
Decide whether or not to get article subtitle value with attribute
“Mass-Screening Cardiac Infarction”
In this case, subj-group-type “features-heading-cat”
is not target.
･Element in value
Cut elements appeared in value. (emphasis elements etc.)
An experimental in vitro study
Article title: “An experimental in vitro study”
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
Both and data can
The day hospital in the community care of the elderly.
JATS Parser Citation data
Extract below and get Link ID
from outside services
get citation data with fulltext link
Sample: MedicalFinder (produced by Igaku-Shoin Ltd.)
JATS for DOI deposit
Deposit DOI through JALC on behalf of publishers.
Parser JALC XML
assign DOI prefix
request to get DOI
･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.
Thank You !