September 2005 - tdwg-tag - lists.tdwg.org

guids
by Kevin Richards 27 Sep '05

27 Sep '05

A few thoughts... To me, the only way I can see GUIDs being used effectively is to assign a GUID to all data objects that will be exposed outside the local system where it is stored, eg database records, image files, document files - I cant see how you could assign GUIDs to specimens themselves as the specimen itself cannot be returned via a query (unless it is a loan request?). This will result in a lot of GUIDs, distributed through a lot of systems. This may seem a concern due to objects in different systems referring to the "same" object but having different GUIDs. But it is not really a problem - all we have acheived at this stage is giving every data object in all systems a globally unique ID, and one that is hopefully resolvable. Whether they may refer to the same "entity"/"concept" as another object in the system does not matter at this point. (by "concept" I dont mean "taxon concept") Objects that refer to the same "concept", such as the same taxonomic name represented in two different systems, needs to be "cross referenced" in some other way. One way this could be done is by building up a table of mappings between systems where the qualified person in each of those systems has decided the objects refer to the same "concept". These mappings can then be returned as metadata for either of the GUIDs in the two systems, as "other data objects that refer to the same thing". This will result in a fairly complex global network of mappings, and will be difficulat to maintain. Another way to do this is to have a central authoritative table of "concepts" with GUIDs that all other synonymic objects in other systems point to. Then when an object is access via its GUID, part of the metadata will be the central "concept" GUID, and therefore can be compared to other objects in other systems with the same "concept" GUID. This will also allow queries to be executed against the different systems for example "give me all objects with the central concept GUID x". It seems DOI and LSIDs are the preferred options at this stage. I personally prefer LSIDs for several reasons including their standard URN format and the fixed 1:1 mapping of objects and IDs. I see that DOIs allow, through the handle system, to query for "different" objects of an entity depending on what you want to query for. Eg for a specimen, you could query for the image of that specimen. This allows multiple objects to be accessed through a single GUID (this also seems to be how a lot of people I have talked to "view" a GUID system to work). I can see this being useful in the biodiversity informatics world but I can also see problems it may cause - each of the objects accessed through the single DOI, should have their own GUIDs otherwise they will end up being referenced from somewhere "through" another object - the maintenance of the GUIDs then becomes more challenging. My main concern with LSIDs is the "must return the exact same set of bytes everytime" requirement of LSIDs. This can be overcome however by providing all the data in the metadata of the LSID (which seems a bit backward) and only returning a "label/name" that will never change for the data of the LSID. Otherwise the versioning component of LSIDs can be used to handle changes within the data. Kevin Richards ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 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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Re: Status of LSID
by Roderic Page 27 Sep '05

27 Sep '05

The SourceForge site (http://lsid.sourceforge.net/ ) does contain quite a bit of background on the project, and some examples of how to implement clients and servers. At least some of the code is in production use. The web resolver provided by Biopathways.org (http://lsid.biopathways.org/resolver/ ) uses IBM's Perl code. The LTER LSID authority (http://lsid.limnology.wisc.edu/ ) builds on IBM's Java code. I'm assuming that BioMoby and Taverna are built on IBM's code. I also use LSIDs in my Taxonomic Search Engine. One can also gauge activity from browsing the CVS repository at SourceForge (http://cvs.sourceforge.net/viewcvs.py/lsid/ ). Most commits happened two years ago, but there are more recent commits (e.g., 7 days ago). This suggests IBM is still doing some work on it. Lastly, LSIDs are mentioned in a recent article on the Semantic Web and life sciences (http://dx.doi.org/10.1126/stke.2832005pe22). Regards Rod On 27 Sep 2005, at 09:44, Robert Huber wrote: > Dear all, > > I wonder a bit about the status of LSID. Some links lead to a > sourcefourge site, but there > is little or no information there. Some googling brougt me to a former > IBM site and to some > projects (these are also at the WIKI) which seem to promote and/or use > LSIDs. > > I am now a bit confused and would like to know how you judge the > current status of the LSID > system? Did it ever reach production status, is it still maintained > and did this system ever leave > the project status? > > best regards, > > 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(a)wdc-mare.org, robert.huber(a)stratigraphy.net 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 at http://darwin.zoology.gla.ac.uk/~rpage/portal/

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Status of LSID
by Robert Huber 27 Sep '05

27 Sep '05

Dear all, I wonder a bit about the status of LSID. Some links lead to a sourcefourge site, but there is little or no information there. Some googling brougt me to a former IBM site and to some projects (these are also at the WIKI) which seem to promote and/or use LSIDs. I am now a bit confused and would like to know how you judge the current status of the LSID system? Did it ever reach production status, is it still maintained and did this system ever leave the project status? best regards, 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(a)wdc-mare.org, robert.huber(a)stratigraphy.net

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Re: interest in guid workshop
by Ricardo Scachetti Pereira 22 Sep '05

22 Sep '05

Matt, Many thanks for expressing your interest in our discussion and workshop on GUIDs. Also thanks for adding your project information to our wiki. As far as I'm concerned there is nothing that would exclude the data items you mention from the discussion (except for some wording on the wiki - sorry). As a matter of fact, one of the aspects of the discussion here has been not only to assign and resolve globally unique identifiers to data items but also to cross-reference them in a meaninful and useful way. Certainly field observations and experiments are part of that web. Again, welcome to our group. Regards, Ricardo Matt Jones wrote: >I sent an email the other day expressing my interest in this workshop, >but it didn't seem to go through to the list. In the meantime, I >created a wiki page with the answers to your questions about why I am >interested at: > >http://wiki.gbif.org/guidwiki/wikka.php?wakka=MattJones > >I also added descriptions of GUID issues for the SEEK EcoGrid and Kepler >projects and some details about the TCS. I also will eventually add in >information about use of LSIDs in the SEEK Taxonomic Object Server (TOS) >that complements the TCS work. > >http://wiki.gbif.org/guidwiki/wikka.php?wakka=ExistingProjects > >I guess my first question is to what extent GBIF and the members of this >list think that this discussion should include use cases outside >specimen collections? Much of my work with LSIDs has been focused on >archiving field observations and experiments done by ecologists and >environmental biologists. It seems like this should be in scope for >GBIF, but thus far the limited discussion on this list has focused on >specimen collections and taxonomic nomenclature/concept issues. Should >we broaden it? > >Thanks, and looking forward to the discussion. > >Matt >-- >~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ >Matt Jones >jones(a)nceas.ucsb.edu >National Center for Ecological Analysis and Synthesis (NCEAS) >UC Santa Barbara http://www.nceas.ucsb.edu/ecoinformatics >~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ > > > _______________________________________________________ Novo Yahoo! Messenger com voz: ligações, Yahoo! Avatars, novos emoticons e muito mais. Instale agora! www.yahoo.com.br/messenger/

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interest in guid workshop
by Matt Jones 22 Sep '05

22 Sep '05

I sent an email the other day expressing my interest in this workshop, but it didn't seem to go through to the list. In the meantime, I created a wiki page with the answers to your questions about why I am interested at: http://wiki.gbif.org/guidwiki/wikka.php?wakka=MattJones I also added descriptions of GUID issues for the SEEK EcoGrid and Kepler projects and some details about the TCS. I also will eventually add in information about use of LSIDs in the SEEK Taxonomic Object Server (TOS) that complements the TCS work. http://wiki.gbif.org/guidwiki/wikka.php?wakka=ExistingProjects I guess my first question is to what extent GBIF and the members of this list think that this discussion should include use cases outside specimen collections? Much of my work with LSIDs has been focused on archiving field observations and experiments done by ecologists and environmental biologists. It seems like this should be in scope for GBIF, but thus far the limited discussion on this list has focused on specimen collections and taxonomic nomenclature/concept issues. Should we broaden it? Thanks, and looking forward to the discussion. Matt -- ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Matt Jones jones(a)nceas.ucsb.edu National Center for Ecological Analysis and Synthesis (NCEAS) UC Santa Barbara http://www.nceas.ucsb.edu/ecoinformatics ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

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Re: Questions and Suggestions to the ongoing discussion
by Donald Hobern 20 Sep '05

20 Sep '05

> Therefore I have the following suggestions for the 1.5 Million $ > project: I'll add my thoughts on Michael's real questions later, but I need to clarify one small thing. The Moore Foundation has generously made available nearly 1.5 million USD over a 30-month period to address several aspects of the operation of TDWG. This includes some funding for investigation of GUIDs, and there is some additional funding for this from GBIF, but the available funds add up to much less than USD 1.5M. 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 ---------------------------------------------------------------

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Re: Questions and Suggestions to the ongoing discussion
by Roderic Page 19 Sep '05

19 Sep '05

On 19 Sep 2005, at 12:59, Michael Malicky wrote: > ad. 3) > > Just a simple statement, as Peter already pointed out, by using > Linnean code carefully and with high quality within > our databases, we have already a working GUID in place! The thing > Linne has already invented. IMHO it is only a > question of database quality, whether the info given is a realy GUID > or only a part of it. Existing taxonomic names are not GUIDs (Globally Unique Identifiers), in that they are not always globally unique. There are numerous generic and higher level names that are the same for plants and animals, and even some species names, e.g. Agathis montana, which is the name of both a wasp and a tree. Failure to grasp this point has doomed some efforts to put taxonomy on the web, such as Wikispecies (http://species.wikipedia.org/wiki/Main_Page), and the Tree of Life pages (http://tolweb.org/tree/). These sites use names to identify pages, leaving them open to the problem of homonyms. Regarrds Rod 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 at http://darwin.zoology.gla.ac.uk/~rpage/portal/ ___________________________________________________________ Yahoo! Messenger - NEW crystal clear PC to PC calling worldwide with voicemail http://uk.messenger.yahoo.com

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Re: Questions and Suggestions to the ongoing discussion
by Peter Dawyndt 19 Sep '05

19 Sep '05

Dear Michael, > a) Growth of the specimen > b) Sampling of the specimen > c) Labeling of the specimen (locality, date, leg, etc.) > d) Conserving of the specimen > e) Determination > f) Digitisation (in house database) > g) Linking up the information to a database network > h) Analysis of the linked up specimen information > i) Revision (loop back to point f)) > > Where exactly should an artificial GUID be implemented? First of all, there's something called 'granularity' in the assignment of unique identifiers, meaning that it is application-dependent and domain-dependent to determine the first-class objects that will need unique identification through the assignment of identifiers. Some application may require more detailed cross-referencing than others. Secondly, the actual point in time where global unique identifiers come into play in the workflow you have given above is when there's a need to move from local scope to global scope. Every data manager assigns identifiers that are usually only unique withing the scope of his local database. Safeguarding unicity on in a global namespace needs a common approach, which is exactly what G in GUID is standing for. > What is the potential impact on the rest of the productlife-cicle? Turning human-readable information into information that can be interpreted (not just reproduced) by machines opens perspectives for data mining and knowledge discovery in databases to assist in exploring and further exploiting the reams of information that is generated in the life science field. The complexity of this fast growing information-jungle limits the processing capabilities of humans dramatically. > ad. 2) > > Learing a lot of latin names with a meaning is much more easy for > humans then to learn some obscure artificial codes. > Just try to rememeber 10 5 digit numbers! And no, not everybody is > eager to run around on a field trip equiped like > a high-tech soldier. GUIDs are not intended to replace the Latin names, but just serve the purpose of machine identification. Human interpretable information and machine interpretable information are to parallel worlds that go hand in hand ever since digitization of information was introduced. Have ISBN numbers replaced book titles ? Do you look at the binary code of a Word document if you want to read it ? Human interpretable information and machine interpretable information are to parallel worlds that go hand in hand ever since digitization of information was introduced. Have ISBN numbers replaced book titles ? Do you look at the binary code of a Word document when reading it ? If your answer is no to both questions, is the conclusion that there is no need for ISBN numbers or binary document formats? Peter ----------------------------------------------------------- Dr. Peter Dawyndt Laboratorium voor Microbiologie Universiteit Gent Ledeganckstraat 35 B9000 Gent, Belgie Tel.: (32)9.264.51.32 Fax.: (32)9.264.50.92 Email: Peter.Dawyndt(a)UGent.be -----------------------------------------------------------

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Questions and Suggestions to the ongoing discussion
by Michael Malicky 19 Sep '05

19 Sep '05

Dear all! Reading through the present discussion on the GUID topic has left me somehow dissapointed about the whole thing, because of the following reasons: 1) Before talking about the actual implementation of a new technology into a product, one has to look on the impact on the WHOLE life-cicle (including all major players in the cicle) of the product! Just because of a better qualtity in one production stage, the porduct will NOT nessesarely gain, the whole product may even end up worse! The implementation stage is usually the very last of a whole series of developing stages! 2) IT technology is here to close the gap between men and machine by enhancing programs to come closer to mens world, but NOT by bringing men closer to computers! 3) Before we try to build in some fancy new things, just have a close look, wether they are already there. ad. 1) Just to start a discussing my few of the whole product life cycle in the databased specimen is roughly like this: a) Growth of the specimen b) Sampling of the specimen c) Labeling of the specimen (locality, date, leg, etc.) d) Conserving of the specimen e) Determination f) Digitisation (in house database) g) Linking up the information to a database network h) Analysis of the linked up specimen information i) Revision (loop back to point f)) Just two simple question: Where exactly should an artificial GUID be implemented? and What is the potential impact on the rest of the product life-cicle? ad. 2) Learing a lot of latin names with a meaning is much more easy for humans then to learn some obscure artificial codes. Just try to rememeber 10 5 digit numbers! And no, not everybody is eager to run around on a field trip equiped like a high-tech soldier. ad. 3) Just a simple statement, as Peter already pointed out, by using Linnean code carefully and with high quality within our databases, we have already a working GUID in place! The thing Linne has already invented. IMHO it is only a question of database quality, whether the info given is a realy GUID or only a part of it. Therefore I have the following suggestions for the 1.5 Million $ project: 1) Build a schema, that enforces better overall quality, but not only in the taxon information. Dealing with analysis tools in ENBI showed me some horrible weeknesses. E.g. No one is enforced to provide the info whether a record is specimen or observation based, and the field, where this info can be OPTIONALLY given is not standardised. Building analyze tools on the top of such info is nearly impossible. 2) Help and convince database holders to raise the quality of their contributions 3) Enhance the database wrappers to speed up the network (I had to look into this for a GBIF Austria protal and found out, that the software can be improved in terms of speed just by rewriting some parts of it in C). I am looking foreward for the further discussion on the topic with great interest. sincerely yours Michael Malicky DI Michael Malicky System Administrator ZOBODAT Biologiezentrum der Oberösterreichischen Landesmuseen Johann Wilhelm Klein Str. 73 A-4040 Linz Oesterreich Tel.: +43/732/759733/33 oder +43/664/8298192 Fax.: +43/732/759733/99 Homepage: http://www.biologiezentrum.at

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Re: Questions and Suggestions to the ongoing discussion
by Richard Pyle 19 Sep '05

19 Sep '05

Hi Michael, > a) Growth of the specimen > b) Sampling of the specimen > c) Labeling of the specimen (locality, date, leg, etc.) > d) Conserving of the specimen > e) Determination > f) Digitisation (in house database) > g) Linking up the information to a database network > h) Analysis of the linked up specimen information > i) Revision (loop back to point f)) > > Just two simple question: > Where exactly should an artificial GUID be implemented? I would suspect somewhere between steps f & g (I'd lean more towards f). But in many institutions (and in my own taxonomic work), step c is merged with step f; and may come before or after steps d & e. > What is the potential impact on the rest of the product life-cicle? I would hope that it would result in increased efficiency & accuracy of steps g & h. > Learing a lot of latin names with a meaning is much more easy for > humans then to learn some obscure artificial codes. > Just try to rememeber 10 5 digit numbers! And no, not everybody is > eager to run around on a field trip equiped like > a high-tech soldier. I think this is one of the most misunderstood aspects of GUIDs. They should *NOT* be optimized for human reading. I personally don't think they should ever even be viewed by a pair of human eyes (except the occassional database manager). The scientific names (and associated information) are what the Human should read. The GUIDs are intended for computers, which are extraordinarily adept at remembering billions of 5-digit numbers, let alone 10. But I would rather see the GUIDs as 19-digit (10^64) numbers. > Just a simple statement, as Peter already pointed out, by using > Linnean code carefully and with high quality within > our databases, we have already a working GUID in place! The thing > Linne has already invented. IMHO it is only a > question of database quality, whether the info given is a realy GUID > or only a part of it. I think it's less a question of database quality than of taxonomic quality. With a few very noteworthy exceptions, the taxonomic information we need for consistent reliance on "natural key" unique identifiers for names (Nomenclatural Code + Monomial/Binomial/Trinomial + Author(s)/Year/Page) is not organized to the point where this complex key can be used as a unique identifier by a computer with any reasonable degree of certainty and repeatability. As I said above, the GUIDs should be optimized for computer usage, not human usage. > Therefore I have the following suggestions for the 1.5 Million $ > project: > > 1) Build a schema, that enforces better overall quality, but not only > in the taxon information. [...] > 2) Help and convince database holders to raise the quality of their > contributions > 3) Enhance the database wrappers to speed up the network (I had to > look into this for a GBIF Austria protal > and found out, that the software can be improved in terms of speed > just by rewriting some parts of it in C). All excellent suggestions, and all of which would, I firmly believe, be enhanced through the establishment of universal GUIDs for biologically-relevant data objects. Aloha, Rich Richard L. Pyle, PhD Database Coordinator for Natural Sciences Department of Natural Sciences, Bishop Museum 1525 Bernice St., Honolulu, HI 96817 Ph: (808)848-4115, Fax: (808)847-8252 email: deepreef(a)bishopmuseum.org http://hbs.bishopmuseum.org/staff/pylerichard.html

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