<Simon> Slideshare URL for todays presentation: http://www.slideshare.net/stwigger/ncbo-dbp

scribenick kei

ncbo biological project rat model

a variety of data including gene annotation data

good use of ontologies to help annotate these data

phenotype, trait, etc

rate genome database

linking bench work to informatics

use rat model for hypertension

quantitative trait loci

link genes within the loci to high blood pressure phenotype

gene expression in different genes, different rat strains, ...

use of geo microarray data at ncbi

use ncbo anntotator

run geo data through annotator

get ontology anntotation

rat strain ontology (obo format)

mouse anatomy ontology (small difference between mouse and rat)

rat strain, tissue (metadata)

give an example (slide 7) of geo series entry

<Simon> gminer.mcw.edu

gminer shows the results

web application to provide tag cloud

who has done particular experiments on certain rat samples

for example, neuromicroarray experiment metadata

annotator tool is used with some noise term removal

provide the ability to pick ontology during the automatic anntation process

nomenclature inconsistency create some problem with annotation

some problem with annotation in affy chips

slide 12 probsets corresponding to babra1 receptor

link to genecard database

ontologies may help make the interpretation of data meaningful

data aggregation based on QTL

genes with QTL may be linked to hypertension

hypergraph structure is created using semantic web

slide 14: use of allegragraph

linking phenotype and disease

multiple sources of data are formatted in rdf and loaded into rdf store

ruby/rail was used

a number of owl ontology are used

in addition to rat data, annotations are collected for humn

annotated data are updated periodically

ontologies are access via bioportal

how to take functional info about genes and use sparql to do queries

rdg in relational database converted to rdf

with alignment with existing ontologies such as SO

try to figure the best way to model entities

support front end interface development

future work: register PURL for RGD

how to represent RGD data in RDF

avoid blank nodes in the RDF representation

rdf provenance

make data accessible and reliable

eric: how to resolve ambuiguity

simon: in some case, curators need to go back to the paper for answer

eric: how upstream one can push annotation

simon: full automation is difficult because the nature of annotation can be complex
... excel might be ontologized
... curation is a challenge even with the use of ontologies

eric: ontology alignment when mutliple alternative ontologies are available

simon: ontology mappings are increasingly available through ncbo

eric: relational vs rdf -- painful (short term vs long term)

scott: swobject might be helpful
... tie with geo?
... arrayexpress aims at rdf format in the future

michael: biologists need to add detailed enough annotation into geo and arrayexpress

<Lena> (I'm sorry... I will have to leave to another meeting :-( I will send the co-authors a list of notes I have on written on the paper's reviewer comments)

<Lena> (bye)

thanks, lena

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