Overview of eMonocot and Scratchpads

From systematics

Jump to: navigation, search

You can reach the main project page for the BioSynC meeting at BioSynC 2011.

One of the things that has changed since we put in our BioSynC proposal is that we are now working explicitly with eMonocot and Scratchpads, a project out of Kew, Oxford, and the British Natural History Museum to document monocot diversity worldwide. This is exciting on several levels.

  • First, the eMonocot Project is committed to creating the infrastructure to develop and deliver information on monocot biodiversity, and is throwing concentrated resources at it -- we’ll benefit significantly from the tools and structure they are creating.
  • Second, they have as part of this project a goal of creating 300 European Carex pages in fairly short order, which will complement the Western Great Lakes (North American) species pages we are creating as part of our BioSynC grant.
  • Third, we will gain a couple of representatives to our meeting from the eMonocot group as part of the deal -- Dave Simpson and Odile Weber (Kew) as representatives from eMonocot (Dave is a world expert on Cyperaceae, and Odile is coordinating Cyperaceae for eMonocot); and Edward Baker as a representative from Scratchpad / Vibrant, which is the database system we will ultimately be moving our checklist, photos, references, and species pages into. (This is discussed more below in this email, in the section on “Informatics tools.”) We’ve had ongoing conversations with Dave Simpson et al., and everyone’s excited about the fact that this is all happening at once.
  • Finally, we met with Bob Corrigan, who is the Product Manager for the Encyclopedia of Life Project, and have agreed to work with them to migrate our current Carex data out of the LifeDesks framework into eMonocot’s Drupal-based Scratchpad framework. (This benefits EOL in that they want an active “content” group with which to collaborate and proof the best methods for the transition mechanism; and it benefits us because we get additional resources and attention from EOL and the eMonocot-Vibrant teams to ensure that all our content gets into their frameworks efficiently and with the kinds of formatting and prominence we desire.)

Contents

From Simpson Lecture, 28 sept 2011

DAvid Simpson gave a talk on eMonocot at the BioSynC meeting in Chicago.

Background

  • Started 2010, runs to Nov 2013
  • Funded by NERC via consortium grant. This was a surprise. It turns out there was a parliamentary committee looking into the state of taxonomy at the time; the timing was fortuitous.
  • Large scale, coherent, sustainable taxonomically based information resource on the monocots
  • Primarily aimed towards biodiversity scientists. This is not being done for taxonomists alone, but to make the data available in a broader format.
  • Why monocots? good size group for a three year project

Aims

  • Aid identification ofmonocots worldwide
  • provide wealth of info about monocot taxa
  • Address the needs of different users
  • Link together monocot taxononmists to enhance productivity; to get data together and get it out.
  • Provide a model for web taxonomy. At Kew in particular, we've been looking at web taxonomy and how we can improve things, make it more recognized, and reward people for putting data online. This is a crucial thing; people need recognition.

Organization

  • Content team at Kew
    • Content devt
    • Integration with strategic and ICT programs
    • Post project sustainability
  • ICT team at Oxford
    • Software devt
    • LInk with bioinf and eScience
  • Outreach team and Nat Hist Museum
    • Scratchpads
    • Extension to zoology
    • web metrics

Existing resources

Deliverables

  • APGIII families keys / pages (77 families)
  • Generic keys / pages for 8 families, ca. 2100 genera:
    • Araceae
    • Arecaceae
    • Asparagaceae
    • Cyperaceae
    • Dioscoreaceae
    • Llieaceae
    • Orchidaceae
    • Poaceae
  • Species level resources
    • European monocots (2000 spp)
    • Cypripedioideae (130 spp)
    • Sampled red list index project (1500 spp)

Expected outputs include the above, plus key to genera, genus pages, etc... Cyperaceae community can contributed much more. The role of the community here is open.

Content progress

  • Developing keys in LUCID to monocot families, Dioscoreaceae (almost done, some illustrations missing), Cypripedioideae
  • Identifying content sources and acquiring content; and administration database has been constructed
  • Report on communities and content
  • Establishing a collaborative link with the Swiss Orchid Foundation to deliver Orchid content
  • Dioscoreaceae scratchpad in development; one researcher in Madagascar
  • for Cyperaceae:
  1. Protologs: 611 links to BHL, 214 digitized
  2. 104 generic descriptions from Kubitzki
  3. 9 additional genera to be processed
  4. 35 species descriptions from Sedges of the British Isles (out of 106)
  • ICT progress
  1. Stakeholder survey
  2. Documentation of existing systems
  3. Existing systems functionality workshop
  4. Content documentation
  5. Data exchange standards, tools and technloglogies
  6. eMonocot development
  7. Prototype architecture
    1. Portal plus data editing system
    2. Scratchpad role
    3. eMonocot portal is read only, presents cross-cutting views of source content. Scratchpads feed content up to the portal. You can restrict access to the Scratchpads; the eMonocot portal displays data to the web and provides an annotation mechanism that pushes data back to the content provider.
  • Outreach progress
  1. Impact plan - UK monoco ID guide
  2. Lyme Regis Fossil Festival
  3. Developing links to UK biodiversity scientists and volunteer scientists
  4. Workshops for Monocot systematists
    1. Call for proposals in summer 2011
    2. First workshop in Chicago in September: Carex
    3. Subsequent workshops in London and potentially worldwide in late 2011 and 2012

From Ed Baker, 28 Sept 2011 lecture

Why Scratchpads?

  • Goals:
  1. Inventory earth's spp
  2. Document relationships
  3. Publish and apply these data
  • Data set:
  1. 1.8 M described spp. (10M names)

Scratchpads started under the EDIT project, 29 leading European, N Am'n and Russian Nat History colelctions based institutions, ca. 12 M euros; Scratchpads was developed as part of the computer resources. The idea is that you put your data into the system, tag it with taxonomy, and it's immediately pushed out on the web. The product is a set of hosted websites for taxonomists, where you can collaborate to do research. There are ca. 250 Scratchpad communities, with ca. 2-3 new sites per week. 2500 + users from 2007. The project is modular (Drupal) based. Ultimately, under ViBRANT, there will be combined bibliographies.

The Scratchpad sites are pretty open; eMonocot sites are branded as eMonocot sites, but there is plenty of flexibility still in what you want to do. There are currently eBooks being worked on on the web, as well as eJournals, DNA, Phylogeny and specimens.

Sustaining Scratchpads ViBRANT: buidling on EDIT and Scratchpads. The goals are:

  • A virtual research env (Scratchpads)
  • Analytical services for users to build identification keys and phylogenetic trees
  • Publication platform for users to automatically compile taxonomic manuscripts for resaerch database
  • A portal for users to centrally access publically accessible biodiversity research information and literature.
  • Training, support, and sociological study, helping research communities to use these tools and services.
  • Standards-compliant architecture.

The project starts Dec 2010, runs 36 months. Collaborations include:

  • ESFRI proejcts
  • GBIF
  • PESI, 4D4Life and related EU project
  • EOL, Barcode of life and biodiversity heritage library
  • South AFrican NAtional biodviersyt institute and Atlas of living Australia

Technical overview:

Personal tools