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General
by Gregor Hagedorn 05 Nov '01

05 Nov '01

Dear colleagues, this message is from the so-called convener of the sdd group, who feels very guilty about his incapacity to organize more and invest more work. As you probably know, the topic of the group is very close to my interest, being also the topic of my proposed thesis. However, in my current situation this seems to make it rather more difficult for me. The GLOPP project I am leading here in Germany is over demanding my resources, i.e. the project is in danger of failing. I can not keep the deadlines there, and I do not find the time to continue the thesis work. So SDD has become part of a big guilt complex. I would love to do more, but I am afraid I have not done enough for a long time now. So, I will be at the TDWG congress in Sydney, and I hope we have a working group discussion there. If anybody wants to take up the lead of the group, she or he will have my support for that task. I hope we can still use the time in Sydney for fruitful discussions! Best wishes Gregor ---------------------------------------------------------- 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: SDD XML discussion in Sydney
by John C. Turnbull 24 Oct '01

24 Oct '01

I'd be interested Bob :-) ----- Original Message ----- From: "Robert A. (Bob) Morris" <ram(a)CS.UMB.EDU> To: <TDWG-SDD(a)USOBI.ORG> Sent: Thursday, October 04, 2001 9:57 AM Subject: SDD XML discussion in Sydney > I found last year that I was torn between the accessions working group > and the sdd working group, so > I wonder if anyone is interested in about a half-day pre-meeting > discussion of XML schemas/DTD for descriptive data on the afternoon of > November 8, to continue in the regular meeting. Based on our own > experience in our Electronic Field Guide project, my current belif is > that descriptive data will generally need much smaller schemas than > accession data, largely because > > (a). the latter is likely to have tags for a lot of stuff descriptive > pages need anyway and (b). mostly what is needed is some stuff to be > able to provide data typing information to characters. XSchema is > quite good at this. > > Because of (a) I will lobby in the accessions group for a clean > separation of markup that's about biological and spatio/temporal > concepts from markup that's about records. It may be that events, > e.g. collection events is another area of overlap. Indeed, one focus > of a premeeting might be to take the output of the accessions work and > see what overlap there is in desired markup. > > Bob Morris

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Re: SDD XML discussion in Sydney
by Stinger Guala 23 Oct '01

23 Oct '01

I'm interested Bob > ----- Original Message ----- > From: "Robert A. (Bob) Morris" <ram(a)CS.UMB.EDU> > To: <TDWG-SDD(a)USOBI.ORG> > Sent: Thursday, October 04, 2001 9:57 AM > Subject: SDD XML discussion in Sydney > > > > I found last year that I was torn between the accessions working group > > and the sdd working group, so > > I wonder if anyone is interested in about a half-day pre-meeting > > discussion of XML schemas/DTD for descriptive data on the afternoon of > > November 8, to continue in the regular meeting. Based on our own > > experience in our Electronic Field Guide project, my current belif is > > that descriptive data will generally need much smaller schemas than > > accession data, largely because > > > > (a). the latter is likely to have tags for a lot of stuff descriptive > > pages need anyway and (b). mostly what is needed is some stuff to be > > able to provide data typing information to characters. XSchema is > > quite good at this. > > > > Because of (a) I will lobby in the accessions group for a clean > > separation of markup that's about biological and spatio/temporal > > concepts from markup that's about records. It may be that events, > > e.g. collection events is another area of overlap. Indeed, one focus > > of a premeeting might be to take the output of the accessions work and > > see what overlap there is in desired markup. > > > > Bob Morris >

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SDD XML discussion in Sydney
by Robert A. (Bob) Morris 03 Oct '01

03 Oct '01

I found last year that I was torn between the accessions working group and the sdd working group, so I wonder if anyone is interested in about a half-day pre-meeting discussion of XML schemas/DTD for descriptive data on the afternoon of November 8, to continue in the regular meeting. Based on our own experience in our Electronic Field Guide project, my current belif is that descriptive data will generally need much smaller schemas than accession data, largely because (a). the latter is likely to have tags for a lot of stuff descriptive pages need anyway and (b). mostly what is needed is some stuff to be able to provide data typing information to characters. XSchema is quite good at this. Because of (a) I will lobby in the accessions group for a clean separation of markup that's about biological and spatio/temporal concepts from markup that's about records. It may be that events, e.g. collection events is another area of overlap. Indeed, one focus of a premeeting might be to take the output of the accessions work and see what overlap there is in desired markup. Bob Morris

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Re: Announcement of the I3C (but where are the taxonomists?)
by Vincent, Leszek 27 Jul '01

27 Jul '01

Dear TDWG folk The note below caught my interest in that I'm a taxonomist/plant systematist by vocation and am currently working in the area of ontology and controlled vocabulary development for monocots & dicots (this is an extension of the Gene Ontology paradigm - see: www.geneontology.org) Lest you're feeling hopeless about the lack of taxonomists represented in this area of endeavor (which overlaps I think with the I3C - I need to study it's mandate further), there is my voice along with those of several other biological ontologists who are collaborating with me. The relevance & inputs from taxonomy/systematics are already being realised amongst some of my colleagues - so there's hope. I'd argue that at least one taxonomist has already got his 'sleeves rolled up' (IMHO) & is working with other colleagues with similar goals (as being focused on by the I3C group). We're hoping to form the Plant Ontology Consortium to extend our tools, paradigm & 'influence', for the benefit of the users of plant-based databases. Regards, - Leszek Vincent xoxoxoxoxoxoxoxoxoxoxoxoxoxoxox P. Leszek D. Vincent Ph.D., FLS Plant Science Unit, Dept. of Agronomy, 209 Curtis Hall, University of Missouri-Columbia, Columbia, MO 65211-7020, USA. Ph: (573) 884-3716 (Agronomy), Fax:(573) 884-7850; Ph/Fax (Home): (573) 441-1228; Email: Leszek(a)missouri.edu Plant Systematist on the Maize Mapping Project - NSF award 9872655 - (http://www.cafnr.missouri.edu/mmp/ and http://www.agron.missouri.edu/) xoxoxoxoxoxoxoxoxoxoxoxoxoxoxox > -----Original Message----- > From: Eric Zurcher [mailto:Eric.Zurcher@PI.CSIRO.AU] > Sent: Monday, July 23, 2001 9:45 PM > To: TDWG-SDD(a)USOBI.ORG > Subject: Announcement of the I3C (but where are the taxonomists?) > > > >This newsgroup might not be quite the correct forum for the > following, but > >as there has been no activity of late, I hope I will be forgiven. > > At the end of June, the formation of the Interoperable Informatics > Infrastructure Consortium (I3C for short) was announced. So > what is it? The > I3C's own material states "The I3C's mission is to facilitate > and enable > data exchange, data management, and knowledge management > across the entire > life science community by promoting common protocols that ensures > interoperability in an open, consistent and robust manner." > The "common > protocols" are largely XML based. See > http://i3c.open-bio.org/ for details. > > Unfortunately, the "entire life science community" does not, > at least at > this stage, appear to include taxonomists. The emphasis is strongly on > genomics, with a substantial side interest in drug discovery. > Nevertheless, > this effort might be worth watching. It includes a number of > heavyweights > from the IT industry (IBM, Sun, Oracle), along with major players in > pharmaceuticals and genomics, so there're a lot of resources > to draw from. > Whether their efforts might someday extend to include > taxonomy, and whether > taxonomists can learn from this initiative, remains to be > seen. But that > mission statement does sound remarkably like that of TDWG... > > > > Eric Zurcher > CSIRO Livestock Industries > Canberra, ACT Australia > E-mail: Eric.Zurcher(a)pi.csiro.au >

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Re: Announcement of the I3C (but where are the taxonomists?)
by Donat Agosti 25 Jul '01

25 Jul '01

Why aren't we trying to hook us onto this bandwagon? I think we do have a real strong case with our systematics to make to be included in any of such a system! Why just be passive? Why not draft a little memo to get in touch with them, explaining what we do, how we could complement their efforts. If they are in drug recovery, a good systematics is, or will become a very important tool for them, as well as easily accessible description of taxa, synonymies, distribution patterns and models. Why be shy - we all think, we are important - so confess and come out! donat agosti antbase.org ----- Original Message ----- From: Eric Zurcher <Eric.Zurcher(a)PI.CSIRO.AU> To: <TDWG-SDD(a)USOBI.ORG> Sent: Tuesday, July 24, 2001 5:45 AM Subject: Announcement of the I3C (but where are the taxonomists?) > >This newsgroup might not be quite the correct forum for the following, but > >as there has been no activity of late, I hope I will be forgiven. > > At the end of June, the formation of the Interoperable Informatics > Infrastructure Consortium (I3C for short) was announced. So what is it? The > I3C's own material states "The I3C's mission is to facilitate and enable > data exchange, data management, and knowledge management across the entire > life science community by promoting common protocols that ensures > interoperability in an open, consistent and robust manner." The "common > protocols" are largely XML based. See http://i3c.open-bio.org/ for details. > > Unfortunately, the "entire life science community" does not, at least at > this stage, appear to include taxonomists. The emphasis is strongly on > genomics, with a substantial side interest in drug discovery. Nevertheless, > this effort might be worth watching. It includes a number of heavyweights > from the IT industry (IBM, Sun, Oracle), along with major players in > pharmaceuticals and genomics, so there're a lot of resources to draw from. > Whether their efforts might someday extend to include taxonomy, and whether > taxonomists can learn from this initiative, remains to be seen. But that > mission statement does sound remarkably like that of TDWG... > > > > Eric Zurcher > CSIRO Livestock Industries > Canberra, ACT Australia > E-mail: >

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Re: Announcement of the I3C (but where are the taxonomists?)
by Leigh Dodds 25 Jul '01

25 Jul '01

Hi, As an outside observer it seems like there's two approaches, to either develop something as a grass-roots community effort and build running code/consensus, and then work upwards to standardisation. Or begin with a formal consortium and beginning defining standards with code to follow. The chemical community has taken the former approach, and have been quite successful. http://xmlhack.com/read.php?item=1315 Cheers, L.

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Announcement of the I3C (but where are the taxonomists?)
by Eric Zurcher 24 Jul '01

24 Jul '01

>This newsgroup might not be quite the correct forum for the following, but >as there has been no activity of late, I hope I will be forgiven. At the end of June, the formation of the Interoperable Informatics Infrastructure Consortium (I3C for short) was announced. So what is it? The I3C's own material states "The I3C's mission is to facilitate and enable data exchange, data management, and knowledge management across the entire life science community by promoting common protocols that ensures interoperability in an open, consistent and robust manner." The "common protocols" are largely XML based. See http://i3c.open-bio.org/ for details. Unfortunately, the "entire life science community" does not, at least at this stage, appear to include taxonomists. The emphasis is strongly on genomics, with a substantial side interest in drug discovery. Nevertheless, this effort might be worth watching. It includes a number of heavyweights from the IT industry (IBM, Sun, Oracle), along with major players in pharmaceuticals and genomics, so there're a lot of resources to draw from. Whether their efforts might someday extend to include taxonomy, and whether taxonomists can learn from this initiative, remains to be seen. But that mission statement does sound remarkably like that of TDWG... Eric Zurcher CSIRO Livestock Industries Canberra, ACT Australia E-mail: Eric.Zurcher(a)pi.csiro.au

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"taxonomic rank" ?
by Robert A. (Bob) Morris 23 May '01

23 May '01

Our Electronic Field Guide has data in which we organize a number of sub-specific instances placing them in the hierarchy below the species, but these are not sub-specific in the sense of, say, plant varieties. Rather they are mainly sex and life-stage. I suppose calling these a taxonomic rank would not please taxonomists, but I wonder if there is any common terminology that encompasses both these and conventional taxonomic ranks, with which we could conveniently tag XML externally and object names internally. Bob Morris

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Re: DIG35 Digital Image Metadata Standard
by Robert A. (Bob) Morris 26 Apr '01

26 Apr '01

Actually, "government and educational institutions" can get it free, according to the web site. Probably most readers of TDWG and Taxacom would qualify. Stan Blum writes: > Date: Thu, 26 Apr 2001 12:33:00 -0700 > From: Stan Blum <sblum(a)calacademy.org> > To: TDWG-SDD(a)usobi.org > Subject: Re: DIG35 Digital Image Metadata Standard > > ... > Unfortunately, the DIG35 group now charges $35(USD) for the PDF of version > 1.0. The draft of v. 1.1, however, is FREE. (So get it now if you're > interested.) > > -Stan >

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