<jun> scribenick mscottm

scribenick mscottm

James: Haven't been able to get sample RDF for you yet
... We have created Experimental Factor Ontology (EFO) as a bridging ontology

James introduce EFO

James: You can see an example of an application of EFO in the Gene Atlas that lets you look for microarray studies with certain specific attributes
... pulling out genes as they relate to disease and experiments using EFO
... So, EFO is a subset of the sort of data that we have in Gene Atlas
... Not sure if we how soon we will create a SPARQL endpoint. We will begin with export of RDF.
... We have a position open at the moment for student internship with funding.
... Some attributes of interest are disease, genes, cell types, cell lines, compounds, acids, instrumentation, software

Jun: We are also trying to model disease, brain region, etc. Would be interesting to link to other related data sets through extra attributes.
... I don't see specific statistical values modeled yet in EFO.

James: We don't have statistics in EFO yet. We could do that if you have a small list of things to add.

Lena: Yes, I would like to refer to statistics as provenance.

James: What sort of values would you like to use?

Lena: fold change and corrected p-value

James: Yes, these are some of the sorts of classes that OBI is meant to cover. We could add these.

<jun> scott: it's quite important to express the method or the software used to derive the p-value

Scott: Would like to refer to the method/software that was used to arrive at the p-values

Lena: But studies sometimes use more than one method.

Scott: Most don't, and this level of detail is not required.

Lena: But software packages change so any reference to the software will be stale over the years.

Scott: Many types of provenance will go stale but essential information about the origins of the information (provenance), such as the method used to produce the p-values, is important to anyone reusing the data. They want to know whether it's from LIMMA or MANOVA, just as they want to know Affy vs. other types of arrays.

Jun: RESTful API?

James: Yes, RESTful API's are available.

<jun> Jun: how to access ArrayExpress programmatically?

<jun> James: through Restful APIs, but no SPARQL endpoint yet

<jun> James: There are some provenance kind of information, tracking e.g. probes used in the experiments, publications, etc, but not expressed using ontologies

Scott: Do you notice any differences between our RDF and others that you are aware of?

<jun> James: we say a lot less about the statistical information about the experiments, about the data

<jun> James: sometimes not all the information is submitted, because it's not required as part of the minimum information

<jun> James: we think species, diseases, regions, etc, as high priority

<jun> James: we are not curating the same level of details as the BioRDF use case

<jun> Scott: where do you see as the bottleneck as using RDF to express the information (general speaking)?

<jun> James: EFO takes bits and pieces from the community that are useful for our cases. and it has been useful

<jun> Jun: have you had any difficulties of dealing with changes of ontologies

<jun> James: we have tools to help us deal with that; so it's not a big problem for us

<jun> Scott: in our application we are interested in linking to related data, for cases, such as translational medicine

<jun> James: we are on the same page for this. that's one of the primary reasons for us to convert datasets into RDF

<LenaDeus> (good job scribing, Scott, you may not need coffee after all ;) )

tx!

<jun> scribenick jun

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