- tdwg-content - lists.tdwg.org

Re: [tdwg-content] tdwg-content Digest, Vol 63, Issue 6
by Ramona Walls 28 Aug '14

28 Aug '14

I think Matt hit the nail on the head. Although Darwin Core can be used to exchange survey data, it lacks the semantics and structure necessary to archive the data without loss of information. I think the biodiversity community would be better served devoting energy to harmonizing existing technologies such as OGC, OBOE, and BCO, not to mention the many database for storing plot or survey data. The goal should be to preserve the data in the most informative manner possible. There is a strong a case for wanting to search across all evidence for occurences, including surveys and point occurences, so I can see possible demand for a tool that would extract occurences from survey data to a DwC archive. However, I am very concerned that making a DwC archive the primary exchange format for survey or plot data commits us to a path of losing information from the start, for all but the simplest sampling schemas. Ramona ------------------------------------------------------ Ramona L. Walls, Ph.D. Scientific Analyst, The iPlant Collaborative, University of Arizona Research Associate, Bio5 Institute, University of Arizona Laboratory Research Associate, New York Botanical Garden On Fri, Aug 22, 2014 at 3:00 AM, <tdwg-content-request(a)lists.tdwg.org> wrote: > Send tdwg-content mailing list submissions to > tdwg-content(a)lists.tdwg.org > > To subscribe or unsubscribe via the World Wide Web, visit > http://lists.tdwg.org/mailman/listinfo/tdwg-content > or, via email, send a message with subject or body 'help' to > tdwg-content-request(a)lists.tdwg.org > > You can reach the person managing the list at > tdwg-content-owner(a)lists.tdwg.org > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of tdwg-content digest..." > > > Today's Topics: > > 1. Re: Darwin Core: proposed news terms for expressing sample > data (Matt Jones) > 2. Re: Darwin Core: proposed news terms for expressing sample > data (Donald Hobern [GBIF]) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Thu, 21 Aug 2014 18:52:06 -0800 > From: Matt Jones <jones(a)nceas.ucsb.edu> > Subject: Re: [tdwg-content] Darwin Core: proposed news terms for > expressing sample data > To: ?amonn ? Tuama [GBIF] <eotuama(a)gbif.org> > Cc: TDWG Content Mailing List <tdwg-content(a)lists.tdwg.org> > Message-ID: > <CAFSW8xkx7uRP9PC2g3= > JT_VJanqujH8nPXoz8GXwh+JwKw5Ccw(a)mail.gmail.com> > Content-Type: text/plain; charset="utf-8" > > This proposal is treading on ground that is quite similar to other > observations and measurements standards for data exchange that are already > mature, in particular: > > * OGC Observations and Measurements ( > http://www.opengeospatial.org/standards/om) > * Extensible Observation Ontology (OBOE; > https://semtools.ecoinformatics.org/oboe) > > The former is a standard and broadly deployed, whereas the latter is part > of a research program in the use of ontologies for measurements. Through > collaboration between the two projects, they've been modified to be > reasonably isomorphic, but O&M uses an XML serialization while OBOE uses an > OWL-DL serialization. They largely express the same measurements and > sampling model once one gets beyond the terminology differences. > > So, I'm wondering if it make much sense to extend Darwin Core, which is at > heart an Occurrence exchange syntax, into this measurements area that is > well represented by these other existing specifications? I'm curious to > hear why people would even want to do this. And if we do go down this > path, won't we just end up with a new syntax that does essentially what O&M > and OBOE do now? > > Matt > > > > On Thu, Aug 21, 2014 at 12:22 AM, ?amonn ? Tuama [GBIF] <eotuama(a)gbif.org> > wrote: > > > Hi Rob, Anne, Rich, > > > > > > > > I think Markus has answered your question as to why we opted for an Event > > core which is being used in the sense described by Anne and Rich. For any > > event, you can have a list of species in an Occurrence extension and for > > each species, you can include quantity and quantityType, e.g., biomass, > > etc. The proposed term eventSeriesID was intended for linking together > > related events, although it now looks like parentEventID might be a > better, > > more flexible term. The measurementOrFact extension is a good fit for > > capturing environmental information relating to an event. See, e.g., the > > Gialova Lagoon brackish water invertebrate test data set [1] where a set > > of 18 environmental variables, including temp, pH, Rdx, particulate > organic > > matter, dissolved oxygen, salinity, chlorophyll-a were measured for each > > sampling station-sampling period combination. An example mapping is: > > > > > > > > Id measurementType measurementValue > > measurementUnit measurementRemarks > > > > IA Tmp (sed) 21.5 > > degree C Tmp > > (sed): temperature at the bottom surface > > > > > > > > **Controlled vocabularies** > > > > Ideally, the values for samplingUnit and quantityType would be selected > > from controlled vocabularies. This is, effectively, what we do by > > presenting a small list of values in a drop-down menu. The current values > > are what we derived for example data sets and discussion but they can > > undoubtedly be extended and improved. > > > > > > > > We capture ?bucket? type measures through a combination of > samplingEffort, > > samplingGeometry and samplingUnit. For example, a pitfall trap (in a > point > > location) left out for 16 days might have samplingEffort: 16, > > samplingGeometry: point and samplingUnit: day. Three m^2 quadrats in a > > shore survey might have samplingEffort: 3, samplingGeometry: area and > > samplingUnit: m^2. > > > > > > > > It would be very useful to see your compilation of scope, effort and > > completeness measures to see if we can express them in our model and/or > if > > we need to reconsider our approach. > > > > > > > > ?amonn > > > > > > > > [1] http://eubon-ipt.gbif.org/resource.do?r=ionian-brackish-lagoon > > > > > > > > *From:* tdwg-content-bounces(a)lists.tdwg.org [mailto: > > tdwg-content-bounces(a)lists.tdwg.org] *On Behalf Of *Markus D?ring > > *Sent:* 20 August 2014 23:47 > > *To:* Robert Guralnick > > > > *Cc:* TDWG Content Mailing List > > *Subject:* Re: [tdwg-content] Darwin Core: proposed news terms for > > expressing sample data > > > > > > > > Rob, > > > > > > > > this proposal if for monitoring surveys really, not to be confused with > > material samples like environmental or tissue samples which have a > distinct > > new dwc class MaterialSample. > > > > > > > > We tend to overload the term sampling a lot and it helps treating > material > > samples different from pure observational "sampling". That is why the > > existing Event class was used as the core and classic Occurrence records > as > > extensions. A classic example is a vegetation survey where each plot > > represents an Event record and each recorded species in that plot will be > > an Occurrence extension record with a given quantity. Darwin Core already > > offers individualCount to specify quantity, but it is a very specific way > > of measuring "abundance" restricted to only some use cases. Abiotic > > measurements about the plot (e.g. soil type, pH, temperature) can be > > published using the measurements or facts extension linked to the Event > > core. > > > > > > > > Markus > > > > > > > > > > > > > > > > On 20 Aug 2014, at 20:08, Robert Guralnick < > Robert.Guralnick(a)colorado.edu> > > wrote: > > > > > > > > > > > > Anne -- I don't know the answers! These are questions for Eamonn. I > > would presume that a sample could be a jumble of species or even just > water > > or soil samples, and biomass would refer to that sample - but maybe that > > isn't a use case being considered? The examples given in the longer > > document all link an event_id to species name and some measure of > quantity > > for that species (to the species, not an individual specimen), so I > assume > > that is the prevailing (or only) case? > > > > Best, Rob > > > > > > > > > > > > On Wed, Aug 20, 2014 at 11:56 AM, Anne Thessen <annethessen(a)gmail.com> > > wrote: > > > > Hi Rob > > I would like to respond to your item number 2. > > From my perspective, I deal with lots of published descriptions of taxa. > > The text might say something like "I saw species A in the Chesapeake Bay, > > the Adriatic Sea and the Indian Ocean and the biomass is 5 - 9 grams". > The > > biomass range obviously corresponds to at least three different > > occurrences, but how to divide the biomass data? I would love to be able > to > > have an *event* to attach it all to. There is almost two different levels > > of events - a sampling event and a "study event". The "study event" would > > correspond to the type of event I would like to use in the above example. > > It may not be ideal, but for the old literature that might be the best we > > can do. > > I have to admit that I don't know enough about trawl data to understand > > why an event core would be a problem. It seems that the trawl would be an > > event and each biomass measure (of each fish) would be attached to a > > separate occurrence which is attached to that event. Am I understanding > > this wrong? > > btw - I found a workaround for the example I gave, so it's not impossible > > to model with the current structure.... > > Anne > > > > > > > > On 8/20/2014 1:16 PM, Robert Guralnick wrote: > > > > > > > > ?amonn et al. --- Thanks for the clarifications. I think these help a > ton > > but it raises a couple more questions for me. > > > > > > > > 1) I am surprised that you plan to use of MeasurementorFact extension > in > > relation to the Event core, which seems like a novel (or perhaps awkward > or > > unintended?) mechanism for capturing environmental data, but the same > > extension was not be seen as relevant for describing samples? Can you > > explain more about the thinking there? > > > > > > > > 2) There may be a subtle issue here extending "Event" to be more what > you > > call a "Sampling Event Core". My read of this is that Darwin Core serves > > as a way to deal with point occurrences and Event reflects the context > of a > > single capture event (whether a single observation, or a bulk sample > > capture). The changes recommended seem to dramatically extend and change > > that meaning? Its simply a question that I don't have answer to, but is > > Darwin Core, the right vehicle to start capturing repeated measures of > > biomass values from trawls? I don't have answer but man, terms like > > quantityType (as a property of occurrence?) give me pause. > > > > > > > > 3) Is Sampling Unit a controlled vocabulary? For another project, I have > > looked through - and captured scope, effort and completeness measures > from > > - a large number of published biotic area inventories. The vast > majorities > > of these are measured in units like bucket hours, or trap nights. Is a > > "bucket" part of SamplingGeometry or Sampling Unit? I'd be happy to send > > along all the many examples of how biotic inventories of an area are > > completed and perhaps it might be good to see how those might be > > represented using the terms you are proposing? > > > > > > > > Best, Rob > > > > > > > > > > > > > > > > > > > > > > > > On Wed, Aug 20, 2014 at 10:16 AM, Richard Pyle < > deepreef(a)bishopmuseum.org> > > wrote: > > > > Same here ? Events are central to the work that we do. > > > > > > > > Aloha, > > > > Rich > > > > > > > > *From:* tdwg-content-bounces(a)lists.tdwg.org [mailto: > > tdwg-content-bounces(a)lists.tdwg.org] *On Behalf Of *Anne Thessen > > *Sent:* Wednesday, August 20, 2014 2:59 AM > > *To:* tdwg-content(a)lists.tdwg.org > > > > > > *Subject:* Re: [tdwg-content] Darwin Core: proposed news terms for > > expressing sample data > > > > > > > > Hello > > I would just like to comment on *event core*. > > I've been doing a lot of work translating published data into Darwin > Core. > > During that process I've wished several times that I could use Event as > > core. I am happy to hear about that proposed change. It will make it > easier > > to model the data I am working with. > > Anne > > > > On 8/20/2014 7:04 AM, ?amonn ? Tuama [GBIF] wrote: > > > > Hi Rob, > > > > > > > > Thank you for the feedback. I have tried to address the two main issues > > you raise below. At the outset, I would like to emphasise that much of > this > > work is taking place in the context of the EU BON project which includes > a > > task on developing/enhancing tools and standards for data sharing with a > > particular focus on the IPT for publishing sample-based data. So, we were > > constrained by the need to publish sample-based data sets in the Darwin > > Core Archive format and to demonstrate practical application using a > > working prototype. When the discussion on the TDWG list faded out, we > took > > it to our EU BON partners whose requirements were essential input to > > further development. We recognise that these discussions took place away > > from TDWG (although the TDWG/EU BON contributors overlapped) and this is > > the reason we are presenting the outcomes here for further > consideration. > > > > > > > > **Event core** > > > > As the SIGS report indicated, sample data can be modelled in Darwin Core > > Archives using either Occurrence or Event as core. This was the starting > > point for our evaluation but as things progressed the data wrangling > pushed > > the model back towards the Event core. We actually went through the > > exercise of mapping multiple test datasets in an iterative process > spanning > > several months' work. In the end, we found that using an Event core > better > > matched the typical sample data we were dealing with, allowing use of a > > measurement-or-fact extension to be included for the efficient expression > > of environmental information associated with the event. The choice comes > > down to an Occurrence core or an Event core + Occurrence extension. In > both > > cases, the true observation records are Occurrences. The big difference > is > > what type the core has and therefore to which kind of records you can > > attach further facts and extra information with DwC-A extensions. Many > > sampling datasets have very rich information about the site and event, so > > it is very natural to hang facts from an Event core. When picking the > > Occurrence core those facts would have to be repeated for each and every > > occurrence record. Moreover, our approach doesn?t stop anyone from using > > the Occurrence core if they so wish. This just provides a different > option > > for datasets that better fit an Event core model. > > > > > > > > I want to stress that we are not building a ?specific IPT version? to > > support an Event core but, rather, we adapted the IPT so that it can be > > configured to support any generic ?core + extension? format to enable its > > use for exploration of more data formats. This is part of the core > > codebase and there were no custom forks of the IPT for this work. Our > view > > at GBIF is that if there are significant numbers of data publishers who > are > > keen to adopt, promote and use a (any) format, and the tools can be > > configured to do so, then we should support it, and, if necessary, use a > > custom namespace. > > > > > > > > **New terms around abundance** > > > > Yes, the discussion on TDWG did fade out but it was clear that the term > > ?abundance? as recommended by the SIGS report (along with > > abundanceAsPercent) was confusing many when we were looking for term(s) > > that reported quantitative measures of organisms in a sample. It also > > became clear we would need to be able to state the type of quantity being > > measured. An alternative suggestion for using the MeasurementsOrFact > class > > was immediately shot down. > > > > As some of our main use cases were coming from the EU BON project, > > discussion shifted to that forum and consensus formed about the currently > > proposed terms. It was within this group that the additional terms > > (samplingGeometry, samplingUnit, eventSeriesID) were proposed and where > we > > began testing with sample data sets. > > > > > > > > Best regards, > > > > ?amonn > > > > > > > > > > > > *From:* robgur(a)gmail.com [mailto:robgur@gmail.com <robgur(a)gmail.com>] > *On > > Behalf Of *Robert Guralnick > > *Sent:* 19 August 2014 16:56 > > *To:* ?amonn ? Tuama [GBIF] > > *Cc:* TDWG Content Mailing List > > *Subject:* Re: [tdwg-content] Darwin Core: proposed news terms for > > expressing sample data > > > > > > > > > > > > Hi ?amonn --- I am curious about the outcomes presented in the SIGS > > paper, in particular, this portion of the paper: > > > > > > > > "Solutions without introducing an event core in Darwin Core Archives: > > During the review of the solutions for the uses cases, it became > apparent > > that either model could be applied to every use case. The core and > > extensions bore a complementary relationship and between them could > express > > all the required information. The core simply provided the central anchor > > in the star schema from which to join the additional information. > > Therefore, using the Occurrence core, well established in the GBIF > network > > through uptake of the IPT, seemed more appropriate than inventing > > CollectingEvent as an additional core type." > > > > > > > > That SIGS paper has John Wieczorek and you both as authors, including > > many luminaries across the biodiversity standards spectrum. Given the > > above, its curious to see the EventCore come back again, along with a > > specific IPT version to support it. > > > > > > > > So I see two issues, conflated, in this post you just made. One is > > the need for an EventCore at all, and the nature of relating Event and > > Occurrence/Material Sample. The second is the introduction of new terms, > > which seemingly have arrived after debate on similar terms - but framed > > around abundance - stalled a year ago. To my mind, these both require > some > > further discussion, because I don't (necessarily) see TDWG community > > coherence around either issue? > > > > > > > > Best, Rob > > > > > > > > > > > > On Tue, Aug 19, 2014 at 6:11 AM, ?amonn ? Tuama [GBIF] <eotuama(a)gbif.org > > > > wrote: > > > > Dear All, > > > > > > > > GBIF is committed to exploring ways in which the IPT and Darwin Core > > Archive format can be extended for publishing sample-based data sets. In > > association with the EU BON project [1], a customised version of the IPT > > [2] has been deployed to test this using a special type of Darwin Core > > Archive in which the core is an ?Event? with associated taxon occurrences > > in an ?Occurrence? extension. > > > > > > > > The Darwin Core vocabulary already provides a rich set of terms with many > > relevant for describing sample-based data. Synthesising several sources > of > > input (GBIF organised workshop on sample data, May 2013 [3], discussions > on > > the TDWG mailing list in late 2013; internal discussion among EU BON > > project partners), five new terms relating to sample data were identified > > as essential. The complete model including these new terms are fully > > described with examples in the online document ?Publishing sample data > > using the GBIF IPT? [4]. > > > > > > > > As a first step towards ratification, we would like to register the new > > terms in the DwC Google Code tracker [5] if there are no major objections > > on this list. The five terms are: > > > > > > > > 1. *quantity*: the number or enumeration value of the quantityType > > (e.g., individuals, biomass, biovolume, BraunBlanquetScale) per > > samplingUnit or a percentage measure recorded for the sample. > > > > > > > > 2. *quantityType*: : the entity being referred to by quantity, > > e.g., individuals, biomass, %species, scale type. > > > > > > > > 3. *samplingGeometry*: an indication of what kind of space was > > sampled; select from point, line, area or volume. > > > > > > > > 4. *samplingUnit*: the unit of measurement used for reporting the > > quantity in the sample, e.g., minute, hour, day, metre, metre^2, metre^3. > > It is combined with quantity and quantityType to provide the complete > > measurement, e.g., 9 individuals per day, 4 biomass-gm per metre^2. > > > > > > > > 5. *eventSeriesID*: an identifier for a set of events that are > > associated in some way, e.g., a monitoring series; may be a global unique > > identifier or an identifier specific to the series. > > > > > > > > > > > > Best regards, > > > > > > > > ?amonn > > > > > > > > [1] http://eubon.eu > > > > [2] http://eubon-ipt.gbif.org > > > > [3] > > > http://www.standardsingenomics.org/index.php/sigen/article/view/sigs.4898640 > > > > [4] http://links.gbif.org/sample_data_model > > > > [5] https://code.google.com/p/darwincore/issues/list > > > > > > > > > > > > > > > > ____________________________________________________ > > > > *?amonn ? Tuama, M.Sc., Ph.D. (eotuama(a)gbif.org <eotuama(a)gbif.org>), * > > > > *Senior Programme Officer for Interoperability, * > > > > *Global Biodiversity Information Facility Secretariat, * > > > > *Universitetsparken 15, DK-2100, Copenhagen ?, DENMARK* > > > > *Phone: +45 3532 1494 <%2B45%203532%201494>; Fax: +45 3532 1480 > > <%2B45%203532%201480>* > > > > > > > > > > _______________________________________________ > > tdwg-content mailing list > > tdwg-content(a)lists.tdwg.org > > http://lists.tdwg.org/mailman/listinfo/tdwg-content > > > > > > > > > > > > _______________________________________________ > > > > tdwg-content mailing list > > > > tdwg-content(a)lists.tdwg.org > > > > http://lists.tdwg.org/mailman/listinfo/tdwg-content > > > > > > > > -- > > > > Anne E. Thessen, Ph.D. > > > > The Data Detektiv, Owner and Founder > > > > Ronin Institute, Research Scholar > > > > 443.225.9185 > > > > > > _______________________________________________ > > tdwg-content mailing list > > tdwg-content(a)lists.tdwg.org > > http://lists.tdwg.org/mailman/listinfo/tdwg-content > > > > > > > > > > > > -- > > > > Anne E. Thessen, Ph.D. > > > > The Data Detektiv, Owner and Founder > > > > Ronin Institute, Research Scholar > > > > 443.225.9185 > > > > > > > > _______________________________________________ > > tdwg-content mailing list > > tdwg-content(a)lists.tdwg.org > > http://lists.tdwg.org/mailman/listinfo/tdwg-content > > > > > > > > _______________________________________________ > > tdwg-content mailing list > > tdwg-content(a)lists.tdwg.org > > http://lists.tdwg.org/mailman/listinfo/tdwg-content > > > > >

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Darwin Core: proposed news terms for expressing sample data
by Éamonn Ó Tuama [GBIF] 22 Aug '14

22 Aug '14

Dear All, GBIF is committed to exploring ways in which the IPT and Darwin Core Archive format can be extended for publishing sample-based data sets. In association with the EU BON project [1], a customised version of the IPT [2] has been deployed to test this using a special type of Darwin Core Archive in which the core is an Event with associated taxon occurrences in an Occurrence extension. The Darwin Core vocabulary already provides a rich set of terms with many relevant for describing sample-based data. Synthesising several sources of input (GBIF organised workshop on sample data, May 2013 [3], discussions on the TDWG mailing list in late 2013; internal discussion among EU BON project partners), five new terms relating to sample data were identified as essential. The complete model including these new terms are fully described with examples in the online document Publishing sample data using the GBIF IPT [4]. As a first step towards ratification, we would like to register the new terms in the DwC Google Code tracker [5] if there are no major objections on this list. The five terms are: 1. quantity: the number or enumeration value of the quantityType (e.g., individuals, biomass, biovolume, BraunBlanquetScale) per samplingUnit or a percentage measure recorded for the sample. 2. quantityType: : the entity being referred to by quantity, e.g., individuals, biomass, %species, scale type. 3. samplingGeometry: an indication of what kind of space was sampled; select from point, line, area or volume. 4. samplingUnit: the unit of measurement used for reporting the quantity in the sample, e.g., minute, hour, day, metre, metre^2, metre^3. It is combined with quantity and quantityType to provide the complete measurement, e.g., 9 individuals per day, 4 biomass-gm per metre^2. 5. eventSeriesID: an identifier for a set of events that are associated in some way, e.g., a monitoring series; may be a global unique identifier or an identifier specific to the series. Best regards, Éamonn [1] http://eubon.eu [2] http://eubon-ipt.gbif.org [3] http://www.standardsingenomics.org/index.php/sigen/article/view/sigs.4898640 [4] <http://links.gbif.org/sample_data_model> http://links.gbif.org/sample_data_model [5] https://code.google.com/p/darwincore/issues/list ____________________________________________________ Éamonn Ó Tuama, M.Sc., Ph.D. (eotuama(a)gbif.org), Senior Programme Officer for Interoperability, Global Biodiversity Information Facility Secretariat, Universitetsparken 15, DK-2100, Copenhagen Ø, DENMARK Phone: +45 3532 1494; Fax: +45 3532 1480

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Initiation of public comment on proposed Darwin Core changes
by joel sachs 11 Aug '14

11 Aug '14

All, As Steve pointed out [1], the Darwin Core Term Change Policy [2] specifies that a 30-day public comment period is required before significant changes are made to the standard. I always thought that this 30 day period automatically begins when proposed changes are summarized and entered into the Issue Tracker. Steve, however, believes that the public-comment period must be initiated via an email to tdwg-content, sent by either John (in his capacity as DwC steward), or by the executive. Maybe the best reading of the policy is that public comment periods should be initiated via email to tdwg-content, and that anyone can initiate a public comment period for a proposal that is contained in the Issue Tracker. Taking this reading, I hereby initiate public comment on the changes outlined in issues 204 - 226 in the Darwin Core issue tracker [3]. Best to everyone, Joel. 1. http://lists.tdwg.org/pipermail/tdwg-content/2014-July/003277.html 2. http://rs.tdwg.org/dwc/terms/namespace/index.htm#classesofchanges 3. https://code.google.com/p/darwincore/issues/list

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Proposed changes to Darwin Core
by joel sachs 25 Jul '14

25 Jul '14

Hi Everyone, I’d like to direct everyone’s attention to issues 204 - 226 in the Darwin Core issue tracker [1]. These issues describe proposed changes to the Darwin Core standard, and were entered back in January in follow up to the Documenting Darwin Core workshop held at TDWG 2013. These proposals reflect what the organizers of that workshop believe to be the consensus that was reached during the workshop’s four sessions in Florence. The background for this is that, for some time, a number of TDWGers have been working towards an applicability statement to provide guidance on expressing Darwin Core data using RDF. In the course of this work, it became apparent that the semantics of Darwin Core itself needed a slight re-think, in order to be usable on the semantic web. The goal was to be backward-compatible, i.e. to introduce and re-define terms in a way that does not affect the meaning of existing Darwin Core spreadsheet data, but which provides the semantic grounding necessary for meaningful RDF. I think this goal has, for the most part, been realized. If you have examples to the contrary, please share them. Steve Baskauf provides a good overview of the proposals in Issue 204. Of all of them, only Issue 205 (the introduction of a class to represent the taxonomically homogenous units that are described in Darwin Core occurrence data) was contentious, primarily because we disagreed on a good name for the class. (“We” refers to the ad-hoc group that worked on translating the notes from the workshop into concrete proposals - John Wieczorek, James Macklin, Markus Döring, Rich Pyle, Tim Robertson, Bob Morris, Hilmar Lapp, Steve Baskauf, Gregor Hagedorn, and myself.) I’ve mentioned my own concerns as a comment on that issue. There is one proposal that had the support of the group, but that is not yet entered into the Issue Tracker - the deprecation of dwc:basisOfRecord. The motivation for this proposal is that dwc:basisOfRecord is widely misunderstood and inconsistently used, coupled with the fact that GBIF currently uses basisOfRecord with the semantics of the (to be proposed) dwc:hasEvidence term. However, we have held back on proposing "hasEvidence", as there remain some unresolved issues regarding how it would be used. This will likely be left as future work, perhaps to be tackled at TDWG 2014. Many thanks to all who participated in the workshop, and to all who take the time to review its outcomes. Joel. 1. https://code.google.com/p/darwincore/issues/list ["ID" -> "Sort Down" to see in order]

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You're Invited - Data Management Interest Group - Kickoff Webinar 7 August
by Debbie Paul 20 Jul '14

20 Jul '14

Hello Everyone!, Got data in your database? Have you shared it? Is your data available via one or more other websites? Can you get enhanced, modified, standardized, georeferenced, annotated data from these sites back into your database? Re-integrating data can be challenging for many reasons. A new Data Management Interest Group at iDigBio plans to discuss issues surrounding shared data. We'd like to document the help, information, and infrastructure the community needs in order to re-integrate data. If you need help, please come to this meeting and share what issues you face. If you have ideas for how to help, please join us. *What:* Webinar to kickoff a new iDigBio Data Management Interest Group <https://www.idigbio.org/content/data-management-interest-group-kickoff-webi…> *What format*: A short presentation will be followed by open discussion for all participants. *When:* Thursday 7 August 2014, 1:00 - 2:00 PM EDT *Where: *http://idigbio.adobeconnect.com/datamgmt (nothing to install, use any browser) Headsets are recommended (they help remove echo). *Who: *All are welcome, please invite your colleagues, no registration needed. *Questions?* Please send to any member of the group: Data Management Interest Group <https://www.idigbio.org/wiki/index.php/IDigBio_Working_Groups#Data_Manageme…> See you soon! Deb Paul, et al *Wiki: *https://www.idigbio.org/wiki/index.php/Data_Management_Interest_Group (please excuse cross-postings) -- Upcoming iDigBio Events https://www.idigbio.org/calendar --Deborah Paul, on Twitter @idbdeb iDigBio Technology Specialist Institute for Digital Information, 234 LSB Florida State University Tallahassee, Florida 32306 850-644-6366

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[Job Announcement Bonn, Germany] 2 Information Scientists - DFG Project "eScience-Compliant Standards for Morphology"
by Lars Vogt 19 Jun '14

19 Jun '14

Job Announcement -------------------------------------------------------------------------------------------------------------------------------------------------------- The *Institute of Evolutionary Biology and Ecology* of the *Friedrich-Wilhelms University of Bonn, Germany*, invites applications for the positions of *2 Information Scientists (f/m; TV-L 13 = app. 42.000€ year's salary, pre-tax; 100%)* for three years for the *DFG projekt „eScience-Compliant Standards for Morphology“*, anticipated *starting date August 1^st 2014*. --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- *Project Aims and Scope:*Following a user-centered-design approach and in close coordination with four use-cases, new modules for ontology-based morphological descriptions, taxonomic descriptions, and image annotation will be developed for the morphological data repository /Morph·D·Base/ (www.morphdbase.de). It should be possible to create the descriptions either through natural language processing and semantic annotation (text markup) or by entering RDF triplets using ontologies. The development of these modules is done in close collaboration with the US-American project „TaxonWorks“ (taxonworks.org). For additional information about the project please refer to http://emorphology.morphdbase.de. *Work Environment:*We provide the opportunity to work for a large national project, in a team of three programmers and other scientists from scientific research collections and biodiversity informatics. You will work in the interdisciplinary, still very young and exciting field of research of ontology applications. You will develop new approaches for solving very complex questions of comparative morphology and taxonomy. *Responsibilities:*Setting up an ontology-server and reasoner, adaptation of different modules for display and input of ontologies and the development of missing functionality for the Web interface of Morph·D·Base. Furthermore, participating in regular meetings of all persons involved in the project is necessary. For the most part, these meetings will be held in Germany. *Requirements: *If you have knowledge in dealing with ontologies and programming of ontology applications, you are welcome in our team! Further, we would like applicants to have experience in setting up an ontology-server and reasoner, in the implementation of Web interfaces, as well as in the design of databases. In case the applicant is correspondingly qualified, payment will be according to German TV-L 13 pay scale (app. 42.000€ year's salary, pre-tax). Part-time work is possible. Disabled applicants will be given preference when equal qualifications are present.To increase the number of women in the scientific staff, female candidates are especially asked to apply. Please forward your applications including CV, list of successfully completed projects, references and copies of certificates *online until 10th of July 2014* to: *Mrs. K. Hennes (**secretary(a)evolution.uni-bonn.de* <mailto:secretary@evolution.uni-bonn.de>*)*. For further questions please contact Dr. Lars Vogt (lars.m.vogt(a)googlemail.com) or Dr. Peter Grobe (p.grobe(a)zfmk.de). --- Diese E-Mail ist frei von Viren und Malware, denn der avast! Antivirus Schutz ist aktiv. http://www.avast.com

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DataONE Users Group Meeting, Registration Closing Soon
by David Bloom 05 Jun '14

05 Jun '14

*DMPTool v2 workshop at the DataONE Users Group Meeting* The DMPTool partners are pleased to announce a half-day workshop at the upcoming DataONE Users Group (DUG) meeting in Frisco, CO July 6th and 7th. The DUG meeting is co-located with the ESIP summer meeting. The half day workshop on the afternoon of Monday July 7th will introduce the recently released version 2 of the widely used DMPTool. It will introduce new and existing users to data management plan requirements, features of the new tool for the completion of comprehensive Data Management Plans that meet funder requirements, highlight key features for specific user groups, and will culminate with hands-on practice using the tool. All stakeholders are invited, with particular emphasis on researchers, research administrators, funders, and librarians/IT managers. Registration for the workshop, and the broader DataONE User Group (DUG) meeting, is free. Further information on the DUG, meeting and workshop agendas (see also below) and registration information is available at: http://www.dataone.org/dataone-users-group . Attendees can register directly at: http://www.dataone.org/dataone-users-group-meeting-registration-2014 . Reduced rate hotel reservations can be made at: http://inntopia.travel/aspnet/09/packageselect.aspx?salesid=912471&packagec… until *Today, Thursday June 5th*. The workshop will be led by Andrew Sallans (Center for Open Science), Patricia Cruse (California Digital Library) and Amber Budden (DataONE). The DataONE Users Group Meeting will include sessions led by Bill Michener, Dave Vieglais, Amber Budden, Chris Jones, Laura Moyers, Bruce Wilson among others. We look forward to seeing you there. *DMPTool Workshop Agenda* 1. Overview of data management planning requirements 2. Creating a plan with the DMPTool; funder templates, collaborative workspace, supporting materials 3. Specialized tracks (hands-on section): Researchers: writing and collaborating on data management plans Research administrators/funders/librarians/IT managers: customization of the DMPTool for institutions, funders, etc. 4. Next Steps and feedback; round table discussion exploring usability of the current tool and desired functionality for v3. David Bloom VertNet Coordinator Museum of Vertebrate Zoology University of California, Berkeley 3101 Valley Life Sciences Building Berkeley, CA 94720-3160 Phone: 510.643.1620 Fax: 510.643.8238 Email: dbloom(a)vertnet.org Email: dbloom(a)berkeley.edu URL: http://www.vertnet.org VertNet Portals: MaNIS: http://www.manisnet.org HerpNET: http://www.herpnet.org ORNIS: http://www.ornisnet.org FishNet2: http://www.fishnet2.net

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Biodiversity Informatics Course open to Nordic graduate students, postdocs, and researchers
by Deb Paul 05 Jun '14

05 Jun '14

Hi Everyone, Thought you'd all like to know about this upcoming Biodiversity Informatics course, offered to Nordic graduate students, postdocs, and researchers. Kilpisjärvi calling: Order and Sense to Your Data at the Polar Frontier ForBio: proudly presents the first-time-ever course on biodiversity informatics and data management *More info:* http://www.forbio.uio.no/events/courses/2014/biodiv_informatics.html *When:* 29 July -1 August 2014 *Where:* Kilpisjärvi Biological Station, University of Helsinki, Finland http://www.helsinki.fi/kilpis/english/ *What:* A course for Nordic graduate students, postdocs, and researchers which explores data tools beyond MS Excel and R! What are the modern, efficient, mistake-proof ways to collect and manage field and lab data, identifiers, traits, and environmental variables? How can you store your data to easily integrate with external databases? This course covers basics of data collecting and data management but leaves out data analysis to other courses. *How much:* No course fee. Danish, Swedish, Norwegian, or Finnish PhD students and postdocs are encouraged to join ForBio - the Research School in Biosystematics, since members are reimbursed for course-related travel costs and accommodation in shared rooms and food at Kilpisjärvi Station. ForBio may also support masters students registered at Danish, Swedish, Norwegian, or Finnish universities who provide compelling evidence that they need the course for their thesis work. ForBio will not cover any expenses (e.g., food, travel, or accommodation costs) for other participants who have to be registered as ForBio associates to attend the course. Please pass along to any who might be interested in taking the course -- or developing a similar one. Best, Deb -- Upcoming iDigBio Events https://www.idigbio.org/calendar --Deborah Paul iDigBio Technology Specialist Institute for Digital Information, 234 LSB Florida State University Tallahassee, Florida 32306 850-644-6366

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delimiter characters for concatenated IDs
by "Dröge, Gabriele" 06 May '14

06 May '14

Hi everyone, I guess there might have been some discussions about proper delimiter characters in the past that I have missed. In several projects, first of all in GGBN (Global Genome Biodiversity Network, http://www.ggbn.org), there is a need for making a decision now. We need to reference between different records and databases and within Darwin Core we want to use the relatedResourceID to do so. During our GGBN workshop at TDWG last year we agreed on concatenating the traditional triple ID (Catalogue Number, Collection Code, Institution Code) and add further parameters if required too (e.g. GUID, access point). We have checked those parameters and can definitely not use a single character as delimiter. So my question to you is, if there are already some suggestions on using two characters together as delimiters. It would be great if we could find a solution more than one community could agree on. Otherwise I would like to open the discussion and suggest "\\", "||", "\|", "§|", "§§", or "\§". Best wishes, Gabi ----------------------------------------------------------------- Gabriele Droege Coordinator - DNA Bank Network Global Genome Biodiversity Network (GGBN) Berlin-Dahlem DNA Bank Women's Officer ZE BGBM Botanic Garden and Botanical Museum Berlin-Dahlem Freie Universität Berlin Koenigin-Luise-Str. 6-8 14195 Berlin Germany +49 30 838 50 139 www.dnabank-network.org<http://www.dnabank-network.org> www.ggbn.org<http://www.ggbn.org> www.bgbm.org<http://www.bgbm.org>

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Re: [tdwg-content] delimiter characters for concatenated IDs
by "Dröge, Gabriele" 06 May '14

06 May '14

Thanks Gregor! I must say I really like this idea for our short term solution! Will discuss this with my team. Best, Gabi Von: Gregor Hagedorn [mailto:gregor.hagedorn@mfn-berlin.de] Gesendet: Dienstag, 6. Mai 2014 13:57 An: Dröge, Gabriele Cc: tdwg-content(a)lists.tdwg.org Betreff: Re: [tdwg-content] delimiter characters for concatenated IDs On the original question: my preference when creating an identifier for the triplet would be to be transparent, and create the identifer with the dwc terms embedded, i.e. use institutionCode=BGBM&collectionCode=xxx&catalogNumber=289742874239872 as the "self-coined" identifier string. While "&" may not be unique, the delimiter &collectionCode= is very likely so. And it is transparent, self-documenting what is going on (and I do not mean that people need to parse it - which they could in either case) Gregor On 5 May 2014 15:24, "Dröge, Gabriele" <g.droege(a)bgbm.org<mailto:g.droege@bgbm.org>> wrote: Hi everyone, I guess there might have been some discussions about proper delimiter characters in the past that I have missed. In several projects, first of all in GGBN (Global Genome Biodiversity Network, http://www.ggbn.org), there is a need for making a decision now. We need to reference between different records and databases and within Darwin Core we want to use the relatedResourceID to do so. During our GGBN workshop at TDWG last year we agreed on concatenating the traditional triple ID (Catalogue Number, Collection Code, Institution Code) and add further parameters if required too (e.g. GUID, access point). We have checked those parameters and can definitely not use a single character as delimiter. So my question to you is, if there are already some suggestions on using two characters together as delimiters. It would be great if we could find a solution more than one community could agree on. Otherwise I would like to open the discussion and suggest "\\", "||", "\|", "§|", "§§", or "\§". Best wishes, Gabi ----------------------------------------------------------------- Gabriele Droege Coordinator - DNA Bank Network Global Genome Biodiversity Network (GGBN) Berlin-Dahlem DNA Bank Women's Officer ZE BGBM Botanic Garden and Botanical Museum Berlin-Dahlem Freie Universität Berlin Koenigin-Luise-Str. 6-8 14195 Berlin Germany +49 30 838 50 139<tel:%2B49%2030%20838%2050%20139> www.dnabank-network.org<http://www.dnabank-network.org> www.ggbn.org<http://www.ggbn.org> www.bgbm.org<http://www.bgbm.org> _______________________________________________ tdwg-content mailing list tdwg-content(a)lists.tdwg.org<mailto:tdwg-content@lists.tdwg.org> http://lists.tdwg.org/mailman/listinfo/tdwg-content -- --------------------------- Dr. Gregor Hagedorn Head of Digital World and Information Science Museum für Naturkunde Berlin Leibniz-Institut für Evolutions- und Biodiversitätsforschung Invalidenstrasse 43, 10115 Berlin +49 (0)30 2093 8576 (work) +49-(0)30-831 5785 (private) gregor.hagedorn(a)mfn-berlin.de<mailto:gregor.hagedorn@mfn-berlin.de> http://www.naturkundemuseum-berlin.de http://linkedin.com/in/gregorhagedorn This communication, together with any attachments, is intended only for the person(s) to whom it is addressed. Redistributing or publishing it without permission may be a violation of copyright or privacy rights.

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