The collaborative working environment an envisaged new level of knowledge transfer and innovative collaboration

Transcription

1 Leibniz-Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH The collaborative working environment an envisaged new level of knowledge transfer and innovative collaboration Erko Stackebrandt, Manuela Schüngel, Dunja Martin and MIRRI partners MIRRI Coordination Bureau, Leibniz-Institute DSMZ, Braunschweig, Germany

2 Leibniz-Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH Beijing Declaration in Microbial Resources Information Sharing (version August 2016) Recognizing c. That in the age of microbial data diversification and explosion, an effective information environment that promotes and sustains microbial research data activities, sharing and use to help advance progress and bridge the gaps within and outside the microbial communities is prerequisite. Link to the Network of Microbial Resources Data Sharing Network

3 Leibniz-Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH

4 Leibniz-Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH 26 million citations in PubMed 50 Million citations for microorganisms 104 million citations for bacteria, citations for Cellulomonas in

5 Leibniz-Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH Origin Habitat User deposit PubMed Clearing House training education Mycobank StrainInfo CABRI ABS,CBD User access User retrieval Bibliography Approved Lists Integrated catalogs Public catalogs mbrcs others OECD Best practice QM, Biosecurity Knowledge transfer Data mining Non-public deposits Tools, BLAST ANI Biosecurity Biosafety Additional properties Patents Molecular data Gold, Brenda Silva WIPO chemotaxonomy EBI NCBI Safe deposit Secured holdings Bioindustry Elixir MALDI-TOF PL, PA Peptidoglycan Fatty acids

6 Leibniz-Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH Isn t this worthwhile trying?

7 Leibniz-Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH Lets assume we want to describe a new taxon or do a comparative survey on application Where are the data for comparative analysis? Easy search for newly described species: original description in e.g. IJSEM, only abstract available for non-subscribers. Abstracts lists many features except physiology. Comprehensive overviews in Bergey s Manual and The Prokaryotes, mainly restricted to type strains. Time-consuming literature search for species and strains (PubMed, Google via Internet).

8 Leibniz-Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH Publication search results for Cellulomonas flavigena Topic Total hits Abstract Full text Full text PDF Medical Ecology Taxonomy Chemotaxonomy Genes, Genomes Physiology Application Enzymes xylanase glucosidase others Review Articles Book Reviews 11 Total

9 Leibniz-Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH Data search in BacDive* (DSMZ) for Cellulomonas flavigena Name and taxonomic classification Morphology and physiology (API20, API coryne, API ZYM) Culture and growth conditions Peptidoglycan type: A4ß, L-Orn-D-Asp Full genome sequence Strain availability: DSM 20109, ATCC 482, CCM 1926, NCIB 8073 *

10 Leibniz-Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH Links to Search for species Cellulomonas flavigena in external resources SILVA - 16S rrna sequences (quality checked) BRENDA - protein data PANGAEA - 0 data on Earth and Environment StrainInfo history, availability, link to databases, recommended 16S rrna sequence GBIF 11 entries, mainly on taxonomy But: no easy search for specific strains

11 Recommended Name Organism Leibniz-Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH e.g. Brenda Results 1-9 EC Recommended name Organisms (plus synonyms) cellulase Cellulomonas flavigena cellulase Cellulomonas flavigena endo-1,4-beta-xylanase Cellulomonas flavigena endo-1,4-beta-xylanase Cellulomonas flavigena CDBB endo-1,4-beta-xylanase Cellulomonas flavigena CDBB beta-glucosidase Cellulomonas flavigena glucuronoarabinoxylan endo-1,4-beta-xylanase Cellulomonas flavigena glucuronoarabinoxylan endo-1,4-beta-xylanase Cellulomonas flavigena CDBB acetolactate decarboxylase Cellulomonas flavigena But: no easy search for specific strains, each entry must be checked individually

12 Leibniz-Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH Chemotaxonomic and physiological traits Peptidoglycan types Databases DSMZ Catalog under species names Availability Species description, Prokaryotes, Bergey s MALDI TOF Bruker, Shimadzu Commercial Fatty acids Midi-System Commercial. Species description. Prokaryotes, Bergey s Biolog, API Biolog Commercial. Species description. Prokaryotes, Bergey s Isoprenoid quinones, polar lipids, polyamines - Species description Prokaryotes, Bergey s

13 Leibniz-Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH Entries of actinobacterial genome sequences Number of genome sequences Actinobacteria 9556 Micrococcales 1161 Cellulomonadaceae 62 Cellulomonas 48 Cellulomonas flavigena 1 Cellulomonas flavigena, type 1 Reddy et al. The Genomes OnLine Database (GOLD) v.5: a metadata management system based on a four level (meta)genome project classification. Nucl. Acids Res. (2014

14 16 Partners, 11 countries 28 Collaborating Parties, 8 additional countries

15 The European MIRRI project The Microbial Resource Research Infrastructure aims at removing the fragmented European mbrc landscape by creating a single European overarching legal entity (Central Coordinating Unit, CCU) in which users are served through a single portal for accessing services provided by the distributed mbrcs working together: the depth and breadth of holdings and data will be increased, redundancies avoided, gaps filled, compliant access to resources provided, etc. 15

16 MIRRIs extended Knowledge Transfer Identify, collect and archive knowledge. Capture Share Present and share knowledge. Add complementary information to increase value of knowledge. Enrich Use Analyze, map and exploit knowledge. Evaluate market and future needs in knowledge. Assess MIRRI is adding value to traditional knowledge transfer by mapping complementary knowledge and serving customized demands. The enriched knowledge landscape is increasing the efficiency of innovative research. 16

17 MIRRIs envisaged novel way of knowledge transfer and collaboration MIRRI Collaborative Work Environment Infrastructure Information Gate to Resources & Data Gate to Collaboration & Experts Gate to Training & Education Public Website Microbial Resources Expert Clusters On-site Trainings Partners Area Data Events elearning Services Knowledge base MIRRI: the gate to innovation and success! 17

18 MIRRI CWE matching effectivly demand and supply MIRRI Collaborative Work Environment Gate to Resources & Data Microbial Resources Data Services Public Website Gate to Collaboration & Experts Expert Clusters Events Partners Area Gate to Training & Education On-site Trainings elearning Knowledge base

19 The Mall concept Single-item shopping idea Data Literature Habitat Provider Expert e-learning Access Strains Rules, regulations Application Collaboration isolation Bio- Industry Multi-item retrieval strategy

20 The virtual Mall concept of the MIRRI offer Single-item shopping idea Data Literature Habitat Provider Expert e-learning Access Strains Rules, regulations Application Collaboration isolation Bio- Industry Multi-item retrieval strategy

21 CWE implementing visability Production Expertise Service Resources & Data Where do you find? Biological Material Services Data Communication Exchange Expertise Production Facilities 21

22 CWE a culture of transparency and empowerment Production Expertise Service Resources & Data Where do you find? Biological Material Services Data Communication Exchange Expertise Production Facilities MIRRI CWE Combines the entire world of biological ressources and knowhow on a single platform Easily creates a massive surplus in transparency for scientists worldwide Saves valuable time in research Broadens the horizon and creates new ideas and products 22

23 CWE gate to the microbial world X (Re)Search Genetic Resource: Cellulomonas flavigena spp Search Options: Resources Literature Sequence Data Service Offers Experts Training Search all or Select individually 23

24 MIRRI has not yet obtained a legal status, hence MIRRI has no funds at present Ideas on requirements are ripening but implementation, i.e. IT architecture (front end, back ends), is delayed (find the most appropriate developer: > 1 mill. + individual solutions) Search for funds From Ideas to Actions Realization may benefit from previous experience and/or available systems Individual solutions (e.g. text mining of literature or design of interactive databases) may already be explored Question: How to work together, not in parallel? 24

25 Thank you 25 The preparatory phase of MIRRI supported by the European Commission (grant agreement no )

26 Leibniz-Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH PubMed Central search for key words on Cellulomonas flavigena T Key words Hits ATCC ATCC 482, ATCC and 482, ATCC each ATCC_482, ATCC each Cellulomonas flavigena ATCC DSMZ DSM DSM and 20109, DSM each DSM_20109, DSM each Cellulomonas flavigena DSM