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To do

  • Map parts database schema to RDF/OWL (D2R Map/Server)
  • HCLSIG BioRDF subgroup tasks - interesting projects
  • Use LSID for parts identification
    • setup LSID resolution service
  • How to represent sequence features (do they belong to sequence or part)?
    • Part has features and has a sequence (piece of DNA with molecular function combined by BB assembly)
    • Sequence has features but a part already has sequence
  • Tools to create and edit ontology and RDF instances?
    • Protege from Stanford?
    • IsaViz from W3C?
  • existing RDBMS <-> RDF <-> objects (e.g., Javascript)
  • Do we need "Device"?
  • I want to build a NOR gate vs. I have a NOR gate
  • Find a way to use MediaWiki software to work with the Semantic Web ontology of biological parts: create a UI from the description of a part in the ontology that would check the entered information for correctness according to the part definition in the ontology.

To read

As biologists increasingly rely upon computational tools, it is imperative that they be able to appropriately apply these tools and clearly understand the methods the tools employ. Such tools must have access to all the relevant data and knowledge and, in some sense, “understand” biology so that they can serve biologists' goals appropriately and “explain” in biological terms how results are computed.

BBF standards

External projects

  • ConnectingMe project will develop a new application architecture that uses a semantic web information repository and data integration engine along with a user customizable presentation engine
  • Jourknow - semantic web personal info organizer (FAQ)


Data or metadata

(from LSID best practices) Data is defined as a sequence of unchanging bytes. Examples of data are microscope images, a protein sequence, a text file, etc. Metadata is usually information that describes the data either literally (date created, MD5 check sum, size) or contains information describing the relationship between the data and other objects. If you cannot determine what should be data and what should be metadata from your data model, follow this rule of thumb: Large byte sequences are easier to manipulate as data, while short byte sequences can be included as data, metadata, or made available in both forms.

From XML to RDF

From XML to RDF: how semantic web technologies will change the design of 'omic' standards

  • ?



  • Semantics - the meaning that is implied by words and sentences.
  • Software agent can search distributed registries using an ontology. This is impossible right now because storage schema is unknown.
  • Data is represented by a graph of triples (statements about resources)
  • Syntax doesn't matter: there are many ways to serialize the data (XML, N3, etc).
  • HCLS task forces:
    • BIORDF (Structured data to RDF) - Susie Stephen, Joanne Luciano co-leads
    • T2S (Text to Structured RDF) - Robert Futrelle, Matthew Cockerill
  • Architecture of the World Wide Web @ W3C
  • Reification @ Wikipedia
  • Metadata
    • Semantic mapper is tool or service that aids in the transformation of data elements from one namespace into another namespace.
    • Metadata registry is a central location in an organization where metadata definitions are stored and maintained in a controlled method.
  • XSLT vs XQuery
  • A Semantic Web Primer for Object-Oriented Software Developers - OO vs SW, links to software, etc
  • rdfs:label vs rdfs:comment
    • used to describe a resource with human readable text in addition to "pure" RDF properties (may have multiple values for internationalization needs)
    • rdfs:label is used to give a human-readable name of a resource
    • rdfs:comment is used to give a longer description
  • rdf:about and rdf:ID in RDF/XML
  • Resource manipulation and description: URIQA, REST, WebDAV, WSDL, etc
  • Logic studies the laws of valid inference (the act or process of deriving a conclusion based solely on what one already knows).
  • Closed world assumption is the presumption that what is not currently known to be true is false.
  • Open World Assumption assumes that its knowledge of the world is incomplete. If something cannot be proved to be true, then it doesn't automatically become false.