Community web sites: small pieces loosely joined

Virtual BiodiversityViBRANT

SEVENTH FRAMEWORK PROGRAMME -infrastructure

Community web sites: small pieces loosely joinedDave Roberts, Simon Rycroft & Vince Smith


-infrastructureSEVENTH FRAMEWORK PROGRAMME



Small pieces loosely joined Has many potential meanings:

Joining contributors together to form communities

Joining the data together that go towards forming a Scratchpad

Joining Scratchpad content with the landscape of biodiversity informatics data on the web



Goal ...

Data set ...

People ...

Addressing the challenges of taxonomy

Inventory the Earth’s speciesDocument their relationships“Publish” & apply these data

1.8 M described spp. (10M names)300M pages (over last 250 years)1.5-3B specimens

4-6,000 taxonomists30-40,000 “pro-amateurs”Many more citizen scientists?



Magic

Your data Your web site

A website for you & your community



Dynamic web pages

Taxonomy import, management and navigation

Reference manager / Endnote support for bibliographies

Image galleries, image upload & annotation

Nexus / Newick import for visualising phylogenies

Character matricies (discrete, morphometric and text characters)

Presence / absence country maps

Specimen & location records (DwC)

Newsletters & Web fora with e-mail integration

User blogs



Import from CSV text file to any content type



Taxonomy & LiteratureLice, mosquitos, freeloader flies, ...

(rapid upload and management of names, synonyms & bibliographic data)

Freeloader Flies, fungus gnats, ...(publication of Scratchpad data in the ZooKeys journal and export to Encyclopedia of Life)

Taxon descriptions & Publications

European Mosquito Bulletin, Phasmid Studies, ...(submission, review & dissemination of articles)

eJournals

Termites, bryozoa, ... (character matrices exporting to SDD and Nexus format, phylogenies, specimen records & maps)

Characters, Phylogeny & Specimens

Image GalleriesDragon trees, nanno fossils, cockroaches, fungi, polychaetes, ...

(rapid upload, annotation & display of images)

ICZN, GBIF, Sampled Red List Index for Plants, Global Plants Initiative ...(space for data collection, services, discussion & organisation)

Societies, Organisations & Projects

240

200

160

120

80

40

0

Year 1 Year 2 Year 3 Year 4

3000

2500

2000

1500

1000

500

0

Registered UsersSites

SitesUsers



A Virtual Research Environment (Scratchpads)where users can safely store, share and manage their research information.

Analytical servicesfor users to build identification keys and phylogenetic trees.

A publication platformfor users to compile taxonomic manuscripts automatically from their site.

A portalfor users to access public biodiversity research information and literature.

Training, support & sociological studyhelping research communities to use these tools and services.

A standards compliant technical architecturethat can be sustained by biodiversity research community.

ViBRANT Products



ScratchpadsVirtual Research

EnvironmentPhylogenetic

analysisBioclimaticmodelling& metrics

Identificationtools

Matrix dataeditor

Biodiversity data

publishingScholarlymanuscriptpublishing

DistributedScratchpad

hostingSoftwaremodule

integration

Sustainabilityplan

Communalbiodiversity

literature

Biodiversityliteraturemarkup

Biodiversitydatamining

Citizenscience

programme

Fieldrecordingsupport

Usersociology

study

Userfeedbacksystems

Training& outreachprogramme

Biodiversitydata

standards

Dataaggregation

portal

GBIFintegrationactivities

Biodiversityvisualisation

layers

Controlledvocabulary

platformNetworking

WP3. TrainingWP4. Standards

WP8. Mobilisation

ResearchWP2. ArchitectureWP7. Literature

ServiceWP5. Data

WP6. Publishing

The “chromosome”



ScratchpadsVirtual Research

EnvironmentPhylogenetic

analysisBioclimaticmodelling& metrics

Identificationtools

Matrix dataeditor

Biodiversitydata

publishingScholarlymanuscriptpublishing

DistributedScratchpad

hostingSoftwaremodule

integration

Sustainabilityplan

Communalbiodiversity

literature

Biodiversityliteraturemarkup

Biodiversitydatamining

Citizenscience

programme

Fieldrecordingsupport

Usersociology

study

Userfeedbacksystems

Training& outreachprogramme

Biodiversitydata

standards

Dataaggregation

portal

GBIFintegrationactivities

Biodiversityvisualisation

layers

Controlledvocabulary

platformNetworking

WP3. TrainingWP4. Standards

WP8. Mobilisation

ResearchWP2. ArchitectureWP7. Literature

ServiceWP5. Data

WP6. Publishing

GBIF

GBIF

GBIF

GBIF

GBIF

The “chromosome”



More reliable (e.g., distribute the servers)More functional (e.g., phylogenetic & publication services) Easier to use (better workflows)Prettier (better graphical design - more intuitive)More integrated (for data stored inside & outside the Scratchpad framework)More sustainable (simple administration, distribute developers, development sandbox)

“making the Scratchpads better”

“making natural history better”Easier to compile, manage and reuse your dataEasier to find and reuse other peoples data Promoting your data inside & outside the taxonomic communityGetting people to work for you (crowdsourcing)



Manuscript preparation on a Scratchpad

Submit as XML

Produce PDF

Enhanced XML

Register with ZooBank,

GBIF, EoL etc.

Printed paper

PDF

Enhanced HTML

Send to reviewers

AuthorAuthor

Publisher

Public



https://git.scratchpads.eu/viewgit



Thank you for your attention.

Any questions

http://vbrant.eu http://scratchpads.eu

e-mail: [email protected]

Technology

Community web sites: small pieces loosely joined