- tdwg-content - lists.tdwg.org

[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

5 4

[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

1 0

[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 >> >> >> >

1 0

[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

1 0

[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

2 1

[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

1 0

[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.

1 0

[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>>

1 0

[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

1 0

[tdwg-ncd] RE: NCD toolkit
by Neil Thomson 23 Apr '07

23 Apr '07

Hi Ruud, Many thanks for providing the URL to the test site - don't worry about its looks, we are all aware that the functionality needs to be in place first. For your questions below: - We decided to drop <PercentageDatabased> as being an unhelpful element. It is one that would need constant updating, which we thought would not happen. The URLs in the Related Materials Group could alert a user to the fact that a database exists and could then go direct to it. As to EAD, Barabara Mathé at the AMNH has prepared a mapping between EAD and NCD which you may find helpful once it reaches its final form. - Yes, this approach sounds good. I did try to put some dummy data into the test site, but I got thrown out with an SQL error. No matter, having an organisation and a person as a precursor to a collection description sounds perfectly reasonable and is similar to the approach taken by NoDIT. - Yes, the lists will be in English, but we could may get other European language equivalents from GEMET? One for use to discuss with Roger. - There may be more than one agent per site that will be creating and editing records. At my own place there may be a dozen or more authors. Perhaps we should have an "open issues" page on the TDWG wiki, otherwise it is going to become difficult to keep track of queries, responses and decisions on emails? All best wishes, Neil -----Original Message----- From: Ruud Altenburg [mailto:ruud@eti.uva.nl] Sent: 20 April 2007 15:19 To: Neil Thomson Cc: tdwg-ncd(a)lists.tdwg.org Subject: Re: NCD toolkit Hallo Neil, I don't think I'm on the list your cc'ed, so if this bounces could you please forward my reply? I have combined both of your answers of today into one mail. But before I get to that I have an important announcement: I have made our NLBIF metadatabase maintenance site available on a public server, so you and other NCD participants can have a look. Please note that my first concern has been the functionality, not its looks! This should easily be improved with style sheets but frankly I never heard complaints from our ETI people about its 'Spartan look' ; ) The system is available at http://www.nlbif.nl/ncd-preview/ It currently contains no data, but anyone can have a try at adding/ updating/deleting records. The login is test/test. A final note: I would not play too much with the "Send mailing" option, as this may seriously annoy people you have entered as test persons! :) Then the Q&A revisited. I only reply to issues that have remained open or that I feel need some more discussion. > ----------- > 3. The contract mentions import from NoDIT databases as a requirement > (plus the EAD standard which I'm not familiar with). To cater for > this we have added several fields to the metadatabase, otherwise we > would not have been able to migrate all data. However, strictly > speaking the metadatabase therefore does not match the NCD standard > one-on-one. How do we deal with this? > > ## NHT: Would you be able to let me have a list of the elements that > do not match, please? Then we can evaluate whether they should be > added to NCD or whether it does not matter. Since NCD was derived > from the schema that underlies NoDIT they should be very similar. > Markus may be able to advise on this, since he built NoDIT for > BioCASE. These are elements such as PercentageDatabased. We could maintain them in the database (so they are not lost) but omit them from the web service. > ------------ > 4. Which fields in the NCD standard are required and which are not? I > assume ones which have a closed box in XML Spy, but this may be too > loose for a database setup. In the NLBIF metadatabase, a collection > must be connected to either a person or an organisation, otherwise it > would be orphaned. If I interpret the NCD schema well, information > about a collection can be entered without providing information about > the organisation or person to which/whom it belongs. > > ## NHT: Your are right in your interpretation of the schema. We have > tried to keep the number of required elements to a minimum to > encourage data entry - there are currently only 8 required elements > and 5 of these are about who created the entry and when. The > <FamilyName> of a person is required if a person is entered. It > would > be easy enough (and makes sense) to make an institution required and > should not be any hardship for data entry folk since for a > session, at > least, the instutition details will be the same and so entered just > once. This IMO needs further discussion. A collection can also be related to a person, not exclusively to an organisation (private collections!). Also, please keep in mind that information on collections by themselves may be virtually useless if there is no information stored about where the collection is stored (for access) and whom to address for further information. The virtue of a database is that you can search for information, but if only an extremely limited set of data is required, this will seriously impede its use. Please have a look at the setup of the metadatabase maintenance site. It's easy to add collections to existing organisations or persons, which only have to be created once. > ----------- > 5. We have copied some value lists from the NoDIT database to our > database, e.g. keywords describing collections. However, the NCD > standard has a broader scope than the NoDIT database and the NLBIF > metadatabase. In the interface, I assume that many values too should > be selected from popups menus, to guarantee a uniform database -- > e.g. AgentRole, CollectionPurpose, UnitOfMeasure, DigitalFileFormats > to name but a few. To create such lists, we need to have these values > stored in the database, so somehow these lists should be compiled. If > multiple languages should be supported, we may need to have these > values in other languages but English as well. > > ## NHT: These terminology lists and their association with the TDWG > ontology > are the subject of a separate development being undertaken at the > Smithsonian Institution by Carol Butler in association with Roger > Hyam and Markus. They will result in sets of terms that can be used > as pick-lists for those elements that should have just a few > terms or > for which consistency is important. > We should see the first draft of these at the NCD Workshop, if not > before. It would be good for anyone interested to make > suggestions for > such terms and their definition through this list to help Carol to > compile them. This is good news! I could start with the basic set we have compiled for NLBIF and replace these with the NCD entries once these have been determined. I assume these lists will be in English and will not be translated to other languages? > ---------- > 2. More or less the same applies to Agents. My idea is that this is > filled in once when setting up the database and that this is returned > only when the database is accessed externally. But as apparently more > than one agent with one or more roles can be responsible for a single > record, so possibly this solution is incomplete. However, many > changes have to be made to the current database to implement agents > to a record level. E.g. consider that a collection is appended to an > organisation that has previously been created by another agent. > > ## NHT: You are right that someone entering new records should only > need to record their details once for the session. The agents > section of the NCD Header (which is based on the METS header) is > intended to record metadata about the record itself, rather than > the collection that the record describes. The date of record > creation should default to "today" and be fixed. However, an > agent can come along later and amend the record, maybe adding to > it or correcting it. In this case the role of the person is > "editor". > Appending a collection to an existing organisation record should not > affect the organisation record, since the relationship is > established simply by recording the organisation ID in the > collection > record. Nothing is added to or changed in the organisation record. Thanks for the explanation. The system tracks which records (organisations, collections and persons) have been updated by whom (by Users). The Agent information e.g. is fixed for each site proving a web service on their local database. This could be entered once when setting up the database. Correct me if I'm wrong! > ---------- > 3. Shouldn't PostalAddressText and PhysicalAddressText each have an > independent zipcode and town? In reverse, is it necessary to use > language attributes to towns and regions? We have stored this data in > a non-language-dependent field. > > ## NHT: Not sure about this one - are there cases where an > organisation > has a postal address in a different town from the organisation? This > may be solved, as the annotation text suggests, by having the > complete > address text in the postal element. The ZIP code and town are > intended > for your wizzy Google Maps link and for folk to determine what > collections > they may visit in a particular area. So if we are agreed that > only one > of these is required, the documentation will need to make it clear > that the ZIP code and Town refer the to actual organisation, rather > than its postbox. > While we are on the topic, does anyone have a preference for > "organisation" > over "institution", or does it not matter? Well, normally both towns are the same, but not always. From a database point of view, it not desirable to enter data that ideally should be stored in separate fields into one field. E.g. it would probably make Google Maps queries much more complicated if not impossible, as addresses can be entered in various forms. Best regards, Ruud

1 0