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[tdwg-ncd] NCD developments
by Neil Thomson 14 May '07

14 May '07

Dear all, Here is a short update on developments that are taking place with NCD. Wouter Addink and Ruud Altenburg at ETI are developing the NCD Toolkit and are currently ensuring that it will work with two languages - English plus a local language. Along with myself and Markus Döring in Berlin we are tidying up the NCD schema into a stable version to be used as the basis for the toolkit. The toolkit itself, along with the other developments outlined below, is expected to be ready for demonstration at this year's TDWG annual conference in mid-September. Markus is also working on the RDF aspects and integration with the TDWG ontology. He has added the emtpy basic classes of NCD to the TDWG ontology and is working on the following: http://rs.tdwg.org/ontology/voc/Collection.rdf http://rs.tdwg.org/ontology/voc/Institution.rdf http://rs.tdwg.org/ontology/voc/CollectionType.rdf http://rs.tdwg.org/ontology/voc/InstitutionType.rdf http://rs.tdwg.org/ontology/voc/ObjectType.rdf http://rs.tdwg.org/ontology/voc/PreservationMethodType.rdf Carol Butler at the Smithsonian is starting to assemble termlists for those elements that will benefit from having controlled vocabulary and these will also be integrated into the TDWG ontology. Connie Rinaldo at Harvard is working on the documentation set. She has reviewed the current introduction, documentation, and schema to see where changes need to be made. She has also reviewed the background TDWG material so that the new documentation will fit the TDWG standards. The implementation guide will be created in collaboration with ETI. I have completed the mapping of the Index Herbariorum data into NCD and next will be selecting which fields will be used so that an NCD Institution record can act as a business card for corporates in the biodiversity collections domain. The NCD 2007 Workshop will take place in June and the report from that will provide further details on progress. In the meantime, the list of deliverables for 2007 is available on the NCD wiki at: http://wiki.tdwg.org/twiki/bin/view/NCD/NCDListOfDeliverables With thanks, Neil --------- Neil Thomson NCD Interest Group Convenor

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[taxon-model] Re: [tdwg-tag] Re: TDM Ontology
by Renato De Giovanni 12 May '07

12 May '07

Hi Roger, I'm not sure I share this vision of a "law of conservation of pain". It's true that one of the points in the other message was to ease the process of sharing data, but this doesn't mean that clients will necessarily have trouble (I hope not!). >>>From the TAPIR perspective, we handle extensibility by allowing providers to work with multiple conceptual schemas. If you produce a list of concepts from the TDM terms, anyone is free to produce other complementary lists in the future, without breaking compatibility. You know that in TAPIR it's also possible to produce outputs in different XML formats, even RDF. This should facilitate the work of clients. I suppose that clients will usually request data in formats that include elements that they know something about. But anyway, nothing prevents them to request things that they don't have any knowledge about. The TapirLink browser that I demonstrated during the TAPIR workshop is one of those clients: it dynamically builds an output model based on what the provider declared to have, and it simply displays this data in a tabular form. Now let's assume that we decide to work with a generic conceptual schema with two main concepts, category of InfoItem and InfoItem value. Let's also assume that providers will be able to easily share their data according to this conceptual model. In TAPIR, the output formats will be very limited - they will need to follow this generic approach. But let's suppose that this will not be a problem. What is going to happen is that clients will get amost anything from there - basically values of things that can be categorised in many ways. If clients want to perform validation they will need to do it themselves (the output format will be too generic, so we cannot use XML validation). Perhaps RDF validation will offer more possibilities, but then you're only considering data exchange in an RDF world. The meaning of InfoItems you would get from a dictionary of categories, in the same way that you could get the meaning of elements from a dictionary (DarwinCore for instance, or some ontology). In this case, it's not clear to me what would be the big benefits of using the generic model approach, but maybe I'm missing something. The more knowledge you have about the elements or concepts, the more interesting and powerful the applications will be. It's a philosophical issue. If we decide to avoid the more "traditional" way of structuring and modelling data because we feel it somehow limits our applications, then I think we first need to clearly understand what are these limitations. Otherwise, by doing things in a very different way we may miss the opportunity of using existing tools and resources - but still running the risk of facing again in a different road the same data structuring issues that we tried to avoid. Best Wishes, -- Renato PS: I'm sorry for crossposting. I'll send any follow-ups only to the new taxon-model mailing list: http://lists.tdwg.org/mailman/listinfo/taxon-model On 8 May 2007 at 9:35, Roger Hyam wrote: > > Renato, > > Thanks for your comments. That is an interesting view of the problem > and I think you may be correct for the supplier databases (though I > don't have first hand knowledge of these database schemas). Generally > the nearer the exchange format is to the supplier's schema the easier > it will be for them to publish. Taking the approach Markus suggests > would produce the result you are after I believe. > > There is just one problem that you didn't address. > > Who wants to consume the data and what do they want to do with it? > > To have something that is easy to produce, easy to consume and easy > to extend is more or less impossible. There has to be some pain > somewhere! > > What is your vision of a client application? How would it handle > elements it hadn't seen before - or is this not a requirement? > > All the best, > > Roger

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[taxon-data-model] Notice: the group mailing list and wiki addresses have changed
by Ricardo Pereira 11 May '07

11 May '07

Dear Taxon Data Model group members, This is to inform you that the group mailing list web and email addresses as well as the group wiki web address have changed. The new addresses are: http://wiki.tdwg.org/TaxonDataModel (wiki homepage - short URL) http://wiki.tdwg.org/twiki/bin/view/TaxonDataModel/WebHome (wiki homepage - full URL) http://lists.tdwg.org/mailman/listinfo/taxon-data-model (mailing list information web page) taxon-data-model(a)lists.tdwg.org (mailing list web address) Please use the new email address above to post messages to all mailing list members. The old addresses of the resources above (that use the abbreviation Taxon Model, including the mailing list email address) have all been redirected to the new versions so that no external links are broken. The changes were made to address some concerns that have been raised that the abbreviation from Taxon Data Model to Taxon Model might lead to confusion and suggest that the group is concerned with taxonomy theory. Best regards, Ricardo Pereira TDWG Systems Administrator

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[taxon-model] Re: Owl polymorphism
by Markus Döring 11 May '07

11 May '07

Roger, this was not targeted directly at TDM. I was mainly exploring OWL and definitely not suggesting multiple inheritance! But in regards to TDM I was thinking about the consequences of allowing any defined term as a "controlled" value for InfoItems.hasValue. Is this desired? Having individual classes for the InfoItem categories now would allow us to define a specific controlled vocabulary for each category - or None if we dont think this is a good idea. These vocabularies, like CyclicityTerm, can easily be extended by anyone who really needs to. And all InfoItems are allowed to contain uncontrolled values via the hasContent property in any case. -- Markus On 11.05.2007, at 11:30, Roger Hyam wrote: > > Hi Markus, > > Sounds like interesting and complex stuff and exactly what I am > trying to avoid ;) > > If this is for exchange standards we want to keep things as simple > as possible. We also need our ontology to entail as little as > possible so people can understand it and (if they are up on the > technology) import it into their own business ontologies. > > The role of the exchange ontology is to denote the meaning of > simple fields it is not to enable connotations but to avoid them. > > This is why I was sticking to simple properties with domains and > ranges. Really just one up from RDFS. If it is important for a > consumer to assert a hierarchy of properties then they can do that > in their own ontology and import it. Who is to say that all > consumers will have the same notion of that hierarchy and what is > the business case for trying to impose one at this point? > > If there were polymorphism of properties (overriding them in sub > classes) then it would get confusing because of the multiple > inheritance. I am not sure what would happen to meaning with the > diamond problem - where the same property is inherited via several > routes but has it's meaning changed differently on each route. It > is always possible to subclass the property though and it may be > possible to forbid the use of the parent property in a class - > perhaps - but this is getting beyond my reading level. > > Not sure if this helps, > > All the best, > > Roger > > > > > On 11 May 2007, at 09:54, Markus Döring wrote: > >> Roger, >> is it possible with OWL to have polymorph class properties? >> As properties are global and only bound to classes via range/ >> domain it doesnt seem to be possible to me, but maybe Im wrong. >> Can I redefine a propertys range depending upon the class it >> belongs to, so its domain? Well, that would mean to declare the >> same property twice with different domains and ranges. Probably >> impossible. It is different from classic OO thinking... >> -- >> Markus >> >> >> >

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[taxon-model] Taxon Data Model wiki updated
by Eamonn O Tuama 09 May '07

09 May '07

I have updated the Taxon Data Model wiki at http://wiki.tdwg.org/TaxonModel. The species model workshop presentations and report are now available there. Feel free to edit and add your own content. Best regards, Éamonn

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[Biogeosdi] itineraries in openmodeller
by Meganck Bart 03 May '07

03 May '07

Hi Tim, I have been thinking about how to make the "itinerary" project a use-case for our GeoAppInter workflow. It's clear that until now I've been working a bit too enclosed - so the Campinas workshop was an eye-opener. In fact the itinerary implementation would not be that different from the demo we did. It's just another way of looking at the modeling part. For that I have some questions about OpenModeler : * how easy or how difficult is it to make your own algorithms for OM ? In what language do they have to be implemented ? * could OM take in data layers other than environmental data ? best regards, Bart. -- Bart Meganck, ICT & GIS engineer, African Zoology Department. Royal Museum for Central Africa, Leuvensesteenweg 13, B-3080 Tervuren, Belgium. Tel : +32(0)2 769 56 92 Fax : +32(0)2 767 02 42 Email : bart.meganck(a)africamuseum.be Website : www.africamuseum.be ########################################### This message has been scanned by ICT - Africa Museum ________________________________________ 3/5/2007 - Filtered through antispam by ICT

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[tdwg-ncd] Preview NLBIF metadatabase
by Ruud Altenburg 01 May '07

01 May '07

Hallo all, at ETI there have been (or still are) problems with the mail server, so some email to or from me may have bounced last week. I would like to announce that a demonstration of the metadatabase developed for NLBIF is available for preview. I had already put up a version last week but that suffered from migration problems. The preview now should work as advertised. If not, please let me know and I'll look at it ASAP. Please note that not all fields catered for in the NCD standard are included. In fact quite many are missing, as they were considered not necessary for this specific project. The interface still is rudimentary. http://www.nlbif.nl/ncd-preview/ Best regards, Ruud Altenburg

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[Biogeosdi] Re: question WFS/WMS layer occurrences search
by Javier de la Torre 28 Apr '07

28 Apr '07

Hi Bart, Lets start using our mailing list to talk about these topics ok? > Now, I think that the occurence service stores a WFS layer (e.g. the > Cocos_nucif_28977530 layer) the moment you do the search, so I just > need > to know : > > * is this done automatically for each and every search ? In GBIF, > in WFS > and in TAPIR ? Yes they are. > > * how do I get the name of this layer in OccurencesDisplay.php - short > of doing a GetCapabilities and parsing the whole XML ? > Uhmmm...no, in the XML report you get after fetching the data it is included the name of the layer that has been registered in the WFS server. Look at the contents of a report to grab it. Cheers.

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[tdwg-ncd] NCD - new version v0.51
by Neil Thomson 24 Apr '07

24 Apr '07

Dear All, A new version of NCD is attached and will be placed on the wiki and in rs.tdwg.org/ncd/dev There are no major changes, but some much-needed tidying up. I am grateful to Markus for making the following changes: - all attribute names start with lower character - all xs:anySimpleType data types have been replaced with xs:string, xs:positiveInteger or xs:language where appropriate - missing types have been added - version="0.51" because all attribute names have changes to lower case In addition, I have amended the header to reflect the new version and date and altered <CollectionExtent> from being a container element (in error) to being a string element. There may be additional changes required to harmonise the schema with the NCD Toolit requirements. For those of you unable to work with .xsd files, I also enclose a cribsheet in Excel that provides a straight listing of the elements and their attrbutes. The names of elements currently deemed to be required are shaded pale blue All best wishes, Neil ------- Neil Thomson Head of Data & Digital Systems The Natural History Museum, Cromwell Road, London SW7 5BD Tel: +44 (0)20 7942 5294, Fax: +44 (0)20 7942 5559, Email: n.thomson(a)nhm.ac.uk http://www.nhm.ac.uk <<NCDv0pt51.xsd>> <<NCDv0pt51.xls>>

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[tdwg-ncd] NCD preview site
by Ruud Altenburg 24 Apr '07

24 Apr '07

Hallo, I must confess that I have been too optimistic about the "NCD preview" database working properly after a server migration. The system was developed in the MySQL 4/PHP 4 tandem and appears not to work flawlessly in MySQL 5/PHP 5. In fact it appears a lot of minor modifications are necessary... So for the time being please consider that link not sent. I will send a message when I get the system working without problems on the new server. Best regards, Ruud Altenburg

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