[tdwg-content] Darwin Core Proposal - environment terms (joel sachs)

joel sachs jsachs at csee.umbc.edu
Fri May 29 19:10:50 CEST 2015


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 at 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 at 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 at 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 at lists.tdwg.org>
>>>> wrote:
>>>>       Send tdwg-content mailing list submissions to
>>>>               tdwg-content at 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 at csee.umbc.edu>
>>>>       Subject: Re: [tdwg-content] Darwin Core Proposal - environment
>>>>       terms
>>>>       To: John Wieczorek <tuco at berkeley.edu>
>>>>       Cc: TDWG Content Mailing List <tdwg-content at lists.tdwg.org>
>>>>       Message-ID:
>>>>
>>>>       <Pine.LNX.4.64.1504231321240.18117 at 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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