TBRC: an online networking platform for biological collections in Thailand

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Microbial culture collections are important for the development of scientific research and industrial exploitation. In order to provide easier access to the collection, the list of microbial cultures should be made available online. A survey on the CCINFO, powered by the WDCM reveals that 60 collections from Thailand registered into CCINFO database during 1983-2013, and only 2 collections: BCC (BIOTEC culture collection) and TISTR provide the online access directly to their microbe information. In addition, at WDCM, 48 from 60 Thai collections are affiliate at universities, but their information in CCINFO is totally outdated. Likewise, only BCC and TISTR published their information in the GCM with the total number of 4,948 and 1,032 strains respectively. It is observed that some data of 4 collections including BCC, TISTR, DOA and DMST can be online accessed through the Thailand Network on Culture Collections (TNCC) website. Established since 2000, TNCC is the first data network of the aforementioned four culture collections in Thailand. The main activity of TNCC is to integrate information from four members and disseminate microbial information to public. To transfer their data into an integrated database, TNCC members can submit the data file in excel or enter each record into a web application. Now there are only 5,550 strains available at TNCC website that is far from what registered at CCINFO, WDCM. The lack of up-to-date information is the main problem at both WDCM and TNCC, although WDCM and TNCC focus at different network levels: individual collections and country service collections. The data and system integration across levels of network might help to co-create the integrated information for understanding the microbial diversity, and integrated services for connecting to industrial networks.
From the network integration perspective, BIOTEC has launched Thailand Bioresource Research Center (TBRC) initiative in 2012 to deliver the co-creating services to bridge a gap between academic research and industry. TBRC aims to (1) leverage the network strength of service collections (2) create a research network based biological resource center and (3) establish a common technology infrastructure to provide open standards and interoperable information systems across the network levels. TBRC network applies the concept for cooperative work based on a hosted solution using a shared server. The collection registered at TBRC will get a software called iCollect to be used in managing the data from their preservation activities, update the list of microbial cultures to TBRC online catalogs and retrieve orders from TBRC via SOAP-based Web services. Alternatively, the members can manage, process their data and transmit back and forth through TBRC website. Integrated data and information will then be curated, annotated and categorized using data mining techniques and made accessible through TBRC online distribution service, www.tbrcnetwork.org.

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TBRC: an online networking platform for biological collections in Thailand

  1. 1. TBRC:  an  online  networking  pla3orm   for  biological  collec8ons  in  Thailand   9/11/13 Copyright  2012-­‐2013  BIOTEC 1 TBRC: a National BRC Supawadee Ingsriswang Bioresources Technology Research Unit, National Center for Genetic Engineering and Biotechnology (BIOTEC), Thailand http://www.biotec.or.th/btu Thailand Bioresource Research Center (TBRC), Thailand http://www.tbrcnetwork.org
  2. 2. 9/11/13Copyright  2012-­‐2013  BIOTEC 2 Country   Culture  Collec8ons   Cultures   Service  Collec8ons   Indonesia   18   11,476   5   Malaysia   7   2,915   2   Philippines   6   3,456   5   Singapore   3   1,389   0   Thailand   60   43,251   4   Viet  Nam   1   6,449   1   ASEAN   94   68,791   17      Sources:  h@p://www.wfcc.info/ccinfo/sta8s8cs/ updated  23  August  2013 Culture  Collec8ons  in   Thailand  and  ASEAN  
  3. 3. 9/11/13 Copyright  2012-­‐2013  BIOTEC 3 www.biotec.or.th/bcc/ Only BCC and TISTR have their own e-Catalog and join the GCM. (2 of 60) www.Kstr.or.th/Kstr_culture/  
  4. 4. 9/11/13 Copyright  2012-­‐2013  BIOTEC 4 Culture   Collec8ons   #Cultures   registered   in  CCINFO   #Cultures     available  in   TNCC   BCC   (wdcm  783)   5,010   3,430   DMST   (wdcm  707)   10,000   442   DOA   (wdcm  704,  705)   76     1,163   TISTR   (wdcm  383)   2,425   515   Total  (TNCC)   17,511   5,550   UNIVERSITIES   25,740   TOTAL   43,251   Thailand Network on Culture Collections (TNCC) 4 of 60 : Service Collections (7%) http://www.biotec.or.th/tncc/
  5. 5. 9/11/13 Copyright  2012-­‐2013  BIOTEC 5 http://www.biotec.or.th/tncc/ Culture   Collec8ons   #Cultures   registered   in  CCINFO   #Cultures     available  in   TNCC   BCC   (wdcm  783)   5,010   3,430   DMST   (wdcm  707)   10,000   442   DOA   (wdcm  704,  705)   76     1,163   TISTR   (wdcm  383)   2,425   515   Total  (TNCC)   17,511   5,550   UNIVERSITIES   25,740   TOTAL   43,251   Thailand Network on Culture Collections (TNCC) Thai Service Collections
  6. 6. TNCC e-catalog Direct Data Entry l Easy to implement, but laborious data conversion, data entry at data node TNCC ( established since 2000) Internal     DB   Data Conversion File Transfer =TNCC Data standard = Data Update- (Modify in-house DB, Convert data, submit or input the data) Member 9/11/13 Copyright  2012-­‐2013  BIOTEC 6
  7. 7. 9/11/13 Copyright  2012-­‐2013  BIOTEC 7 Culture   Collec8ons   #Cultures   registered   in  CCINFO   #Cultures     available  in   TNCC   BCC   (wdcm  783)   5,010   3,430   DMST   (wdcm  707)   10,000   442   DOA   (wdcm  704,  705)   76     1,163   TISTR   (wdcm  383)   2,425   515   Total  (TNCC)   17,511   5,550   UNIVERSITIES   25,740   TOTAL   43,251   54 of 60 Research/ Specialized Collections
  8. 8. 9/11/13     Copyright  2012-­‐2013  BIOTEC   8   TBRC,  Thailand  Bioresource  Research   Center  has  been  iniKated  by  BIOTEC,   to     •  facilitate  the  integraKon  and  the   access  of  biomaterial  and  related   informaKon  beyond  the  scope  of  a   single  BRC,  and     •   fill  the  missing  link  between  BRC   and  industry
  9. 9. 9/11/13 Copyright  2012-­‐2013  BIOTEC 9 TBRC  aims  to     (1)  leverage  the  network   strength  of  service  collecKons     (2)  create  a  network  of   research  collecKons    (3)  establish  a  common   technology  infrastructure  to   provide  standards  and   interoperable  informaKon   systems  across  the  network   levels    
  10. 10. 9/11/13 Copyright  2012-­‐2013  BIOTEC 10 TBRC and Network of Research Collections
  11. 11. 9/11/13 Copyright  2012-­‐2013  BIOTEC 11 TBRC member/hub Management System TBRC Central Management System TBRC Internet Distribution System TBRC-miner TBRC-Link TBRC-catalog Microbe++ Retrieve orders Avail. Cultures Mine for associated info Categorization Categorized microbe++ Submit orderDispatch order TBRC-node
  12. 12. 9/11/13 Copyright  2012-­‐2013  BIOTEC 12 TBRC Web services iCollect: Software for TBRC Member TBRC-node TBRC-Link
  13. 13. 9/11/13 Copyright  2012-­‐2013  BIOTEC 13 Microbe++: Using text mining to build TBRC strain catalog TBRC-miner TBRC-Link TBRC-catalog
  14. 14. 9/11/13     14   Ref: Enzymes at Work, Novozyme, www.novozymes.com/en/about-us/brochures/.../enzymes_at_work.pdf‎ accessed 9/15/2013 Megazyme, http://www.megazyme.com/docs/analytical-applications-downloads/ enzymes_indsutrial_and_analytical_appliation_eng.pdf?sfvrsn=2, accessed 9/15/2013 Categorized by Enzyme Copyright  2012-­‐2013  BIOTEC  
  15. 15. Tagged abstracts Abstracts ” from PubMed PMID- 22782181 OWN – NLM DP - 2012 Jul 11 TI - In vitro human cell-free expression system for synthesis of malaria proteins. AB - Malaria rhoptry genes (PFc14_0344, PFc0120w, PY01759, PY00763, PY07482, and PY04666) and a Maurer's cleft gene (PfA0680c) identified from proteome analysis studies were cloned into the pT7CFE1-Chis ... AD - Department of Biological, Geological, And Environmental Sciences, PMID- 22782471 OWN – NLM DP - 2012 Jul 11 TI - In vitro human cell-free expression system for synthesis of malaria proteins. AB - Malaria rhoptry genes (PFc14_0344, PFc0120w, PY01759, in Plasmodium faciparum, .. AD - Department of Biological, Geological, And Environmental Sciences, Enzyme Ontology Pathway Ontology KEGG pathways, PANTHER pathways, … Taxonomy & gene info from NCBI PMID- 22782181 OWN – NLM DP - 2012 Jul 11 TI - In vitro human cell-free expression system for synthesis of malaria proteins. AB - Malaria rhoptry genes (PFc14_0344, PFc0120w, PY01759, PY00763, PY07482, and PY04666) and a Maurer's cleft gene (PfA0680c) identified from proteome analysis studies were cloned into the pT7CFE1-Chis ... AD - Department of Biological, Geological, And Environmental Sciences, PMID- 22782471 OWN – NLM DP - 2012 Jul 11 TI - In vitro human cell-free expression system for synthesis of malaria proteins. AB - Malaria rhoptry genes (<START: GENE> PFc14_0344 <END>, <START:GENE> PFc0120w <END> <START:GENE>PY01759 <END> , in <START: SPECIES> Plasmodium faciparum <END>... AD - Department of Biological, Geological, And Environmental Sciences, Microbe++ Search Engine 1 2 3 4 TBRC-­‐miner:  Ontology-­‐driven  Indexing  and  tagging  of  publicaKons     Enzyme   nomenclature   Industrial   ClassificaKon   9/11/13     Copyright  2012-­‐2013  BIOTEC   15  
  16. 16. 9/11/13 Copyright  2012-­‐2013  BIOTEC 16 TBRC  :  Opening  2014 Become  the  informaKon  hub  for  microbial  resources  in  Thailand     Deliver  diverse  microbial  cultures  and  services  for  science  and  industry   www.tbrcnetwork.org

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