scratchpad 2, virtual research environment: project update

Scratchpad 2, VirtualResearch Environment:

Project Update

Vince SmithNatural History Museum, London

vince@vsmith.info

EOL Content SummitPanama, 17-20 Jan. 2012

The problem

Science is global• It needs global standards• Global workflows• Cooperation of global players

Science is carried out “locally”• By local scientists• Being part of local infrastructures• Having local funders

Scratchpads• EDIT (07-11), ViBRANT / eMonocot (11-13)

• Hosted websites for taxonomists• Taxonomic, regional or societal • Research & publication platform • Supports the taxonomic workflow • Modular (Drupal) & flexible • Two full time developers • Ecosystem of communities (~300)

http://scratchpads.eu

Categories of Scratchpads

Taxa(Classifications, taxon profiles, specimens, literature, images, maps, phenotypic,

genotypic & morphometric datasets, keys, phylogenies)

ProjectsConservation Regions Societies

Sites 326Users 6279Active Users 5139(273 w / 759 m)

Pages 424,972

Site

s

Use

rs

Range: 1-1049Mean: 15Mode: 1

• Prof. scientists• Amateur naturalists• Citizen scientists (soon)

Scratchpad usage (2007-2011)

ViBRANT SP 2

Scratchpad 2 Overview

Justification for SP2

Release Timeline

• Backend enhancements (technical sustainability & scalability)

• Frontend enhancements (improved functionality & ease of use)

• Move from Drupal 6 to Drupal 7 (4 year upgrade cycle, UI + entities)

Goal“a scholarly communication system that is intertwined with the pursuit of natural history, rather than its after-thought or annex”

• Feb. 3rd (Sandbox release for testing, comments & bug fixes )

• March 2nd (released for new site requests)

• April 2nd (opt in switch over for SP1 users)

• Mid 2012 (opt out of automatic migration for all SP1 users)

• Aegir hosting environment (automated site management & migration)

• Themed project profiles (e.g. GBIF NPT, COMBER & potentially LifeDesks)

• Git code management (distributed source code version control)

• Scratchpad wide search (Apache Lucene, dedicated VM)

• Distributed physical hosting (not just at the NHM)

• Data services (Darwin Core Archives & Extensions)

• Scratchpad site registry with metadata and usage metrics• Integrated Single Sign On (SSO) (e.g. Google, Facebook, author-ID)

• Proper GUIDS beyond URL’s (LSIDs, DataCite DOI’s?)

Scratchpad 2 backend enhancements

Still to come…

• Consistent theming, navigation & less clutter (more scholarly, still flexible)

• Easier administration (editing overlays, simple content & user management)

• Tabular data management (1 step Excel import & export) • Guided workflows (linking site functionality)

• Faceted search (with multisite search options)

• New multi-media gallery (including video support)

• New EOL linked taxon pages (inspired by Natural History guides)

• Consistent mapping (integrating points, polygons, regions & 3rd party data)

• Manuscript & data publication (enhanced publication module)

• Key construction, analysis toolbox and more data publishing outlets

Scratchpad 2 frontend enhancements

Still to come…

Scratchpad 2 theming

SP1 SP2

Garland

Idiosyncratic

colours & layouts• Consistent• Clear navigation• Less clutter

• More professional• Highly flexible

Scratchpad 2 flexibility

• Easy content customization

• Pre-defined swatches

Scratchpad 2 editing & administration

SP1 SP2

• Consistent• Editing overlays

Complex & not intuitive

• No “lost” content• Easier

Scratchpad 2 data management

• Tabular management• One-step Excel import & export• Dynamic Excel templates• Add, edit & update all content types• Integrated search• Intuitive filters

Scratchpad 2 guided workflows

SP1 SP2

• Support common tasks• Link site functions• Optional for advanced users• Still being themed

Not intuitive

12

3

4

5

o Site setupo Adding userso Groups & permissionso Importing taxonomyo Creating serviceso Creating views

Scratchpad 2 faceted search

• Rapid content discovery• Systematic browsing• Content specific facet

display (e.g. biblo, media)• Slickgrid filters for other

content types

Scratchpad 2 multimedia gallery

• New look• Video support• Faceted search & browse• Embed YouTube &

Vimeo

Scratchpad 2 taxon pages

SP1 SP2

• Improved layout (tabs)• EOL trusted content

• Single page• Poor 3rd partly content• Hard to customise

Scratchpad 2 taxon pages

• Easy publishing to EOL• Better content control• Direct editing• Parent-child data inheritance• Inspired by Natural History Guides

Scratchpad 2 mapping

Three map types supported in SP1

User defined TDWG regions(up to Level 4)

GBIF Maps

User definedPoint localities via DwCrecords

Scratchpad 2 mapping

• Point & TDWG region maps • Flexible polygon maps & annotations• GBIF point imports (record limits)• Edit point location & metadata

Scratchpad 2 “publication” options

• Manuscripts from Scratchpads to ZooKeys & PhytoKeys • Produced directly from the database• Three exemplar papers produced via SP1• Comprehensive new data structure in SP2

Taxon descriptions

1. Define the publication

2. Enter metadata

3. Select taxa & content

4. Organise manuscript

5. Submit to journal

Scratchpad 2 “publication” options

• New Pensoft data publication journal• Published metadata descriptions of structured datasets• Dataset pushed to 3rd party repository

Datasets

Scratchpad 2 “publication” options

• Name & metadata to ZooBank (GNA)• Taxon SPM data to EOL• 1-Click publication (subject to minimum data standard)

Data items

EOL Issues – discussion points

• Incomplete• Multiple records• Licensing complexity• Seeding Scratchpad SPM fields ???

API

• Profile development• Mapping content• Resources• Timing & policy

LifeDesks

• Often has better content, less duplication & no licensing issues • Would like to see greater integration with EOL

Wikipedia