uBio presentation given to Species 2000 in May 2004

1. Universal Biological Indexer and Organizer
Research Funded by the Andrew W. Mellon Foundation
MBL / WHOI LIBRARY
Universal Biological Indexer and Organizer
Research Funded by the Andrew W. Mellon Foundation
MBL / WHOI LIBRARY

2. Universal Biological Indexer and Organizer
Research Funded by the Andrew W. Mellon Foundation
MBL / WHOI LIBRARY
MBL/WHOI Library
• Stewards of natural
history information
• Provide services to our
patrons
• Access to information

3. Universal Biological Indexer and Organizer
Research Funded by the Andrew W. Mellon Foundation
MBL / WHOI LIBRARY
What information
• Local Data
– Special Literature Collections
– Specimen databases, herbaria,
sequence data
• Remote data
– Journals
– ILL
– Serial Databases
• (ASFA, JSTOR, etc.)

4. Universal Biological Indexer and Organizer
Research Funded by the Andrew W. Mellon Foundation
MBL / WHOI LIBRARY
Information Delivery
• Primary access interfaces
– Brute Force - Read it
– Search:
– Browse by hierarchical taxonomic category
• Animalia
• Vertebrates
• Birds
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5. Universal Biological Indexer and Organizer
Research Funded by the Andrew W. Mellon Foundation
MBL / WHOI LIBRARY
Problem: Multiple Names
• Common names
• Scientific Names
• N:N
• Persistent
• Pervasive
– Pectinaria gouldii
– Cistenides gouldii
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6. Universal Biological Indexer and Organizer
Research Funded by the Andrew W. Mellon Foundation
MBL / WHOI LIBRARY
Problem: Multiple categories
• No taxonomic opinion
• Patron opinions are what counts
• Multiple basis for derivation
• Dynamic
• Require any/all
ITIS
Animalia
Chordata
Osteichthys
Actinopterygii
Perciformes
Pomatomidae
Pomatomus
saltatrix
NCBI
Eukaryota
Fungi/Metazoa group
Metazoa
Eumetazoa
Bilateria
Coelomata
Deuterostomia
Chordata
Craniata
Vertebrata
Gnathostomata
Teleostomi
Euteleostomi
Actinopterygii
Actinopteri
Neopterygii
Teleostei
Elopocephala
Clupeocephala
Euteleostei
Neognathi
Neoteleostei
Eurypterygii
Ctenosquamata
Acanthomorpha
Euacanthomorpha
Holacanthopterygii
Acanthopterygii
Euacanthopterygii
Percomorpha
Perciformes
Percoidei
Pomatomidae
Pomatomus
saltatrix

7. Universal Biological Indexer and Organizer
Research Funded by the Andrew W. Mellon Foundation
MBL / WHOI LIBRARY
Generalized Solution
• Ad-hoc Fix
• Systematic Fix
• Network thesaurus
• “Plug” in applications
• Any name
• Any classification

8. Universal Biological Indexer and Organizer
Research Funded by the Andrew W. Mellon Foundation
MBL / WHOI LIBRARY
What it should do
• Account for any “name” relevant to the defined
“community”
• Provides taxonomic metadata to biological information
providers
– Libraries
– Publishers
• Provides detailed accounting of usage of taxonomic
metadata to contributors of knowledge

9. Universal Biological Indexer and Organizer
Research Funded by the Andrew W. Mellon Foundation
MBL / WHOI LIBRARY
WHY do we want a solution
• Increase access to biological information assets
• Too much information is inaccessible
• It should directly benefit contributors of
knowledge
• Directly link usage to attribution

10. Universal Biological Indexer and Organizer
Research Funded by the Andrew W. Mellon Foundation
MBL / WHOI LIBRARY
Increase Access: How?
• Supplement name information that is available for
searching and matching name strings
– (Example)
– Vernacular, homotypic, heterotypic
• Provide hierarchical structures for browsing large
biological data collections
– (Example)
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11. Universal Biological Indexer and Organizer
Research Funded by the Andrew W. Mellon Foundation
MBL / WHOI LIBRARY
What we came up with:uBio
• Database of taxonomic metadata (TNS)
• Network Service (SOAP)
• Workgroup management system
• Intent:
– Demonstrate a need through pilot system
– Add enough names to show that the system works at
scale
– Look for partners who can curate names

12. Universal Biological Indexer and Organizer
Research Funded by the Andrew W. Mellon Foundation
MBL / WHOI LIBRARY
TNS

13. Universal Biological Indexer and Organizer
Research Funded by the Andrew W. Mellon Foundation
MBL / WHOI LIBRARY
TNS: NameBank
• Nomenclature -
– Scientific -> basionym
– Vernacular -> scientific
• Objective Relationships
– Vernacular mappings based on associations
– Homotypic
– Lexical variants
– Management Classification
• No name left behind
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14. Universal Biological Indexer and Organizer
Research Funded by the Andrew W. Mellon Foundation
MBL / WHOI LIBRARY
TNS: ClassificationBank
• Subjective
• Hierarchies
• Synonymies
• Varying degrees of granularity
– Checklists (-Example)
– Junior Synonyms (-Example)
– Full bibliographic review (-Example) QuickTime™ and aTIFF (Uncompressed) decompressorare needed to see this picture.
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15. Universal Biological Indexer and Organizer
Research Funded by the Andrew W. Mellon Foundation
MBL / WHOI LIBRARY
TNS: Accounting
• Multiple sources may be responsible for a single
data object
• Any data change is linked to a source
• Links all TNS data to a contributing Agent
– NameBank/ClassificationBank specific
– Each interacts with it independently
– (Example)
• Names belong to sources
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16. Universal Biological Indexer and Organizer
Research Funded by the Andrew W. Mellon Foundation
MBL / WHOI LIBRARY
Network Service: Methods
• SOAP
– http-based
• Four primary methods
– nameBank_search (locate factual instance of name)
– nameBank_object (objective metadata)
– classificationBank_search (locate interpretations of name)
– classificationBank__object (subjective metadata)
– …more to come
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17. Universal Biological Indexer and Organizer
Research Funded by the Andrew W. Mellon Foundation
MBL / WHOI LIBRARY
Network Service :Attribution
• Every datum sent out via
service is logged
– nameBankID
– datestamp
– Client IP
– Calling method
– requestorIP
• <client optional>

18. Universal Biological Indexer and Organizer
Research Funded by the Andrew W. Mellon Foundation
MBL / WHOI LIBRARY
Log is Processed
• Network service <-> Contributing Agent
– By date
– By IP
– By method
– Full Accounting of usage
• Intent is to be a proxy for these data
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19. Universal Biological Indexer and Organizer
Research Funded by the Andrew W. Mellon Foundation
MBL / WHOI LIBRARY
Why
• Increase utility
– Put data to work in multiple ways
• Increase value
– When benefits are clear
• Increase support for it
– We can garner support from these communities

20. Universal Biological Indexer and Organizer
Research Funded by the Andrew W. Mellon Foundation
MBL / WHOI LIBRARY
Workgroup Management System
Platypus
Networked
Multi-platform
Multiple Users
Ease management burden
Input parser

21. Universal Biological Indexer and Organizer
Research Funded by the Andrew W. Mellon Foundation
MBL / WHOI LIBRARY
Collaborate
• Reduce duplication of effort
• Maximize accountability to those that DO the work
• Utilize funding resources for new work
• New uses for existing work

22. Universal Biological Indexer and Organizer
Research Funded by the Andrew W. Mellon Foundation
MBL / WHOI LIBRARY
Multiple Initiatives
• Range of focus
• Different priorities
• Different scales
• Multiple opinions
• Yet there is common data
• Any name in list is useful
to all

23. Universal Biological Indexer and Organizer
Research Funded by the Andrew W. Mellon Foundation
MBL / WHOI LIBRARY
Layered Systems Work

24. Universal Biological Indexer and Organizer
Research Funded by the Andrew W. Mellon Foundation
MBL / WHOI LIBRARY
Encapsulate: NameBank
• Nomenclature reference core
• Independent from any specific
application/system
• Maintain full attribution to
source and edits
• Makes our TNS portable
• Collaborative foundation

25. Universal Biological Indexer and Organizer
Research Funded by the Andrew W. Mellon Foundation
MBL / WHOI LIBRARY
Federate
• Layered architecture
• Common Foundation
• Multiple Directions
• Interchange
• Cooperation
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26. Universal Biological Indexer and Organizer
Research Funded by the Andrew W. Mellon Foundation
MBL / WHOI LIBRARY
Domain Layer

27. Universal Biological Indexer and Organizer
Research Funded by the Andrew W. Mellon Foundation
MBL / WHOI LIBRARY
Next
• Formalize the NameBank split from TNS
• Empty it and start over
– uBio is only a prototype
• Look for taxonomic partners
• Focus on solutions for libraries
• Bring library community to partnership