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[tdwg-ncd] NCD news and list of deliverables for 2007
by Neil Thomson 25 Jan '07

25 Jan '07

Dear all, Here is a final list of the NCD deliverables that will be expected under the two contracts that are currently being negotiated. Please let me know as soon as possible if changes need to be notified. Once finalised, I will post this to the NCD wiki, after I get that launched, so that they can be used as topic headings for discussion and progress reporting. Some, if not all, will also be mirrored on the RAVNS Basecamp. I am pleased to say the the French GBIF node have expressed an early interest in making use of the toolkit and have joined this mailing list so that they can participate in the discussions - welcome Gaël Lancelot. It would be good to start discussing the timing and content of the 2007 NCD Workshop and I will send a separate email to this list about that shortly. --------------------- NCD deliverables - 2007 Part 1: TDWG harmonisation 1. LSID Vocabulary for organisations and collections in the rs.tdwg.org namespace. (Berlin) 2. Report on potential sources of information about biodiversity organisations. (London) 3. Memo of Understanding on uses of organisation metadata. (London) 4. Initial set of organisation records in the Berlin implementation of the NCD tool kit. (London & Berlin) 5. Documentation: - Introduction to NCD - User Guide - Data Creation & Migration Guide - Crosswalk with Dublin Core, EAD and MARC21. (Boston, with New York & St. Louis) 6. A set of terms and definitions included in LSID vocabulary developed under 1 above. (Washington) 7. Meeting report from NCD 2007 Workshop as per TDWG template. (London) 8. Workshop training presentation on using RDF. (Berlin) 9. Review of 1st drafts of documents produced under 5 and vocabulary produced under 1. (Boston) Part 2: NCD Toolkit 1. The NCD Toolkit Macintosh and Windows installation executable, including interfaces as described below, based on MySQL, PHP and include an installation guide and full documentation. (Netherlands) 2. Interfaces will be developed for: a. PHP Web interface for data editing b. OAI harvesting interface, including an RDF response based on a templating language. c. Extraction of data in NCD schema-compliant XML files, through a REST Webservice d. Pywrapper NCD configuration e. Helpdesk with support for Mac and Windows (Netherlands) 3. Documentation and Help Desk to lead organisations through the implementation process and provide ongoing support. (Note that a User Guide is also in preparation (see 5 above), which will guide those preparing data on the use and purpose of each data field or element.) (Netherlands) 4. Central database established at the Berlin Botanic Gardens (BGBM) pre-seeded with data currently in the BioCASE NoDIT database for use in testing and to act as a repository for data from organisations that do not wish to host their own. (Berlin) ----------------- 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] Fwd: Auto-discard notification
by Javier de la Torre 21 Jan '07

21 Jan '07

I have the impression that this message was not received... I will write Ricardo to know what is going on... Comment on the email later... Cheers. Begin forwarded message: > From: biogeosdi-bounces(a)lists.tdwg.org > Date: 21 de enero de 2007 19:18:08 GMT+01:00 > To: biogeosdi-owner(a)lists.tdwg.org > Subject: Auto-discard notification > > The attached message has been automatically discarded. > From: "David Neufeld" <david.neufeld(a)colorado.edu> > Date: 21 de enero de 2007 19:17:58 GMT+01:00 > To: <biogeosdi(a)lists.tdwg.org> > Subject: RE: [Biogeosdi] meeting > > > Hello, > > > Date are likewise “OK’ish” for me. I might head out at the end of > the day on the 5th if that week in April comes together. Otherwise > June looks good. > > > I’ve worked with WCS some via Map Server for the environmental > extraction service we put together for MAPA last year. It uses the > httpclient from Jakarta commons which is nice in that it can pull > from disparate WCS services and collate the results for specimen > occurrence records. We recently received a little more funding to > further develop this, and I’d be happy to coordinate/collaborate > with others on this piece prior to the meeting. In particular it > might be fun to make a range of “environmental” servers available > at a couple of remote locations using MapServer and WCS and test > collating the results… > > > I’m imaging a python script located in Spain submitting a list of > LSIDS and x,y coords to the EVE service in Boulder (environmental > values extraction service) which distributes the query out to WCS > servers at KU, CRIA, others and makes a CSV text file of specimen > LSIDS, followed by the environmental values available back to the > calling python client. Any interest? > > > cheers, > Dave > > > > -----Original Message----- > From: biogeosdi-bounces(a)lists.tdwg.org [mailto:biogeosdi- > bounces(a)lists.tdwg.org] On Behalf Of Javier de la Torre > Sent: Saturday, January 20, 2007 12:21 PM > To: biogeosdi(a)lists.tdwg.org > Subject: [Biogeosdi] meeting > > > Hi All, > > > I am still waiting for Vanderlei's approval to have the meeting at > CRIA. I have applied for the 1st week of April as we already > discussed. > > > I haven't done anything since our last talk. But know I start > having some more free time so I will start as soon as possible to > discuss with Tim to further envision the use case. I have already > seen that GDAL has already released WCS support, has anybody tried > it? OpenModellers people? > > > I hope the dates are still fine for everybody. > > > Javi. > > > PD: By the way Peter your messages seems to be refuse by the list > server :?? > > > > On 18/01/2007, at 22:07, biogeosdi-bounces(a)lists.tdwg.org wrote: > > > > > The attached message has been automatically discarded. > > From: Peter Brewer <p.w.brewer(a)reading.ac.uk> > > Date: 18 de enero de 2007 22:07:23 GMT+01:00 > > To: biogeosdi(a)lists.tdwg.org > > Subject: Re: [Biogeosdi] SubStandards workshop > > > > I was thinking the same. Dates are ok(ish) with me, but does > everyone realise this falls over Easter? Not sure if that will be > an issue for anyone. > > > Pete > > > Aimee Stewart wrote: > >> Hi all, >> >> >> We should probably start some email or irc discussions regarding >> our upcoming workshop so that we can prepare. I have April 2-6 as >> our target dates. Does this still work for everyone, or do we need >> to revisit the timing? US participants will also need to get a >> visa to enter Brazil, I'm not sure about other countries. >> >> >> Aimee >> >> >> _______________________________________________ >> >> biogeosdi mailing list >> >> biogeosdi(a)lists.tdwg.org >> >> http://lists.tdwg.org/mailman/listinfo/biogeosdi >> >> > > > >

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[Biogeosdi] openModeller Desktop version 1.0.3 Released!
by Tim Sutton 03 Jan '07

03 Jan '07

Hi All (with apologies for cross posting) I am very pleased to announce the release of openModeller Desktop version 1.0.3. openModeller is a fundamental ecological niche modelling library, providing a uniform method for modelling distribution patterns using a variety of modelling algorithms. The openModeller Desktop application is a user friendly front-end to the openModeller library. openModeller library and the openModeller Desktop application are free, open source software published under the GPL license. This version of openModeller Desktop is a complete rewrite of the original Wizard based GUI we previously made available. This version is being designed to support large experiments where multiple species can be modelled using multiple algorithms. Future versions will also support projecting models into multiple environmental scenarios. openModeller Desktop makes use of an embedded GIS model browser (based on Quantum GIS, a free and open source GIS - see http://qgis.org) in order to facilitate panning and zooming around the model outputs. This release is available as a windows binary set up file and in source form. In future versions we will make Mac OSX and GNU / Linux versions of the software available in binary form too. The software can be downloaded directly from http://sourceforge.net/project/showfiles.php?group_id=101808&package_id=142… You can find more information including links to our mailing list and news about updates as and when they become available by visiting our website at: http://openmodeller.sf.net. Best regards, -- Tim Sutton The openModeller Team

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[Biogeosdi] Minutes from meeting held Dec 05 2006 on IRC
by Tim Sutton 06 Dec '06

06 Dec '06

Hi All Hopefully everyone from the old yahoo list is now subscribed here too! I've posted my minutes from the meeting we held on irc today onto th eTDWG wiki. Please feel free to correct any grossly misguided assessments of the discussion I may have made. http://wiki.tdwg.org/twiki/bin/view/Geospatial/BioGeoSDIMeeting05Dec2006 Regards -- -- Tim Sutton Visit http://qgis.org for a great Open Source GIS Home Page: http://linfiniti.com Skype: timlinux MSN: tim_bdworld(a)msn.com Yahoo: tim_bdworld(a)yahoo.com Jabber: timlinux Irc: timlinux on #qgis at freenode.net

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[tdwg-ncd] FW: TIP Round-2 proposals
by Neil Thomson 01 Dec '06

01 Dec '06

Dear NCD'ers, This is fantastic news from Lee! I'm out of the Museum today and Monday, but will be in touch with Roger after that to pin down the refinements that are required. Speak with you soon, Neil -----Original Message----- From: Lee Belbin [mailto:leebel@netspace.net.au] Sent: Fri 01/12/2006 03:14 To: Neil Thomson Cc: 'Roger Hyam (tdwg)' Subject: TIP Round-2 proposals Hi Neil The TDWG Infrastructure Project Team has finally evaluated all the Round-2 proposals. As mentioned earlier, we had 28 proposals for a total of US$704,255 for a pot of ~US$250,000. The good news is that the Team has supported the funding of all of your projects- #16 - 'RDFS for NCD' #17 - 'Identify and database biodiversity organisations' #18 - 'Intro to NCD document' #19 - 'Ontology-NCD integration' #20 - 'NCD Workshop' There are a number of possible enhancements and some tuning that the Team wanted to discuss with you. We all believed that 'tweaking' of your projects should result in outcomes with greater benefit to the community. Roger has been tasked with this and reporting back to me. I have reserved additional funding that could be applied to ensure that the projects maximize their potential. Congratulations and best wishes Neil! Lee Lee Belbin Manager, TDWG Infrastructure Project Email: lee(a)tdwg.org Phone: +61(0)419 374 133

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[tdwg-ncd] NCD Toolkit bid
by Neil Thomson 28 Nov '06

28 Nov '06

Dear Larry, I have received no further requests for amendments to the bid document for the development of the NCD Toolkit and we would therefore be very grateful if you would submit the attached document to GBIF for consideration. Note that it is proposed that the work be carried out over the second and third quarters of 2007. Please let me know if there is anything else that the NCD Subgroup can provide in support of this bid. With many thanks, Neil <<NCD-GBIFToolkitBid-Final.doc>> ------- 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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[tdwg-ncd] NCD Toolkit bid - draft for comment
by Neil Thomson 23 Nov '06

23 Nov '06

NCD, Attached is the first full draft of the bid to develop the NCD Toolkit which is being prepared for GBIF. Please look it over and let me have your comments before I submit it to Larry next week. I am particularly grateful to Wouter and Markus for tackling the technical issues and would ask them to examine the text to see whether I have accurately captured the proposal, since this goes beyond my own technical knowledge. With many thanks, Neil <<NCD-GBIFToolkitBid-Draft2.doc>> ------- 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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[tdwg-ncd] RE: Moore Foundation Round II bid from NCD Task Group
by Neil Thomson 21 Nov '06

21 Nov '06

Hi Lee, As requested, here are the outputs that are expected from the NCD 2007 workshop: 1. Introduction to RDF/OWL modelling - may also be useful for TDWG-Education purposes 2. First draft of NCD RDF schema and agreement on implementation 3. Agreed list of terms for use with NCD picklists and for definition in the TDWG ontology 4. Final draft of NCD User Guide and first draft of Migration Guide. User Guide to include new section on the use og NCD for describing organisations. 5. Workshop Report Hope this helps, Neil ________________________________ From: Lee Belbin [mailto:leebel@netspace.net.au] Sent: 17 November 2006 05:35 To: Neil Thomson Subject: RE: Moore Foundation Round II bid from NCD Task Group Hi Neil I've spent the day summarising the proposals and will get a statement about them to all the submitters sometime next week. On your part 5 (the NCD meeting), I really need to know specifically what will be done at the meeting/workshop or by the people attending the meeting. I can't fund meetings, only what will be produced as a consequence of them. I've cut out part of an e-mail to Aimee Stewart (below) about this that may help. "Meetings and Workshops shouldn't be talkshops. I have found a simple process very effective for productive meetings. The cost of entry is the provision of a significant component of work. That work may be determining and documenting how to communicate between two components, outlining a portion of the workflow, providing data, writing software, researching options and presenting conclusions etc. The other key point is to come away from the meeting with the outcome. Done. Written up. The works. This tends to focus the mind, determine what is really needed, and ensure that it gets done." I've also broken your proposal into 5 components as we may end up having to pick and choose in some cases. I've done the same with a few others. On a related subject, Roger, Donald, Adrian, Stan and I have had some discussion yesterday on what the 'observations' may encompass. We currently have quite a few proposals (no charters as yet!) for Interest Groups. The structure is flat in that there has not been a 'horizontal perspective' on how any of these proposed IGs relate. I doubt we (the Exec) can do much on that until we have the charters. Catch-22. I mentioned that one perspective could put NCD into observations. Anyway, as I said early on, I strongly suggest you discuss the options with Adrian. We really need to keep the discussions flowing on this issue. Cheers Lee Lee Belbin Manager, TDWG Infrastructure Project Email: lee(a)tdwg.org Phone: +61(0)419 374 133

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[tdwg-ncd] FW: Round-2 Proposals
by Neil Thomson 21 Nov '06

21 Nov '06

NCD, Thank you for your suggestions for specific outcomes for the 2007 Workshop - I'll be forwarding them as a supplemental today. For information, the Moore Foundation bids come to nearly three times the money that is available, so we may not get everything that we requested. Neil -----Original Message----- From: Lee Belbin [mailto:leebel@netspace.net.au] Sent: 21 November 2006 00:32 To: benjamin.clark(a)imperial.ac.uk; CooperJ(a)landcareresearch.co.nz; jatorre(a)gmail.com; renato(a)cria.org.br; J.Kennedy(a)napier.ac.uk; ram(a)cs.umb.edu; ICZN-AP; RichardsK(a)landcareresearch.co.nz; asimpson(a)usgs.gov; astewart(a)ku.edu; Neil Thomson; vieglais(a)ku.edu; ghw(a)anbg.gov.au; r.j.white(a)cs.cardiff.ac.uk Subject: Round-2 Proposals To all Round-2 funding applicants- I received 28 proposals that totalled US$704,255. Evaluation is currently underway and should be completed by the end of the month. I've split a number of the proposals into logical independent components. Each will be treated on its merit. Cheers Lee Lee Belbin Manager, TDWG Infrastructure Project Email: lee(a)tdwg.org Phone: +61(0)419 374 133

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[tdwg-ncd] FW: Moore Foundation Round II bid from NCD Task Group
by Neil Thomson 17 Nov '06

17 Nov '06

Hi NCD'ers, Please see the initial feedback from Lee on our bid to the Moore Foundation. Please send me your ideas for outcomes expected from the 2007 Workshop, as indicated in the second paragraph. With thanks, Neil ________________________________ From: Lee Belbin [mailto:leebel@netspace.net.au] Sent: 17 November 2006 05:35 To: Neil Thomson Subject: RE: Moore Foundation Round II bid from NCD Task Group Hi Neil I've spent the day summarising the proposals and will get a statement about them to all the submitters sometime next week. On your part 5 (the NCD meeting), I really need to know specifically what will be done at the meeting/workshop or by the people attending the meeting. I can't fund meetings, only what will be produced as a consequence of them. I've cut out part of an e-mail to Aimee Stewart (below) about this that may help. "Meetings and Workshops shouldn't be talkshops. I have found a simple process very effective for productive meetings. The cost of entry is the provision of a significant component of work. That work may be determining and documenting how to communicate between two components, outlining a portion of the workflow, providing data, writing software, researching options and presenting conclusions etc. The other key point is to come away from the meeting with the outcome. Done. Written up. The works. This tends to focus the mind, determine what is really needed, and ensure that it gets done." I've also broken your proposal into 5 components as we may end up having to pick and choose in some cases. I've done the same with a few others. On a related subject, Roger, Donald, Adrian, Stan and I have had some discussion yesterday on what the 'observations' may encompass. We currently have quite a few proposals (no charters as yet!) for Interest Groups. The structure is flat in that there has not been a 'horizontal perspective' on how any of these proposed IGs relate. I doubt we (the Exec) can do much on that until we have the charters. Catch-22. I mentioned that one perspective could put NCD into observations. Anyway, as I said early on, I strongly suggest you discuss the options with Adrian. We really need to keep the discussions flowing on this issue. Cheers Lee Lee Belbin Manager, TDWG Infrastructure Project Email: lee(a)tdwg.org Phone: +61(0)419 374 133 ________________________________ From: Neil Thomson [mailto:N.Thomson@nhm.ac.uk] Sent: Thursday, 16 November 2006 9:54 PM To: leebel(a)netspace.net.au Subject: RE: Moore Foundation Round II bid from NCD Task Group Hi Lee, Thank you for confirming receipt. Neil ________________________________ From: Lee Belbin [mailto:leebel@netspace.net.au] Sent: 16 November 2006 02:18 To: Neil Thomson Subject: RE: Moore Foundation Round II bid from NCD Task Group Hi Neil Thanks for the proposal. I'll be evaluating them over the next few weeks and will get back you on the outcomes ASAP. Cheers Lee Lee Belbin Manager, TDWG Infrastructure Project Email: lee(a)tdwg.org Phone: +61(0)419 374 133 ________________________________ From: Neil Thomson [mailto:N.Thomson@nhm.ac.uk] Sent: Wednesday, 15 November 2006 1:53 AM To: lee(a)tdwg.org Cc: tdwg-ncd(a)lists.tdwg.org; leebel(a)netspace.net.au Subject: Moore Foundation Round II bid from NCD Task Group Hi Lee, I attach a one-page bid for funding from the Gordon and Betty Moore Foundation on behalf of the Natural Collections Descriptions Task Group. I look forward to hearing the outcome, in due course. Thank you for considering this bid, Neil <<NCD-MooreRound2Bid-Final.doc>> ------- 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 <http://www.nhm.ac.uk>

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