User:Ilya

Registry of Biological Parts software architecture.

Semantic Web: RDF/XML and RDF Schema

Data access interface requirements:

• standardized
• extensible
• human and machine readable
• scalable (distributed registries)

Semantic Web

• allows to model real things, not just documents or database tables
• consists of statements about resources in the form of triples:

SUBJECT -> PROPERTY -> VALUE

• identifies every resource with a globally unique URI: don't say "color", say <http://example.com/2005/std6#col>
• allows “serendipitous reuse”: integration with data sources in other fields (“web join”)

Ontology: controlled vocabulary of concepts and their relationships.

Examples of ontologies:

• Dublin Core
  • Namespace: http://purl.org/dc/elements/1.1/
  • Properties: title, creator, publisher, identifier
• Gene Ontology
  • Namespace: ftp://ftp.geneontology.org/pub/go/xml/dtd/go.dtd
• Properties: name, definition, isa, association, evidence
• Sequence Ontology: features on a nucleotide or protein sequence
• BioPAX: biological pathway data
• UniProt (planning)

References:

1. Berners-Lee - Semantic Web Life Sciences - BioIT World
2. Web Service - Semantic Web by Tim-Berners Lee
3. Introduction to the Semantic Web and RDF by A.M. Kuchling

Bioinformatics extensions for Firefox:

• Biobar
• LSID

Wiki ideas:

• blacklist certain pages from public viewing and/or editing (Blacklist pages from viewing)

• use "endy members group" to restrict access to certain pages