Apologies: The previous post from me with this
title was an unfinished version sent off prematurely by my email editor.
Please ignore and use this one instead.
-----------------------------
Hi Trevor - thanks very much for your comments
and comparative document - this is really useful, and we need to get much more
feedback like this.
The main difference between SDD and
Prometheus seems to be that you are working specifically on the basis of
defining a controlled terminology whereas SDD explicitly decided early on that
a controlled terminology was outside our scope. History will judge which
approach is best.
[Paterson, Trevor]
a controlled terminology was not such a large feature
of our work initially - we were more interested in the model
for saving 'character' data - however it became obvious that the only way to
allow unambiguous interpretation of data - for reuse, comparison etc -
was to provide full definitions. it then seemed desirable that people would
share definitions to allow compatability.......whether this will be achieved
by bottom up adoption is an open question. Taxonomists don seem to like the
idea of top down imposition - tho they may be happier when it is restricted
to quite a small domain of
users
We did have early discussions about a
controlled terminology (see the list archives for a history of this).One
dificulty for us is that SDD is designed to be biology-wide (indeed, we have
even removed specific references to biology, such as "taxon", because SDD is
equally applicable to descriptions of non-taxa such as diseases, nutrient
deficiency syndromes, soils and minerals. Perhaps here we have drawn our bow
too wide, but we were informed by the fact that at our Lisbon meeting all but
one of the contributors who were working with identification tools had removed
their biology-specific tags to become more general). Prometheus (as I
understand it from your document) is specifically botanical. This would be an
intolerable restriction for us given our brief.
[Paterson,
Trevor]
We are constrained by the expertise of whoever we are
collaborating with... the taxonomists at RBGE are full partners in this
project so the 'test domains' reflect their interests and expertise ( or we will never get real test data). We hope
that our character model will be applicable to the whole field of biological
taxonomy - - and that specific ontologies/terminologies could be
developed to allow description of other groups ( mammals, insects
etc)
Obviously, a botany-wide controlled
terminology is more achievable than a biology-wide one. Personally, however, I
think that you run the danger even in botany with any controlled terminology
of trying to force nature kicking and screaming into small boxes, and do it an
injustice therewith. I don't know how any botany-wide controlled terminology
could cope with the leaves of Drosera auriculata, for instance, or
the morphology of Podostemaceae. (In fact, I wonder whether the dream of a
controlled terminology is more likely in a cold Northern Hemisphere
climate than in the biodiverse South or tropics?).
[Paterson,
Trevor]
Yes - we know that diverse taxa would probably require
specific ontologies. We may be able to develope a system that allows a core
central terminology - with taxon specific extensions.....We want to allow
MEANINGFUL comparison of data - and often there is no need or sense in
comparing data across widely divergent taxa
ie you would might want to compare the properties of stalks on angiosperm
flowers, but it is probably of no taxonomic interest to compare these with the
stalks of a slime mould fruiting
body...............
In general, we have taken the view that a
controlled terminology in particular domains (e.g. legumes) may develop as an
emergent property of SDD, rather than imposed top-down.
[Paterson,
Trevor]
Yes - this is the working model we have come round
to...users develope an ontology and share it with colleagues in a closely
related field etc....
On more specific points from your
document:
Complexity: SDD was scoped to be
a superset of existing systems and standards e.g. DELTA, Lucid, DeltaAcess,
and also to accommodate future developments that those of us working in the
field can envisage but no-one's really done yet (particularly federation
issues - and you may be further down this track than we are). This is part of
the reason for the complexity,
>It is not clear to me whether SDD is proposing this schema as
>a unifying schema to which different description formats would
map their own schema
>or
>whether the SDD schema is being proposed as a schema for
developers to (partially) implement when designing applications
>and repositories for capturing descriptive
data.
It is designed as a unifying standard, to allow lossless
roundtripping between applications. At the same time, we are struggling with
how much should be mandatory and how much optional (your second
option)
>From our own collaborative experiences with botanical
taxonomists, data models and structures hold no interest to them in
>practice, and they find even our simple conceptual model of
character description complex to understand. Probably few working
>taxonomists would wish to interact at any level with the SDD
schema and applications would have to achieve this mapping
>transparently.
On this I'm sure you're right, and
we have had many discussions within SDD about this problem. There are
differing views as to the importance of taxonomists themselves coming to grips
with SDD, as the standard itself will generally be invisible
to a taxonomist using an SDD-compliant application.
[Paterson,
Trevor]
The problem is that someone has
to write and implement the applications ( e.g. me !) - and they have
to do this in collaboration with taxonomists - or it will be perceived as an
irrelevant imposition - -therefore it will always be necessary to get at least
some taxonomists from a variety of fields to understand
the schema...
From my perspective actually it
seems much easier for computer scientists to get to grips with taxonomy rather
than vice versa - ( although taxonmists would be a bit defensive about
this....)
Translation and multiple language
representations: allowing multiple languages is seen as a
fundamental part of the SDD brief. Life would indeed be much simpler if
everyone spoke the same language, but they don't so we need to handle that.
>It
is not clear whether SDD proposes that a single document can include multiple
language representations, or whether these
>would
form separate documents, conforming to the same
standard
SDD
can handle multiple language representations of every character string within
the one document.
[Paterson,
Trevor]
Still not convinced allowing
multiple language representations would mace for good/accurate
science
Multiple expertise
levels
>I am
similarly suspicious of the necessity for including the ability for recording
different expertise levels in one document format.
>Is SDD
proposing/allowing multiple representations within the same document : or just
that the same format/standard can be
>used for
documents aimed at different expertise level.
>
>There
clearly is value in being able to extract/translate simple language
descriptions from complex data resources - as is
>necessary
for compiling flora and keys from monographs and original descriptions.
However, is including the ability to describe
>descriptive data in language suitable for primary
schoolchildren relevant to an accurate scientific database of taxonomic data.
>[Again
this would appear to be a political requirement??]
This is not a political requirement, but an attempt to
broaden the application of taxonomy beyond taxonomists (surely a requirement
if the taxonomic crisis is to be resolved). It also derives neatly from
the XML underpinning (XML is based on the idea of multiple
representations of a single document)
[Paterson,
Trevor]
Yes I see
where you are coming from - i think the probelm is that taxonomists are
concerned about accurate representation of their data for their purposes -
making a shareable version of this is not perceived as of any value to
them - they want a scientific tool to do their job - i am not sure how /if we
could encourage a dual markup approach - or whether different 'markets'
for descriptive data would exist independently -
Defining the descriptive terminology
>Are you suggesting that the SDD
Terminology Section will be adequate and appropriate to store
>and represent any (allowed) defined
terminology?
Yes, we hope so. Do you think it will
be inadequate?
[Paterson,
Trevor]
It probably would be adequate to store Prometheus
terminologies - with minor tinkering, the
semantics of the terminolgies could be saved just with glossary entries and
relationships etc - but would obviously require interpetation by suitable
applications. I cant understand concept trees well enough to get a feel for
whether they could store the semantics of a terminolgy more
explicitly.....
However, that is not to say SDD could cope with
other terminolgies that might have further unforseen relationships -
there might need to be a facility for recording 'user defined' relationships
such as our stategroup membership and restrictions between these and sets of
structures - i think that these type of relationships are representable
in concept trees - but would need a primer/ turotial to show me
how.
>Is the standard going to allow
descriptions to reference other defined terminologies?
It will be possible to outsource the
terminology section, so if a group creates a controlled vocabulary, that
could be referenced in multiple SDD documents. So presumably Prometheus could
be the source of a controlled vocabulary that other users (of they found it
adequate) could reference.
>Would SDD only accept Data marked up in
an SDD terminology?
Yes - or do I misunderstand this
question?
[Paterson,
Trevor]
If i understand your previous remark - you could have completely
external termnologies - that SDD 'knows' nothing about the structure and
semantics - so it would have to accept 'non-SDD'
terminology
>Would existing terminologies have to be
translated/mapped/redescribed in SDD format?
Any existing terminology can be
represented in SDD, so there will be no remapping necessary.
[Paterson,
Trevor]
Again this will only be knowable if people try doing it.
Obviously if there is a standard structure people would be encouraged to use
it - but prexisting description ontologies ( eg PlantOnology and GeneOntology)
would not want to retrofit to the standard....even if there is no ' rdesign or
remapping necessary - there is the matter of re-expressing it in an SDD
format
>Who is going to create terminologies,
e.g.gusers on an adhoc basis, or expert user groups?
As above, these may develop
particularly for some groups (e.g. ferns, legumes), but some users may choose
to stay outside such a system (there will be benefits and costs of using a
controlled vocabulary, so people will have to weigh it up for themselves). SDD
itself is agnostic.
[Paterson,
Trevor]
Almost our opinion - but we are not agnostic - we believe
'interpretability' and 'reusability' are Gods, and we should proselytize on
their behalfs - gently of course - by offering only carrots and no
sticks...
>Is it an aim to promote re-use and
sharing of terminologies?
It would be a desirable outcome, but
we hope it evolves bottom-up rather than being imposed top-down.
[Paterson,
Trevor]
Sure
>Is there going to be policing of SDD
terminologies, e.g. maintaining versioning, additions etc?
Versioning will be handled within SDD, but
there can be no possibility of policing a system
[Paterson,
Trevor]
This what really worries the taxonomists - imposed standards
reducing the flexibility and expressivity of their descriptions - and
hatred of a police state. I think standardisation WILL be perceived to
lead to a loss of expressivity - but as often one person's expressivity is
another'; s incomprehensivity to an outsider this seems like potentially 'a
good thing' ( in small doses
obviously)........
>How was the terminology section created
- by examining examples of terminology specifications,
>ontology representations
etc?
We have had a mix of
off-the-top-of-the-head speculation as to how best to do things, and proofing
of concepts against real-world examples. I would have liked to see more
proofing going on during development, but this has been hard to maintain, and
may be to our cost. We are nbow at a phase where several groups are trting to
implement SDD-compliance for their systems - this will be the proof of the
pudding.
Note also that SDD is currently v0.9 - with
the explicit statement on release that everything may change if we find that
the proofing fails.
>Does it form a standard template for
storing a terminology?
What do you mean by this. It provides the
standard schema for representing an (undefined)
terminology.
>Is it compatible with any existing
tools, standards or formats - e.g. ontology editors?
We have specifically made it very
general. There is currently no existing tool that can handle SDD. Hopefull
this will change shortly.
[Paterson,
Trevor]
Keep me posted
----------------------------------
So does Prometheus have any data yet,
or is it still at the model stage? It would be very interesting to try
representing Prometheus data in SDD.
[Paterson, Trevor] to date we
have
-
the model ( and a data base implementation to save
model compliant data)
-
a tool for creating simple terminologies -
with definitions, PartOf, Typeof, Stategroup relations
etc
-
a prototype angiosperm
terminology/ontology
-
a prototype tool for using onologies to specify
project description templates (
proformas)
-
which also allows recordng of specimen
descriptions
-
the ability to save these descriptions to the
database in the model compliant
format
and we are currently getting user testing done on the
prototype by the taxonomists, who are making proformas adn saving specimen
descriptions. We are just about ready to use the tool for a 'real' project if
we can get time and interest to do this...eg for a small taxonomic revision.
We are rapidly approaching the end of our project funding however.. so it may
switch to being a 'back burner' project....
Cheers - k
----- Original Message -----
Sent: Monday, March 15, 2004 9:41
PM
Subject: SDD Schema in relationship to
Prometheus
Gregor
I have written a
rough document considering several aspects of the SDD-schema - largely
interpreted with reference to our Prometheus Database model for descriptive
data. It seems easier to keep this all together, rather than post it to
various sections on twiki, so i am attaching it here
My main problems
in interpreting the schema were the lack of documentation ( as always...)
especially for the conceptually complex parts like concept trees. I think
clear, visual summary models for description, characters, concept
trees etc would help a novice to get to grips with the concepts, and might
make some of the complexities more tractable. I do worry that the overall
schema is over complex and 'trying to do too much in one go' - eg
considering multiple language and expertise representations, although I am
sure that there are good political reasons for
everything.....
yours
trevor
Trevor Paterson PhD
t.paterson@napier.ac.uk
School of Computing
Napier University
Merchiston
Campus
10 Colinton
Road
Edinburgh
Scotland
EH10 5DT
tel:
+44 (0)131 455-2752
www.dcs.napier.ac.uk/~cs175
www.prometheusdb.org