HCLSIG BioRDF Subgroup/Meetings/2009/09-28 Conference Call

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Conference Details

  • Date of Call: Monday September 28, 2009
  • Time of Call: 10:00 am Eastern Time
  • Dial-In #: +1.617.761.6200 (Cambridge, MA)
  • Dial-In #: + (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)
  • Duration: ~1 hour
  • Frequency: bi-weekly
  • Convener: Kei Cheung
  • Scribe: Eric Prud'hommeaux


Kei Cheung, Eric Prud'hommeaux, Matthias Samwald, Adrian Paschke, Scott Marshall, Satya Sahoo, Huajun Chen, Jun Zhao


Rob Frost


  • Introduction [Kei]
  • HCLS KB upate [Matthias, Adrian]
  • F2F meeting -- biordf [All]
  • Semantic Web Development for Traditional Chinese Medicine: a Report for Current Status [Huajun] (slides)


<ericP> topic: KB update

<mscottm> I just skyped the new code to Matthias.

<ericP> kei: matthias migrating to a new server and virtuoso instance

<mscottm> Matthias is trying to dialin.

<ericP> adrianpaschke: we're migrating to a new server and new version of allegrograph

<ericP> ... should be more stable

<jun> Adrian is also updating his server in Berlin, and software. will perform much better

<ericP> ... (enterprise edition)

<ericP> topic: F2F 2-3Nov

<ericP> kei: attending: kei, mscottm, ericP, others?

<ericP> ... we'll be doing a joint activity with LODD

<ericP> ... would could work on traditional chinese medicine

<mscottm> Zakim, who is here?

<Zakim> apparently Team_(HCLS)13:49Z has ended, mscottm

<Zakim> On IRC I see adrianpaschke, jun, ssahoo2, mscottm, RRSAgent, kei, huajun, Cloud, AlexPassant, Zakim, ericP

<ericP> ... we invite other ideas

<ericP> topic: KB update

<ericP> matthias: we're using virtuoso six

<ericP> ... the amount of data is large (too many named graphs)

<ericP> mscottm: ~200 named graphs

<ericP> matthias: there's no dedicated mechanism for dumping a graph?

<Zakim> sorry, adrianpaschke, I don't know what conference this is ericP adrianpaschke, you need to join #hcls3 to talk to zakim

<mscottm> you have to issue that command on #hcls3 to get results

<mscottm> http://esw.w3.org/topic/HCLSIG_BioRDF_Subgroup?action=AttachFile&do=get&target=W3C-Group.pdf 16:12 kei http://esw.w3.org/topic/HCLSIG_BioRDF_Subgroup?action=AttachFile&do=get&target=W3C-Group.ppt

<ericP> topic: TCM slides

<ericP> -> http://esw.w3.org/topic/HCLSIG_BioRDF_Subgroup?action=AttachFile&do=get&target=W3C-Group.ppt TCM slides

<ericP> [slide 7: The ultimate vision of the TCM Semantic Web]

<kei> cheung: chinese academy of tcm is located in Beijing

<ericP> Huajun: we've helped developed many TCM databases

<ericP> ... there are many which have been developed by local communities

<ericP> ... will be very useful to make a connection between TCM knowledge and western medicine

<kei> cheung: great interest in linking TCM and western medicine

<ericP> ... chinese medicine has its own logic derived from traditional chinese philosophy

<kei> cheung: many technical/cultural challenges

<ericP> ... there is a wide gulf between western medical culture and chinese philosophy

<jun> cheung: also does data mining and analysis

<jun> cheung: tcm ontology engineering started in 2001

<ericP> ... dartgrid uses semantic tech to integrate diverse databases

<jun> cheung: currently focused on building a semantic query engine

<ericP> [slide 10: TCM Ontology Engineering]

<ericP> kei: [re slide 12: TCM ontologies] who created these?

<ericP> Huajun: collaborative project between my univ and China Academy of TCM

<ericP> ... we provide technical support

<ericP> ... they have a committee

<ericP> ... a small percentage of these have corresponding english names

<ericP> ericP: so you have translations to English *and* correspondances with western medical terms

<jun> cheung: it's hard to translate, because the concept is different

<ericP> Huajun: mostly we have the english translation of the chinese concept

<ericP> mscottm: e.g. chi-related terms like "dampness" and "heat"

<ericP> kei: LODD folks attacking this from the chemical ingredient angle

<ericP> s/re slide 12:/re slide 11:/

<ericP> [slide 12: Ontology visualization and query engine]

<ericP> Huajun: allows you to graphically browse semantic connections

<ericP> [slide 14: System Architecture]

<ericP> Huajun: provide a semantic mapping from db to high-level concepts

<ericP> ... compiles into an SQL query plan

<ericP> ... doesn't do materialized views, uses query mapping instead

<jun> huajun: transformation by query, using query rewritter

<mscottm> It is here: http://sourceforge.net/projects/swobjects/

<mscottm> (That is Eric's approach to federated query)

<ericP> Huajun: offer full-text-search in all DB's

<ericP> ... have a new version which integrates more data

<ericP> [slide 15: Visualized Mapper]

<ericP> Huajun: makes user's job easier

<ericP> [slide 16: Semantic Search Portal Version 1]

<ericP> huajun: user enters terms

<ericP> ... gets mapped to semantic terms

<ericP> ... TCM ontology provides search suggestions based on connections

<ericP> ... combining new resources

<ericP> ... major feature: uses the ontology as a sort of search index

<ericP> ... easier for user to retrieve data sets and related items

<ericP> kei: is this released to the public or to a consortium?

<ericP> huajun: rules are changing

<ericP> ... traditionally didn't want to make data public

<ericP> ... they're providing open access to some of this data

<ericP> ... e.g. data coming from public web pages

<ericP> ... we're working on semantic integration of these DBs

<ericP> ... asking what can we do with this huge web of data

<ericP> [slide 19: Graph vs Semantic Graph]

<ericP> huajun: in graph, the basic data element is a node. in RDF, it's an arc

<ericP> ... we can view a graph from two different perspectives

<matthias_samwald> (need to leave now, bye!)

<kei> bye, matthias, thanks for attending

<ericP> ... migrating by looking for most common patterns

<huajun> hello

<huajun> am i lost

<ericP> yep

<ssahoo2> kei I need to leave

<kei> bye sahoo

<mscottm> Huajun - can you dial in again?

<kei> huajun can you deal in again

<mscottm> bye sahoo

<huajun> I am trying

<huajun> but it is restricted

<mscottm> Huajun - we will have to get another code.

<jun> me

<huajun> what do we do?

<jun> we all hang up now

<huajun> I am about to be finished

<mscottm> We will get another code. Wait a minute

<ericP> Zakim, space for 7?

<Zakim> sorry, ericP; could not schedule an adhoc conference; passcode overlap; if you do not have a fixed code you may try again

<huajun> It has past 11, is that ok?

<kei> it's ok ...

<kei> if it's ok to you

<ericP> 22631

<ericP> sorry

<kei> i'm dialing in now ...

<mscottm> New code is: 26631

<ericP> 25531

<mscottm> New code is: 25531

<ericP> s/5/6/g

<mscottm> New code is: 26631

<jun> i am in now

<ericP> [slide 21: An example]

<ericP> huajun: we're try mining approaches

<ericP> [slide 22: Semantic data analysis]

<ericP> [slide 23: DartSpora: a interactive mining engine for TCM]

<ericP> huajun: allows user to combine [and present] different data

<ericP> huajun: connecting TCM and western medicine at the data level will help both communities find and use patterns

<ericP> mscottm: is someone working on a map from western disease names and conditions to TCM symptoms?

<ericP> huajun: we couldn't find many direct correlations

<ericP> ... we're using a statistical approach

<ericP> ... e.g. identify a set of associated symptoms in TCM and find a corresponding [symptoms for a] disease

<ericP> ... tells you that there are relationships, but not that they are equal

<ericP> kei: e.g. TCM "hot" maps to {fever, inflamation, }

<ericP> ... getting deeper, the mapping probably becomes more difficult

<ericP> ericP: the heuristic mappings should meet most of the use cases, so long as the interface indicates that the association was derived heuristically

<ericP> kei: example: alzheimer's is well known in western med, but you need to look by it's synonym "dimentia" to find mappings in TCM

<mscottm> I have to go. Thank you Huajun.

<mscottm> Bye.

<ericP> huajun: [mentions plan for TCM XG]

<kei> bye scott

<kei> eric and huajun explore the query mapping