<kei> agena+ intro [kei]

<kei> scribnick scott

Kei: Agenda: 1) Introductions 2) Microarray Use Case
... We have made some progress in the Microarray Use Case. Maybe we can talk a little about a possible demo.

<ssahoo2> NIH project at Kno.e.sis: http://wiki.knoesis.org/index.php/Trykipedia

<ssahoo2> Priti works at: http://knoesis.wright.edu/

<kei> priti: wright state u.

Priti: I am working as a postdoc here at Wright University (Knoeisis). I did my PhD work in food microbiology at Virginia Tech.

Kei: Sounds like you have a biology background. Experience with microarrays?

Priti: I have some and plan to learn more at Wright.

<ssahoo2> http://esw.w3.org/topic/HCLSIG_BioRDF_Subgroup/QueryFederation2

Kei: Thank you Priti. Now let's talk about the Microarray Use Case.
... There is an example that focuses on Alzheimer's and others that focus on other neurological diseases.
... There are microarray experiments cited from the NIH Neuroscience Microarray Consortium http://np2.ctrl.ucla.edu/np2/home.do

<kei> http://esw.w3.org/topic/HCLSIG_BioRDF_Subgroup/MicroarrayExperimentContext

Kei: I have used the NCBO Annotator with NIFSTD http://bioportal.bioontology.org/annotator
... Hi, Don, would you give an introduction for some new people here?

Donald Doherty: <Introduction> I have been involved with the group since the beginning. Lately, pretty busy with my company BrainStage. Have done some work on Parkinson's Disease with this group.

Kei: We are looking at the Provenance page of the wiki ( http://esw.w3.org/topic/HCLSIG_BioRDF_Subgroup/MicroarrayExperimentContext )
... and the 4 examples that we annotated with NCBO's Annotator using NIFSTD ontology to identify terms in the abstracts.
... This is to explore what can be done with these types of tools.
... As you look down the page, you will encounter the Provenance terms that we gathered together with Jun and Satya. Below that, you will find terms identified by NCBO's annotator.

<kei> prefrontal and temporal cortex

Kei: It didn't identify some brain regions such as prefrontal and temporal cortex

<kei> dopamine neuron

Scott: Maybe we should document some of the things that are missed by the Named Entity Recognizer (Annotator).

Satya: The queries that you list in the main case. Are these queries that we will try to answer?

Kei: Yes, to begin with.

<kei> Find experiments involving the same disease/phenotype, brain region, and species

<kei> Find particular types of genes that are expressed in a given brain region

<kei> Find experiments that involves patients of certain disease states (e.g., mild vs severe AD patients)

Scott: Does NIFSTD include "dopamine neuron"
... ?

Kei: I will look into the specifics in the near future.

Scott: I will also learn more about Annotator in the coming months at NCBO.
... Maybe Don can suggest some additional ontologies.

Kei: Don?

<ssahoo2> Scott: Don can you identify additional ontologies for this use case?

<kei> SAO -- neuroscience terms

<ssahoo2> Don: Will try to suggest additional ontologies

Don: There are a number of issues to consider. Anatomical issues. SAO is one that comes to mind. Also, NIF. There are some disease oriented ontologies that I will look into and post to the group.

Kei: So, do we generally agree on this initial approach?

Satya: We also have a Provenance ontology that we can use.

<ssahoo2> upper level provenance ontology: http://wiki.knoesis.org/index.php/Provenir_Ontology

Kei: Sometimes you need to create new relations between terms in ontologies.

Satya: Yes, we will use domain experts such as Priti who can explain specific needs for new relations.
... Also, we will continue to consult the Relation Ontology of OBI

<kei> actions: Don suggests more ontologies; look at the example queries

<kei> domain experts help define new relationships if any

Kei: I skipped over the HCLS KB status because Matthias and Adrian couldn't make it today.

<kei> http://esw.w3.org/topic/HCLSIG_BioRDF_Subgroup/QueryFederation2?action=AttachFile&do=get&target=genelist_ex1.pdf

Kei: Scott, do you have anything to report?

Scott: Nothing significant. The DERI KB was down the other day and Matthias fixed it in a few hours.

Kei: Yes, that brings up the issue of reliability in federated query. That's one advantage of data warehouses for demonstrations.
... <discussing gene lists with example, see URI above>

<kei> gene list representation

Scott: Question: It seems like we need to manually extract gene lists because there is no standard representation of gene lists associated with a data set (i.e. MAGETAB).
... Is that a TODO list item, to create gene lists in RDF to be integrated with our queries?

Kei: Yes, this should be an ACTION item.

Satya: Do we have a standard way of identifying genes? Such as EntrezGene.

Kei: It isn't standardized so we will have to choose something.
... I will update the wiki, prob by end of today to reflect these new tasks.
... Let's move on to discussing the demo.
... We need a way to present the results of our work that appeals to a variety of backgrounds.
... Scott, Don: Do you have ideas about possible ways of creating a demo?

Don: For the iPhone application, you want to keep the amount of computation on the iPhone to a minimum and shift it to the server.
... In contrast, more is done on the web client side in the BrainStage application.

Kei: I don't think that the demo will involve large amounts of computation.
... About triples: We could store some of the relevant data in a triple store.
... Are we still planning to query Linked Data sets?

Don: I would be willing to look at integrating the iPhone app with either one of those.

Satya: iPhone seems like a good way to show the results, perhaps of canned queries.

Kei: How do we divide up the work?

Satya: We have collected some of the terms for provenance. We can add to that.

Scott: I will try to discover more relevant terminologies and ontologies by consulting people at both NIF and NCBO.

Satya: Listing 1) Kei selects queries 2) Using the queries Jun, Kei, myself and Scott, we identify new ontologies and terms 3) We work on generating the RDF to express the experimental context and gene lists.

Kei: We can also talk to Matthias about aTags in this application.
... Next call on Jan. 4 sound ok?

Satya: Could we try for the week after?

<discussion> Kei will look into it. Possibly in 3 weeks.

<kei> 1. example queries; 2. ontologies/terms 3. RDF structure

Kei: This was the last BioRDF call of the year. Wishing you a nice holiday and Happy New Year.

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