July 2007 - tdwg-content - lists.tdwg.org

[tdwg-ncd] Re: Terminology version 2
by Markus Döring 16 Jul '07

16 Jul '07

Hi, Id like to reformulate some queries cause they seem to be targeted at specimens (unit level) rather than collections. I think all queries are good real world use cases, but to be honest I think most of them are way too complex to be answered by NCD datasets. This is mostly due to the lack of standardised keywords (India, SE Asia, fallout area of cherynoble) but also because of too detailed questions (species names like 'bufo bufo' are unlikely to be listed for collections). But one lesson learned here is again the need for keyword standardisation. We should at least recommend ISO country codes or kind of enforce them through the editor. Not sure if NCD should mandate this cause you really might want to use different region schemas. Markus > Here are some sample queries to consider, and I'm sure you have > others in mind: > - All the birds from India all collections having birds from india > - All the instances of Bufo bufo resources in a single > institution's holdings all collections of the institution X that have specimens of Bufo bufo (what is a resource ???) > - All specimens collected in the fall-out area within a year after > the Cherynoble disaster all collections that have specimens collected in the fall-out area within a year after the Cherynoble disaster > - Specimens from SE Asia all collections that have specimens from SE Asia > - Endangered species, worldwide all collections that have worldwide endagered species > - All the herbarium collections in Europe > - All the herbarium and insect collections in Africa > - Published and unpublished resources relating to Darwin's collections > - Molecular collections available for destructive analysis > - Living collections of plants and animals > - Living collections for which observation of mating displays exists > > > I'm hoping we can come to a conclusion on this soon, to give Ruud > and Wouter what they need to keep moving on their work, and Connie > what she needs towards documentation. > > Best wishes to all! > Carol > > > > > > -----Original Message----- > From: Markus Döring [mailto:m.doering@bgbm.org] > Sent: Wednesday, July 11, 2007 9:39 AM > To: Constance Rinaldo; Neil Thomson; Butler, Carol; > Guenter.Waibel(a)rlg.org; Barbara Mathe; Doug Holland; Natural > Collections Descriptions mailing list; Wouter Addink; Ruud Altenburg > Subject: Re: Terminology version 2 > > Hi, > I've been talking to Anton Güntsch about the use of NCD and the > different proposals about controlled keywords. > We came to the conclusions that from an biological point of view we > would need an easy way to enter and extract at least the information > which collection is a herbarium, zoo, garden, aquarium, mineral > collection. > Some terms are specialisations of broader terms we had (herbarium < > specimen collection). We can model this in the ontology so that > applications know that every herbarium is also a specimen collection > (or "dead" collection as opposed to living collection?) and simply > keep all terms in the schema list. Would that be an option? We will > have all the broad terms and some frequently occuring > specialisations. for example: > > archive > library > facsimile > digital data # what exactly is this? arent observations also data, > maybe just a specialisation > observation > specimen > - herbarium > - nat.hist.collection # or how you call those dead animal > collections in general? > living collection > - garden > - zoo > - aquarium > > > > The other option to know whether a collection is a herbarium is to > say its a specimen collection and have a taxonomic indication of > "plants". For this we would need a short list of very broad taxonomic > terms. I think that would be very useful anyways. something along the > lines of plants, animals, fungus, bacteria, viruses and minerals. And > of course additionally the free taxonomic keywords list. Does this > sound strange from a librarian point of view? > > Markus > > > > > On Jul 9, 2007, at 3:37 PM, Döring, Markus wrote: > >> I do like the idea of having a very short high level list for a first >> categorisation. I would like to add "Living collection" and maybe >> also "DNA >> samples" or more generic "molecular samples" to the list though. So >> we have >> dead specimens, living beings and some molecular (?) samples like >> DNA, cell >> culture, proteins and alike. Well, cell cultures are not really >> molecular >> samples. Anyone with a better term for this? >> >> Markus >> >> >> Am 09.07.2007 15:17 Uhr schrieb "Constance Rinaldo" unter >> <crinaldo(a)oeb.harvard.edu>: >> >>> Have we absolutely agreed to merge ctype and pfocus? I still think >>> there is value in keeping them separate. Carol had an idea about >>> Ctype having a few, high-level choices with pfocus as a modifier. >>> The two fields really are different, although it is easy to see how >>> they can be a bit confusing. If we offer the right choices, though, >>> it will not be so confusing. Carol suggested to me: <ctype> " >>> should >>> become a very short, high level list - - only having: Archive, >>> Library, specimen/Object, Observation, Data/Information, >>> Representation/Facsimilie. Then <pFocus> would be something of a >>> modifier. " >>> >>> Can we still talk about this? I am not convinced that merging them >>> is the best idea. It seems even more confusing to me. >>> >>> >>> ************************************************************ >>> Constance Rinaldo, Librarian of the Ernst Mayr Library >>> Museum of Comparative Zoology, Harvard University, >>> 26 Oxford St., Cambridge, MA 02138 >>> voice: 617-495-4576; fax: 617-496-6838 >>> email: crinaldo(a)fas.harvard.edu >>> http://library.mcz.harvard.edu >>> ************************************************************ >>> "To a person uninstructed in natural history, his country or seaside >>> stroll is a walk through a gallery filled with wonderful works of >>> art, nine-tenths of which have their faces turned to the wall" >>> Thomas >>> Henry Huxley >>> >>> >>> On Jul 9, 2007, at 5:28 AM, Neil Thomson wrote: >>> >>>> Hi Carol, >>>> >>>> I'm happy that we have the right elements now and a good selection >>>> of terms within each. >>>> >>>> Just one comment on the collectionType terms - since they refer to >>>> collections, then maybe some of them should be in the plural? For >>>> example, image should be images. This wouldn't apply to all, for >>>> example event and expedition should remain as they are. >>>> >>>> Any other views? >>>> >>>> With thanks, >>>> Neil >>>> >>>> From: Butler, Carol [mailto:ButlerCR@si.edu] >>>> Sent: 06 July 2007 19:04 >>>> To: Neil Thomson; Guenter.Waibel(a)rlg.org; Markus Döring; Barbara >>>> Mathe; Constance Rinaldo; Doug Holland; Wouter Addink; Ruud >>>> Altenburg >>>> Subject: Terminology version 2 >>>> Importance: High >>>> >>>> Hi All, >>>> >>>> Thanks for your comments. I've attached version 2. You'll see >>>> that it collapses <primaryFocus> into <collectionType> (which we >>>> had in the past called "collection class"). I included examples >>>> for the terms that correspond to this revised element. >>>> >>>> >>>> As we're on a time schedule and need to agree on the property/ >>>> elements so that Ruud and Wouter can proceed, would you please send >>>> me your final comments on 1) the Property Comment definitions, and >>>> 2) updated Terms, no later than the end of your day on Monday, July >>>> 9th? My recollection is that we needed to complete this review by >>>> July 10th. I expect we may want to tune the term definitions and >>>> examples a bit, which Neil tells me can have a bit more time as >>>> long as the elements themselves are agreed. If I don't hear from >>>> you, I'll conclude that you don't have comments or edits on this >>>> version. >>>> >>>> >>>> I've also sent this to our wiki. >>>> >>>> >>>> Thanks! >>>> >>>> Carol >>>> >>>> >>>> >>>> >>> >> > > <NCD terms version 3_July11.xls>

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[Biogeosdi] Someone attending TDWG
by Javier de la Torre 15 Jul '07

15 Jul '07

Hi all, is there anybody thinking in attending TDWG this year? I was just lookig at the program and wondering if we should present and abstract to present this. Renato already asked me to present in his slot for "Integrating biodiversity data - 2" at 11:00 12:30. That is ok for me. This year i will not be able to make it the whole week so i plan to travel on wednesday late 19th. But if there is people from the team around... we could make try to find a slot to work further on this... specially on creating documentation to go for funding for next workshop :) If there is many people away we can maybe ask for conference equipment (they do it a lot here in OGC and is cool). Sooo what about Friday at 17:30 for a meeting? Cheers.

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[tdwg-ncd] Re: Terminology version 2
by Markus Döring 11 Jul '07

11 Jul '07

Hi, I've been talking to Anton Güntsch about the use of NCD and the different proposals about controlled keywords. We came to the conclusions that from an biological point of view we would need an easy way to enter and extract at least the information which collection is a herbarium, zoo, garden, aquarium, mineral collection. Some terms are specialisations of broader terms we had (herbarium < specimen collection). We can model this in the ontology so that applications know that every herbarium is also a specimen collection (or "dead" collection as opposed to living collection?) and simply keep all terms in the schema list. Would that be an option? We will have all the broad terms and some frequently occuring specialisations. for example: archive library facsimile digital data # what exactly is this? arent observations also data, maybe just a specialisation observation specimen - herbarium - nat.hist.collection # or how you call those dead animal collections in general? living collection - garden - zoo - aquarium The other option to know whether a collection is a herbarium is to say its a specimen collection and have a taxonomic indication of "plants". For this we would need a short list of very broad taxonomic terms. I think that would be very useful anyways. something along the lines of plants, animals, fungus, bacteria, viruses and minerals. And of course additionally the free taxonomic keywords list. Does this sound strange from a librarian point of view? Markus On Jul 9, 2007, at 3:37 PM, Döring, Markus wrote: > I do like the idea of having a very short high level list for a first > categorisation. I would like to add "Living collection" and maybe > also "DNA > samples" or more generic "molecular samples" to the list though. So > we have > dead specimens, living beings and some molecular (?) samples like > DNA, cell > culture, proteins and alike. Well, cell cultures are not really > molecular > samples. Anyone with a better term for this? > > Markus > > > Am 09.07.2007 15:17 Uhr schrieb "Constance Rinaldo" unter > <crinaldo(a)oeb.harvard.edu>: > >> Have we absolutely agreed to merge ctype and pfocus? I still think >> there is value in keeping them separate. Carol had an idea about >> Ctype having a few, high-level choices with pfocus as a modifier. >> The two fields really are different, although it is easy to see how >> they can be a bit confusing. If we offer the right choices, though, >> it will not be so confusing. Carol suggested to me: <ctype> " should >> become a very short, high level list - - only having: Archive, >> Library, specimen/Object, Observation, Data/Information, >> Representation/Facsimilie. Then <pFocus> would be something of a >> modifier. " >> >> Can we still talk about this? I am not convinced that merging them >> is the best idea. It seems even more confusing to me. >> >> >> ************************************************************ >> Constance Rinaldo, Librarian of the Ernst Mayr Library >> Museum of Comparative Zoology, Harvard University, >> 26 Oxford St., Cambridge, MA 02138 >> voice: 617-495-4576; fax: 617-496-6838 >> email: crinaldo(a)fas.harvard.edu >> http://library.mcz.harvard.edu >> ************************************************************ >> "To a person uninstructed in natural history, his country or seaside >> stroll is a walk through a gallery filled with wonderful works of >> art, nine-tenths of which have their faces turned to the wall" Thomas >> Henry Huxley >> >> >> On Jul 9, 2007, at 5:28 AM, Neil Thomson wrote: >> >>> Hi Carol, >>> >>> I'm happy that we have the right elements now and a good selection >>> of terms within each. >>> >>> Just one comment on the collectionType terms - since they refer to >>> collections, then maybe some of them should be in the plural? For >>> example, image should be images. This wouldn't apply to all, for >>> example event and expedition should remain as they are. >>> >>> Any other views? >>> >>> With thanks, >>> Neil >>> >>> From: Butler, Carol [mailto:ButlerCR@si.edu] >>> Sent: 06 July 2007 19:04 >>> To: Neil Thomson; Guenter.Waibel(a)rlg.org; Markus Döring; Barbara >>> Mathe; Constance Rinaldo; Doug Holland; Wouter Addink; Ruud >>> Altenburg >>> Subject: Terminology version 2 >>> Importance: High >>> >>> Hi All, >>> >>> Thanks for your comments. I’ve attached version 2. You’ll see >>> that it collapses <primaryFocus> into <collectionType> (which we >>> had in the past called “collection class”). I included examples >>> for the terms that correspond to this revised element. >>> >>> >>> As we’re on a time schedule and need to agree on the property/ >>> elements so that Ruud and Wouter can proceed, would you please send >>> me your final comments on 1) the Property Comment definitions, and >>> 2) updated Terms, no later than the end of your day on Monday, July >>> 9th? My recollection is that we needed to complete this review by >>> July 10th. I expect we may want to tune the term definitions and >>> examples a bit, which Neil tells me can have a bit more time as >>> long as the elements themselves are agreed. If I don’t hear from >>> you, I’ll conclude that you don’t have comments or edits on this >>> version. >>> >>> >>> I’ve also sent this to our wiki. >>> >>> >>> Thanks! >>> >>> Carol >>> >>> >>> >>> >> >

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[Biogeosdi] Problem with getting avaialble algorithms in OMWS
by Javier de la Torre 08 Jul '07

08 Jul '07

Hi all, Well this is from Tim and Renato... I have troubles dealing with the response from the getAvailableAlgorithms method. The XML it returns is invalid (some & not scaped in biographies and things like that). I am going to try to fake it for my demostration but you probably have forgotten to include code to escape text. Cheers.

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[Biogeosdi] Wiki editing
by Javier de la Torre 07 Jul '07

07 Jul '07

Hi all, I have edited the wiki of the group to try to keep it kind of consistent. Start looking at it http://wiki.tdwg.org/twiki/bin/view/ Geospatial/WebHome . I would like to keep it fine so that interested people after the OGC presentation can find it useful. We have to start looking for fundings for the next workshop in Bahia ;) Cheers. Javier

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[Biogeosdi] Report and aknowledgements
by Javier de la Torre 07 Jul '07

07 Jul '07

Hi all, I have added the aknowledgements section as Dave proposed but maybe some editing from a native speaker or something on this part would be great... apart of this I think I am done... I have to do some cleaning-up on the website and we are ready with it. Check it out on subversion or here in the PDF. Ahh!! Also I gave credits to the instituions I thought you might want to give credits but it would be good if you can check if it is fine for you ;) Then I will be working on the prototype. Tim has created a parallels image with a debian running everything that is very convient from demostration... it does not work perfectly yet but I will be working on the code this afternoon. Tomorrow I do the presentation and I hope to be ready for rocking at OGC! I will try to circulate as soon as possible the presentation so that I can get comments on it :) Cheers.

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[Biogeosdi] Hey guys, last chance to touch the report...
by Javier de la Torre 06 Jul '07

06 Jul '07

Hey guys, Here I send you the latest version of the report with serious editings and adapted for the txt2tags that we agree on use. I have produced the PDF and HTML and everything is in subversion. Please edit as soon as possible as I plan to start circulating this now now!! Javi.

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[Biogeosdi] report
by Javier de la Torre 05 Jul '07

05 Jul '07

this is how it looks like... in PDF and in HTML check it on subversion... (HTML looks nicer)

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[tdwg-ncd] NCD Workshop report and deliverables
by Neil Thomson 05 Jul '07

05 Jul '07

Dear NCD'ers, The meeting report from the NCD 2007 Workshop is available, along with other workshop deliverables, on the NCD wiki. Please take a look at: http://wiki.tdwg.org/twiki/bin/view/NCD/NCDWorkShop and let me know if any changes are required, With thanks, 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

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[Biogeosdi] Re: biogeosdi Digest, Vol 8, Issue 4
by Meganck Bart 05 Jul '07

05 Jul '07

Hi Javier, It has become a neat report ! The text seems ok, I had nothing really to add - I only put the definitions and links for PHP and SPICE in the Terms Definition part. best regards, Bart. On Thu, 2007-07-05 at 07:51 +0200, biogeosdi-request(a)lists.tdwg.org wrote: > Send biogeosdi mailing list submissions to > biogeosdi(a)lists.tdwg.org > > To subscribe or unsubscribe via the World Wide Web, visit > http://lists.tdwg.org/mailman/listinfo/biogeosdi > or, via email, send a message with subject or body 'help' to > biogeosdi-request(a)lists.tdwg.org > > You can reach the person managing the list at > biogeosdi-owner(a)lists.tdwg.org > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of biogeosdi digest..." > > > Today's Topics: > > 1. Hey guys, last chance to touch the report... (Javier de la Torre) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Thu, 5 Jul 2007 07:51:09 +0200 > From: Javier de la Torre <jatorre(a)gmail.com> > Subject: [Biogeosdi] Hey guys, last chance to touch the report... > To: biogeosdi(a)lists.tdwg.org, Lee Belbin <leebel(a)netspace.net.au> > Message-ID: <FA773FD2-C4BE-48A1-8824-F273370F79DE(a)gmail.com> > Content-Type: text/plain; charset="us-ascii" > > Hey guys, > > Here I send you the latest version of the report with serious > editings and adapted for the txt2tags that we agree on use. I have > produced the PDF and HTML and everything is in subversion. > > Please edit as soon as possible as I plan to start circulating this > now now!! > > Javi. > > >

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