Re: [tdwg-content] Darwin Core: proposed news terms for expressing sample data
Hi Ramona -
I understand your concern, though I would counterpoint that the only real reason to collect and curate a specimen is to support observations, either contemporaneously or at some future time. So it could be seen as slightly perverse to suggest that a model for specimens and samples could be divorced from the notion of observations.
FWIW I'm right now trying to develop a simplified SamplingFeatures ontology, still conceptually based on the ISO 19156 model, but with no commitments to marginal ontologies (i.e. lift it out of the ISO 19100 ghetto). This has led me to consider re-use of more standard ontologies. W3C Prov-O is interesting. Since a lot of the information that you would want to record about a specimen concerns its provenance, then it probably makes sense to align with prov. Currently I have
sam:Specimen a owl:Class ; rdfs:comment "A Specimen is a physical sample, obtained for observation(s) normally carried out ex-situ, sometimes in a laboratory."^^xsd:string ; rdfs:label "Specimen"@en ; rdfs:subClassOf prov:Entity , sam:SamplingFeature ; rdfs:subClassOf [ a owl:Restriction ; owl:cardinality "1"^^xsd:nonNegativeInteger ; owl:onProperty sam:samplingTime ] .
Simon
=============== Date: Mon, 1 Sep 2014 20:38:33 -0700 From: Ramona Walls rlwalls2008@gmail.com Subject: Re: [tdwg-content] tdwg-content Digest, Vol 63, Issue 14 To: TDWG Content Mailing List tdwg-content@lists.tdwg.org Message-ID: CAJYF1k6wcwPWtUt6ZHr8OgEcBJVYHUq0jiYc0hqEJeMY_kQ=1A@mail.gmail.com Content-Type: text/plain; charset="utf-8"
Thank you, Simon, for that explanation and the links. They were very helpful. Amen to the point: "There is no ?sample? class, because it is such an overloaded word (noun, verb, statistical sample vs ex-situ sample, etc)." The documents you shared highlight the very important point that OGC and OBO-E were designed specifically to describe observations.
Darwin Core, on the other hand, was designed to capture information about "taxa, their occurrence in nature as documented by observations, specimens, samples, and related information" [1]. As such, observations are not central to Darwin Core, but rather are included as evidence of the occurrence of a taxon in nature. It works for communicating basic information about an observation or other evidence of a taxon's occurrence, but I think it would be mis-using and abusing DwC to try to shoe-horn the complexity of observation data/metadata into it. It also does some dis-service to the communities who have spent so much time developing OGC and OBO-E.
Eamonn, this is not meant to discredit the work that you and your colleagues have done to develop a DwC archive schema for sampling data. I think it is an important step toward developing a comprehensive framework for biodiversity data, and just by proposing it, we have moved a step in the right direction (even if I disagree about adopting it). Your point that OBO-E is far more complex is true, and we may have to adopt more terms if we accurately want to describe observation data in DwC. On the other hand, we do not need to necessarily adopt every aspect of OBO-E to exchange observation data.
What the BCO participants -- and thanks to all the GBIF people who have participated! -- are trying to do is build a framework that can work across many (not necessarily all) types of biodiversity data, including specimen collection and observations, while considering existing efforts such as DwC, MIxS, OBO-E, and OBO Foundry ontologies. We started with specimens, but the intention has always been to link to observation data as well [2]. Although the full BCO model probably will be large and complex, we fully intend to offer views that are basically subsets of the ontology filtered for applications. This is regular practice now in application ontologies. Views makes it possible to provide a controlled vocabulary for data annotation without burdening annotators with a confusing array of terms and logical definitions.
However, the point that BCO is not yet ready for your needs is correct, and I would never tell anyone to just "hold on to your data until the ontology is ready". Did you examine the possibility of using EML as an exchange format for the sampling/survey related data? DwC-A already has an EML component, so I wonder if some combination of an occurrence core with an extended EML document (based on OGC) would work.
Ramona
[1] http://rs.tdwg.org/dwc/index.htm [2] http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0089606
------------------------------------------------------ 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
Simon --- Perhaps your email also illustrates Ramona's point about the complexity of the landscape right now when it comes to the _details_ of how we might model samples, and sampling processes. Darwin Core recently added a materialSample term, that was a refinement of OBI's "specimen" ( http://purl.obolibrary.org/obo/OBI_0100051) and with a description: "A resource describing the physical results of a sampling (or subsampling) event. In biological collections, the material sample is typically collected, and either preserved or destructively processed" ( http://rs.tdwg.org/dwc/dwctype/MaterialSample)
Maybe what you and what others are developing are equivalent expressions and perhaps they are not, but my initial reaction was that separating specimens and observations is a remarkably important and clarifying idea, and not perverse at all. I think the difference is that what you might call an observation is what the Biocollections Ontology community would refer to as a "sampling process" and what we call an "observation" is more related to some documentation of a "thing" in nature.
I say this recognizing that others, even those working on the Biocollections Ontology or Darwin Core, may have radically different notions of those same concepts. I hope not, but this is not simple to model. What I would like to see is some clarity among those putting in all this effort to do so more strategically, with bridges built across efforts and locations.
Best, Rob
On Mon, Sep 1, 2014 at 10:31 PM, Simon.Cox@csiro.au wrote:
Hi Ramona -
I understand your concern, though I would counterpoint that the only real reason to collect and curate a specimen is to support observations, either contemporaneously or at some future time. So it could be seen as slightly perverse to suggest that a model for specimens and samples could be divorced from the notion of observations.
FWIW I'm right now trying to develop a simplified SamplingFeatures ontology, still conceptually based on the ISO 19156 model, but with no commitments to marginal ontologies (i.e. lift it out of the ISO 19100 ghetto). This has led me to consider re-use of more standard ontologies. W3C Prov-O is interesting. Since a lot of the information that you would want to record about a specimen concerns its provenance, then it probably makes sense to align with prov. Currently I have
sam:Specimen a owl:Class ; rdfs:comment "A Specimen is a physical sample, obtained for observation(s) normally carried out ex-situ, sometimes in a laboratory."^^xsd:string ; rdfs:label "Specimen"@en ; rdfs:subClassOf prov:Entity , sam:SamplingFeature ; rdfs:subClassOf [ a owl:Restriction ; owl:cardinality "1"^^xsd:nonNegativeInteger ; owl:onProperty sam:samplingTime ] .
Simon
=============== Date: Mon, 1 Sep 2014 20:38:33 -0700 From: Ramona Walls rlwalls2008@gmail.com Subject: Re: [tdwg-content] tdwg-content Digest, Vol 63, Issue 14 To: TDWG Content Mailing List tdwg-content@lists.tdwg.org Message-ID: <CAJYF1k6wcwPWtUt6ZHr8OgEcBJVYHUq0jiYc0hqEJeMY_kQ= 1A@mail.gmail.com> Content-Type: text/plain; charset="utf-8"
Thank you, Simon, for that explanation and the links. They were very helpful. Amen to the point: "There is no ?sample? class, because it is such an overloaded word (noun, verb, statistical sample vs ex-situ sample, etc)." The documents you shared highlight the very important point that OGC and OBO-E were designed specifically to describe observations.
Darwin Core, on the other hand, was designed to capture information about "taxa, their occurrence in nature as documented by observations, specimens, samples, and related information" [1]. As such, observations are not central to Darwin Core, but rather are included as evidence of the occurrence of a taxon in nature. It works for communicating basic information about an observation or other evidence of a taxon's occurrence, but I think it would be mis-using and abusing DwC to try to shoe-horn the complexity of observation data/metadata into it. It also does some dis-service to the communities who have spent so much time developing OGC and OBO-E.
Eamonn, this is not meant to discredit the work that you and your colleagues have done to develop a DwC archive schema for sampling data. I think it is an important step toward developing a comprehensive framework for biodiversity data, and just by proposing it, we have moved a step in the right direction (even if I disagree about adopting it). Your point that OBO-E is far more complex is true, and we may have to adopt more terms if we accurately want to describe observation data in DwC. On the other hand, we do not need to necessarily adopt every aspect of OBO-E to exchange observation data.
What the BCO participants -- and thanks to all the GBIF people who have participated! -- are trying to do is build a framework that can work across many (not necessarily all) types of biodiversity data, including specimen collection and observations, while considering existing efforts such as DwC, MIxS, OBO-E, and OBO Foundry ontologies. We started with specimens, but the intention has always been to link to observation data as well [2]. Although the full BCO model probably will be large and complex, we fully intend to offer views that are basically subsets of the ontology filtered for applications. This is regular practice now in application ontologies. Views makes it possible to provide a controlled vocabulary for data annotation without burdening annotators with a confusing array of terms and logical definitions.
However, the point that BCO is not yet ready for your needs is correct, and I would never tell anyone to just "hold on to your data until the ontology is ready". Did you examine the possibility of using EML as an exchange format for the sampling/survey related data? DwC-A already has an EML component, so I wonder if some combination of an occurrence core with an extended EML document (based on OGC) would work.
Ramona
[1] http://rs.tdwg.org/dwc/index.htm [2] http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0089606
Ramona L. Walls, Ph.D. Scientific Analyst, The iPlant Collaborative, University of Arizona Research Associate, Bio5 Institute, University of Arizona Laboratory Research Associate, New York Botanical Garden
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Robert Guralnick -
Simon.Cox＠csiro.au