Building Data

Building Data
Yasunori Yamamoto

NCBI Taxonomy 4,000 biomedical journals
Database indexed at NLM

1994
4 DBs GenBank
SWISSPROT
PIR
EMBL PRF
DDBJ PDB
dbEST GenBank
dbSTS EMBL
DDBJ 3442 Nucleic Acids Research, 1994, Vol. 22, No. 17
LANL
Patent LANL
Patent

35 DBs

2012

http://www.ncbi.nlm.nih.gov/sites/gquery
Database Center for Life Science

NAR database issue
1400 1380
1330
1300 1230

1200 1170

1078
1100

2008 2009 2010 2011 2012

Source: Oxford University Press
92 databases added every year

93
dullhunk


How to ﬁnd a relevant database is an important topic,

and, at the same time,

to discuss what kind of databases are “good” is also signiﬁcant.


Data before applications / services

NASA Goddard Photo and Video


Good ﬁshes ﬁrst

y !
m
u m !
Y y
m
u m
Y


Aziz T. Saltik

Nature provides good ﬁshes

Chef mashes up good materials

mrjorgen


What should be considered?
and how can these be assessed?
Interesting, useful & reliable

Reliable in terms of content and structure

Peer-reviewed
→ Published on NAR database issue or another scientiﬁc journal.

Sustainable, reusable & discoverable

Appropriate licenses, bulk downloadable via the Internet, Linked Data...

Fresh & stable

Frequent updates with the least amount of down time.


We should focus on building “good” data or developing tools to help it.


Allie
Abbreviation / long form pairs in life sciences

Japanese translation

CC 2.1 (Japan) Allie
Monthly update http://allie.dbcls.jp/

SPARQL endpoint / bulk downloadable
(N-triples or tab delimited plain text)

Links to PubMed and DBpedia (currently, RDF data only)

Web search service

7000+ unique visits / mo to the search service


Allie data model absorption of lexical variants

PairCluster
ShortForm LongForm
SPF specific pathogen-free
appearsIn PubMedIDList

contains
CoocurringShort
cooccursWith
PairList FormList
Pair
ShortForm LongForm
SPF specific pathogen-free inResearch
AreaOf
ResearchArea
Pair
ShortForm LongForm
spf specified pathogen free
frequency


Allie class hierarchy
http://purl.org/allie/ontology/201108


Allie RDF data excerpted
"特定病原体除去の"@ja allie:LongForm
Abbreviation
SPF "speciﬁc pathogen-free"@en rdfs:label rdf:type
Long form rdfs:label
speciﬁc pathogen-free http://purl.org/allie/id/longform/1528191
English
allie:hasLongFormOf
特定病原体除去の
Japanese
http://purl.org/allie/id/pair/1547869

rdf:type
allie:hasShortFormOf

allie:EachPair
http://purl.org/allie/id/pair/1547869

rdfs:label rdf:type

"SPF"@en allie:ShortForm

Useful / reliable?
Database, Vol. 2011, Article ID bar013, doi:10.1093/database/bar013
.............................................................................................................................................................................................................................................................................................

Original article
Allie: a database and a search service of
abbreviations and long forms
Yasunori Yamamoto1,*, Atsuko Yamaguchi1, Hidemasa Bono1 and Toshihisa Takagi2
1
Database Center for Life Science, Bunkyo-ku, Tokyo and 2Department of Computational Biology, University of Tokyo, Kashiwa, Chiba, Japan

*Corresponding author: Tel: +81 (0)3 5841 0251; Fax: +81 (0)3 5841 8090; Email: yy@dbcls.rois.ac.jp

Downloaded from http://database.oxfordjournals.org/ at University of Tokyo on
Submitted 25 November 2010; Revised 25 March 2011; Accepted 28 March 2011

.............................................................................................................................................................................................................................................................................................

Many abbreviations are used in the literature especially in the life sciences, and polysemous abbreviations appear
frequently, making it difficult to read and understand scientific papers that are outside of a reader’s expertise. Thus, we
have developed Allie, a database and a search service of abbreviations and their long forms (a.k.a. full forms or definitions).
Allie searches for abbreviations and their corresponding long forms in a database that we have generated based on all
titles and abstracts in MEDLINE. When a user query matches an abbreviation, Allie returns all potential long forms of the
query along with their bibliographic data (i.e. title and publication year). In addition, for each candidate, co-occurring
abbreviations and a research field in which it frequently appears in the MEDLINE data are displayed. This function helps
users learn about the context in which an abbreviation appears. To deal with synonymous long forms, we use a dictionary
called GENA that contains domain-specific terms such as gene, protein or disease names along with their synonymic
information. Conceptually identical domain-specific terms are regarded as one term, and then conceptually identical
abbreviation-long form pairs are grouped taking into account their appearance in MEDLINE. To keep up with new abbre-
viations that are continuously introduced, Allie has an automatic update system. In addition, the database of abbreviations
and their long forms with their corresponding PubMed IDs is constructed and updated weekly.
Database URL: The Allie service is available at http://allie.dbcls.jp/.
.............................................................................................................................................................................................................................................................................................


Discoverable?

http://thedatahub.org/dataset/allie-abbreviation-and-long-form-database-in-life-science

Reliable?

http://www4.wiwiss.fu-berlin.de/lodcloud/ckan/validator/validate.php

Reliable/stable?

http://stats.lod2.eu/rdfdocs

Stable?

http://labs.mondeca.com/sparqlEndpointsStatus/
http://labs.mondeca.com/sparqlEndpointsStatus/details/allie-abbreviation-and-long-form-database-in-life-science.html

consider to be on the right track.


Projects in this hackathon


RDFization of Life Science Dictionary

Life Science Dictionary

English - Japanese / Japanese - English dictionary in life sciences

Thesaurus and concordance

Project started in 1993.

110k English words and 120k Japanese words (as of Mar. 2011)

Can be used to inter- or intra-connect life science databases

Bridge English-Japanese resources in life sciences

Preﬁx would be http://purl.org/lsd/


http://lsd.pharm.kyoto-u.ac.jp/en/service/weblsd/index.html


RDFization of Colil

Comments on Literature in Literature (Colil)

Citation data extracted from PMC OA subset

Citing comments on each cited literature (Citation context)

Relevant literature based on co-citation data

Similar to the MS academic search service

Can be used to a literature recommendation service

Curation/annotation assistance services

Bulk downloadable


Colil


Enjoy hack & Toyama!

digicacy

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Notes de l'éditeur