- tdwg-content - lists.tdwg.org

Re: [tdwg-content] status of uBio
by Chuck Miller 16 Oct '15

16 Oct '15

I’d be glad to host it here as well. Chuck From: jonathan.rees(a)gmail.com [mailto:jonathan.rees@gmail.com] On Behalf Of Jonathan A Rees Sent: Thursday, October 15, 2015 11:39 AM To: Chuck Miller Cc: Steve Baskauf; tdwg-content(a)lists.tdwg.org Subject: Re: [tdwg-content] status of uBio Even just providing a dump file of it somewhere would be a big advance over the current situation. I'd be happy to host it, if I can get ahold of it (of course assuming the blessing of whomever is responsible).

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Re: [tdwg-content] status of uBio
by Steve Baskauf 16 Oct '15

16 Oct '15

Nicky, Thanks, I'm looking forward to checking it out! But no animals. :-( Steve Nicky Nicolson wrote: > > Hello Steve, > > Thanks for triggering an interesting thread. > > Just waving the IPNI flag for a minute: > > > > 1. They have managed to stick around for a long time and are stable in > their format (as LSIDs and HTTP proxied LSIDs). > > At ipni.org we support our own HTTP proxy for LSIDs: > > http://ipni.org/urn:lsid:ipni.org:names:12345-1 > > … and it’s been an age since I tried to resolve an LSID using the > formal LSID spec but a quick run-through today shows that all the > steps appear to be in working order. > > > 2. The coverage of names is really good for plants, animals, different > geographic locations, etc. I also use ITIS identifiers but it's > fairly common for me to not be able to find one for the name I need, > which almost never happens with uBio. > > > > IPNI is comprehensive for vascular plants (at species level). We’ll be > addressing the data gaps at infra-specific level – but it’s very > useful for us to be armed with reasons (from users like yourself) as > to why we should spend time doing this. > > > 3. It's somewhat clear what uBio identifiers refer to: names vs. > something more nebulous involving taxa or ... something. (Not trying > to push your button, Rich Pyle). > > IPNI only serves data about names, no taxa here. > > We are pushing IPNI IDs into our taxonomic resources so that a user > can flexibly match a name and get an IPNI identifier (the > nomenclatural part), and then as a later step query a taxonomic > resource for their current view as to the taxonomic status of that > name. We are aiming for a clean separation of names matching from the > (multiple, potentially different) uses of those names to form taxonomies. > > > 4. You can actually get RDF associated with the LSID version of the > uBio identifiers. I was wanting to download some to play with in our > new triplestore (http://rdf.library.vanderbilt.edu) when I discovered > that the server was down. The RDF is somewhat ad hoc, but hey, it's > there. > > > > The HTTP proxy above returns RDF metadata for the specified record. > > New developments (most of the functionality outlined above is 8-10 > years old), I’ve been working on exposing IPNI data through standard > match services – namely the Open Refine reconciliation API, which > permits much more flexible names look-ups using a lot of heuristics > gathered from matching data port exercises carried out at Kew over the > past few years. Currently the main hitch with this service is that it > includes duplicate records. This is something we’re working on > resolving right now. > > The service is outlined here: http://data1.kew.org/reconciliation/ and > details of the IPNI service in particular are here: > http://data1.kew.org/reconciliation/about/IpniName > > > > If you’re interested in using IPNI, I’d be happy to hear any comments > on the functionality above and / or any requests as to how we can make > it more useful for you. > > > > cheers, > > Nicky > > > > > > *From:* tdwg-content-bounces(a)lists.tdwg.org > [mailto:tdwg-content-bounces@lists.tdwg.org] *On Behalf Of *Steve Baskauf > *Sent:* 16 October 2015 14:09 > *To:* Dmitry Mozzherin <dmozzherin(a)gmail.com> > *Cc:* Chuck Miller (Contact) <chuck.miller(a)mobot.org>; > tdwg-content(a)lists.tdwg.org; Jonathan A Rees <rees(a)mumble.net>; > Shorthouse, David <david.shorthouse(a)umontreal.ca> > *Subject:* Re: [tdwg-content] status of uBio > > > > Thanks all for the information and comments about the status of uBio. > I'm glad to hear that the server will probably come back up. If not, > then I hope the data will be made available to those who said they > would be willing to host it. > > I have been interested in using the uBio identifiers for several reasons: > 1. They have managed to stick around for a long time and are stable in > their format (as LSIDs and HTTP proxied LSIDs). > 2. The coverage of names is really good for plants, animals, different > geographic locations, etc. I also use ITIS identifiers but it's > fairly common for me to not be able to find one for the name I need, > which almost never happens with uBio. > 3. It's somewhat clear what uBio identifiers refer to: names vs. > something more nebulous involving taxa or ... something. (Not trying > to push your button, Rich Pyle). > 4. You can actually get RDF associated with the LSID version of the > uBio identifiers. I was wanting to download some to play with in our > new triplestore (http://rdf.library.vanderbilt.edu) when I discovered > that the server was down. The RDF is somewhat ad hoc, but hey, it's > there. > > There isn't really any other source that has all of these > characteristics. So please keep uBio going indefinitely, if at all > possible. > Steve > > Dmitry Mozzherin wrote: > > I had been administering uBio for the last year, but now I am > moving from MBL. uBio machine is in a bad shape, and it crashes > after a few hours of work. My plan is to create Docker containers > for database, code and data, which should make whole system much > more stable, and much more manageable. Good news I will definitely > try my best to do it, the bad news I am spread thinner than usual > with move, transferring hardware and grant, GN things, EOL things, > and figuring out what to do with the house etc. uBio 'code' part > is about 35 Gb, which makes the task more complicated, but I am > quite optimistic that I will be able to make containers and put > them either on an MBL machine, run it from University of > Illinois, or give it to Naturalis -- depending on what will make > more sense for Dave Remsen, MBL and all interested in the project. > > > > > > -- > Steven J. Baskauf, Ph.D., Senior Lecturer > Vanderbilt University Dept. of Biological Sciences > > postal mail address: > PMB 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) 322-4942 > If you fax, please phone or email so that I will know to look for it. > http://bioimages.vanderbilt.edu > http://vanderbilt.edu/trees > -- Steven J. Baskauf, Ph.D., Senior Lecturer Vanderbilt University Dept. of Biological Sciences postal mail address: PMB 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) 322-4942 If you fax, please phone or email so that I will know to look for it. http://bioimages.vanderbilt.edu http://vanderbilt.edu/trees

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status of uBio
by Steve Baskauf 15 Oct '15

15 Oct '15

Does anybody know the status of uBio? The web server has been down now for weeks. I've been using it for a long time to find uBio ID numbers to use as a locally unique identifier for names. If the uBio server is not coming back up, does anybody know if there is a data dump somewhere? Steve -- Steven J. Baskauf, Ph.D., Senior Lecturer Vanderbilt University Dept. of Biological Sciences postal mail address: PMB 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) 322-4942 If you fax, please phone or email so that I will know to look for it. http://bioimages.vanderbilt.edu http://vanderbilt.edu/trees

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RDF Task Group: next steps
by joel sachs 28 Sep '15

28 Sep '15

Greeting to everyone in Nairobi and to TDWGers everywhere, Members of the RDF task group [1] are already aware that Steve Baskauf stepped down as co-convenor earlier this year. It would be hard to overstate the extent and significance of Steve's efforts as co-convenor, culminating in the ratification of the Darwin Core RDF Guide [2] this past March. Steve is continuing his efforts towards clarity in biodiversity informatics as head of the Vocabulary Maintenance Specification task group [3]. With the release and ratification of the guide, together with the earlier work on term documentation [4, 5] we face the question "What next?". Options include i) disbanding; ii) reconvening as an Interest Group [6] with the broad mandate of keeping abreast of developments in RDF technology and best practises, and discussing how those developments could/should affect TDWG practises; and iii) continuing as a task group with a fresh, narrow mandate from the TAG. I invite perspectives and opinions on this, both from current task group members, and also from TDWG as a whole. To those in Kenya, I wish you all a wonderful meeting! Cheers, Joel. 1. https://code.google.com/p/tdwg-rdf/ 2. http://rs.tdwg.org/dwc/terms/guides/rdf/index.htm 3. https://github.com/tdwg/vocab/blob/master/README.md 4. overview of rationale: http://lists.tdwg.org/pipermail/tdwg-content/2014-July/003274.html 5. summary of decision: http://lists.tdwg.org/pipermail/tdwg-content/2014-November/003381.html 6. Recall that, in TDWG, Interest Groups foster discussion, seek to develop consensus around approaches to information sharing, and maintain and update products as required; Task Groups are created by Interest Groups to create specific products (such as best practices documents or vocabulary standards).

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examples or further reading on ac:subtypeLiteral?
by Stoner, Dan 24 Aug '15

24 Aug '15

Hi, I am looking for more info or examples on the subtypeLiterals listed here: http://terms.tdwg.org/wiki/AC_Subtype_Examples Some of these are more obvious than others: Drawing, Painting, Logo, Icon, Illustration, Graphic, Photograph, Animation, Film, SlideShow, DesignPlan, Diagram, Map, MusicalNotation, IdentificationKey, ScannedText, RecordedText, RecordedOrganism, TaxonPage, MultimediaLearningObject, VirtualRealityEnvironment, GlossaryPage Thanks, - Dan Stoner

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Darwin Core RDF Guide published.
by John Wieczorek 19 Jun '15

19 Jun '15

Dear all, I would like to announce, with pleasure, the incorporation of the RDF Guide [1] into the body of the Darwin Core standard [2]. For this we have Steve Baskauf to thank especially among a cast of characters in the TDWG RDF Task Group [3]. Thanks to all. Go out and relate. Enjoy! [1] http://rs.tdwg.org/dwc/terms/guides/rdf/ [2] http://rs.tdwg.org/dwc/ [3] https://code.google.com/p/tdwg-rdf/wiki/CharterOfTG

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Monitoring data DwC
by Camila Plata 12 Jun '15

12 Jun '15

Dear colleagues, At SiB Colombia we are standardizing a resource of vegetation plots that are going to be monitored for several years, the data includes both measurements of the event and the organisms. So, we are currently discussing how to address this kind of data through the occurrenceCore and the new eventCore. We propose to create two related resources, the first describing the biotic and abiotic data of each plot (eventCore + meassurementOrFacts + relevé), and the second describing the organisms and it’s functional traits (occurrenceCore + meassurementOrFacts). The resources will be related through eventID and parentEventID. We would like to know what do you think about this approach and if anyone is dealing with the same kind of data and how did you address this issue, or if we also will need to relate the resources through the resourceRelationship extension? Looking forward for your assessment. Kind Regards! *Camila Plata*Interoperabilidad y Admón. de Contenidos EC-SiB. *Instituto de Investigación de Recursos BiológicosAlexander von Humboldt**Avenida Paseo Bolivar (Circunvalar) 16-20 * *PBX: (57) 1 320 2767 Ext. 1157Bogotá, D.C., Colombia* Antes de imprimir este mensaje, piensa si realmente necesitas hacerlo. ¡Gracias!

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Re: [tdwg-content] Darwin Core Proposal - environment terms (joel sachs)
by joel sachs 29 May '15

29 May '15

Hi Pier, I'll be happy to put my comments in the issue tracker. I also wanted to follow up on your comment that "ENVO's guidelines suggest that there should be *at least* one class from each hierarchy used. Indeed, multiple feature and material classes can and should be used to fully characterize an entity's environment." I remember now that the ENVO paper mentions this, and gives, as an example, a duck in the water. Such a duck would have properties like <dorsally_surrounded_by> <water> <ventrally_surrounded_by> <air> However, the sample data records provided as supplemental material to the MIXS paper all have one and only one value for each of "environmental feature", "environmental material", and "biome". The MIXS paper itself appears to be silent on the question of whether multiple values are allowed. The prototype annotation interface that my colleagues at AAFC are developing currently allows only a single value for each field. Do you know if this is right? wrong? unspecified? Maybe the real question is not what the standard permits/requires, but what will the repositories allow? Do you know what the repositories are thinking on this? As an aside, I notice that MIXS uses the terms "biome", "environmental_material", and "environmental_feature" as properties, while ENVO uses them as classes. I like that, because I believe that we should allow semantics to be derived from syntax, and other forms of context. I attended the Open Data conference here in Ottawa this week, and was a bit pressed for time, but would be happy to join a call about habitats. Best, Joel. On Thu, 21 May 2015, Pier Luigi Buttigieg wrote: > Hi Joel, > > These are valuable thoughts. > Could you post them to the ENVO issue tracker? It can be found here: > https://github.com/EnvironmentOntology/envo/issues > > We can develop from there more effectively. > > The habitat issue is one I plan to work on with Grant Godden next week in > Claremont. > I'm in Berkeley/Oakland right now working with a group interesting in urban > environments. > Shall we perhaps arrange a call? > > Best, > Pier > > > On Wed, 20 May 2015 14:28:40 -0700, Ramona Walls <rlwalls2008(a)gmail.com> > wrote: >> Hi Joel, >> >> I completely agree about the need to unpack the multiple dimensions of >> "habitat" in DWC, while not making DWC into an ontology. I suggest the >> discussion of ENVO terms should probably move to the ENVO list (then come >> back here, if/when we are ready to deal with adding them to DWC. >> >> I'd be very happy to work with you on BCO/DWC stuff and here your needs. >> Please feel free to just email me off list or email >> bco-discuss(a)googlegroups.com. We have bi-weekly calls that are open to >> anyone who wants to participate. >> >> Ramona > [...] >> On Mon, May 18, 2015 at 5:50 AM, joel sachs <jsachs(a)csee.umbc.edu> wrote: >> >>> Ramona, >>> >>> Thanks for engaging. My thinking is this: >>> >>> Our goal is to address the mess that is “habitat”. So much - >>> environmental >>> conditions, associated taxa, geography, geology - gets crammed into that >>> one poor term. >>> >>> We want to either replace or augment or subclass “habitat” with some new >>> terms, with each new term capturing some key dimension of information >>> that >>> “people” are interested in. Before talking specifically about the terms >>> under consideration, let me disclose some of my biases: >>> >>> <statement of biases> >>> i. I’d like to see terms that will help organize the thousands of > habitat >>> terms used by the authors of taxonomic treatments in the Flora of North >>> America. You can see some of these terms here - http://bit.ly/1Fnow3E >>> >>> We’re currently categorizing these terms to enable semantic search over >>> habitat; as we do so, we are also thinking about the user interface of >>> treatment templates for future contributors. Our opinion is that we >>> should >>> look at existing habitat terms, answer the question “what have authors >>> been >>> trying to tell us?”, and then design interfaces that make it easier for >>> them to tell us those things. (This isn’t to say that we shouldn’t also >>> coax new types of information out of treatment authors, based on our >>> understanding of what data consumers want to know.) >>> >>> The habitat dimensions that, for plants, keep coming up are: wet vs dry; >>> open canopy vs closed canopy; soil type; sloped vs. flat; and associated >>> taxa. We also see a range of geography/geology related dimensions. >>> >>> ii. I think the semantics of Darwin Core terms should be clear from > their >>> natural language definitions. Ontologies that can be used to provide >>> values >>> for the terms should not be relied upon as documentation for the terms >>> themselves. >>> >>> iii. I’ve long argued that Darwin Core should not make commitments to > any >>> particular upper ontologies. I explained some of my reasons in my 2013 >>> TDWG >>> talk (http://bit.ly/1FjCimJ) I recall that you spoke with me about this >>> last year, and expressed support for the idea of creating ontological >>> layers on top of Darwin Core. I’ve since tried to do this for BCO, but >>> struggled. I’ve been meaning to ask for your help with this. >>> </statement of biases> >>> >>> Back to the proposed terms: >>> >>> Biome. As has been noted by others, the currently proposed >>> definition is at odds with common understanding of the term, and is >>> somewhat confusing due to its dependance on evolution. I think I >>> understand >>> what the definition is getting at - namely, expanding the traditional >>> notion of biome to include microbiomes. >>> >>> Environmental feature. We often see habitat terms such as “rocky >>> outcrops”; “arroyos”; “bogs”; etc. So I can see a lot of utility in a >>> “feature” term. My preference would be to call it “geographic feature” > or >>> “geologic feature”, since I think that’s how most people think of such >>> features (see, e.g. geonames). The currently proposed definition is “A >>> material entity which determines an environmental system.” This >>> requirement >>> that the feature “determine” the environmental system strikes me as too >>> strong. >>> >>> Environmental material. The currently proposed definition is “A >>> portion of environmental material is a fiat object which forms the > medium >>> or part of the medium of an environmental system.” A much clearer >>> definition is one that I’ve heard Pierre give, which was along the lines >>> of >>> “The substance that was displaced by the sample prior to its being >>> removed >>> from its environment”. In addition to being clearer, this second >>> definition >>> has the advantage of not relying on the BFO notion of “fiat object”. >>> >>> >>> Happy Victoria Day to all my fellow British subjects! >>> Joel. >>> >>> >>> >>> On Wed, 13 May 2015, Ramona Walls wrote: >>> >>> This is my first chance to reply to this thread, but I think several of >>>> Joel's comments need to be addressed. >>>> >>>> 1. re.: ENVO terms: "As far as I can tell, no one knows how to use > these >>>> them." >>>> -- I know how to use them, and I know a community of people who know >>>> how >>>> to >>>> use them. True, that just like Darwin Core, they are often used >>>> incorrectly, >>>> but further documentation and outreach can help with that. >>>> >>>> 2. "There was a lot of confusion over whether particular aspects of an >>>> environment constituted an environmental feature, an environmental >>>> material, >>>> or a biome. The correct answer was often dependent on context. For >>>> example >>>> if a small mammal were found in leaf litter, then "leaf litter" would > be >>>> the >>>> environmental material, and >>>> the biome would be "forest". But if a microbe were sampled from the > same >>>> leaf litter, then "leaf litter" would be the biome, and I'm not sure >>>> what >>>> the environmental material would be." >>>> -- ENVO very clearly distinguishes between a biome, a feature, and a >>>> material. It is never the case that the same ENVO class can be use as >>>> both a >>>> biome and a feature or a feature and a material. Although the same >>>> entity, >>>> depending on its role, may serve as either a biome or material (or >>>> feature >>>> for that matter), in that case, it would be an instance of two > different >>>> classes in ENVO. Take the leaf litter example. A correct annotation >>>> would >>>> need to point to both a "leaf litter biome" class and a "leaf litter >>>> material" class. It is really crucial not to confuse material entities >>>> in >>>> world with the roles they take on as instances of classes in ENVO. >>>> -- Joel and I seem to remember outcomes of that RCN meeting quite >>>> differently (probably we were in different break-out groups). As I >>>> recall, >>>> the major problem was that people couldn't use ENVO because the classes >>>> they >>>> needed were not in there, not because they didn't know how. This is a >>>> problem that would actually be helped by DwC adopting ENVO, because it >>>> would >>>> create more users, and therefore more contributors to the ontology. >>>> Another >>>> major problem was that people often want to describe environments in >>>> terms >>>> of parameters like light level, salinity, temperature, etc. ENVO does >>>> not >>>> currently include classes like this, but a movement is underfoot to >>>> perhaps >>>> add such a branch to ENVO. >>>> >>>> 3. "Creating tripartite (biome/feature/material) decompositions of >>>> habitats >>>> sometimes makes sense. Certainly, it made sense for some of the early >>>> metagenomic assays that gave rise to ENVO. But it doesn't always make >>>> sense, and there are often better ways to characterize an environment." >>>> -- True, there are cases when you cannot specify a biome, feature, and >>>> material for an organism, but usually you can provide at least one of >>>> two >>>> of >>>> them, which goes a long way toward standardizing environmental records >>>> and >>>> making large-scale queries possible. I have not yet seen a better way > to >>>> classify environment on this scale. As I mentioned above, when it comes >>>> to >>>> describing environments in terms of their physico-chemical paramaters, >>>> ENVO >>>> does not serve, but that does not negate the utility of ENVO-style >>>> descriptions. Furthermore, as with most DwC terms, these are optional, >>>> and >>>> people/institutions who don't have to provide them if they are not >>>> relevant. >>>> >>>> 4. "The terms "env_biome", "env_feature", and "env_material" already >>>> exist >>>> in >>>> the MIxS Sample extension to Darwin Core (along with "submitted to >>>> INSDC", >>>> etc.). Why do they need to be moved into the core?" >>>> -- The main reason I can see is that they have a lot of applicability >>>> outside of MIXS, that is, for occurrences that do not have any > sequences >>>> associated with them, and should not be hidden away in a place that >>>> suggests >>>> they can only be applied to sequence data. >>>> >>>> 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, Apr 24, 2015 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 >>>> >>>> >>>> >>>> Today's Topics: >>>> >>>> 1. Re: Darwin Core Proposal - environment terms (joel sachs) >>>> >>>> >>>> ---------------------------------------------------------------------- >>>> >>>> Message: 1 >>>> Date: Thu, 23 Apr 2015 13:29:47 -0400 (EDT) >>>> From: joel sachs <jsachs(a)csee.umbc.edu> >>>> Subject: Re: [tdwg-content] Darwin Core Proposal - environment >>>> terms >>>> To: John Wieczorek <tuco(a)berkeley.edu> >>>> Cc: TDWG Content Mailing List <tdwg-content(a)lists.tdwg.org> >>>> Message-ID: >>>> >>>> <Pine.LNX.4.64.1504231321240.18117(a)linuxserver1.cs.umbc.edu> >>>> Content-Type: TEXT/PLAIN; charset=US-ASCII; format=flowed >>>> >>>> John, >>>> >>>> I have some concerns with these terms. As far as I can tell, no >>>> one knows >>>> how to use these them. I was at a phenotype RCN meeting last >>>> year where >>>> the theme was environmental ontologies. The attendees were >>>> pretty savvy in >>>> terms of both ontologies, and environmental terminology. We were >>>> given an >>>> overview of ENVO, and then, as an experiment, we broke into >>>> groups, and >>>> each group tried to use ENVO to describe particular >>>> environments. I don't >>>> recall any group being successful. There was a lot of confusion >>>> over >>>> whether particular aspects of an environment constituted an >>>> environmental >>>> feature, an environmental material, or a biome. The correct >>>> answer was >>>> often dependent on context. For example if a small mammal were >>>> found in >>>> leaf litter, then "leaf litter" would be the environmental >>>> material, and >>>> the biome would be "forest". But if a microbe were sampled from >>>> the same >>>> leaf litter, then "leaf litter" would be the biome, and I'm not >>>> sure what >>>> the environmental material would be. >>>> >>>> Due to the confusion, Pier Luigi gave us a more in-depth >>>> tutorial when we >>>> re-convened. We didnt break back out into groups, but I wish we >>>> had, >>>> because I wonder if we would have had much more success. >>>> >>>> Creating tripartite (biome/feature/material) decompositions of >>>> habitats >>>> sometimes makes sense. Certainly, it made sense for some of the >>>> early >>>> metagenomic assays that gave rise to ENVO. But it doesn't always >>>> make >>>> sense, and there are often better ways to characterize an >>>> environment. I >>>> think it was a mistake for these terms to be made mandatory in >>>> MIxS/MIMARKS. >>>> >>>> But the question isn't "What should MIxS do four years ago?", >>>> but "What >>>> should TDWG do now?". One wrinkle is that dwc:Habitat already >>>> exists. Will it stay in the core? Is the idea to create usage >>>> guides that >>>> explain when to use dwc:Habitat and when and how to use biome, >>>> feature, >>>> and material? Such an approach could work, but I'd like to see >>>> our usage >>>> guides differ from current ENVO/MIxS guidelines which mandate >>>> one and only >>>> one value for each of the terms. "Environmental feature", in >>>> particular, >>>> often merits multiple uses within the same record, and I think >>>> disallowing >>>> such usage would impede uptake of the term set. (As far as I can >>>> see >>>> from browsing metagenomic sampling metadata, it *has* impeded >>>> uptake of the term set.) >>>> >>>> So I'm not necessarily opposed to the addition of these terms, >>>> but I do >>>> wonder why we need them. >>>> >>>> You wrote that "there is currently no possibility of a Darwin >>>> Core >>>> PreservedSpecimen or MaterialSample record to meet the minimum >>>> requirements of a Mimarks Specimen record[6], as there is >>>> currently no way >>>> to share required environment terms." But MIMARKS specimen >>>> records are >>>> also required to have the fields "Submitted to INSDC", >>>> "Investigation-type", "Project name", "Nucleic acid sequence >>>> source", >>>> "Target gene or locus", and "Sequencing method". So won't it >>>> still be the >>>> case that there will be no possibility of a Darwin Core record >>>> being MIMARKS compliant, without appropriate >>>> augmentation? >>>> >>>> The terms "env_biome", "env_feature", and "env_material" already >>>> exist in >>>> the MIxS Sample extension to Darwin Core (along with "submitted >>>> to INSDC", >>>> etc.). Why do they need to be moved into the core? >>>> >>>> Cheers, >>>> Joel. >>>> >>>> >>>> >>>> On Thu, 26 Mar 2015, John Wieczorek wrote: >>>> >>>> > Dear all, >>>> > >>>> > This message pertains to a proposal[1] set forth in September >>>> 2013 >>>> > concerning the environment terms biome, environmentalFeature, >>>> and >>>> > environmentalMaterial. I'm renewing the proposal because so >>>> much time has >>>> > passed and the original proposal was not carried through to >>>> completion. >>>> > There were no objections to the addition of those terms during >>>> the initial >>>> > public commentary. Discussion revolved around how the >>>> recommendations for >>>> > how to populate them. >>>> > >>>> > The recommendations for all three terms will suggest using a >>>> controlled >>>> > vocabulary such as ENVO. The examples will be based on the set >>>> of >>>> > subclasses of the corresponding ENVO terms for biome[2], >>>> > environmentalFeature[3], and environmentalMaterial[4]. As with >>>> all Darwin >>>> > Core terms, the constraints on content are not part of the >>>> definition - >>>> > they are only illustrative recommendations. >>>> > >>>> > The importance of these terms was recognized anew at a Darwin >>>> Core and MIxS >>>> > Hackathon in Florence in Sep 2014[5]. One important outcome of >>>> that >>>> > workshop was the the realization that there is currently no >>>> possibility of >>>> > a Darwin Core PreservedSpecimen or MaterialSample record to >>>> meet the >>>> > minimum requirements of a Mimarks Specimen record[6], as there >>>> is currently >>>> > no way to share required environment terms. This creates a >>>> huge and easy to >>>> > solve barrier to integration of data across the collection, >>>> sample, and >>>> > sequence realms. >>>> > >>>> > This proposal is not substantively different from the one >>>> discussed in >>>> > 2013. It differs from the final amended previous proposal in >>>> two ways, 1) >>>> > only the three terms biome, environmentalFeature, and >>>> environmentalMaterial >>>> > are proposed here (the proposal to change to the term >>>> 'habitat' has been >>>> > dropped), and 2) the term definitions have been updated to >>>> agree with those >>>> > in ENVO. The terms will be in the Darwin Core namespace >>>> (following the TDWG >>>> > community consensus in the previous discussion as well the >>>> consensus to >>>> > coin the MaterialSample class in the Darwin Core namespace >>>> rather than use >>>> > obi:specimen, with the equivalency being made on the ontology >>>> side in >>>> > BCO[7]). >>>> > >>>> > The complete definitions of the three proposed terms is given >>>> below the >>>> > following references. This reopens the 30-day public >>>> commentary period for >>>> > the addition of new terms as described in the Darwin Core >>>> Namespace >>>> > Policy[8]. >>>> > >>>> > [1] Original tdwg-content proposal for environment terms. >>>> > >>>> >>>> http://lists.tdwg.org/pipermail/tdwg-content/2013-September/003066.html >>>> > [2] ENVO biome. http://purl.obolibrary.org/obo/ENVO_00000428 >>>> > [3] ENVO environmentalFeature. >>>> http://purl.obolibrary.org/obo/ENVO_00002297 >>>> > [4] ENVO environmentalMaterial. >>>> http://purl.obolibrary.org/obo/ENVO_00010483 >>>> > [5] DwC MIxS Meeting Notes. >>>> > >>>> > https://docs.google.com/document/d/1Zexgsiol6WC83vDzMTCF3uUB7DcFmKL15DFEPbw >>>> 5w6c/edit?usp=sharing >>>> > [6] Table of the core items of Mimarks checklists. >>>> > >>>> http://www.nature.com/nbt/journal/v29/n5/fig_tab/nbt.1823_T1.html >>>> > [7] Biological Collections Ontology. >>>> https://github.com/tucotuco/bco >>>> > [8] Darwin Core Namespace Policy. >>>> > >>>> http://rs.tdwg.org/dwc/terms/namespace/index.htm#classesofchanges >>>> > >>>> > >>>> > Term Name: biome >>>> > Identifier: http://rs.tdwg.org/dwc/terms/biome >>>> > Namespace: http://rs.tdwg.org/dwc/terms/ >>>> > Label: Biome >>>> > Definition: An environmental system to which resident >>>> ecological >>>> > communities have evolved adaptations. >>>> > Comment: Recommended best practice is to use a controlled >>>> vocabulary such >>>> > as defined by the biome class of the Environment Ontology >>>> (ENVO). Examples: >>>> > "flooded grassland biome", >>>> > "http://purl.obolibrary.org/obo/ENVO_01000195". >>>> > Type of Term: >>>> http://www.w3.org/1999/02/22-rdf-syntax-ns#Property >>>> > Refines: >>>> > Status: proposed >>>> > Date Issued: 2013-09-26 >>>> > Date Modified: 2015-03-26 >>>> > Has Domain: >>>> > Has Range: >>>> > Refines: >>>> > Version: biome-2015-03-26 >>>> > Replaces: >>>> > IsReplaceBy: >>>> > Class: http://rs.tdwg.org/dwc/terms/Event >>>> > ABCD 2.0.6: not in ABCD >>>> > >>>> > Term Name: environmentalFeature >>>> > Identifier: http://rs.tdwg.org/dwc/terms/environmentalFeature >>>> > Namespace: http://rs.tdwg.org/dwc/terms/ >>>> > Label: Environmental Feature >>>> > Definition: A material entity which determines an >>>> environmental system. >>>> > Comment: Recommended best practice is to use a controlled >>>> vocabulary such >>>> > as defined by the environmental feature class of the >>>> Environment Ontology >>>> > (ENVO). Examples: "meadow", >>>> > "http://purl.obolibrary.org/obo/ENVO_00000108". >>>> > Type of Term: >>>> http://www.w3.org/1999/02/22-rdf-syntax-ns#Property >>>> > Refines: >>>> > Status: proposed >>>> > Date Issued: 2013-09-26 >>>> > Date Modified: 2015-03-26 >>>> > Has Domain: >>>> > Has Range: >>>> > Refines: >>>> > Version: environmentalFeature-2015-03-26 >>>> > Replaces: >>>> > IsReplaceBy: >>>> > Class: http://rs.tdwg.org/dwc/terms/Event >>>> > ABCD 2.0.6: not in ABCD >>>> > >>>> > Term Name: environmentalMaterial >>>> > Identifier: http://rs.tdwg.org/dwc/terms/environmentalMaterial >>>> > Namespace: http://rs.tdwg.org/dwc/terms/ >>>> > Label: Environmental Material >>>> > Definition: A portion of environmental material is a fiat >>>> object which >>>> > forms the medium or part of the medium of an environmental >>>> system. >>>> > Comment: Recommended best practice is to use a controlled >>>> vocabulary such >>>> > as defined by the environmental feature class of the >>>> Environment Ontology >>>> > (ENVO). Examples: "scum", >>>> > "http://purl.obolibrary.org/obo/ENVO_00003930". >>>> > Type of Term: >>>> http://www.w3.org/1999/02/22-rdf-syntax-ns#Property >>>> > Refines: >>>> > Status: proposed >>>> > Date Issued: 2013-09-26 >>>> > Date Modified: 2015-03-26 >>>> > Has Domain: >>>> > Has Range: >>>> > Refines: >>>> > Version: environmentalMaterial-2015-03-26 >>>> > Replaces: >>>> > IsReplaceBy: >>>> > Class: http://rs.tdwg.org/dwc/terms/Event >>>> > ABCD 2.0.6: not in ABCD >>>> > >>>> >>>> >>>> >

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Invitation to participate in the work of the Vocabulary Maintenance Specification TG
by Steve Baskauf 28 May '15

28 May '15

The charter of the Vocabulary Maintenance Specification Task Group was approved by the TDWG Executive on 2015-05-11. The purpose of this group is to produce Standards Documentation Specification and Vocabulary Maintenance Specification standards that will clarify the processes by which TDWG vocabulary standards would be documented, amended, and maintained. The work of the task group will be documented on the TDWG GitHub site at https://github.com/tdwg/vocab where you can read the group's charter for more details and background. If you would like to participate in the work of the group, go the GitHub link for the group and "watch" the repository. This will allow you to receive email notifications when issues are raised and comments are made. Discussion will be facilitated and documented by raising issues and commenting on them using the GitHub Issues tracker. If you have further questions, please contact the task group convener, Steve Baskauf at steve.baskauf(a)vanderbilt.edu . -- Steven J. Baskauf, Ph.D., Senior Lecturer Vanderbilt University Dept. of Biological Sciences postal mail address: PMB 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) 322-4942 If you fax, please phone or email so that I will know to look for it. http://bioimages.vanderbilt.edu http://vanderbilt.edu/trees

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Re: [tdwg-content] Darwin Core Proposal - environment terms (joel sachs)
by Ramona Walls 20 May '15

20 May '15

Hi Joel, I completely agree about the need to unpack the multiple dimensions of "habitat" in DWC, while not making DWC into an ontology. I suggest the discussion of ENVO terms should probably move to the ENVO list (then come back here, if/when we are ready to deal with adding them to DWC. I'd be very happy to work with you on BCO/DWC stuff and here your needs. Please feel free to just email me off list or email bco-discuss(a)googlegroups.com. We have bi-weekly calls that are open to anyone who wants to participate. 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 Mon, May 18, 2015 at 5:50 AM, joel sachs <jsachs(a)csee.umbc.edu> wrote: > Ramona, > > Thanks for engaging. My thinking is this: > > Our goal is to address the mess that is “habitat”. So much - environmental > conditions, associated taxa, geography, geology - gets crammed into that > one poor term. > > We want to either replace or augment or subclass “habitat” with some new > terms, with each new term capturing some key dimension of information that > “people” are interested in. Before talking specifically about the terms > under consideration, let me disclose some of my biases: > > <statement of biases> > i. I’d like to see terms that will help organize the thousands of habitat > terms used by the authors of taxonomic treatments in the Flora of North > America. You can see some of these terms here - http://bit.ly/1Fnow3E > > We’re currently categorizing these terms to enable semantic search over > habitat; as we do so, we are also thinking about the user interface of > treatment templates for future contributors. Our opinion is that we should > look at existing habitat terms, answer the question “what have authors been > trying to tell us?”, and then design interfaces that make it easier for > them to tell us those things. (This isn’t to say that we shouldn’t also > coax new types of information out of treatment authors, based on our > understanding of what data consumers want to know.) > > The habitat dimensions that, for plants, keep coming up are: wet vs dry; > open canopy vs closed canopy; soil type; sloped vs. flat; and associated > taxa. We also see a range of geography/geology related dimensions. > > ii. I think the semantics of Darwin Core terms should be clear from their > natural language definitions. Ontologies that can be used to provide values > for the terms should not be relied upon as documentation for the terms > themselves. > > iii. I’ve long argued that Darwin Core should not make commitments to any > particular upper ontologies. I explained some of my reasons in my 2013 TDWG > talk (http://bit.ly/1FjCimJ) I recall that you spoke with me about this > last year, and expressed support for the idea of creating ontological > layers on top of Darwin Core. I’ve since tried to do this for BCO, but > struggled. I’ve been meaning to ask for your help with this. > </statement of biases> > > Back to the proposed terms: > > Biome. As has been noted by others, the currently proposed > definition is at odds with common understanding of the term, and is > somewhat confusing due to its dependance on evolution. I think I understand > what the definition is getting at - namely, expanding the traditional > notion of biome to include microbiomes. > > Environmental feature. We often see habitat terms such as “rocky > outcrops”; “arroyos”; “bogs”; etc. So I can see a lot of utility in a > “feature” term. My preference would be to call it “geographic feature” or > “geologic feature”, since I think that’s how most people think of such > features (see, e.g. geonames). The currently proposed definition is “A > material entity which determines an environmental system.” This requirement > that the feature “determine” the environmental system strikes me as too > strong. > > Environmental material. The currently proposed definition is “A > portion of environmental material is a fiat object which forms the medium > or part of the medium of an environmental system.” A much clearer > definition is one that I’ve heard Pierre give, which was along the lines of > “The substance that was displaced by the sample prior to its being removed > from its environment”. In addition to being clearer, this second definition > has the advantage of not relying on the BFO notion of “fiat object”. > > > Happy Victoria Day to all my fellow British subjects! > Joel. > > > > On Wed, 13 May 2015, Ramona Walls wrote: > > This is my first chance to reply to this thread, but I think several of >> Joel's comments need to be addressed. >> >> 1. re.: ENVO terms: "As far as I can tell, no one knows how to use these >> them." >> -- I know how to use them, and I know a community of people who know how >> to >> use them. True, that just like Darwin Core, they are often used >> incorrectly, >> but further documentation and outreach can help with that. >> >> 2. "There was a lot of confusion over whether particular aspects of an >> environment constituted an environmental feature, an environmental >> material, >> or a biome. The correct answer was often dependent on context. For example >> if a small mammal were found in leaf litter, then "leaf litter" would be >> the >> environmental material, and >> the biome would be "forest". But if a microbe were sampled from the same >> leaf litter, then "leaf litter" would be the biome, and I'm not sure what >> the environmental material would be." >> -- ENVO very clearly distinguishes between a biome, a feature, and a >> material. It is never the case that the same ENVO class can be use as >> both a >> biome and a feature or a feature and a material. Although the same entity, >> depending on its role, may serve as either a biome or material (or feature >> for that matter), in that case, it would be an instance of two different >> classes in ENVO. Take the leaf litter example. A correct annotation would >> need to point to both a "leaf litter biome" class and a "leaf litter >> material" class. It is really crucial not to confuse material entities in >> world with the roles they take on as instances of classes in ENVO. >> -- Joel and I seem to remember outcomes of that RCN meeting quite >> differently (probably we were in different break-out groups). As I recall, >> the major problem was that people couldn't use ENVO because the classes >> they >> needed were not in there, not because they didn't know how. This is a >> problem that would actually be helped by DwC adopting ENVO, because it >> would >> create more users, and therefore more contributors to the ontology. >> Another >> major problem was that people often want to describe environments in terms >> of parameters like light level, salinity, temperature, etc. ENVO does not >> currently include classes like this, but a movement is underfoot to >> perhaps >> add such a branch to ENVO. >> >> 3. "Creating tripartite (biome/feature/material) decompositions of >> habitats >> sometimes makes sense. Certainly, it made sense for some of the early >> metagenomic assays that gave rise to ENVO. But it doesn't always make >> sense, and there are often better ways to characterize an environment." >> -- True, there are cases when you cannot specify a biome, feature, and >> material for an organism, but usually you can provide at least one of two >> of >> them, which goes a long way toward standardizing environmental records and >> making large-scale queries possible. I have not yet seen a better way to >> classify environment on this scale. As I mentioned above, when it comes to >> describing environments in terms of their physico-chemical paramaters, >> ENVO >> does not serve, but that does not negate the utility of ENVO-style >> descriptions. Furthermore, as with most DwC terms, these are optional, and >> people/institutions who don't have to provide them if they are not >> relevant. >> >> 4. "The terms "env_biome", "env_feature", and "env_material" already exist >> in >> the MIxS Sample extension to Darwin Core (along with "submitted to INSDC", >> etc.). Why do they need to be moved into the core?" >> -- The main reason I can see is that they have a lot of applicability >> outside of MIXS, that is, for occurrences that do not have any sequences >> associated with them, and should not be hidden away in a place that >> suggests >> they can only be applied to sequence data. >> >> 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, Apr 24, 2015 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 >> >> >> >> Today's Topics: >> >> 1. Re: Darwin Core Proposal - environment terms (joel sachs) >> >> >> ---------------------------------------------------------------------- >> >> Message: 1 >> Date: Thu, 23 Apr 2015 13:29:47 -0400 (EDT) >> From: joel sachs <jsachs(a)csee.umbc.edu> >> Subject: Re: [tdwg-content] Darwin Core Proposal - environment >> terms >> To: John Wieczorek <tuco(a)berkeley.edu> >> Cc: TDWG Content Mailing List <tdwg-content(a)lists.tdwg.org> >> Message-ID: >> >> <Pine.LNX.4.64.1504231321240.18117(a)linuxserver1.cs.umbc.edu> >> Content-Type: TEXT/PLAIN; charset=US-ASCII; format=flowed >> >> John, >> >> I have some concerns with these terms. As far as I can tell, no >> one knows >> how to use these them. I was at a phenotype RCN meeting last >> year where >> the theme was environmental ontologies. The attendees were >> pretty savvy in >> terms of both ontologies, and environmental terminology. We were >> given an >> overview of ENVO, and then, as an experiment, we broke into >> groups, and >> each group tried to use ENVO to describe particular >> environments. I don't >> recall any group being successful. There was a lot of confusion >> over >> whether particular aspects of an environment constituted an >> environmental >> feature, an environmental material, or a biome. The correct >> answer was >> often dependent on context. For example if a small mammal were >> found in >> leaf litter, then "leaf litter" would be the environmental >> material, and >> the biome would be "forest". But if a microbe were sampled from >> the same >> leaf litter, then "leaf litter" would be the biome, and I'm not >> sure what >> the environmental material would be. >> >> Due to the confusion, Pier Luigi gave us a more in-depth >> tutorial when we >> re-convened. We didnt break back out into groups, but I wish we >> had, >> because I wonder if we would have had much more success. >> >> Creating tripartite (biome/feature/material) decompositions of >> habitats >> sometimes makes sense. Certainly, it made sense for some of the >> early >> metagenomic assays that gave rise to ENVO. But it doesn't always >> make >> sense, and there are often better ways to characterize an >> environment. I >> think it was a mistake for these terms to be made mandatory in >> MIxS/MIMARKS. >> >> But the question isn't "What should MIxS do four years ago?", >> but "What >> should TDWG do now?". One wrinkle is that dwc:Habitat already >> exists. Will it stay in the core? Is the idea to create usage >> guides that >> explain when to use dwc:Habitat and when and how to use biome, >> feature, >> and material? Such an approach could work, but I'd like to see >> our usage >> guides differ from current ENVO/MIxS guidelines which mandate >> one and only >> one value for each of the terms. "Environmental feature", in >> particular, >> often merits multiple uses within the same record, and I think >> disallowing >> such usage would impede uptake of the term set. (As far as I can >> see >> from browsing metagenomic sampling metadata, it *has* impeded >> uptake of the term set.) >> >> So I'm not necessarily opposed to the addition of these terms, >> but I do >> wonder why we need them. >> >> You wrote that "there is currently no possibility of a Darwin >> Core >> PreservedSpecimen or MaterialSample record to meet the minimum >> requirements of a Mimarks Specimen record[6], as there is >> currently no way >> to share required environment terms." But MIMARKS specimen >> records are >> also required to have the fields "Submitted to INSDC", >> "Investigation-type", "Project name", "Nucleic acid sequence >> source", >> "Target gene or locus", and "Sequencing method". So won't it >> still be the >> case that there will be no possibility of a Darwin Core record >> being MIMARKS compliant, without appropriate >> augmentation? >> >> The terms "env_biome", "env_feature", and "env_material" already >> exist in >> the MIxS Sample extension to Darwin Core (along with "submitted >> to INSDC", >> etc.). Why do they need to be moved into the core? >> >> Cheers, >> Joel. >> >> >> >> On Thu, 26 Mar 2015, John Wieczorek wrote: >> >> > Dear all, >> > >> > This message pertains to a proposal[1] set forth in September >> 2013 >> > concerning the environment terms biome, environmentalFeature, >> and >> > environmentalMaterial. I'm renewing the proposal because so >> much time has >> > passed and the original proposal was not carried through to >> completion. >> > There were no objections to the addition of those terms during >> the initial >> > public commentary. Discussion revolved around how the >> recommendations for >> > how to populate them. >> > >> > The recommendations for all three terms will suggest using a >> controlled >> > vocabulary such as ENVO. The examples will be based on the set >> of >> > subclasses of the corresponding ENVO terms for biome[2], >> > environmentalFeature[3], and environmentalMaterial[4]. As with >> all Darwin >> > Core terms, the constraints on content are not part of the >> definition - >> > they are only illustrative recommendations. >> > >> > The importance of these terms was recognized anew at a Darwin >> Core and MIxS >> > Hackathon in Florence in Sep 2014[5]. One important outcome of >> that >> > workshop was the the realization that there is currently no >> possibility of >> > a Darwin Core PreservedSpecimen or MaterialSample record to >> meet the >> > minimum requirements of a Mimarks Specimen record[6], as there >> is currently >> > no way to share required environment terms. This creates a >> huge and easy to >> > solve barrier to integration of data across the collection, >> sample, and >> > sequence realms. >> > >> > This proposal is not substantively different from the one >> discussed in >> > 2013. It differs from the final amended previous proposal in >> two ways, 1) >> > only the three terms biome, environmentalFeature, and >> environmentalMaterial >> > are proposed here (the proposal to change to the term >> 'habitat' has been >> > dropped), and 2) the term definitions have been updated to >> agree with those >> > in ENVO. The terms will be in the Darwin Core namespace >> (following the TDWG >> > community consensus in the previous discussion as well the >> consensus to >> > coin the MaterialSample class in the Darwin Core namespace >> rather than use >> > obi:specimen, with the equivalency being made on the ontology >> side in >> > BCO[7]). >> > >> > The complete definitions of the three proposed terms is given >> below the >> > following references. This reopens the 30-day public >> commentary period for >> > the addition of new terms as described in the Darwin Core >> Namespace >> > Policy[8]. >> > >> > [1] Original tdwg-content proposal for environment terms. >> > >> >> http://lists.tdwg.org/pipermail/tdwg-content/2013-September/003066.html >> > [2] ENVO biome. http://purl.obolibrary.org/obo/ENVO_00000428 >> > [3] ENVO environmentalFeature. >> http://purl.obolibrary.org/obo/ENVO_00002297 >> > [4] ENVO environmentalMaterial. >> http://purl.obolibrary.org/obo/ENVO_00010483 >> > [5] DwC MIxS Meeting Notes. >> > >> https://docs.google.com/document/d/1Zexgsiol6WC83vDzMTCF3uUB7DcFmKL15DFEPbw >> 5w6c/edit?usp=sharing >> > [6] Table of the core items of Mimarks checklists. >> > >> http://www.nature.com/nbt/journal/v29/n5/fig_tab/nbt.1823_T1.html >> > [7] Biological Collections Ontology. >> https://github.com/tucotuco/bco >> > [8] Darwin Core Namespace Policy. >> > >> http://rs.tdwg.org/dwc/terms/namespace/index.htm#classesofchanges >> > >> > >> > Term Name: biome >> > Identifier: http://rs.tdwg.org/dwc/terms/biome >> > Namespace: http://rs.tdwg.org/dwc/terms/ >> > Label: Biome >> > Definition: An environmental system to which resident >> ecological >> > communities have evolved adaptations. >> > Comment: Recommended best practice is to use a controlled >> vocabulary such >> > as defined by the biome class of the Environment Ontology >> (ENVO). Examples: >> > "flooded grassland biome", >> > "http://purl.obolibrary.org/obo/ENVO_01000195". >> > Type of Term: >> http://www.w3.org/1999/02/22-rdf-syntax-ns#Property >> > Refines: >> > Status: proposed >> > Date Issued: 2013-09-26 >> > Date Modified: 2015-03-26 >> > Has Domain: >> > Has Range: >> > Refines: >> > Version: biome-2015-03-26 >> > Replaces: >> > IsReplaceBy: >> > Class: http://rs.tdwg.org/dwc/terms/Event >> > ABCD 2.0.6: not in ABCD >> > >> > Term Name: environmentalFeature >> > Identifier: http://rs.tdwg.org/dwc/terms/environmentalFeature >> > Namespace: http://rs.tdwg.org/dwc/terms/ >> > Label: Environmental Feature >> > Definition: A material entity which determines an >> environmental system. >> > Comment: Recommended best practice is to use a controlled >> vocabulary such >> > as defined by the environmental feature class of the >> Environment Ontology >> > (ENVO). Examples: "meadow", >> > "http://purl.obolibrary.org/obo/ENVO_00000108". >> > Type of Term: >> http://www.w3.org/1999/02/22-rdf-syntax-ns#Property >> > Refines: >> > Status: proposed >> > Date Issued: 2013-09-26 >> > Date Modified: 2015-03-26 >> > Has Domain: >> > Has Range: >> > Refines: >> > Version: environmentalFeature-2015-03-26 >> > Replaces: >> > IsReplaceBy: >> > Class: http://rs.tdwg.org/dwc/terms/Event >> > ABCD 2.0.6: not in ABCD >> > >> > Term Name: environmentalMaterial >> > Identifier: http://rs.tdwg.org/dwc/terms/environmentalMaterial >> > Namespace: http://rs.tdwg.org/dwc/terms/ >> > Label: Environmental Material >> > Definition: A portion of environmental material is a fiat >> object which >> > forms the medium or part of the medium of an environmental >> system. >> > Comment: Recommended best practice is to use a controlled >> vocabulary such >> > as defined by the environmental feature class of the >> Environment Ontology >> > (ENVO). Examples: "scum", >> > "http://purl.obolibrary.org/obo/ENVO_00003930". >> > Type of Term: >> http://www.w3.org/1999/02/22-rdf-syntax-ns#Property >> > Refines: >> > Status: proposed >> > Date Issued: 2013-09-26 >> > Date Modified: 2015-03-26 >> > Has Domain: >> > Has Range: >> > Refines: >> > Version: environmentalMaterial-2015-03-26 >> > Replaces: >> > IsReplaceBy: >> > Class: http://rs.tdwg.org/dwc/terms/Event >> > ABCD 2.0.6: not in ABCD >> > >> >> >>

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