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The nature of bioinformatics databases

The nature of bioinformatics databases. Provide Open Access, free to academics, for data generated by publicly funded research Few databases have assured long-term funding; many run on a shoestring

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The nature of bioinformatics databases

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  1. The nature of bioinformatics databases • Provide Open Access, free to academics, for data generated by publicly funded research • Few databases have assured long-term funding; many run on a shoestring • None are run for the purpose of generating profit, although some generate income to offset costs by selling services to commercial companies • Data are rarely replicated between databases (with the exception of basic sequence and crystal structure data), so little need for multiple resolution • Many add value to raw data by providing expert annotations, organizing data according to protein families, etc. • Databases typically use distinct data models and lack interoperability • Some are actively adopting new Semantic Web technologies • All are ripe for the use of universal resolvable identifiers

  2. The aims of the BioImage Database Project The aims of the BioImage Database (www.bioimage.org), funded by the European COmmission ORIEL project (www.oriel.org) are: • To be a searchable database of high-quality multidimensional research images of biological specimens, both ‘raw’ and processes, with detailed supporting metadata concerning: • the biological specimen itself • the experimental procedure • details of image formation and subsequent digital processing • the people, institutions and funding agencies involved • the curation and provenance of the image and its metadata • To integrate such multi-dimensional digital image data with other life science resources by providing links to literature and ‘factual’ databases • To store, use and conform with standard external identifiers such as DOIs where these are available, particularly when referencing articles

  3. The basic BioImage metadata model (with thanks to <indecs>) Cell or organism Researcher Experimental conditions or manipulations Experiment or study Subject or specimen Photographer or microscopist Camera or microscope Image capture Image sets of multidimensional images, including videos

  4. TheBioImage home page www.bioimage.org Note the hierarchical browse categories and the alternative Browse / Search arrangement

  5. Search result, showing Studies

  6. What are Life Science Identifiers? • LSIDs have been developed by IBM and I3C (the Interoperable Informatics Infrastructure Consortium; www.i3c.org) to serve the life sciences • They uniquely identify single digital objects • They provide persistent URNs resolvable though normal DNS mechanisms • They are location independent • They permit provenance records (versioning) • While developed for the life sciences, they are in fact completely generic

  7. What do LSIDs look like? • A five-part format: urn:lsid:Authority:Namespace:Object_ID[:Revision-ID] • urn:lsid: This network identifier (NID) is a mandatory prefix • Authority is the root DNS name of the issuing authority • Namespace is chosen by the issuing authority and constrains the scope of the object • Object_ID is an alphanumeric object ID unique to the namespace • Revision is an optional version of the object For example: • urn:lsid:bioimage.org:BIOIMAGE:76 refers to entry 76 in the BioImage Database • urn:lsid:ncbi.nlm.nih.gov:pubmed:12571434 references a PubMed article • urn:lsid:ncbi.nlm.nig.gov:GenBank:T48601:2 refers to the second version of an entry in GenBank

  8. How do they work? • LSIDs are in a sense just a sociological con trick, since they are nothing more than cheap and cheerful URNs • They can be published and resolved, either over the Web using DNS mechanisms, or using Web Services protocols (UDDI, WSDL, SOAP) • If an LSID names an abstract concept, such as a protein name, for which multiple relevant datasets may exist, that LSID will not have any byte data associated with it, but instead will have metadata pointing to other LSIDs that themselves name ‘concrete’ versions of the object, e.g. the protein sequence, the crystal structure. Those LSIDs do name actual byte data • They share many of the weaknesses of conventional Web mechanisms, particularly regarding security and access control

  9. Who are using LSIDs? • LSIDs wer first introduced in 2003 • LSIDs are being adopted by highly respected and influential leaders in the bioinformatics Web Services and Semantic Web community, including • Mark Wilkinson of BioMOBY (www.biomoby.org), • Carol Goble of MyGrid (www.mygrid.org.uk), and • and Eric Neumann, Global Head of Knowledge Management for Aventis • They form the resolution mechanism behind Haystack, the first Semantic Web browser, based on Eclipse (haystack.lcs.mit.edu)

  10. Why are people choosing LSIDs • LSIDs can be retro-fitted to existing databases, permitting you to convert your own internal identifiers into unique resolvable identifiers, without altering your existing naming system • Open Source software exists to permit you to establish DNS and Web Services resolution services for your URNs, such that anyone addressing your URL can send an LSID and have returned an RDF document describing what that LSID represents • Like being a Web publisher, anyone can become an LSID registration agency • No central third-party registration agency is required, and there are no fees to pay • This no-cost decentralized mechanism, while lacking many of the safeguards and refinements of DOIs, has the same ingredients for success as Tim Berners-Lee’s original Web protocols • We have adopted LSIDs for the BioImage Database and will establish our own LSID resolution authority as soon as we go public

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