See also BiodiversityCollectionsIndexKickOffMeetingFunctionality and BiodiversityCollectionsIndexKickOffMeetingImplementation

Monday 28th January

GBIF - Vishwas Chavan

• Motivations for GBIF
• Resource discovery.
• Data mobilization
• Estimate 'Universe of Biological Collections'
• Gap analysis for digitization.
• Encourage non-participant activities
• Tangible contributions to GTI, GSPC and thus to CBD
• Decentralized approach to registry for data discovery
• Multilingual?
• Leverage of existing collections important
• How will we keep this going past the first year.

NCD/RAVNS - Neil Thomson /Carol Butler

• Summary of the NCD and RAVNS activities
• NCD is Exchange/Interchange standard.
• Cross Domain
• Between EAD and DC in complexity
• "Business Card" for collection
• Developed under BioCASE?, Sythesys, RAVNS and became TDWG Interest Group
• RDF version 2007
• ToolKit? from ETI 2007/8
• Go for TDWG standards approval 2008
• RAVNS = Resources Available in the Natural Sciences
• Work distributed across continents with conferences calls and wikis
• "Looking at the forest not the trees"
• Fields of NCD and controlled vocabularies designed for cross disciplinary resource discovery.

Motivation for BCI - Roger Hyam

• A summary of why the project has been instigated.
• Original plan was for national nodes to feed into GBIF.

NCBI/GenBank - Scott Federhen/Larry Chlumsky/Ilene Mizrachil

Index Herbariorum - Barbara Theirs

• Curating the standard list of herbaria
• Issue in 19th Century
• 1935 initiated. First pub 1937 updated 1939
• 1974
• Last hard copy 1990
• 1997 on line
• 3,373 herbaria, 10,368 staff
• 105 added since 2004
• 1,189 staff added since 2004
• 200 changes per year (mainly staff)
• inactive herbaria - 800ish
• Regional editors gathered data up to 2004
• Since 2004 updating has been more passive.
• Minimum criteria
  • public institution
  • at least 10,000 specimens
  • demonstrate activity in terms of number of loans, visitors, annual accessions.
• Applicant suggest acronym. Modified as needed
• Only then added to the database
• Tour of IH website.
• Important collections does not use standard names for collectors - can't
• Address book for the world's herbaria.
• Listing in IH is required by other herbaria for loans and collecting permits
• Expertise finding.
• Trends in systematic research.
• Challenges
  • 10k specimen rule can be awkward but does reduce chances of abandonment.
  • Changing, combining and use of acronyms
  • Political requests. Disputes over who is listed as contact.
  • Data doesn't fit. Staff at multiple herbaria. Separate mailing and physical locations
  • Some people change data too often. Some never supply info.
  • "Advocate role" - can we help with collections in danger.

CBOL - David Schindel/Bob Hanner

• Disambiguation example through airport codes
• Two level system.
• Not all airports get codes.
• Barcodes are center for linking names and specimens
• Uses of barcode.
  • Improve species-level taxonomy
  • Identifying regulated species
  • "Triage" tool for potential new species
• Do not use separate database. Use standard DNA databases
• BOLD holds associated data
• Barcode data standard. Structured link to a voucher specimen ( + sequence metadata)
• Three part link to specimen. Inst/Collection/Catalog ID
• Private collectors are all 'personal'/personName/spec ID
• Only looking at Institution codens
• BioRepositories?.org
• contract developer
• Two staff to run data for next 6 months to a year
• All personal collections come within the institution called "personal"
• Institutions with only one numbering system treated as a single collection
• Institutions with different numbering systems for different collections have collections records.
• Building feedback mechanisms

ETI NCD Toolkit - Wouter Addink

• 2007 - ETI developed toolkit (http://145.18.162.52/ncd/manage, login: "admin" or "user", password: "test")
• NCD reference implementation for managing NCD compliant collections data targeted at institutions like GBIF nodes
• Ready for use but not for import/export
• Nodit is support (but not production)
• Two languages are supported (English + optional local language)
• Two Roles: admin and editor
• Log in as admin can add Institutions & Collections & People also user management.
• Development in 2007 at ETI was focused on web services: NLBIF portal, Catalog of Life webservice created
• Development in 2008 will be focused on community driven portals: Portal Toolkit, Cultivar Finder portal
• Going to embed toolkit in open source content management / community building tools (Drupal)
• Demo of prototype (http://145.18.162.103/ncddrupal, login: "test admin" or "test user", password: "test")
• NCD toolkit embedded in Drupal can do multi-language and change look and feel.
• Five Roles: Visitor, Registered User (can add comments), Editor (edit, translate, revisions), Admin (rights for managing content, rights and users), Superadmin (full access for changing system functions (for developers).
• No syncro mechanisms yet
• Would be good basis for BCI.
• Can upload images etc

EoL - Paddy Patterson

• Want to use something that is available now. Will pick up the first available source.
• 1 million pages
• Digital object are the target.
• Service discovery
• Think of EoL? as a client who wants information.
• Minimal metadata
  • Name of the taxon
  • kind of object
  • biological context of the information.
• Synonymies of acronyms.

NBII - Annette Olson

• NBII is federation of multiple organisations
• Help these people get data on line
• Infrastructure - promote standards, public portal, sponsor workshops
• Partnership networks
• North American mirror for GBIF
• Host for OBIS-USA
• etc
• Data and Information Projects.
• Example building South East Herbaria Network in support of digitizing data
• Helping digitize collections.
• collections of images becoming important.
• NBII role is providing info to support collections and discover lesser known collections
• Evolving requirements for NCD collections

OBIS - Edward Vanden Berghe

• Marine species online - biogiographic info
• As open as possible
• Integrating data is important - on a large scale
• Not just big things - protists too
• Partners with GBIF and Species 2000 and WoRMS?, marinespecies.org
• IOC, FAO etc
• Standards: DwC? (briefly at ABCD).
• MetadataL? Global Change Master Directory - NASA
• MEDI - IODE; FGDC- US GOV
• WoRMS? has specimen (type) info. Need institute identifiers
• DwC? added Depth. Begin and end point, Sample size.
• OBIS 238 data sets 14m records
• 3 part code plus basis of record
• 10m are observations
• 1m are specimens
• People are confusing three fields.
• Collaboration to build controlled vocabulary
• Some useful info available within the system.

Remote submissions - Roger Hyam

CollectionsWeb

• Hank Bart -Tulane University Museum of Natural History
• The goal of CollectionsWeb? is to improve lines of communication among curators of U.S. natural history collections (NHC), researchers using the collections, other programs dealing with collections issues, and other stakeholders, in order to build a more effective NHC community and increase the base of support for NHC.
• To accomplish this goal, we are developing a number of web resources, and planning a series of workshops and symposia on important collections-related issues. All of the products of these activities will be accessible through the project web site, www.CollectionsWeb.org, the portal for communicating and disseminating information about the project.
• One of the CollectionsWeb? workshops (tentatively scheduled for 2009-2010) will focus on databasing and networking and we see good opportunities to collaborate with and learn about best practices from Biodiversity Collections Index (BCI) in this area.
• Another obvious area of overlap and potential collaboration is the design and implementation of collection information systems. CollectionsWeb? plans to conduct a survey of U.S. NHC. The purpose of this is to pull together basic information on holdings, curators and other staff, support, research and collection issues. This effort would benefit from any standard descriptors of NHC developed in connection with BCI.

Atlas of Living Australia

• Donald Hobern - CSIRO
• Australian government-funded science project to develop computing infrastructure for integrating biological knowledge
• Core data types: specimens/observations, names/taxonomy, molecular, descriptive, multimedia
• Goal is to maximise discovery and accessibility of biodiversity data
• Need well-managed reference lists to organise and interpret data records, particularly specimen records
• Accurate identification of collections is a critical step in locating specimens from references

ZooBank

• Rich Pyle - ICZN/Bishop Museum
• The Official Online Registry for Zoological Nomenclature.
• Names are anchored by type specimens.
• Need a unambiguous way of expressing the location of type specimens.
• Location needs to be tracked even when collections are moved or merged.

Insect and Spider Collections of the World

• Neal Evenhuis - Bishop Museum
• List of ~2000 collections with abbreviations.
• Searchable and downloadable on web.
• Assisting the arthropod community with a set of standard abbreviations to use in communicating depositories.
• Tracking collections not institutions (some institutions have multiple collections).
• Currently no cross checking with other zoological or botanical lists for use of the same abbreviation.
• Personal/temporary collections don't warrant ISCW abbreviations - must be 'permanent'.

Tuesday 29th January

-- RogerHyam - 27 Jan 2008