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Re: SDD Schema in relationship to Prometheus
by Kevin Thiele 16 Mar '04

16 Mar '04

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. 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. 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?). 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. 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. 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. 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) 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? >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? >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. >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. >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. >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. >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. ---------------------------------- 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. Cheers - k ----- Original Message ----- From: Paterson, Trevor To: TDWG-SDD(a)LISTSERV.NHM.KU.EDU 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(a)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

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Re: SDD Schema in relationship to Prometheus
by Kevin Thiele 16 Mar '04

16 Mar '04

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. 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. 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?). 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. 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. 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. 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??] ----- Original Message ----- From: Paterson, Trevor To: TDWG-SDD(a)LISTSERV.NHM.KU.EDU 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(a)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

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SDD Schema in relationship to Prometheus
by Paterson, Trevor 15 Mar '04

15 Mar '04

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(a)napier.ac.uk <mailto: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 <http://www.dcs.napier.ac.uk/~cs175> www.prometheusdb.org <http://www.prometheusdb.org/>

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Re: SDD Schema in relationship to Prometheus
by Rob Stevenson 15 Mar '04

15 Mar '04

Dear Trevor, I watched from a far intellectual distance (not being a computer scientist or a taxonomist) as my colleague Bob Morris helped develop the SDD schema. Occasionally Bob and I would discuss the the broader issues of how standards are recieved by a community and how or why they get adopted I know there was a great deal of time and thought put into the proposed standard and that your comments will be very helpful to the committee and to someone like me trying to understand the issues. Your email also highlights the equally important communication and sociological issues with standards. I hope your comments will stimulate a broader dialogue. Rob Stevenson Paterson, Trevor wrote: > 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(a)napier.ac.uk <mailto: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 > <http://www.dcs.napier.ac.uk/%7Ecs175>www.prometheusdb.org > <http://www.prometheusdb.org/> > > -- R.D. Stevenson Dept. of Biology UMass Boston MA 02125-3393 tel 617-287-6572 fax 617-287-6650 http://www.cs.umb.edu/efg/

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Re: glossary
by Jim Croft 04 Feb '04

04 Feb '04

maybe not - Mary Colravy is the new and current director try mary.colreavy(a)deh.gov.au jim At 04:27 AM 4/02/2004, you wrote: >I have got a little ways with the glossary, and was trying to get in >touch with Fl. Aust. over the possibility of integrating their >piccies - is the person with whom I should be in touch the same (I >have forgotten her name - sent an e-mail, but no reply) as it was a >year ago? > >FYI http://www.mobot.org/MOBOT/Research/APweb/glossary1.html should >show you where we are at. > >P. ~ Jim Croft ~ jrc(a)anbg.gov.au ~ 02-62465500 ~ www.anbg.gov.au/jrc/ ~

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Re: glossary
by Peter Stevens 03 Feb '04

03 Feb '04

>Apologies - this should have gone to Jim Croft... P. >I have got a little ways with the glossary, and was trying to get in >touch with Fl. Aust. over the possibility of integrating their >piccies - is the person with whom I should be in touch the same (I >have forgotten her name - sent an e-mail, but no reply) as it was a >year ago? > >FYI http://www.mobot.org/MOBOT/Research/APweb/glossary1.html should >show you where we are at. > >P.

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glossary
by Peter Stevens 03 Feb '04

03 Feb '04

I have got a little ways with the glossary, and was trying to get in touch with Fl. Aust. over the possibility of integrating their piccies - is the person with whom I should be in touch the same (I have forgotten her name - sent an e-mail, but no reply) as it was a year ago? FYI http://www.mobot.org/MOBOT/Research/APweb/glossary1.html should show you where we are at. P.

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Re: Virus apologizes
by Peter Stevens 03 Feb '04

03 Feb '04

>The address of yr institute seems appropriate... I changed the >subject somewhat. P. >Hello all, > >My apologies for the spread of a damaging virus! > >Gregor > >PS: I was actually completely offline for the last 2 weeks, and my >own computer seems to be clean. Our firewall-and-virus-scan-and-all >protected intranet was infected, however, and I suspect that acutally >a mail server became infected. >---------------------------------------------------------- >Gregor Hagedorn (G.Hagedorn(a)bba.de) >Institute for Plant Virology, Microbiology, and Biosafety >Federal Research Center for Agriculture and Forestry (BBA) >Koenigin-Luise-Str. 19 Tel: +49-30-8304-2220 >14195 Berlin, Germany Fax: +49-30-8304-2203 > >Often wrong but never in doubt!

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Virus apologies
by Gregor Hagedorn 02 Feb '04

02 Feb '04

Hello all, My apologies for the spread of a damaging virus! Gregor PS: I was actually completely offline for the last 2 weeks, and my own computer seems to be clean. Our firewall-and-virus-scan-and-all protected intranet was infected, however, and I suspect that acutally a mail server became infected. ---------------------------------------------------------- Gregor Hagedorn (G.Hagedorn(a)bba.de) Institute for Plant Virology, Microbiology, and Biosafety Federal Research Center for Agriculture and Forestry (BBA) Koenigin-Luise-Str. 19 Tel: +49-30-8304-2220 14195 Berlin, Germany Fax: +49-30-8304-2203 Often wrong but never in doubt!

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Re: Hi VIRUS!!
by Chuck.Miller＠MOBOT.ORG 20 Jan '04

20 Jan '04

You've got the Beagle virus. http://news.yahoo.com/news?tmpl=story&u=/nm/20040120/tc_nm/tech_internet_vir us_dc_6 Sorry, Chuck -----Original Message----- From: ram(a)CS.UMB.EDU [mailto:ram@CS.UMB.EDU] Sent: Sunday, January 18, 2004 10:33 PM To: TDWG-SDD(a)LISTSERV.NHM.KU.EDU Subject: Hi Test =) bxfeyewpugobn -- Test, yep.

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