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EarthScienceOntolog: Panel Session-04 - Thu 2012-11-01

Mini-Series Theme: An Earth Science Ontology Dialog ("EarthScienceOntolog")

Session Topic: A Review of Ontologies for Earth Sciences

Session Co-chairs: Dr. DaliaVaranka (USGS) and Dr. MarkSchildhauer (NCEAS, UC Santa Barbara) - intro slides

Panelists / Briefings:

  • Dr. LuisBermudez (OGC) - "Use of Ontologies within the Open Geospatial Consortium (OGC)" slides
  • Dr. BoyanBrodaric (Geological Survey of Canada) - "Toward an integrated surface and subsurface water ontology" slides
  • Dr. NormanMorrison (U of Manchester, UK) - "The Environment Ontology: What sort of a place was it?" slides
  • Mr. ThomasHuang (JPL/NASA) - "From Modeling the Earth to Terrain Simulation" slides
  • Dr. MarkSchildhauer (UC Santa Barbara) - "Where do we go from here with Earth and Environmental Science Ontologies?" (joint work by Mark Schildhauer & BenAdams) slides

Archives

Abstract

A Review of Ontologies for Earth Sciences - intro slides

This is the 4th session of the Joint EarthCube-Ontolog Mini-series on "Ontology and Semantic Technology for the Earth Science Community" - a series of panel sessions dubbed: "EarthScienceOntolog" - an Earth Science Ontology Dialog.

This mini-series of events are co-organized/supported by members of the Earth Cube community, Ontolog community, SOCoP community, IAOA community.

Challenges in the earth sciences to meet research and societal needs require creative ways of integrating data for complex analysis. This session is the 4th in a series of informative presentations to bring science and ontology communities together in an exchange of ideas and collaborative networks. This session will look into some of the current ontology efforts in the earth and environmental sciences, and showcase examples of earth science problems being tackled by the use of ontologies for synthesis and exploratory knowledge discovery.

More details about this mini-series at: EarthScienceOntolog (home page for this mini-series)

Briefings

  • Dr. LuisBermudez (OGC) - "Use of Ontologies within the Open Geospatial Consortium (OGC)" slides
    • Abstract: ... This presentation will provide an overview of ontologies been used by OGC. It will discuss the formal representations of concepts within OGC standards and the ontology behind the new GeoSPARQL.
  • Dr. BoyanBrodaric (Geological Survey of Canada) - "Toward an integrated surface and subsurface water ontology" slides
    • Abstract: ... Pressing scientific and societal issues, coupled with the increasing availability of water data, require an integrated approach to surface and subsurface water representations. However, emerging representations are largely disconnected at present, most notably within geospatial data standards, thus impeding joint use of data for key aspects such as estimating water balances. This presentation discusses work in progress on the development of an ontology for these water domains. It identifies five basic primitives common to the domains and illustrates how these can be specialized from DOCLE toward an integrated water ontology.
  • Dr. NormanMorrison (U of Manchester, UK) - "The Environment Ontology: What sort of a place was it?" slides
    • Abstract: ... The Environment Ontology (EnvO) is a community-developed ontology which provides a controlled, structured approach to support the annotation of any organism or biological sample with environment descriptors. EnvO contains terms for biomes, environmental features, and environmental material which enable the description of environments from coarse to fine levels of granularity. We hope that the community will adopt EnvO and benefit from its potential to promote standardised data integration and access. As an open project, we welcome your use of and participation in this project at http://www.environmentontology.org
  • Mr. ThomasHuang (JPL/NASA) - "From Modeling the Earth to Terrain Simulation"" slides
    • Abstract: ... Using knowledgebase technology to drive design decisions and as an instrument for validation not only cuts cost in product development, but it also enables much more thorough validation of the design prior to fabrication. An ongoing development effort is underway in building a knowledgebase system to model terrains for vehicle designs. The popular Semantic Web for Earth and Environmental Terminology (SWEET) ontologies is a collection of ontologies and concepts design to improve discovery and application of Earth science data, which provides the foundation in modeling such ontological system. This talk presents a brief overview on SWEET and discusses some of the designs and challenges in building this domain knowledge system.
  • Dr. Mark Schildhauer & Mr. BenjaminAdams (NCEAS, UC Santa Barbara) - "Where do we go from here with Earth and Environmental Science Ontologies?" slides
    • Abstract: ... An ecosystem of Earth and environmental science vocabularies, markup languages, and ontologies has arisen in recent years. These representations of the meanings of Earth science terms vary greatly in thematic scope, intended uses, foundational design principles, and axiomatic structures and inferencing capabilities. In this talk we identify some important considerations as we move forward in developing semantic cyberinfrastructure for the Earth and environmental sciences. Common issues that we will address include the need for definitions of terms that come from authoritative sources, better use of richer, formalized representations for describing relations among concepts (such as disjoint, classes with two parents, etc.), and a need for clearer governance mechanisms that enable systematic approaches to evaluating, populating, updating and using vocabularies and ontologies. We will conclude with thoughts on the possibilities and value of harmonizing the numerous ongoing community semantic development efforts, rather than continuing to create a new Babel of semantically enriched but mutually incomprehensible dialects.

Agenda

EarthScienceOntolog - Panel Session-04

  • Session Format: this is a virtual session conducted over an augmented conference call

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 --

[09:10] Peter P. Yim: Welcome to the

EarthScienceOntolog: Panel Session-4 - Thu 2012-11-01

Mini-Series Theme: An Earth Science Ontology Dialog ("EarthScienceOntolog")

Session Topic: A Review of Ontologies for Earth Sciences

Session Co-chairs:

Panelists:

  • Dr. Luis Bermudez (OGC) - "Use of Ontologies within the Open Geospatial Consortium (OGC)"
  • Dr. Boyan Brodaric (Geological Survey of Canada) - "Toward an integrated surface and subsurface

water ontology"

  • Dr. Norman Morrison (U of Manchester, UK) - "The Environment Ontology: What sort of a place was

it?"

  • Dr. Thomas Huang (JPL/NASA) - "From Modeling the Earth to Terrain Simulation"
  • Dr. Mark Schildhauer (UC Santa Barbara) - "Where do we go from here with Earth and Environmental

Science Ontologies?" (a joint work by Mark Schildhauer & BenAdams)

Logistics:

  • Refer to details on session page at:

http://ontolog.cim3.net/cgi-bin/wiki.pl?ConferenceCall_2012_11_01

  • (if you haven't already done so) please click on "settings" (top center) and morph from

anonymous to your RealName

  • Mute control: *7 to un-mute ... *6 to mute
  • Can't find Skype Dial pad? ** for Windows Skype users: Can't find Skype Dial pad? ... it's under

the "Call" dropdown menu as "Show Dial pad" ** for Linux Skype users: please stay with (or downgrade

to) Skype version 2.x for now (as a Dial pad seems to be missing on Linux-based Skype v4.x for

skype-calls.)

Proceedings:

[09:14] anonymous morphed into Bruno Emond

[09:20] anonymous morphed into Deborah Nichols

[09:21] anonymous morphed into Ben Adams

[09:25] anonymous1 morphed into CeciliaZanniMerk

[09:28] anonymous1 morphed into Tom Tinsley

[09:30] anonymous1 morphed into Joel Sachs

[09:30] anonymous2 morphed into GenhanChen

[09:32] Dan morphed into Dan Dong

[09:32] anonymous2 morphed into Fran Lightsom

[09:32] anonymous1 morphed into Luis Bermudez

[09:32] Norman Morrison morphed into Norman Morrison

[09:32] anonymous4 morphed into Dalia Varanka

[09:32] anonymous5 morphed into Boyan Brodaric

[09:32] anonymous3 morphed into Torsten Hahmann

[09:32] Deborah Nichols morphed into DeborahLNichols

[09:33] anonymous morphed into MarshallXMa

[09:34] anonymous1 morphed into Hilmar Lapp

[09:35] anonymous morphed into Semir Sarajlic

[09:35] anonymous1 morphed into Uma

[09:36] anonymous2 morphed into Joel Bender

[09:38] anonymous1 morphed into Krzysztof Janowicz

[09:38] anonymous2 morphed into Alex Sorokine

[09:38] Semir Sarajlic morphed into Semir Sarajlic

[09:40] anonymous morphed into DeborahMacPherson

[09:40] anonymous1 morphed into DeborahMcGuinness

[09:41] anonymous morphed into Yan Liu

[09:43] anonymous morphed into Whitenack

[09:40] Peter P. Yim: == Dalia Varanka opening the session with the intro slides ...

[09:41] List of members: Alex Sorokine, Alex Shkotin, Ben Adams, Bobbin Teegarden, Bob Smith,

Boyan Brodaric, Bruno Emond, CeciliaZanniMerk, Chuck Ward, Dalia Varanka, Dan Dong, David Valentine,

DeborahMcGuinness, DeborahLNichols, DeborahMacPherson, Frank Olken, Fran Lightsom, GaryBergCross,

GenhanChen, Hilmar Lapp, Joel Sachs, Joel Bender, Ken Baclawski, Krzysztof Janowicz, Luis Bermudez,

Mark Schildhauer, MarshallXMa, Norman Morrison, Peter P. Yim, Scott Hills, Semir Sarajlic, Terry Longstreth,

Todd Schneider, Tom Tinsley, Torsten Hahmann, Yan Liu, Uma, vnc2,

[09:44] Peter P. Yim: == Luis Bermudez presenting ...

[09:46] Peter P. Yim: whoever posted into the box next to the "hand" button, please re-post into the

editing box on the left of the "send" button

[09:47] Peter P. Yim: your question: "is there chat support ..." - the answer is, the in-session

chat-support is right here; after the session, the conversation can continue - see:

http://ontolog.cim3.net/cgi-bin/wiki.pl?ConferenceCall_2012_11_01#nid3HA5

[09:47] anonymous morphed into Carlos Rueda

[09:48] anonymous morphed into Krishna Sinha

[09:48] anonymous1 morphed into Cyber-[[ShARE]]

[09:51] Norman Morrison: Out of interest, is there a twitter hashtag in use for the session ... [

PeterYim: not yet, Norman ]

[09:53] Todd Schneider: Luis, does OGC recommend use of, or alignment to, a foundational ontology to

facilitate interoperability or integration?

[10:15] Luis Bermudez: Hi Todd. OGC doesn't currently recommended alignment to a foundational

ontology. The only related OGC standard (recommendation) is GeoSPARQL. My sense is that we cannot

call it a foundational ontology.

[10:17] Todd Schneider: Luis, is OGC considering such a recommendation? I'm sure it would help,

eventually:)

[10:20] Luis Bermudez: Todd, I will take your recommendation back to OGC.

[10:04] Peter P. Yim: @LuisBermudez - what open "use license" is used (by default) on OGC's open

Intellectual Properties (IP's)

[10:20] Luis Bermudez: Peter, OGC IP document is here:

http://portal.opengeospatial.org/files/?artifact_id=32268

[10:08] Peter P. Yim: == Boyan Brodaric presenting ...

[10:10] anonymous morphed into Thomas Huang

[10:14] anonymous morphed into Doug Foxvog

[10:29] Krishna Sinha: Krishna Sinha :Boyan, is it possible to extend this to oceans? Are there any

obvious links?

[10:31] Boyan Brodaric: Krishna---we haven't looked at oceans, but my sense is that at least some of

it is directly applicable. Boyan

[10:28] Peter P. Yim: == Norman Morrison presenting ...

[10:31] GaryBergCross: For people interested in working more on semantics of a container idea it is

a topic at the Nov 28-30 workshop at USGS in Reston VA see http://vocamp.org/wiki/GeoVoCampSOCoP2012

[10:38] Torsten Hahmann: Krisha, I guess it depends on what exactly you want to model. For example

reefs or underwater ridges (as Norman is talking about) could be modeled similarly using certain

kinds of voids (hollows) based on containment.

[10:47] Norman Morrison: Torsten, Boyan & Krishna, yes, it was encouraging to see that we have

independently adopted the same formalism of (voids) holes and containment.

[10:50] Mark Schildhauer: interesting to know, though, whether these formalisms are identical or

merely similar

[11:02] Torsten Hahmann: Mark, I totally agree that this is a key question. Norman: in that regard,

to what extent is Envo formalized? Is it restricted to a IS-A taxonomy right now? That's what I

found on the website you mentioned (in the download section).

[11:00] Boyan Brodaric: Norman---the conceptual convergence is nice to see. Do you use BFO for the

hole/containment schema, or did you enhance BFO in that direction? My look at BFO in this respect is

that it has some hooks that need fleshing out.

[11:11] Norman Morrison: Torsten: Yes, EnvO does leverage it's concepts and relations from BFO. There

is an 'EnvO2' in the pipeline that will do so more rigourously.

[11:08] GaryBergCross: The connection to BFO suggests that EnvO leverages its concepts and

relations.

[10:44] GaryBergCross: @Norman does EnvO cover the idea of a site as in ecological site or other

types of sites?

[10:55] Norman Morrison: @Gary yes we have sites represented in EnvO, but I would say this is an area

that is not that well covered. We also incorporate a number of Biome classification systems that are

non orthogonal. This is certainly an area that would benefit from further work.

[11:01] GaryBergCross: @Norman Thank you. Perhaps we can exchange ideas about this later. Site is a

topic at the Nov 28-30 workshop at USGS in Reston VA see http://vocamp.org/wiki/GeoVoCampSOCoP2012

[10:45] Peter P. Yim: @Norman (& all) - your slides are now updated (in particular the garble on slide#6

is now gone)

[10:45] Peter P. Yim: == Thomas Huang presenting ...

[11:07] Peter P. Yim: == Mark Schildhauer presenting ...

[11:11] Alex Shkotin: What about this authority http://www.merriam-webster.com/dictionary/definition?

[11:11] Peter P. Yim: @Mark, Ben & All - ref. your slides #3 & 4 - there is an ongoing effort under the

Open Ontology Repository (OOR) initiative, that makes an attempt to build a federated network of

those who are running ontology repositories, so that there can be a "logical" go-to place to access

them, and where other value-added services can be applied ... among the repositories, some of those

of interest to this group like MMISW-ORR, SOCoP-OOR, ORNL-DAAC, BioPortal, etc. are also on board

there - see: http://oor.net/

[11:16] Peter P. Yim: the OOR effort welcomes participation of projects that are running ontology

repository ("open" ones, especially) ... join us!

[11:20] Peter P. Yim: == Q&A and Open Discussion now ...

[11:21] GaryBergCross: Note VoCamps in spirit do try to research existing vocabularies. Then build

on these refining and extending these as part of the effort.

[11:21] anonymous morphed into Myunghwa Hwang

[11:22] anonymous1 morphed into Alex Mirzaoff

[11:23] Alex Sorokine: to Boyan: how do you treat granularity in relation to your concept of gaps and

voids?

[11:36] Torsten Hahmann: as follow-up to Boyan answer to Alex's question [11:23]: I suppose you meant

granularity of voids? we currently only distinguish two levels of granularity: the object level

(physical objects) and the matter level. Those we formalized in the FOIS paper (2012). It is a

simplified version of the DOLCE concept of constituency.

[11:24] anonymous morphed into Ramona Walls

[11:23] Torsten Hahmann: Btw, the ontologies Boyan and I developed will be available next week in the

COLORE ontology repository (one of the OOR Peter was referring to) available at

http://code.google.com/p/colore/

[11:24] GaryBergCross: @Torsten, so these are formalized in common logic?

[11:24] Torsten Hahmann: @Gary: yes.

[11:24] Mark Schildhauer: thanks, Boyan...

[11:25] Michael Grüninger: It will be important to explicitly use the axioms of the ontologies so

that we can show that the commonalities are more than an intuitive similarity.

[11:26] Michael Grüninger: Identical concepts in two ontologies would mean that from the axioms alone

we can entail the axioms satisfied by one concept can be entailed by the axioms satisfied by the

other ontology, together with specifications of the mappings

[11:27] Torsten Hahmann: @Gary: for clarification: the DOLCE ontology that Boyan presented is

generated from the Common Logic ontology, it obviously only captures only a subset of what we

formalized in Common Logic

[11:28] GaryBergCross: @MichaelGruninger So yours and Torsten's work on spatial ontologies is an

example where you have done this type of mapping and close look at axioms. Right?

[11:30] Michael Grüninger: @Gary: Exactly. The challenges posed by today's speakers is to identify

all of the different ontologies that people are working on, and to figure out what the possible

mappings could be

[11:28] Mark Schildhauer: http://obofoundry.org

[11:31] Mark Schildhauer: http://oor.net

[11:28] Alex Shkotin: @Mark, it looks like we need to create a formal theory one for every particular

science?

[11:30] Mark Schildhauer: @alex-- I see more a need for common design principles in ontology

construction *across* disciplines, and shared concepts wherever possible

[11:33] Boyan Brodaric: @Alex---the degree of formality will be use-governed; for some purposes high

formality it might not be necessary. But, to leverage reasoning it would be desirable.

[11:35] Alex Shkotin: @Mark, it looks like common sense knowledge formalization. Like Ernst Davis.

[11:34] Krishna Sinha: MarkSchildhauer---I think developing a general ontology based solely on

vocabulary is difficult to accomplish. I dont see how non specialists with respect to a given

discipline could even begin to discover data.. We need something beyond just terms

[11:43] Mark Schildhauer: @Krishna-- agreed; but well-defined terms developed by experts, and

currently housed in thesauri like the AGI example you pointed out to us, can be borrowed and

embedded where appropriate in richer constructs? That's what I was intending, sorry it wasn't clear.

[11:33] CeciliaZanniMerk: Michael and Torsten, can I have a link or some biblio on your spatial

ontologies ?

[11:37] Torsten Hahmann: @Cecilia: sure, what format would you like? They are buried in the really

long bibliography of my thesis.

[11:40] CeciliaZanniMerk: Torsten, if you could send me some articles, it would be great ... merk

[at] unistra.fr

[11:39] CeciliaZanniMerk: Torsten, OWL and PDF will be fine ... :-D) OWL to play with, PDF to

understand ... ... we have just begun to work on an urban ontology for remote sensing, and the

spatial relationships are one of the key aspects

[11:43] Torsten Hahmann: @cecilia: I can email you a pdf.

[11:43] CeciliaZanniMerk: @torsten : thanks ! it would be great !

[11:34] Norman Morrison: On this topic MIREOT (Minimum information to reference an external ontology

term): http://obi-ontology.org/page/MIREOT

[11:34] Norman Morrison: Ramona Walls (who's online now) knows more about this

[11:36] Doug Foxvog: @Michael, I think we can distinguish theories from definitional ontologies. If

that is done, then different theories with different axioms could be defined, so that two terms from

different ontologies can be accepted as identical concepts, even though the axioms defined for one

(with one theory) are not necessarily entailed by the axioms of the other (defined with a different

theory).

[11:36] Doug Foxvog: This entails reifying the different theories in different theory ontologies.

[11:38] Torsten Hahmann: @Luis: is there any effort to formalize the semantics of the GeoSPARQL

concepts any further?

[11:44] Luis Bermudez: @Torsten. The GeoSPARQL semantics are already formalized in OWL

http://www.opengis.net/ont/geosparql.

[11:46] Torsten Hahmann: @Luis: I meant to formalize it beyond what is already there. In particular

whether to formalize the descriptions of each concepts that are currently in English, for example

statements like: <skos:definition xml:lang="en">Exists if the subject SpatialObject spatially

contains the object SpatialObject. DE-9IM: T*****FF*</skos:definition>

[11:37] Peter P. Yim: -- (conference call) session ended: 11:37am PDT --

[11:37] Mark Schildhauer: oops-- sorry Joel. Good point- we didn't have time to go into the usage of

these ontologies, in terms of semantic annotation and mediation!

[11:40] Mark Schildhauer: @joel-- for example, one typical application of an ontology term would be,

via annotation, asserting that some data value or column in a data set "IS" a (set of) instances of

that term.

[11:40] Peter P. Yim: @Joel ... would you post your question here (we can leave the chat-room going for

a few more minutes) or put that out to the community for further discussion - see:

http://ontolog.cim3.net/cgi-bin/wiki.pl?ConferenceCall_2012_11_01#nid3HA5

[11:40] Norman Morrison: Thanks again to the organisers. As a first timer to the Ontolog session I

found this to be an excellent forum and certainly hope to join future discussions. @Joel - next time

perhaps... :-)

[11:41] CeciliaZanniMerk: I agree with Norman ... it was my first time also, and i've really

appreciated the quality of the presentations and of the discussions ... thanks a lot !

[11:41] List of attendees: Alex Mirzaoff, Alex Shkotin, Alex Sorokine, Ben Adams, Bob Smith,

Bobbin Teegarden, Boyan Brodaric, Bruno Emond, Bruno Emond, Carlos Rueda, CeciliaZanniMerk, Chuck Ward,

Cyber-[[ShARE]], Dalia Varanka, Dan Dong, David Valentine, Deborah Nichols, DeborahMcGuinness,

DeborahLNichols, DeborahMacPherson, Doug Foxvog, Fran Lightsom, Frank Olken, GaryBergCross, GenhanChen,

Joel Sachs, Joel Bender, Ken Baclawski, Krzysztof Janowicz, Luis Bermudez, Mark Schildhauer, MarshallXMa,

Michael Grüninger, Myunghwa Hwang, Nancy Wiegand, Norman Morrison, Peter P. Yim, Ramona Walls, Scott Hills,

Semir Sarajlic, Terry Longstreth, Thomas Huang, Todd Schneider, Tom Tinsley, Torsten Hahmann, Uma,

Whitenack, Yan Liu, Hilmar Lapp, Krishna Sinha, vnc2

[12:00] Peter P. Yim: closing chat-room now!

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

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