User:Ilya/Registry

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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.

Abstraction Hierarchy

• Part - simple biological function encoded in DNA
• Device - simple logical function; collection of parts
• System - collection of devices
• Device is_a part in context of the system but also device has_a part.
• Device is_a subclass of Part, System is_a subclass of Device
• How to represent barriers and interfaces betwee levels of abstration?
• Genetic, protein and cell devices
• :RBS :subclassOf :BasicPart OR :RBS :typeOf :BasicPart (instance)
• Basic parts: detailed specs and sequence data
• Composite parts: basic parts plus assembly (composite parts have are the same if they have the same basic parts)
• Device: not necessary on a single piece of DNA
• Separate spaces: set of hierarchies
  • Physical (DNA sequence assembly)
  • Design
  • Standards (Performance)
• Class of Standards: assembly standards, performance standards?

Current Design

Biobricks come in three flavors:

• Parts/basic parts/subparts encode basic biological functions (RBS, CDS)
• Devices/composite parts are made from a collection of parts and encode some human-defined functions, such as logic gates in electronic circuits) (inverter)
• Systems perform tasks, such as counting (oscillator)

• No need to specify deep_components vs component_list
• Right now: composite parts have only components listed; deep components produced from that list

Types: what type are Plasmid, Cell and T7?

Registry Parts Index

• A part is not allowed to contain both its own sequence and other parts
• Subparts - ordered set

Naming convention

• Part name/number - unique ID
• BB a _ X nnnnnn
• BB: BioBricks
• a: alpha stage of development
• X: part type
• nnnnnn: 4-6 digit part number
• Normally, the part name contains the letter associated with the part's type. Confusion is possible when a part fits into multiple categories.

Part properties (example) (* marks properties that belong to composite, possible value(s) are in parenthesis)

• name
• short_description (Promoter (lacI regulated, lambda pL hybrid))
• description
• type (Regulatory)
• status/availability (Available)
• results/usefulness (None|Fails|Works)
• component_list (NULL | BBa_B0032 BBa_C0051 BBa_B0010 BBa_B0012 BBa_R0063 BBa_B0030)*
• base_components (0 | 9)*
• deep_components (NULL | 149 156 603 145 193 147 161 603 145)*
• deep_components_2 (own part_id | _149_156_603_145_193_147_161_603_145_)* ?
• deep_component_count (1 | 9)*
• device_name (NULL | inverter)*
• sequence (why is sequence available for the composite parts)
• feature(s)
  • type
  • start
  • stop
  • label
• usage
  • lastmod_user
  • lastmod_date
• biology (Very weak promoter)
• functional parameters
  • efficiency 0.6
• design
  • author (names(s) or id)
  • owner (number: owner_id)
  • creation_date
  • container_id
  • version
  • source (Bacteriophage 434 right operator)
  • notes
  • reference?
  • owning groups
• physical DNA (instances?)
  • plasmid
  • plasmid_length
  • part_and_plasmid_length
  • VF2-VR
• location(s) - This part may be found in these wells/tubes
  • library
  • well
  • plate
  • plasmid - this the same plasmid as in physical DNA section above?
  • cell
• files
• references
• licenses

Miscellaneous

• 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).
• Ontology vs taxonomy vs thesaurus vs list
• Ontology vs Taxonomy vs Folksonomy vs Collabulary
  • Taxonomy - concepts and relationships but no attributes.
  • Controlled vocabulary - only concepts.
• Microformats
  • "lowercase semantic web"
  • humans first, machines second
• 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

To Do

• Map parts database schema to RDF/OWL (D2R, other?)
  • Use RDF/OWL to describe neuronal data available in SenseLab - similar project
• 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

From XML to RDF

(from [1])

• ?

Knowledge Management

• Thinking XML: Basic XML and RDF techniques for knowledge management
  • Part 1: Generate RDF using XSLT
  • Parl 2: Combining files into an RDF model, and basic RDF querying
  • Part 3: Knowledge from semantics
  • Part 4: Issue tracker schema
  • Part 5: Defining RDF and DAML+OIL
  • Part 6: RDF Query using Versa
  • Part 7: Review and relevance of the techniques discussed
• IBM Systems Journal - Knowledge Management

Description Logic

• Description Logic - a cornerstone of the Semantic Web for its use in the design of ontologies
  • Tutorial course
• Semantic network is often used as a form of knowledge representation. It is a directed graph consisting of vertices which represent concepts and edges which represent semantic relations between the concepts. An example of a semantic network is WordNet, a lexical database of English.

Links

• RDF in Mozilla

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