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[TDWG-SDD] TDWG SDD Wiki
by Bob Morris 09 May '06

09 May '06

The SDD Wiki has moved to the TDWG Twiki platform http://wiki.tdwg.org/twiki/bin/view/SDD/WebHome If you don't care, you can stop reading now. For a number of technical reasons, time constraints, and privacy issues, it is difficult to move wiki presences from one organization to another, so if you are a registered user at the old umb wiki but not already at the tdwg wiki platform, you need to re-register. Note however that I \have/ copied the email notification list to the new wiki, and if you merely register with the same wiki name, notification will resume. You can check out http://wiki.tdwg.org/twiki/bin/view/SDD/WebNotify. If your name appears there with a "?" it means that there is not presently a registration for you at the tdwg wiki. If you choose a different wiki name than you had at umb, you will need to edit that page if you want mail notification. -- Robert A. Morris Professor of Computer Science UMASS-Boston http://www.cs.umb.edu/~ram phone (+1)617 287 6466

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[Tdwg-img] Fwd: Image Annotation on the Semantic Web
by Kevin Richards 31 Mar '06

31 Mar '06

A w3c article that sounded relevant to the image sub group - images and the semantic web http://www.w3.org/TR/2006/WD-swbp-image-annotation-20060322/. I received this from a semantic web mailing group that are currently in the process of setting up Sem Web/RDF standards for the Health care / Life science domain (public-semweb-lifesci(a)w3.org) Kevin Richards >>> "Eric Neumann" <eneumann(a)teranode.com> 31/03/2006 12:32 a.m. >>> I wanted to bring this working draft to the attention of folks working on various HCLSIG Tasks: http://www.w3.org/TR/2006/WD-swbp-image-annotation-20060322/ This could prove very useful regarding the proposed Brain Atlas work, as well as more general microscopy applications. They do not explicitly mention the Open Microscopy Environment (OME, http://www.openmicroscopy.org/) but it is probably relevant to them and us as well. cheers, Eric ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ WARNING: This email and any attachments may be confidential and/or privileged. They are intended for the addressee only and are not to be read, used, copied or disseminated by anyone receiving them in error. If you are not the intended recipient, please notify the sender by return email and delete this message and any attachments. The views expressed in this email are those of the sender and do not necessarily reflect the official views of Landcare Research. Landcare Research http://www.landcareresearch.co.nz ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++

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[Tdwg-obs] GBIF SURVEY: generalizing / randomizing sensitive data (deadline April 1, 2006)
by Lynn Kutner 27 Mar '06

27 Mar '06

Hi all - Apologies if you've already received this; I wanted to make sure it was widely distributed. Lynn Lynn Kutner NatureServe www.natureserve.org (303) 541-0360 lynn_kutner(a)natureserve.org ******* New on-line survey <http://www.surveymonkey.com/s.asp?u=861321784377> on how data custodians are overseeing the sharing of Sensitive Primary Species Occurrence Data The GBIF Secretariat <http://www.gbif.org/> recognises concerns about the unprotected distribution of Sensitive Primary Species Occurrence Data (for example the exact localities of rare, endangered or commercially valuable taxa). This as an important issue to be addressed related to data to be shared through the GBIF network and made visible through the GBIF Data Portal <http://www.gbif.net> . We urgently need to review current approaches to obscuring or generalizing such data, and to develop best practice recommendations in this area. It is also important to understand the possible impact that such approaches may have on biodiversity science. This review will lead to a discussion paper which will be made available later this year on the GBIF web site. The GBIF Secretariat wishes to examine: * which data are regarded as 'sensitive' * which approaches are currently used by GBIF data providers to protect sensitive data (and the associated advantages and disadvantages of these approaches) * the extent to which each approach may be reversed through co-relational analysis * the extent that generalization may restrict various analyses * the level of generalization that may be appropriate for different types of data * the best ways of documenting generalization of data and the methods used * whether a standard approach can be promoted for all sensitive data provided through the GBIF network * whether changes should be made to the TDWG ABCD and Darwin Core schemas (used by GBIF for exchange of Primary Species Occurrence Data) to facilitate sharing generalised data We are offering an on-line survey <http://www.surveymonkey.com/s.asp?u=861321784377> (http://www.surveymonkey.com/s.asp?u=861321784377) and invite representatives of all institutions holding Primary Species Occurrence Data (specimen data, observations, living collections, and survey and monitoring data) to fill out this survey. The deadline for completion is April 1, 2006. After this date the survey will be closed and we will compile the responses to contribute to the review process. Further background on the survey can be found in the introduction to the survey <http://www.surveymonkey.com/s.asp?u=861321784377> . All respondents will receive a link to the draft Discussion Paper when it becomes available and there will be an opportunity to provide additional comments and reflections before the report becomes public. Larry Speers Senior Programme Officer Digitization of Natural History Collections Global Biodiversity Information Facility Copenhagen, Denmark Arthur D. Chapman (Consultant to GBIF on Sensitive Data) Australian Biodiversity Information Services Toowoomba, Australia

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Re: [Tdwg-tag] RDF instead of xml schema
by Roderic Page 24 Mar '06

24 Mar '06

Dear Gregor, Various comments: Relationship to ER ------------------------- In many ways RDF is very like ER-modelling (e.g., http://bit.csc.lsu.edu/~chen/pdf/Chen_Pioneers.pdf) indeed the W3C states that "RDF is a member of the Entity-Relationship modelling family." One could think of the modelling the link between two entities as a triple. There's also a comment on this on Danny Ayers' blog (http://dannyayers.com/2005/03/16/xml-andor-rdf/) - embedded in some other extraneous stuff. You might also want to look at D2R Map (http://www.wiwiss.fu-berlin.de/suhl/bizer/d2rmap/D2Rmap.htm) for mapping between database schema and RDF. One way I like to think of this is that I think RDMS are geared towards locally held data, hence the emphasis on primary keys and normalisation. If, however, much of the data is elsewhere (as I believe it is in biodiversity informatics) then you need ways to refer to remotely held objects (i.e., URIs, which is another way of saying GUIDs). Hence, instead of locally defined primary keys you start to store GUIDs (which, by definition, are unique). If you then start to think about relationships between the objects identified by GUIDs, then you've pretty much got RDF. I would also say that in terms of managing local data, RDBMS are not going away. RDF, in my opinion, only really becomes relevant once you want to make the data available to others, and once you want to enable people to be able to aggregate that data. RDMS and triple stores ------------------------------- Regarding triple stores, most ones that I'm aware of are actually built on top of a RDBMS. For example, I use 3store, which uses MySQL as the backend. Would we be first in line? ---------------------------------- Well, I've been serving RDF for taxonomic names since mid-2005, uBio are serving their own LSIDs, and DiGIR is moving that way. So, there are functioning examples to play with, and people making a start in this area. Does bioinformatics use it? ------------------------------------ The biggest use I've seen is the port of UniProt to RDF (http://expasy3.isb-sib.ch/~ejain//rdf/) by Eric Bain. The EBI has some interest in RDF via the BioMoby project. Another project is BioPax (see commentary at Nodalpoint - http://www.nodalpoint.org/2006/03/12/ integrating_biopax_compliant_pathway_data). GML/SVG not RDFS -------------------------- (no idea) Importing RDF ------------------- Well, this is sort of what triple stores do. Given that RDF is composed of triples the trivial mapping to a relational database is to store the triples in one table with three columns (subject, predicate, object). I guess for most people the issue is getting data out of RDBMS into RDF, not the other way around. Tools ------- As one who positively hates the diagrams XMLSpy produces I'm biased, but when I played with Altova SemanticWorks I was distinctly underwhelmed. Hope this helps, Regards Rod On 24 Mar 2006, at 17:36, Gregor Hagedorn wrote: > Hi all, > > RDF to me appears on a level of abstraction making it very hard for me > to > follow the documentation and discussion. Most of the examples are > embedded in > an artificial intelligence / reasoning use cases that I have no > experience > with. > > I am a biologist and I feel comfortable with UML, ER-modeling, > xml-schema- > modeling, and - surprise - relational databases. I believe many others > are as > well - how many datastores are actually build upon RDBMS technology? > > To me xml-schema maps nicely to both UML-like OO-modeling and > Relational DBMS. > I can guess about the advantages of opening this all up and seeing the > world as > a huge set of unstructured statement tupels. But it also scares me. > > Angst is a bad advisor. But then if only a minority of the current few > people > involved can follow on the RDF abstraction level. A few questions I > have: > > * Would we be first in line to try rdf for such complex models as > biodiversity > informatics? > > * Do Genbank/EMBL with their hundreds of employees and programmers use > rdf? > Internally/externally? The molecular bioinformatics is probably 1000 > times > larger than our biodiversity informatics. > > * Why are GML, SVG etc. based on xml schema and not RDFS? Is this just > historical? > > * Are there any tools around that let me import RDF into a relational > database > (simple tools for xml-schema-based import/export are almost standard > part of > databases now, or you can use comfortable graphical tools like Altova > MapForce). > > -- I am just trying to test some tools to help me to visualize RDFS > productions > (like Roger has send around) on a level comparable with the UML-like > xml-schema > editors (Spy, Stylus, Oracle, etc.) I will try Altova SemanticWorks > and Protege > over the next week. The screenshot seem to be about AI and semantic > web much > more than about information models (those creatures where you try to > simplify > the world to make it manageable...). > > Gregor---------------------------------------------------------- > Gregor Hagedorn (G.Hagedorn(a)bba.de) > Institute for Plant Virology, Microbiology, and Biosafety > Federal Research Center for Agriculture and Forestry (BBA) > Königin-Luise-Str. 19 Tel: +49-30-8304-2220 > 14195 Berlin, Germany Fax: +49-30-8304-2203 > > > _______________________________________________ > Tdwg-tag mailing list > Tdwg-tag(a)lists.tdwg.org > http://lists.tdwg.org/mailman/listinfo/tdwg-tag_lists.tdwg.org > > ------------------------------------------------------------------------ ---------------------------------------- Professor Roderic D. M. Page Editor, Systematic Biology DEEB, IBLS Graham Kerr Building University of Glasgow Glasgow G12 8QP United Kingdom Phone: +44 141 330 4778 Fax: +44 141 330 2792 email: r.page(a)bio.gla.ac.uk web: http://taxonomy.zoology.gla.ac.uk/rod/rod.html reprints: http://taxonomy.zoology.gla.ac.uk/rod/pubs.html Subscribe to Systematic Biology through the Society of Systematic Biologists Website: http://systematicbiology.org Search for taxon names: http://darwin.zoology.gla.ac.uk/~rpage/portal/ Find out what we know about a species: http://ispecies.org Rod's rants on phyloinformatics: http://iphylo.blogspot.com ___________________________________________________________ Yahoo! Messenger - NEW crystal clear PC to PC calling worldwide with voicemail http://uk.messenger.yahoo.com

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Re: [Tdwg-lit] PublicationBank - requirements evaluation
by Donald Hobern 24 Mar '06

24 Mar '06

Dear Anna, Thank you for making the connection between these two groups. I think it would help if I explained (particularly for the TDWG-LIT group) what questions are being addressed by the TDWG-GUID work under the general heading of "PublicationBank". During the first GUID workshop, we recognized that different classes of information require (for want of a better term) different strengths of GUIDs. It is a great help for us to be able to recognise that two references are to the same piece of data because they use the same GUID to reference it. Let me give some examples. If I state that my taxon concept includes a specimen with LSID urn:lsid:my.org:specimen:123 and someone else also includes the same LSID in the list of specimens examined as part of their revision, it helps us to make some firm deductions about shared material. It seems reasonable that we will be able to associate identifiers with specimens in a way that ensures that the vast majority of specimens can receive a single identifier, meaning that all references to that identifier refer to that specimen and that all references to that specimen use that identifier. This second part is what I mean when I speak of a strong identifier. Now consider the situation with taxon names. Many people are going to wish to refer to the same names (or nomenclatural acts). It will clearly be really valuable if we can work towards having a single GUID for each validly published name, so that we can maximize the interconnectedness of our data. If I say that refer to the name with the LSID urn:lsid:my.org:names:xyz and that LSID has data or metadata indicating that it relates to Aus bus Jones, 2004, and you use the LSID urn:lsid:another.org:names.abc to refer to the same Aus bus Jones, 2004, then we are still left with the same string matching problems we have right now with names. It therefore seems sensible to work with the nomenclators as the "preferred" issuers of LSIDs for taxon names (recognising the gaps we have today for zoological names) and to encourage a move to using those identifiers whenever we wish to provide a secure reference to each name. (Of course this implies an urgent need for tools and services to make this easy.) Turning to taxon concepts, we had a long debate as to whether it was plausible to try to enforce the same degree of preferred issuers for LSIDs for taxon concepts. If I publish the first LSID-enabled revision of a group, I may need to assign LSIDs to refer to many different taxon concepts. Someone else databasing the taxonomy of the group will have a similar task. Unless we manage a central easy-to-search registry for people quickly to find out whether someone has already assigned an LSID to Aus bus Jones, 2004 sensu Smith, 2006, we will never be able to make any assumptions based on the fact that I have used urn:lsid:my.org:concepts:123.1 and you have used urn:lsid:my.org:concepts:abc.001. Even though the two identifiers are different there is still a good chance that they may refer to the same concept (expressed as name-according to-publication). It seems much more reasonable instead to tackle the problem of getting really strong LSIDs for names (through the nomenclators) and doing the same thing for the taxonomic literature (through someone for whom we used the placeholder name "PublicationBank"). Any concept LSID can resolve through its metadata to two LSIDs, one for a name and one for a publication. Comparing concept LSIDs can therefore be based on the comparisons between these two more fundamental objects. So, from the standpoint of the GUID group, the requirement here is a very specific one. We need to find a way to manage assigning LSIDs to the publications that make up the taxonomic literature, so that we can all have what would amount to a master list of relevant publications. From this angle, "all" that is needed is a secure registry into which the bibliographic data can be stored, cleaned and assigned identifiers. Of course such a resource could also be an excellent place to register the location of online digital versions of each publication. At that point it becomes something even more valuable. On the other hand, considering it this way suggests that it may already naturally be addressed as part of the BHL or a similar effort, and part of what we would like to do is to identify any existing initiatives which may serve as a part or all of what is required for the LSID work. As I see it, the TDWG-LIT work gives a framework for the exchange of these bibliographic data, but we also need to understand the best way to get the kind of integrated biodiversity bibliography we would like to have. Does that all make sense? Best wishes, Donald --------------------------------------------------------------- Donald Hobern (dhobern(a)gbif.org) Programme Officer for Data Access and Database Interoperability Global Biodiversity Information Facility Secretariat Universitetsparken 15, DK-2100 Copenhagen, Denmark Tel: +45-35321483 Mobile: +45-28751483 Fax: +45-35321480 --------------------------------------------------------------- _____ From: Taxonomic Databases Working Group GUID Project [mailto:TDWG-GUID@LISTSERV.NHM.KU.EDU] On Behalf Of Anna Weitzman Sent: 21 March 2006 20:10 To: TDWG-GUID(a)LISTSERV.NHM.KU.EDU Subject: Re: PublicationBank - requirements evaluation Dear Robert, You may not be aware that TDWG has a list devoted to taxonomic literature standards. It would be great if you (and anyone else interested) would join in that discussion ( TDWG Literature standards mailing list tdwg-lit(a)lists.tdwg.org; sign up at http://lists.tdwg.org/mailman/listinfo/tdwg-lit_lists.tdwg.org/general ) and add your expertise. The list has only been active since early February, and the complete correspondence is in the archives ( http://lists.tdwg.org/pipermail/tdwg-lit_lists.tdwg.org/ ). Anna L. Weitzman, Ph.D. Informatics Branch Chief, National Museum of Natural History Smithsonian Institution, PO Box 37012 Natural History Building, Room W-623, MRC 136 Washington, DC 20013-7012 U.S.A. phone: (202) 633-0846 fax: (202) 786-3180 email: weitzman(a)si.edu INOTAXA - http://www.sil.si.edu/digitalcollections/bca/status.cfm electronic Biologia Centrali-Americana - http://www.sil.si.edu/digitalcollections/bca/ >>> rhuber(a)WDC-MARE.ORG 21-Mar-2006 5:06:30 AM >>> Dear all, Below is a short 'survey' which hopefully can help to get an overview on how bibliographic information currently is stored in your databases. If you don't like to fill such forms, any other info on your current literature db is also welcome, just send it to me by email! The list maybe incomplete, if you think important questions are missing there just let me and the others know. I will try to sumarize the results on the wiki later. best regards, Robert 1) How is your literature database/module organised? - [ ]Database structure completely normalized - [ ]Database structure not/incomplete normalized 2) How do you hold your bibliographic information? - [ ]Complete set of Bib info (Author, Title,Source, Volume, Pages) - [ ]Incomplete set of Bib info - [ ]Abbreviations (e.g. Stafleu&Cowan) - [ ]Bib Info and Abbreviations - Specify which bibliographic fields you hold in your db: --[ ]Author(s) --[ ]Title --[ ]Source (Journal/Book) --[ ]Pages --[ ]Date(s) --[ ]Volume --[ ]Issue --[ ]Series --[ ]URL/GUID --[ ]Source Editors --[ ]Series Editors --[ ]Other: 3) How do you store author names: - [ ]Abbreviations (e.g. Brummitt & Powell) - [ ]Complete Name as String, one author per string - [ ]Complete Name as String, all authors in one string - [ ]Last Name, First Name separated 4) How do you store journal names/ other sources - [ ]Complete Name - [ ]Abbreviation - [ ]Both - [ ]If you hold abbreviations acc. to which standard? Dr. Robert Huber WDC-MARE / PANGAEA - www.pangaea.de <http://www.pangaea.de/> , www.wdc-mare.org <http://www.wdc-mare.org/> Stratigraphy.net - www.stratigraphy.net <http://www.stratigraphy.net/> _____________________________________________ MARUM - Institute for Marine Environmental Sciences (location) University Bremen Leobener Strasse POP 330 440 28359 Bremen Phone ++49 421 218-65593, Fax ++49 421 218-65505 e-mail rhuber@@wdc-mare.org , robert.huber(a)stratigraphy.net

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[Tdwg-lit] Level 1 summary and proposal
by Anna Weitzman 09 Mar '06

09 Mar '06

Greetings all, Following on from Gregor's message, it appears that there is some consensus from those who have contributed, that the Level 1 standard should be a recommendation for the format of a microcitation, as commonly used in biological taxonomic works, most often in synonymies. It will be used in a variety of ways, but it is, in a sense, being created in order to maintain some human-readable version of an GUID for citations of published material. This is important, as Gregor points out "technically it would be sufficient to simple store a uri. However, considering we want to express scientific data, I believe it would be wise to store a uri plus a single string representation. If the uri breaks (say in 50 years), we still have the scientific data". Basically, we are, in a sense, codifying 200+ years of tradition into a recommendation. There is little in the Codes of Botanical or Zoological nomenclature to help us since the Codes are about names (especially about their 'availability' (zoo) or 'valid publication' (bot) rather than about where in the literature they were used. Nevertheless, we have cited at the bottom of this message, some relevant recommendations, which, while not directly aimed at citations in synonymy, are nonetheless relevant. It should also be noted that authors and titles are usually be abbreviated. Botany has standardized lists, which have been adopted nearly universally, for both of these, and the group may want to recommend following those lists. Zoology does not have a single list, and in most cases the lists that are used are more informal than formal. Should we recommend that TDWG work on compiling and merging those lists and proposing those as a separate standard? We make the following recommendation for the "Level 1 standard" based on that tradition along with some examples. We are not proposing the following list as named elements within the microcitation string, only the recommended components, with an initial thought as to whether each is required or optional, and their recommended order. Level 1 (Microcitation) standard recommendation Author(s) of citation (required; this could be the author(s) of a new taxon or new combination, or just that portion of the work being cited) Author(s) of work (optional; the author(s) of a book, chapter, or article, if different from citation author(s)) Title of work (required; the title of the book, book series, journal, etc.) volume indicator (optional, though required if applicable) part or issue number indicator (optional; though required if applicable) page(s) (required) image indicator (optional) Note 1: Article and/or chapter title have been omitted as they are rarely, if ever, used in microcitations; they will be included, along with many other things in level 2. Note 2: We should perhaps include some recommendation about a reference to the permanent archive for an electronic publication. How such a permanent archive is set up and probably how to cite is one of the major issues for those discussing long-term electronic data curation issues, but at least we should make reference to that ultimate goal and add an appropriate recommendation when there are community standards. Note 3: Should an LSID for the microcitation be added? Should there be an LSID that links to the level 2 standard reference with metadata that probably exists at the level of article, chapter, volume in a book series, a single book, etc.? Cheers, Anna & Chris ++++++++ Zoological Code: Recommendation 22A.2.3. if wishing to cite both the actual and the imprint dates, should first cite the actual date (...), followed by the imprint date for information and enclosed in parentheses or other brackets and quotation marks.... Recommendation 51B. Transliteration of author's name. When the author's name is customarily written in a language that does not use the Latin alphabet it should be given in Latin letters with or without diacritic marks. Recommendation 51E. Citation of contributors. If a scientific name and the conditions other than publication that make it available [...] are the responsibility not of the author of the work containing them, but of some other person(s), or less than all of joint authors, the authorship of the name, if cited, should be stated as "B in A", or "B in A & B", or in whatever form is appropriate to facilitate information retrieval.... Botanical Code: Article 46.2. A name of a new taxon must be attributed to the author or authors to whom both the name and the validating description or diagnosis were ascribed, even when authorship of the publication is different.... Note 1. When authorship of a name differs from the authorship of the publication in which it was validly published both are sometimes cited, connected by the word "in". In such a case, "in" and what follows are part of a bibliographic citation and are better omitted unless the place of publication is also being cited. Article 46.4. A name of a new taxon must be attributed to the author or authors of the publication in which it appears only when the name but not the validating description or diagnosis was ascribed to a different author or different authors.... However, ... authorship as ascribed, followed by "ex", may be inserted before the name(s) of the publishing author(s). Recommendation 46A.1. For purposes of author citation, prefixes indicating ennoblement (...) should be suppressed unless they are an inseparable part of the name. Recommendation 46A.2. When a name in an author citation is abbreviated, the abbreviation should be long enough to be distinctive, and should normally end with a consonant that, if the full name, precedes a vowel. The first letters should be given without any omission, but one of the last characteristic consonants may be added when this is customary. Recommendation 46A.3. Given names or accessory designations serving to distinguish two botanists of the same name should be abridged in the same way. Recommendation 46A.4. When it is a well-established custom to abridge a name in another manner, it is advisable to conform to custom. Note 1. Brummit & Powell's Authors of plant names (1992) provides unambiguous standard abbreviations, in conformity with the present Recommendation.... Recommendation 46B.1. In citing the author of the scientific name of a taxon, the romanization of the author's name given in the original publication should normally be accepted. Where an author failed to give a romanization, or where the author has at different times used different romanizations, then the romanization known to be preferred by the author or that most frequently adopted by the author should be accepted. In the absence of such information the author's name should be romanized in accordance with an internationally available standard.

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[Tdwg-lit] Level 2 summary
by Anna Weitzman 09 Mar '06

09 Mar '06

Greetings all, In the case of Level 2, we still have a good deal of work to do to decide on the recommendation for a standard for content and metadata. To try to start some conversation about this, we'd like to offer some ideas on what we have heard from others about why this standard is important. First, let's think about a couple of uses for this standard. In Christchurch at the TDWG meeting in 2004, Rich Pyle suggested the need for a central repository for references of taxonomic works so that taxonomists (and others) could simply pick the references that they needed from a list and they would get a bibliographic or literature cited citation in a form that they need for submission of a publication, building a CV, etc. I believe he was hoping for an open access version of EndNote or the like, that would support us all so we don't each have to build such lists. Gregor has just made much the same point. To have this functionality, we would need several things, but first, we would need the standard. In the formation of the Biodiversity Heritage Library (http://bhl.si.edu/) which Neil mentioned earlier today, the group working on it, largely from the libraries, are, apparently for the first time, attempting to catalogue biodiversity literature (larger than taxonomic, but including taxonomic) at the level of article, chapter, or volume of a book series, and not only at the higher level as libraries have traditionally done. At the same time, they are working on what the metadata will need to be to added, etc. Those working on the BHL have expressed an interest in joining our work on the level 2 standard, so it will serve all of our needs. They are currently working on getting funding for a Union Catalog of these publications. It seems to us, that this is the ideal opportunity for librarians and taxonomists to finally settle on a common way of indexing, cataloguing, describing, and finding taxonomic literature (and beyond). If the BHL can fund and build such a system that contains all of the information needed for their catalogue, we hope that it can be built upon in such ways that taxonomists will be able to use it as Rich described, as well as to generate level 1 strings and hold metadata related to language, and to contain and generate LSIDs in such a way as to link all of these. There will, of course, then be a relation to level 3, which will also need to link the level 2 database(s) and be able to used the scanned material that the BHL is generating to create the larger database(s) using the level 3 standard to make all literature interoperable and to make it further interoperable with other biodiversity data (names, concepts, specimens, barcodes, etc). Cheers, Anna & Chris

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[Tdwg-lit] Boundaries: Levels 1 & 2
by Anna Weitzman 09 Mar '06

09 Mar '06

Hi all, In this and the next couple of messages, we're going to try to summarize what has been discussed so far and refocus the discussion somewhat. There has been some level of discussion, especially from Donald, Gregor, and Roger about the form the standards should take. For now, we would like to leave that aside from this particular discussion as, I think we all agree, that seems to be a more generalized discussion that is going to affect all ongoing TDWG standards. We think it would be more productive if the group puts its focus on contents of the standards rather than form at the current time. It also appears that there is some confusion between what is included in levels 1 & 2. Level 1, as originally defined, is not intended to include metadata about the publication. To us that seems to include original language and translation/transliteration metadata which, while it is certainly relevant, might better be placed in level 2 with the rafts of other metadata. We can see an argument for inclusion of certain metadata in Level 1, although this goes against taxonomic custom and opens the door to adding lots of metadata to Level 1, which seems inappropriate. That does bring up the issue of relationship between the two standards. Should one of the uses of Level 2 be the generation of Level 1 citation(s) in various languages which then tie back to metadata in Level 2 about the language used as well as all of the other level 2 metadata? Cheers, Anna & Chris

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Re: [Tdwg-lit] Boundaries: Levels 1 & 2
by Neil Thomson 09 Mar '06

09 Mar '06

Anna & Chris, The generation of Level 1 records is a possibility, although I'm not sure in which circumstances that would be used. As I understood it, Level 1 was to be a citation and level 2 a full bibliographic record. If that is so, it would seem to make more sense to go in the opposite direction, so that the details of a publication could be tracked down from the citation for those that want to get them. The citation then has a resource discovery role, leading to richer data - a fairly common scenario. One of level 1 or 2 could usefully contain an LSID which would resolve to full text from (for example) the Biodiversity Heritage Library (BHL) once it gets going, or to other sources of the digitised version. Does that sound likely? Neil -----Original Message----- From: TDWG-Lit-bounces(a)lists.tdwg.org [mailto:TDWG-Lit-bounces@lists.tdwg.org]On Behalf Of Anna Weitzman Sent: 08 March 2006 17:42 To: TDWG-Lit(a)lists.tdwg.org Subject: [Tdwg-lit] Boundaries: Levels 1 & 2 Hi all, In this and the next couple of messages, we're going to try to summarize what has been discussed so far and refocus the discussion somewhat. There has been some level of discussion, especially from Donald, Gregor, and Roger about the form the standards should take. For now, we would like to leave that aside from this particular discussion as, I think we all agree, that seems to be a more generalized discussion that is going to affect all ongoing TDWG standards. We think it would be more productive if the group puts its focus on contents of the standards rather than form at the current time. It also appears that there is some confusion between what is included in levels 1 & 2. Level 1, as originally defined, is not intended to include metadata about the publication. To us that seems to include original language and translation/transliteration metadata which, while it is certainly relevant, might better be placed in level 2 with the rafts of other metadata. We can see an argument for inclusion of certain metadata in Level 1, although this goes against taxonomic custom and opens the door to adding lots of metadata to Level 1, which seems inappropriate. That does bring up the issue of relationship between the two standards. Should one of the uses of Level 2 be the generation of Level 1 citation(s) in various languages which then tie back to metadata in Level 2 about the language used as well as all of the other level 2 metadata? Cheers, Anna & Chris

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Re: [Tdwg-lit] Level 1 starting point
by Anna Weitzman 16 Feb '06

16 Feb '06

Hi Gregor, I must be getting dense, but I'm not sure I completely follow what you are getting at here. Perhaps the word description is confusing me. A 'micro'citation should follow some standard, which is what, I think we are trying to set here for the community as a whole, whether it matches what one journal dictates that we put into a taxonomic treatment or not. When it comes to languages, a work (as we all realize) may contain several languages. Even a single taxonomic treatment may contain several languages (if the overall language is, for example, German, a description or diagnosis in Latin, and localities are written in the language of their country of origin). Are you suggesting that we include all languages here (I can see the point of that for level 3, but for level 1 and probably even for level 2, I can't see much point in having anything more than the overall language added (in the example above, German). Cheers, Anna >>> "Gregor Hagedorn" <G.Hagedorn(a)BBA.DE> 15-Feb-2006 7:46:45 AM >>> > Thanks for this. The main question I think needs to be clarified is how > much flexibility a data provider is to be allowed in completing the > human-readable string. Clearly we do not expect to be able to perform > direct string comparisons between two provider's citations, so are these > just recommendations of components that should be included, or is the > intention to mandate a particular sequence of elements? Which ones are > considered (at least more or less) mandatory, and which are optional? I > guess we should provide some actual examples of "complete" and "partial" > citations and state whether they are regarded as sufficient. I agree and think in the contrast to the list cited by Anna a typical free-form source description would rather follow established printed publication standards (some Journal standard) and would typically NOT include a "type of publication" (in software like RefMan or EndNote typically an enumerated value, but no common language vocabulary in printed publications exists to my knowledge). So reformulating it as recommendation, I suggest to recommed adding information if the description is in a different language than the publication itself. This is quite common, most English/German/French etc. publications will cite Russion/Greek/Japanese/Chinese etc. publications either transliterated or translated. Preferred way to indicate this would be welcome. Gregor---------------------------------------------------------- Gregor Hagedorn (G.Hagedorn(a)bba.de ) Institute for Plant Virology, Microbiology, and Biosafety Federal Research Center for Agriculture and Forestry (BBA) Königin-Luise-Str. 19 Tel: +49-30-8304-2220 14195 Berlin, Germany Fax: +49-30-8304-2203 _______________________________________________ TDWG-Lit mailing list TDWG-Lit(a)lists.tdwg.org http://lists.tdwg.org/mailman/listinfo/tdwg-lit_lists.tdwg.org

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