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Re: [ontology-summit] [Quality] What means "open" in "Open Ontology Repo

To: Ontology Summit 2008 <ontology-summit@xxxxxxxxxxxxxxxx>
From: Bill Bug <wbug@xxxxxxxxxxxxxx>
Date: Wed, 19 Mar 2008 10:16:56 -0400
Message-id: <1CAE9EA2-1006-4037-9BDD-812824E486E6@xxxxxxxxxxxxxx>
Sorry to add more to the thread, but I believe Rex is making an important point worth highlighting.  Some of what I say below builds on comments by others, including the post John Sowa has just made in response to Barry.

Rex makes the point:

On Mar 19, 2008, at 9:31 AM, Rex Brooks wrote:
Participation does not imply that everyone's contribution will be included in an open ontology

This - along with the statement "cooperative" - implies that an ontology, to meet these criteria, needs must have a "governing" body of some sort, probably also establish a developer role for the active, contributing participants, and then a means whereby the governing body can decide how to admit new "developers" to the group, which would likely include having that person agree to conform to a set of rules for participating developers.  Contributions would then be accepted by "developers" based on a vetting process that involves the participation of the collective of "developers" in part or whole.  This is in fact the process we've adopted in the development of the Ontology of Biomedical Investigation (OBI) - and to some extent, the Biomedical Informatics Research Network ontology, BIRNLex.

Given the level of work and complexity this implies, we certainly shouldn't expect all ontologies of value to an OOR will fully conform to such a process. This implies the need for participating OOR ontologies to provide some description of their level or means of coming into conformance with these desired requirements, so that users can judge for themselves, whether they can afford to commit to using a given ontology - essentially the suggestion by John and others that an OOR would need to focus specifically on tracking the metadata related to prior use and conformance to these recommended practices - 

On Mar 19, 2008, at 9:47 AM, John F. Sowa wrote:
... a repository ... (needs to) contain a large amount of metadata, among which would be records about who developed, used, revised, and extended it and the results that were obtained in various applications.

Ideally, there would even be an OOR review board that could use a coding scheme to evaluate these descriptions, so that the OOR repository could include some scoring metric as an aid to users.  An OOR review board would also be responsible for providing some advice/guidance on how to remediate issues that result in poor scores, based on existing examples of other OOR ontologies that have dealt better with the requirement at issue.  For example, I believe this is one of the intended activities for the OBO Foundry reviewers being assembled.

Building on John's point cited above, I'd then go back to my statement regarding the uses of ontologies - a very "thin" view for certain given the depth of experience of Ontolog participants.  Still, one could use a general list of use cases as a means of specifying how an ontology with a particular set of scores might fair when applied to that application domain (this is a non-trivial issue, but one where at least a limited amount of useful advice might be possible).  This would help potential users to determine - depending on their intended application (e.g., broadly scoped data annotation and federation/integration, tightly scoped decision support, NLP/Text Mining, e-Commerce data exchange, controlled UI design, etc.) and their potential participation as developers of an ontology based on their semantic domain coverage requirements (scope & granularity) - whether a given ontology would suit their purposes.


On Mar 19, 2008, at 9:31 AM, Rex Brooks wrote:
Hi Folks,

I thought the idea was to discuss these issues on the appropriate 
lists as much as possible so as the make the most effective use of 
our time together in conference. I certainly disapprove of hoarding 
our opinions until we get a chance to play tag with the floor on a 
concall that goes an hour or more beyond the time we have allotted 
for it. We have an active community here. The point is that we need 
to get our opinions out for examination before we have live 

I like i-v with the caveat that ii needs to be in a subversion-type 
environment with a clear decision-making process for what is included 
in the ontology, or else in some well-established and transparent 
process. Participation does not imply that everyone's contribution 
will be included in an open ontology. A transparent process only 
means that the public can view/listen/access the documents and 
recordings involved in the process.


Hi All,

I would strongly agree with Fabian's suggestion we table some of 
this discussion for the meeting.

Personally, I find i - v precisely what I'd hope to get from an 
"open" ontology repository (OOR) [with the exception that 
"virtually" in 'v' may lead to a lack of clarity], but I've no 
intension of dragging everyone over the coals of this long thread 
again, as many insightful points pro & con have been thoroughly 
presented.  As Matthew suggests, we all bring an agenda to the table 
that needs must color our sense of what would truly make an OOR more 
a valued resource than a hindrance to gaining wider acceptance and 
use for the ontologies it contains.

Many thanks for the concise and clear summary, Fabian.  :-)

Bill Bug

On Mar 17, 2008, at 1:19 PM, Fabian Neuhaus wrote:

Okay, let me try to summarize. Everybody, please let me know  if  I
misrepresented  your position.

We are discussing the scope of the OOR, thus the minimal requirements an
ontology has to meet.

Peter Yim and Ravi Sharma  suggest the following:
(i) the ontology is based on open standards AND
(ii) an ontology that is created and maintained in a cooperative process
that is, in principle, open to everybody who wants to participate AND
(iii) an ontology that is created and maintained in a transparent
process AND
(iv) the ontology is accessible to all who can be identified or
authenticated (at least Read only) AND
(v) the ontology is available under a license that includes virtually no
restrictions on the use and distribution of the ontology.

[I assume that a standard is considered to be "open" if and only if it
meets analogs of criteria (ii)-(v), FN]

Matthew West objects to (v).
Pat Hayes objects to (ii) and (iii).

It seems to me that this discussion won't be resolved easily. If nobody
objects, I will put it on the list of topics to be discussed on the
Ontological Summit during the "Quality and Gatekeeping" section.


Pat Hayes wrote:

At 12:09 AM +0000 3/15/08, 

Dear Pat,

 The first. Only the ISO has this absurd policy of
 charging cash for standards;

MW: There are others.

MW: But lets be precise about this. The problem has its
roots in ISO essentially seeing itself as a publishing house.
That at least is how it gets its income. The up side is that it
does not charge to participate in standards development. Try the
OMG charges if you want to see how much that can be, even if
their specs are free to users (or W3C for that matter).

I don't see why that matters, in the case of ontologies. The process
that gave rise to ontology is really not of any relevance: what
matters is the final product and the ability to use it. That is what
we should be focused upon.

MW: Now I think that ISO is outdated in thinking like this, and
many of us are trying to persuade them to change, but that is
still the current situation.

MW: Now, in ISO TC184/SC4 we have managed to get dispensation
to make all the computer interpretable stuff, i.e. what you need
to implement the standard. So suppose someone makes their
OWL ontology available free, but then publishes a book through
a publisher (who naturally charges for it) explaining its use.
How would you see that?

If the same source published the book and the ontology, and if the
book was the only 'manual' or documentation available, I think this
would be close to inadmissible, and certainly bad practice. The issue
here is not charging for the book, but withholding what should be
part of the openly accessible ontology itself.

How would that be different from what
ISO TC 184/SC4 does.

 moreover, I would
 not say that Matthew's interpretation of 'open'
 is universally accepted. The W3C is not open in
 this sense, for example.

MW: Indeed I would certainly NOT see W3C as open. This concerned
some enough that they moved to OASIS.

But the results of the W3C process are openly available to anyone
without any payment, which for standard adoption is surely the main
point. Agencies pay a membership fee to join the W3C, but that makes
sense to me: parties that are interested enough to want to influence
a standard for commercial reasons tend to be those that can easily
afford such membership fees. And the process is 'open' in the sense
of being conducted in public: all the email archives, minutes of
meetings. etc. are publicly available and archived.

Is the OOR supposed restricted to ontologies that are developed in an
open process and come with very light weight copyright

 licenses (e.g. *

*Creative Commons Attribution )?

 Certainly the latter. Lets take a stand on this.
 It does not eliminate ISO participation, but it
 does require them to make any relevant standards
 freely available. They can do this, and have done
 it in the past.

MW: Indeed, see above.

 Putting something into the OOR
 should make it automatically available for access
 and use without restriction; like the GNU
 licences, it should not permit other copyright
 restrictions to be 'passed through' its open

Or is OOR open for all ontologies that are developed in an

 open process

regardless of their copyright license?
Would the OOR be open for ontologies that are developed and


by a group of people who don't want to participate in an open process
but are willing to publish their ontology as a freely

 available resource

for the community?

 I have no problem with that part. We should
 permit ontologies that were constructed by one
 person in total privacy, or written on stone
 tablets by God, as long as they are freely
 available for public use without restriction.
 This is what 'open' means in 'open cyc', for

MW: I think the lack of an open process is a problem

Why? If someone writes a useful ontology, or one is developed by a
small team, what possible harm can there be in making this publicly

but I'm actually prepared to be more permissive.
For most of these issues above, I think the most
important thing is to be clear about what the
situation is. So there is a clear statement as to
- There is an open process for development
- How much do you have to pay to participate in that process?
- What is free, and what is not, and how much that is

MW: I do not suffer from the illusion that there are
no costs in developing an ontology. The only real
question is what is the business model?
- pay to join the development organization
- donate own time and resources to contribute
- sell services based on deliverables
- pay for deliverables
- ...

MW: In fact what I dislike most are the organizations
that charge for membership to participate in development.

Well, in defense of the W3C, it has managed to extract a quite
remarkable amount of participation from me without my paying a red
cent. On the other hand, I havn't been paid a red cent, either.


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William Bug, M.S., M.Phil.                                          

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Rex Brooks
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William Bug, M.S., M.Phil.                                          email: wbug@xxxxxxxxxxxxxx
Ontological Engineer work: (610) 457-0443
Biomedical Informatics Research Network (BIRN)
National Center for Microscopy & 
Imaging Research (NCMIR)
Dept. of Neuroscience, School of Medicine
University of California, San Diego
9500 Gilman Drive
La Jolla, CA 92093

Please note my email has recently changed

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