HCLSIG/Meetings/2010-06-03 Conference Call

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Conference Details

  • Date of Call: Thursday June 3, 2010
  • Time of Call: 11:00am Eastern Daylight Time (EDT), 16:00 British Summer Time (BST), 17:00 Central European Time (CET)
  • 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: Click on mibbit for instant IRC access.
  • Duration: ~1h
  • Convener: Scott
  • Scribe: Matthias Samwald

Agenda

Minutes

scott: let us start with updates from the task forces.
... let us start with TMO
... there is some work on interfacing with EHR, the OpenVista system
... the intention is to look at what kind of software and interfaces are available to integrate EHRs into the TMO demo

elgar: there are a number of issues in terms of clinical data utilisation. there are some use-cases to define around presentation of TMO-based data.
... we have worked with luke and worked out a few simple use-cases.

bosse: we started out with focus on user interaction, but we found that without connection to EHR data it is difficult, so we need to get some data into RDF format.

scott: did you also assume that some of the data resides in relational databases. did you think about creating an RDF view with SWObjects?

bosse: don't know all the details.

scott: it could be interesting to involve EricP in this.
... the TMO ontology file is now available from bioportal
... there is a paper in the BioOntologies SIG. any other plans for papers?

elgar: not that i know of
... the collaboration with marshfiel highlights two issues: utilization of our tools in order to derive better value from various datasets. in this regard we are very comfortable to work with other groups. the other issue is getting access to patient data.
... we don't have a streamlined process for that. what are the legal implications? i think the whole HCLS community needs a more streamlined approach in this regard.

<mscottm>http://www.patientslikeme.com/

<mscottm> http://www.nytimes.com/2010/05/30/business/30stream.html?src=tptw

scott: patientslikeme are also selling data to industry.
... partnering could be of interest to us.
... next topic, TERMINOLOGY
... john madden and i discussed the possibility of creating a demo.
... he has a database that he searches for data that we could use (needs to take care of privacy etc.)
... e.g., discrepancy between reports (radiologist report vs. endocrinology report)
... john is a pathologist.
... daniel rubin (stanford) is also interested in this notion of checking discrepancies.
... next topic, SCIENTIFC DISCOURSE

tim: we have five subtasks, we are in the process of adding a sixth
... 1) formalizing SWAN, SWAN/SIOC integration
... 2) bibliographic citations
... 3) discourse representation and experiments
... the idea is not to come up with something from scratch, but re-use
... for bibliography, we made use of CITO, the SWAN citation module, and PRISM
... made a preliminary alignment between SWAN and CITO, preliminary alignment with PRISM, there are a few outstanding issues.
... the actual alignment work is done, we are waiting for david at the moment. we want to publish IG notes.
... there was also discussion about writing a paper.
... 4) rhetorical document model.
... we discussed the annotation ontology from Paolo, which is based on Annotea
... we had some discussions with potential users of the ontology
... the ontology will be presented at BioOntologies
... it is designed to support taking sections of text in a document, and mapping them to a terminology. including provenance.
... had talks with text mining people at Elsevier, Nature, EBI. they offered ideas for making it more useful to them.
... we hope to get a small community.
... once we have a group, we might write an IG note
... the group connected to EBI was also involved in the distributed annotation server.

<TIm> This is a link to the previously-referenced "AO - Annotation Ontology" discussed in the Scientific Discourse task

<TIm> http://esw.w3.org/images/4/48/AO_paper_bio-ontologies_preprint.pdf

scott: i will soon join a workshop co-organized by dietrich rebholz-schuhmann. should discuss that further.

tim: in the next call on rhetorical documents, we will have a presentation on an RDF representation of the NLM DTD, done by alex.
... we want to capture semantics of article sections, e.g., to avoid mining proteins from reference section.

scott: did paola et al. consider putting ontologies on BioPortal?

tim: before we do that, we need to have all the critique from publishers. feedback so far is very positive.

<mscottm> http://sparql.bioontology.org/webui/

<mscottm>http://sparql.bioontology.org/sparql/

scott: NCBO has now put up a SPARQL endpoint.
... next topic, BioRDF.
... we have been collaboratin the area of provenance.
... use case: federating micorarray data and related knowledge.
... we want to represent experimental conditions together with gene lists.
... we came back to the notion of gene expression, but put that on the shelf, focus on lists of differentially expressed genes
... using concepts from Provenir, EFO and other ontologies.
... we can also review how aTags fit into this.
... any news from LODD? ... (no participants reply)
... next topic, PACKAGING AND MARKETING OF HCLS AS A WHOLE
... one thing that seems to hinder progress is the reputation as a group of "semantic web geeks".
... HCLS can be perceived as too complex, six task forces etc., it could be packaged more simply.
... we have considered packaging our activities with a focus on translational medicine.
... this could help us to have a simpler and more appealing outside appearance.
... framing the work of current task forces based on translational medicine seems easy to do.
... feedback?

bosse: when you have the heading "translational medicine", people seem to think about it from a pharmaceutical perspective. does this really capture the healthcare side of the things we are doing?

scott: that would be good.
... it also includes translation between different domains and instrumentations, e.g. lab and patient records. this still fits into the definition of translational medicine.
... does everybody agree?

elgar: is it really a good connotation?
... HCLS should have a wider mandate than just serving pharma.

tim: i agree with elgar, in part.
... translational medicine is a hot topic, but it does not cover all the interesting stuff going on to semantic web solutions. e.g. people doing basic neuroscience are not doing translational medicine.
... yes. also, EHR demos are not necessarily associated with translational medicine. but we create a number of scenarios where a clinican has, for example, access to data in SWAN format.

scott: besides the EHR scenario, you could also have a scenario of linking patient data about ongoing studies such as drug development. this would be an innovation compared to current EHR systems.

<TIm> thanks

janos: another example from EHR could be linking to drugs. ATC code - RxNorm datasets - link to DrugBank etc.
... that is something that traditional EHRs don't do.
... we could also link two distinct demos (e.g. "EHR" and "patient eligibility")
... we need to start from the bottom, the datasets. first triplestores and ontologies. then build the demo on that.

scott: i agree, we need thins available via SPARQL.
... but what i am talking about is defining a frame for all this work.

tim: something positive about the translational medicine idea. i get what you are trying to accomplish -- providing a unifying framework that is focused on a cluster of use-cases.
... it does have a pharma angle, but it gives you the use-case for cross-disciplinary data integration. that is positive.

<mscottm> scribenick: mscottm

Matthias: What kind of concrete next steps would we take in the next few months?

<matthias_samwald> scribenick: matthias_samwald

scott: at the moment we are trying to get feedback.
... the next step is to establish that we have some consensus and mutual understanding.
... an EHR demo could be of interest.

bosse: could i propose something else for the overarching topic?
... i propose 'tailored medicine'

scott: this also sounds like a good name. one thing that seems to be missing from clinical research is informing clinicans directly from EHR, personalized medicine also fits into 'tailored medicine'.

<michel> the idea of "personalized medicine" is that it must necessarily transcend clinical and life sciences - this is a worthy objective

scott: thanks for coming everybody!

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