Presentation forpd bj_1

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Published on February 20, 2014

Author: maoringo

Source: slideshare.net

Presentation Materials http://l.bitcasa.com/ayav_jSQ Cross Search Service for Life Science and Semantic web National Institute of Biomedical Innovation Maori Ito 1

Sagace Search for Biomedical Data & Resources in Japan

Features •  •  •  •  Focus on biomedical database Semi-automated Ranking Refining search results with facets More informative search results with metadata

h"p://integbio.jp/en/ 4

Mechanisms of Search Engine 1.  Crawling 2.  Indexing 3.  Query Processing 4.  Scoring

Crawling Databases Crawling Program 6

Indexing •  Split data convenient size and store own server Indexing Data Internal Server

Query Processing and Scoring

Search System NIBIO NBDC  /  DBCLS AgriTogo   MEDALS Collaborate by using P2P architecture JCGGDB   9

Log Analysis and Reflect Search Results •  The members of top 8 databases are almost the same. –  Patents –  KEGG MEDICUS –  Medicine and pharmaceutical proceedings –  Drug emergency call –  Ingredients information of health food –  Merck Manual –  Medical Information Network Distribution Service –  The Encyclopedia of Psychoactive Drugs 10

Comparison of Databases •  Popular databases are Medical or Pharmaceutical “literal rich” databases. •  Top databases run away with the winnings! •  More than half of databases have never clicked! 11

Unpopular databases •  Sagace has started the service in March 2012. •  Some databases have never clicked since then. •  Eliminate these databases. •  Databases –  272 DB -> 122 DB 12

Results •  Accuracy for users must have improved. •  Reducing databases also caused speed up. 13

Specific databases in life science •  Some databases in life science is lacked “literal information” . •  Cross search engine is suitable to show literal information. •  Semantic web will help these databases. 14

Semantic Web? 15

What is semantic web? Semantic web is constructed by Web of Meaningful and Machine Understandable Data 16

Web of Document h"p://pdbj.org/mine/summary/2yi1 17

Search Engine Results Query  “2yi1  pdbj”  search  on  google Search  engine  can  reflect  only  text  data. 18

Web of Document to Web of Data Data Data Data Data Data Data Data Data Data Data Data Data Data Data h"p://pdbj.org/mine/summary/2yi1 19

How should the computer recognize these data? 20

A.(Focus on search service) Mark-up with Metadata by Database Developer 21

What is metadata? •  Data about Data Entry  ID See  Also Keywords Species Reference Experimental   method Image Entry ID: 2YI1 Species:HOMO SAPIENS Reference: PubMed ID 22343627 See Also:2YHY,2YHW Experimental method: X-RAY DIFFRACTION Image: http://pdbj.org/pdb_images/ 2yi1.jpg 22

Reflect Search Results •  Metadata encourage encounter Users and Database Image 23

How to markup? (microdata) •  Add metadata with html tag Declare  Vocabulary <div  itemscope=“”  itemtype=“h"p://schema.org/BiologicalDatabaseEntry”>    <span  itemprop=“entryID”>2YI1</span>   </div> Property   Content   (Predicate)   (Object) http://pdbj.org/mine/summary/2yi1 2YI1 http://schema.org/BiologicalDatabaseEntry/entryID 24

How to reflect? •  Crawler program can find metadata easily! <div  itemscope=“”  itemtype=“h"p://schema.org/BiologicalDatabaseEntry”>    <span  itemprop=“entryID”>2YI1</span>   </div> •  Add indexed data @BiologicalDatabaseEntry_entryID=2YI1 •  Reflect search results 25

Machine Understandable Data •  Declaration of vocabulary is important. biological?   E.g. entryID book? products? recipe? 26

Machine Understandable Data •  Declaration of vocabulary is important. <div  itemscope=“”  itemtype=“h"p://schema.org/BiologicalDatabaseEntry”>    <span  itemprop=“entryID”>2YI1</span>   </div> E.g. entryID=2YI1 Biological   DatabaseEntry!! 27

What is schema.org? •  "Schema.org is a set of extensible schemas that enables webmasters to embed structured data on their web pages for use by search engines and other applications.” –  (http://schema.org/) 28

It’s not only in Sagace. •  "Search engines including Bing, Google, Yahoo! and Yandex rely on this markup to improve the display of search results, making it easier for people to find the right web pages.” (h"p://schema.org/)   29

•  Google support these content types: –  Reviews –  People –  Products –  Businesses and organizations –  Recipes –  Events –  Music 30

Current Situation •  Define original properties for Biological Database and Biological Database Entry for schema.org –  entryID, isEntryOf, taxon, seeAlso, reference –  Schema.org proposal –  http://www.w3.org/wiki/WebSchemas/BioDatabases •  Sagace can reflect them to search results. •  Search Collaboration organization will also reflect them to search results. –  NBDC –  MEDALS (molprof) •  How to mark up and search results examples in Sagace •  http://sagace.nibio.go.jp/press/metadata/markup/ 31

Sagace reflects these properties •  •  •  •  •  •  •  •  image   isEntryOf  (Database name) entryID taxon(Species) disease seeAlso (Reference database entry) dateModified (last modified) reference (Reference article) 32

To reflect biological data into major search engine, it requires adding schema.org. schema.org Reflect Search Results Biological Database and Biological Database Entry schema.org Proposal 33

•  To achieve adding our proposal into schema.org,“Need more people who think it is a good idea.” (by organizers @ schema.org) •  We need more databases! 34

9 DBs have applied microdata! •  DoBISCUIT (Database Of BIoSynthesis clusters CUrated and InTegrated) •  JCRB Cell Bank •  Functional Glycomics with KO mice database •  Glyco-Disease Genes Database •  Carbohydrate Interaction Database (Carint) •  •  •  •  JCGGDB Report MEDALS Integbio Database Catalog Life Science Database Archive 35

Search Results Example 1 36

Search Results Example 2 37

Issues (Cons) for Microdata •  Microdata strongly recommend using schema.org vocabulary. •  Microdata is W3C working group not recommendation •  If we integrate RDF data, we have to consider again which vocabularies are suitable.

RDFa Lite •  RDFa Lite is a minimal subset of RDFa, the Resource Description Framework in attributes (http://www.w3.org/TR/rdfa-lite/) –  Affected by Microdata –  W3C recommendation 07 June 2012 •  Ability to specify more than one vocabulary (not only schema.org) •  Easy to mark up 39

How to markup? (RDFa Lite) •  Add metadata with html tag Declare  Vocabulary <div  vocab=“h"p://schema.org”  typeof=“BiologicalDatabaseEntry”>    <span  property=“entryID”>2YI1</span>   </div> Property   Content   (Predicate)   (Object) http://pdbj.org/mine/summary/2yi1 2YI1 http://schema.org/BiologicalDatabaseEntry/entryID 40

If you use PDBo as extension vocabulary Declare  Vocabulary <div prefix="PDBo : http://rdf.wwpdb.org/schema/pdbx-v40.owl#"> <span property="PDBo:exptl.method">X-RAY DIFFRACTION</span> </div> Content   Property   (Predicate)   (Object) Image 41

If metadata add into database..., •  Search engine can pick up many important data. •  Database developers can appeal their service more effectively. •  Users can find easily which they are looking for. 42

Current Situation •  KNApSAcK has applied RDFa Lite. •  We’d like to reflect more information by using RDFa Lite. •  If you add metadata into your databases, please contact NBDC or me (maori@nibio.go.jp) •  Please collaborate with us ! •  Please tell me what kind of information is suitable to show and refine. 43

Acknowledgement •  National Institute of Biomedical Innovation –  Mizuguchi Kenji –  Morita Mizuki –  Igarashi Yoshinobu –  Sakate Ryuichi –  Nagao Chioko –  Chen Yi-an –  Akiko Fukagawa –  Tohru Masui –  Johan Nystrom-Persson •  •  •  •  National Bioscience Database Center (NBDC) National Institute of Agrobiological Sciences database (NIAS) Molecular Profiling Research Center for Drug Discovery (molprof) Japan Consortium for Glycobiology and Glycotechnology DataBase (JCGGDB) •  This project is supported by a collaboration "Database integration in NIBIO and cooperation with outside organizations" with the NBDC. 44

45

Web of Data (Concept) 46

xxxx http://pdbj.org/mine/summary/xxxx http://schema.org/BiologicalDatabaseEntry/entryID http://schema.org/BiologicalDatabaseEntry/isEntryOf http://schema.org/BiologicalDatabaseEntry/reference PDBj PubMed:xxxxxxx http://schema.org/BiologicalDatabaseEntry/reference http://schema.org/BiologicalDatabaseEntry/isEntryOf http://databaseA.org/publication Database A 47

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