introduction

https://transfer.med.yale.edu/upload/data/39YObdi808qV4ftL3FY1588AL5AAC2AKLpS/Baker_-_BioRDF_-_W3C_-_HCLS_Lipid-Ontology_and_Reuse_Cases.pptx

https://transfer.med.yale.edu/upload/data/39YObdi808qV4ftL3FY1588AL5AAC2AKLpS/Baker_-_BioRDF_-_W3C_-_HCLS_Lipid-Ontology_and_Reuse_Cases.pdf

Cheers,

-Kei

<rfrost> kei, would you mind repasting the slide link?

kei: lipid ontology -- started with text mining and then formal ontology
... data integration is important and challenging in the context of lipid

IUPAC is older (1970's) challenge in adoption

LIPIDMAPS came along but still has issues such as inconsistencies

objectives: available through OBO

OBO compliance (e.g., continuant entity ... small molecule)

semantically expressive

use of owl in terms of necessary and sufficient condiitions and cardinality

started with 32 organic groups and another 63 are needed to define lipids

different functional groups can be defined

some entities are from the lipidmap and new entities have been added

reasoning can be performed based on the owl structure

use of checkmol and open babel for conversion into n3 format from mol files

go through all the instances and use rules/axioms to reason over the structure

to make sure structural group assignments are correct

this is an iterative process with interaction/collaboration/curation with community

715 classes, 901 restrictions, and 41 properties

scientists discovering new lipids can submit through web services

position the ontology as a bridge between lipid community, obo, and chebi

leverage the skills of the ontology community and the expertise of lipid community

semantic assistant

use of racer, sparql, and other related tools

use of text mining to help populate the ontology

normalizing terms into canonical names

looked at 8000 abstracts involving ovarian cancer

linked dimensions of lipid/protein to classes

linked to the sentence level

signal pathways are also included

knowledge finder: user can submit keyword can be mapped to a set of natural language queries for users to select

in addition, visual query tool has been developed

semantic desktop assistant: web service paradigm

lipid annotation: input can be abstract text for example

using the GATE annotation pipeline

client side application is open office

semantic assistant is free for download

acknowledgement: mutliple institutions are involved

<matthias_samwald> (need to leave now as well. bye!)

thanks, matthias

scott, could you also do the scribing from this point on?

I'm leaving now ...thanks!

<mscottm> possible followup meeting to look at genelists: Thu morning HCLS timeslot 11AM ET

<mscottm> Lena: Have some concerns about the current relation between genes and samples

<mscottm> Scott: Yes, let's talk about that some more - possibly this week?

<mscottm> ..anybody else interested in this?

<mscottm> MichaelMiller: I would be interested

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Got date from IRC log name: 07 Jun 2010
Guessing minutes URL: http://www.w3.org/2010/06/07-hcls-minutes.html
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