Analyzer of Bio-resource Citations. World Data Center of Microorganisms(WDCM)

Transcription

1 Analyzer of Bio-resource Citations World Data Center of Microorganisms(WDCM)

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3 Outlines Introduction of ABC Homepage and function of ABC Text mining for microorganism : classification, clustering, and applications

4 ABC -- Analyzer of Bio-resource Citations Find out the citations information for microorganism strains, culture collections from papers and patents. Find out the sequences information for strains and culture collections

5 ABC Data resources Dates In Resource In ABC Journal Paper Patent Journal Paper Patent Derwent Innovations IndexSM 1963~ >3 million ,349 PubMed 1940~ >25,000 >22 million --- 2,048 49, Highwire 1953~ 1,774 >2 million --- 1, , Web of science 1900~ ~10,000 >40 million

6 Analyzer of Bio-resource Citations Data resources Papers Resources patents Sequences CGMCC ATCC PubMed HighWire PMC Derwent Innovations Index Genome Genbank

7 Introduction of ABC Paper resources We totally gather 1,880,853 papers meta-info from these sources about this 437 culture collections. And we could extract 128,667 strains from 173,901 papers of this paper set. Source Highwire PubMed PMC Highwire&PubMed Highwire&PMC PubMed&PMC Highwire&PM&PMC Papers 1,412,691 papers 692,807 papers 113,038 papers 298,523 papers 31,333 papers 15,750 papers 7,923 papers

8 Literature resource Finding the sources which are valuable Resource Pubmed Highwire PMC Journal Ranking classify Paper PDF Retrieval 580 culture collections have been searched using the prefix of their strains, 111,240 strains are described in 144,134 papers We listed top 200 journals for culture strains (from 1953 January to 2011 July). More than 11,000 papers PDF in 17 journals be download in our severs. And full text search engineer be built based on LUCENE.

9 Data mining from public resources Pubmed/PMC: Securing data by CGI Pubmed/P MC Perl script Accessing remote server Storing data in XML XML HighWire: Securing data by web HighWire Web Crewlers Data download Storing data in html HTML

10 Data mining in full text The workflow of Lucene The flat files in our server Index files Target paper list Build index by Lucene Keyword search by Lucene Perl script query strain, organism in mysql database For others query MySQL pre_fix_tex t Perl script MySQL table: doc_strain_ref_id,title_ hash,strain_org,strain_ org_id,match_times

11 Strains count: Level 1 > Level 2 > Level 3 Quality control for strain citation Level 1 Mining strain ID using the acronym of culture collection e.g. JCM CBS CGMCC Level 2 Filtering strain ID according to the pattern e.g. JCM + number CBS+number ; CBS+number+.+number ; CGMCC+number ; CGMCC+number+.+number; Level 3 Matching strain ID in catalogue of culture collection e.g. JCM CBS CGMCC

12 Data filter for strain citation We completed strains filter of 24 culture collections. CBS, JCM, BCC, CCARM, LIPIMC, VTCC, MCC- MNH,ITDI,UL,UPCC, NBRC For example: JCM(paper/strain) CBS(paper/strain) CGMCC(paper/strai n) Level / / /504 Level / / /451 Level / / /64

13 New Functions in ABC --Microorganism search

14 New Functions in ABC --Dynamic statistics for each culture collection

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20 ABC User can upload paper information and PDF document which is related to his/her culture collection.

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23 Text Mining & Application Preprocessing: To Get Keywords

24 Text Mining & Application Example:

25 Text Mining & Application Application: Automatic Text Classification Method: a. First, define the category, and set up the training set. b. Second, represent each document as a vector, compute their similarity. c. Assign a document to the category which has the biggest similarity value.

26 Text Mining & Application Example: Documents From PubMed Central Class number percent Bacteriology % Environmental Microbiology % Genetics,Microbial % Industrial Microbiology % Mycology % Plant Pathology % Virology % Other %

27 Text Mining & Application Score the documents: For short:ijsem Extract those terms have relation to strains.

28 Text Mining & Application Score the documents: term weight strain 3625 temperature 404 acid 1741 atcc 393 growth 1407 optimum 379 genus 1388 microbiology 370 sequence 1382 evolutionary 370 fatty 1302 carbon 312 gene 1298 bacteria 303 type 1244 cell 302 medium 777 tree 290 analysis 720 production 287 novel 551 description 281 international 497 family 254 journal 441 systematic 244

29 Text Mining & Application Result Page Show:

30 Thanks for your attention!