May 2015 - tdwg-content - lists.tdwg.org

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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Re: [tdwg-content] Darwin Core Proposal - environment terms (biome)
by Daniel Janzen 18 May '15

18 May '15

Pier, yes please you put this wherever it might be useful to anyone. I am drowning. Dan Janzen On May 18, 2015, at 3:59 PM, Pier Luigi Buttigieg <pbuttigi(a)mpi-bremen.de> wrote: > @Dan, > Thanks for the feedback. Could you add this as an issue on our tracker? > https://github.com/EnvironmentOntology/envo/issues > Copy-pasting your text would be great (if you don't have and don't wish to > create a github account, I could post it on your behalf). > At the very least, we (the ENVO editors) should add a comment to this class > reflecting these concerns. > > @Steve, > Thanks for your thinking on this. I suppose there's an element of > historical intertia here, and a relabelling is probably wise. Would it > possible to post this to our issue tracker? > > On Sun, 17 May 2015 16:46:00 -0600, Daniel Janzen <djanzen(a)sas.upenn.edu> > wrote: >> 17 May 2015 >> >> Folks, you are inserting "evolution" in a definition that has never had >> one. Worse, frankly, you have zero way of really knowing if a species in >> hand evolved in or in response to the place where you are finding it. > And >> evolved what? MANY species arrive in this or that ecosystem under their >> own steam, and simply "ecologically fit" into them according to their own >> traits, with no evolution involved. Introduce the agouti into Africa >> without telling anyone and all future biologists will tell you that it is >> highly evolved as a seed disperser for African rain forest trees (just as >> people tell you today for the neotropics), which will be absolute > nonsense. >> It may of course evolve further once it has arrived somewhere, but it >> certainly need not, and you (and I) have no way of knowing if it has. > And >> furthermore, what particular trait are you thinking you can evaluate as >> "evolved" at your site (and not elsewhere) and just how many of them need >> there be, visible or invisible (to Homo sapiens) before it is "evolved" > in >> that ecosystem (or biome if you like)? P.S. Note that the "biome" >> terminology is a peculiar mutant of extra-tropical northern biologists, > and >> "ecosystem" has vastly more geographic and social coverage around the >> globe. >> >> For whatever. Not able or willing to enter into some massive discussion > of >> all this. Just tossing this on the table in case it fits somewhere, > since >> it appears to me, as a lurker, that it has not been. >> >> Dan Janzen >> >> >> On May 17, 2015, at 4:13 PM, Steve Baskauf <steve.baskauf(a)vanderbilt.edu> >> wrote: >> >>> Thanks to all for the clarifying comments. I think that what we are >>> seeing here is a manifestation of what we've seen previously on this > list >>> in discussions about terms: that people make assumptions about what a >>> term means based on its label (mea culpa). The solution, as in previous >>> cases, is to look carefully at the definition to make sure the term >>> actually means what you think it does. >>> >>> I don't have a problem with the ENVO text definition "an environmental >>> system to which resident ecological communities have evolved >>> adaptations." if that's what ENVO wants the term ENVO:00000428 to mean. >>> But I'm not sure that I would necessarily have gotten a clear picture of >>> what ENVO wants "biome" to mean solely from the documentation. The .obo >>> file includes "Wikipedia:Biome" as a citation for the ENVO definition, >>> but the Wikipedia definition of bioime [1] doesn't really seem to bear >>> any resemblence to the ENVO definition. The ENVO term description also >>> includes "synonym: 'major habitat type' EXACT [WWF:Biome]", but WWF [2] >>> doesn't define biomes as ENVO does either. Both Wikipedia and WWF talk >>> about biomes in the traditional sense of large geographic regions. If >>> the ENVO definition of biome is intended to broaden biome beyond its >>> traditional meaning, then I think it would be better to give the >>> ENVO:00000428 some different label ("evolved environmental system"?) and >>> reserve the label "biome" for biome in the traditional sense (with the >>> declared WWF and Wikipedia equivalencies). Then declare "biome" >>> rdfs:subClassOf "evolved environmental system". >>> >>> Also, if the various ENVO subclasses of ENVO:00000428 are intended to be >>> equivalent to all or part of WWF biomes, then why not note this in the >>> term description. Unlike Wikipedia, which could change tomorrow, the > WWF >>> bioimes are well-described in stable publications such as Ricketts et > al. >>> (1999) [3]. >>> >>> Steve >>> >>> [1] "Biomes are climatically and geographically defined as contiguous >>> areas with similar climatic conditions on the Earth, such as communities >>> of plants, animals, soil organisms, and viruses and are often referred > to >>> as ecosystems. Some parts of the earth have more or less the same kind > of >>> abiotic and biotic factors spread over a large area, creating a typical >>> ecosystem over that area. Such major ecosystems are termed as biomes. >>> Biomes are defined by factors such as plant structures (such as trees, >>> shrubs, and grasses), leaf types (such as broadleaf and needleleaf), >>> plant spacing (forest, woodland, savanna), and climate. " >>> >>> [2] "Biomes are the various regions of our planet that can best be >>> distinguished by their climate, fauna and flora. There are different > ways >>> of classifying biomes but the common elements are climate, habitat, >>> animal and plant adaptation, biodiversity and human activity." >>> > http://wwf.panda.org/about_our_earth/teacher_resources/webfieldtrips/major_… >>> >>> [3] http://islandpress.org/terrestrial-ecoregions-north-america >>> >>> Pier Luigi Buttigieg wrote: >>>>> The ENVO definition of biome is : "A biome is an environmental system >>>>> to >>>>> which resident ecological communities have evolved adaptations." >>>>> (http://purl.obolibrary.org/obo/ENVO_00000428) >>>>> >>>> >>>> We try to be agnostic to spatial scale with this definition as we >>>> encountered numerous instances of the term being used outside of >>>> 'classical' biome classification systems with reasonable rationale > (e.g. >>>> many environments - such as marine and lacustrine environments - are > not >>>> adequately covered by existing schemes). Even within classical systems, >>>> identifying the scale threshold is hardly precise (if anyone knows of >>>> anything that defines this, please let me know) and definitions are >>>> revised >>>> from time to time as new technologies (e.g. remote sensing) emerge. > Some >>>> have suggested using prevailing climate as a way to stabilise 'large' >>>> scales, but this is problematic as microclimates (e.g. near large water >>>> bodies) can result in the emergence of different biomes (in the >>>> classical >>>> sense) existing at comparatively small regions. The presence of an >>>> ecological community which has adapted to a given environment seems to >>>> be >>>> the common theme. A successful, in situ adaptation process indicates >>>> that >>>> the environment a) can sustain viable populations over multiple >>>> generations >>>> and b) persists long enough for these populations to undergo >>>> evolutionarily >>>> consequential changes, distinguishing it from other environment types. >>>> If >>>> users wish to use a 'classical' biome type, they have access to an >>>> adapted >>>> version of the WWF classification (see below). >>>> >>>> >>>>> A resident ecological community from the perspective of a microbe >>>>> likely >>>>> does not care about the large-scale plant and animal communities, so > it >>>>> >>>> is >>>> >>>>> a matter of perspective taken from the point of view of the subject. >>>>> To >>>>> that end, leaf litter as the biome seems entirely reasonable if the >>>>> microbes resident there have evolved adaptations to leaf litter. >>>>> >>>> [...] >>>> >>>>>> Steve Baskauf wrote: >>>>>> I haven't looked at the definition given to "biome" in ENVO, but >>>>>> based >>>>>> on what I believe is the common consensus on what a biome is (a > major, >>>>>> large-scale set of plant and animal communities occupying a > geographic >>>>>> region), it doesn't seem right to apply that term to "leaf litter". >>>>>> >>>> [...] >>>> >>>>>> There are a number of standard lists of the world's biomes and they >>>>>> include large-scale regions like "temperate deciduous forest", not >>>>>> small-scale features. >>>>>> >>>> >>>> ENVO includes a representation of the WWF biome classification system. >>>> At >>>> one stage, the Udvardy, WWF, and Bailey systems were all in ENVO (which >>>> was >>>> quite confusing). We opted to use the WWF system (obsoleting the other >>>> classes) as it was the most current and had the highest global > coverage. >>>> The WWF categories were modified to make them more suitable for an >>>> ontology >>>> (e.g. compound classes were split). >>>> >>>> As a microbial ecologist, I think that the position outlined by John is >>>> a >>>> valid one. The scales used in the 'classical' definition are, >>>> ultimately, a >>>> function of our own observational capacities and various forms of >>>> ecosystem >>>> can be nested across scales. However, Steve's right in saying that this >>>> is >>>> a fairly profound change in the usage of a well-established term (with > a >>>> substantial literature base behind it). Further, just because a >>>> microbial >>>> ecologist (or anyone else, but I'm going with this example) declares >>>> something to be a biome, doesn't make it so: the communities of > microbes >>>> living in leaf litter may not have evolved in that particular >>>> environment, >>>> they may simply have adaptations to other environments that allow them >>>> to >>>> colonise a one with sufficient similarities. >>>> >>>> In our annotation guidelines >>>> (http://www.environmentontology.org/annotation-guidelines) we do ask >>>> that >>>> such "small scale" biomes are requested with reference to some form of >>>> empirical data supporting the notion that the communities have adapted >>>> to >>>> that particular environment. ENVO doesn't try to dictate what is > "right" >>>> here, but attempts to represent how different communities (who are >>>> creating >>>> new conventions which reflect their phenomena they study) are talking >>>> about >>>> environments. Whether they turn out to be correct in their usage of a >>>> given >>>> term is a somewhat different question and we're always happy to receive >>>> critiques and input. >>>> >>>> I think it's best if we declare or produce subset of biome classes that >>>> are >>>> approved by a certain body (e.g. the WWF). Conversely, classes that are >>>> somehow 'nascent' or 'experimental' can also be marked. Plans to > produce >>>> subsets of ENVO that are relevant to specific working bodies are > already >>>> queued. >>>> >>>> >>>>>> Ramona Walls wrote: >>>>>> >>>>>> >>>> [...] >>>> >>>>>> -- 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. >>>>>> >>>> >>>> A "leaf litter biome" would, roughly, refer to the environmental system >>>> that is determined by (~ must include) the community of organisms that >>>> have >>>> adapted to the conditions in leaf litter. As noted above, there should >>>> be >>>> some sort of evidence that this environment-specific adaptation >>>> occurred. >>>> >>>> As a material, "leaf litter" is referring to some portion of 'stuff' >>>> primarily composed of (but not necessarily limited to) fallen, dead or >>>> dying plant material. As another example, when you use ENVO:water you >>>> roughly mean "a volume of material primarily composed of H2O, but which >>>> is >>>> likely to include stuff other than H2O found in some environment". >>>> >>>> I'm not sure that leaf litter works as a feature as it doesn't seem to >>>> have >>>> countable parts that would be called, e.g. "pieces of leaf litter" > (does >>>> it?). One would rather say "dead leaf" or "dead twig". As an > alternative >>>> example, "rock", as a mass noun, is a material, but a "piece of rock" >>>> can >>>> be a feature. >>>> >>>> >>>>>>> Joel sachs wrote: >>>>>>> >>>> [...] >>>> >>>>>>> I have some concerns with these terms. As far as I can tell, no one >>>>>>> knows how to use these them. >>>>>>> >>>> [...] >>>> >>>> I feel that creating interfaces for annotators to use ontologies > without >>>> delving too deeply into (the individual) ontology are sorely needed. >>>> Some >>>> of us have discussed something like a GUI-based wizard to help people >>>> use >>>> ENVO (gamifying it to increase 'uptake' and annotation accuracy), but >>>> haven't had the time to put it together. >>>> In the meantime, I can certainly help write more sets of annotation >>>> guidelines for different communities (linking to them from the ENVO >>>> website >>>> to show that there are multiple ways to use the ontology). >>>> >>>> >>>>>>> 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. >>>>>>> >>>> >>>> The main arguments for using the tripartite annotation (and its >>>> mandatory >>>> status) were: 1) many of the better ways of describing environments >>>> (e.g. >>>> hard data) were non-recoverable and 2) adding more than one term for >>>> each >>>> of ENVO's main hierarchies would add too much to the already long >>>> checklist. Even when other data is missing, there is usually enough >>>> information around to compose a 'three-phase zoom in' (from biome to >>>> material) on an entity's environment. This way, at least rough >>>> comparative >>>> studies could be performed using an ontology (or, at the very least, a >>>> controlled vocabulary). It's clear, however, that many MIxS report >>>> submitters don't use ENVO very well, even after directed to the >>>> annotation >>>> guidelines. Again, some sort of nifty annotation interface would >>>> probably >>>> make this more successful. >>>> >>>> >>>>>>> ... 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.) >>>>>>> >>>> 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 characterise an entity's environment. There is certainly more > than >>>> one feature that is likely to exert a strong >>>> causal influence on (i.e. determine) an entity's environment and all >>>> those >>>> that are deemed relevant should all be recorded. Ideally, they would be >>>> 'ranked', but this requires some further thinking and implementation. >>>> For >>>> materials, entities can be partially surrounded by multiple materials >>>> (Chris' duck swimming in water example, for instance). >>>> >>>> >>>>>>> So I'm not necessarily opposed to the addition of these terms, but I >>>>>>> do >>>>>>> wonder why we need them. >>>>>>> >>>> I think there are some good reasons to use some form of ontology in >>>> annotations to enhance comparative power across granularities and > shades >>>> of >>>> meaning. Naturally, ontologies like ENVO are constantly developing and >>>> if >>>> they don't meet a community's needs, there are usually ways to either >>>> report and discuss issues (e.g. >>>> https://github.com/EnvironmentOntology/envo/issues) or become a >>>> co-developer. >>>> [...] >>>> >>>> I hope this has helped rather clarify our thinking. As always, we're >>>> very >>>> interested in insight (especially on our issue tracker) to help enhance >>>> the >>>> usefulness of the ontology. >>>> Best, >>>> Pier >>>> >>>> PS: For general interest, I'll be meeting some urban environment >>>> specialists next week and intend to add more city-based environment >>>> classes >>>> (e.g. "urban prairies" such as those proliferating in Detroit). >>>> . >>>> >>>> >>> >>> -- >>> 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 >>> >>> _______________________________________________ >>> tdwg-content mailing list >>> tdwg-content(a)lists.tdwg.org >>> http://lists.tdwg.org/mailman/listinfo/tdwg-content > > -- > Dr. Pier Luigi Buttigieg > HGF-MPG Group for Deep Sea Ecology and Technology > Alfred-Wegener-Institut, Helmholtz-Zentrum für Polar- und Meeresforschung > c/o Max Planck Institute for Marine Microbiology > Celsiusstrasse 1, 28359 Bremen, Germany > Tel: +49 421 2028 984 > Email: pbuttigi(a)mpi-bremen.de >

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Darwin Core Proposal - environment terms (joel sachs)
by Ramona Walls 18 May '15

18 May '15

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… > > [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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Re: [tdwg-content] Darwin Core Proposal - environment terms (biome)
by Steve Baskauf 17 May '15

17 May '15

Thanks to all for the clarifying comments. I think that what we are seeing here is a manifestation of what we've seen previously on this list in discussions about terms: that people make assumptions about what a term means based on its label (mea culpa). The solution, as in previous cases, is to look carefully at the definition to make sure the term actually means what you think it does. I don't have a problem with the ENVO text definition "an environmental system to which resident ecological communities have evolved adaptations." if that's what ENVO wants the term ENVO:00000428 to mean. But I'm not sure that I would necessarily have gotten a clear picture of what ENVO wants "biome" to mean solely from the documentation. The .obo file includes "Wikipedia:Biome" as a citation for the ENVO definition, but the Wikipedia definition of bioime [1] doesn't really seem to bear any resemblence to the ENVO definition. The ENVO term description also includes "synonym: 'major habitat type' EXACT [WWF:Biome]", but WWF [2] doesn't define biomes as ENVO does either. Both Wikipedia and WWF talk about biomes in the traditional sense of large geographic regions. If the ENVO definition of biome is intended to broaden biome beyond its traditional meaning, then I think it would be better to give the ENVO:00000428 some different label ("evolved environmental system"?) and reserve the label "biome" for biome in the traditional sense (with the declared WWF and Wikipedia equivalencies). Then declare "biome" rdfs:subClassOf "evolved environmental system". Also, if the various ENVO subclasses of ENVO:00000428 are intended to be equivalent to all or part of WWF biomes, then why not note this in the term description. Unlike Wikipedia, which could change tomorrow, the WWF bioimes are well-described in stable publications such as Ricketts et al. (1999) [3]. Steve [1] "Biomes are climatically and geographically defined as contiguous areas with similar climatic conditions on the Earth, such as communities of plants, animals, soil organisms, and viruses and are often referred to as ecosystems. Some parts of the earth have more or less the same kind of abiotic and biotic factors spread over a large area, creating a typical ecosystem over that area. Such major ecosystems are termed as biomes. Biomes are defined by factors such as plant structures (such as trees, shrubs, and grasses), leaf types (such as broadleaf and needleleaf), plant spacing (forest, woodland, savanna), and climate. " [2] "Biomes are the various regions of our planet that can best be distinguished by their climate, fauna and flora. There are different ways of classifying biomes but the common elements are climate, habitat, animal and plant adaptation, biodiversity and human activity." http://wwf.panda.org/about_our_earth/teacher_resources/webfieldtrips/major_… [3] http://islandpress.org/terrestrial-ecoregions-north-america Pier Luigi Buttigieg wrote: >> The ENVO definition of biome is : "A biome is an environmental system to >> which resident ecological communities have evolved adaptations." (http://purl.obolibrary.org/obo/ENVO_00000428) >> > > We try to be agnostic to spatial scale with this definition as we > encountered numerous instances of the term being used outside of > 'classical' biome classification systems with reasonable rationale (e.g. > many environments - such as marine and lacustrine environments - are not > adequately covered by existing schemes). Even within classical systems, > identifying the scale threshold is hardly precise (if anyone knows of > anything that defines this, please let me know) and definitions are revised > from time to time as new technologies (e.g. remote sensing) emerge. Some > have suggested using prevailing climate as a way to stabilise 'large' > scales, but this is problematic as microclimates (e.g. near large water > bodies) can result in the emergence of different biomes (in the classical > sense) existing at comparatively small regions. The presence of an > ecological community which has adapted to a given environment seems to be > the common theme. A successful, in situ adaptation process indicates that > the environment a) can sustain viable populations over multiple generations > and b) persists long enough for these populations to undergo evolutionarily > consequential changes, distinguishing it from other environment types. If > users wish to use a 'classical' biome type, they have access to an adapted > version of the WWF classification (see below). > > >> A resident ecological community from the perspective of a microbe likely >> does not care about the large-scale plant and animal communities, so it >> > is > >> a matter of perspective taken from the point of view of the subject. To >> that end, leaf litter as the biome seems entirely reasonable if the >> microbes resident there have evolved adaptations to leaf litter. >> > [...] > >>> Steve Baskauf wrote: >>> I haven't looked at the definition given to "biome" in ENVO, but based >>> on what I believe is the common consensus on what a biome is (a major, >>> large-scale set of plant and animal communities occupying a geographic >>> region), it doesn't seem right to apply that term to "leaf litter". >>> > [...] > >>> There are a number of standard lists of the world's biomes and they >>> include large-scale regions like "temperate deciduous forest", not >>> small-scale features. >>> > > ENVO includes a representation of the WWF biome classification system. At > one stage, the Udvardy, WWF, and Bailey systems were all in ENVO (which was > quite confusing). We opted to use the WWF system (obsoleting the other > classes) as it was the most current and had the highest global coverage. > The WWF categories were modified to make them more suitable for an ontology > (e.g. compound classes were split). > > As a microbial ecologist, I think that the position outlined by John is a > valid one. The scales used in the 'classical' definition are, ultimately, a > function of our own observational capacities and various forms of ecosystem > can be nested across scales. However, Steve's right in saying that this is > a fairly profound change in the usage of a well-established term (with a > substantial literature base behind it). Further, just because a microbial > ecologist (or anyone else, but I'm going with this example) declares > something to be a biome, doesn't make it so: the communities of microbes > living in leaf litter may not have evolved in that particular environment, > they may simply have adaptations to other environments that allow them to > colonise a one with sufficient similarities. > > In our annotation guidelines > (http://www.environmentontology.org/annotation-guidelines) we do ask that > such "small scale" biomes are requested with reference to some form of > empirical data supporting the notion that the communities have adapted to > that particular environment. ENVO doesn't try to dictate what is "right" > here, but attempts to represent how different communities (who are creating > new conventions which reflect their phenomena they study) are talking about > environments. Whether they turn out to be correct in their usage of a given > term is a somewhat different question and we're always happy to receive > critiques and input. > > I think it's best if we declare or produce subset of biome classes that are > approved by a certain body (e.g. the WWF). Conversely, classes that are > somehow 'nascent' or 'experimental' can also be marked. Plans to produce > subsets of ENVO that are relevant to specific working bodies are already > queued. > > >>> Ramona Walls wrote: >>> >>> > [...] > >>> -- 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. >>> > > A "leaf litter biome" would, roughly, refer to the environmental system > that is determined by (~ must include) the community of organisms that have > adapted to the conditions in leaf litter. As noted above, there should be > some sort of evidence that this environment-specific adaptation occurred. > > As a material, "leaf litter" is referring to some portion of 'stuff' > primarily composed of (but not necessarily limited to) fallen, dead or > dying plant material. As another example, when you use ENVO:water you > roughly mean "a volume of material primarily composed of H2O, but which is > likely to include stuff other than H2O found in some environment". > > I'm not sure that leaf litter works as a feature as it doesn't seem to have > countable parts that would be called, e.g. "pieces of leaf litter" (does > it?). One would rather say "dead leaf" or "dead twig". As an alternative > example, "rock", as a mass noun, is a material, but a "piece of rock" can > be a feature. > > >>>> Joel sachs wrote: >>>> > [...] > >>>> I have some concerns with these terms. As far as I can tell, no one >>>> knows how to use these them. >>>> > [...] > > I feel that creating interfaces for annotators to use ontologies without > delving too deeply into (the individual) ontology are sorely needed. Some > of us have discussed something like a GUI-based wizard to help people use > ENVO (gamifying it to increase 'uptake' and annotation accuracy), but > haven't had the time to put it together. > In the meantime, I can certainly help write more sets of annotation > guidelines for different communities (linking to them from the ENVO website > to show that there are multiple ways to use the ontology). > > >>>> 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. >>>> > > The main arguments for using the tripartite annotation (and its mandatory > status) were: 1) many of the better ways of describing environments (e.g. > hard data) were non-recoverable and 2) adding more than one term for each > of ENVO's main hierarchies would add too much to the already long > checklist. Even when other data is missing, there is usually enough > information around to compose a 'three-phase zoom in' (from biome to > material) on an entity's environment. This way, at least rough comparative > studies could be performed using an ontology (or, at the very least, a > controlled vocabulary). It's clear, however, that many MIxS report > submitters don't use ENVO very well, even after directed to the annotation > guidelines. Again, some sort of nifty annotation interface would probably > make this more successful. > > >>>> ... 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.) >>>> > 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 characterise an entity's environment. There is certainly more than > one feature that is likely to exert a strong > causal influence on (i.e. determine) an entity's environment and all those > that are deemed relevant should all be recorded. Ideally, they would be > 'ranked', but this requires some further thinking and implementation. For > materials, entities can be partially surrounded by multiple materials > (Chris' duck swimming in water example, for instance). > > >>>> So I'm not necessarily opposed to the addition of these terms, but I do >>>> wonder why we need them. >>>> > I think there are some good reasons to use some form of ontology in > annotations to enhance comparative power across granularities and shades of > meaning. Naturally, ontologies like ENVO are constantly developing and if > they don't meet a community's needs, there are usually ways to either > report and discuss issues (e.g. > https://github.com/EnvironmentOntology/envo/issues) or become a > co-developer. > [...] > > I hope this has helped rather clarify our thinking. As always, we're very > interested in insight (especially on our issue tracker) to help enhance the > usefulness of the ontology. > Best, > Pier > > PS: For general interest, I'll be meeting some urban environment > specialists next week and intend to add more city-based environment classes > (e.g. "urban prairies" such as those proliferating in Detroit). > . > > -- 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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Fwd: Darwin Core Proposal - environment terms (biome)
by Ramona Walls 16 May '15

16 May '15

Forwarding Pier's response, because he is not on the TDWG list. Thanks, Pier! ------------------------------------------------------ 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 ---------- Forwarded message ---------- From: Pier Luigi Buttigieg <pbuttigi(a)mpi-bremen.de> Date: Fri, May 15, 2015 at 7:51 PM Subject: Re: [tdwg-content] Darwin Core Proposal - environment terms (biome) To: John Deck <jdeck88(a)gmail.com> Cc: Steve Baskauf <steve.baskauf(a)vanderbilt.edu>, Ramona Walls < rlwalls2008(a)gmail.com>, TDWG Content Mailing List < tdwg-content(a)lists.tdwg.org>, Suzanna Lewis <suzi(a)berkeleybop.org>, Chris Mungall <cjmungall(a)lbl.gov> Hi all, I've restricted my responses (in line, below) to the usage of ENVO classes as I can't really comment on DwC strategy. > John Deck wrote: [...] > The ENVO definition of biome is : "A biome is an environmental system to > which resident ecological communities have evolved adaptations." ( > http://purl.obolibrary.org/obo/ENVO_00000428) We try to be agnostic to spatial scale with this definition as we encountered numerous instances of the term being used outside of 'classical' biome classification systems with reasonable rationale (e.g. many environments - such as marine and lacustrine environments - are not adequately covered by existing schemes). Even within classical systems, identifying the scale threshold is hardly precise (if anyone knows of anything that defines this, please let me know) and definitions are revised from time to time as new technologies (e.g. remote sensing) emerge. Some have suggested using prevailing climate as a way to stabilise 'large' scales, but this is problematic as microclimates (e.g. near large water bodies) can result in the emergence of different biomes (in the classical sense) existing at comparatively small regions. The presence of an ecological community which has adapted to a given environment seems to be the common theme. A successful, in situ adaptation process indicates that the environment a) can sustain viable populations over multiple generations and b) persists long enough for these populations to undergo evolutionarily consequential changes, distinguishing it from other environment types. If users wish to use a 'classical' biome type, they have access to an adapted version of the WWF classification (see below). > A resident ecological community from the perspective of a microbe likely > does not care about the large-scale plant and animal communities, so it is > a matter of perspective taken from the point of view of the subject. To > that end, leaf litter as the biome seems entirely reasonable if the > microbes resident there have evolved adaptations to leaf litter. [...] >> Steve Baskauf wrote: >> I haven't looked at the definition given to "biome" in ENVO, but based >> on what I believe is the common consensus on what a biome is (a major, >> large-scale set of plant and animal communities occupying a geographic >> region), it doesn't seem right to apply that term to "leaf litter". [...] >> There are a number of standard lists of the world's biomes and they >> include large-scale regions like "temperate deciduous forest", not >> small-scale features. ENVO includes a representation of the WWF biome classification system. At one stage, the Udvardy, WWF, and Bailey systems were all in ENVO (which was quite confusing). We opted to use the WWF system (obsoleting the other classes) as it was the most current and had the highest global coverage. The WWF categories were modified to make them more suitable for an ontology (e.g. compound classes were split). As a microbial ecologist, I think that the position outlined by John is a valid one. The scales used in the 'classical' definition are, ultimately, a function of our own observational capacities and various forms of ecosystem can be nested across scales. However, Steve's right in saying that this is a fairly profound change in the usage of a well-established term (with a substantial literature base behind it). Further, just because a microbial ecologist (or anyone else, but I'm going with this example) declares something to be a biome, doesn't make it so: the communities of microbes living in leaf litter may not have evolved in that particular environment, they may simply have adaptations to other environments that allow them to colonise a one with sufficient similarities. In our annotation guidelines (http://www.environmentontology.org/annotation-guidelines) we do ask that such "small scale" biomes are requested with reference to some form of empirical data supporting the notion that the communities have adapted to that particular environment. ENVO doesn't try to dictate what is "right" here, but attempts to represent how different communities (who are creating new conventions which reflect their phenomena they study) are talking about environments. Whether they turn out to be correct in their usage of a given term is a somewhat different question and we're always happy to receive critiques and input. I think it's best if we declare or produce subset of biome classes that are approved by a certain body (e.g. the WWF). Conversely, classes that are somehow 'nascent' or 'experimental' can also be marked. Plans to produce subsets of ENVO that are relevant to specific working bodies are already queued. >> Ramona Walls wrote: >> [...] >> -- 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. A "leaf litter biome" would, roughly, refer to the environmental system that is determined by (~ must include) the community of organisms that have adapted to the conditions in leaf litter. As noted above, there should be some sort of evidence that this environment-specific adaptation occurred. As a material, "leaf litter" is referring to some portion of 'stuff' primarily composed of (but not necessarily limited to) fallen, dead or dying plant material. As another example, when you use ENVO:water you roughly mean "a volume of material primarily composed of H2O, but which is likely to include stuff other than H2O found in some environment". I'm not sure that leaf litter works as a feature as it doesn't seem to have countable parts that would be called, e.g. "pieces of leaf litter" (does it?). One would rather say "dead leaf" or "dead twig". As an alternative example, "rock", as a mass noun, is a material, but a "piece of rock" can be a feature. >>> Joel sachs wrote: [...] >>> I have some concerns with these terms. As far as I can tell, no one >>> knows how to use these them. [...] I feel that creating interfaces for annotators to use ontologies without delving too deeply into (the individual) ontology are sorely needed. Some of us have discussed something like a GUI-based wizard to help people use ENVO (gamifying it to increase 'uptake' and annotation accuracy), but haven't had the time to put it together. In the meantime, I can certainly help write more sets of annotation guidelines for different communities (linking to them from the ENVO website to show that there are multiple ways to use the ontology). >>> 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. The main arguments for using the tripartite annotation (and its mandatory status) were: 1) many of the better ways of describing environments (e.g. hard data) were non-recoverable and 2) adding more than one term for each of ENVO's main hierarchies would add too much to the already long checklist. Even when other data is missing, there is usually enough information around to compose a 'three-phase zoom in' (from biome to material) on an entity's environment. This way, at least rough comparative studies could be performed using an ontology (or, at the very least, a controlled vocabulary). It's clear, however, that many MIxS report submitters don't use ENVO very well, even after directed to the annotation guidelines. Again, some sort of nifty annotation interface would probably make this more successful. >>> ... 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.) 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 characterise an entity's environment. There is certainly more than one feature that is likely to exert a strong causal influence on (i.e. determine) an entity's environment and all those that are deemed relevant should all be recorded. Ideally, they would be 'ranked', but this requires some further thinking and implementation. For materials, entities can be partially surrounded by multiple materials (Chris' duck swimming in water example, for instance). >>> So I'm not necessarily opposed to the addition of these terms, but I do >>> wonder why we need them. I think there are some good reasons to use some form of ontology in annotations to enhance comparative power across granularities and shades of meaning. Naturally, ontologies like ENVO are constantly developing and if they don't meet a community's needs, there are usually ways to either report and discuss issues (e.g. https://github.com/EnvironmentOntology/envo/issues) or become a co-developer. [...] I hope this has helped rather clarify our thinking. As always, we're very interested in insight (especially on our issue tracker) to help enhance the usefulness of the ontology. Best, Pier PS: For general interest, I'll be meeting some urban environment specialists next week and intend to add more city-based environment classes (e.g. "urban prairies" such as those proliferating in Detroit).

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[Fwd: Re: Darwin Core Proposal - environment terms]
by Steve Baskauf 12 May '15

12 May '15

I have lost track of where we were on the public comment period on this proposal. I don't think that there was ever a declared end to to comment period, so I'm going to go ahead and make another comment. On 2015-03-27 I objected to this proposal on the basis that it was not clear how the terms would be used with literal and IRI values. Although the ratification of the DwC RDF Guide has not yet been formally announced, since it has been approved by the Executive Committee, I withdraw my objections to the proposed addition of the environment terms. Under the system outlined in the RDF guide, a term such as dwc:biome would be used with a string literal value, while the analogous term dwciri:biome would be used with an IRI value. Steve -------- Original Message -------- Subject: Re: [tdwg-content] Darwin Core Proposal - environment terms Date: Fri, 27 Mar 2015 09:37:25 -0500 From: Steve Baskauf <steve.baskauf(a)vanderbilt.edu> Organization: Vanderbilt University Dept. of Biological Sciences To: <tuco(a)berkeley.edu> CC: TDWG Content Mailing List <tdwg-content(a)lists.tdwg.org> References: <CAHwKGGdu=qaC0SBdGqF95VvBCxwmk2zrgWAmYmux9vrL2ut71g(a)mail.gmail.com> <55155B13.3080602(a)vanderbilt.edu> Actually, let me be more blunt. I object to the adoption of these terms as currently proposed because the recommendation in the comment is not clear. I think that these three term adoption issues are blocked by the adoption of the RDF guide. If the RDF guide is accepted by the Executive, then there is default mechanism for addressing my issue: there will be dwc:biome, which would have a literal value and dwciri:biome, which would have a value that is an IRI. If the RDF guide is not accepted by the executive, then there needs to be some other solution, such as the Audubon Core mechanism: dwc:biome and dwc:biomeLiteral. I don't know what the holdup is on the RDF guide. It had jumped through every hoop required for adoption and was submitted for approval by the Executive on 2014-12-29. There is no reason why it should take three months for a decision on this. Steve Steve Baskauf wrote: > For clarification, each example shows one string value that is free > text and another that is an ENVO IRI. Does this mean that if a user > wants to indicate the ENVO class for flooded grassland biome that they > can chose to provide either the text label for the class or the IRI? > Or is the example showing free text intended to show how a user might > provide a value if they aren't following the recommended best > practice (i.e. using some system other than ENVO that doesn't have > IRIs)? It seems to me counterproductive to provide two choices. I > would rather see the recommendation be to provide an IRI unless one > isn't available. Otherwise, consumers will be stuck with having to > try to interpret what free text means. > > Alternatively, provide two terms: one intended for use with literal > names (i.e. free text) and one intended for use with IRIs. That > precedent has been set in Audubon Core (e.g. ac:provider and > ac:providerLiteral). In DwC we have the dwc: and dwciri: solution in > the RDF guide (which appears once again to be stuck in Executive > Committee limbo). In the Audubon Core case, this isn't really an RDF > issue since AC doesn't assume any particular representation and I > think you could have a spreadsheet with an IRI value for ac:provider. > I suppose it would be kosher to have dwciri:biome expressed as an IRI > in string form in a spreadsheet for people who don't care about RDF. > I don't think this has actually been discussed. > > Steve > > John Wieczorek wrote: >> >> >> 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 > > -- > 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 -- 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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Postdoctoral fellow in Computable Semantics for the Tree of Life
by Cellinese,Nico 04 May '15

04 May '15

A Postdoctoral position is available to work with Hilmar Lapp and Nico Cellinese on building phyloreferences for the Tree of Life. All details can be found here: http://www.flmnh.ufl.edu/museum-voices/cellinese-lab/2015/05/03/postdoctora… Spread the word so we can start having fun asap. Thanks! Nico <><><><><><><><><><><><><><><><><><><><><><><><> Nico Cellinese, Ph.D. Associate Curator, Botany & Informatics Joint Associate Professor, Department of Biology University of Florida Florida Museum of Natural History 354 Dickinson Hall, 1659 Museum Rd. Gainesville, FL 32611-7800, U.S.A. Tel. 352-273-1979 Fax 352-846-1861 http://www.flmnh.ufl.edu/museum-voices/nico-cellinese/ Twitter @ncellinese _______________________________________________ tdwg-phylo mailing list tdwg-phylo(a)lists.tdwg.org<mailto:tdwg-phylo@lists.tdwg.org> http://lists.tdwg.org/mailman/listinfo/tdwg-phylo

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