January 2010 - tdwg-content

Re: [tdwg-content] [tdwg-tag] Indicating living versus deceased status in Darwin Core
by Bob Morris 30 Jan '10

30 Jan '10

Jason The GBIF Multimedia Resource Task Group (MRTG) is shortly to begin the process of submission to TDWG of its draft proposal for metadata on multimedia objects and collections. Later this year GBIF expects to support this in the Integrated Publishing Toolkit, so it might be of particular interest to you for any of the image management in your tools. The current draft is at http://www.keytonature.eu/wiki/MRTG_Schema_v0.9 The TDWG standards process will present further opportunity to comment on the proposal, but the aforementioned wiki also solicits comments (To do so, you will need to register for that wiki to comment, but not to view). Bob Morris On Fri, Jan 29, 2010 at 1:35 PM, Jason Holmberg <holmbergius(a)gmail.com> wrote: > Thanks for the responses! > > If I'm understanding this correctly...should I then propose a new term as > discussed by John? > > As background, we have a successful multi-user, Web-based mark-recapture > software platform at www.whaleshark.org that we would like to open source. > Before open sourcing it, I would like it to be as "standards-based" as > possible. One measure of this is to use DarwinCore attributes in the > database tables, allowing for the easy mapping of TapirLink into the db and > therefore easier data exposure. > > If this group can think of other standards that it would be goods to > support, please let me know. I would like to build interoperability directly > into the software before releasing it, allowing adopters of the platform to > expose data meaningfully with minimal effort. > > Thanks, > Jason > > > On Thu, Jan 28, 2010 at 5:25 PM, Phillip C. Dibner <pcd(a)ecosystem.com> > wrote: >> >> On Jan 28, 2010, at 4:17 PM, Kevin Richards wrote: >> >>> There is probably another (external to TDWG) vocab / ontology that could >>> handle this?? >> >> I'm not certain at this time. However .... >> >>> (which, I think, we ought to be encouraging anyway???) >> >> Concur. We are falling into the realm where a generic observation model >> would be useful. Otherwise, we will encounter an increasing number of ad >> hoc treatments for other attributes, without a consistent underlying >> framework. >> >> May I point, as a matter of interest, to the SONet Project: >> https://sonet.ecoinformatics.org/ >> >> Best regards, >> Flip >> >> > > > _______________________________________________ > tdwg-tag mailing list > tdwg-tag(a)lists.tdwg.org > http://lists.tdwg.org/mailman/listinfo/tdwg-tag > > -- Robert A. Morris Professor of Computer Science (nominally retired) UMASS-Boston 100 Morrissey Blvd Boston, MA 02125-3390 Associate, Harvard University Herbaria email: ram(a)cs.umb.edu web: http://bdei.cs.umb.edu/ web: http://etaxonomy.org/FilteredPush http://www.cs.umb.edu/~ram phone (+1)617 287 6466

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Re: [tdwg-content] [tdwg-tag] Indicating living versus deceased status in Darwin Core
by John R. WIECZOREK 29 Jan '10

29 Jan '10

Hi Jason, The (only) slightly more appropriate place to post this is the tdwg-content list, which I've cc'd. You've posed an interesting scenario that I suspect was never imagined during Darwin Core development. I know I didn't. More and more discussion about individuals and their status over time is emerging, and I find the process of "testing" Darwin Core against these interesting. I think there are lots of ways to accommodate the information you've mentioned using the Darwin Core as it is. Some are more satisfying and reusable than others. And if Darwin Core as it now stands ends up failing, there are ways to extend it. Here are a few ways the sighting information could be accommodated now. 1) Use the dwc:behavior term. This would be particularly suitable if you had a richer vocabulary that just alive or dead, but could be used nevertheless as long as no one gets too upset about alive and dead not being traditional behavior descriptors. Well, maybe if we assume that "dead" is a hypothesis and think about the animal "acting dead" then there might be fewer objections. ;-) 2) Use the dwc:eventRemarks term. I'm loathe to suggest this because I hate putting data with analytical potential into an ad hoc field where it can get lost or misunderstood for not having a strong context. 3) Use the dwc:dynamicProperties term. The intention of this term is pretty well documented on the Simple Darwin Core page under "Doing More with Simple Darwin Core" (http://rs.tdwg.org/dwc/terms/simple/index.htm#domore). Here's the relevant verbiage from the Simple Darwin Core page to get the full idea, along with the pros and cons of this technique. "Another way to get more out of the Darwin Core without adding a term is to "payload" the dynamicProperties term as shown in the example below, to contain a list of key-value pairs. The keys in this case would act as new unofficial terms. This is perfectly legal, since it doesn't compromise the meaning of the term. Some of the weaknesses of payloading are that it is prone to errors, inconsistencies, and lack of stable or well-defined semantics. Still, this might be a reasonable way to at least allow you to share all of your data, even if there might be problems with people using it reliably." Basically, for your example, you could include in this field the key-value pair for your data field, whatever you call it. Suppose you called it liveStatus. You could load information in Darwin Core records via the dwc:dynamicProperties term that included "liveStatus=alive" or "liveStatus=dead". In XML that could look something like this: <dwc:dynamicProperties>liveStatus=alive</dwc:dynamicProperties> 4) Finally, if none of the above are fully satisfying, you can propose that a new term be added to the Darwin Core. The process for doing so is documented on the Namespace Policy page under the Term Change Policy section (http://rs.tdwg.org/dwc/terms/namespace/index.htm#classesofchanges), specifically section 3.4 Addition of Darwin Core term declarations to existing Darwin Core namespaces. And though that section says that requests for changes should be submitted to the TDWG-TAG, there is a well-documented procedure and infrastructure for it on the Darwin Core Project Site for Discussion and Development. The details can be found on the wiki page about Submitting Issues (http://code.google.com/p/darwincore/wiki/SubmittingIssues). It's worth reading the whole thing, despite that the section of particular interest in this case is the one called "New Term Request", accessible from the link with that title. 5) Of course, you can start making your own library of terms and give them a namespace to use in tandem with Darwin Core. This may be necessary if you can't make a strong enough case for a new term - for example, because it is too specialized to be of use across communities. I'm not saying that's the case here, only that this would be cause to have to define your own namespace and terms for those specialized concepts. The advantage of creating a new Darwin Core term is that it will definitely reach a wider audience than something project based, and will thereby promote re-use and integration between data sets. Temptations I would avoid include the following: I would not use occurrenceStatus, as its meaning is pretty clear. An animal would be present, whether alive or dead. I also wouldn't use dwc:lifeStage, not because death couldn't be argued to be a life stage, but because it would be a mix of semantics to include "alive" when the term is meant to capture something about categorical ages. Now you're an expert! Good luck and respond here to tdwg-content if you have further queries about this or similar Darwin Core Issues. Cheers, John On Wed, Jan 27, 2010 at 10:32 AM, Jason Holmberg <holmbergius(a)gmail.com> wrote: > > Hello! Apologies for the newbie question, which I am hoping has reached the > correct list. > > I'm altering the names of tables in a mark-recapture database to reflect > Darwin Core labels as part of a larger open source initiative. I need to > indicate in a new field whether a whale shark sighting (occurrence) > represents a living or deceased whale shark. Which Darwin Core field would > best represent this? A look through the terms in the Quick Reference did not > yield an immeidate match for me, but apologies if I missed the obvious. Can > you recommend an appropriate field? > > Thanks in advance! > Jason Holmberg > ECOCEAN Whale Shark Photo-identification Library > http://www.whaleshark.org > > > > _______________________________________________ > tdwg-tag mailing list > tdwg-tag(a)lists.tdwg.org > http://lists.tdwg.org/mailman/listinfo/tdwg-tag > >

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Proposal to create a new DwC term for the class Individual
by Steve Baskauf 23 Jan '10

23 Jan '10

This issue is with reference to http://code.google.com/p/darwincore/issues/detail?id=69 I have proposed the creation of a new Darwin Core term, Individual, that is a class representing individual organisms in their environment (as opposed to live organisms in collections which would be Occurrences of type LivingSpecimen). The justification for this new term is given at the link above, but to summarize, this class is needed: 1. to establish the concept of an individual (in the sense of the object of dwc:individualID) and its relationship to other classes in the TDWG ontology. 2. to provide a way for users who assign a GUID as a value for the dwc term individualID to meet Recommendation 11 (regarding GUID typing) of the draft TDWG GUID Applicability Statement. I should also note that the problem that my proposal is intended to resolve may exist for other terms in the new Darwin Core standard that can refer to resources that can be identified with GUIDs. In particular, there may be no existing classes in the TDWG ontology http://tdwg-ontology.googlecode.com/svn/trunk/ontology/voc/ for GUID-labeled resources that are referenced by identificationID datasetID, eventID, and locationID . The lack of an appropriate means to type objects identified by GUIDs is only one of the impediments to the implementation of GUIDs in the biodiversity community, but it is one that can be solved relatively quickly by appropriate action on the part of the TDWG technical architecture group. Steve Baskauf -- Steven J. Baskauf, Ph.D., Senior Lecturer Vanderbilt University Dept. of Biological Sciences postal mail address: VU Station B 351634 Nashville, TN 37235-1634, U.S.A. delivery address: 2125 Stevenson Center 1161 21st Ave., S. Nashville, TN 37235 office: 2128 Stevenson Center phone: (615) 343-4582, fax: (615) 343-6707 http://bioimages.vanderbilt.edu

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Has Domain and Has Range for DwC Terms
by Moen, William 18 Jan '10

18 Jan '10

As part of our work on the Apiary Project, http://www.apiaryproject.org/content/apiary-home, we are using DwC as the foundational vocabulary for our metadata requirements. The question we currently have relates to the Has Domain and Has Range parameters for the DwC terms as listed in the Complete Historical Record: http://rs.tdwg.org/dwc/terms/history/index.htm We have been reading a number of Dublin Core as well as DwC docs to get an understanding, but it would be very helpful to hear from those of you who have worked with these parameters in DwC. Thanks. Bill ---------------------------------------------------------------------------------------------- William Moen, Ph.D. Director of Research Director, Texas Center for Digital Knowledge (TxCDK) Associate Professor, Department of Library and Information Sciences College of Information, University of North Texas 1155 Union Circle 311068, Denton, Texas 76203-5017 Email: William.Moen(a)unt.edu Website: http://www.unt.edu/wmoen Voice: 940-565-2473 (TxCDK) or 565-3563 (LIS) Fax: 940-369-7872

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Re: [tdwg-content] Any RDF example? Is this what the standard authors intended?
by Paul.Alexander＠csiro.au 14 Jan '10

14 Jan '10

Hi Pete, Thank you for your example. I'm confused by the example's use of dcterms:identifier mainly because I understand that Identifier should point to the resource being described (resource from Dublin Core point of view). My interpretation of DublinCore is that title and publisher describe the resource if it is specifically referenced, i.e. the resource is pointed to by dcterms:identifier (An unambiguous reference to the resource within a given context.) On the other hand if the rdf:Description is pointing to the resource being described, then some alternatives to dcterms:identifier would be dcterms:References, dcterms:Abstract or dcterms:Source. Each indicate we are pointing to a resource that is associated in some way with the rdf:Description resource. One possibility is to discard dcterms:Identifier, so dcterms:title will not be specifically tied to a resource outside its own namespace and will therefore be associated with its containing element i.e. rdf:Description. I clicked through the various parts via uriburner, viewed the source code, looked at the dcterms:Title of each of the RDF files in the example, and re-read the posts on 23 and 24 December but I don't get it. I will have a more thorough look at Darwin Core. Perhaps it would help my understanding if you could put the files dcterms:titled: Pedilus serratus, Bufo americanus and Shivering Sands Natural Area Beach into context. Thank you in advance. Paul ----------------------------------------------------------- On Tue, 12 Jan 2010 02:33:08, Peter DeVries <pete.devries(a)gmail.com> wrote: Hi Jamie, I have mocked up this example, but I am not sure it is what the standard authors were intending. See my post on December 23rd. Here is my example http://rdf.geospecies.org/datasets/Bcb50c3c-13f5-4c0c-A6de-5f422e2b88c7.rdf <http://rdf.geospecies.org/datasets/Bcb50c3c-13f5-4c0c-A6de-5f422e2b88c7.rdf>You can click through the various parts via uriburner http://linkeddata.uriburner.com/about/html/http://rdf.geospecies.org/datase… I also have a lot of species information in RDF, (about 2 million triples) but it is not in DarwinCore at: http://lod.geospecies.org/ The about page is here: http://about.geospecies.org/ This data set is part of the Linked Open Web or LOD, which is explained here: http://linkeddata.org/ Here is the diagram of the Linked Open Data Cloud: http://www4.wiwiss.fu-berlin.de/bizer/pub/lod-datasets_2009-03-05.html I have some examples of SPARQL queries here: http://about.geospecies.org/sparql.xhtml Here the page for one of my species http://lod.geospecies.org/ses/iuCXz.html Here is the RDF for that species http://lod.geospecies.org/ses/iuCXz.rdf I have tried to follow the DarwinCore as close as I can without breaking what I have working. In the future, I plan to rework my occurrence RDF into something like my example above, but with some additional fields. I think I can come up with a version of RDF for occurrences in DarwinCore that also follows Linked Data best practices. Hope this helps. :-) - Pete

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Any RDF example?
by Jaime Bosque 13 Jan '10

13 Jan '10

Dear list, As far as I've been working with DWC I've been just using Simple Darwin Core in XML files but now I'd like to add semantic information and therefore I've planned to use RDF. I've been looking around but couldn't find any good example of a DWC RDF, could you please provide me with one? Even better if it contains the FOAF info of the author... :) Thanks in advance, Jaime

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character encodings
by Bob Morris 11 Jan '10

11 Jan '10

Does SDD (resp. tdwg) have any best-practice about character encodings and character sets in XML. The sad fact of life is that many printed, and word processing, systematics and ecology documents have odd symbols even in characters and states, e.g. the degree sign, +- sign, the circled 'x', em-dashes, ..., which are not always rendered by browsers. -- Robert A. Morris Professor of Computer Science (nominally retired) UMASS-Boston 100 Morrissey Blvd Boston, MA 02125-3390 Associate, Harvard University Herbaria email: ram(a)cs.umb.edu web: http://bdei.cs.umb.edu/ web: http://etaxonomy.org/FilteredPush http://www.cs.umb.edu/~ram phone (+1)617 287 6466

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Cross referencing of TDWG's rank terms in an OBO rank vocabulary
by Peter Midford 04 Jan '10

04 Jan '10

Hello, A few weeks ago I inquired about the stability of URI's for the rank terms that appear in the TDWG ontology. Here's why - I am preparing to submit a rank vocabulary to the OBO foundry that includes rank terms from both NCBI and terms from TDWG. In the case of terms that came from TDWG, I have included the TDWG URIs as OBO cross references for the terms. This message is to let the TDWG community know that, barring any objection from the TDWG maintainers, I will be submitting vocabulary, including terms I picked up from TDWG, to the OBO foundry for review. If you are someone involved in both TDWG and OBO foundry, the OBO request will follow soon. Let's please keep discussion of OBO-specific issues on obo-discuss. Thanks, Peter Peter E. Midford Phenoscape Ontology Curator Peter.Midford(a)gmail.com

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clarification of the use of dwc:recordedBy
by Steve Baskauf 04 Jan '10

04 Jan '10

John et al., I have been pondering the difference of the use of the terms dwc:recordedBy and dcterms:creator (http://purl.org/dc/terms/creator). dcterms:creator is defined as: "An entity primarily responsible for making the resource." dwc:recordedBy is defined as: A list (concatenated and separated) of names of people, groups, or organizations responsible for recording the original Occurrence. The primary collector or observer, especially one who applies a personal identifier (recordNumber), should be listed first. Except for the one word "original" in dwc:recordedBy, I would believe that these two terms would mean the same thing in the case of Occurrence resources. In some cases, such as the collection of a physical specimen or photographing a live organism, I think that they are the same thing. The entity that creates the resource (specimen or image) is the same entity that has recorded the Occurrence. However, in the situation where a specimen is imaged, the resulting image resource would have a dcterms:creator that was the person or institution that did the specimen imaging, while according to the way that I read the definition, dwc:recordedBy for the specimen image would have a value that specified the collector of the specimen (not the photographer). If I am correct in this interpretation, this distinction would be useful in the case of images because it would allow for a simple mechanism to distinguish between images that directly record the appearance of individual organisms and images that are simply digital representations of some other thing that records the appearance of an individual organism, i.e. if dcterms:creator= =dwc:recordedBy then the resource was collected directly from an organsim and if dcterms:creator !=dwc:recordedBy then the resource might represent some other resource that was collected directly from an organism. I am not sure how this would apply in situations other than images. For example, if a spider were collected and assigned a persistent identifier, then later for a character documentation project the body parts were separated and considered separate specimens with their own identifiers, would the metadata for a leg specimen resource have dcterms:creator as the person who made the leg prep and dwc:recordedBy be the person who collected the spider? Basically, I would like to know the intention of the use of the word "original" in the definition of dwc:recordedBy. Steve Baskauf -- Steven J. Baskauf, Ph.D., Senior Lecturer Vanderbilt University Dept. of Biological Sciences postal mail address: VU Station B 351634 Nashville, TN 37235-1634, U.S.A. delivery address: 2125 Stevenson Center 1161 21st Ave., S. Nashville, TN 37235 office: 2128 Stevenson Center phone: (615) 343-4582, fax: (615) 343-6707 http://bioimages.vanderbilt.edu

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