ORNIS: Looking into the Future

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ORNISLooking into the Future
Accipiter gularis

• Principal Investigators A. Town Peterson Carla
  Cicero
• Lead Programmer John Wieczorek
• Web Site Portal http//ornisnet.org

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What is ORNIS?
An integrated, multi-institutional,
cross-disciplinary information resource
(ORNithological lnformation System) providing
state-of-the-art, up-to-the-minute information
about bird biology and bird diversity worldwide
that can address pressing questions in
Ornithology and in broader policy decisions
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ORNIS Scope

• NSF Biological Databases and Informatics Program
• 5 years (from 1 Sep 2004)
• 1.5M (65 cut from original budget)
• 29 institutions funded
• 33 participating
• open to additional participants (U.S./foreign)
• gt5M specimens, gt21M observations

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Taxonomic data
Scientific literature
Gene sequence data Genomics
Recordings, images, videos
Stable isotope data
Primary Species Occurrence Data
Field notes, other ancillary information
Parasites etc.
Stomach contents, etc.
Geospatial data describing locality
Remote-sensing data showing locality in space
and time
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ORNIS Improved resource for

• Identifying gaps in taxonomic and/or geographic
  sampling
• need for additional collecting for genetic or
  other studies
• Tracking emerging diseases (e.g., WNV, avian flu)
• Correlating changes in species distributions
  and/or abundances with environmental changes (GIS
  analysis)
• inclusion of observational (monitoring) data
  improves power of analysis

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ORNIS Rationale

• Multiple sources of data
• under local control
• with concepts in common
• Distributed nature of biodiversity data requires
  collaboration across institutions for efficient
  access
• similar efforts for mammals, herps, fish, etc.
• registered with GBIF for global access

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Example Mexico
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ORNIS Goals

• Project Web Site http//ornisnet.org
• Distributed Data Network
• 19 of 33 providers currently online
• Georeferencing (promised North America, can do
  more)
• automated georeferencing via Biogeomancer
  (http//www.biogeomancer.org)
• Data Validation (taxonomy, geography, collecting
  events)
• error detection
• outlier detection

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ORNIS Network Architecture
Sasia ochracea
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DiGIRDistributed Generic Information Retrieval

• Distributed - A protocol for retrieving
  structured data from multiple, heterogeneous
  databases across the Internet.
• Generic - A protocol independent of the data
  retrieved and of the software to retrieve it.

Developed collaboratively by University of Kansas
Biodiversity Research Center, California Academy
of Sciences, Museum of Vertebrate Zoology. Used
widely by similar initiatives (MaNIS, HerpNET,
FishNet, GBIF, etc.).
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DWC2Darwin Core 2 Schema

• A simple set of data element definitions designed
  to support the sharing and integration of primary
  biodiversity data
• Relevant extensions for ORNIS include
• Curatorial
• Geospatial
• (new version still under review
  http//darwincore.calacademy.org)

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Relevance for DNA barcoding

• Allows querying of tissues across multiple
  institutions
• now a separate field
• new version of DWC2 includes tissues as part of
  specimen preparation in the curatorial extension
• need standardized way of storing tissue data
• Allows linking to Genbank Accession numbers if
  supported by institutional database
• new version of DWC2 includes GenbankNum as
  standard field in the curatorial extension

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Provider

• Receives requests
• Logs requests
• Retrieves data from database
• Sends results to requester
• Can be registered

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Registry

• Provides a yellow pages to advertise the
  existence and capabilities of a provider
• Provides a means to discover potential providers
  of interest
• May be public or private
• Need not be a part of the architecture

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Portal/Dispatcher

• Queries a registry to discover potential
  providers
• Determines, based on provider metadata, whether a
  provider should be queried
• Sends requests to multiple providers
• Assembles responses from providers
• Returns packaged results to the requesting
  application
• Logs activity

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Construct query on data portal








ORNIS DiGIR Dispatcher


ORNIS Data Portal
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Dispatcher distributes request








ORNIS DiGIR Dispatcher


ORNIS Data Portal
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Providers query databases








ORNIS DiGIR Dispatcher


ORNIS Data Portal
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Databases respond to providers








ORNIS DiGIR Dispatcher


ORNIS Data Portal
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Providers respond to dispatcher








ORNIS DiGIR Dispatcher


ORNIS Data Portal
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Last response returns to dispatcher








ORNIS DiGIR Dispatcher


ORNIS Data Portal
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Dispatcher sends results to portal








ORNIS DiGIR Dispatcher


ORNIS Data Portal
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Key Issues

• Ownership maintained locally
• data controlled locally
• varying data quality and standards (e.g.,
  taxonomic names, geographic names, specimen part
  names)
• not all fields supported by all institutions
• mapping of fields across institutions may be a
  problem
• Institutions may restrict classes of data
• entire records (e.g., proprietary research
  material)
• certain fields (e.g., locality, collector)
• Updated data served in real time
• frequency of updates depends on local institution

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What does this mean forDNA Barcoding?

• Data on tissues will vary depending on local
  databases (how data are stored)
• Access to data IS NOT access to tissues
• institutional policies
• institutional decision-making
• Critical link between barcoding data and original
  provenance of samples (NO centralization)
• barcode sequences should be voucher-based
• data should be maintained at institution where
  voucher is deposited (taxonomic/identification
  updates, etc.)
• Genbank sequences should link directly back to
  vouchers and institutional data

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Success of DNA barcoding initiative depends on
community collaboration to provide data and
genetic resources!
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Downstream Costs

• Support for maintenance, enhancement, growth, and
  use of genetic resource collections
• Support for institutions that manage and serve
  data
• computerization of collections (staff time,
  dedicated computers)
• secure servers to enhance online access
• programming time to add institutions to the
  network

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ORNIS portalhttp//ornisnet.org
Glaucidium brodei
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Query Steps

• Select one or multiple providers
• Select one or more query conditions
• Concepts, e.g., Genus, Country
• Comparators, e.g., equals, contains
• Select result set structure
• Mapping
• allows mapping, table views, downloads
• subset of fields displayed
• only georeferenced points mapped
• Full result set
• all fields displayed
• currently not mappable
• Custom result set
• Selected (custom) fields displayed
• currently not mappable
• use to output Genbank numbers
• Specify record limit (default to display 10)

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ORNIS portalhttp//ornisnet.org
Glaucidium brodei