Hi Roger,

Supporting many representation formats would be really cool, but I have doubts as to whether the benefit of such a system will outweigh the costs.

The initial goal behind modular schemata was that, if we had them, we could build a network of data providers and consumers that could carry any type of data (type independence). In essence we would build a data network that would allow anyone to talk about anything. This by itself is not an easy thing to do.

Then the issue of representation language cropped up; first XML or RDF and now different types of XML, different RDF ontology languages, microformats, and semantic tags (why not JSON, SQL tables, serialized Java objects, C structs, and any other representation people might want). To resolve this issue without restricting representation language requires a huge increase in the scope of work; not only type independence, but independence of representation; building a data network that allows anyone to talk about anything in any language.

On the one hand you're absolutely right that such a system, if we could build it, might work as a bridge between different technologies. But I worry that it will be a massively difficult and expensive undertaking that might not ever work. I'll list a few of my concerns.

The first is whether or not it will support automatic translation:

1.) If the system does not do automatic translation between representation languages, then it's more like a schema repository. In my view, schema repositories don't help to integrate tools that use different representation languages. Instead each representation language becomes a silo. The schema repository helps to document what has to be done when people need to write code that will cut across silos for a one-time task, but it doesn't actually encourage people to do so.

2.) If the system does automatic translation between representations then it adds a layer of complexity and a large processing and transport cost to each transaction on the network. Imagine that you want to do some niche modeling. Assume you have some taxonomic group in mind. First you'd have to find the names for this group, including synonyms. Next you'd have to get specimens and observations for these names. So, two large sets of transactions are necessary to acquire the data you need. Each name and observation provider might be using a different representation language. When you contact them you have to figure out what representation they've given you and ship the data off to a translation service before you can merge the results. This adds a large (at best linear) cost to acquiring data. Additionally, someone has to pay for the huge amount of bandwidth used by the translation service. We can propose to use a local library instead of a remote service to do the translation, but this adds a burden on the developers of all software, requires that the library is updated often as new types and representation languages are adopted, and requires that the library exists or has bindings to many programming languages; in short this is a software maintenance nightmare.

My second set of concerns are about the representations themselves:

3.) Each representation will require some effort to construct and maintain. If the system will provide guidelines (rules expressed in natural language) for how to translate each representation into other representations, the cost (in effort, time, and money) will increase. If the system will provide automatic translation, the cost will increase further. However, not all representations will be used equally. If there are only two people who want TCS in format X, then is it worth the expense of providing it to them? Who decides whether or not a particular representation format has enough demand to justify the work involved in supporting it?

4.) If the goal is to provide guidelines or automatic services for translation between representations of a given data type, then we have to map X * X-1 * Y possible translations where X is the number of allowed representations for a given data type and Y is the number of data types. The TDWG biodiversity informatics ontology may end up with 30 classes. If we support 5 representations (maybe OWL, RDFS, semantic tags, XML metadata, and GML Feature Types) that's 5 * 4 * 30 = 600 possible translation mappings to create and maintain. Each time we have a new representation or a new data type we have to update the set of translation mappings.

My final set of concerns regards knowledge representation, modeling, and the expressive power of representation languages:

5.) Different representation languages have different language features and expressive powers. For instance, there are things you can do with OWL that you can't do with semantic tags. This is because OWL has language features for representing inheritance, property-value constraints, etc. that simply don't exist in the world of semantic tagging. If we have to be able to represent the platonic ideal of our data types (as defined in the TDWG ontology) in any representation language and also have to be able to translate between representations, we run into a dilemma.

If we use all the features of a particular representation language we benefit from them when using that particular format. The software that is constructed to natively consume that representation can use all of the available language features to automate tasks on behalf of the user. However, translation becomes very difficult. Imaging translating OWL-style inheritance into microformats or XML-Schema data type constraints into a system of semantic tags. It's simply not possible. Translating between languages of differing expressive powers can be problematic. The alternative approach is to use only those language features that are common to all representation languages. In practice this usually means using only those features that exist in the most weakly-expressive language. If our bag of representation languages includes both semantic tagging and OWL, then we're not really using the power of OWL. In fact, if we have to use only the common features of the two, we might as well implement our OWL ontology so that there is only one type of class with a single property called "tagvalue".

6.) Different representation languages enable different functionality in the software that consumes them. For instance, client software that consumes RDFS or OWL instances often expand searches to encompass instances of superclasses. In other words, software designed to use semantic web technologies can do some of the work a human user might otherwise have to do by exploiting the features of semantic web languages. Software designed to use semantic tags often doesn't do much more than search and statistical correlation between tag instances. This is quite powerful in it's own way, but because semantic tags were designed to indicate the context of a document, not necessarily its contents, semantic tagging really only helps a user to locate documents of interest. A document with tags is ultimately read by a human, not a machine. Every representation language carries with it assumptions about how "documents" that are instances of that language will be used.

To navigate you need a fixed point. To move the world you need a fulcrum. Because representation languages provide different features and make different assumptions about how their instances will be used, it makes sense to use representation language as the fixed point of our designs and leave data types and service interfaces free to vary. Some have argued that the TDWG ontology is the fixed point in our constellation of services, but I disagree. It is the umbrella under which data integration will occur; there will always be extensions to the core ontology and it too will change over time as it is expanded.

Overall I think it's a laudable goal to support as many representation languages as possible, but there are so many headaches and compromises involved that we may end up with an expensive solution that, because it only supports the lowest common denominator of functionality, doesn't really work right for anybody. A case in point is the current discussion of namespaces. In order to make namespaces work across the widest range of representation languages, it's been proposed that they can no longer be used as packages to logically partition the larger ontology. This makes it harder to manage extensions to the ontology and makes it likely that we'll end up using veryLongClassAndPropertyNamesToTryToAvoidNamespaceClashes. And you still can't represent namespaces in semantic tags.

It's hard enough to write software that can cope with any data type and I'd rather spend energy, time, and money on getting it right with only one or two feature-rich representations. What I'd really like to see is a network of heterogeneously typed, highly integrated data objects and a rich set of services that operate on them. Once this is built, the real fun can begin, creating software that uses these data to answer important scientific questions.

-Steve

Roger Hyam wrote:

Thanks for forwarding this Sally.

What I am proposing at St Louis - though I seem to been having to propose it long before - is that we have an application for managing the ontology that will expose the underlying semantics in multiple 'formats' i.e. as RDFS or OWL ontologies as GML application schemas, as custom XML Schemas as OBO ontologies etc etc. I see no other way of integrating multiple technologies. (Suggested alternatives welcome).

One of the things on my list is micro formats along with tagging. It seems crazy to define a 'specificEpithet' in a TDWG ontology and then not use exactly the same concept in a micro format or as a tag.

So this is timely. I just can't act on it very well before St Louis. I'll add something to the wiki page to flag my/our interest.

Thanks,

Roger

Sally Hinchcliffe wrote:

...

Hi all

This is probably on the wrong list (Maybe TAG?) but it strikes me that what this guy needs is an ontology that he can use in his microformats ...

Possibly an example of a real world need for ontologies ?

Sally

------- Forwarded message follows ------- Date sent: Tue, 26 Sep 2006 09:34:04 -0000 To: sh00kg@rbgkew.org.uk Subject: Fwd: [TDWG] Announce: Proposal for "microformat" for marking-up taxonomic names in HTML: comments and contributions sought From: M.Jackson@kew.org Send reply to: M.Jackson@rbgkew.org.uk

Sally,

Do you think you might respond to this? Just curious what you think.

Mark

Forwarded From: Andy Mabbett andy@pigsonthewing.org.uk

...

Hello - my first post to this mailing list.

I'm not a taxonomist, but I've been told by one that you might be interested in recent proposals for a formula (a "microformat" http://microformats.org) for marking-up, in HTML, the names of species (and other ranks, varieties, hybrids, etc.).

Microformats are a way of adding additional, simple markup to human-readable data items on web pages, using common and open HTML standards, so that the information can be extracted by software and indexed, searched for, saved, cross-referenced or aggregated. Microformats are also open standards, freely available for anyone to use.

The proposed format respects all existing biological taxonomies, and is not intended to change or supplant any of them - it merely provides webmasters with a method of either:

1. marking-up a taxonomical name (or taxon-common name pair) in such a way that its components can be recognised by computers

or

2. marking up a common name, so as to associative with it a taxonomical name, in such a way that the latter's components

can be recognised by computers

For instance, if I mark up a list of common names on a page I maintain:

http://www.westmidlandbirdclub.com/staffs/tittesworth/latest.htm

using that microformat, a visitor might have browser tool which lists all the species on the page, sorted into alphabetical order within taxonomic class, or in taxonomic order, and then creates links to, say (for Joe Public) their entries in Wikipedia, or the British Trust for Ornithology, or (for scientists) some academic database of the users choosing.

Early thoughts on the format are on an editable "wiki", here:

    <http://microformats.org/wiki/species>

Please feel free to participate - the proposal needs both messages of support (particularly from people or organisations who have websites on which they might use them) and, especially, comments and constructive criticisms - does the proposal understand and use taxonomy correctly; is the terminology right, are there any omissions or overlooked, unusual naming conventions?

You can use the above wiki, or the microformats mailing list:

    <http://microformats.org/wiki/mailing-lists>

and/ or please feel free to pass this e-mail to other interested parties.

Thank you.

-- Andy Mabbett Birmingham, England

---

TDWG mailing list TDWG@mailman.nhm.ku.edu http://mailman.nhm.ku.edu/mailman/listinfo/tdwg

---

---

TDWG-GUID mailing list TDWG-GUID@mailman.nhm.ku.edu http://mailman.nhm.ku.edu/mailman/listinfo/tdwg-guid

People can use OWL or GML or TAPIR or ... but which do the clients actually want to use? It would be a lot easier if we only used one. A few client applications would certainly clarify things.

I know this won't surprise regular readers, but if any client is thinking of using more than one data source, is there anything as simple and as general as RDF? I spend most of my time mangling all sorts of weird stuff (Darwin Core in all its variants, Google Earth KML, CrossRef XML, PubMed XML, Genbank XML, HTML, Yahoo Images XML, etc., much of it all nicely defined with - gack - XML schemas, that of course I don't actually read) into RDF so I can actually do something.

Within a single domain people can pretty much do what they like (and have done so), but once we start sharing and aggregating (e.g., specimens, images, sequences, publications, observations, people) then why not aim for one data format and a few simple, shared vocabularies.

I'm sure this is naive, but it seems that we persist in making things just about as difficult as we possibly can.

Rod

------------------------------------------------------------------------ ---------------------------------------- Professor Roderic D. M. Page Editor, Systematic Biology DEEB, IBLS Graham Kerr Building University of Glasgow Glasgow G12 8QP United Kingdom

Phone: +44 141 330 4778 Fax: +44 141 330 2792 email: r.page@bio.gla.ac.uk web: http://taxonomy.zoology.gla.ac.uk/rod/rod.html iChat: aim://rodpage1962 reprints: http://taxonomy.zoology.gla.ac.uk/rod/pubs.html

Subscribe to Systematic Biology through the Society of Systematic Biologists Website: http://systematicbiology.org Search for taxon names: http://darwin.zoology.gla.ac.uk/~rpage/portal/ Find out what we know about a species: http://ispecies.org Rod's rants on phyloinformatics: http://iphylo.blogspot.com Rod's rants on ants: http://semant.blogspot.com

Has anyone asked/responded to Andy Mabbet (the guy who proposed the microformat in the first place)? He might have an opinion Sally

Hi Steve,

Great posting. I agree just about 100%. The only point I disagree on is whether it is possible to develop a metamodel that is expressive enough to be useful but simple enough to be mapped into multiple languages. This is for two reasons:

1. The metamodel does not have to define application logic it is only

for supplying meaning.

There is a split between denotation and connotation in formal logic. The ontology is to enable people to denote that something is, for example, a specific epithet. It does not have to define (connote) what a specific epithet IS so that people can test things against the ontology.

The example I gave in an earlier posting to the TAG was of cardinality. Everyone has a mother so the semantics of the Person.hasMother property should be 1. This is useless from a application logic point of view. No Person instance could be exchanged without first defining another instance to act as the person's mother. Every ontology containing instances of Person would be invalid. (We could create a subclass of Person called Eve that has a constraint on hasMother - but that is just getting silly) From an application perspective hasMother should have a cardinality of 0 or more - which is semantically nonsense because we all have at least one mother. The Person class doesn't have to have a mother but then we are talking about the semantics of the class not the person... For this reason I would argue that cardinality should not be in the metamodel. It adds nothing to the meaning of the property but is very useful for application logic.

The purpose of the network is to allow transfer of data between heterogeneous applications which by definition have different application logic and therefore different notions of validity. Individual applications therefore have to have their own ontologies that import the general shared ontology. Your application may say hasMother has cardinality of 0 or 1 but it is not a general truism of all applications. The social services application has 0 to many because it handles birth mothers, adoptive mothers and foster mothers.

This does not negate the need to produce shared application logic. Herbaria may well need their own ontologies to constrain the data they share but why should climate prediction models constrain data in exactly the same way? A field recording application may allow the specific epithet field to contain punctuation (such as a question mark) but a taxonomic revision application may prevent it. If we have to agree on whether punctuation is permitted in a specific epithet field we will never benefit from the fact that both applications agree there is such a thing as a specific epithet field.

2. Not all mappings have to be totally expressive.

If some one is going to come up with a way of tagging a span element in HTML as being a specific epithet it would be convenient if they used something that could be mapped back to the vocabulary used to describe TaxonNames in LSID metadata. This does not mean that the tagging system has to support hierarchies.

---

I don't think the ontology should provide data transformation services. I think primarily it will make it possible for providers to make data available in multiple formats (using PyWrapper and Wasabi). Whether this is worth the bother is up to the clients who use the data - and we don't have enough of them to make a decision.

People can use OWL or GML or TAPIR or ... but which do the *clients *actually want to use? It would be a lot easier if we only used one. A few client applications would certainly clarify things.

If some one has an alternative approach I would certainly like to hear it!

All the best,

Roger

Steve Perry wrote:

...

Hi Roger,

Supporting many representation formats would be really cool, but I have doubts as to whether the benefit of such a system will outweigh the costs. The initial goal behind modular schemata was that, if we had them, we could build a network of data providers and consumers that could carry any type of data (type independence). In essence we would build a data network that would allow anyone to talk about anything. This by itself is not an easy thing to do. Then the issue of representation language cropped up; first XML or RDF and now different types of XML, different RDF ontology languages, microformats, and semantic tags (why not JSON, SQL tables, serialized Java objects, C structs, and any other representation people might want). To resolve this issue without restricting representation language requires a huge increase in the scope of work; not only type independence, but independence of representation; building a data network that allows anyone to talk about anything in any language.

On the one hand you're absolutely right that such a system, if we could build it, might work as a bridge between different technologies. But I worry that it will be a massively difficult and expensive undertaking that might not ever work. I'll list a few of my concerns.

The first is whether or not it will support automatic translation:

1.) If the system does not do automatic translation between representation languages, then it's more like a schema repository. In my view, schema repositories don't help to integrate tools that use different representation languages. Instead each representation language becomes a silo. The schema repository helps to document what has to be done when people need to write code that will cut across silos for a one-time task, but it doesn't actually encourage people to do so.

2.) If the system does automatic translation between representations then it adds a layer of complexity and a large processing and transport cost to each transaction on the network. Imagine that you want to do some niche modeling. Assume you have some taxonomic group in mind. First you'd have to find the names for this group, including synonyms. Next you'd have to get specimens and observations for these names. So, two large sets of transactions are necessary to acquire the data you need. Each name and observation provider might be using a different representation language. When you contact them you have to figure out what representation they've given you and ship the data off to a translation service before you can merge the results. This adds a large (at best linear) cost to acquiring data. Additionally, someone has to pay for the huge amount of bandwidth used by the translation service. We can propose to use a local library instead of a remote service to do the translation, but this adds a burden on the developers of all software, requires that the library is updated often as new types and representation languages are adopted, and requires that the library exists or has bindings to many programming languages; in short this is a software maintenance nightmare.

My second set of concerns are about the representations themselves:

3.) Each representation will require some effort to construct and maintain. If the system will provide guidelines (rules expressed in natural language) for how to translate each representation into other representations, the cost (in effort, time, and money) will increase. If the system will provide automatic translation, the cost will increase further. However, not all representations will be used equally. If there are only two people who want TCS in format X, then is it worth the expense of providing it to them? Who decides whether or not a particular representation format has enough demand to justify the work involved in supporting it?

4.) If the goal is to provide guidelines or automatic services for translation between representations of a given data type, then we have to map X * X-1 * Y possible translations where X is the number of allowed representations for a given data type and Y is the number of data types. The TDWG biodiversity informatics ontology may end up with 30 classes. If we support 5 representations (maybe OWL, RDFS, semantic tags, XML metadata, and GML Feature Types) that's 5 * 4 * 30 = 600 possible translation mappings to create and maintain. Each time we have a new representation or a new data type we have to update the set of translation mappings.

My final set of concerns regards knowledge representation, modeling, and the expressive power of representation languages:

5.) Different representation languages have different language features and expressive powers. For instance, there are things you can do with OWL that you can't do with semantic tags. This is because OWL has language features for representing inheritance, property-value constraints, etc. that simply don't exist in the world of semantic tagging. If we have to be able to represent the platonic ideal of our data types (as defined in the TDWG ontology) in any representation language and also have to be able to translate between representations, we run into a dilemma.

If we use all the features of a particular representation language we benefit from them when using that particular format. The software that is constructed to natively consume that representation can use all of the available language features to automate tasks on behalf of the user. However, translation becomes very difficult. Imaging translating OWL-style inheritance into microformats or XML-Schema data type constraints into a system of semantic tags. It's simply not possible. Translating between languages of differing expressive powers can be problematic. The alternative approach is to use only those language features that are common to all representation languages. In practice this usually means using only those features that exist in the most weakly-expressive language. If our bag of representation languages includes both semantic tagging and OWL, then we're not really using the power of OWL. In fact, if we have to use only the common features of the two, we might as well implement our OWL ontology so that there is only one type of class with a single property called "tagvalue".

6.) Different representation languages enable different functionality in the software that consumes them. For instance, client software that consumes RDFS or OWL instances often expand searches to encompass instances of superclasses. In other words, software designed to use semantic web technologies can do some of the work a human user might otherwise have to do by exploiting the features of semantic web languages. Software designed to use semantic tags often doesn't do much more than search and statistical correlation between tag instances. This is quite powerful in it's own way, but because semantic tags were designed to indicate the context of a document, not necessarily its contents, semantic tagging really only helps a user to locate documents of interest. A document with tags is ultimately read by a human, not a machine. Every representation language carries with it assumptions about how "documents" that are instances of that language will be used.

To navigate you need a fixed point. To move the world you need a fulcrum. Because representation languages provide different features and make different assumptions about how their instances will be used, it makes sense to use representation language as the fixed point of our designs and leave data types and service interfaces free to vary. Some have argued that the TDWG ontology is the fixed point in our constellation of services, but I disagree. It is the umbrella under which data integration will occur; there will always be extensions to the core ontology and it too will change over time as it is expanded.

Overall I think it's a laudable goal to support as many representation languages as possible, but there are so many headaches and compromises involved that we may end up with an expensive solution that, because it only supports the lowest common denominator of functionality, doesn't really work right for anybody. A case in point is the current discussion of namespaces. In order to make namespaces work across the widest range of representation languages, it's been proposed that they can no longer be used as packages to logically partition the larger ontology. This makes it harder to manage extensions to the ontology and makes it likely that we'll end up using veryLongClassAndPropertyNamesToTryToAvoidNamespaceClashes. And you still can't represent namespaces in semantic tags.

It's hard enough to write software that can cope with any data type and I'd rather spend energy, time, and money on getting it right with only one or two feature-rich representations. What I'd really like to see is a network of heterogeneously typed, highly integrated data objects and a rich set of services that operate on them. Once this is built, the real fun can begin, creating software that uses these data to answer important scientific questions.

-Steve

Roger Hyam wrote:

...

Thanks for forwarding this Sally.

What I am proposing at St Louis - though I seem to been having to propose it long before - is that we have an application for managing the ontology that will expose the underlying semantics in multiple 'formats' i.e. as RDFS or OWL ontologies as GML application schemas, as custom XML Schemas as OBO ontologies etc etc. I see no other way of integrating multiple technologies. (Suggested alternatives welcome).

One of the things on my list is micro formats along with tagging. It seems crazy to define a 'specificEpithet' in a TDWG ontology and then not use exactly the same concept in a micro format or as a tag.

So this is timely. I just can't act on it very well before St Louis. I'll add something to the wiki page to flag my/our interest.

Thanks,

Roger

Sally Hinchcliffe wrote:

...

Hi all

This is probably on the wrong list (Maybe TAG?) but it strikes me that what this guy needs is an ontology that he can use in his microformats ...

Possibly an example of a real world need for ontologies ?

Sally

------- Forwarded message follows ------- Date sent: Tue, 26 Sep 2006 09:34:04 -0000 To: sh00kg@rbgkew.org.uk Subject: Fwd: [TDWG] Announce: Proposal for "microformat" for marking-up taxonomic names in HTML: comments and contributions sought From: M.Jackson@kew.org Send reply to: M.Jackson@rbgkew.org.uk

Sally,

Do you think you might respond to this? Just curious what you think.

Mark

Forwarded From: Andy Mabbett andy@pigsonthewing.org.uk

...

Hello - my first post to this mailing list.

I'm not a taxonomist, but I've been told by one that you might be interested in recent proposals for a formula (a "microformat" http://microformats.org) for marking-up, in HTML, the names of species (and other ranks, varieties, hybrids, etc.).

Microformats are a way of adding additional, simple markup to human-readable data items on web pages, using common and open HTML standards, so that the information can be extracted by software and indexed, searched for, saved, cross-referenced or aggregated. Microformats are also open standards, freely available for anyone to use.

The proposed format respects all existing biological taxonomies, and is not intended to change or supplant any of them - it merely provides webmasters with a method of either:

1. marking-up a taxonomical name (or taxon-common name pair) in such a way that its components can be recognised by computers

or

2. marking up a common name, so as to associative with it a taxonomical name, in such a way that the latter's

components can be recognised by computers

For instance, if I mark up a list of common names on a page I maintain:

http://www.westmidlandbirdclub.com/staffs/tittesworth/latest.htm

using that microformat, a visitor might have browser tool which lists all the species on the page, sorted into alphabetical order within taxonomic class, or in taxonomic order, and then creates links to, say (for Joe Public) their entries in Wikipedia, or the British Trust for Ornithology, or (for scientists) some academic database of the users choosing.

Early thoughts on the format are on an editable "wiki", here:

    <http://microformats.org/wiki/species>

Please feel free to participate - the proposal needs both messages of support (particularly from people or organisations who have websites on which they might use them) and, especially, comments and constructive criticisms - does the proposal understand and use taxonomy correctly; is the terminology right, are there any omissions or overlooked, unusual naming conventions?

You can use the above wiki, or the microformats mailing list:

    <http://microformats.org/wiki/mailing-lists>

and/ or please feel free to pass this e-mail to other interested parties.

Thank you.

-- Andy Mabbett Birmingham, England

---

TDWG mailing list TDWG@mailman.nhm.ku.edu http://mailman.nhm.ku.edu/mailman/listinfo/tdwg

---

---

TDWG-GUID mailing list TDWG-GUID@mailman.nhm.ku.edu http://mailman.nhm.ku.edu/mailman/listinfo/tdwg-guid

--

---

Roger Hyam Technical Architect Taxonomic Databases Working Group

---

http://www.tdwg.org roger@tdwg.org

+44 1578 722782

*** Sally Hinchcliffe *** Computer section, Royal Botanic Gardens, Kew *** tel: +44 (0)20 8332 5708 *** S.Hinchcliffe@rbgkew.org.uk