This paper defends a view of the Gene Ontology (GO) and of Basic Formal Ontology (BFO) as examples of what the manufacturing industry calls product-service systems. This means that they are products bundled with a range of ontology services such as updates, training, help desk, and permanent identifiers. The paper argues that GO and BFO are contrasted in this respect with DOLCE, which approximates more closely to a scientific theory or a scientific publication. The paper provides a detailed overview of ontology services and concludes with a discussion of some implications of the product-service system approach for the understanding of the nature of applied ontology. Ontology developer communities are compared in this respect with developers of scientific theories and of standards (such as W3C). For each of these we can ask: what kinds of products do they develop and what kinds of services do they provide for the users of these products?
The success of an ontology can be measured using a range of
metrics, including number and variety of associated software
applications; quantities of data and literature annotated using
terms from the ontology; and number, size and degree of
utilization of major databases incorporating terms from the
ontology. By any of these metrics, the Gene Ontology (GO) (
These principles can, I believe, help us to account for the remarkable success of the GO, which still, after 20 years, continues on its upward trajectory as concerns numbers of users and applications, and scientific influence and utility.
The most important of the Ashburner-Lewis principles for our purposes here are: Before you start building an ontology learn what is out
there. Assess extant ontologies critically and realistically. Do not reinvent. Start building – but not in isolation. Collaborate. The computable representation must be shared. Ontology
development is inherently collaborative. Ensure that there is access to help. Does a warm body answer help email within a reasonable time (say 2 working days)? Every ontology improves when it is applied to actual
instances of data. There will be fewer problems in the ontology and more commitment to fixing remaining problems when important research data is involved that scientists depend upon.
The basic thesis underlying these principles is that an ontology becomes more valuable to the extent that it is aggressively used.
Ashburner and his associates accordingly devised a multipronged strategy designed to maximize GO usage, including: 1. developing a simple ontology editing tool (called OBO
Edit) designed to suit the needs of biologists (
domain
3. making the results of using the GO in annotating biological
literature and data easy to find, by creating the GO
Annotation (GOA) database (
identifiers and repositories for ontology content (
Ontologies) Foundry at http://obofoundry.org. 10. ensuring an effective modular architecture for these ontologies, including providing each ontology with a name (such as “Cell Ontology”, “Protein Ontology”) that would make it easily findable by new users 11. ensuring an effective division of labor by devising procedures to support resolution of overlaps between ontology modules and an editorial process that allows each OBO ontology to be managed by scientists with corresponding subject-matter expertise 12. contributing to the development of ontology software (for
example ROBOT (
certainty for users and reusers of the ontologies.
This strategy has yielded (and continues to yield) a positive snowball effect whereby, when one community encounters gaps or errors when using the GO or one of its sister ontologies, these gaps and errors are rapidly fixed. This increases the value of the ontology, thereby making it attractive to further users, who in turn identify further gaps and errors thereby initiating a new cycle of improvement. Such fixes occur in a way that preserves the integrity of the GO as a resource on which existing and future users can rely as it develops over time and addresses new sets of user needs.
While the role played by ontology services is familiar to all ontology practitioners, such services have not thus far been an explicit topic of theoretical reflection. In the advanced manufacturing industries, in contrast, a set of parallel developments has engendered a new organizational paradigm with considerable impact both practically and theoretically.
The term ‘product-service system’ was introduced in the early
2000s, when producers of, for instance, aircraft engines or
photocopying machines had been experimenting with new business
models focused on the marketing of bundled services.
On one model, GE does not sell engines. Rather it charges for
the use of its engines per hour of flying time. As pointed out in
(
to develop sophisticated algorithms for predicting likely sources of
future engine failure and the optimal time to service the engine to
prevent such failures. The more data and experience GE
accumulates, the better these algorithms become, and the more effective GE
will become in delivering these services. (
The business model underlying the activities of GE, as well as – somewhat later – IBM, Microsoft, Adobe, is that each of these organizations wants to provide services. They are, in effect, using the products that they create as delivery mechanisms for services. This model contributes to a move away from the throw-away approach characteristic of manufacturing in the second half of the 20th century, to a situation in which one product is maintained in active use for as long as possible and is continually updated to ensure a maximally productive life.
requires a higher level of customer involvement and education by producers. For producers and service providers, product-service systems mean a higher degree of responsibility for the product’s full life cycle, the early involvement of consumers in the design of the product-service system, and design of the closed-loop system. A product-service system is thus not simply the result of associating products with services. Rather, it constitutes an architecture where artifacts and processes are deliberately designed in such a way that they fit together in a single system, which may involve multiple enterprises and multiple user communities joined together in complex networks.
In an interesting parallel to such developments in the advanced
manufacturing and commercial software industries, we can now
see that the GO developer community has been providing the
Gene Ontology to its users as a (free) product bundled with a
range of user services. This reflects the fact that the incentives
of the GO developers were from the very beginning aligned
with the incentives of its users. Indeed, many of these users
formed part of the very same GO Consortium that was
responsible for developing and maintaining the ontology itself.
From the very beginning the GO pursued a strategy of assisting
its users in solving the problems that arise, for example, when
a new release of the ontology involves changes that might
disrupt existing workflows, or when new scientific results or new
sorts of data arise which need to be accommodated within the
GO and GOA frameworks. Both GO developers and GO users
want to minimize the amount of downtime of the ontology of
the sort that would arise, for instance, if the GO failed to correct
errors or to provide terms relating to newly discovered
biological phenomena in a reliable manner and with a rapid turnaround
time. The GO has helped its users also by developing software,
such as the AmiGO browser (
The creation of the UniProt and other databases (
BFO was created to serve as the top-level ontology of the OBO
Foundry, and its three principal categories, of (i) independent
and (ii) dependent continuants and (iii) occurrents, correspond
to the three Gene Ontology modules for Cellular Component,
Molecular Function, and Biological Process, respectively (
The BFO developer community provides these services as a
reflection of its conviction that an ontology benefits when it has
a user community that is both large and diverse. Many of the
services are provided through the OBO Foundry (of which BFO
forms a part). However, there are now significant numbers of
BFO-compliant ontologies outside the domain of the life
sciences (
The BFO product consists of the ontology itself, in both
formalized and natural language versions, which is presented to its
users as a domain-neutral starting point for ontology creation in a
way that brings the advantage of having been employed as TLO
in many peer ontology initiatives with a correspondingly broad
cohort of experts in BFO-based ontology development.
Services provided by the BFO developer community and its
collaborators include:
helping such users
- to formulate definitions (
There are a number of items which could be added to this list as
desiderata, including targeted software tools for checking the
BFO compliance of a domain ontology and also tools to assist
in the creation of BFO-conformant ontologies following the
proposals sketched in (
One service that is indispensable to those who need to use an
ontology over long periods of time is a traceable revision
history. This enables annotations of data to be kept up to date as
the ontology used in these annotations changes. For this
purpose it must be possible to establish the present meanings of
annotations created at an earlier date and using an earlier
version of the ontology. Like the GO, BFO has a traceable history
of this sort, and it has provided guidance to users of successive
versions both to support consistency of use from one version to
the next and also to provide the rationale for specific changes
(
Given the large number of ontology development groups using
BFO as their common top level, it is important that updates
involve minimal disruption and that they are carefully managed
in such a way that they do not disrupt existing workflows.
Often, issues can be resolved without any necessary change in the
ontology itself, for example through additional commentary on
the release document, or through associated changes in an
extension ontology such as the IAO (
The consequences of proposed changes in BFO are thoroughly evaluated before these changes are incorporated in the next public release. If such changes affect, for example, the ways English-language definitions are formulated, the BFO developers are careful to ensure that terms and relational expressions refer persistently from one version to the next and that examples of usage provided in earlier versions continue to be applicable in later versions.
Some 300 domain ontologies have been built using BFO as top
level (
Most recently, the Allotrope Foundation (
NSF Center for e-Design and the Realization of Engineered
Products and Systems (
In March 2019, BFO was selected, after an extensive review
process managed by the National Institute of Standards and
Technology (NIST), to serve as top-level ontology of the
Industrial Ontologies Foundry (IOF) suite (
Finally, in the military and intelligence domains, BFO is being
used above all through the Common Core Ontology (CCO)
suite (
BFO and ISO/IEC 21838
A further type of service that can be of value in almost any area
of organized human activity is the establishment of standards.
The International Standards Organization was founded on the
idea of answering the question: what’s the best way of doing
this? (
Standard terminologies can promote more effective communication; electrotechnical standards can promote interoperability of hardware and software. They can promote improved understandability of third‐party content formulated in accordance with the standard, allow new sorts of quality measures to be developed and applied, and promote transportability of expertise.
- Common Logic (CL, ISO/IEC 24707:2018) (
Compliance to the ISO rules for the formulation of definitions
required also a number of improvements in the treatment of
natural language definitions of terms and relational expressions in
BFO 2 (
a collection of terms, relational expressions and associated
naturallanguage definitions together with one or more formal theories
designed to capture the intended interpretations of these definitions.
Part of the goal of this definition is to take account of the fact
that an ontology – for example the Gene Ontology, or BFO –
can exist in multiple successive versions and yet remain one and
the same ontology. One solution to this problem views the
ontology as a document, analogous for example to a textbook, that
exists in several successive editions (
Top-level ontologies deal with categories, which are general classes or types represented by domain-neutral terms such as ‘object’ or ‘process’.
On this basis ISO/IEC 21838-1 defines a top-level ontology as an ontology that deals with categories shared across a maximally broad range of domains.
The standard must then provide a procedure for determining whether a candidate TLO satisfies this definition. To meet this need, Part 1 of the standard provides a list of types of entities ranging from entities relating to time, space and spacetime, to change and process; qualities and quantities; material and informational artefacts, and so forth. That an ontology O succeeds in covering a ‘maximally broad range’ is shown by providing documentation demonstrating that, given a type or class of entity of one or other of the listed sorts, either (i) there exists a corresponding parent (or ancestor) term for this type of entity in O itself, or (ii) a definition of this class of entity can be created through logical combination (for example disjunction) of terms from O representing types or classes satisfying (i).
ISO/IEC 21838-1 therefore does not require that the TLO contains detailed treatments of entities under all the mentioned headings. Thus, for example it is sufficient if it is possible to point to some extension ontology which serves this purpose, and which establishes the needed chain of subtype relations to some term or terms in the TLO. Thus, for example there are no terms for information artifacts in BFO – thus no terms for data, signs, symbols, software, and so on. However, many terms in this family are provided in the Common Core Ontology suite (CCO) and in the Information Artifact Ontology (IAO), which provide definitions of the mentioned terms as representing subtypes or subclasses of BFO:generically dependent continuant.
As Guarino himself outlines in (
BFO and DOLCE differ also with respect to the issue of
ontological realism (
The reason for using such benchmarks as the basis for creating ontologies is (simplifying considerably) to arrive at a situation in which there will be just one authoritative ontology for each domain of reality. This goal can be achieved only if we can persuade ontology developers to accept certain shared constraints on how they build ontologies and for this we need to employ a strategy that does not endanger, for example, the flexibility that is needed to keep pace with scientific advance. The OBO Foundry has been at least partially successful in meeting these conditions, and in ways that essentially involve the use of BFO.
In 2008, I defended the proposition that ontologies like the GO,
which are created to support the retrieval, integration and
analysis of scientific data, are a part of science (
A counterpart view, as applied to a top-level ontology such as BFO, would see the latter as providing terminological resources at a more general level, which is to say, above the level of the specific sciences. This is to enable domain ontologies at lower levels to be linked together. What subject-matter experts in, for example, molecular biology or clinical medicine will see are terms in GO, or in some clinical ontology such as SNOMED CT. BFO will remain invisible.
Certain requirements must be satisfied, however, If an ontology
is to serve as “terminological scaffolding” of a scientific theory
or of some counterpart thereof for example in the field of
manufacturing industry (
Above all, it will require provision of services of the sort that will give users confidence that the ontology will be reliably disseminated and maintained, and will continue to offer needed serviced, in the future. Only thus can we overcome a range of familiar obstacles standing in the way of adoption of an ontology by new users, captured in complaints for example to the effect that this or that ontology “was not being kept up to date”; that it “was not clear to me how the ontology would fit my particular data”; that it “would not be able to incorporate the terms I needed in time for my funding deadline”; or that “I did not have the confidence that the ontology will still be supported when I need it in the future”. Too often, potential new users of an existing ontology are motivated to build ontologies of their own, resulting almost always in ad hoc contrivances with a very short half-life.
The views of the developers of DOLCE on the topic of
ontological realism are formulated as follows:
the aim of DOLCE is to capture the intuitive and cognitive bias
underlying common-sense … DOLCE does not commit to a strong
referentialist metaphysics (it does not make claims on the intrinsic
nature of the world) and does not take a scientific perspective (it is not
an ontology of, say, physics or of social sciences). Rather, it looks
at reality from the mesoscopic and conceptual level aiming at a
formal description of a particular, yet fairly natural, conceptualization
of the world. (
A more charitable, and I believe more adequate, view of
DOLCE, however, sees it as a scientific ontology of human
common sense, with needed benchmarks provided, for
example, by linguistics, perceptual psychology and action theory.
DOLCE can in this way be viewed as a contribution to science,
that has served as inspiration for the development of many new
ontologies, both domain ontologies based on DOLCE in its
FOL version, as well as spin-offs from DOLCE, such as the
Unified Foundational Ontology (
In support of a view of this sort is the remarkable degree to
which DOLCE (FOL) has remained stable across its entire
history, reflecting the degree to which human common sense, too,
has also – for reasons relating to the evolutionary survival of
the species – manifested little change over long periods. (
In the matter of update history, now, BFO lies somewhere
intermediate between DOLCE (FOL) on the one hand and
DOLCE (OWL) on the other. For BFO has been maintained as
one thing through a series of updates over time motivated by
the experiences of its users. The one “version” of DOLCE, in
contrast, has been without update for some 17 years, which
means that it has been unaffected by the changes in the field of
ontology around it. Thus while DOLCE provided the
ontological foundations for important work in a series of multi-partner
projects (
The domain ontology contributions created on the basis of
DOLCE thus survive largely as fragments, documented in
scientific papers, rather than as ontological going concerns.
In sum, the various domain ontologies built around the official
DOLCE have not been provided with the services needed to
make the domain ontologies defined in its terms work well
together in a sustainable, publicly accessible way. Matters are
somewhat different in the case of DOLCE in its OWL
formalizations, which have a richer history of usage than the FOL
version of DOLCE. This is in part because most users of ontologies
work with OWL rather than FOL. But it is in part also because
of differences in management policy, reflected in the multiple
sorts of user assistance documented for example at (
Conclusion
and, it is sometimes said, there are scientific interdisciplines
(
Let us therefore assume that ontology itself is an interdiscipline. What is to be said now of each single ontology? Is there some single type or class whose instances are the GO, and BFO, and IAO, and UFO, and DOLCE, and DOLCE+DnS Ultralite v. 3.31? Or do we rather need something like an ontology of ontologies that would have no single root?
rested on what I think is a novel view of ontology developer teams as analogous to business enterprises.
The latter, as we have seen, have as their outputs both products and services, more or less closely bundled together. Products are of two sorts: material products such as laptops and servers; and digital products such as Adobe Acrobat. Some enterprises – such as business consultants – produce no products at all but only services. Some enterprises product products – such as IBM’s Watson – but they give them away free, and provide services to support their use.
I conclude merely by noting that this perspective can be applied not only to teams of ontology developers. Standards organizations, too, can be viewed under this heading, given that NIST, CEN, ASME, ISO, IEC, W3C and even HL7 are both production systems, producing standards, and service systems, providing support for the users of these standards.
And communities of scientists, too, can be viewed as providing product-service systems, containing both production elements – producing scientific results, publications – and service elements, for example training each new cohort of scientists.