Einfrastructure for organism names to facilitate data sharing

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E-infrastructure for organism names to facilitate
data sharing

• Project presentation
• Joint project of the Nordic GBIF Nodes by
  NordForsk 2008-2010

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Why regional cooperation makes sense?

• Neighbours need to learn from each other because
  they share biodiversity
• Share similar problems and are often at same
  level of science and technology
• Language and cultural barriers and cost of
  meetings are low
• There often is need data sharing within regions
• In the Nordic region data is being shared, but
  data flows are moving to European level
• There are funding sources that work at regional
  level
• Several sources in the Nordic region

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A Nordic Code Centre Operated in 1981-94. It
issued unique numbers for taxa and 9 letter codes
(ab-breviations for field work) for names. These
can still be downloaded, but they are updated on
several places and updates are not publicly
available.
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Proposal funded by
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Scientific names in observational databasespose
problems

• Cannot identify taxonomic concept unequivocally
• Antropomorphic, mix contents with the key, and
  thus prone to change
• Do not scale up to integrate hundreds of
  databases automatically
• Life Science Identifier technology seen as
  solution

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Life Science Identifiers (LSID) for every
taxonomic concept

• Example urnlsidgbif.fitaxon12345678901
• Identifier for a taxon concept for example
  Vanessa cardui L., sensu Saarenmaa Saarenmaa
  2027.
• The six elements of an LSID are separated by a
  colon sign
• States that this is an Universal Resource Name
  (URN).
• Denotes that this URN is an LSID.
• Authority identification (normally, who has
  issued the LSID and that provides the web service
  to resolve it).
• Namespace identification (normally, name of a
  database at the authority).
• Object identification (meaningless GUID or
  database key).
• Optional revision number.
• Resolving LSID means retrieving the description
  from an authority.
• LSID authorities are now being set up by many
  Species Databases and regional centres.

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Purpose of the joint project

• Build an e-infrastructure for resolving
  scientific names of organisms to facilitate
  biodiversity data use and data sharing in the
  Nordic region and beyond.
• Set up service on Internet that will issue
  globally unique identifiers for scientific names
  (?) and the underlying taxonomic concepts (!)
  based on the LSID specification.
• Environmental authorities, research groups, and
  mobile observers out in the wild can then use
  these identifiers to remove ambiguities in data
  exchange. Among the benefits will be that large
  integrated studies that need to combine data, for
  instance for global change studies, become more
  feasible.
• Project increases the interaction of the
  participants that already are major research
  infrastructure elements into new electronic
  frontiers. This is the first joint project of
  the Nordic GBIF nodes and the project is aimed
  also at strengthening Nordic cooperation in the
  global GBIF process.

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The proposed e-infrastructure will offer the
following services

• Issue LSID for each scientific name and each
  circumscription, and resolve the LSIDs upon
  request.
• Integrate globally the services through the TDWG
  infrastructure project.
• Coordinate integration of name lists in the
  Nordic region, initially for Lepidoptera.
• Develop guidelines for incorporating LSIDs in
  datasets. Offer helpdesk and training.
  Disseminate results.
• Promote data sharing in the region.

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Participants are GBIF Nodes in the region plus NW
Russia

• Natural History Museum of Denmark
• Estonian Life Sciences University
• Finnish Museum of Natural History (coordinator)
• University of Oslo, Natural History Museums
• Swedish Museum of Natural History
• Russian Academy of Sciences, Zoological
  Insititute, Sankt Petersburg

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Advisory Group

• Starri Heidmarsson (GBIF-Iceland)
• Liisa Tuominen-Roto (Finnish Environment
  Institute)
• Søren Roug (European Environment Agency)
• Kevin Richards (GBIF New Zealand)
• Per Alström (Artdatabanken)
• Ricardo Pereira (TDWG)
• Frank Bisby (Species 2000)

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Timeline - Steps

• Month 1 Hire workforce. Hold kick-off meeting
  with the Steering Group.
• Month 3 Acquire and set up server computers.
  Install LSID software tools. Study experiences
  from other LSID projects. Acquire relevant name
  lists.
• Month 6 Issue LSIDs for all names and
  tentatively generate naked LSID (without link to
  description) for the corresponding concept. Link
  simple synonyms together. Using several test
  databases for observations, integrate them
  together. Have entered 25 descriptions by hand
  from literature for homonyms and split species.
• Month 9 Open test service for LSID issuance for
  new names and their resolution. Present
  demonstration of simple data integration. Design
  linking to descriptions from literature. Have
  entered 50 descriptions by hand from literature
  for homonyms and split species. Hold meeting of
  IT Advisory Group.
• Month 12 Acquire links to literature references
  from uBio and BHL, and link them to the concept
  LSIDs. Have entered 100 descriptions by hand from
  literature. Start linking together split species
  and homonyms. Set up the TAPIR/TCS name
  provider. Hold meeting of the Coordinating Group
  in particular looking at lessons learnt and new
  opportunities for Nordic GBIF cooperation.
• Month 15 Have entered 150 descriptions by hand
  from literature and automatic sources. Write
  guidelines how to incorporate LSIDs in
  observation databases and data collection tools.
  Test these guidelines with global fish and
  Danish, Estonian, and Norwegian all species
  lists.
• Month 18 Open service on Internet for LSID
  resolution. First operational use of LSID in
  data exchange. Write papers. Present results at
  TDWG and other meetings. Prepare proposals
  Steering Group about continuation projects.
• Month 24 Have entered 300 descriptions by hand
  from literature and automatic sources. Start
  working on other lists than Lepidoptera to test
  the procedures. Hold meeting of Steering Group
  and explore for continuation the feasibility of a
  Nordic Catalogue of Life project that would build
  permanent infrastructure for biodiversity
  informatics in the region.
• Month 30 Experiment with using LSIDs in
  observation databases. Write thesis. Write
  about lessons learned. Propose latest at this
  stage further Nordic GBIF projects.
• Month 36 Final meeting of the Coordinating
  Group. Training workshop to disseminate results.
  Transition of project to other bodies.

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Contributions by Partner

• Denmark (SNM-UKBH) Contribute names of all
  Danish taxa (preparations for a national dataset
  of all species is being finalised, to be shared
  through the Danish node portal of GBIF
  www.danbif.dk in the near future). Feed updates
  on Danish inventory of Lepidoptera to the
  Norwegian dynamic checklist of Nordic
  Lepidoptera.
• Estonia (EMU) Contribute names of all Estonian
  taxa. Test observation databases to increase
  availability of data.
• Finland (FMNH) Good Lepidoptera data exists and
  is already being shared. Contribute names for
  Finnish Lepidoptera. Carry out project
  management and technical development.
• Norway (University of Oslo and Artsdatabanken)
  Some Lepidoptera data exists and is already being
  shared. Possibly establish data collection
  portal to increase availability of data.
  Contribute names for all Norwegian taxa.
• Russia (ZIN) Contribute Lepidoptera names. Test
  observation databases and digitize sample
  collection data.
• Sweden (NRM) Good Lepidoptera data exists and
  is already being shared. Contribute names for
  Nordic Lepidoptera and global fish.
• All Put LSIDs in selected observation datasets
  according to guidelines that will be developed by
  the project. Share experience between GBIF nodes
  in the region.

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Project organisation

• Project leader will oversee the work of the
  technological development unit, communicate with
  the Coordinating Group, Advisory Group, and the
  funding organisation, and ensure the quality of
  the project deliverables.
• Coordinating Group will be set up of project
  leaders of all partners. This group is six
  people, and will meet at least annually, but will
  work intensively on email.
• Advisory Group consisting of major users and
  experts of informatics solutions will be invited
  internationally. It will constitute of about 5
  people from international organisations, such as
  GBIF, TDWG, Catalogue of Life, European
  Environment Agency, national environment
  authorities, and research groups who are well
  known leaders of this area. This group will meet
  at least once in person, but will comment on
  plans and deliverables electronically.
• Technological development unit Nina Markus.

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Use of funds

• 1 million NOK 125,000
• Finland 71.8
• 79 to salaries, 8 travel, 3 computers, 10
  overhead
• Others 5.6 each
• One travel annually
• Deliver name lists
• Enter LSIDs in databases
• Mobilise databases

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Questions

• How are name databases handled in the
  participating countries?
• Do these databases make explicit the taxonomic
  concepts?
• Can we increase availability of data in targeted
  groups?
• Any LSID experience so far?