- tdwg-content - lists.tdwg.org

Fwd: Fw: PLOS Early Career Travel Award Program is Back!
by Cynthia Parr 05 May '16

05 May '16

This might be of interest for travel to TDWG. ------------------------------ *From:* PLOS <feedback(a)e.plos.org> *Sent:* Tuesday, May 3, 2016 3:39 PM *To:* Parr, Cynthia - ARS *Subject:* PLOS Early Career Travel Award Program is Back! PLOS is once again pleased to announce its Early Career Travel Award Program View this email in your browser <http://view.e.plos.org/?qs=8c6b5ea0b6a1243c24d38be2836dffd3aabeed1a44faba52…> [image: PLOS] <http://click.e.plos.org/?qs=bd46dfd56cae90fe3e0e5a254fe3bd67f6d9319c5923821…> PUBLISH WITH PLOS <http://click.e.plos.org/?qs=bd46dfd56cae90fe167ed6b3ad9d3c676454d10151fae94…> ------------------------------ PLOS Early Career Travel Award Program is Back! Presenting research findings and participating in the scientific dialogue are important experiences in the career development of researchers. To support their growth as effective communicators, PLOS is once again pleased to announce its Early Career Travel Award Program. New this year are multiple award cycles. ARE YOU ELIGIBLE? If you are... • Presenting at a conference taking place between July 1, 2016 – March 31, 2017 • An author on an article published in any PLOS journal by the application date, AND • Currently part of a graduate program or have received a graduate degree within the last five years as of the application deadline ...apply to be considered for the PLOS Early Career Travel Award Program. APPLICATION DEADLINE: MAY 31, 2016 More information is available at plos.org/ecr-travel-awards <http://click.e.plos.org/?qs=bd46dfd56cae90fefd197046c785890f20d72902a8467b6…>. Watch this space for announcements on future Award cycles. *Share with us the subject area(s) that most interest you* Biology and life sciences <http://click.e.plos.org/?qs=bd46dfd56cae90fe10cfd43c519be40123d5c75d91f7891…> Ecology and Earth sciences <http://click.e.plos.org/?qs=bd46dfd56cae90fe212e96c0e3601ff6a94b208425b1529…> Medicine and health sciences <http://click.e.plos.org/?qs=bd46dfd56cae90feb28a0ce588aabb651e2d4c4560ce55b…> Physical sciences <http://click.e.plos.org/?qs=bd46dfd56cae90fe8df12b07dd38f747af4a6919c5d1df5…> Research methods and science policy <http://click.e.plos.org/?qs=bd46dfd56cae90fe52a6b02494e7bd3790b4ed11dbc7f65…> Social sciences <http://click.e.plos.org/?qs=bd46dfd56cae90fe1310872581c0ecda75e90b073be0748…> Other <http://click.e.plos.org/?qs=bd46dfd56cae90fe286759123c749cc45833a6ae8396122…> APPLY NOW <http://click.e.plos.org/?qs=bd46dfd56cae90feac2a40114c7f1eb4c45be0196d0407b…> Public Library of Science 1160 Battery St. Suite 100 San Francisco, CA 94111-1233 US [image: Facebook] <http://click.e.plos.org/?qs=bd46dfd56cae90fe7b5b8ca644c7bd09eeecd7fc40375ad…> Facebook <http://click.e.plos.org/?qs=bd46dfd56cae90fe7b5b8ca644c7bd09eeecd7fc40375ad…> [image: Twitter] <http://click.e.plos.org/?qs=bd46dfd56cae90fe7bb2335b31e04ae0b2dc7307e8c195a…> Twitter <http://click.e.plos.org/?qs=bd46dfd56cae90fe7bb2335b31e04ae0b2dc7307e8c195a…> [image: Website] <http://click.e.plos.org/?qs=bd46dfd56cae90fe01746768f2d37ed1599080d1f23d7b8…> Website <http://click.e.plos.org/?qs=bd46dfd56cae90fe01746768f2d37ed1599080d1f23d7b8…> [image: Email] <feedback(a)plos.org> Email <feedback(a)plos.org> You are receiving this email because you opted to receive PLOS updates and information. Privacy Policy <http://click.e.plos.org/?qs=bd46dfd56cae90fec102242e10488524a4c459098a8c927…> | Unsubscribe <http://click.e.plos.org/unsub_center.aspx?qs=2cc4d08de3cfd95849cfb456239cba…> | Update Preferences <http://click.e.plos.org/profile_center.aspx?qs=2cc4d08de3cfd958def7b9a29790…> | Sign Up <http://click.e.plos.org/?qs=bd46dfd56cae90fede0030842b8328c6639d37f5e491e92…> This electronic message contains information generated by the USDA solely for the intended recipients. Any unauthorized interception of this message or the use or disclosure of the information it contains may violate the law and subject the violator to civil or criminal penalties. If you believe you have received this message in error, please notify the sender and delete the email immediately.

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Re: [tdwg-content] Taxonomic name usage files
by Richard Pyle 20 Apr '16

20 Apr '16

Thanks, Terry; and agreed! I’ll claim full-credit for the over-verbosity. But when it comes to taxon names, and how to structure the information appropriately, I’ve tried every strategy for communicating from super-thin to super-verbose (the recent thread epitomizing the latter); and on balance, none of them are effective because there is SO MUCH noise out there in terminology, and concepts of concepts, and such. It’s a perpetual uphill battle. My hope is that, in this case, the information was decipherable to primary audience (Nico). Now… on the topic of uphill battles… we had some great conversations in Florence and Jönköping on how to improve TaxPub to capture the core elements of TNUs (both Protonyms and subsequent usages); but I’m not sure we ever got anywhere. However, given the recent (excellent) progress with the PLAZI workflow, and some other things that are happening later this year in GNUB-space; perhaps it’s time to revisit those conversations, in the context of Nico’s original question, and hammer-out a functional solution (or, if not a “solution”, at least a quantum step forward). Aloha, Rich From: Terry Catapano [mailto:catapanoth@gmail.com] Sent: Wednesday, April 20, 2016 1:30 AM To: Donat Agosti Cc: tdwg-content(a)lists.tdwg.org; vocab(a)noreply.github.com; Michael Rosenberg (Faculty); Chuck Miller (Chuck.Miller(a)mobot.org) Robert Guralnick; Nico Franz; deepreef(a)bishopmuseum.org Subject: Re: [tdwg-content] Taxonomic name usage files Donat, Where did Chuck ask about TaxonX? I'd like to see what the specific question is. In general, it's more effective to clearly and briefly describe *what* we do and *why* and to not discuss what we *dont* currently do, or plan on doing. There is danger to credibility in sustained over-promising. As is evidenced by the verbosity of this thread, there is an even greater danger to communication in over-writing. On Wed, Apr 20, 2016 at 6:13 AM, Donat Agosti <agosti(a)amnh.org> wrote: I am trying to answer two questions in this tread. Taxonx. Chuck asked about TaxonX. We are moving away from TaxonX to use an archival version of TaxPuB, TaxPub-green ( <https://github.com/plazi/TaxPubJATS-green> https://github.com/plazi/TaxPubJATS-green ), which is related to TaxPub that Pensoft already uses for the publishing, and which is based on NLM JATS, that is a widely used “standard” albeit in different flavors. But to have all based on JATS-TaxPub makes it easier to make use of legacy (articles converted into TaxPub) and prospective (born digital based on TaxPub) articles. Once we have this move finished we will release and note and explain in detail. But in brief, let’s focus on TaxPub. Taxonomic names For our work with taxonomic publications we tag all scientific taxonomic names we discover in the articles. Our main focus are names for which a taxonomic treatment is provided in the respective article, or which are cited as a reference to an earlier usage and with that a taxonomic treatment. As an example: <http://treatment.plazi.org/id/87F5BDFA-6C63-C7B7-4A85-A1B39AE6CACE> http://treatment.plazi.org/id/87F5BDFA-6C63-C7B7-4A85-A1B39AE6CACE Agosti (1990) provides a treatment of Catagylphis turcomanicus (Emery). He cites all the earlier usages of this name, beginning from the protonym to all the latter changes in combination. With that he says, that under this understanding of this taxon, he subsumes all the earlier name usages. He does this by citing them. A visualization is provided on the right hand und “taxonomy” A more recent example is this crab: <http://treatment.plazi.org/id/F017F605-AC1E-BB43-FF2A-90F9555CF9CD> http://treatment.plazi.org/id/F017F605-AC1E-BB43-FF2A-90F9555CF9CD This treatmentCitation allows us to build a citation graph which is specific in a sense that this type of taxonomic names have a relationship to an earlier specified usage. Whilst names that are found in the next have this relationship implicit, known probably to the author in most cases, and few exceptional cases to a community that maintains a name server including the currently accepted name (and then there the history that eventually leads to the protonym, such as is the case for ants (and mony more hymenoptera) on the Hymenopter Name Server). But this is a discussion in itself. In Taxpub this is dealt with (somewhat cryptic) <nomenclature-citation-list> <nomenclature-citation> </nomenclature-citation> <nomenclature-citation> </nomenclature-citation> </nomenclature-citation-list> See <https://htmlpreview.github.io/?https://raw.githubusercontent.com/tcatapano/…> https://htmlpreview.github.io/?https://raw.githubusercontent.com/tcatapano/… In RDF we make use of CITO ( <http://purl.org/spar/cito/> http://purl.org/spar/cito/) to model this relationship <https://github.com/plazi/TreatmentOntologies> https://github.com/plazi/TreatmentOntologies and here an example <http://tb.plazi.org/GgServer/rdf/87F5BDFA6C63C7B74A85A1B39AE6CACE> http://tb.plazi.org/GgServer/rdf/87F5BDFA6C63C7B74A85A1B39AE6CACE Donat From: tdwg-content [mailto: <mailto:tdwg-content-bounces@lists.tdwg.org> tdwg-content-bounces(a)lists.tdwg.org] On Behalf Of Richard Pyle Sent: Wednesday, April 20, 2016 12:30 AM To: 'Nico Franz' < <mailto:nico.franz@asu.edu> nico.franz(a)asu.edu> Cc: <mailto:tdwg-content@lists.tdwg.org> tdwg-content(a)lists.tdwg.org; <mailto:vocab@noreply.github.com> vocab(a)noreply.github.com; 'Michael Rosenberg (Faculty)' < <mailto:msr@asu.edu> msr(a)asu.edu> Subject: Re: [tdwg-content] Taxonomic name usage files Good questions! Note that the stuff I was describing isn’t just GNUB; it’s embedded in the DwC terms as well. And the few elements that are missing from DwC are embedded in TCS. The main other aspects are the Reference metadata (the ill-fated TDWG Reference standard; now looking towards NLMS), and Agents (most people I know follow FOAF). Other than those, the main missing holes (in both GNUB and DwC) are the Appearance stuff, and perhaps a more robust approach to the relationshipAssertion stuff. Maybe a task for TCS 2.0? Once the standards fleshed out, I imagine the way to implement this stuff in new literature is via something along the lines of Pensoft’s PWT (now arpha): <http://arpha.pensoft.net/> http://arpha.pensoft.net/ The natural group to focus on this would be PLAZI, which has been going gangbusters in recent months on capturing structured treatments from existing literature. [Pssst… Donat…. That’s your cue….] Rich From: Nico Franz [ <mailto:nico.franz@asu.edu> mailto:nico.franz@asu.edu] Sent: Tuesday, April 19, 2016 11:58 AM To: Richard Pyle Cc: Gaurav Vaidya; greg whitbread; <mailto:tdwg-content@lists.tdwg.org> tdwg-content(a)lists.tdwg.org; <mailto:vocab@noreply.github.com> vocab(a)noreply.github.com; Michael Rosenberg (Faculty) Subject: Re: [tdwg-content] Taxonomic name usage files Thanks, Rich, for catching me up. So then if we can apparently cover a good bit of ground (with what I assume you'd call a "smart [or the only] way of implementing GNUB"), this does raise the question of how to bring this as close as possible to the peer-review/publication process where an author team may be motivated to express their intentions related to name usages in various explicit, structurally recorded ways. Best, Nico On Tue, Apr 19, 2016 at 2:09 PM, Richard Pyle <deepreef(a)bishopmuseum.org> wrote: > 1. Given a multitude of well established and precise historical name usages, I explicitly don't want to commit to one in particular > that my present usage is congruent with, or not. (Indeed, I kind of think this is what the name withOUT a sec. does, "explicitly"). Yes! Exactly! > I choose to be vague - any past usage is ok with me, here. During the TCS days, this is what we referred to as a "Nomenclatural Concept", which is roughly the sum/average of all historical treatments, more or less (ambiguity and vagueness deliberate/intentional). > I think we can presently model the vagueness (by integrating on the strings alone), but not the deliberateness thereof (in contrast to other situations where vagueness is not intended)? Yes - a TNU without any relationshipAssertions. Basically, the only implied associations with other TNUs is via the Protonym link (i.e., a Nomenclatural Assertion). > 2. Franz. 2010. Revision of Apotomoderes (Insecta: Coleoptera). => Actually, "Insecta" here is more of a social concession to an outdated data filing paradigm than > a claim to an active speaker role (related to name usages that I actually care about). I am not intending to apply my taxonomic expertise to "Insecta"; > that is *out of scope* (though the string is being written). So... in that case, the question is whether to represent "Insecta" as used in Franz 2010 as a scientific name, or vernacular name (two different ways of modelling names, as the latter do not have structured Codes). Even if you fall on the side of using it as a scientific (taxon) name, you can still create a TNU for it. In the spirit of Walter's pioneering work on this stuff, TNUs only represent "potential" taxa. Aloha, Rich

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Taxonomic name usage files
by Nico Franz 20 Apr '16

20 Apr '16

Hi TDWG Content group: Perhaps someone can answer these question? Suppose I submitted a new biodiversity study to a journal for peer review and ultimately publication. My study mentions taxonomic names, but some names are used in more than one specific sense throughout the manuscript. As part of my study's data body, I want to say things like: at this point or these sections in my manuscript, I am using the name in the sense of authors X. And: later on in the Discussion, I am using the name in "my new sense" (as an example). I want to submit a table with structured metadata on the various usages of names in my manuscript, as part of the supplementary data provided to the Journal. I believe part of what the table would have to reflect, for each usage, is whether this is my usage, or that of someone else that I am ok with (=> define speaker role). Is there a best TDWG standard to glean terms and definitions from to draft up that table? I assume it is Darwin Core and/or the TCS, but then has someone actually tried this (= extract the subset of terms needed to identify names, usages, speaker roles) in conjunction with (e.g.) a biodiversity inventory or taxonomic revision to be published? The key purpose here would be to facilitate better name usage data practices, tied to the process of publishing new data via journals. To make data about name usages part of the supplementary data, in a structured and rather explicit format. Thanks and best, Nico

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Symposium & Workshop Proposals due today TDWG 2016
by Kampmeier, Gail E 11 Apr '16

11 Apr '16

A quick reminder that for best consideration and promotion*, proposals for symposia and workshops** for TDWG 2016 are due today in another 12 hours (UTC - 5). See the TDWG Conference page http://www.tdwg.org/conference2016/ for more information on the call, including what you need to include in your abstract text https://mbgserv18.mobot.org/ocs/index.php/tdwg/tdwg2016/schedConf/trackPoli… and the link to submitting your abstract https://mbgserv18.mobot.org/ocs/index.php/tdwg/tdwg2016/schedConf/cfp. *Although proposals may be accepted after the deadline as space and time allows, submitting proposals by the deadline will allow them to be featured in advertising for the conference and may encourage contributed submissions and participation in your topic. **Note that this is NOT a call for contributed oral or poster presentations. That will open later in April. Hope to see you in Costa Rica at TDWG 2016!! Gail Kampmeier Erick Mata Co-Chairs TDWG 2016 Program Committee conference [at] tdwg.org<http://tdwg.org>

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mailing list migration
by Markus Döring 22 Jan '16

22 Jan '16

Dear all, in an attempt to migrate all TDWG mail services to a new server I will shutdown mailing lists for a while. Please excuse and ignore one or two upcoming test mails. I will announce the availability of the list again when migration has completed. Best, Markus

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Application deadline extended for Practical Hacking On Identifiers at BiOSphere 2 (PHOIBOS2), Feb. 17-19, 2015, Oracle, Arizona, USA
by Ramona Walls 24 Nov '15

24 Nov '15

The deadline for applications has been extended to Dec. 6th. Please apply online at http://bit.ly/1knvYoR Also, a reminder that there is funding available to support several participants from developing countries! 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 Tue, Nov 10, 2015 at 1:24 PM, Ramona Walls <rlwalls2008(a)gmail.com> wrote: > In the era of big data and informatics, there is growing awareness among > scientists and scientific data managers of the need for permanent, globally > unique identifiers for both physical specimens and digital data, leading to > the development of new systems for minting, tracking, resolving, and > querying identifiers. However, existing identifier systems have not yet > been put to the test with the types of very large, multidisciplinary > datasets that loom on the horizon, and developing an identifier > infrastructure for really big data (pre- and post-publication) is crucial > next step. > > During the three day PHOIBOS2 > <https://github.com/identifier-services/phoibos2/wiki> workshop at the > world-renowned Biosphere 2 <http://b2science.org/> in Oracle, Arizona, > identifier practitioners and data generators will come together to > summarize the current state of the field, identify and elucidate the > technical issues, and develop solutions. PHOIBOS2 will incorporate elements > of a hackathon, but outputs may also include non-technical products like a > draft proposal, a survey, or educational materials. The agenda for the > meeting is modeled after the successful MIT Hacking Medicine > <http://hackingmedicine.mit.edu/>, in which groups of participants are > asked to identify a problem and articulate what a system that solved the > problem would look like, including technologies, support material, and a > business model. We aim to develop a vision of an identifier infrastructure > that spans the entire data lifecycle in the context of very large, complex, > multi-disciplinary, research-oriented datasets. > > If you are a scientist, or user or developer of identifier systems, and > would like to take part in this innovative experience, please complete the > online application available here > <https://docs.google.com/forms/d/1m1paDJjRigPLw0PaLFlS5D2bfvJ2iGwP6W_bsvcMEY…> > by November 30, 2015. The meeting is open to all, with room and board > covered for up to 30 participants, and limited funding available to support > travel costs, particularly for early career or under-represented > participants. Funding requests will be considered in early December, after > all applications are received. > > This workshop is funded by the U.S. National Science Foundation, with > logistical support provided by the iPlant Collaborative. > ------------------------------------------------------ > 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 >

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Practical Hacking On Identifiers at BiOSphere 2 (PHOIBOS2), Feb. 17-19, 2015, Oracle, Arizona, USA
by Ramona Walls 10 Nov '15

10 Nov '15

In the era of big data and informatics, there is growing awareness among scientists and scientific data managers of the need for permanent, globally unique identifiers for both physical specimens and digital data, leading to the development of new systems for minting, tracking, resolving, and querying identifiers. However, existing identifier systems have not yet been put to the test with the types of very large, multidisciplinary datasets that loom on the horizon, and developing an identifier infrastructure for really big data (pre- and post-publication) is crucial next step. During the three day PHOIBOS2 <https://github.com/identifier-services/phoibos2/wiki> workshop at the world-renowned Biosphere 2 <http://b2science.org/> in Oracle, Arizona, identifier practitioners and data generators will come together to summarize the current state of the field, identify and elucidate the technical issues, and develop solutions. PHOIBOS2 will incorporate elements of a hackathon, but outputs may also include non-technical products like a draft proposal, a survey, or educational materials. The agenda for the meeting is modeled after the successful MIT Hacking Medicine <http://hackingmedicine.mit.edu/>, in which groups of participants are asked to identify a problem and articulate what a system that solved the problem would look like, including technologies, support material, and a business model. We aim to develop a vision of an identifier infrastructure that spans the entire data lifecycle in the context of very large, complex, multi-disciplinary, research-oriented datasets. If you are a scientist, or user or developer of identifier systems, and would like to take part in this innovative experience, please complete the online application available here <https://docs.google.com/forms/d/1m1paDJjRigPLw0PaLFlS5D2bfvJ2iGwP6W_bsvcMEY…> by November 30, 2015. The meeting is open to all, with room and board covered for up to 30 participants, and limited funding available to support travel costs, particularly for early career or under-represented participants. Funding requests will be considered in early December, after all applications are received. This workshop is funded by the U.S. National Science Foundation, with logistical support provided by the iPlant Collaborative. ------------------------------------------------------ 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

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Re: [tdwg-content] [IPT] Reverting the process of DwC standardization
by Menashe' Eliezer 29 Oct '15

29 Oct '15

Hello, Resending the same message due to a subscription problem. -- Menashè 2015-10-29 12:15 GMT+01:00 Menashe' Eliezer <menashe.eliezer(a)gmail.com>: > Hello, > Please see my updated suggestion at > https://github.com/gbif/ipt/issues/1165 > IMHO Open Refine is not the right tool. One can simply use org.apache.poi > in his Java application for reading all the information from the different > files inside the DwC, and create an ODS file with the combined matrix, > which takes into consideration also possible parentEventID. I'm sorry I > don't have time to do it myself. > I hope it's clear. > -- > Menashè > > > 2015-10-28 18:57 GMT+01:00 Shorthouse, David < > david.shorthouse(a)umontreal.ca>: > >> All, >> >> Is part of the issue being expressed here because the raw ecological data >> sets we're discussing are small-ish matrices rather than occurrences, with >> site codes as columns, taxa as rows and measures of density/abundance as >> cells (and similar for environmental variables)? Such structures are often >> used as input for software that executes eg ordinations, classification & >> regression trees, species richness estimates. The shortcoming of such a >> structure is the inherent idiosyncratic nature of "site codes", with >> variable numbers of them, i.e. an arbitrary number of columns. I doubt it >> was ever designed for ease of dataset integration, but rather for ease of >> computation. Representing this structure as Event core requires significant >> transposition & potential for error if it were manual. Open Refine is one >> such tool that could permit bi-directional transpositions (DwC -> matrix >> and then matrix -> DwC), but it is still clunky and accommodation of >> extensions is virtually non-existent. But, perhaps Open Refine recipes and >> guides gets us one step closer to finding a balance between the need for >> standardized representation & efficient transport (DwC) vs. end-users who >> want matrices for ease of computation. >> >> David P. Shorthouse >> >> On Tue, Oct 27, 2015 at 7:36 AM, David Valentim Dias <dvdias(a)sibbr.gov.br >> > wrote: >> >>> Hi again, >>> >>> I think the problem target both. DwC because is a solution to a problem >>> creating another problem to researchers less "skilled" in table >>> manipulation. Ecological data with occurrence is resulting in three tables >>> and manipulation of these are getting harder with the number of core or >>> extensions used. >>> Two possible solutions comes in mind: create a new term describing the >>> original layout of the columns (so we can use csvjoin like Menashe suggest) >>> or ipt with option to store the original table associated with resource. >>> We can always use external links in eml and save the file somewhere but >>> this means creating another service and managing more login (aka resource >>> cost and new problems). >>> >>> I think any solution will need ipt changes. >>> >>> 2015-10-27 9:08 GMT-02:00 Menashe' Eliezer <menashe.eliezer(a)gmail.com>: >>> >>>> Hi Tim, >>>> I believe that the IPT feature I've requested long ago could be helpful >>>> for David: https://github.com/gbif/ipt/issues/1165 >>>> Consumers and also the data providers don't have a DwC-A viewer, and >>>> they need to join the separate csv files for having one table in a >>>> worksheet. >>>> Web applications like the one at OBIS website do let end users download >>>> one big table. >>>> >>>> Best regards, >>>> Menashè >>>> >>>> >>>> 2015-10-27 9:53 GMT+01:00 Tim Robertson <trobertson(a)gbif.org>: >>>> >>>>> Hi David >>>>> (CC’ing the IPT list as this might be an IPT specific thread - >>>>> http://lists.gbif.org/mailman/listinfo/ipt) >>>>> >>>>> For clarification - is your question specific to the DwC-A standard >>>>> which is possible as Alex says or is it specific to the IPT tool please? >>>>> >>>>> Do you imagine a scenario where you’d effectively map the same >>>>> extension 2 times - once to interpreted and once to verbatim - or do you >>>>> envisage a different data schema for each? >>>>> >>>>> Thanks, >>>>> Tim >>>>> >>>>> >>>>> >>>>> On 23 Oct 2015, at 16:00, Alex Thompson <godfoder(a)acis.ufl.edu> wrote: >>>>> >>>>> David, >>>>> >>>>> It's certainly possible, within the context of a Darwin Core Archive, >>>>> to include other files within the ZIP file that lie outside the schema of >>>>> the archive. Both GBIF and iDigBio do this when generating downloads for >>>>> various reasons (RIGHTS & LICENSE files, additional EML metadata, etc). >>>>> However, I do not believe it is possible to do this within IPT. You might >>>>> submit an issue on the IPT issue tracker ( >>>>> https://github.com/gbif/ipt/issues) for potential inclusion of this >>>>> feature in a future version of IPT. >>>>> >>>>> There are workarounds you can use to include additional data in Darwin >>>>> Core archives, but none of them will exactly match your old format. For >>>>> instance, including an additional Occurrence file with the values as JSON >>>>> in dynamicProperties or in some other verbatim format in the >>>>> occurrenceRemarks field. Both of those would at least give some method of >>>>> single-row access (vs joining multiple measurementOrFacts to a single event >>>>> id) if that is the primary concern, even if they would require additional >>>>> parsing steps to be useful. >>>>> >>>>> Alex Thompson >>>>> iDigBio Infrastructure >>>>> >>>>> >>>>> On 10/23/2015 09:40 AM, David Valentim Dias wrote: >>>>> >>>>> Dear colleagues, >>>>> >>>>> Here on SiBBr we're using the new eventCore and measurementOrFacts and >>>>> after the process of standardization to DwC and publishing we think some >>>>> users/researchers will want the "original" table format because of multiple >>>>> reasons. >>>>> >>>>> Is possible to have a vertabimTable or some place where we can store >>>>> the original table/column format? >>>>> >>>>> Regards >>>>> >>>>> >> _______________________________________________ >> IPT mailing list >> IPT(a)lists.gbif.org >> http://lists.gbif.org/mailman/listinfo/ipt >> >> >

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Re: [tdwg-content] [IPT] Reverting the process of DwC standardization
by David Valentim Dias 28 Oct '15

28 Oct '15

Hi again, I think the problem target both. DwC because is a solution to a problem creating another problem to researchers less "skilled" in table manipulation. Ecological data with occurrence is resulting in three tables and manipulation of these are getting harder with the number of core or extensions used. Two possible solutions comes in mind: create a new term describing the original layout of the columns (so we can use csvjoin like Menashe suggest) or ipt with option to store the original table associated with resource. We can always use external links in eml and save the file somewhere but this means creating another service and managing more login (aka resource cost and new problems). I think any solution will need ipt changes. 2015-10-27 9:08 GMT-02:00 Menashe' Eliezer <menashe.eliezer(a)gmail.com>: > Hi Tim, > I believe that the IPT feature I've requested long ago could be helpful > for David: https://github.com/gbif/ipt/issues/1165 > Consumers and also the data providers don't have a DwC-A viewer, and they > need to join the separate csv files for having one table in a worksheet. > Web applications like the one at OBIS website do let end users download > one big table. > > Best regards, > Menashè > > > 2015-10-27 9:53 GMT+01:00 Tim Robertson <trobertson(a)gbif.org>: > >> Hi David >> (CC’ing the IPT list as this might be an IPT specific thread - >> http://lists.gbif.org/mailman/listinfo/ipt) >> >> For clarification - is your question specific to the DwC-A standard which >> is possible as Alex says or is it specific to the IPT tool please? >> >> Do you imagine a scenario where you’d effectively map the same extension >> 2 times - once to interpreted and once to verbatim - or do you envisage a >> different data schema for each? >> >> Thanks, >> Tim >> >> >> >> On 23 Oct 2015, at 16:00, Alex Thompson <godfoder(a)acis.ufl.edu> wrote: >> >> David, >> >> It's certainly possible, within the context of a Darwin Core Archive, to >> include other files within the ZIP file that lie outside the schema of the >> archive. Both GBIF and iDigBio do this when generating downloads for >> various reasons (RIGHTS & LICENSE files, additional EML metadata, etc). >> However, I do not believe it is possible to do this within IPT. You might >> submit an issue on the IPT issue tracker ( >> https://github.com/gbif/ipt/issues) for potential inclusion of this >> feature in a future version of IPT. >> >> There are workarounds you can use to include additional data in Darwin >> Core archives, but none of them will exactly match your old format. For >> instance, including an additional Occurrence file with the values as JSON >> in dynamicProperties or in some other verbatim format in the >> occurrenceRemarks field. Both of those would at least give some method of >> single-row access (vs joining multiple measurementOrFacts to a single event >> id) if that is the primary concern, even if they would require additional >> parsing steps to be useful. >> >> Alex Thompson >> iDigBio Infrastructure >> >> >> On 10/23/2015 09:40 AM, David Valentim Dias wrote: >> >> Dear colleagues, >> >> Here on SiBBr we're using the new eventCore and measurementOrFacts and >> after the process of standardization to DwC and publishing we think some >> users/researchers will want the "original" table format because of multiple >> reasons. >> >> Is possible to have a vertabimTable or some place where we can store the >> original table/column format? >> >> Regards >> >> -- >> >> >> >> [image: ass_sibbr] >> >> *David Valentim Dias* >> >> *Biodiversity Data Management* >> >> SiBBr | MCTI | PNUMA (UNEP) >> >> Phone: +55 61 3329 6045 >> Phone: +55 61 9359 6151 >> Skype: ctenidae >> >> dvdias(a)sibbr.gov.br >> >> www.sibbr.gov.br >> >> >> _______________________________________________ >> tdwg-content mailing listtdwg-content@lists.tdwg.orghttp://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 >> >> >> >> _______________________________________________ >> IPT mailing list >> IPT(a)lists.gbif.org >> http://lists.gbif.org/mailman/listinfo/ipt >> >> > > _______________________________________________ > IPT mailing list > IPT(a)lists.gbif.org > http://lists.gbif.org/mailman/listinfo/ipt > > -- [image: ass_sibbr] *David Valentim Dias* *Biodiversity Data Management* SiBBr | MCTI | PNUMA (UNEP) Phone: +55 61 3329 6045 Phone: +55 61 9359 6151 Skype: ctenidae dvdias(a)sibbr.gov.br www.sibbr.gov.br

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Reverting the process of DwC standardization
by David Valentim Dias 27 Oct '15

27 Oct '15

Dear colleagues, Here on SiBBr we're using the new eventCore and measurementOrFacts and after the process of standardization to DwC and publishing we think some users/researchers will want the "original" table format because of multiple reasons. Is possible to have a vertabimTable or some place where we can store the original table/column format? Regards -- [image: ass_sibbr] *David Valentim Dias* *Biodiversity Data Management* SiBBr | MCTI | PNUMA (UNEP) Phone: +55 61 3329 6045 Phone: +55 61 9359 6151 Skype: ctenidae dvdias(a)sibbr.gov.br www.sibbr.gov.br

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