Reference Ontologies in support of Semantic Interoperability
Gary Berg-Cross
Mike Bennett
Mike
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Kingsley Idehen
The Financial Industry Business Ontology (FIBO) was created according to exactly these principles, specifically so it can be used as a reference ontology e.g. for reporting, risk management, compliance, integration and so on.
Mike
Is this ontology now easily available for perusal and exploration ? If so, I just need a URL that identifies its current location on the Web.
Kingsley
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Obrst, Leo J.
Yes, there are currently many such in the biomedical community, in fact, most of those in the OBO Foundry.
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Chris Mungall
I'm not sure what a "vigorous" axiomatization is, but some of the
ontologies here may meet these criteria in the life sciences domain:
http://obofoundry.org/
For example, GO and Uberon (cellular biology and multi-species anatomy)
have a high degree of axiomatization, albeit largely within EL++
On 31 Mar 2016, at 12:56, Gary Berg-Cross wrote:
> One of the longer conversations at today's Ontology Summit session
> concerned Reference Ontologies.
> In their talk Shirly Stephen
> <http://ontologforum.org/index.php/TorstenHahmann> (University of
> discussed this as part of "Semantic Alignment of the Groundwater
> Markup
> Language with the Emerging Reference Hydro Ontology HyFO"
>
> Among the requirements for such a RO they cite:
> * Foundational Grounding
> * broad coverage of their domain
> * Detailed and vigorous axiomization of the needed semantics in a
> representation language that affords automated verification and
> reasoning.
>
> We couldn't come up with other examples from the GeoScience domain but
> perhaps others on the forum can or can provide candidates from other
> domains.
> We agree that this is an important thing to develop for progress
> on Semantic Interoperability.
>
> Certainly there seem to be candidates in the BioMed domain and
> sub-domains
> such as:
>
> Rosse, Cornelius, and José LV Mejino Jr. "A reference ontology for
> of
> biomedical informatics* 36.6 (2003): 478-500.
>
>
> Gary Berg-Cross, Ph.D.
> gberg...@gmail.com
>
>
> <http://ontolog.cim3.net/cgi-bin/wiki.pl?GaryBergCross>*http://ontolog.cim3.net/cgi-bin/wiki.pl?GaryBergCross
> <http://ontolog.cim3.net/cgi-bin/wiki.pl?GaryBergCross>*
> All contributions to this forum by its members are made under an open
> content license, open publication license, open source or free
> or its successors.
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Matthew West
Dear Gary,
ISO 15926 of course. Main domain is process engineering. Weak on axiomatization, though an OWL version is currently in development. The main use of axioms and reasoning is expected to be verification of additions.
Regards
Matthew West
Information Junction
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From: ontolo...@googlegroups.com [mailto:ontolo...@googlegroups.com] On Behalf Of Gary Berg-Cross
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To: ontolog-forum <ontolo...@googlegroups.com>; ontolog...@googlegroups.com
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Cory Casanave
I would also like to point out the OMG initiative for threat and risk information sharing and federation which uses conceptual reference models (a.k.a. ontologies) and mappings to specific data structures. More information can be found on www.threatrisk.org.
From: ontolog...@googlegroups.com [mailto:ontolog...@googlegroups.com]
On Behalf Of James Davenport
Sent: Thursday, March 31, 2016 9:12 PM
To: ontolog...@googlegroups.com; ontolog-forum <ontolo...@googlegroups.com>
Subject: RE: [Ontology Summit] Reference Ontologies in support of Semantic Interoperability
Can I draw attention to www.openmath.org which is not incorporated in MathML3, and at least attempts to satisfy
“Detailed and vigorous axiomization of the needed semantics in a representation language that affords automated verification and reasoning”.
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Cory Casanave
The OMG initiative for threat and risk information sharing and federation which uses conceptual reference models (a.k.a. ontologies) and mappings to specific data structures. More information can be found on www.threatrisk.org.
John F Sowa
GBC
Among the requirements for [a reference ontology] :
> * broad coverage of their domain
> * Detailed and vigorous axiomization of the needed semantics in
> a representation language that affords automated verification
> and reasoning.
or comparison with some other specification. What is the notation
used for that other spec? Is it some NL? Or another formalism?
MB
Leo
> Yes, there are currently many such in the biomedical community...
MW
> ISO 15926 of course. Main domain is process engineering...
CC
> I would also like to point out the OMG initiative for threat and risk...
Summary of the issues:
1. Digital systems have been successfully interoperating on shared
data for over a century -- ever since punched-card equipment
was designed and implemented for the 1890 census.
2. The primary requirement for successful interoperability has been
and always will be agreement on syntax -- from punched-card
formats to XML, JSON, or whatever.
3. The only widely accepted notation for defining the semantics
has been some version of natural language supplemented with
various diagrams and notations. Many of the notations were
formalized by some standards bodies. But the semantics of
those notations were expressed in NLs -- supplemented with
other diagrams and notations.
4. Even today, the most widely used standards for data sharing
and interoperability -- Schema.org and the Amazon DB schema,
for example -- are based on formally defined syntax with
informal NL definitions for the semantics.
5. More detailed axiomatizations can only be enforced for projects
that are governed by some authority that can exert financial pain
for noncompliance.
6. More often than not, strictly enforced standards lead to "silos"
with enhanced interoperability among systems within a silo, but
a severe *reduction* in interoperability among silos.
7. Attempts to promote interoperability among silos usually lead
to YASPI (Yet Another Standard to Promote Interoperability).
Repeat from step #3.
I discussed some related topics in the slides I presented at the
first session of the Ontology Summit in February, and I extended
them with more slides after the next couple of sessions:
http://www.jfsowa.com/talks/interop.pdf
For further discussion of the semantic issues, see below.
John
_____________________________________________________________________
From p. 19 of http://www.jfsowa.com/pubs/worlds.pdf
5. Making Possible Worlds Meaningful
One of the oldest controversies about Aristotle's categories was
whether they represent the kinds of things that exist or the way
people perceive, think, and talk about things that exist.
Theophrastus, Aristotle's successor as head of the Lyceum, said that
the categories were intended in all those ways — in modern terms,
ontological, epistemological, and lexical. Yet the fragmented
methodologies of those subjects are scattered across the fields of
philosophy, linguistics, and artificial intelligence, in each of
which the researchers who work on formal semantics or lexical
semantics are disjoint sets. For linguistics, Partee (2005) hoped
that "these different approaches can be seen as complementary and
not necessarily antagonistic."
One reason for hoping that Peirce's semiotics can help relate the
fragmented subfields is that the scope of his research was as broad
as Aristotle's. In addition to his research on mathematics, physics,
and logic, he had been an associate editor of the Century Dictionary,
for which he wrote, revised, or edited over 16,000 definitions. The
combined influence of logic and lexicography is apparent in a letter
he wrote to to B. E. Smith, the editor of that dictionary:
The task of classifying all the words of language, or what's
the same thing, all the ideas that seek expression, is the most
stupendous of logical tasks. Anybody but the most accomplished
logician must break down in it utterly; and even for the strongest
man, it is the severest possible tax on the logical equipment and
faculty.
In this remark, Peirce equated the lexicon with the set of expressible
ideas and declared logic the primary means of analysis. Unlike Frege,
Husserl, and Russell, he did not avoid the challenge of characterizing
the language people actually use by escaping to some purified realm of
formal semantics or ontology.
Semiotics is a unified subject that addresses all possible uses of
signs by all possible species. Various students of the subject may
prefer to analyze different aspects or to adopt a philosophical,
mathematical, or applied approach, but academic compartmentalization
should not create artificial barriers...
Mike Bennett
The OMG standards parts of FIBO are available on the web, though these don't contain all the material that covers the foundational grounding, as yet.
For instance this URI gives an "About" file that imports all of FIBO Foundations (not quite current - a version 1.1 is soon to be published there):
http://www.omg.org/spec/EDMC-FIBO/FND/AboutFND-1.0.rdf
Similarly there's an OMG page for FIBO Business Entities, with listings of the inividual ontology URIs (but not About file in this version, which is superseded by another version that the OMG site has not yet published).
http://www.omg.org/spec/EDMC-FIBO/BE/1.0/Beta2/index.htm
The more conceptually complete material I was referring to, with all the foundational abstractions and the rest of the industry draft content (securities etc.), is currently being worked on so that we can expose this as RDF/OWL files, but that work won't be complete until around the end of April as a first draft. This will subsequently be expressed in SKOS for further business subject matter expert review and completion over the coming months. The draft concepts are all available as graphics and spreadsheets but not yet as RDF/OWL.
Mike
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Kingsley Idehen
Hi Kingsley,
The OMG standards parts of FIBO are available on the web, though these don't contain all the material that covers the foundational grounding, as yet.
For instance this URI gives an "About" file that imports all of FIBO Foundations (not quite current - a version 1.1 is soon to be published there):
http://www.omg.org/spec/EDMC-FIBO/FND/AboutFND-1.0.rdf
Similarly there's an OMG page for FIBO Business Entities, with listings of the inividual ontology URIs (but not About file in this version, which is superseded by another version that the OMG site has not yet published).
http://www.omg.org/spec/EDMC-FIBO/BE/1.0/Beta2/index.htm
The more conceptually complete material I was referring to, with all the foundational abstractions and the rest of the industry draft content (securities etc.), is currently being worked on so that we can expose this as RDF/OWL files, but that work won't be complete until around the end of April as a first draft. This will subsequently be expressed in SKOS for further business subject matter expert review and completion over the coming months. The draft concepts are all available as graphics and spreadsheets but not yet as RDF/OWL.
Mike
Great!
See the following docs that provide Ontology browsing:
[1] http://linkeddata.uriburner.com/c/8GTEFI -- FIBO
[2] http://linkeddata.uriburner.com/c/9GXSIQ2 -- People .
Basically, you can drill-down using the usual follow-your-nose approach over the entity relationship graph that's now web-accessible :)
Kingsley
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Gary Berg-Cross
or comparison with some other specification. What is the notation
used for that other spec? Is it some NL? Or another formalism?
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John F Sowa
> perhaps relevant work is in the paper Weitl, Franz, Mirjana Jakšić, and
> Burkhard Freitag. "Towards the automated verification of semi-structured
That's a good article. I found a copy at the authors' university:
https://www.fim.uni-passau.de/fileadmin/files/lehrstuhl/freitag/verdikt/WeitlJaksicFreitagDKE09.pdf
But they are only addressing a small part of the issues of semantic
interoperability. As they say in the title, they are relating NL
documents that are "semi-structured" -- i.e., they have annotations
that some humans inserted in the NL text.
And by verification, they are only using a rather simple logic
(a temporal DL) to check the consistency of annotations of the
documents on a single web site. That is useful, but much simpler
than the task of verifying that a large software system conforms
to its specifications.
Furthermore, the following sentence is taken out of context:
> They argue that "Criteria expressed in natural language as above
> are quite ambiguous"
that the information on the previous page, by itself, is insufficient.
The authors have degrees in computer science, and their references
do not cite anything about NLs or their syntax and semantics.
Their first reference is to the KAON2 project, which is "an
infrastructure for managing OWL-DL, SWRL, and F-Logic ontologies"
for the Semantic Web: http://kaon2.semanticweb.org/
The bald statement "Natural languages are ambiguous" is often bandied
about by computer scientists who have never studied the relationships
of NLs to logic, ontology, reasoning, or communication:
1. Every feature (syntactic or semantic) of every version of formal
logic is a *disciplined* abstraction from and simplification of
some NL feature.
2. The structure of a formal logic is designed to enforce the
discipline. It is not possible to use the logic to state
anything ambiguous or imprecise.
3. Because of point #2, it is *always* possible to translate
any statement in any formal logic to an equivalent statement
in an NL that is just as precise and unambiguous.
4. But point #2 does not guarantee that statements written in
the logic express what what the author had intended to say --
*especially* if the author is not fluent in the notation.
5. Although I recommend controlled NLs for *output* from computer
systems, writing a CNL requires the same amount of discipline
as writing in a formal logic. CNLs are most useful for readable
output. CNLs as input requires a very well designed user
interface (which few systems have).
See below for a summary of the issues from my note of April 3.
John
___________________________________________________________________
Gary Berg-Cross
I think, however, in addition to what you say the ordinary practice of expressing things in natural language does bandy about many things from what is intended. Formal languages and controlled NL brings with them (or we hope should in practice) a focus on"thinking clearly" about topics & intentions.
John F Sowa
> Formal languages and controlled NL bring with them (or we hope should
certainly helpful to "thinking clearly". That kind of discipline,
which is usually called *mathematics*, has enabled people to think
clearly for thousands of years.
The Babylonian mathematicians, for example, were able to do some
very sophisticated math thousands of years ago. That point was
known for a long time. But some recently discovered cuneiform
tablets provided additional evidence:
> A reanalysis of markings on Babylonian tablets has revealed that
> astronomers working between the fourth and first centuries BC
> used geometry to calculate the motions of Jupiter — a conceptual
> leap that historians thought had not occurred until fourteenth-
> century Europe.
http://www.nature.com/news/babylonian-astronomers-used-geometry-to-track-jupiter-1.19261
Summary: Discipline is essential to "think clearly", and logic,
mathematics, computer science, etc. are valuable for enforcing
discipline. But discipline alone does not provide new ideas.
You also need observation, insights, creativity, experiments,
testing, reading, and discussions with other people.
For more on these issues, see slides 28 to 31 of
http://www.jfsowa.com/talks/interop.pdf
John
Bruce Schuman
I thought it was fascinating to discover this morning this "Islamic mandala" or "sunburst" described by an author as a symbol for "the ninety-nine names of God in Islam"
What was once Babylonia is now Iraq. https://en.wikipedia.org/wiki/Babylonia
The word “algebra” is derived from the Arabic. I wonder how those ancient Babylonian mathematicians would view ontological studies of modern sunburst diagrams….
“Algebra—meaning “reunion of broken parts”
https://en.wikipedia.org/wiki/Algebra
Bruce Schuman, Santa Barbara CA USA
-----Original Message-----
From: ontolo...@googlegroups.com [mailto:ontolo...@googlegroups.com] On Behalf Of John F Sowa
Sent: Tuesday, April 12, 2016 7:48 AM
To: ontolo...@googlegroups.com
Cc: Jay Bennett <jben...@aitia.io>
Subject: Re: [ontolog-forum] RE: [Ontology Summit] Reference Ontologies in support of Semantic Interoperability
On 4/11/2016 5:33 PM, Gary Berg-Cross wrote:
> Formal languages and controlled NL bring with them (or we hope should
> in practice) a focus on"thinking clearly" about topics & intentions.
They are indeed important tools, and the discipline they enforce is certainly helpful to "thinking clearly". That kind of discipline, which is usually called *mathematics*, has enabled people to think clearly for thousands of years.
The Babylonian mathematicians, for example, were able to do some very sophisticated math thousands of years ago. That point was known for a long time. But some recently discovered cuneiform tablets provided additional evidence:
> A reanalysis of markings on Babylonian tablets has revealed that
> astronomers working between the fourth and first centuries BC used
> geometry to calculate the motions of Jupiter — a conceptual leap that
> historians thought had not occurred until fourteenth- century Europe.
http://www.nature.com/news/babylonian-astronomers-used-geometry-to-track-jupiter-1.19261
Summary: Discipline is essential to "think clearly", and logic, mathematics, computer science, etc. are valuable for enforcing discipline. But discipline alone does not provide new ideas.
You also need observation, insights, creativity, experiments, testing, reading, and discussions with other people.
For more on these issues, see slides 28 to 31 of http://www.jfsowa.com/talks/interop.pdf
John
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John F Sowa
> The word “algebra” is derived from the Arabic. I wonder how those
> ancient Babylonian mathematicians would view ontological studies of
> modern sunburst diagrams….
its syllable-structures were based on Sumerian phonetics, which
is very different from the Semitic phonetics of Akkadian, then
Assyrian, and then Aramaic.
After the Persians conquered that region, they used the same scribes
to communicate with the entire region in Aramaic, since it was then
the lingua franca. But when Alexander conquered the Persians, he
forced the scribes to use Greek. Kings, empires, and languages came
and went, but the scribes had job security.
Re sunburst diagrams: They're useful for representing some kinds
of structures. But the variety of useful diagrams is as open ended
as the kinds of structures. In the orders of infinity, the set of
points on a plane is uncountably infinite, but the set of curves
(diagrams) on a plane is the next higher infinity.
John
Bruce Schuman
Thank you.
I think what is fascinating me about sunburst diagrams-- is their similarity with so many ancient or "profound" symbols all of which strike me as "pre-mathematical" -- but probably pointing in a profound and simplifying direction, that I personally suspect is very significant -- and if generally ignored, it's most for myopic reasons. There's a lot of bridge-building to do here, obviously -- and a long history of windmill tilting.
It seemed another fascinating serendipity this morning when my friend called me about a talk she had just heard at Toastmasters, on the subject of "executable philosophy". I laughed when she told me that -- but I looked at the web site. This is a smart guy: http://www.executablephilosophy.org/ I don't know whether it's feasible -- but it's interesting. He's driven by a primary concern that I've been chasing for many years: ambiguity in the interpretation of abstractions. That's the killer problem -- in politics and in religion.
Regarding sunburst diagrams, I don't mean to imply that "we only need one kind of diagram" or anything like that -- but I do think there is a stunning and very significant similarity between SO many facets of contemporary semantic ontology -- ALL of which seem to revolve around -- or be centrally organized by -- the same concept: levels of abstraction. Level of abstraction IS a linear variable. We can quickly come up with a long list of standard epistemological or logical or mathematical concepts that can immediately be organized on the same framework. Taxonomy is the obvious starting point.
Maybe the subject is confused because the question "what is abstraction" remains confused and controversial. People with a bottom-up perspective -- and it's probably correct to suppose that most professional working ontologists in responsible paid positions are required to take that point of view or risk their professional status -- are not likely to get entangled in this kind of issue. But the issue of defining "abstraction" is more a political problem than it is a technical one.
I have been looking at this stuff a long time, and I think the whole enchilada ("ontological space") can be linearized -- IF we give up the adamant insistence on bottom-up empiricism and understand that we are talking about stipulation, which is a whole different thing. Don’t talk about "how it is out there" -- because how it is out there is a mess -- an undisciplined chaos of semi-random free-association connections in any direction anybody thinks is interesting for any local reason -- and that's the prevailing human standard at the moment because nobody can or does take responsibility for the whole. But what we should be doing is not talking about "how it is" (confused and fragmented and noisy) but about "how it should be" (harmonically collaborative) -- and building a map to get from here to there.
So -- any claim that even a top-down masterpiece of brilliant integration can subsume or integrate ALL of that stuff -- would be depend on actually interpreting every last bit of this fragmented stuff as local subsets running on their own private or bounded law -- and then politely showing 1) why their stuff makes sense in a bounded local environment, though it is fragmented and incommensurate in the whole, and then 2) showing how that local subset maps to the integral tree, creating a sweet-spirited pathway into the one-size-fits-everything whirly-gig...
It's kind of like saying -- absolutely any point can be the starting point -- totally ignoring the large implicit containing framework that holds all these developments. Just drive your stake in the ground and go. If you can sell your products, nice going. But we're in a global space now. We gotta get smarter -- not to mention nicer...
PS -- I've started making another database -- drawn totally from Wikipedia -- and this thing IS a kind of free-association gismo. I build a list of terms I think are interesting, and then I add another Wikipedia article and my little search algorithm runs the complete list of terms through the article, and if the term is found, the algorithm creates a link. A little crude maybe, but probably in the statistical ballpark. http://origin.org/database.cfm
Hang the entire civilized internet universe from one non-relativistic coordinate origin??? Just because “it’s the right thing to do??” Either crazy or mind-blowing....
Bruce Schuman, Santa Barbara CA USA
-----Original Message-----
From: ontolo...@googlegroups.com [mailto:ontolo...@googlegroups.com] On Behalf Of John F Sowa
Sent: Tuesday, April 12, 2016 12:03 PM
To: ontolo...@googlegroups.com
Subject: Re: [ontolog-forum] RE: [Ontology Summit] Reference Ontologies in support of Semantic Interoperability
On 4/12/2016 11:46 AM, Bruce Schuman wrote:
> The word “algebra” is derived from the Arabic. I wonder how those
> ancient Babylonian mathematicians would view ontological studies of
> modern sunburst diagrams….
The scribes who used cuneiform had to learn some Sumerian, since its syllable-structures were based on Sumerian phonetics, which is very different from the Semitic phonetics of Akkadian, then Assyrian, and then Aramaic.
After the Persians conquered that region, they used the same scribes to communicate with the entire region in Aramaic, since it was then the lingua franca. But when Alexander conquered the Persians, he forced the scribes to use Greek. Kings, empires, and languages came and went, but the scribes had job security.
Re sunburst diagrams: They're useful for representing some kinds of structures. But the variety of useful diagrams is as open ended as the kinds of structures. In the orders of infinity, the set of points on a plane is uncountably infinite, but the set of curves
(diagrams) on a plane is the next higher infinity.
John
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