GUID-1 Workshop National Evolutionary Synthesis Center Durham, NC, Feb 1-3, 2006 Digital Object Identifiers as a technology Implementation of a full working prototype The NamesforLife model George M. Garrity Microbiology and Molecular Genetics Michigan State University
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GUID-1 WorkshopNational Evolutionary Synthesis Center
Durham, NC, Feb 1-3, 2006
Digital Object Identifiers as a technology
Implementation of a full working prototype
The NamesforLife model
George M. GarrityMicrobiology and Molecular Genetics
Michigan State University
GUID-1 WorkshopNational Evolutionary Synthesis Center
Durham, NC, Feb 1-3, 2006
During the next 25 minutes
An overview Digital Object IdentifiersWhat is an identifier?Comparison of DOI features to a native Handle implementationAddress Ricardo’s general questions
ExtensibilityHandling of metadataStrengthsWeaknessesOther relevant issues
Introduce the NamesforLife prototypeDevelopment of the modelA complete prokaryotic taxonomy implemented with DOIs
GUID-1 WorkshopNational Evolutionary Synthesis Center
Durham, NC, Feb 1-3, 2006
“Dual” interestsTrustee and Editor-in-Chief
Founded in 1936501 c3 Non-profit educational trustHeadquartered at Michigan State University
Produce reference works in prokaryotic biologyBergey’s Manual of Systematic Bacteriology
Principal monographic work in the field
Validly published, named taxa
> 650 international expert authors
Published by Springer, NY
Bergey’s Manual of Determinative Bacteriology
Diagnostic
Traditional “ink on paper” products
Taxonomic Outline of the Prokaryotes
Derived from MSU/DOE sponsored research
Backbone of the Systematics
Distributes as a locked PDF file
http:
//www.bergeysoutline.com
GUID-1 WorkshopNational Evolutionary Synthesis Center
Durham, NC, Feb 1-3, 2006
“Dual” interests (cont.)The major source of curated 16S rRNA sequences and on-
line tools used in building prokaryotic phylogenies and identifying cultivated and yet to be cultivated prokaryotes.
Funding by DOE Office of Science (BER) and NSFhttp://rdp.cme.msu.edu
Visualization tools for exploratory data analysis of large sequence data set, a taxonomic atlas of the prokaryotes, and a repository of vetted 16S sequences.
Funding by DOE Office of Science (BER)
http://taxoweb.mmg.msu.edu
Semantic resolution services for life sciences using digital object identifiers
Funding by the Michigan University Commercialization InitiativeUS and WIPO patents pendingProperty of the Board of Trustees of Michigan State
University
GUID-1 WorkshopNational Evolutionary Synthesis Center
Durham, NC, Feb 1-3, 2006
I represent the following parties
An IUMS COMCOF
Body that oversees the nomenclature of prokaryotesPublication of the “Code” and the International Journal of
Systematic and Evolutionary Microbiology
Judicial Commission
Oversees application and modification of the code
Taxonomic subcommittees
The Digital ObjectIdentifier System
International Committee on Systematics of Prokaryotes
The International DOI FoundationEstablished in 1998Develop and manage the DOI SystemSupport the needs of the IP community in the digital
environment by development and promotion of DOI system as a common infrastructure for content management
An open member consortiumNamesforLife, LLC is a general member of the IDF
GUID-1 WorkshopNational Evolutionary Synthesis Center
Durham, NC, Feb 1-3, 2006
Comparing identifiersA label that identifies an entity
ISBN 0-387-98771-1
ATCC 27126L-681,572
A single unambiguous string
A method of providing consistent syntax to denote a class membership of an entity.A formal standard or industry convention
ISBN numbers follow an international industry conventionAn arbitrary internal system
Collection accession numbers and sample tracking numbers are typically institution specific Establishes a 1:1 correspondence between labels and membersEnumeration
The number or label is simply a string
A numbering scheme
GUID-1 WorkshopNational Evolutionary Synthesis Center
Durham, NC, Feb 1-3, 2006
Comparing identifiers (cont.)
A syntax by which an identifier can be expressed in a form suitable for use within a specific infrastructure.Actionable identifiers
URI (URN and URL)ISBN numbers as UPC/EAN identifiers
Does not mandate a method of creating labelsDoes not create a managed environment
An infrastructure specification
Includes Unique identifiersA formalized infrastructureManagement policies for registration, structured
interoperable metadata, policy, and governance mechanisms.
ExamplesUPC/EAN barcodes and RFID tagsDigital object identifiers (digital identifiers of
objects)
A fully implementedidentifier system
GUID-1 WorkshopNational Evolutionary Synthesis Center
Durham, NC, Feb 1-3, 2006
The Digital ObjectIdentifier System
The DOI - Handle relationship
Handle System is one component of the DOI SystemGlobal name serviceSecure name resolution over the Internet and Grid
DOI System uses the Handle System as part of a value-added applicationDOIs provide persistent, semantically interoperable identification of IP resourcesThe DOI system provides a ready to use
Numbering syntaxResolution serviceData modelPolicies and procedures for implementationExpanded technical infrastructure and features specific to DOI applications
GUID-1 WorkshopNational Evolutionary Synthesis Center
Durham, NC, Feb 1-3, 2006
Persistence
The Digital ObjectIdentifier System
The IDF extends the technical infrastructure of the Handle System by provides a social infrastructure guaranteeing persistenceFunction of organizations, not technologyFederation of Registration Agencies
IDF policies ensure DOIs “live” even if RAs failRAs provide the process of DOI transfer
IDF is persistent as it is self-fundingDOI System is backed by several major public companies, multiple RAs, and a large customer base
Persistence is not requiredNo appropriate social structure is
provided
GUID-1 WorkshopNational Evolutionary Synthesis Center
Durham, NC, Feb 1-3, 2006
Consistency
The Digital ObjectIdentifier System
Adds consistent rules for multiple applicationsIDF set rules for DOI assignment
What DOIs can be applied toRestrictions on arbitrary/temporary assignmentRestrictions on removal
Management by a Directory Manager to enforce QCDOI API defines consistent way of accessing and managing DOI applications and servicesConsistent use of DOI prefix and numbering syntax provides numbering interoperability in the IP sector, brand recognition,
understanding of what a DOI conceptOptimal data model provides semantic consistency for true interoperability
Ensures interoperability for resolution purposes across Handle System implementations
No requirements for interoperability at the application level
GUID-1 WorkshopNational Evolutionary Synthesis Center
Durham, NC, Feb 1-3, 2006
Ease of use
The Digital ObjectIdentifier System
Turn-key applicationIDF and RAs maintain technical support staff
Interacts with users, standards community and others
Resolve problems of RAs and broader user community
Underwrites cost of directory manager
Support to RAs
Guidance, troubleshooting, etc
DOI Handbook
Policies and procedures for various actors
Guidelines for RAs, developers
Developed by federation of DOI agencies, guaranteed by detailed legal agreements.
No ongoing technical supportHandle server must be installed and managed by
local technical staffFree, but not without real costs
GUID-1 WorkshopNational Evolutionary Synthesis Center
Durham, NC, Feb 1-3, 2006
Expressing relationships
The Digital ObjectIdentifier System
Provides framework to achieve practical application of multiple resolutionApplication of Handle System that adds the necessary constraintsConstraints provided by metadata, which defines the entities
(data dictionary approach) and expresses the relationships.
Provides support for multiple resolutionParent-child relationshipsOther relationships
No preexisting constraints to make useful relationships
GUID-1 WorkshopNational Evolutionary Synthesis Center
Durham, NC, Feb 1-3, 2006
Technical infrastructure
The Digital ObjectIdentifier System
Adds dedicated and improved technical infrastructureReplication servers for RAs, secondary sites, mirror servers, proxy servers all housed in a secure commercial hosting facility
More robust and scalable databaseDOI Directory Manager to provide technical oversight and evolutionary
growth
Provides a shared resolution service Global root servers, local Handle servers, clients, proxy serversScalable and interoperableLicense provides a reference implementation but the database does
not scale above a few million handles
GUID-1 WorkshopNational Evolutionary Synthesis Center
Durham, NC, Feb 1-3, 2006
Semantic interoperability
The Digital ObjectIdentifier System
Adds semantic interoperability across application space
Feature of advanced DOI applicationsProvides metadata kernel to specify entity identified by DOI
Optional tool to map existing schema through a structured ontology
Ensures DOI can be the key in building multi component media objects or managing multiple assets
Data dictionary and application frameworkEnsures that DOIs act predictably in applications with defined series
IDF maintains indecs data dictionary and will likely maintain MPEG-21 data dictionary
No requirements as to what is being identified
No assurance of semantic interoperability across resources
GUID-1 WorkshopNational Evolutionary Synthesis Center
Durham, NC, Feb 1-3, 2006
Development activities
The Digital ObjectIdentifier System
Adds to this resource for active development of DOI applications and advanced features
Working groups and technical support staffUse of DOIs in commercial settings
RAs have an incentive to allocate their own resources to develop new features, collaborate with other RAs and share with the wider DOI community
Provides upgrades of the global general-purpose naming system
GUID-1 WorkshopNational Evolutionary Synthesis Center
Durham, NC, Feb 1-3, 2006
Costs to replicate a comparable system
The Digital ObjectIdentifier System
Preceding features are part of a turn-key system
RAs provide value added services to their clients
IDF holds production Handle license with right to sublicense
Cost of DOI assignmentVary across RAs and depend on their business model Can be free as part of a service offering
Need to add all preceding features not included in the general purpose software
Cost of a production Handle licenseOther licenses to enabling technologies
GUID-1 WorkshopNational Evolutionary Synthesis Center
Durham, NC, Feb 1-3, 2006
Governance
The Digital ObjectIdentifier System
Independent not-for-profit organizationCNRI provides services under commercial agreement Elected board and nominated working groupsOpen membership
NamesforLife, LLC is a general member
Independent of IDFHandle System Advisory Committee
Major users and interested partiesIDF is a member
GUID-1 WorkshopNational Evolutionary Synthesis Center