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Ontology Summit 2012: Session-09 - Thu 2012-03-08

Summit Theme: OntologySummit2012: "Ontology for Big Systems"

Track (4) Title: Large-Scale Domain Applications

Session Topic: Large-scale domain applications - Biomedical, earth & environmental science & engineering

Session Chair: Dr. TrishWhetzel (NCBO; Stanford) and Dr. SteveRay (CMU) - intro slides

Panelists:

  • Mr. DavidPrice (TopQuadrant) - "Experiences from a Large Scale Ontology-Based Application Development for Oil Platforms" - slides
  • Dr. MichaelKellen (Sage Bionetworks) - "Collaborative Clinical Genomics Data Analysis with Sage Bionetworks Synapse" - slides
  • Dr. DamianGessler (iPlant Collaborative) & Dr. BlazejBulka (Clark & Parsia) - "The iPlant Collaborative Semantic Web Platform: Using OWL and SSWAP (Simple Semantic Web Architecture and Protocol) for On-Demand Semantic Pipelines" - slides
  • Dr. IlyaZaslavsky (SDSC) - "Managing observation semantics in CUAHSI Hydrologic Information System" - slides
  • Dr. LinePouchard (ORNL) - "Linked Science as a producer and consumer of big data in the Earth Sciences" - slides

Archives

Conference Call Details

  • Date: Thursday, 8-March-2012
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Attendees

Abstract

Large-Scale Domain Applications - II : Biomedical, earth & environmental science & engineering

This is our 9th Ontology Summit, a joint initiative by NIST, Ontolog, NCOR, NCBO, IAOA & NCO_NITRD with the support of our co-sponsors. The theme adopted for this Ontology Summit is: "Ontology for Big Systems." The event today is our 9th virtual session.

The principal goal of the summit is to bring together and foster collaboration between the ontology community, systems community, and stakeholders of some of "big systems." Together, the summit participants will exchange ideas on how ontological analysis and ontology engineering might make a difference, when applied in these "big systems." We will aim towards producing a series of recommendations describing how ontologies can create an impact; as well as providing illustrations where these techniques have been, or could be, applied in domains such as bioinformatics, electronic health records, intelligence, the smart electrical grid, manufacturing and supply chains, earth and environmental, e-science, cyberphysical systems and e-government. As is traditional with the Ontology Summit series, the results will be captured in the form of a communiqué, with expanded supporting material provided on the web.

The large-scale domain applications track will help to ground the discussions in the other tracks and bring key challenges to light by describing current large-scale systems and systems of systems that either use, or could use, ontologies in their deployment. "Large-scale" can mean either very large data sets, very complex data sets, federated systems, highly distributed systems, or real-time, continuous data systems. Examples of large data sets might include scientific observations and studies; complex data sets could be technical data packages for manufactured products, or electronic health records; federated systems could include information sharing to combat terrorism, highly distributed systems includes items such as the smart electrical grid (aka Smart Grid), and real-time systems include network management systems. Of course, some big systems might include all five aspects.

Today's speakers will describe experiences in adapting ontology technology for biomedical applications, biological plant studies, earth science, a hydrology system, and the oil and gas industry. As with the prior session in this track, each presentation will try to highlight what systems engineering or operational functions were impacted by the use of ontology, and how. These examples have been chosen to help ground the discussions in the other summit tracks of where ontology could or should be used.

More details about this Summit at: OntologySummit2012 (home page for the summit)

Agenda

Ontology Summit 2012 - Panel Session-09

  • Session Format: this is a virtual session conducted over an augmented conference call
  • 1. Opening - co-chairs [5 min.] ... [ slides ]
  • 2. Panel briefings - [12 min. each]
    • David Price
    • Mike Kellen
      • Abstract: The past two decades have seen an exponential growth in the technical ability to generate genetic and biomolecular data fueled by advances in measurement technologies. However, with a few exceptions, these data have failed to improve prevention or treatment of common human disease. A fundamental reason for this discrepancy between data generation and clinical improvement is the immature development of analytical techniques to meaningfully interpret these new data types. As with any new field, analytical methodologies need to be iteratively developed and refined. The difficulty of accessing, understanding, and reusing data, analysis methods, or models of disease across multiple labs with complimentary fields of expertise is a major barrier to the effective interpretation of genomic data today. Additionally, much of the relevant data to answer a particular research question is spread among multiple public and private repositories. Sage Bionetworks' mission is to catalyze a cultural transition from the traditional single lab, single-company, and single-therapy research paradigm to a model founded on broad precompetitive collaboration on analysis of large-scale biological data. In this talk we will focus on the technology component of Sage Bionetworks' solution strategy, Synapse, an informatics platform for open data-driven collaborative research. Synapse provides programmatic access to a variety of clinical and genomic data sets, tracking of analysis workflows, and integration with common analysis tools like R/Bioconductor.
    • Damian Gessler & Blazej Bulka
    • Ilya Zaslavsky
    • Line Pouchard
  • 3. Q & A and open discussion [All: ~30 min.] -- please refer to process above
  • 4. Wrap-up / Announcements - (co-chairs)

Proceedings

Please refer to the above

IM Chat Transcript captured during the session

see raw transcript here.

(for better clarity, the version below is a re-organized and lightly edited chat-transcript.)

Participants are welcome to make light edits to their own contributions as they see fit.

-- begin in-session chat-transcript --

Peter P. Yim: Welcome to the

Ontology Summit 2012: Session-09, Thursday 2012-03-08

Summit Theme: Ontology Summit 2012: "Ontology for Big Systems"

Track (4) Title: Large-Scale Domain Applications

Session Topic: Large-scale domain applications - Biomedical, earth & environmental science & engineering

Session Chairs: Dr. Trish Whetzel (NCBO; Stanford) and Dr. Steve Ray (CMU)

Panelists:

- "Experiences from a Large Scale Ontology-Based Application Development for Oil Platforms"

- "Collaborative Clinical Genomics Data Analysis with Sage Bionetworks Synapse"

- "The iPlant Collaborative Semantic Web Platform: Using OWL and SSWAP (Simple Semantic Web Architecture and Protocol) for On-Demand Semantic Pipelines"

- "Managing observation semantics in CUAHSI Hydrologic Information System"

- "Linked Science as a producer and consumer of big data in the Earth Sciences"

Session page: http://ontolog.cim3.net/cgi-bin/wiki.pl?ConferenceCall_2012_03_08

Mute control: *7 to un-mute ... *6 to mute (please make sure your own phone is not muted as well)

Can't find Skype Dial pad? ... it's under the "Call" dropdown menu as "Show Dial pad"

Proceedings:

anonymous morphed into Damian Gessler

anonymous morphed into Christopher Spottiswoode

anonymous1 morphed into David Flater

anonymous morphed into Jim Schoening

anonymous morphed into David Price

anonymous morphed into Michael Kellen

anonymous morphed into Jim Rhyne

anonymous morphed into Scott Hills

anonymous morphed into ByronDavies

anonymous morphed into Pavithra Kenjige

Line Pouchard: testing

Peter P. Yim: == David Price presenting ...

anonymous morphed into Elisa Kendall

Mike Bennett: Does the reported data include SCADA data from on-platform systems such as Fire and

Gas, ESD and so on? Just curious.

David Price: The date is about Drilling and Production. Some of it is measurement, but not really

SCADA.

Mike Bennett: @David thanks. Just seeing an opportunity there.

Ernani Santos morphed into Ernani Santos

anonymous morphed into Thomas Getgood

Doug Foxvog: What is "warm fallover"?

Harold Boley: Re Slide 10: Would the 300 million triples be structured/modularized in some way, e.g.

as named graphs?

David Price: The triples are managed in graphs based on Licenses for Fields in the sea. This allows

us to control the set of data over which aggregations and queries are allowed and also allows us to

use these graphs as the basis for access control and security.

Michael Grüninger: @David -- you say that it is hard to test an ontology. Can you share any of your

ontologies which we can test?

anonymous morphed into DWiz

Amanda Vizedom: @David - to what extend do you think the "vague/ambiguous" character of the

ontologies or their documentation (your slide 17) is a result of the application type being

comparatively shallow (that is, not too much axiomatization or reasoning)?

David Price: I attribute vague-ness entirely to projects running out of money - in fact I have heard

that from the people who created some of the background ontologies/reference data we are re-using.

David Price: I cannot yet share the ontologies, but they will be made public eventually ... probably

3Q2012. The project is not yet complete, the Drilling stuff is going into production use this month.

The Production use will follow between now and June/July.

DWiz: David: Do you have a mandatory XDS? Otherwise, how to you generate a true ontology from XML?

David Price: Our 'XSD Proxy Ontology' capability does not try to create a 'true ontology' - as the

name suggests it's a proxy for the XSD that allow us to import an XML data file into the workspace

and do SPARQL over it directly through the proxy ontology-based triples.

Amanda Vizedom: @David - Have you tried developing test beds and test apps with which to evaluate the

ontologies? Given the well-developed application context, this seems like an approach you could use

to ontology testing & proofing.

David Price: We are just now getting into the detailed use of proper software testing tools to try to

do a better job wrt testing our ontology. We are working on large, complete test cases, test

scenarios, automated tests using REST-like services, etc. to make testing the ontology fit into the

more traditional testing apparatus used by our software team.

Amanda Vizedom: @David - Ah, yes, I see what you mean. Not unlike undocumented code from abandoned

software projects, then.

David Price: FWIW we use Github for the source code/ontology management and SpiraTest for the testing

tool.

David Price: TopBraid Composer is an eclipse-based tool and that's what we use to develop ontology

and SPIN/SPARQL/SWP.

David Price: I have to leave for a while but will respond to any other questions in 30 mins or so.

Thanks!

Steve Ray: Thanks David. Fascinating talk.

Amanda Vizedom: @David - I can't remember who it was, now, but one presenter earlier in the summit

discussed an approach in which they used "real" (sound, computational) ontologies but also

intermediate artifacts that are ontological in format (OWL) but are not used (or usable) as

ontologies; rather, they are fairly direct models of the data source's data model. This is similar

to what you describe, yes?

David Price: @Amanda For ontologies of a domain, we usually follow Leo Orbst use of the term 'Strong

ontologies' meaning they are about the domain of interest.

David Price: @Amanda - wrt direct models of the data source ... yes, we call that a proxy ontology.

Amanda Vizedom: @David - Thanks. I think a similar approach is used for the DoD EIW. Independently,

we discussed using something like "proxy ontologies" on the USAF project. Though non-technical

factors/authorities mooted that discussion, I thought (think) that it was promising. I sense a

pattern.

David Price: @Amanda For us the main thing is to use a semantic language like SPARQL to define the

transforms between data sources and targets and so everything must be presented as at least RDF, and

preferably as an OWL ontology.

David Price: We also have ontologies of SPARQL, etc. which we often call 'system ontologies' as in

software system ... just to confuse things even more

Amanda Vizedom: @David - though I did and do think there needs to be some explicit (meta)data on/in

the proxy ontology to make clear that it is not a full ontology - that is, under the formal

semantics of the language used, it would not likely be computationally sound.

Mike Bennett: @Amanda et al - we need a metaontology. Or at least an ISO 1087 compliant terminology

and vocabulary setting out rather less messy uses of words like "Ontology" - people think they are

listening about the same thing when someone is talking about a different thing - dog food much?

David Price: We have a taxonomy of ontology-related artifacts we use (and modify as required in

various projects). It can be used as metadata but we also use it in the base of the URIs for things

and even in the name of graphs so it's visible to the ontologies/software developer.

David Price: We actually often use the phrase 'schema' when we mean the 'ontology' in many projects

because customers are more familiar with that terminology. We then have graphs that are

transforms', that are 'swp', that are 'spin', that are 'testcase', etc. as you would in a typical

software development team.

Amanda Vizedom: @Mike - Yup. And we've probably gotten far enough along since we started saying that

that we could actually build one, identifying main types of artifact. We would then run into the

problem of every domain, in that we would disagree over what to call the various types. Were we then

to get over the names problem (via multiple, contextual labels and/or other techniques), we'd then

have a very useful product *and* a useful methodological example!

David Price: @Amanda We have published some work on a metadata for ontology at

http://linkedmodel.org/doc/vaem/1.2/ Vocabulary for Essential Metadata ... Ralph Hodgson has pushed

that effort.

Peter P. Yim: == Mike Kellen presenting ...

anonymous morphed into GiulianoLancioni

Simon Spero: @MichaelKellen: SKOS is for controlled vocabularies; SKOS concepts are "Subjects", not

the things that subjects are about"

Simon Spero: @Michael: is that the intended semantics

Michael Kellen: Yes, we aren't trying to create a model of the relationships among domain objects

that we can reason about

Michael Kellen: We are simply trying to consistently structure information to help scientists pull

together appropriate data so that they can reason about it

Simon Spero: @Michael: as long as it's just for guiding people to data sets, that's a safe use

Michael Kellen: There are other projects in life sciences trying to use the richer semantics to

actually model the domain

Michael Kellen: The problem they hit is that there are so many unknowns in our domain that this is

hard to do

Simon Spero: @Michael: right - it's just important to keep the distinctions clear so that a KOS isn't

used directly an ontology

Mike Bennett: @Simon @Michael we have a labeling problem: if we get into the habit of referring to

everything that is in triple-store formats as "An ontology" then we need a new word for ontologies.

Syntax is not semantics...

Peter P. Yim: == Damian Gessler presenting ...

Bobbin Teegarden: @Damian where is are the transformation decisions made between services in the

pipeline?

Damian Gessler: @BobbinTeegarden third-parties hosting SSWAP semantic web services run a servlet that

we provide from our Software Development Kit. This servlet handles the semantics and ensures that

both input and output follow the protocol. So at the pipeline end, we can look at the outputs and

required inputs, and orchestrate the interaction. Third-party data need not pass through us: it goes

directly from the upstream service to the downstream service.

Bobbin Teegarden: @Damian Thank you, grand.

Doug Foxvog: How do you deal when a large number of possible services are available at one point?

E.g., there may be hundreds of services available for converting images from Format A to Format B.

Damian Gessler: @DougFoxvog The key is in service choice prioritization--just like Google prioritizes

web pages on its search results page. But here, we are not nearly as sophisticated as Google and

currently use a very simple algorithm. We'll put focus here down the road a little.

Amanda Vizedom: @Damian - There are many similarities between the iPlant approach you describe and

the Semantic SOA - service discovery approach being developed by USAF. I think that the approach

used in the DoD EIW is also strongly similar (perhaps DWiz - Dennis Wisnosky - will comment). In each

case, ontologies are primarily being used to provide semantic description, model, or wrapper for

(mostly natively non-semantic) data services, and ontological reasoning and search technologies are

used to enable service discovery given user needs. Your statement about ontology alignment, however,

stands out. I understand service matching operationally and ephemerally based on reasoning over

lightly-aligned ontologies. But you seem to be saying something else, that the alignment of the

locally-developed ontologies in which the services are described is not manual, not static, and not

axiomatic. Can you say something more about how you align, or connect, or reason across such

ontologies without any prior / stable alignment points?

Damian Gessler: @AmandaVizedom The key is that we are not aligning ontologies on *data* per se; we

let services make the mapping statements (e.g., the (possibly complex) data they take in and the

(possibly complex) data they give back. So we "simply" need to determine and operate on subsumption

questions: can this service operate on my data and return what I want? This is essentially a

dynamic, operational alignment question.

Peter P. Yim: == Ilya Zaslavsky presenting ...

anonymous morphed into Carlos Rueda

Simon Spero: @Ilya: if the hierarchies are genuine hierarchies - that is, subordinate terms always

entail the superordinate term, then you have traditional Knowledge Organization System semantics

Elisa Kendall: @Ilya, have you used any vocabulary such as ISO 1087 to define relationships such as

synonomy, polysemy, etc.? Just wondering ...

Matthew West: Sorry I have to go.

Bobbin Teegarden: @Ilya what did you use for the visualizations, and how well received were they?

Ilya Zaslavsky: @BobbinTeegarden: Inxight startree, semantic wiki, also recently Silverlight.

Hydrologists were comfortable using Inxight startree in the tagging application

Ilya Zaslavsky: @ElisaKendall: no, we haven't. This sounds interesting. The current plan is to use

SKOS

Ilya Zaslavsky: @SimonSpero. No, in many cases these are not trees. We try to present them as trees

where possible

Harold Boley: @Elisa, do you use SBVR rules for mapping?

Elisa Kendall: @Ilya: I have a draft ontology for ISO 1087 that we're planning to standardize at OMG,

together with ISO TC 37. I'm guessing that we will be publishing a draft sometime this

spring/summer, with one of the goals being to use it to assist in mapping SBVR vocabularies to

ODM/OWL. If you'd like to chat more about this offline, please feel free to contact me directly, at

ekendall at thematix.com.

Ilya Zaslavsky: @ElisaKendall, thanks Elisa, I'd be interested

Elisa Kendall: @Harold, not so far, but Mark Linehan (IBM) has been doing some work in this area for

a Date Time vocabulary we're creating at OMG. The current alpha (or maybe beta) spec is available at

http://www.omg.org/spec/DTV/1.0/Beta1/, but doesn't include much of the OWL work we've been doing

more recently in finalization.

Elisa Kendall: @Harold, you might take a look even at the Beta spec for the Date Time effort, as it

does include some OCL and CLIF statements for the SBVR definitions, which we're still refining, but

could give you a better sense of what the SBVR actually is intended to say .

Harold Boley: @Elisa, thanks, I just opened the huge http://www.omg.org/spec/DTV/1.0/Beta1/ PDF.

Frank Olken: @ElisaKendall The URL you posted for DTV yields a 404 (page missing) error ...

Elisa Kendall: @Frank, hmmm... for me it downloads, so I'm glad you were able to get to it.

Elisa Kendall: @Harold, Sorry , but hopefully you'll find it useful. When we've added the OWL it will

only get bigger ... as you might imagine, but I think the result could provide a next generation OWL

Time ontology, and includes a number of business oriented definitions.

Mike Bennett: Is it the mental model of hydraulogists that doesn't map to Protege, or that fact that

to use Protege you first need a mental model of ontology, since Protege in no way presents a visual

or other model of ontology to the person looking at it.

Frank Olken: @ElisaKendall The DTV link that Harold Boley posed seems to work.

Harold Boley: @Frank, my quote of the URL omitted the comma, wrongly assumed to be part of the URL by

the chat software.

Mike Bennett: @Frank et al - there is a rogue comma in the original URL.

Harold Boley: @Elisa, yes it looks very exhaustive. Can I mentioned it in the OASIS TC on

LegalRuleML?

Elisa Kendall: @Harold - Yes, of course, and please give people the link to the specification. Our

next iteration will have more OWL, and ultimately we will have a set of OWL ontologies corresponding

to the SBVR

Peter P. Yim: == Line Pouchard presenting ...

Line Pouchard: @Peter: I sent you a new set of slides that contain page numbers. Would you have time

to upload them?

Peter P. Yim: @Line - ack .... will try now

Michael Grüninger: my copy has page numbers

GiulianoLancioni: mine too

Jim Rhyne: So does mine.

Amanda Vizedom: Copy just downloaded from refreshed call page does have the page numbers.

Doug Foxvog: The link to the slides is the same. Re-download & you'll get the page numbers

Steve Ray: Strange, I just did this and do not get slide numbers...

anonymous morphed into Nancy Wiegand

Doug Foxvog: @Line: attaching multiple textual terms to individual ontology terms would assist in

search, not relying on searching only on the ontology term's name.

Peter P. Yim: == Steve Ray moderating the open discussion ...

Simon Spero: [ref. MichaelGruninger's verbal comment] Testing; Competency or performance?

Line Pouchard: DataONE is offering an Internship program for Summer 2012 at

http://www.dataone.org/internships. I am co-mentoring for Project #7 to continue the work described

today. In particular, this work needs to extend parts of the SWEET ontologies w.r.t soil science,

and a candidate with domain knowledge would be ideal. The intern works remotely from their own

institution for ten weeks. The deadline is March 12. Please share with your students.

Peter P. Yim: @ALL - the memory and the work of Dr. Robert Raskin

(http://ontolog.cim3.net/cgi-bin/wiki.pl?RobRaskin ) who passed away last Friday, will be with us.

Rob was the PI of the SWEET Ontology (Semantic Web for Earth and Environmental Terminology) project,

and an active contributor to this community

Mike Bennett: [ref. IlyaZaslavsky's comment about domain experts having problems with Protege, and

PeterYim's comment about limitations imposed by the expressivity of the tools or the language being

used] Expressivity versus what is expressed - these are two distinct matters.

Larry Lefkowitz: And formalism vs content is another distinction. Having a great grammar but a small

vocabulary is certainly going to limit expressivity. Yes, in theory you can create new vocabulary on

the fly, but that could easily overtake the initial modeling task.

Mike Bennett: Exactly. you can have a very expressive model of data, but it's still a model of data.

Or you can have a more or less expresive model of real things in the problem domain, and it's an

ontology.

Elisa Kendall: @Frank, the units/dimensions part of the model is limited, fyi, but the SysML effort

for quantities and units and this units model are in the process of being aligned now at OMG, with

the SysML version being more comprehensive, as you might imagine/hope.

David Flater: @Steve What happened with OASIS Quantities & Units of Measure Ontology?

David Price: There is also the QUDT ontology from NASA Ames that was input to the OASIS QUOMOS

activity ... http://qudt.org/

Elisa Kendall: @David, Folks from OMG who are working on the SysML QUDV effort are looking at

alignment with that as well, fyi, but I don't know much about the differences. I have heard there

are some, which they are working through, and that JPL is involved along with ESA.

Ilya Zaslavsky: @LinePouchard: do you know if there are already soil vocabularies available in some

form? Is there any relationship with SoilML? CZO project would be interested in this.

Line Pouchard: @Ilya: yes, I had talked to Nancy W. about this, and last Fall, SoilML was not

released yes.

Damian Gessler: Thank you

GaryBergCross: bye all

Peter P. Yim: great session!

Steve Ray: Thanks everybody for making the session stimulating.

Peter P. Yim: -- session ended: 11:26am PST --

-- end of in-session chat-transcript --

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