HCLSIG BioRDF Subgroup/Meetings/2010/01-04 Conference Call

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Conference Details

  • Date of Call: Monday January 4, 2010
  • Time of Call: 11:00 am Eastern Time
  • Dial-In #: +1.617.761.6200 (Cambridge, MA)
  • Dial-In #: +33.4.89.06.34.99 (Nice, France)
  • Dial-In #: +44.117.370.6152 (Bristol, UK)
  • Participant Access Code: 4257 ("HCLS")
  • IRC Channel: irc.w3.org port 6665 channel #HCLS (see W3C IRC page for details, or see Web IRC), Quick Start: Use http://www.mibbit.com/chat/?server=irc.w3.org:6665&channel=%23hcls for IRC access.
  • Duration: ~1 hour
  • Frequency: bi-weekly
  • Convener: Kei Cheung
  • Scribe: Kei Cheung

Attendees

Kei Cheung, Helena Deus, Rob Frost, Priti Parikh, Eric Prud'hommeaux, Satya Sahoo, Matthias Samwald, Jun Zhao

Regrets

Scott Marshall, Adrian Paschke

Agenda

  • Introduction [Kei]
  • Microarray use case -- exploring the RDF structure [All]

Minutes

Introduction: today’s call is a working telcon focused on coming up with an initial version of the ontology structure for answering a range of semantic federated queries posed by the microarray use case.

Satya presents the provenir ontology for representing experiment parameters, data, and provenance while reusing existing ontological terms/relationships.

Lena talks about her experience on how to represent gene lists derived from raw data.

Kei introduces some examples involving entities such as organisms, brain regions, neurons, genes and diseases and how they might be related to one another.

Entities such as brain regions and neurons may be modeled as experiment parameters (domain parameters). We will reference NIFSTD for these neuroscience entities and their relationships.

Array platforms (e.g., Affymetrix) should be captured as an experiment parameter.

Gene lists can be viewed as output of experiment. Expressed genes can be related to brain regions and neurons located in brain regions. We should represent both gene lists and individual genes for query flexibility (e.g., find genes that are involved in certain pathways).

Protocols (e.g., the steps/methods involved in computing the gene lists) should also be captured and shown as part of the query output.

Neurons (subclass of biosamples?) may be classified as normal vs. disease neurons (e.g., ones with NFT) extracted from the brain tissues of patients/normal controls/model organisms.

Next steps: Satya will continue to refine the ontology. Lena will continue to work on the genelist aspect and help populate the ontology with the use case examples. We will test it with some sparql queries.

Next telcon call will be held in two weeks.