uBio 
What’s in a name? For Biological researchers a lot. Taxonomic information spans centuries. The information contained in
the journals of a research expedition to Africa in 1923 may be the key to locating a rare species
The trick is to find the name.
Common usage, even for scientific names, evolves over time as specimens names and genera are updated over the years. If the reference is to a vernacular name, the problem is even
more difficult given the fact that it might appear in over 100 languages. Regional usage adds even more complexity to the problem. To top it all off, there are also subjective
interpretations. An expert on fish may consider that something classified as separate species are in fact the same creature.
Searching for a bluefish is not as easy as you might think.
uBio is a research effort create a name service and an international indexing scheme that will map the many to one relationship between a creature and its names.
The names themselves are also distributed. Experts, some with differing opinions, maintain a vast number of disjoint databases all over the world. The formats, data models, and
details of these repositories are almost as diverse as the species they contain.
The union of this knowledge contains the keys needed to mine the world’s libraries, electronic stores and museum collections as well as foster relationships to enhance the collaborative
nature of taxonomic science.
The uBio solution has gained a great deal of international support and is working jointly with the Global Biodiversity Information Facility (GBIF)
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Key Project Data
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Project Duration
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9 months (on-going)
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Key Technologies
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Server, multi-platform clients, web client, security, encryption, database, distributed database, peer to peer syncronization, event based repository
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Major Technologies
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Dynamic Indexing Keys, Universal ID model, Asyncronous collaborative model, disconnected networking
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Key Success Factors
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Acceptance by the international community
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Surprises
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Thats why they call it research
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Client Platforms
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Windows NT, 2000, XP, Mac OS 7.1-9.2, Mac OS X, Linux/32
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Development
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RealBasic, Java, PHP
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Server Platforms
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Primary: Linux/mySQL, Mac OS X/mySQL. Secondary: Anything.
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The Solution
A number of innvovative models, components and concepts have been created for uBio. The data repository uses a Data Model that accommodates all of the information models for the distributed research data
stores. There is a three tier persistent dynamic key structure that links names to objective synonyms and vernaculars in any published language.
The ID structure is designed to be globally unique without requiring a clearinghouse and can be used as the local indexing scheme for multiple peer-to-peer data repositories even when they are disconnected.
Key linkage can inherit additional many-to-1 relationships are remain valid for life. The dynamic keys, once created can be mapped directly into a very responsive atomic set of standard SQL queries.
The repository, which is secured on a per attribute basis,
maintains a threaded journal that allows changes to roll both forward and backward with a fine degree of granularity. In the case of scientific research, the matter of who changed what in which order adds a great deal of information to the process.
There are also SOAP, JavaXML, and private protocols for accessing the information, and a security model to protect intellectual properity.
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Branching out |
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The uBio project is a Mellon funded effort that has already spawned the Taxonomic name server project (TNS), the NameBank project, and Classification Bank as well as proposals for additional Mellon, NSF, and NIM
research.
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RealBasic |
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uBio makes extensive use of RealBasic. For more info take a look at our RealBasic Develpment Notes
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Collaboration |
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uio has established relations with many library, museum, biodiversity, global initiative and research efforts. including the Americian Musium of Natural History, the Smithsonion, GBIF, Species 2000, ECAT.
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Libraries at the leading edge of IT |
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This effort was started by the libraries at The Marine Biological Laboratory (MBL) and the Wood’s Hole Oceanigraphic Institute.
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