March 2006 - tdwg-tag - lists.tdwg.org

AW: PublicationBank - requirements evaluation
by Robert Huber 27 Mar '06

27 Mar '06

Dear Anna, Thank you for that information, I will subscribe to that mailing list today and am happy to have the opportunity to join your discussion! best regards, Robert -----Ursprungliche Nachricht----- Von: Taxonomic Databases Working Group GUID Project [mailto:TDWG-GUID@LISTSERV.NHM.KU.EDU]Im Auftrag von Anna Weitzman Gesendet: Dienstag, 21. Marz 2006 20:10 An: TDWG-GUID(a)LISTSERV.NHM.KU.EDU Betreff: 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 , www.wdc-mare.org Stratigraphy.net - 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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Re: [Tdwg-tag] RDF instead of xml schema
by Bob Morris 25 Mar '06

25 Mar '06

There are very interesting observations about this relationship on the final pages (pp. 313-314 sic!) of the current revision of the submission by IBM and others to OMG of an Ontology Definition Metamodel (ODM) http://www.omg.org/docs/ad/05-08-01.pdf Metamodels are mechanisms from Model Directed Architecture which, among other things, are designed to promote interoperability of models, not merely interoperability of the systems which implement them (which then comes for free in rigorous MDA, because implementations are a special kind of model). Users of modeling tools which convert from one model to another, e.g. code generation from UML, are often the beneficiaries of formal or informal metamodels in the conversion framework. [Here I must confess to having read only the TOC and these two pages of the ODM submission. But from those, I am prepared to speculate that the rest of it has a lot to say about the topics at hand. Indeed, if it is a successful metamodel proposal, it will have identified every single issue raised here in the last few weeks, and more....]. Bob Roderic Page wrote: > 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. > > [...] -- Robert A. Morris Professor of Computer Science UMASS-Boston http://www.cs.umb.edu/~ram phone (+1)617 287 6466

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xml-schema and RDFS
by Gregor Hagedorn 24 Mar '06

24 Mar '06

Roger wrote off-list: > We might have a complexType for a 'personType' and then create an > element within 'bookType' called 'author' that is of type 'personType'. > Is the notion of "an author" a property of a bookType or the extension > of the notion of a person? I think neither. If in any given OO-model you define a class or struct "Coordinates" with lat and long, and you use it for two properties (say TranssectStart, TransectEnd) of another class, you are not extending "Coordinates". Both xml-elements and xml-attributes are OO-properties of the current OO-class (called "Type" in xml-schema). Attributes are always simple types (OO: value- types), whereas elements can be simple or complex (or mixed, but let us forget that - all TDWG standards avoid mixed type). Confusing is that XML schema often allows you to be implicit about this, by defining "anonymous types". So you can make complex nested structures without giving the types names. Or even define global elements. But in principle, you are creating a composition of class- definitions - just that type-naming can be omitted. > In an instance document the thing encoded > within the book>author element gets the meaning of person from the type > hierarchy but the meaning of author from its position within a bookType > and the name of the element. Should we really create a complexType > called authorType that extends personType and the author element should > be of type authorType. (i.e. are the semantics in the complexType > hierarchy) or should we just have a author element of type person (i.e. > some of the the semantics are in the document structure and some in the > type hierarchy)? I think not. Otherwise in current OO programming you would have to extend the class "string" for each property where you want to use the type string. > Simply put: Are the semantics encoded in the XML Schema or in the > structure of the XML instance documents that validate against that > schema? Is it possible to 'understand' an instance document without > reference to the schema? You are correct that the semantics of a property are not defined in an ontological way, but they are implied by the property that is using a type. (They are implied in the *schema*, not the "instance"). If you add several string properties to a class in any Java, C++, Python, Visual Basic, etc. this is what you do. That is why I at the moment feel that xml-schema is intuitive to users of OO languages like the ones named. RDFS seems strange - at least to me. I realize that more OO-languages exist, I just perceive the ones "mainstream" and know little about the others. > How do we map 'concepts' in two schemas to each other if one encodes > meaning in the document structure and the other in the type hierarchy? > Even doing it manually how do we express that authorType in one schema > is equivelent to book>author(of type person) in another. This gets very > complex as the Tapir team have found. Is there are concept for every > possible element in every possible instance document for a given schema? > What about iterative nested structures? I have no answer other than simple xml transformation based on a one time (per schema combination) analysis. Although I do not believe we will truly achieve backward compatibility (it could be nominal, but not useful!) very soon, regardless of technology, these questions are certainly important for schema evolution. Do we have to go to the length of atomizing our models into subject-predicate- object tupels, or do we have other options? I find xml-schema a much simpler technology, despite all its shortcoming, some of which we have encountered ourself. Can we answer Roger's question about mapping concepts from one schema to another based on xml-schema standards like TDWG has produced so far? Gregor BTW: I just wonder how you do inheritance of a class with properties in RDFS. It seems to me that since in RDF/RDFS you do not know the number of properties a class may have, you can always only extend an abstract ("property-less") concept, but never communicate an agreement that two pieces of software desire to use an agreed set of properties. Is that correct?---------------------------- ------------------------------ 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

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Re: PublicationBank - requirements evaluation
by Donald Hobern 24 Mar '06

24 Mar '06

Thanks, Chuck. I agree that this is the best approach and that our goal should simply be to find the right communities with whom to align this activity. 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 Chuck Miller Sent: 24 March 2006 16:43 To: TDWG-GUID(a)LISTSERV.NHM.KU.EDU Subject: Re: PublicationBank - requirements evaluation Roger and Donald, Roger's list gets even worse because there are multiple editions and formats (eg. quartile) for many books/journals. The same information may thus occur on different pages across the different editions. Librarians maintain the publication records at this detailed level - ie. which editions and formats are in the library and where. I agree with Roger. This area of publication information belongs to the library community. In our Botanicus project we are digitizing 18th and 19th center botanical references. For the higher level coding information we have looked to our library management system and engaged our librarians to supply the correct information. There are existing standards and standards bodies for book/journal codification. We should not reinvent the wheel. I think this says we need to engage some library professionals into biodiversity informatics and TDWG, like we have engaged the geographical information professionals. Chuck -----Original Message----- From: Roger Hyam To: TDWG-GUID(a)LISTSERV.NHM.KU.EDU Sent: 3/24/2006 4:54 AM Subject: Re: [TDWG-GUID] PublicationBank - requirements evaluation Hi Donald, This makes perfect sense to me but I'd like to introduce one comment that might muddy the waters or help clear them. We need an understanding of the granularity of a publication in any such publication bank as I think 'publication' means different things to different people. Looking at a monograph I have in front of me: A Revision of Rhododendron VI subgenus Pentanthera (Sections Sciadorhodion, Rhodora and Viscidula) W.S. Judd and K.A. Kron (1995) Edinburgh Journal of Botany (ISSN 0960-4286), Volume 52, Number 1, Pages 1-54. On page 15 we have a good description of Rhododendron schlippenbachii (a TaxonConcept as this is not a sp nov or comb nov). The scope of publication bank could be at several levels: 1. LSID for the Journal/Book 2. LSID for the volume 3. LSID for the part 4. LSID for the article 5. LSID for the actual description on page 15. I would argue quite strongly that taking it beyond level 1 is moderately pointless as we can have a simple vocabulary of fields that can contain nice integers to uniquely identify a place within a Journal (or book). Taking it beyond 1 is also incredibly difficult. An analogy is the use of postal or zip codes. The postal code refers to a block not a single address and must be qualified by house and flat number (in the UK). Perhaps PublicationBank should really be BookAndJournalBank but identifying books and journals definitely feels to me like it is outside the scope of TDWG and firmly in the scope of the library community. I don't want to preempt the outcome of any white paper on the subject but it may be that a simple applicability statement is required on how to cite references electronically using existing numbering systems accompanied by several integer fields (year, volume, part etc). i.e. not relying on titles or author names. The above references is uniquely identified by ISSN:0960-4286:52:1:1-54. It may be accompanied by the text as well of course - for humans! Just my 2 cents. Roger Donald Hobern wrote: 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 <mailto:dhobern@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 <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 <mailto:TDWG-GUID@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 <mailto:tdwg-lit@lists.tdwg.org> ; sign up at http://lists.tdwg.org/mailman/listinfo/tdwg-lit_lists.tdwg.org/general <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/ <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 <mailto:weitzman@si.edu> INOTAXA - http://www.sil.si.edu/digitalcollections/bca/status.cfm <http://www.sil.si.edu/digitalcollections/bca/status.cfm> electronic Biologia Centrali-Americana - http://www.sil.si.edu/digitalcollections/bca/ <http://www.sil.si.edu/digitalcollections/bca/> >>> rhuber(a)WDC-MARE.ORG <mailto:rhuber@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 <mailto:rhuber@@wdc-mare.org> , robert.huber(a)stratigraphy.net <mailto:robert.huber@stratigraphy.net> -- ------------------------------------- Roger Hyam Technical Architect Taxonomic Databases Working Group ------------------------------------- http://www.tdwg.org <http://www.tdwg.org> roger(a)tdwg.org <mailto:roger@tdwg.org> +44 1578 722782 -------------------------------------

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TAPIR pywrapper.org site launched
by "Döring, Markus" 24 Mar '06

24 Mar '06

Dear all, Sorry for cross-posting. We are happy to announce the new collaborative home of the PyWrapper.org open source project: http://www.pywrapper.org Probably most of you don't know that pywrapper is the library behind the BioCASe Provider Software and the new TAPIR implementation that Markus had been working on with GBIF support in the last year. The first priority is to support the revised TAPIR protocol, but we are also working on support for the WFS and SPICE protocols. A basic Configuration Tool to help data providers with their configuration and hopefully to update from previous BioCASe versions is under development with the help of SYNTHESYS funding. We hope to include at some point also a local web-based search interface, the Query Tool. This will allow data providers to gain instant webaccess to their databases with customisable skins (html templates) to integrate in existing designs. The pywrapper library has always been released under the open source Mozilla Public License, but the development of it has mainly been done by one person alone. We want to alter this and become a truly open source project where everybody is invited to participate in the development. For this we have created a new working environment under http://www.pywrapper.org There you will find public access to the latest source code, a roadmap of the development, a report system to submit bugs and request and a new documentation system. We have also created two mailing lists: pywrapper-users(a)lists.sourceforge.net and pywrapper-devel(a)lists.sourceforge.net to improve communication between users and developers. Please feel free to join them at: http://trac.pywrapper.org/pywrapper/wiki/MailingLists If you are interested in supporting the PyWrapper development you are very welcome and can do so in a variety of ways. We would be happy to welcome: * developers who want to participate in the core python components or just simple submodules like additional database syntax support. * testers and people interested in helping us with the documentation. * decision makers helping us to prioritize development according to the different project demands. * financial supporters to speed up development or add new compontents to the software We hope you will like the new site and are excited to see the community grow. We are looking forward to work with you. Markus & Javier

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Re: PublicationBank - requirements evaluation
by Roger Hyam 24 Mar '06

24 Mar '06

Hi Donald, This makes perfect sense to me but I'd like to introduce one comment that might muddy the waters or help clear them. We need an understanding of the granularity of a publication in any such publication bank as I think 'publication' means different things to different people. Looking at a monograph I have in front of me: A Revision of Rhododendron VI subgenus Pentanthera (Sections Sciadorhodion, Rhodora and Viscidula) W.S. Judd and K.A. Kron (1995) Edinburgh Journal of Botany (ISSN 0960-4286), Volume 52, Number 1, Pages 1-54. On page 15 we have a good description of Rhododendron schlippenbachii (a TaxonConcept as this is not a sp nov or comb nov). The scope of publication bank could be at several levels: 1. LSID for the Journal/Book 2. LSID for the volume 3. LSID for the part 4. LSID for the article 5. LSID for the actual description on page 15. I would argue quite strongly that taking it beyond level 1 is moderately pointless as we can have a simple vocabulary of fields that can contain nice integers to uniquely identify a place within a Journal (or book). Taking it beyond 1 is also incredibly difficult. An analogy is the use of postal or zip codes. The postal code refers to a block not a single address and must be qualified by house and flat number (in the UK). Perhaps PublicationBank should really be BookAndJournalBank but identifying books and journals definitely feels to me like it is outside the scope of TDWG and firmly in the scope of the library community. I don't want to preempt the outcome of any white paper on the subject but it may be that a simple applicability statement is required on how to cite references electronically using existing numbering systems accompanied by several integer fields (year, volume, part etc). i.e. not relying on titles or author names. The above references is uniquely identified by ISSN:0960-4286:52:1:1-54. It may be accompanied by the text as well of course - for humans! Just my 2 cents. Roger Donald Hobern wrote: > > 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 <mailto:dhobern@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 <mailto:tdwg-lit@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 <mailto:weitzman@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 <mailto:rhuber@@wdc-mare.org>_ , > _robert.huber(a)stratigraphy.net <mailto:robert.huber@stratigraphy.net>_ > -- ------------------------------------- Roger Hyam Technical Architect Taxonomic Databases Working Group ------------------------------------- http://www.tdwg.org roger(a)tdwg.org +44 1578 722782 -------------------------------------

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Re: PublicationBank - requirements evaluation
by Chuck Miller 24 Mar '06

24 Mar '06

Roger and Donald, Roger's list gets even worse because there are multiple editions and formats (eg. quartile) for many books/journals. The same information may thus occur on different pages across the different editions. Librarians maintain the publication records at this detailed level - ie. which editions and formats are in the library and where. I agree with Roger. This area of publication information belongs to the library community. In our Botanicus project we are digitizing 18th and 19th center botanical references. For the higher level coding information we have looked to our library management system and engaged our librarians to supply the correct information. There are existing standards and standards bodies for book/journal codification. We should not reinvent the wheel. I think this says we need to engage some library professionals into biodiversity informatics and TDWG, like we have engaged the geographical information professionals. Chuck -----Original Message----- From: Roger Hyam To: TDWG-GUID(a)LISTSERV.NHM.KU.EDU Sent: 3/24/2006 4:54 AM Subject: Re: [TDWG-GUID] PublicationBank - requirements evaluation Hi Donald, This makes perfect sense to me but I'd like to introduce one comment that might muddy the waters or help clear them. We need an understanding of the granularity of a publication in any such publication bank as I think 'publication' means different things to different people. Looking at a monograph I have in front of me: A Revision of Rhododendron VI subgenus Pentanthera (Sections Sciadorhodion, Rhodora and Viscidula) W.S. Judd and K.A. Kron (1995) Edinburgh Journal of Botany (ISSN 0960-4286), Volume 52, Number 1, Pages 1-54. On page 15 we have a good description of Rhododendron schlippenbachii (a TaxonConcept as this is not a sp nov or comb nov). The scope of publication bank could be at several levels: 1. LSID for the Journal/Book 2. LSID for the volume 3. LSID for the part 4. LSID for the article 5. LSID for the actual description on page 15. I would argue quite strongly that taking it beyond level 1 is moderately pointless as we can have a simple vocabulary of fields that can contain nice integers to uniquely identify a place within a Journal (or book). Taking it beyond 1 is also incredibly difficult. An analogy is the use of postal or zip codes. The postal code refers to a block not a single address and must be qualified by house and flat number (in the UK). Perhaps PublicationBank should really be BookAndJournalBank but identifying books and journals definitely feels to me like it is outside the scope of TDWG and firmly in the scope of the library community. I don't want to preempt the outcome of any white paper on the subject but it may be that a simple applicability statement is required on how to cite references electronically using existing numbering systems accompanied by several integer fields (year, volume, part etc). i.e. not relying on titles or author names. The above references is uniquely identified by ISSN:0960-4286:52:1:1-54. It may be accompanied by the text as well of course - for humans! Just my 2 cents. Roger Donald Hobern wrote: 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 <mailto:dhobern@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 <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 <mailto:TDWG-GUID@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 <mailto:tdwg-lit@lists.tdwg.org> ; sign up at http://lists.tdwg.org/mailman/listinfo/tdwg-lit_lists.tdwg.org/general <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/ <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 <mailto:weitzman@si.edu> INOTAXA - http://www.sil.si.edu/digitalcollections/bca/status.cfm <http://www.sil.si.edu/digitalcollections/bca/status.cfm> electronic Biologia Centrali-Americana - http://www.sil.si.edu/digitalcollections/bca/ <http://www.sil.si.edu/digitalcollections/bca/> >>> rhuber(a)WDC-MARE.ORG <mailto:rhuber@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 <mailto:rhuber@@wdc-mare.org> , robert.huber(a)stratigraphy.net <mailto:robert.huber@stratigraphy.net> -- ------------------------------------- Roger Hyam Technical Architect Taxonomic Databases Working Group ------------------------------------- http://www.tdwg.org <http://www.tdwg.org> roger(a)tdwg.org <mailto:roger@tdwg.org> +44 1578 722782 -------------------------------------

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Re: 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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Re: PublicationBank - requirements evaluation
by Ricardo Scachetti Pereira 23 Mar '06

23 Mar '06

Dear all, I'm posting Matt Jones' reply to Robert Huber's survey because we are having problems with Matt's GUID list subscription. ------------------- Here I've provided responses for EML. Its not a database per se, but it is an exchange format that is in common use among ecological field sites in the US. The format basically follows End Note which is a commonly used bibliography manager at field stations. The bibliographic section of EML is described here: http://knb.ecoinformatics.org/software/eml/eml-2.0.1/eml-literature.html and here is an image of the schema which is easier to interpret: http://knb.ecoinformatics.org/software/eml/eml-2.0.1/eml-literature.png Matt Robert Huber wrote: > 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 Not a db, not 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 complete set of bib info > > - 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: All, and much more. See links above for details. > > 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 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? Complete name > > Dr. Robert Huber > WDC-MARE / PANGAEA - www.pangaea.de, www.wdc-mare.org > Stratigraphy.net - 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 -- ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Matt Jones Ph: 907-789-0496 jones(a)nceas.ucsb.edu SIP #: 1-747-626-7082 National Center for Ecological Analysis and Synthesis (NCEAS) UC Santa Barbara http://www.nceas.ucsb.edu/ecoinformatics ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

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RDF resources
by Javier de la Torre 23 Mar '06

23 Mar '06

Hi all, Now that so much is being discussed about RDF I was wondering if someone could point me to some good resources where I can learn more about it. I think there are several people right now trying to catch up with this technology so some help would be really appreciated. Thanks in advance. Javier.

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