SlideShare une entreprise Scribd logo

Roberts leiden110213

•
•
V
vibrantmanager
Technologie
1  sur  18
Télécharger pour lire hors ligne
Scratchpad virtual research environments: sharing, linking and publishing biodiversity data the ViBRANT way Vince Smith1, Dave Roberts1 & Lyubomir Penev2 1. Natural History Museum, London 2. Pensoft Publishers, Sofia, Bulgaria
Our informatics grand challenge… “Link together evolutionary data… by developing analytical tools and proper documentation and then use this framework to conduct comparative analyses, studies of evolutionary process and biodiversity analyses” Cyndy Parr, Rob Guralnick, Nico Cellinese and Rod Page. TREE. doi:10.1016/j.tree.2011.11.001
Our informatics grand challenge… “Link together evolutionary data… by developing analytical tools and proper documentation and then use this framework to conduct comparative analyses, studies of evolutionary process and biodiversity analyses” Cyndy Parr, Rob Guralnick, Nico Cellinese and Rod Page. TREE. doi:10.1016/j.tree.2011.11.001 This requires data, information & knowledge to be… •  Digital Not printed paper •  Openly accessible Not behind barriers •  Linked-up Not in silos
Most of our output is not digital, open or linked •  •  •  •  •  •  15-20k new spp. described annually (2M total)1 30k nomenclatural acts (12M total) 1 20k phylogenies (750k total)2 31k taxa sequenced (360k taxa total)3 800k BioMed papers (40M total pp. of taxonomy) 4 Countless specimens, images, maps, keys… Typically generated by small communities for “local” research projects Figures from 1) Zhang, Zootaxa 2011 4, 1-4; 2) Web-of-Science; 3) Genbank and 4) PubMed.
ViBRANT Virtual Biodiversity A website for you & your community Magic Your data SEVENTH FRAMEWORK PROGRAMME Your web site -infrastructure
ViBRANT Virtual Biodiversity What are Scratchpads? • Hosted websites for biodiversity data • Virtual research & publication platform • Completely open access & open source • Modular & flexible SEVENTH FRAMEWORK PROGRAMME -infrastructure
ViBRANT Virtual Biodiversity What Scratchpads are not! • A single biodiversity database • Restricted thematically, geographically or taxonomically • A tool just for taxonomists • Owned or controlled by anyone other than the data creator SEVENTH FRAMEWORK PROGRAMME -infrastructure
ViBRANT Virtual Biodiversity How are Scratchpads funded? 2007 2011 2014 ViBRANT Virtual Biodiversity & SEVENTH FRAMEWORK PROGRAMME -infrastructure
ViBRANT Virtual Biodiversity Scratchpads Taxonomy & Literature Lice, mosquitos, freeloader flies, ... (rapid upload and management of names, synonyms & bibliographic data) Characters, Phylogeny & Specimens Termites, bryozoa, ... (character matrices exporting to SDD and Nexus format, phylogenies, specimen records & maps) biodiversity online 7000 6000 5000 4000 Sites Users Active Users 400 300 3000 200 2000 100 Taxon descriptions & Publications 1000 50 Sites 20 eJournals European Mosquito Bulletin, Phasmid Studies, ... (submission, review & dissemination of articles) SEVENTH FRAMEWORK PROGRAMME Dragon trees, nanno fossils, cockroaches, fungi, polychaetes, ... (rapid upload, annotation & display of images) 500 2007 2008 2009 2010 2011 2012 ViBRANT Scratchpads 2 Users Freeloader Flies, fungus gnats, ... (publication of Scratchpad data in the ZooKeys journal and export to Encyclopedia of Life) Image Galleries Societies, Organisations & Projects ICZN, GBIF, Sampled Red List Index for Plants, Global Plants Initiative ... (space for data collection, services, discussion & organisation) -infrastructure
ViBRANT Virtual Biodiversity Training & outreach Support services ViBRANT Goals Vision Connecting the people, data & science of biodiversity http://vbrant.eu SEVENTH FRAMEWORK PROGRAMME Controlled vocabulary Networking Training Standards Mobilisation Sociology Data aggregation Field recording GBIF integration Citizen science Position Open & sustainable development of a federated network of biodiversity informatics infrastructures Mission Facilitate the mobalisation, sharing, reuse and publication of biodiversity data Data standards Visualisation Scratchpads Virtual Research Environment Scratchpad Phylogeny tools hosting Bioclimatic modelling Software integration Identification tools Matrix data editor Data publishing Service Data Publishing Manuscript publishing Sustainability Communal literature Research Literature mark up Architecture Literature Data mining -infrastructure
ViBRANT Virtual Biodiversity Taxonomic Concept Schema XML Nexus Newick CSV/tab Excel file EoL Transfer schema (SPM) SDD, Lucid, DwCA Nexus SEVENTH FRAMEWORK PROGRAMME XML CSV, XLS, RDF Microsoft Word .DOC, TXT -infrastructure
ViBRANT What can Scratchpads do? Virtual Biodiversity • Taxon pages (generated from tagged content) • Distribution maps (from specimens and TDWG regional distributions - Brummitt, 2001) • Specimen records • Bibliography management • Images, video and sound (bulk import) • Excel spreadsheet import • Tabular data editing & Character matrixes • Custom content • User management • Custom webforms • Analytics • Darwin Core Archive export (links to eMonocot Portal and EOL) • EOL data import (taxonomy, species information) • GBIF Map integration SEVENTH FRAMEWORK PROGRAMME -infrastructure
ViBRANT Virtual Biodiversity http://www.comber.hcmr.gr SEVENTH FRAMEWORK PROGRAMME -infrastructure
ViBRANT Virtual Biodiversity Oxford Batch Operations Engine https://oboe.oerc.ox.ac.uk/ SEVENTH FRAMEWORK PROGRAMME -infrastructure
ViBRANT Virtual Biodiversity BDJ The Biodiversity Data Journal Making small data big! SEVENTH FRAMEWORK PROGRAMME -infrastructure
ViBRANT Virtual Biodiversity ISSN 1314-2828 (online) ISSN 1314-2836 (print) 1. Define the publication A peer-reviewed open-access journal Biodiversity D ata Journal Articles Launched to accelerate biodiversity data journal Bibliographies 2. Enter metadata Occurrence 3. Select taxa & content 1t 2011 Taxon treatments Plazi http://www.pensoft.net/biodiversitydata 4. Organise manuscript Editor-in-Chief: VINCENT SMITH Natural History Museum, London, UK Taxon names 5. Submit to journal I . P . N . I SEVENTH FRAMEWORK PROGRAMME -infrastructure
ViBRANT Virtual Biodiversity Acknowledgements • Scratchpad technical development - Simon Rycroft, Ben Scott, Ed Baker, Alice Heaton & Katherine Boulton • Scratchpad outreach - Laurence Livermore & Dimitris Koureas • E-Monocot - Paul Wilkin & the Kew team, Charles Godfray & the Oxford team • ViBRANT - Vince Smith, Dave Roberts & Lucy Reeve • Our 7,000+ users SEVENTH FRAMEWORK PROGRAMME -infrastructure
ViBRANT Virtual Biodiversity Thank you for your attention. Any questions e-mail: enquiries@vbrant.eu e-mail: scratchpad@nhm.ac.uk http://vbrant.eu SEVENTH FRAMEWORK PROGRAMME http://scratchpads.eu -infrastructure

Recommandé

ViBRANT 8th e-Concertation Meeting, CERN
ViBRANT 8th e-Concertation Meeting, CERNViBRANT 8th e-Concertation Meeting, CERN
ViBRANT 8th e-Concertation Meeting, CERNVince Smith
 
No specimen left behind: Collections digitisation at the NHM, London*
No specimen left behind: Collections digitisation at the NHM, London*No specimen left behind: Collections digitisation at the NHM, London*
No specimen left behind: Collections digitisation at the NHM, London*Vince Smith
 
Moving beyond the box: automating the digitisation of insect collections
Moving beyond the box: automating the digitisation of insect collectionsMoving beyond the box: automating the digitisation of insect collections
Moving beyond the box: automating the digitisation of insect collectionsVince Smith
 
Small pieces loosely joined: getting louse research online.
Small pieces loosely joined: getting louse research online.Small pieces loosely joined: getting louse research online.
Small pieces loosely joined: getting louse research online.Vince Smith
 
Tutorial: “How to use ontology repositories and ontology–based services”
Tutorial: “How to use ontology repositories and ontology–based services”Tutorial: “How to use ontology repositories and ontology–based services”
Tutorial: “How to use ontology repositories and ontology–based services”INRAE (MISTEA) and University of Montpellier (LIRMM)
 
Digitised collections: Toward a digital strategy for for the NHM, London
Digitised collections: Toward a digital strategy for for the NHM, LondonDigitised collections: Toward a digital strategy for for the NHM, London
Digitised collections: Toward a digital strategy for for the NHM, LondonVince Smith
 
eMonocot Project Update
eMonocot Project UpdateeMonocot Project Update
eMonocot Project UpdateeMonocot
 
Digital research: Collections, data, tools and methods
Digital research: Collections, data, tools and methods Digital research: Collections, data, tools and methods
Digital research: Collections, data, tools and methods Stella Wisdom
 

Recommandé

ViBRANT 8th e-Concertation Meeting, CERN
ViBRANT 8th e-Concertation Meeting, CERNViBRANT 8th e-Concertation Meeting, CERN
ViBRANT 8th e-Concertation Meeting, CERNVince Smith
 
No specimen left behind: Collections digitisation at the NHM, London*
No specimen left behind: Collections digitisation at the NHM, London*No specimen left behind: Collections digitisation at the NHM, London*
No specimen left behind: Collections digitisation at the NHM, London*Vince Smith
 
Moving beyond the box: automating the digitisation of insect collections
Moving beyond the box: automating the digitisation of insect collectionsMoving beyond the box: automating the digitisation of insect collections
Moving beyond the box: automating the digitisation of insect collectionsVince Smith
 
Small pieces loosely joined: getting louse research online.
Small pieces loosely joined: getting louse research online.Small pieces loosely joined: getting louse research online.
Small pieces loosely joined: getting louse research online.Vince Smith
 
Tutorial: “How to use ontology repositories and ontology–based services”
Tutorial: “How to use ontology repositories and ontology–based services”Tutorial: “How to use ontology repositories and ontology–based services”
Tutorial: “How to use ontology repositories and ontology–based services”INRAE (MISTEA) and University of Montpellier (LIRMM)
 
Digitised collections: Toward a digital strategy for for the NHM, London
Digitised collections: Toward a digital strategy for for the NHM, LondonDigitised collections: Toward a digital strategy for for the NHM, London
Digitised collections: Toward a digital strategy for for the NHM, LondonVince Smith
 
eMonocot Project Update
eMonocot Project UpdateeMonocot Project Update
eMonocot Project UpdateeMonocot
 
Digital research: Collections, data, tools and methods
Digital research: Collections, data, tools and methods Digital research: Collections, data, tools and methods
Digital research: Collections, data, tools and methods Stella Wisdom
 
The VRC Project
The VRC ProjectThe VRC Project
The VRC ProjectFabrizio Giudici
 
Scratchpads training course introduction
Scratchpads training course introductionScratchpads training course introduction
Scratchpads training course introductionDimitrios Koureas
 
Pampel/Bertelnmann/Hobohm: Data Librarianship
Pampel/Bertelnmann/Hobohm: Data LibrarianshipPampel/Bertelnmann/Hobohm: Data Librarianship
Pampel/Bertelnmann/Hobohm: Data LibrarianshipHans-Christoph Hobohm
 
E-ARK: Open Data Mining for Government Archives
E-ARK: Open Data Mining for Government ArchivesE-ARK: Open Data Mining for Government Archives
E-ARK: Open Data Mining for Government ArchivesDanube University Krems, Centre for E-Governance
 
Jim Woolley - Name Registration: One Less Impediment to Taxonomy
Jim Woolley - Name Registration: One Less Impediment to TaxonomyJim Woolley - Name Registration: One Less Impediment to Taxonomy
Jim Woolley - Name Registration: One Less Impediment to TaxonomyICZN
 
NECTAR_VRE1
NECTAR_VRE1NECTAR_VRE1
NECTAR_VRE1Craig Bellamy
 
Building data infrastructures for science
Building data infrastructures for scienceBuilding data infrastructures for science
Building data infrastructures for scienceVince Smith
 
Digital Thesis Unmsm
Digital Thesis UnmsmDigital Thesis Unmsm
Digital Thesis UnmsmLibio Huaroto
 
Introduction to eMonocot (Dave Simpson)
Introduction to eMonocot (Dave Simpson)Introduction to eMonocot (Dave Simpson)
Introduction to eMonocot (Dave Simpson)eMonocot
 
Scaling-up collections digitisation
Scaling-up collections digitisationScaling-up collections digitisation
Scaling-up collections digitisationVince Smith
 
Dagstuhl "Future" sesssion intro slides
Dagstuhl "Future" sesssion intro slidesDagstuhl "Future" sesssion intro slides
Dagstuhl "Future" sesssion intro slidesTim Clark
 
2016-10-12 MUSIT & GBIF - Dataset portals
2016-10-12 MUSIT & GBIF - Dataset portals2016-10-12 MUSIT & GBIF - Dataset portals
2016-10-12 MUSIT & GBIF - Dataset portalsDag Endresen
 
Florence2
Florence2Florence2
Florence2blalbritton
 
Tech Sci
Tech SciTech Sci
Tech Scikateb
 
Tdwg bih
Tdwg bihTdwg bih
Tdwg bihvibrantmanager
 
Kinhto
Kinhto Kinhto
Kinhto Eva Krokidi
 
Scratchpads sustainability berlin220513
Scratchpads sustainability berlin220513Scratchpads sustainability berlin220513
Scratchpads sustainability berlin220513vibrantmanager
 
The Ciliate Species Names List Project
The Ciliate Species Names List ProjectThe Ciliate Species Names List Project
The Ciliate Species Names List Projectvibrantmanager
 
Hardisty roberts 190313_opt
Hardisty roberts 190313_optHardisty roberts 190313_opt
Hardisty roberts 190313_optvibrantmanager
 
Bo l intro_060913_opt
Bo l intro_060913_optBo l intro_060913_opt
Bo l intro_060913_optvibrantmanager
 
Bih session7 panel2_summary
Bih session7 panel2_summaryBih session7 panel2_summary
Bih session7 panel2_summaryvibrantmanager
 
Hardisty roberts tdwg_301013_min
Hardisty roberts tdwg_301013_minHardisty roberts tdwg_301013_min
Hardisty roberts tdwg_301013_minvibrantmanager
 

Contenu connexe

Tendances

Scratchpads training course introduction
Scratchpads training course introductionScratchpads training course introduction
Scratchpads training course introductionDimitrios Koureas
 
Pampel/Bertelnmann/Hobohm: Data Librarianship
Pampel/Bertelnmann/Hobohm: Data LibrarianshipPampel/Bertelnmann/Hobohm: Data Librarianship
Pampel/Bertelnmann/Hobohm: Data LibrarianshipHans-Christoph Hobohm
 
Jim Woolley - Name Registration: One Less Impediment to Taxonomy
Jim Woolley - Name Registration: One Less Impediment to TaxonomyJim Woolley - Name Registration: One Less Impediment to Taxonomy
Jim Woolley - Name Registration: One Less Impediment to TaxonomyICZN
 
Building data infrastructures for science
Building data infrastructures for scienceBuilding data infrastructures for science
Building data infrastructures for scienceVince Smith
 
Digital Thesis Unmsm
Digital Thesis UnmsmDigital Thesis Unmsm
Digital Thesis UnmsmLibio Huaroto
 
Introduction to eMonocot (Dave Simpson)
Introduction to eMonocot (Dave Simpson)Introduction to eMonocot (Dave Simpson)
Introduction to eMonocot (Dave Simpson)eMonocot
 
Scaling-up collections digitisation
Scaling-up collections digitisationScaling-up collections digitisation
Scaling-up collections digitisationVince Smith
 
Dagstuhl "Future" sesssion intro slides
Dagstuhl "Future" sesssion intro slidesDagstuhl "Future" sesssion intro slides
Dagstuhl "Future" sesssion intro slidesTim Clark
 
2016-10-12 MUSIT & GBIF - Dataset portals
2016-10-12 MUSIT & GBIF - Dataset portals2016-10-12 MUSIT & GBIF - Dataset portals
2016-10-12 MUSIT & GBIF - Dataset portalsDag Endresen
 
Tech Sci
Tech SciTech Sci
Tech Scikateb
 

Tendances (14)

The VRC Project
The VRC ProjectThe VRC Project
The VRC Project
 
Scratchpads training course introduction
Scratchpads training course introductionScratchpads training course introduction
Scratchpads training course introduction
 
Pampel/Bertelnmann/Hobohm: Data Librarianship
Pampel/Bertelnmann/Hobohm: Data LibrarianshipPampel/Bertelnmann/Hobohm: Data Librarianship
Pampel/Bertelnmann/Hobohm: Data Librarianship
 
E-ARK: Open Data Mining for Government Archives
E-ARK: Open Data Mining for Government ArchivesE-ARK: Open Data Mining for Government Archives
E-ARK: Open Data Mining for Government Archives
 
Jim Woolley - Name Registration: One Less Impediment to Taxonomy
Jim Woolley - Name Registration: One Less Impediment to TaxonomyJim Woolley - Name Registration: One Less Impediment to Taxonomy
Jim Woolley - Name Registration: One Less Impediment to Taxonomy
 
NECTAR_VRE1
NECTAR_VRE1NECTAR_VRE1
NECTAR_VRE1
 
Building data infrastructures for science
Building data infrastructures for scienceBuilding data infrastructures for science
Building data infrastructures for science
 
Digital Thesis Unmsm
Digital Thesis UnmsmDigital Thesis Unmsm
Digital Thesis Unmsm
 
Introduction to eMonocot (Dave Simpson)
Introduction to eMonocot (Dave Simpson)Introduction to eMonocot (Dave Simpson)
Introduction to eMonocot (Dave Simpson)
 
Scaling-up collections digitisation
Scaling-up collections digitisationScaling-up collections digitisation
Scaling-up collections digitisation
 
Dagstuhl "Future" sesssion intro slides
Dagstuhl "Future" sesssion intro slidesDagstuhl "Future" sesssion intro slides
Dagstuhl "Future" sesssion intro slides
 
2016-10-12 MUSIT & GBIF - Dataset portals
2016-10-12 MUSIT & GBIF - Dataset portals2016-10-12 MUSIT & GBIF - Dataset portals
2016-10-12 MUSIT & GBIF - Dataset portals
 
Florence2
Florence2Florence2
Florence2
 
Tech Sci
Tech SciTech Sci
Tech Sci
 

En vedette

Scratchpads sustainability berlin220513
Scratchpads sustainability berlin220513Scratchpads sustainability berlin220513
Scratchpads sustainability berlin220513vibrantmanager
 
The Ciliate Species Names List Project
The Ciliate Species Names List ProjectThe Ciliate Species Names List Project
The Ciliate Species Names List Projectvibrantmanager
 
Hardisty roberts 190313_opt
Hardisty roberts 190313_optHardisty roberts 190313_opt
Hardisty roberts 190313_optvibrantmanager
 
Bih session7 panel2_summary
Bih session7 panel2_summaryBih session7 panel2_summary
Bih session7 panel2_summaryvibrantmanager
 
Hardisty roberts tdwg_301013_min
Hardisty roberts tdwg_301013_minHardisty roberts tdwg_301013_min
Hardisty roberts tdwg_301013_minvibrantmanager
 

En vedette (8)

Tdwg bih
Tdwg bihTdwg bih
Tdwg bih
 
Kinhto
Kinhto Kinhto
Kinhto
 
Scratchpads sustainability berlin220513
Scratchpads sustainability berlin220513Scratchpads sustainability berlin220513
Scratchpads sustainability berlin220513
 
The Ciliate Species Names List Project
The Ciliate Species Names List ProjectThe Ciliate Species Names List Project
The Ciliate Species Names List Project
 
Hardisty roberts 190313_opt
Hardisty roberts 190313_optHardisty roberts 190313_opt
Hardisty roberts 190313_opt
 
Bo l intro_060913_opt
Bo l intro_060913_optBo l intro_060913_opt
Bo l intro_060913_opt
 
Bih session7 panel2_summary
Bih session7 panel2_summaryBih session7 panel2_summary
Bih session7 panel2_summary
 
Hardisty roberts tdwg_301013_min
Hardisty roberts tdwg_301013_minHardisty roberts tdwg_301013_min
Hardisty roberts tdwg_301013_min
 

Similaire à Roberts leiden110213

Making your data work for you: Scratchpads, publishing & the biodiversity dat...
Making your data work for you: Scratchpads, publishing & the biodiversity dat...Making your data work for you: Scratchpads, publishing & the biodiversity dat...
Making your data work for you: Scratchpads, publishing & the biodiversity dat...Vince Smith
 
Scratchpads Intro: Swiss Orchid Foundation
Scratchpads Intro: Swiss Orchid FoundationScratchpads Intro: Swiss Orchid Foundation
Scratchpads Intro: Swiss Orchid FoundationEdward Baker
 
Scratchpads introductory presentation 45mins
Scratchpads introductory presentation 45minsScratchpads introductory presentation 45mins
Scratchpads introductory presentation 45minsDimitrios Koureas
 
ALIAOnline Practical Linked (Open) Data for Libraries, Archives & Museums
ALIAOnline Practical Linked (Open) Data for Libraries, Archives & MuseumsALIAOnline Practical Linked (Open) Data for Libraries, Archives & Museums
ALIAOnline Practical Linked (Open) Data for Libraries, Archives & MuseumsJon Voss
 
Scripting Life: ViBRANT's Kickoff meeting
Scripting Life: ViBRANT's Kickoff meetingScripting Life: ViBRANT's Kickoff meeting
Scripting Life: ViBRANT's Kickoff meetingVince Smith
 
Scratchpad training
Scratchpad trainingScratchpad training
Scratchpad trainingVince Smith
 
ViBRANT Project Overview
ViBRANT Project OverviewViBRANT Project Overview
ViBRANT Project OverviewVince Smith
 
Danis biosystematics2011
Danis biosystematics2011Danis biosystematics2011
Danis biosystematics2011Bruno Danis
 
ViBRANT—Virtual Biodiversity Research and Access Network for Taxonomy
ViBRANT—Virtual Biodiversity Research and Access Network for TaxonomyViBRANT—Virtual Biodiversity Research and Access Network for Taxonomy
ViBRANT—Virtual Biodiversity Research and Access Network for TaxonomyVince Smith
 
Swiss Orchid Foundation Scratchpads and ViBRANT overview
Swiss Orchid Foundation Scratchpads and ViBRANT overviewSwiss Orchid Foundation Scratchpads and ViBRANT overview
Swiss Orchid Foundation Scratchpads and ViBRANT overviewEdward Baker
 
Wish you were here before!
Wish you were here before!Wish you were here before!
Wish you were here before!David King
 
Web services based workflows to deal with 3D data
Web services based workflows to deal with 3D dataWeb services based workflows to deal with 3D data
Web services based workflows to deal with 3D dataJose Enrique Ruiz
 
Using e-Infrastructures for Biodiversity Conservation
Using e-Infrastructures for Biodiversity ConservationUsing e-Infrastructures for Biodiversity Conservation
Using e-Infrastructures for Biodiversity ConservationBlue BRIDGE
 
NHM Data Portal: first steps toward the Graph-of-Life
NHM Data Portal: first steps toward the Graph-of-LifeNHM Data Portal: first steps toward the Graph-of-Life
NHM Data Portal: first steps toward the Graph-of-LifeEdward Baker
 
NHM Data Portal: first steps toward the Graph-of-Life
NHM Data Portal: first steps toward the Graph-of-LifeNHM Data Portal: first steps toward the Graph-of-Life
NHM Data Portal: first steps toward the Graph-of-LifeVince Smith
 
XldbEuropeEdinburgh-09-jun2011
XldbEuropeEdinburgh-09-jun2011XldbEuropeEdinburgh-09-jun2011
XldbEuropeEdinburgh-09-jun2011Alex Hardisty
 
An introduction to ViBRANT: Virtual Biodiversity Research and Access Network ...
An introduction to ViBRANT: Virtual Biodiversity Research and Access Network ...An introduction to ViBRANT: Virtual Biodiversity Research and Access Network ...
An introduction to ViBRANT: Virtual Biodiversity Research and Access Network ...Vince Smith
 
Introduction to Scratchpads & ViBRANT
Introduction to Scratchpads & ViBRANTIntroduction to Scratchpads & ViBRANT
Introduction to Scratchpads & ViBRANTEdward Baker
 

Similaire à Roberts leiden110213 (20)

Making your data work for you: Scratchpads, publishing & the biodiversity dat...
Making your data work for you: Scratchpads, publishing & the biodiversity dat...Making your data work for you: Scratchpads, publishing & the biodiversity dat...
Making your data work for you: Scratchpads, publishing & the biodiversity dat...
 
Scratchpads Intro: Swiss Orchid Foundation
Scratchpads Intro: Swiss Orchid FoundationScratchpads Intro: Swiss Orchid Foundation
Scratchpads Intro: Swiss Orchid Foundation
 
Scratchpads introductory presentation 45mins
Scratchpads introductory presentation 45minsScratchpads introductory presentation 45mins
Scratchpads introductory presentation 45mins
 
ViBRANT Overview
ViBRANT OverviewViBRANT Overview
ViBRANT Overview
 
ALIAOnline Practical Linked (Open) Data for Libraries, Archives & Museums
ALIAOnline Practical Linked (Open) Data for Libraries, Archives & MuseumsALIAOnline Practical Linked (Open) Data for Libraries, Archives & Museums
ALIAOnline Practical Linked (Open) Data for Libraries, Archives & Museums
 
Scripting Life: ViBRANT's Kickoff meeting
Scripting Life: ViBRANT's Kickoff meetingScripting Life: ViBRANT's Kickoff meeting
Scripting Life: ViBRANT's Kickoff meeting
 
Scratchpad training
Scratchpad trainingScratchpad training
Scratchpad training
 
ViBRANT Project Overview
ViBRANT Project OverviewViBRANT Project Overview
ViBRANT Project Overview
 
Danis biosystematics2011
Danis biosystematics2011Danis biosystematics2011
Danis biosystematics2011
 
ViBRANT—Virtual Biodiversity Research and Access Network for Taxonomy
ViBRANT—Virtual Biodiversity Research and Access Network for TaxonomyViBRANT—Virtual Biodiversity Research and Access Network for Taxonomy
ViBRANT—Virtual Biodiversity Research and Access Network for Taxonomy
 
Swiss Orchid Foundation Scratchpads and ViBRANT overview
Swiss Orchid Foundation Scratchpads and ViBRANT overviewSwiss Orchid Foundation Scratchpads and ViBRANT overview
Swiss Orchid Foundation Scratchpads and ViBRANT overview
 
Wish you were here before!
Wish you were here before!Wish you were here before!
Wish you were here before!
 
Web services based workflows to deal with 3D data
Web services based workflows to deal with 3D dataWeb services based workflows to deal with 3D data
Web services based workflows to deal with 3D data
 
Using e-Infrastructures for Biodiversity Conservation
Using e-Infrastructures for Biodiversity ConservationUsing e-Infrastructures for Biodiversity Conservation
Using e-Infrastructures for Biodiversity Conservation
 
NHM Data Portal: first steps toward the Graph-of-Life
NHM Data Portal: first steps toward the Graph-of-LifeNHM Data Portal: first steps toward the Graph-of-Life
NHM Data Portal: first steps toward the Graph-of-Life
 
NHM Data Portal: first steps toward the Graph-of-Life
NHM Data Portal: first steps toward the Graph-of-LifeNHM Data Portal: first steps toward the Graph-of-Life
NHM Data Portal: first steps toward the Graph-of-Life
 
XldbEuropeEdinburgh-09-jun2011
XldbEuropeEdinburgh-09-jun2011XldbEuropeEdinburgh-09-jun2011
XldbEuropeEdinburgh-09-jun2011
 
An introduction to ViBRANT: Virtual Biodiversity Research and Access Network ...
An introduction to ViBRANT: Virtual Biodiversity Research and Access Network ...An introduction to ViBRANT: Virtual Biodiversity Research and Access Network ...
An introduction to ViBRANT: Virtual Biodiversity Research and Access Network ...
 
130712 antabif workshop
130712 antabif workshop130712 antabif workshop
130712 antabif workshop
 
Introduction to Scratchpads & ViBRANT
Introduction to Scratchpads & ViBRANTIntroduction to Scratchpads & ViBRANT
Introduction to Scratchpads & ViBRANT
 

Dernier

Cloud Frontiers: A Deep Dive into Serverless Spatial Data and FME
Cloud Frontiers: A Deep Dive into Serverless Spatial Data and FMECloud Frontiers: A Deep Dive into Serverless Spatial Data and FME
Cloud Frontiers: A Deep Dive into Serverless Spatial Data and FMESafe Software
 
Repurposing LNG terminals for Hydrogen Ammonia: Feasibility and Cost Saving
Repurposing LNG terminals for Hydrogen Ammonia: Feasibility and Cost SavingRepurposing LNG terminals for Hydrogen Ammonia: Feasibility and Cost Saving
Repurposing LNG terminals for Hydrogen Ammonia: Feasibility and Cost SavingEdi Saputra
 
HTML Injection Attacks: Impact and Mitigation Strategies
HTML Injection Attacks: Impact and Mitigation StrategiesHTML Injection Attacks: Impact and Mitigation Strategies
HTML Injection Attacks: Impact and Mitigation StrategiesBoston Institute of Analytics
 
Apidays New York 2024 - The value of a flexible API Management solution for O...
Apidays New York 2024 - The value of a flexible API Management solution for O...Apidays New York 2024 - The value of a flexible API Management solution for O...
Apidays New York 2024 - The value of a flexible API Management solution for O...apidays
 
TrustArc Webinar - Stay Ahead of US State Data Privacy Law Developments
TrustArc Webinar - Stay Ahead of US State Data Privacy Law DevelopmentsTrustArc Webinar - Stay Ahead of US State Data Privacy Law Developments
TrustArc Webinar - Stay Ahead of US State Data Privacy Law DevelopmentsTrustArc
 
Strategize a Smooth Tenant-to-tenant Migration and Copilot Takeoff
Strategize a Smooth Tenant-to-tenant Migration and Copilot TakeoffStrategize a Smooth Tenant-to-tenant Migration and Copilot Takeoff
Strategize a Smooth Tenant-to-tenant Migration and Copilot Takeoffsammart93
 
How to Troubleshoot Apps for the Modern Connected Worker
How to Troubleshoot Apps for the Modern Connected WorkerHow to Troubleshoot Apps for the Modern Connected Worker
How to Troubleshoot Apps for the Modern Connected WorkerThousandEyes
 
Tata AIG General Insurance Company - Insurer Innovation Award 2024
Tata AIG General Insurance Company - Insurer Innovation Award 2024Tata AIG General Insurance Company - Insurer Innovation Award 2024
Tata AIG General Insurance Company - Insurer Innovation Award 2024The Digital Insurer
 
2024: Domino Containers - The Next Step. News from the Domino Container commu...
2024: Domino Containers - The Next Step. News from the Domino Container commu...2024: Domino Containers - The Next Step. News from the Domino Container commu...
2024: Domino Containers - The Next Step. News from the Domino Container commu...Martijn de Jong
 
Bajaj Allianz Life Insurance Company - Insurer Innovation Award 2024
Bajaj Allianz Life Insurance Company - Insurer Innovation Award 2024Bajaj Allianz Life Insurance Company - Insurer Innovation Award 2024
Bajaj Allianz Life Insurance Company - Insurer Innovation Award 2024The Digital Insurer
 
Exploring the Future Potential of AI-Enabled Smartphone Processors
Exploring the Future Potential of AI-Enabled Smartphone ProcessorsExploring the Future Potential of AI-Enabled Smartphone Processors
Exploring the Future Potential of AI-Enabled Smartphone Processorsdebabhi2
 
Axa Assurance Maroc - Insurer Innovation Award 2024
Axa Assurance Maroc - Insurer Innovation Award 2024Axa Assurance Maroc - Insurer Innovation Award 2024
Axa Assurance Maroc - Insurer Innovation Award 2024The Digital Insurer
 
Deploy with confidence: VMware Cloud Foundation 5.1 on next gen Dell PowerEdg...
Deploy with confidence: VMware Cloud Foundation 5.1 on next gen Dell PowerEdg...Deploy with confidence: VMware Cloud Foundation 5.1 on next gen Dell PowerEdg...
Deploy with confidence: VMware Cloud Foundation 5.1 on next gen Dell PowerEdg...Principled Technologies
 
The 7 Things I Know About Cyber Security After 25 Years | April 2024
The 7 Things I Know About Cyber Security After 25 Years | April 2024The 7 Things I Know About Cyber Security After 25 Years | April 2024
The 7 Things I Know About Cyber Security After 25 Years | April 2024Rafal Los
 
Real Time Object Detection Using Open CV
Real Time Object Detection Using Open CVReal Time Object Detection Using Open CV
Real Time Object Detection Using Open CVKhem
 
A Year of the Servo Reboot: Where Are We Now?
A Year of the Servo Reboot: Where Are We Now?A Year of the Servo Reboot: Where Are We Now?
A Year of the Servo Reboot: Where Are We Now?Igalia
 
Partners Life - Insurer Innovation Award 2024
Partners Life - Insurer Innovation Award 2024Partners Life - Insurer Innovation Award 2024
Partners Life - Insurer Innovation Award 2024The Digital Insurer
 
MINDCTI Revenue Release Quarter One 2024
MINDCTI Revenue Release Quarter One 2024MINDCTI Revenue Release Quarter One 2024
MINDCTI Revenue Release Quarter One 2024MIND CTI
 
GenAI Risks & Security Meetup 01052024.pdf
GenAI Risks & Security Meetup 01052024.pdfGenAI Risks & Security Meetup 01052024.pdf
GenAI Risks & Security Meetup 01052024.pdflior mazor
 
Apidays New York 2024 - The Good, the Bad and the Governed by David O'Neill, ...
Apidays New York 2024 - The Good, the Bad and the Governed by David O'Neill, ...Apidays New York 2024 - The Good, the Bad and the Governed by David O'Neill, ...
Apidays New York 2024 - The Good, the Bad and the Governed by David O'Neill, ...apidays
 

Dernier (20)

Cloud Frontiers: A Deep Dive into Serverless Spatial Data and FME
Cloud Frontiers: A Deep Dive into Serverless Spatial Data and FMECloud Frontiers: A Deep Dive into Serverless Spatial Data and FME
Cloud Frontiers: A Deep Dive into Serverless Spatial Data and FME
 
Repurposing LNG terminals for Hydrogen Ammonia: Feasibility and Cost Saving
Repurposing LNG terminals for Hydrogen Ammonia: Feasibility and Cost SavingRepurposing LNG terminals for Hydrogen Ammonia: Feasibility and Cost Saving
Repurposing LNG terminals for Hydrogen Ammonia: Feasibility and Cost Saving
 
HTML Injection Attacks: Impact and Mitigation Strategies
HTML Injection Attacks: Impact and Mitigation StrategiesHTML Injection Attacks: Impact and Mitigation Strategies
HTML Injection Attacks: Impact and Mitigation Strategies
 
Apidays New York 2024 - The value of a flexible API Management solution for O...
Apidays New York 2024 - The value of a flexible API Management solution for O...Apidays New York 2024 - The value of a flexible API Management solution for O...
Apidays New York 2024 - The value of a flexible API Management solution for O...
 
TrustArc Webinar - Stay Ahead of US State Data Privacy Law Developments
TrustArc Webinar - Stay Ahead of US State Data Privacy Law DevelopmentsTrustArc Webinar - Stay Ahead of US State Data Privacy Law Developments
TrustArc Webinar - Stay Ahead of US State Data Privacy Law Developments
 
Strategize a Smooth Tenant-to-tenant Migration and Copilot Takeoff
Strategize a Smooth Tenant-to-tenant Migration and Copilot TakeoffStrategize a Smooth Tenant-to-tenant Migration and Copilot Takeoff
Strategize a Smooth Tenant-to-tenant Migration and Copilot Takeoff
 
How to Troubleshoot Apps for the Modern Connected Worker
How to Troubleshoot Apps for the Modern Connected WorkerHow to Troubleshoot Apps for the Modern Connected Worker
How to Troubleshoot Apps for the Modern Connected Worker
 
Tata AIG General Insurance Company - Insurer Innovation Award 2024
Tata AIG General Insurance Company - Insurer Innovation Award 2024Tata AIG General Insurance Company - Insurer Innovation Award 2024
Tata AIG General Insurance Company - Insurer Innovation Award 2024
 
2024: Domino Containers - The Next Step. News from the Domino Container commu...
2024: Domino Containers - The Next Step. News from the Domino Container commu...2024: Domino Containers - The Next Step. News from the Domino Container commu...
2024: Domino Containers - The Next Step. News from the Domino Container commu...
 
Bajaj Allianz Life Insurance Company - Insurer Innovation Award 2024
Bajaj Allianz Life Insurance Company - Insurer Innovation Award 2024Bajaj Allianz Life Insurance Company - Insurer Innovation Award 2024
Bajaj Allianz Life Insurance Company - Insurer Innovation Award 2024
 
Exploring the Future Potential of AI-Enabled Smartphone Processors
Exploring the Future Potential of AI-Enabled Smartphone ProcessorsExploring the Future Potential of AI-Enabled Smartphone Processors
Exploring the Future Potential of AI-Enabled Smartphone Processors
 
Axa Assurance Maroc - Insurer Innovation Award 2024
Axa Assurance Maroc - Insurer Innovation Award 2024Axa Assurance Maroc - Insurer Innovation Award 2024
Axa Assurance Maroc - Insurer Innovation Award 2024
 
Deploy with confidence: VMware Cloud Foundation 5.1 on next gen Dell PowerEdg...
Deploy with confidence: VMware Cloud Foundation 5.1 on next gen Dell PowerEdg...Deploy with confidence: VMware Cloud Foundation 5.1 on next gen Dell PowerEdg...
Deploy with confidence: VMware Cloud Foundation 5.1 on next gen Dell PowerEdg...
 
The 7 Things I Know About Cyber Security After 25 Years | April 2024
The 7 Things I Know About Cyber Security After 25 Years | April 2024The 7 Things I Know About Cyber Security After 25 Years | April 2024
The 7 Things I Know About Cyber Security After 25 Years | April 2024
 
Real Time Object Detection Using Open CV
Real Time Object Detection Using Open CVReal Time Object Detection Using Open CV
Real Time Object Detection Using Open CV
 
A Year of the Servo Reboot: Where Are We Now?
A Year of the Servo Reboot: Where Are We Now?A Year of the Servo Reboot: Where Are We Now?
A Year of the Servo Reboot: Where Are We Now?
 
Partners Life - Insurer Innovation Award 2024
Partners Life - Insurer Innovation Award 2024Partners Life - Insurer Innovation Award 2024
Partners Life - Insurer Innovation Award 2024
 
MINDCTI Revenue Release Quarter One 2024
MINDCTI Revenue Release Quarter One 2024MINDCTI Revenue Release Quarter One 2024
MINDCTI Revenue Release Quarter One 2024
 
GenAI Risks & Security Meetup 01052024.pdf
GenAI Risks & Security Meetup 01052024.pdfGenAI Risks & Security Meetup 01052024.pdf
GenAI Risks & Security Meetup 01052024.pdf
 
Apidays New York 2024 - The Good, the Bad and the Governed by David O'Neill, ...
Apidays New York 2024 - The Good, the Bad and the Governed by David O'Neill, ...Apidays New York 2024 - The Good, the Bad and the Governed by David O'Neill, ...
Apidays New York 2024 - The Good, the Bad and the Governed by David O'Neill, ...
 

Roberts leiden110213

  • 1. Scratchpad virtual research environments: sharing, linking and publishing biodiversity data the ViBRANT way Vince Smith1, Dave Roberts1 & Lyubomir Penev2 1. Natural History Museum, London 2. Pensoft Publishers, Sofia, Bulgaria
  • 2. Our informatics grand challenge… “Link together evolutionary data… by developing analytical tools and proper documentation and then use this framework to conduct comparative analyses, studies of evolutionary process and biodiversity analyses” Cyndy Parr, Rob Guralnick, Nico Cellinese and Rod Page. TREE. doi:10.1016/j.tree.2011.11.001
  • 3. Our informatics grand challenge… “Link together evolutionary data… by developing analytical tools and proper documentation and then use this framework to conduct comparative analyses, studies of evolutionary process and biodiversity analyses” Cyndy Parr, Rob Guralnick, Nico Cellinese and Rod Page. TREE. doi:10.1016/j.tree.2011.11.001 This requires data, information & knowledge to be… •  Digital Not printed paper •  Openly accessible Not behind barriers •  Linked-up Not in silos
  • 4. Most of our output is not digital, open or linked •  •  •  •  •  •  15-20k new spp. described annually (2M total)1 30k nomenclatural acts (12M total) 1 20k phylogenies (750k total)2 31k taxa sequenced (360k taxa total)3 800k BioMed papers (40M total pp. of taxonomy) 4 Countless specimens, images, maps, keys… Typically generated by small communities for “local” research projects Figures from 1) Zhang, Zootaxa 2011 4, 1-4; 2) Web-of-Science; 3) Genbank and 4) PubMed.
  • 5. ViBRANT Virtual Biodiversity A website for you & your community Magic Your data SEVENTH FRAMEWORK PROGRAMME Your web site -infrastructure
  • 6. ViBRANT Virtual Biodiversity What are Scratchpads? • Hosted websites for biodiversity data • Virtual research & publication platform • Completely open access & open source • Modular & flexible SEVENTH FRAMEWORK PROGRAMME -infrastructure
  • 7. ViBRANT Virtual Biodiversity What Scratchpads are not! • A single biodiversity database • Restricted thematically, geographically or taxonomically • A tool just for taxonomists • Owned or controlled by anyone other than the data creator SEVENTH FRAMEWORK PROGRAMME -infrastructure
  • 8. ViBRANT Virtual Biodiversity How are Scratchpads funded? 2007 2011 2014 ViBRANT Virtual Biodiversity & SEVENTH FRAMEWORK PROGRAMME -infrastructure
  • 9. ViBRANT Virtual Biodiversity Scratchpads Taxonomy & Literature Lice, mosquitos, freeloader flies, ... (rapid upload and management of names, synonyms & bibliographic data) Characters, Phylogeny & Specimens Termites, bryozoa, ... (character matrices exporting to SDD and Nexus format, phylogenies, specimen records & maps) biodiversity online 7000 6000 5000 4000 Sites Users Active Users 400 300 3000 200 2000 100 Taxon descriptions & Publications 1000 50 Sites 20 eJournals European Mosquito Bulletin, Phasmid Studies, ... (submission, review & dissemination of articles) SEVENTH FRAMEWORK PROGRAMME Dragon trees, nanno fossils, cockroaches, fungi, polychaetes, ... (rapid upload, annotation & display of images) 500 2007 2008 2009 2010 2011 2012 ViBRANT Scratchpads 2 Users Freeloader Flies, fungus gnats, ... (publication of Scratchpad data in the ZooKeys journal and export to Encyclopedia of Life) Image Galleries Societies, Organisations & Projects ICZN, GBIF, Sampled Red List Index for Plants, Global Plants Initiative ... (space for data collection, services, discussion & organisation) -infrastructure
  • 10. ViBRANT Virtual Biodiversity Training & outreach Support services ViBRANT Goals Vision Connecting the people, data & science of biodiversity http://vbrant.eu SEVENTH FRAMEWORK PROGRAMME Controlled vocabulary Networking Training Standards Mobilisation Sociology Data aggregation Field recording GBIF integration Citizen science Position Open & sustainable development of a federated network of biodiversity informatics infrastructures Mission Facilitate the mobalisation, sharing, reuse and publication of biodiversity data Data standards Visualisation Scratchpads Virtual Research Environment Scratchpad Phylogeny tools hosting Bioclimatic modelling Software integration Identification tools Matrix data editor Data publishing Service Data Publishing Manuscript publishing Sustainability Communal literature Research Literature mark up Architecture Literature Data mining -infrastructure
  • 11. ViBRANT Virtual Biodiversity Taxonomic Concept Schema XML Nexus Newick CSV/tab Excel file EoL Transfer schema (SPM) SDD, Lucid, DwCA Nexus SEVENTH FRAMEWORK PROGRAMME XML CSV, XLS, RDF Microsoft Word .DOC, TXT -infrastructure
  • 12. ViBRANT What can Scratchpads do? Virtual Biodiversity • Taxon pages (generated from tagged content) • Distribution maps (from specimens and TDWG regional distributions - Brummitt, 2001) • Specimen records • Bibliography management • Images, video and sound (bulk import) • Excel spreadsheet import • Tabular data editing & Character matrixes • Custom content • User management • Custom webforms • Analytics • Darwin Core Archive export (links to eMonocot Portal and EOL) • EOL data import (taxonomy, species information) • GBIF Map integration SEVENTH FRAMEWORK PROGRAMME -infrastructure
  • 14. ViBRANT Virtual Biodiversity Oxford Batch Operations Engine https://oboe.oerc.ox.ac.uk/ SEVENTH FRAMEWORK PROGRAMME -infrastructure
  • 15. ViBRANT Virtual Biodiversity BDJ The Biodiversity Data Journal Making small data big! SEVENTH FRAMEWORK PROGRAMME -infrastructure
  • 16. ViBRANT Virtual Biodiversity ISSN 1314-2828 (online) ISSN 1314-2836 (print) 1. Define the publication A peer-reviewed open-access journal Biodiversity D ata Journal Articles Launched to accelerate biodiversity data journal Bibliographies 2. Enter metadata Occurrence 3. Select taxa & content 1t 2011 Taxon treatments Plazi http://www.pensoft.net/biodiversitydata 4. Organise manuscript Editor-in-Chief: VINCENT SMITH Natural History Museum, London, UK Taxon names 5. Submit to journal I . P . N . I SEVENTH FRAMEWORK PROGRAMME -infrastructure
  • 17. ViBRANT Virtual Biodiversity Acknowledgements • Scratchpad technical development - Simon Rycroft, Ben Scott, Ed Baker, Alice Heaton & Katherine Boulton • Scratchpad outreach - Laurence Livermore & Dimitris Koureas • E-Monocot - Paul Wilkin & the Kew team, Charles Godfray & the Oxford team • ViBRANT - Vince Smith, Dave Roberts & Lucy Reeve • Our 7,000+ users SEVENTH FRAMEWORK PROGRAMME -infrastructure
  • 18. ViBRANT Virtual Biodiversity Thank you for your attention. Any questions e-mail: enquiries@vbrant.eu e-mail: scratchpad@nhm.ac.uk http://vbrant.eu SEVENTH FRAMEWORK PROGRAMME http://scratchpads.eu -infrastructure