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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 22 May '01

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

26 Apr '01

The DIG35 Initiative Group is circulating for comment a Draft of Version 1.1 of their metadata specificiation for digital images. See http://www.digitalimaging.org/i_dig35.html This extensive XML-based proposal standard allows the specification of content metadata, colorimetric metadata including ICC color profiles of the imaging system and characterization of the illuminant, intellectual property rights (IPR), history of the image, capture data including GPS data,... This is very cool stuff, from a group whose members include Adobe, Agfa, Kodak, Fujifilm, Canon, HP, and Microsoft. Look into this if you are publishing images and want such things down the road as: -distributed catalog access -remote color rendering with a high likelyhood looking like the original -standardized IPR so that micropayment software can pay you everytime somebody uses your image -ease of software comparison of your image to someone else's -.... Don't look into this if: - 200+ standards proposals turn you off - You want to wait until somebody builds the applications that make use of standards and then you want to not care about the standards, just the applications - You think XML is an American TV wrestling organization

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Re: DIG35 Digital Image Metadata Standard
by Stan Blum 26 Apr '01

26 Apr '01

At 02:21 PM 4/26/01 -0400, Robert A. (Bob) Morris wrote: >The DIG35 Initiative Group is circulating for comment a Draft of >Version 1.1 of their metadata specificiation for digital images. See >http://www.digitalimaging.org/i_dig35.html <--Cross-posted to TAXACOM and TDWG-SDD --> Version 1.0 is an excellent example of a metadata standard. It is well documented and (relatively) easily understood, AND strikes an excellent (IMHO) balance between simplicity and completeness. Highly recommended reading for anyone designing databases (not necessarily image databases) or working on data standards. 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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Re: XML gateways
by Rob Stevenson 25 Mar '01

25 Mar '01

Dave, I tried looking at http://tsadev.speciesanalyst.net/DarwinCore/Darwin_core.asp but I was unsuccessful. Is the address wrong? Must I be registered? Rob Stevenson but I was unsuccessful Dave Vieglais wrote: > >-----Original Message----- > >From: TDWG - Structure of Descriptive Data [mailto:TDWG-SDD@USOBI.ORG]On > >Behalf Of Robert A. (Bob) Morris > >Sent: Tuesday, March 20, 2001 10:07 AM > >To: TDWG-SDD(a)USOBI.ORG > >Subject: Re: XML gateways > > > > > >Jim Croft writes: > > > Date: Wed, 21 Mar 2001 00:25:09 +1100 > > > From: Jim Croft <jrc(a)anbg.gov.au> > > > To: TDWG-SDD(a)usobi.org > > > Subject: Re: XML gateways > > > > ... > > > > >Sad, but true. We should kick around other ideas to solve this > >problem, though a conventional port may be the easiest for data > >sources to implement. How about: > > > >- A convention whereby if > > http://<host>/<filePath>/<cgiquery> > >yields HTML then > > http://<host>/<filePath>/xml/<cgiquery> > >yields XML > > > >-A convention whereby people set up virtual hosts---pretty easy in > >most web servers---so that if > > http://<host>/<filePath>/<cgiquery> > >yields HTML then something like > > http://xml-<host>/<filePath>/<cgiquery> > >yields XML > > > >Hopefully all of this is temporary, since a well crafted GBIF should > >provide for discovery of URL, query syntax, and return schema. My real > >point is that current versions of Oracle, SQL-Server, FileMaker, and > >Access(?) can already emit XML without much(?) effort on the part of > >the data source operators, and doing so would let people proceed to > >build interesting distributed applications. > > There are initiatives to resolve each of the issues brought up here that are > being worked on in several industry sectors: > 1. Service discovery is addressed by UDDI (Universal Description, > Description and Integration). > 2. Service description by WSDL (Web Service Description Language) which is > an XML document format for describing methods and data exposed by a web > services. > 3. IGIR (Interface for Generic Information Retrieval) provides a generic > format for information retrieval via HTTP GET or POST requests that is easy > to implement. The queries are sent as a structure easily translated into a > number of common query syntaxes (SQL for example). Results are contained > within a consistently formatted document. IGIR is optionally stateful (it's > up to the server to decide)- so a query that generates a very large result > set need not be sent back to the client all in one hit. IGIR also supports > a SOAP interface (that's what it is originally designed for), so > programmatic access to information resources becomes pretty simple. > > A search and retrieval scenario would work something like this: > A client hits on the UDDI directory, looking for services that support IGIR > and are "biologically relevant". A list of services supporting IGIR are > returned, and the client broadcasts a query to them and waits for results to > start coming back. Since the records are all formatted in a similar manner, > it is a simple process for the client to merge the results and present to > the user a nicely formatted set of results. > > Anyway, that's how things should work. To support a broadcast query, > obviously the targets must understand the contex of the query terms- so > groups within a particular domain (such as biological collections for > example) will need a set of "well known" access points (searchable fields). > Similarly, to simplify the merging of results that come back from such a > query, it would be convenient if there was an agreed record structure that > was shared between data providers. The xml output by most database vendors > is a hack designed to allow easy transport of database records using http. > Things are getting better with xsd and so forth, but the structure of the > resulting xml documents will still reflect the structure of the databases > rather than any agreed upon common format. > > Which brings us back to the "biological collections profile" concept that > was raised at the last TDWG meeting. Would anybody like to volunteer a set > of access points (searchable fields) that are relevant for biological > collections? Similarly for the record structure? The DarwinCore elements > start to address these issues, but are somewhat deficient in several > respects. They might make a reasonable starting place though- The > description with a comment section (add your gripes etc) is available at: > http://tsadev.speciesanalyst.net/DarwinCore/Darwin_core.asp > > Most of you know that the DarwinCore was originally developed as a Z39.50 > profile, hence some of the language may seem a little odd. But the main > thing to take a look at is the list of access points- which are useful from > a biological collections point of view, and what's missing? > > There are obviously other domains of biological databases beside just > collection databases. Any suggestions for commonality between them all? > > Cheers, > Dave V. > > ========================= > David A. Vieglais > University of Kansas > Natural History Museum & > Biodiversity Research Center > http://www.nhm.ukans.edu

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